Query 018828
Match_columns 350
No_of_seqs 153 out of 347
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 04:23:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018828hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08068 MPN_BRCC36 Mov34/MPN/P 100.0 9E-52 1.9E-56 386.5 15.9 163 1-288 81-244 (244)
2 KOG1554 COP9 signalosome, subu 100.0 2E-40 4.4E-45 316.4 3.5 134 2-147 124-261 (347)
3 KOG1555 26S proteasome regulat 100.0 4.9E-37 1.1E-41 295.9 10.8 192 1-312 107-298 (316)
4 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 5.3E-31 1.2E-35 247.9 4.8 134 2-145 80-217 (268)
5 cd08067 MPN_2A_DUB Mov34/MPN/P 99.8 3.1E-21 6.8E-26 174.3 7.7 69 5-74 75-150 (187)
6 cd08058 MPN_euk_mb Mpr1p, Pad1 99.8 6.6E-19 1.4E-23 145.9 5.2 61 3-69 59-119 (119)
7 cd08066 MPN_AMSH_like Mov34/MP 99.6 3.3E-15 7.1E-20 133.6 7.2 60 6-73 72-132 (173)
8 smart00232 JAB_MPN JAB/MPN dom 99.4 3.4E-13 7.3E-18 110.2 6.8 65 3-70 70-134 (135)
9 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.4 3.2E-13 7E-18 127.1 3.1 111 1-121 71-181 (266)
10 cd07767 MPN Mpr1p, Pad1p N-ter 99.3 1.7E-12 3.7E-17 104.1 4.0 49 4-52 58-106 (116)
11 PF01398 JAB: JAB1/Mov34/MPN/P 99.2 2.7E-12 5.8E-17 104.6 2.6 39 3-41 75-113 (114)
12 KOG2880 SMAD6 interacting prot 99.1 4.2E-11 9.2E-16 118.7 1.9 65 4-76 320-384 (424)
13 cd08070 MPN_like Mpr1p, Pad1p 98.9 2.3E-09 5E-14 89.9 5.5 55 6-71 67-121 (128)
14 COG1310 Predicted metal-depend 98.9 3.2E-09 7E-14 89.8 5.5 41 7-51 67-108 (134)
15 cd08057 MPN_euk_non_mb Mpr1p, 98.7 2.8E-08 6.1E-13 86.3 6.6 71 1-73 68-139 (157)
16 cd08062 MPN_RPN7_8 Mpr1p, Pad1 98.3 4.9E-07 1.1E-11 86.7 5.2 63 1-71 74-136 (280)
17 cd08064 MPN_eIF3f Mpr1p, Pad1p 98.1 2.4E-06 5.3E-11 80.6 4.9 104 1-135 68-171 (265)
18 cd08056 MPN_PRP8 Mpr1p, Pad1p 98.1 3.6E-06 7.8E-11 80.5 6.0 60 7-72 104-168 (252)
19 PF14464 Prok-JAB: Prokaryotic 98.1 1.8E-06 3.8E-11 68.8 2.3 42 5-50 55-96 (104)
20 cd08072 MPN_archaeal Mov34/MPN 98.0 1.8E-05 3.9E-10 66.7 6.2 53 6-70 56-109 (117)
21 KOG1555 26S proteasome regulat 97.5 2.1E-05 4.6E-10 77.4 0.5 106 32-149 142-250 (316)
22 KOG1560 Translation initiation 97.4 0.00018 3.9E-09 70.6 4.3 63 5-71 94-156 (339)
23 cd08073 MPN_NLPC_P60 Mpr1p, Pa 97.4 0.00019 4.2E-09 59.9 3.9 36 10-50 60-95 (108)
24 cd08063 MPN_CSN6 Mpr1p, Pad1p 96.9 0.0013 2.9E-08 63.0 5.6 67 1-72 75-141 (288)
25 cd08059 MPN_prok_mb Mpr1p, Pad 96.6 0.0035 7.5E-08 50.5 4.6 40 6-50 53-92 (101)
26 cd08061 MPN_NPL4 Mov34/MPN/PAD 96.2 0.0077 1.7E-07 58.4 5.5 62 6-72 90-161 (274)
27 TIGR02256 ICE_VC0181 integrati 96.1 0.0074 1.6E-07 53.0 4.6 46 4-49 68-113 (131)
28 PLN03246 26S proteasome regula 95.6 0.018 3.9E-07 56.4 5.1 62 1-70 79-140 (303)
29 TIGR03735 PRTRC_A PRTRC system 94.0 0.03 6.4E-07 52.2 2.0 43 5-52 130-172 (192)
30 KOG1556 26S proteasome regulat 93.4 0.062 1.4E-06 52.6 3.0 46 1-50 82-127 (309)
31 cd08060 MPN_UPF0172 Mov34/MPN/ 93.1 0.17 3.6E-06 46.4 5.1 40 7-49 68-111 (182)
32 PF05021 NPL4: NPL4 family; I 88.8 1 2.2E-05 44.7 6.2 60 8-72 57-144 (306)
33 PF11471 Sugarporin_N: Maltopo 75.8 4.4 9.5E-05 31.5 3.8 28 279-306 29-56 (60)
34 TIGR01834 PHA_synth_III_E poly 71.0 22 0.00048 35.9 8.5 82 216-304 225-318 (320)
35 PF11471 Sugarporin_N: Maltopo 71.0 21 0.00046 27.7 6.6 26 277-302 34-59 (60)
36 PF15458 NTR2: Nineteen comple 63.8 64 0.0014 31.1 9.7 78 222-304 152-244 (254)
37 PF13600 DUF4140: N-terminal d 54.8 30 0.00064 28.1 5.1 34 272-305 67-100 (104)
38 PF15659 Toxin-JAB1: JAB-like 51.3 9.8 0.00021 35.0 1.9 29 7-36 114-142 (162)
39 PF01621 Fusion_gly_K: Cell fu 49.9 18 0.00039 36.8 3.6 35 219-258 177-211 (337)
40 PF08826 DMPK_coil: DMPK coile 45.4 60 0.0013 25.5 5.2 30 276-305 26-55 (61)
41 PRK00888 ftsB cell division pr 44.3 96 0.0021 26.2 6.6 45 264-308 7-60 (105)
42 COG5509 Uncharacterized small 44.3 36 0.00077 27.2 3.7 27 284-310 27-53 (65)
43 COG3416 Uncharacterized protei 38.7 1.3E+02 0.0028 29.4 7.3 34 271-304 44-77 (233)
44 PF04977 DivIC: Septum formati 36.2 90 0.0019 23.5 4.8 31 277-307 19-49 (80)
45 PHA03278 envelope glycoprotein 35.9 35 0.00076 35.0 3.2 34 219-257 177-210 (347)
46 COG2132 SufI Putative multicop 35.4 25 0.00055 35.7 2.2 8 14-21 129-136 (451)
47 KOG2975 Translation initiation 35.2 92 0.002 31.3 5.8 62 2-71 91-152 (288)
48 PHA03275 envelope glycoprotein 34.2 39 0.00084 34.6 3.2 35 219-258 175-209 (340)
49 KOG0976 Rho/Rac1-interacting s 33.7 56 0.0012 37.4 4.5 33 273-305 125-157 (1265)
50 PHA03279 envelope glycoprotein 33.3 47 0.001 34.2 3.6 34 219-257 203-236 (361)
51 TIGR03782 Bac_Flav_CT_J Bacter 33.0 69 0.0015 32.6 4.7 39 268-306 78-116 (322)
52 PHA03276 envelope glycoprotein 31.2 46 0.001 34.0 3.2 34 219-257 176-209 (337)
53 PF11853 DUF3373: Protein of u 31.2 72 0.0016 34.1 4.7 28 278-306 21-48 (489)
54 PF00170 bZIP_1: bZIP transcri 29.4 1.5E+02 0.0032 22.3 5.0 29 277-305 28-56 (64)
55 KOG1795 U5 snRNP spliceosome s 29.4 75 0.0016 38.2 4.7 62 7-74 2163-2225(2321)
56 PF07716 bZIP_2: Basic region 29.4 1.5E+02 0.0031 21.8 4.8 24 280-303 30-53 (54)
57 PF06103 DUF948: Bacterial pro 29.0 1.7E+02 0.0037 23.2 5.5 35 271-305 15-49 (90)
58 PF11740 KfrA_N: Plasmid repli 27.5 2.9E+02 0.0064 22.6 6.9 39 267-305 80-118 (120)
59 PF01166 TSC22: TSC-22/dip/bun 27.5 1.8E+02 0.0039 23.1 5.2 29 277-305 16-44 (59)
60 PF10883 DUF2681: Protein of u 27.3 3.3E+02 0.0073 22.8 7.1 35 272-306 13-47 (87)
61 PF14220 DUF4329: Domain of un 27.2 69 0.0015 28.1 3.2 26 8-33 58-88 (123)
62 PF06305 DUF1049: Protein of u 26.1 2.8E+02 0.006 20.6 6.3 22 285-306 44-65 (68)
63 cd00632 Prefoldin_beta Prefold 26.1 1.9E+02 0.0041 23.8 5.5 47 259-305 47-93 (105)
64 KOG0804 Cytoplasmic Zn-finger 25.7 5.2E+02 0.011 27.9 9.7 27 218-244 326-352 (493)
65 smart00338 BRLZ basic region l 25.6 1.8E+02 0.0039 21.9 4.8 29 277-305 28-56 (65)
66 TIGR02338 gimC_beta prefoldin, 25.4 1.6E+02 0.0035 24.6 5.0 50 257-306 49-98 (110)
67 PF14331 ImcF-related_N: ImcF- 24.9 5.5E+02 0.012 24.6 9.1 100 199-312 68-178 (266)
68 PRK04325 hypothetical protein; 24.3 1.4E+02 0.0031 23.8 4.3 20 285-304 33-52 (74)
69 PF06005 DUF904: Protein of un 24.0 1.9E+02 0.0042 23.1 4.9 29 277-305 20-48 (72)
70 PF11945 WASH_WAHD: WAHD domai 23.6 2.9E+02 0.0063 27.6 7.2 54 269-322 30-87 (297)
71 TIGR02376 Cu_nitrite_red nitri 23.4 66 0.0014 31.6 2.7 29 12-51 119-147 (311)
72 PF13815 Dzip-like_N: Iguana/D 22.7 2.8E+02 0.006 23.5 6.0 33 273-305 78-110 (118)
73 PRK10965 multicopper oxidase; 22.6 36 0.00078 36.0 0.7 9 12-20 138-146 (523)
74 PRK10883 FtsI repressor; Provi 22.0 38 0.00082 35.2 0.8 9 13-21 139-147 (471)
75 TIGR02449 conserved hypothetic 21.8 2.2E+02 0.0047 22.8 4.8 29 277-305 2-30 (65)
76 PF08172 CASP_C: CASP C termin 21.5 3.2E+02 0.007 26.5 6.9 35 277-311 1-35 (248)
77 KOG0774 Transcription factor P 21.4 4.8E+02 0.01 26.5 8.0 68 226-293 113-194 (334)
78 PF02388 FemAB: FemAB family; 20.9 6.6E+02 0.014 25.6 9.2 84 218-305 196-296 (406)
79 TIGR02231 conserved hypothetic 20.6 1.7E+02 0.0036 30.5 5.0 34 273-306 69-102 (525)
80 TIGR02209 ftsL_broad cell divi 20.6 2.4E+02 0.0053 21.8 4.9 31 277-307 26-56 (85)
81 PF04102 SlyX: SlyX; InterPro 20.5 2.2E+02 0.0048 22.2 4.6 30 277-306 20-49 (69)
82 PLN02168 copper ion binding / 20.5 64 0.0014 34.4 2.0 8 13-20 123-130 (545)
83 PF06305 DUF1049: Protein of u 20.2 2.8E+02 0.0061 20.6 5.0 25 277-301 43-67 (68)
84 PRK04406 hypothetical protein; 20.2 2.3E+02 0.0051 22.7 4.8 22 284-305 34-55 (75)
85 PRK02119 hypothetical protein; 20.1 2.3E+02 0.0051 22.5 4.7 24 282-305 30-53 (73)
No 1
>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=100.00 E-value=9e-52 Score=386.49 Aligned_cols=163 Identities=52% Similarity=0.917 Sum_probs=151.5
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccc-cccCceEEEEEEeeCCCCccccCC
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDA-NKVGRIQVIAFQSSDGKQNHISKP 79 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~-~s~Gkv~i~AFR~~~~~~~~~~rp 79 (350)
|++.+||++.+||||||||+++||||.+|++||..||+++++||+|||||++.+. +..|+++++|||+.++++
T Consensus 81 ~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~~------ 154 (244)
T cd08068 81 LTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGNK------ 154 (244)
T ss_pred HHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCCC------
Confidence 5678899999999999999999999999999999999999999999999998663 456899999999988532
Q ss_pred cccccCCCcchhcccccCCccccccccccccccCCccccccccccccccccCCCccccCCCccccccCCccccccCCCCc
Q 018828 80 IALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNY 159 (350)
Q Consensus 80 ~~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~N~~~~~~~~~~~ 159 (350)
T Consensus 155 -------------------------------------------------------------------------------- 154 (244)
T cd08068 155 -------------------------------------------------------------------------------- 154 (244)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCcCCCCCCCcchHHHHHhhhccccCCCCceeeeeeeeeeecCCCcccCCCcchhHHHHhHHHHHHHHHHHHHH
Q 018828 160 QTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQA 239 (350)
Q Consensus 160 ~~~~~~~~~~~~~~~d~s~~~qea~hrs~ld~sg~~y~rkEvpl~v~p~~~~~~~~~~l~s~~~Lq~iL~~EE~~ay~qa 239 (350)
|++|+|+||||+|+|+.++.++ ||+++++||+||++||++||++|
T Consensus 155 ---------------------------------~~~~~~~e~pl~i~~~~~~~~~--~~~~~~~l~~~l~~e~~~a~~~~ 199 (244)
T cd08068 155 ---------------------------------AGQYERIEVPLEIVPTSTISEA--CLESLVELPEILYQEEEDAYNKA 199 (244)
T ss_pred ---------------------------------CCcceEEEeeeEEecCcccccc--CHHHHHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999999997 59999999999999999999999
Q ss_pred HHhhcCCCCCCccceeehhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 018828 240 IMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENE 288 (350)
Q Consensus 240 ~~q~~~~~~~hpLt~iHh~sty~~slc~l~e~~l~P~~~~l~drl~~n~ 288 (350)
+.|+.+ ||||+|||++|||++||+|||+|++|++++||+||++|+
T Consensus 200 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~~ 244 (244)
T cd08068 200 LQSCDL----DPLTKIHNGSVYTKSLCHILETISGPLLQLLEARLEQNK 244 (244)
T ss_pred Hhcccc----hHHHHHHhhHHHHHHHHHHHHHHHhhHHHHHHHHHHhcC
Confidence 987654 499999999999999999999999999999999999985
No 2
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=2e-40 Score=316.44 Aligned_cols=134 Identities=21% Similarity=0.250 Sum_probs=123.2
Q ss_pred ccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccc---cC
Q 018828 2 TVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHI---SK 78 (350)
Q Consensus 2 ~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~---~r 78 (350)
.+..||.++|||||||||+|+||+|+|||.||+++|++++||||||+||.+ +.++|++.|+|||++|.++.+. +.
T Consensus 124 ~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~R--tlsagkv~iGAFRTyp~gyk~~d~~~s 201 (347)
T KOG1554|consen 124 AKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTR--TLSAGKVNIGAFRTYPKGYKPPDEPPS 201 (347)
T ss_pred HHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCcc--ccccCceeeceeecccCCCCCCCCCch
Confidence 567899999999999999999999999999999999999999999999986 5678999999999999988654 33
Q ss_pred CcccccCCCcchhcccccCCcccc-ccccccccccCCccccccccccccccccCCCccccCCCccccccC
Q 018828 79 PIALLPVNKSTVIDLESSLSSSES-LSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDA 147 (350)
Q Consensus 79 p~~~~pl~k~siid~~~~~g~~~~-YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~ 147 (350)
.++..|++| |++||.||+ ||+|+|+||++.+|.+.++ .||+|||++|+++++++.|.|-
T Consensus 202 eyqtipl~k------ied~gvHck~yysl~isyfks~ld~kll~----~Lwnkywv~Tlsss~ll~N~dy 261 (347)
T KOG1554|consen 202 EYQTIPLNK------IEDFGVHCKQYYSLEISYFKSSLDMKLLE----LLWNKYWVRTLSSSPLLKNIDY 261 (347)
T ss_pred hhhccchhh------hhhcccceEEeeccchhhhhhhhhHHHHH----HHHhhhhhcccccccccccchh
Confidence 477778887 799999998 9999999999999999999 9999999999999999998763
No 3
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.9e-37 Score=295.85 Aligned_cols=192 Identities=35% Similarity=0.500 Sum_probs=158.4
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCCc
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPI 80 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp~ 80 (350)
|++++||++.|||||||||+|+||||++||+||+.||++.+..++++++|.. +..|++.++|||++.+.....
T Consensus 107 ~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~---S~~g~vv~d~f~~In~~~~~~---- 179 (316)
T KOG1555|consen 107 LLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQ---SPYGKVVPDAFSSINPQWISP---- 179 (316)
T ss_pred HHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeeccc---CCCCCccCChhhhcCcccccC----
Confidence 5789999999999999999999999999999999999998888888888743 456899999999988654211
Q ss_pred ccccCCCcchhcccccCCccccccccccccccCCccccccccccccccccCCCccccCCCccccccCCccccccCCCCcC
Q 018828 81 ALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGNYQ 160 (350)
Q Consensus 81 ~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~N~~~~~~~~~~~~ 160 (350)
T Consensus 180 -------------------------------------------------------------------------------- 179 (316)
T KOG1555|consen 180 -------------------------------------------------------------------------------- 179 (316)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCcCCCCCCCcchHHHHHhhhccccCCCCceeeeeeeeeeecCCCcccCCCcchhHHHHhHHHHHHHHHHHHHHH
Q 018828 161 TGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAI 240 (350)
Q Consensus 161 ~~~~~~~~~~~~~~d~s~~~qea~hrs~ld~sg~~y~rkEvpl~v~p~~~~~~~~~~l~s~~~Lq~iL~~EE~~ay~qa~ 240 (350)
+++-+.....+++|||+++|||++|++| .|.|+|||++|.|......++-|+.++.++|+++|+||+++|.+..
T Consensus 180 ~~eprqtts~~~~m~~~~s~q~~~~g~n------~y~~~ei~~~v~~~~~~~~~nv~~~s~~~~~~~~y~e~~k~~~~~~ 253 (316)
T KOG1555|consen 180 GGEPRQTTSNGGHMDMQESLQEDIHGLN------RYYRIEIPLHVLPYEQLMLLNVPLKSWKSLQDVLYEEKLKAYLQSV 253 (316)
T ss_pred CCCCccccccccccccchhHHhHhhccC------ceEEEEeeEEechhhhhchhccchhhhhhcchhhHHHHHHHhhhhh
Confidence 0122334456789999999999999999 6999999999999777777777899999999999999999999766
Q ss_pred HhhcCCCCCCccceeehhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 018828 241 MQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAFKGSDSS 312 (350)
Q Consensus 241 ~q~~~~~~~hpLt~iHh~sty~~slc~l~e~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~~~~~~~~ 312 (350)
.+... |+++++++.++.++++.++.+++++.++..++-.++....
T Consensus 254 ~~~~s---------------------------L~~~~N~~~~~~k~~~~~~~~i~d~~~~~~kq~l~~~v~~ 298 (316)
T KOG1555|consen 254 PSMKS---------------------------LSKVYNKVCDVCKQMSDFLLMIEDVGEQNPKQHLKEAVTE 298 (316)
T ss_pred hHHHh---------------------------HHHHHHHHHHHHhhccHHHHHHHHhhhhhHHHHhHHHhhh
Confidence 54321 7778888888888888888888888888866655544443
No 4
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.96 E-value=5.3e-31 Score=247.89 Aligned_cols=134 Identities=20% Similarity=0.220 Sum_probs=115.9
Q ss_pred ccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCcc---ccC
Q 018828 2 TVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNH---ISK 78 (350)
Q Consensus 2 ~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~---~~r 78 (350)
++.+++++++||||||||+++||||.+||.||..||++.+|+|+|||||.. +.+.|++.++|||+++..... -..
T Consensus 80 ~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~--t~~~g~~~i~Afr~~~~~~~~~~~~~~ 157 (268)
T cd08069 80 LKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIR--SLVKGKVVIGAFRTIPPGYKPLEPRQT 157 (268)
T ss_pred HHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCc--cccCCcceeeEEEEECccccccCcccC
Confidence 467899999999999999999999999999999999999999999999975 236789999999999988653 123
Q ss_pred CcccccCCCcchhcccccCCcccc-ccccccccccCCccccccccccccccccCCCccccCCCccccc
Q 018828 79 PIALLPVNKSTVIDLESSLSSSES-LSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANV 145 (350)
Q Consensus 79 p~~~~pl~k~siid~~~~~g~~~~-YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~ 145 (350)
..+.+.+.+++++ .++.+++ ||+|+|.||++.+|+.+|. .||+|+|+++|.+++|++|+
T Consensus 158 ~s~~~~~~~~~~~----~~~~~~~~y~~l~i~~~~s~l~~~~L~----~l~~~~w~~~l~~~~~~~~~ 217 (268)
T cd08069 158 TSNIGHLPKPKIE----DFGGHNKQYYSLPIEYFKSSLDRKLLL----NLWNKYWVNTLSLSPLLENS 217 (268)
T ss_pred ccccCccCcHHHH----HhCchhcEEEEeeeEEecCHHHHHHHH----HHHHHhHHHHhhCCchhhhh
Confidence 3555666665444 5566665 9999999999999999999 99999999999999999998
No 5
>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=99.84 E-value=3.1e-21 Score=174.26 Aligned_cols=69 Identities=33% Similarity=0.525 Sum_probs=60.5
Q ss_pred cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCc-------CceEEEeccccccccccCceEEEEEEeeCCCCc
Q 018828 5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-------GFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQN 74 (350)
Q Consensus 5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~-------pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~ 74 (350)
..+++++||||||||.++||||.+||+||..||.+.+ ||||||||||+++.. ..+++|+|||+.++..+
T Consensus 75 ~~~gl~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~-~~~s~i~~f~~~~~~~~ 150 (187)
T cd08067 75 ESRGLSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNS-TPESQITCFWVMPPPEN 150 (187)
T ss_pred HHcCCEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCC-CCCCcEEEEEEECCCCC
Confidence 3677899999999999999999999999999999865 899999999986443 44678999999998764
No 6
>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=99.75 E-value=6.6e-19 Score=145.94 Aligned_cols=61 Identities=41% Similarity=0.590 Sum_probs=55.3
Q ss_pred cccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEee
Q 018828 3 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 69 (350)
Q Consensus 3 ~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~ 69 (350)
+..++++++||||||||++++|||..|++||..||++.+++|+||+||++. +..++|||+.
T Consensus 59 ~~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~------~~~~~a~rl~ 119 (119)
T cd08058 59 VQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR------NKDTGIFRLT 119 (119)
T ss_pred HHhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC------CcccceEEeC
Confidence 457899999999999999999999999999999999999999999999762 4579999963
No 7
>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=99.57 E-value=3.3e-15 Score=133.58 Aligned_cols=60 Identities=25% Similarity=0.360 Sum_probs=54.4
Q ss_pred CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEee-CCCC
Q 018828 6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS-DGKQ 73 (350)
Q Consensus 6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~-~~~~ 73 (350)
.+++.+||||||||..+||||.+|+.||..||.+++++++|||||. .+.++|||+. +.+.
T Consensus 72 ~~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~--------~~~l~afrl~~~~g~ 132 (173)
T cd08066 72 QHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK--------YNEFGIFRLTDPPGL 132 (173)
T ss_pred hCCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC--------CcEEeEEEeecCCcc
Confidence 5789999999999999999999999999999999999999999972 4689999999 4443
No 8
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.42 E-value=3.4e-13 Score=110.24 Aligned_cols=65 Identities=32% Similarity=0.504 Sum_probs=57.9
Q ss_pred cccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeC
Q 018828 3 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD 70 (350)
Q Consensus 3 ~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~ 70 (350)
++..+++.+||||||||..+++||..|+.+|..||.....++.++++|.. +..|++.+.||++.+
T Consensus 70 ~~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~---s~~g~~~~~af~~~~ 134 (135)
T smart00232 70 KKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIK---SFQGRLSLRAFRLTP 134 (135)
T ss_pred HhhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCc---cccCcEEEEEEEecC
Confidence 45678899999999999999999999999999999999999999999864 334889999999865
No 9
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.35 E-value=3.2e-13 Score=127.10 Aligned_cols=111 Identities=12% Similarity=0.088 Sum_probs=83.8
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCCc
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPI 80 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp~ 80 (350)
|+++++..+.+|||||||| +++|.+..++++|..||...+++|+||+||.. ++.|++.+.|||+.+......
T Consensus 71 ~~r~v~~~e~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~---s~~g~l~lkAyrl~~~~~~~~---- 142 (266)
T cd08065 71 LLREVNVDHNHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSK---TSQGSLSLKAYRLSEKFMELY---- 142 (266)
T ss_pred HHHHhCCCCcEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCc---ccccceeeEEEEEcHHHHHHh----
Confidence 3577888999999999999 99999999999999999988999999999864 245788999999987543111
Q ss_pred ccccCCCcchhcccccCCccccccccccccccCCccccccc
Q 018828 81 ALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGD 121 (350)
Q Consensus 81 ~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~ 121 (350)
..+..++..+++....++ +-|+.++|.++.+.+++.+|.
T Consensus 143 ~~~~~~~~~l~~~~~~~~--~if~eiPv~i~n~~l~~~~L~ 181 (266)
T cd08065 143 KEGKFSTESLREANLTFS--NIFEEIPVVIRNSHLVNALLS 181 (266)
T ss_pred hcCCcCHHHHHHhcCchh--cEEEEEEEEEEchHHHHHHHH
Confidence 112222222333322333 229999999999999999987
No 10
>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=99.30 E-value=1.7e-12 Score=104.13 Aligned_cols=49 Identities=24% Similarity=0.452 Sum_probs=45.2
Q ss_pred ccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecccc
Q 018828 4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFS 52 (350)
Q Consensus 4 ~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~ 52 (350)
...+++.+||||||||..++|||..|+.+|..||...+.+|+||+|+-.
T Consensus 58 ~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~ 106 (116)
T cd07767 58 KLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKP 106 (116)
T ss_pred HhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCC
Confidence 4567899999999999999999999999999999988999999999854
No 11
>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=99.25 E-value=2.7e-12 Score=104.58 Aligned_cols=39 Identities=38% Similarity=0.809 Sum_probs=31.9
Q ss_pred cccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCc
Q 018828 3 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT 41 (350)
Q Consensus 3 ~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~ 41 (350)
+++...+.+||||||||.++||||..|+.||..||++.+
T Consensus 75 ~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~ 113 (114)
T PF01398_consen 75 KKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNP 113 (114)
T ss_dssp HHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTT
T ss_pred ccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCC
Confidence 344455999999999999999999999999999999875
No 12
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=99.06 E-value=4.2e-11 Score=118.68 Aligned_cols=65 Identities=25% Similarity=0.387 Sum_probs=56.3
Q ss_pred ccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccc
Q 018828 4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHI 76 (350)
Q Consensus 4 ~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~ 76 (350)
+..+.+-.+||.|.||+.+||+|.||++|+-+||.|.|.+|||||+|-.. ..|.||.++++.+..
T Consensus 320 Qdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~--------~tGiFrLt~~~Gm~~ 384 (424)
T KOG2880|consen 320 QDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSK--------TTGIFRLTDPGGMEV 384 (424)
T ss_pred cccccceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccC--------CcceEEecCCcchHH
Confidence 34567889999999999999999999999999999999999999999531 256799998777644
No 13
>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=98.89 E-value=2.3e-09 Score=89.94 Aligned_cols=55 Identities=33% Similarity=0.413 Sum_probs=44.9
Q ss_pred CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828 6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG 71 (350)
Q Consensus 6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~ 71 (350)
.+++.+||||||||...|+||..|+.++.. .+.+.+|+++... ...+.||+...+
T Consensus 67 ~~g~~~vG~~HSHP~~~~~PS~~D~~~~~~-----~~~~~lIv~~~~~------~~~~~~~~~~~~ 121 (128)
T cd08070 67 ERGLEVVGIYHSHPDGPARPSETDLRLAWP-----PGVSYLIVSLAGG------APELRAWRLEGG 121 (128)
T ss_pred HCCCeEEEEEeCCCCCCCCCCHHHHHhccC-----CCCeEEEEECCCC------CcEEEEEEEcCC
Confidence 356899999999999999999999997643 3799999997541 346999998764
No 14
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=98.86 E-value=3.2e-09 Score=89.82 Aligned_cols=41 Identities=32% Similarity=0.455 Sum_probs=31.6
Q ss_pred CCCceeeeeccCCCCCCCCChHHHHhHHHhhhh-CcCceEEEeccc
Q 018828 7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLL-DTGFIGLIFSCF 51 (350)
Q Consensus 7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~-~~pfVaLIvSP~ 51 (350)
+++.|||||||||+..||||..|+. +|.+ ..+|+.|+..|+
T Consensus 67 ~g~~vvg~yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~~ 108 (134)
T COG1310 67 AGEVVVGWYHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPG 108 (134)
T ss_pred CCCEEEEEEcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCCC
Confidence 4599999999999999999999999 3333 245666666553
No 15
>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=98.71 E-value=2.8e-08 Score=86.33 Aligned_cols=71 Identities=14% Similarity=0.284 Sum_probs=59.5
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhh-CcCceEEEeccccccccccCceEEEEEEeeCCCC
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLL-DTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ 73 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~-~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~ 73 (350)
|.+++.+.+.+|||||+||...++++..|...|..|... .+++|.|++||... ...|+..+.||++.+...
T Consensus 68 ~~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~--~~~~~l~i~ay~~~~~~~ 139 (157)
T cd08057 68 LHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQ--SDSEKLEISTFTSAQREE 139 (157)
T ss_pred HHHHhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcc--cCCCcccEEEEEEecCCC
Confidence 457788999999999999999999999998888888765 78899999999541 345788999999997654
No 16
>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=98.35 E-value=4.9e-07 Score=86.70 Aligned_cols=63 Identities=14% Similarity=0.296 Sum_probs=52.3
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG 71 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~ 71 (350)
|.+++++.+.+||||||||+. +..|+..|..|+...++.|.|++||.. +.++.-+.||...+.
T Consensus 74 ~~kkv~~~e~vVGWY~tg~~~----~~~d~~ih~~~~~~~~~pv~l~vd~~~----~~~~lpi~aY~s~~~ 136 (280)
T cd08062 74 MFKKVNAKEKIVGWYSTGPKL----RPNDLDINELFRRYCPNPVLVIIDVRP----KDLGLPTEAYIAVEE 136 (280)
T ss_pred HHHHhCCCCCeEEEecCCCCC----CcchHHHHHHHHHhCCCCEEEEEecCC----CCCCCceEEEEEeee
Confidence 467889999999999999984 567889999999998889999999853 234567899988763
No 17
>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=98.14 E-value=2.4e-06 Score=80.60 Aligned_cols=104 Identities=13% Similarity=0.084 Sum_probs=67.5
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCCc
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPI 80 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp~ 80 (350)
|.++++..+.+|||||++|.+. ++...|+.|..+|...+..|.|++||.. ..+++.+.||++.+......
T Consensus 68 ~~kkv~~~~~vVGWY~tg~~~~--~~~~~Ih~~~~~~~~~~~pI~L~~D~~~----~~~~l~i~ay~~~~~~~~~~---- 137 (265)
T cd08064 68 LHQKVNPKEVIVGWYATGSEIT--EHSALIHDYYSRECTSYNPIHLTVDTSL----DDGKMSIKAYVSSPLGVPGK---- 137 (265)
T ss_pred HHHHhCCCCcEEeeeeCCCCCC--ccHHHHHHHHHhhCCCCCCEEEEEeCCC----CCCCcceEEEEEEecccCCC----
Confidence 3578899999999999999433 3445555555544332377999999843 23468899999987432100
Q ss_pred ccccCCCcchhcccccCCccccccccccccccCCccccccccccccccccCCCcc
Q 018828 81 ALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRT 135 (350)
Q Consensus 81 ~~~pl~k~siid~~~~~g~~~~YYsl~i~~~~~~~e~~~l~s~~v~l~~K~W~~t 135 (350)
.....|=.+++....+..|+.-++ .+++..|..+
T Consensus 138 -----------------~~~~~F~~ip~~i~~~eaE~i~v~----~l~~~~~~~~ 171 (265)
T cd08064 138 -----------------TLGSMFVPIPLELLYSEAERVALD----LLAKTLASPS 171 (265)
T ss_pred -----------------CcceEEEEcceeeecCcHHHHHHH----HHHhhccCCc
Confidence 001115556666777888888888 6676666554
No 18
>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=98.14 E-value=3.6e-06 Score=80.51 Aligned_cols=60 Identities=22% Similarity=0.242 Sum_probs=53.7
Q ss_pred CCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCc-----CceEEEeccccccccccCceEEEEEEeeCCC
Q 018828 7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-----GFIGLIFSCFSEDANKVGRIQVIAFQSSDGK 72 (350)
Q Consensus 7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~-----pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~ 72 (350)
.++..+||.|.||.-.|++|.+||.||..||.+.+ .+|.++|++- .|.+.++||++++.+
T Consensus 104 ~~Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sft------pGs~sl~ay~LT~~G 168 (252)
T cd08056 104 EDLEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFT------PGSCSLTAYKLTPEG 168 (252)
T ss_pred CCCEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCC------CCceEEEEEecCHHH
Confidence 46889999999999999999999999999999886 7999999962 578899999999754
No 19
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=98.08 E-value=1.8e-06 Score=68.80 Aligned_cols=42 Identities=26% Similarity=0.392 Sum_probs=31.8
Q ss_pred cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828 5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC 50 (350)
Q Consensus 5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP 50 (350)
..+++.+||+|||||...++||..|..+..... +++.||++.
T Consensus 55 ~~~~~~~vg~~HSHP~~~a~pS~~D~~~~~~~~----~~~~iI~~~ 96 (104)
T PF14464_consen 55 RERGLEIVGIWHSHPSGPAFPSSTDIRSMRDLA----PPSYIIVGN 96 (104)
T ss_dssp HHHT-EEEEEEEEESSSSSS--HHHHHTHCCS-----SCEEEEEEE
T ss_pred hcccceeeEEEEcCCCCCCCCCHHHHHhhhccC----CeEEEEEeC
Confidence 356789999999999999999999998654332 889999985
No 20
>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=97.96 E-value=1.8e-05 Score=66.71 Aligned_cols=53 Identities=26% Similarity=0.366 Sum_probs=40.4
Q ss_pred CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEec-cccccccccCceEEEEEEeeC
Q 018828 6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFS-CFSEDANKVGRIQVIAFQSSD 70 (350)
Q Consensus 6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvS-P~~~d~~s~Gkv~i~AFR~~~ 70 (350)
.+++.+||-|||||.-.++||..|+. ++ ..++.+.+|++ |+.. -.+.||+...
T Consensus 56 ~~g~~ivgi~HSHP~~~~~PS~~D~~-~~----~~~~~~~lIvs~~~~~-------~~~~a~~~~g 109 (117)
T cd08072 56 PLDMSIVGSVHSHPSGSPRPSDADLS-FF----SKTGLVHIIVGYPYDE-------DDWRAYDSDG 109 (117)
T ss_pred cCCCeEEEEEEcCCCCCCCCCHHHHH-hh----hcCCCEEEEEECcCCC-------CCEEEEecCC
Confidence 45689999999999999999999976 22 23789999999 4531 1366776644
No 21
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=2.1e-05 Score=77.43 Aligned_cols=106 Identities=10% Similarity=-0.149 Sum_probs=86.6
Q ss_pred hHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCCCccccCC--cccccCCC-cchhcccccCCcccccccccc
Q 018828 32 TQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKP--IALLPVNK-STVIDLESSLSSSESLSARSG 108 (350)
Q Consensus 32 TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~~~~rp--~~~~pl~k-~siid~~~~~g~~~~YYsl~i 108 (350)
-|+....-..+||+.|+||+... ...-...|.|++..+++. +|+ ++.+|+++ ++++..++++| | ||+++|
T Consensus 142 yq~~~~r~~a~~v~~i~S~~g~v-v~d~f~~In~~~~~~~~e---prqtts~~~~m~~~~s~q~~~~g~n-~--y~~~ei 214 (316)
T KOG1555|consen 142 YQALSSRAVAVVVDPIQSPYGKV-VPDAFSSINPQWISPGGE---PRQTTSNGGHMDMQESLQEDIHGLN-R--YYRIEI 214 (316)
T ss_pred HhhhccCCcceeeecccCCCCCc-cCChhhhcCcccccCCCC---CccccccccccccchhHHhHhhccC-c--eEEEEe
Confidence 45556666789999999999743 222345799999999844 454 88999999 99999999999 4 999999
Q ss_pred ccccCCccccccccccccccccCCCccccCCCccccccCCc
Q 018828 109 NVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANH 149 (350)
Q Consensus 109 ~~~~~~~e~~~l~s~~v~l~~K~W~~tl~l~~f~~n~d~N~ 149 (350)
.|.+...|+.|+. +++.+.|.+. ...+|....++|+
T Consensus 215 ~~~v~~~~~~~~~----nv~~~s~~~~-~~~~y~e~~k~~~ 250 (316)
T KOG1555|consen 215 PLHVLPYEQLMLL----NVPLKSWKSL-QDVLYEEKLKAYL 250 (316)
T ss_pred eEEechhhhhchh----ccchhhhhhc-chhhHHHHHHHhh
Confidence 9999999999999 9999999886 6666666677764
No 22
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=97.37 E-value=0.00018 Score=70.62 Aligned_cols=63 Identities=21% Similarity=0.288 Sum_probs=55.1
Q ss_pred cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828 5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG 71 (350)
Q Consensus 5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~ 71 (350)
++-....||||-||- ++.+.|.-=|++|..||.+.+.-|++|.||.. ++.|...+.|||.+|.
T Consensus 94 vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~k---ssqG~L~lrAyrLTp~ 156 (339)
T KOG1560|consen 94 VNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIK---SSQGTLSLRAYRLTPE 156 (339)
T ss_pred cCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEecccc---ccCceEEeehhhcCHH
Confidence 444566899999995 88999999999999999999999999999964 5678999999999884
No 23
>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=97.36 E-value=0.00019 Score=59.94 Aligned_cols=36 Identities=33% Similarity=0.408 Sum_probs=31.0
Q ss_pred ceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828 10 RVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC 50 (350)
Q Consensus 10 ~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP 50 (350)
.+||-|||||.-.+.||..|+. ++ ..++.+.||++.
T Consensus 60 ~ivgi~HSHP~~~a~PS~~D~~-~~----~~~~~~~iIvs~ 95 (108)
T cd08073 60 EIVAVVHSHPDGSPAPSEADRA-QQ----EATGLPWIIVSW 95 (108)
T ss_pred CEEEEEEcCCCCCCCCCHHHHH-Hh----hcCCCcEEEEEc
Confidence 7999999999999999999986 22 337889999995
No 24
>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=96.95 E-value=0.0013 Score=63.01 Aligned_cols=67 Identities=12% Similarity=0.134 Sum_probs=48.6
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCCC
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGK 72 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~ 72 (350)
|.+++...+.+||||++.|. ++.+ .|..-|..|....+.-|.|++||... .+.++.-+.||++....
T Consensus 75 ~~kkV~~~~~vVGWY~tg~~-~~~~--~~~~Ih~~~~~~~~~pv~L~~D~~~~--~~~~~lpi~ay~s~~~~ 141 (288)
T cd08063 75 QFKQVFKDLDFVGWYTTGPG-GPTE--SDLPIHKQILEINESPVLLLLDPEAN--ASGKDLPVTIYESVLEL 141 (288)
T ss_pred HHHHhccCCceEEEEecCCC-CCCH--HHHHHHHHHHhhCCCcEEEEEccccc--cCCCCCceeEEEEEEec
Confidence 35678888999999999998 4444 45555555556667779999998541 13567789999987643
No 25
>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=96.58 E-value=0.0035 Score=50.49 Aligned_cols=40 Identities=28% Similarity=0.392 Sum_probs=31.3
Q ss_pred CCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828 6 GRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC 50 (350)
Q Consensus 6 gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP 50 (350)
..+..+||-|||||.-.+.||..|+..... ....-+|++.
T Consensus 53 ~~~~~~v~i~HsHP~g~~~PS~~D~~~~~~-----~~~~~iIv~~ 92 (101)
T cd08059 53 EIGMKVVGLVHSHPSGSCRPSEADLSLFTR-----FGLYHVIVCY 92 (101)
T ss_pred hCCCcEEEEEecCcCCCCCCCHHHHHHHHh-----cCCeEEEEEC
Confidence 345689999999999999999999983321 3667778763
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=96.22 E-value=0.0077 Score=58.40 Aligned_cols=62 Identities=23% Similarity=0.322 Sum_probs=54.4
Q ss_pred CCCCceeeeeccCCCC----CCCCChHHHHhHHHhhh------hCcCceEEEeccccccccccCceEEEEEEeeCCC
Q 018828 6 GRTTRVIGWYHSHPHI----TVLPSHVDVRTQAMYQL------LDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGK 72 (350)
Q Consensus 6 gR~l~VVGWYHSHP~~----~~~PS~vDV~TQ~~yQ~------~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~ 72 (350)
..++..|||.++|+.- .+++|..+|.+-+.+|. ....||-+|++|-. .|.+.+.|||+.+..
T Consensus 90 ~lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~-----~g~i~~~ayQvSdq~ 161 (274)
T cd08061 90 ALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK-----DGQIHFEAYQVSDQA 161 (274)
T ss_pred HcCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC-----CCceeeeeeeecHHH
Confidence 3568999999999987 89999999999999996 56899999999843 388999999998863
No 27
>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=96.15 E-value=0.0074 Score=52.98 Aligned_cols=46 Identities=24% Similarity=0.329 Sum_probs=35.5
Q ss_pred ccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEec
Q 018828 4 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFS 49 (350)
Q Consensus 4 ~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvS 49 (350)
+.+..+..||=+||||...+-||.+|..+-...=.-...++-||+.
T Consensus 68 ~s~g~~~ylGeWHtHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG 113 (131)
T TIGR02256 68 VSGGVDTYLGEWHTHPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG 113 (131)
T ss_pred HhCCceEEEEecCcCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence 3455689999999999999999999998766543334556667766
No 28
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=95.58 E-value=0.018 Score=56.43 Aligned_cols=62 Identities=18% Similarity=0.309 Sum_probs=46.6
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeC
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD 70 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~ 70 (350)
|.+++...+.+||||++-|..+ ..|+.-|..|....+.-|-|++|+.- ..+++-+.||.+.+
T Consensus 79 ~~k~V~~~~~vVGWY~tg~~i~----~~d~~IH~~~~~~~~~Pv~L~vD~~~----~~~~lpi~aY~s~~ 140 (303)
T PLN03246 79 MFKRINAKEHVVGWYSTGPKLR----ENDLDIHELFNDYVPNPVLVIIDVQP----KELGIPTKAYYAVE 140 (303)
T ss_pred HHHHhCCCCcEEeeecCCCCCC----cchHHHHHHHHhhCCCCeEEEEecCC----CCCCCceEEEEEEE
Confidence 3567888999999999988854 35677778888877777778998632 23456788898765
No 29
>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=94.02 E-value=0.03 Score=52.23 Aligned_cols=43 Identities=16% Similarity=0.137 Sum_probs=33.1
Q ss_pred cCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecccc
Q 018828 5 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFS 52 (350)
Q Consensus 5 ~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~ 52 (350)
..+++..|+-|||||..+++||..|..-- ..+--|+.|+...+
T Consensus 130 ~~~ge~lV~iyHSH~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~ 172 (192)
T TIGR03735 130 LDDGEHLVVDLHSHGTGSAFFSETDDADD-----KGEVKISGVLGCLD 172 (192)
T ss_pred HhCCCeEEEEEcCCCCCCCCCCcccchhh-----cCceEEEEEEEecC
Confidence 36788999999999999999999998722 12346677777554
No 30
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=93.41 E-value=0.062 Score=52.56 Aligned_cols=46 Identities=20% Similarity=0.460 Sum_probs=33.2
Q ss_pred CccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEecc
Q 018828 1 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC 50 (350)
Q Consensus 1 M~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP 50 (350)
|.+++...+.+|||||+=|.. .++.+||+. ++-.+-+--|-+|+|.
T Consensus 82 mfkKvNakekivGWYhTGPkl--~~nDl~In~--l~k~y~pnpvLvIIdv 127 (309)
T KOG1556|consen 82 MFKKVNAKEKVVGWYHTGPKL--RENDLDINE--LLKRYVPNPVLVIIDV 127 (309)
T ss_pred HHHHhcchhheeeeeccCCcc--ccchhhHHH--HHhhcCCCceEEEEec
Confidence 677889999999999998875 456666664 4445555566667774
No 31
>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=93.08 E-value=0.17 Score=46.38 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=24.3
Q ss_pred CCCceeeeeccCCCCC-CCCChHHHHhHHHhhh---hCcCceEEEec
Q 018828 7 RTTRVIGWYHSHPHIT-VLPSHVDVRTQAMYQL---LDTGFIGLIFS 49 (350)
Q Consensus 7 R~l~VVGWYHSHP~~~-~~PS~vDV~TQ~~yQ~---~~~pfVaLIvS 49 (350)
+++.+||+|||||.+. .-|+.+ +.+.-.. ..+..+.++++
T Consensus 68 ~gl~IvG~Yhsh~~~~d~~~~~~---a~kIadki~~~~~~a~ll~vd 111 (182)
T cd08060 68 SGLVIVGYYQANERLDDSSPSPV---AKKIADKIAENFSNACLLMVD 111 (182)
T ss_pred CCCEEEEEEecCCcccCCCCcHH---HHHHHHHHHHhCCCCEEEEEe
Confidence 5789999999999985 233332 2222222 23456666666
No 32
>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=88.81 E-value=1 Score=44.70 Aligned_cols=60 Identities=20% Similarity=0.282 Sum_probs=51.9
Q ss_pred CCceeeeeccCCC---------------CCCCCChHHHHhHHHhhhh-------------CcCceEEEeccccccccccC
Q 018828 8 TTRVIGWYHSHPH---------------ITVLPSHVDVRTQAMYQLL-------------DTGFIGLIFSCFSEDANKVG 59 (350)
Q Consensus 8 ~l~VVGWYHSHP~---------------~~~~PS~vDV~TQ~~yQ~~-------------~~pfVaLIvSP~~~d~~s~G 59 (350)
++..|||.=+|+. -..++|..+|.+=+.+|.. ...||-+|+++ ...|
T Consensus 57 GL~rVG~IfTdl~~~~~~~g~v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg-----~~~g 131 (306)
T PF05021_consen 57 GLERVGWIFTDLTDDGSGDGTVKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSG-----DEEG 131 (306)
T ss_pred CCEEEEEEEecCcccccCCCceeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeC-----CCCC
Confidence 6899999999998 7889999999999999974 35799999997 2468
Q ss_pred ceEEEEEEeeCCC
Q 018828 60 RIQVIAFQSSDGK 72 (350)
Q Consensus 60 kv~i~AFR~~~~~ 72 (350)
++.+.|||+.+..
T Consensus 132 ~i~~~ayQvS~q~ 144 (306)
T PF05021_consen 132 EIHFEAYQVSNQC 144 (306)
T ss_pred ceeeEEeeehHHH
Confidence 9999999998754
No 33
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=75.83 E-value=4.4 Score=31.48 Aligned_cols=28 Identities=29% Similarity=0.344 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 018828 279 ALQDRLKENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 279 ~l~drl~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
++|.||..-|.||+..+.+++.-|+++.
T Consensus 29 tiEqRLa~LE~rL~~ae~ra~~ae~~~~ 56 (60)
T PF11471_consen 29 TIEQRLAALEQRLQAAEQRAQAAEARAK 56 (60)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999999998888873
No 34
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.
Probab=71.03 E-value=22 Score=35.88 Aligned_cols=82 Identities=13% Similarity=0.200 Sum_probs=61.2
Q ss_pred CcchhHHHHhHHHHHHHHHHHHHHHHhhcCCCCCCccceeeh-----hhHHHHHHHHHHHHHHhHH-------HHHHHHH
Q 018828 216 SPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHH-----TSTYQASMCKLIEYCLSPA-------ISALQDR 283 (350)
Q Consensus 216 ~~l~s~~~Lq~iL~~EE~~ay~qa~~q~~~~~~~hpLt~iHh-----~sty~~slc~l~e~~l~P~-------~~~l~dr 283 (350)
.+++++.++..+=.+.=.++|.+++.. ...+++|. .--|++.+-++||..|..+ |..+.+|
T Consensus 225 ~~v~s~re~~d~W~~~ae~~~~e~~~S-------~efak~~G~lvna~m~lr~~~qe~~e~~L~~LnlPTRsElDe~~kr 297 (320)
T TIGR01834 225 KPVKTAKALYDLWVIAAEEAYAEVFAS-------EENAKVHGKFINALMRLRIQQQEIVEALLKMLNLPTRSELDEAHQR 297 (320)
T ss_pred CCchhHHHHHHHHHHHHHHHHHHHHcC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 456777777777766666677776631 33444443 2358888999999999887 7888899
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 018828 284 LKENEIRLAMLTDEAKSLESE 304 (350)
Q Consensus 284 l~~n~~rl~~L~~e~~~L~~e 304 (350)
|.|-+.|++.|+.|+.+|+++
T Consensus 298 L~ELrR~vr~L~k~l~~l~~~ 318 (320)
T TIGR01834 298 IQQLRREVKSLKKRLGDLEAN 318 (320)
T ss_pred HHHHHHHHHHHHHHHHHhhhc
Confidence 999999999999998888865
No 35
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=70.95 E-value=21 Score=27.72 Aligned_cols=26 Identities=31% Similarity=0.408 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLE 302 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~ 302 (350)
+..||.||+++|.|++.-+.++++.+
T Consensus 34 La~LE~rL~~ae~ra~~ae~~~~~~k 59 (60)
T PF11471_consen 34 LAALEQRLQAAEQRAQAAEARAKQAK 59 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 78899999999999999888888764
No 36
>PF15458 NTR2: Nineteen complex-related protein 2
Probab=63.76 E-value=64 Score=31.10 Aligned_cols=78 Identities=22% Similarity=0.366 Sum_probs=44.7
Q ss_pred HHHhHHHHH-------HHHHHHHHHHHhhcCCCCC--------CccceeehhhHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 018828 222 TDLQRVLYE-------EERAAYNQAIMQNMSDGKV--------HPLTYIHHTSTYQASMCKLIEYCLSPAISALQDRLKE 286 (350)
Q Consensus 222 ~~Lq~iL~~-------EE~~ay~qa~~q~~~~~~~--------hpLt~iHh~sty~~slc~l~e~~l~P~~~~l~drl~~ 286 (350)
..+.+.+.+ ||..+|+.|......+|.. -|+..|=---+-...+- =|.=.+..|+.+.++
T Consensus 152 ~~i~e~I~~~~~d~~de~~~~wE~aQ~rkg~~~~~~~~~~~~~~~ip~~tpLP~L~~~~~-----rL~~~l~~le~~~~~ 226 (254)
T PF15458_consen 152 EEIEEAINDDDDDSEDEERAEWEAAQLRKGMDGLSDEKDRYKPPPIPKITPLPSLSECLE-----RLRESLSSLEDSKSQ 226 (254)
T ss_pred HHHHHHHHhcccccchhhHHHHHHHHHHhhccCCccchhccCCCCCcccCCCCchhHHHH-----HHHHHHHHHHHHHHH
Confidence 356667777 8899999877644333333 11111111111111111 122335778888888
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 018828 287 NEIRLAMLTDEAKSLESE 304 (350)
Q Consensus 287 n~~rl~~L~~e~~~L~~e 304 (350)
...||+.|+.|++.|...
T Consensus 227 ~~~~l~~l~~E~~~I~~r 244 (254)
T PF15458_consen 227 LQQQLESLEKEKEEIEER 244 (254)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 888888888888877653
No 37
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=54.79 E-value=30 Score=28.10 Aligned_cols=34 Identities=35% Similarity=0.485 Sum_probs=30.7
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 272 CLSPAISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 272 ~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
-..|.+..|++++++-+.+++.++++.+.+++++
T Consensus 67 ~~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~ 100 (104)
T PF13600_consen 67 SDSPELKELEEELEALEDELAALQDEIQALEAQI 100 (104)
T ss_pred cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999999999999999886
No 38
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=51.32 E-value=9.8 Score=34.99 Aligned_cols=29 Identities=28% Similarity=0.393 Sum_probs=22.8
Q ss_pred CCCceeeeeccCCCCCCCCChHHHHhHHHh
Q 018828 7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMY 36 (350)
Q Consensus 7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~y 36 (350)
....++. +||||.-+..||..|...=...
T Consensus 114 ~~~~iid-iHSHP~~~~~~S~~D~~~~~~~ 142 (162)
T PF15659_consen 114 NGNKIID-IHSHPENSNGPSGNDMKNAKPR 142 (162)
T ss_pred CCceEEE-eccCCCCCCCCCcchhhhhhhc
Confidence 3456677 9999999999999998754433
No 39
>PF01621 Fusion_gly_K: Cell fusion glycoprotein K; InterPro: IPR002567 Human herpesvirus 1 (HHV-1) (Human herpes simplex virus 1) glycoprotein K (gK) plays an essential role in viral replication and cell fusion. gK is a very hydrophobic membrane protein that contains a signal sequence and several hydrophobic regions. gK contains three transmembrane domains (amino acids 125-139, 226-239, and 311-325) and another hydrophobic domain (amino acids 241-265), which is relatively less hydrophobic and much longer compared with the transmembrane sequences located in the extracellular loop. The domains may interact with each other to form a complex tertiary structure that is critical for the biological function of gK [].; GO: 0007155 cell adhesion, 0016020 membrane
Probab=49.91 E-value=18 Score=36.82 Aligned_cols=35 Identities=23% Similarity=0.455 Sum_probs=29.4
Q ss_pred hhHHHHhHHHHHHHHHHHHHHHHhhcCCCCCCccceeehh
Q 018828 219 TSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHT 258 (350)
Q Consensus 219 ~s~~~Lq~iL~~EE~~ay~qa~~q~~~~~~~hpLt~iHh~ 258 (350)
..++.|++.|+ |-+.++||+.|.+ +.||+||.+|-
T Consensus 177 ~pYTK~arlmc--Els~~R~als~~F---~~DPitFl~~h 211 (337)
T PF01621_consen 177 YPYTKMARLMC--ELSIQRQALSRIF---KADPITFLYRH 211 (337)
T ss_pred CChHHHHHHHH--HHHHHHHHHHHHh---ccCCCeeeeeC
Confidence 46899999999 7889999998665 66999998874
No 40
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=45.41 E-value=60 Score=25.45 Aligned_cols=30 Identities=33% Similarity=0.368 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 276 AISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 276 ~~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+-.+++.||++.+.|-..|..|.+.|+.++
T Consensus 26 ~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ 55 (61)
T PF08826_consen 26 ANLAFESKLQEAEKRNRELEQEIERLKKEM 55 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678889999999999999988888877
No 41
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=44.30 E-value=96 Score=26.21 Aligned_cols=45 Identities=13% Similarity=0.047 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 018828 264 SMCKLIEYCLSPA---------ISALQDRLKENEIRLAMLTDEAKSLESEAFKG 308 (350)
Q Consensus 264 slc~l~e~~l~P~---------~~~l~drl~~n~~rl~~L~~e~~~L~~e~~~~ 308 (350)
-+|-++-++.-++ ...++.++++.+.+++.|+++.++|++|+..-
T Consensus 7 vll~ll~~l~y~l~~g~~G~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L 60 (105)
T PRK00888 7 LLLALLVWLQYSLWFGKNGILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDL 60 (105)
T ss_pred HHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455566666554 45577888888888889999999998888543
No 42
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=44.25 E-value=36 Score=27.23 Aligned_cols=27 Identities=33% Similarity=0.389 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 018828 284 LKENEIRLAMLTDEAKSLESEAFKGSD 310 (350)
Q Consensus 284 l~~n~~rl~~L~~e~~~L~~e~~~~~~ 310 (350)
..|-+.|++.|++|.+.|++|+.+...
T Consensus 27 V~El~eRIalLq~EIeRlkAe~~kK~~ 53 (65)
T COG5509 27 VAELEERIALLQAEIERLKAELAKKKA 53 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 346678899999999999999976543
No 43
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.69 E-value=1.3e+02 Score=29.36 Aligned_cols=34 Identities=18% Similarity=0.292 Sum_probs=26.2
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 271 YCLSPAISALQDRLKENEIRLAMLTDEAKSLESE 304 (350)
Q Consensus 271 ~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e 304 (350)
|.|.=.+.-+|.-|+..++++++|+...+.|+++
T Consensus 44 Y~laQ~vliqE~ALk~a~~~i~eLe~ri~~lq~~ 77 (233)
T COG3416 44 YYLAQRVLIQEQALKKASTQIKELEKRIAILQAG 77 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4455555567788888888888998888888886
No 44
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=36.18 E-value=90 Score=23.54 Aligned_cols=31 Identities=19% Similarity=0.252 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEAFK 307 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~~~ 307 (350)
+..++..+++.+.+++.|++|.++|++++..
T Consensus 19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~ 49 (80)
T PF04977_consen 19 YYQLNQEIAELQKEIEELKKENEELKEEIER 49 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446677777888888888888888888754
No 45
>PHA03278 envelope glycoprotein K; Provisional
Probab=35.89 E-value=35 Score=34.97 Aligned_cols=34 Identities=24% Similarity=0.448 Sum_probs=28.7
Q ss_pred hhHHHHhHHHHHHHHHHHHHHHHhhcCCCCCCccceeeh
Q 018828 219 TSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHH 257 (350)
Q Consensus 219 ~s~~~Lq~iL~~EE~~ay~qa~~q~~~~~~~hpLt~iHh 257 (350)
..++.|.+.|+ |-+.++||+.+ +-+.||+||.++
T Consensus 177 ~~YTK~arlmc--Els~~R~alsr---~F~~DPItFl~~ 210 (347)
T PHA03278 177 CTYTKMARLMC--ELSIRRNALSR---DFKEDPITFAFR 210 (347)
T ss_pred CChHHHHHHHH--HHHHHHHHHHH---hhccCCceeeee
Confidence 46899999999 88899999974 567799999876
No 46
>COG2132 SufI Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=35.37 E-value=25 Score=35.65 Aligned_cols=8 Identities=63% Similarity=1.497 Sum_probs=7.6
Q ss_pred eeccCCCC
Q 018828 14 WYHSHPHI 21 (350)
Q Consensus 14 WYHSHP~~ 21 (350)
|||||++.
T Consensus 129 wyh~H~~~ 136 (451)
T COG2132 129 WYHPHTHG 136 (451)
T ss_pred EeccCCCc
Confidence 99999987
No 47
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=35.21 E-value=92 Score=31.25 Aligned_cols=62 Identities=21% Similarity=0.287 Sum_probs=47.0
Q ss_pred ccccCCCCceeeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccccccccccCceEEEEEEeeCC
Q 018828 2 TVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG 71 (350)
Q Consensus 2 ~~~~gR~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~ 71 (350)
.+++.-++.|||||=.=++.+..=|.| |--|-.--+++|-+-+|. ..+.|+..+.||-..+-
T Consensus 91 ~~k~npnE~vvGWyaTg~dvt~~ssli----hdyYare~~~pvhLtVDT----~~~n~rm~ikaYvss~~ 152 (288)
T KOG2975|consen 91 HKKVNPNELVVGWYATGHDVTEHSSLI----HDYYAREAPNPVHLTVDT----SLQNGRMSIKAYVSSLM 152 (288)
T ss_pred hcccCCCceeEEEEecCCCcccchhHH----HHHhhccCCCCeEEEEec----cccCCccceeEEEEecc
Confidence 356778899999999999988887776 666655567788888873 23457888999987653
No 48
>PHA03275 envelope glycoprotein K; Provisional
Probab=34.17 E-value=39 Score=34.58 Aligned_cols=35 Identities=26% Similarity=0.392 Sum_probs=28.9
Q ss_pred hhHHHHhHHHHHHHHHHHHHHHHhhcCCCCCCccceeehh
Q 018828 219 TSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHT 258 (350)
Q Consensus 219 ~s~~~Lq~iL~~EE~~ay~qa~~q~~~~~~~hpLt~iHh~ 258 (350)
..++.|.|.|+ |-+.++|++.+ +-+.||++|.+|-
T Consensus 175 ~~YTK~arllc--Els~~R~als~---~F~~DPItFl~~h 209 (340)
T PHA03275 175 TPYTKLARLLC--EVSLRRVALSK---TFKRDPIGFLCEH 209 (340)
T ss_pred CChHHHHHHHH--HHHHHHHHHHH---hhccCCcEEeeeC
Confidence 46899999999 88899999974 5577999998754
No 49
>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]
Probab=33.74 E-value=56 Score=37.43 Aligned_cols=33 Identities=39% Similarity=0.478 Sum_probs=30.3
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 273 LSPAISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 273 l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
|--+|+.+|+-++||+++|..+..++.+|++|+
T Consensus 125 lQ~ti~~~q~d~ke~etelE~~~srlh~le~eL 157 (1265)
T KOG0976|consen 125 LQDTIQGAQDDKKENEIEIENLNSRLHKLEDEL 157 (1265)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 455788999999999999999999999999998
No 50
>PHA03279 envelope glycoprotein K; Provisional
Probab=33.34 E-value=47 Score=34.21 Aligned_cols=34 Identities=24% Similarity=0.227 Sum_probs=27.3
Q ss_pred hhHHHHhHHHHHHHHHHHHHHHHhhcCCCCCCccceeeh
Q 018828 219 TSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHH 257 (350)
Q Consensus 219 ~s~~~Lq~iL~~EE~~ay~qa~~q~~~~~~~hpLt~iHh 257 (350)
..++.|++.|+ |-+.+++++.+. -+.||++|.++
T Consensus 203 ~pYTK~aRlLc--E~s~~R~alSr~---F~~DPItFl~~ 236 (361)
T PHA03279 203 VPYLKLQRFLR--EFEHRRDCKSLN---FSADPLGFCIC 236 (361)
T ss_pred CchHHHHHHHH--HHHHHHHHHHHh---hccCCceeeee
Confidence 46899999999 777899999754 56799997544
No 51
>TIGR03782 Bac_Flav_CT_J Bacteroides conjugative transposon TraJ protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage. This family is related conjugation system proteins in the Proteobacteria, including TrbL of Agrobacterium Ti plasmids and VirB6.
Probab=32.99 E-value=69 Score=32.62 Aligned_cols=39 Identities=23% Similarity=0.360 Sum_probs=35.4
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 018828 268 LIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 268 l~e~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
.|..+++|+.+.=+.=++.+...++.|+++++.||.|..
T Consensus 78 ~in~v~spvv~gT~~m~~~q~~dl~~l~~qkd~L~~e~~ 116 (322)
T TIGR03782 78 TINGVLSPVVQGTHSMLEGQTLDMNRYREQKDKLEYEAM 116 (322)
T ss_pred HhhhhhHHHHHhHHHHHHccHHHHHHHHHHHHHHHHHHH
Confidence 366788999999999999999999999999999999984
No 52
>PHA03276 envelope glycoprotein K; Provisional
Probab=31.24 E-value=46 Score=33.98 Aligned_cols=34 Identities=24% Similarity=0.460 Sum_probs=28.5
Q ss_pred hhHHHHhHHHHHHHHHHHHHHHHhhcCCCCCCccceeeh
Q 018828 219 TSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHH 257 (350)
Q Consensus 219 ~s~~~Lq~iL~~EE~~ay~qa~~q~~~~~~~hpLt~iHh 257 (350)
..++.|.+.|+ |-+.+++++.+ +-+.||++|.++
T Consensus 176 ~~YTK~arlmc--E~s~~R~als~---~F~~DPitFl~~ 209 (337)
T PHA03276 176 YPYTKITRLLC--ELSVQRQSLVE---IFEADPVTFLYH 209 (337)
T ss_pred CChHHHHHHHH--HHHHHHHHHHH---hhccCCceEeee
Confidence 46899999999 78899999975 557799999875
No 53
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=31.21 E-value=72 Score=34.09 Aligned_cols=28 Identities=14% Similarity=0.291 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 018828 278 SALQDRLKENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 278 ~~l~drl~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
.+.-+.+...| ++++|+.|.++|+++..
T Consensus 21 ~a~~~~~~~~q-kie~L~kql~~Lk~q~~ 48 (489)
T PF11853_consen 21 AAMADDIDLLQ-KIEALKKQLEELKAQQD 48 (489)
T ss_pred hhhhhhhHHHH-HHHHHHHHHHHHHHhhc
Confidence 34445555445 77777777777777753
No 54
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=29.44 E-value=1.5e+02 Score=22.34 Aligned_cols=29 Identities=28% Similarity=0.376 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+..|++++..-+.....|..+...|+.++
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~ 56 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEI 56 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555555444
No 55
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=29.42 E-value=75 Score=38.24 Aligned_cols=62 Identities=21% Similarity=0.253 Sum_probs=48.1
Q ss_pred CCCceeeeeccCCCCCCCCChHHHHhHHHhhh-hCcCceEEEeccccccccccCceEEEEEEeeCCCCc
Q 018828 7 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQL-LDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQN 74 (350)
Q Consensus 7 R~l~VVGWYHSHP~~~~~PS~vDV~TQ~~yQ~-~~~pfVaLIvSP~~~d~~s~Gkv~i~AFR~~~~~~~ 74 (350)
.++.-+||.|.-|.=-+.+|..||.|+.---. -.+.||-|-|+ ...|.+.+.||.+++.++.
T Consensus 2163 ~d~e~Lgw~hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~------~tpgs~sl~ay~lt~~G~e 2225 (2321)
T KOG1795|consen 2163 EDLEPLGWIHTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCS------FTPGSCSLTAYKLTPSGYE 2225 (2321)
T ss_pred cCCcccchhhcCccccccCCHHHhhhhhhhhhcCccceEEEEee------ccCCcceeeeeccCccccc
Confidence 35677999999999999999999999975432 23567666665 2357889999999987764
No 56
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=29.41 E-value=1.5e+02 Score=21.85 Aligned_cols=24 Identities=29% Similarity=0.320 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 280 LQDRLKENEIRLAMLTDEAKSLES 303 (350)
Q Consensus 280 l~drl~~n~~rl~~L~~e~~~L~~ 303 (350)
|+.++.+-+.....|..+...|+.
T Consensus 30 le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 30 LEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344444444444444444444443
No 57
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=29.00 E-value=1.7e+02 Score=23.24 Aligned_cols=35 Identities=17% Similarity=0.286 Sum_probs=22.9
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 271 YCLSPAISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 271 ~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
.++.|.+..|...+++.+..+..|+++...+..|.
T Consensus 15 i~l~~~l~~l~~~l~~~~~ti~~l~~~~~~i~~e~ 49 (90)
T PF06103_consen 15 IFLIKVLKKLKKTLDEVNKTIDTLQEQVDPITKEI 49 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 45666666666667666666666666666666555
No 58
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=27.52 E-value=2.9e+02 Score=22.56 Aligned_cols=39 Identities=28% Similarity=0.239 Sum_probs=26.3
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 267 KLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 267 ~l~e~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+..+--+..+...++.+.++.+.+++.+.++.+.|++++
T Consensus 80 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~e~ 118 (120)
T PF11740_consen 80 EEAEEELEAARAELEQERAAAEAELAEAEAQAEELEAEL 118 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334444455556677777777777777777777777775
No 59
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=27.48 E-value=1.8e+02 Score=23.07 Aligned_cols=29 Identities=28% Similarity=0.416 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+..|.+++++-+.|...|+.|..-|..-+
T Consensus 16 VevLK~~I~eL~~~n~~Le~EN~~Lk~~~ 44 (59)
T PF01166_consen 16 VEVLKEQIAELEERNSQLEEENNLLKQNA 44 (59)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 56788999999999999999888887766
No 60
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=27.26 E-value=3.3e+02 Score=22.82 Aligned_cols=35 Identities=20% Similarity=0.208 Sum_probs=24.2
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 018828 272 CLSPAISALQDRLKENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 272 ~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
++.=++..+.=+++..+.+.+.|.+|.++|..|..
T Consensus 13 v~~~i~~y~~~k~~ka~~~~~kL~~en~qlk~Ek~ 47 (87)
T PF10883_consen 13 VVALILAYLWWKVKKAKKQNAKLQKENEQLKTEKA 47 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444556777777777777888888887777653
No 61
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=27.20 E-value=69 Score=28.05 Aligned_cols=26 Identities=23% Similarity=0.390 Sum_probs=19.8
Q ss_pred CCceeeeeccCCCCCC-----CCChHHHHhH
Q 018828 8 TTRVIGWYHSHPHITV-----LPSHVDVRTQ 33 (350)
Q Consensus 8 ~l~VVGWYHSHP~~~~-----~PS~vDV~TQ 33 (350)
+..+|+=||+|..+.. .||..|+..-
T Consensus 58 g~~~vA~yHTHG~~~~~y~~evfS~~D~~~~ 88 (123)
T PF14220_consen 58 GSTIVASYHTHGAYSDGYDNEVFSPQDIRGD 88 (123)
T ss_pred ccceeeEeecccccCCCccccCCCHHHhhhh
Confidence 4689999999997754 5777777654
No 62
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.09 E-value=2.8e+02 Score=20.61 Aligned_cols=22 Identities=32% Similarity=0.225 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 018828 285 KENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 285 ~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
-..+.+++.+++|.+++|+|+.
T Consensus 44 ~~~r~~~~~~~k~l~~le~e~~ 65 (68)
T PF06305_consen 44 LRLRRRIRRLRKELKKLEKELE 65 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667788888888888873
No 63
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=26.08 E-value=1.9e+02 Score=23.82 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 259 STYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 259 sty~~slc~l~e~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
-+|..-=--+++.-..=|+..|++|++.-+.+++.|..+.+.|++++
T Consensus 47 ~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~ 93 (105)
T cd00632 47 EVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKL 93 (105)
T ss_pred hHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34433333445555556788899999999888888888888888776
No 64
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=25.65 E-value=5.2e+02 Score=27.92 Aligned_cols=27 Identities=37% Similarity=0.480 Sum_probs=22.6
Q ss_pred chhHHHHhHHHHHHHHHHHHHHHHhhc
Q 018828 218 LTSFTDLQRVLYEEERAAYNQAIMQNM 244 (350)
Q Consensus 218 l~s~~~Lq~iL~~EE~~ay~qa~~q~~ 244 (350)
|+|-.+=|+..+++.-..|+|+-.+|.
T Consensus 326 l~sqleSqr~y~e~~~~e~~qsqlen~ 352 (493)
T KOG0804|consen 326 LTSQLESQRKYYEQIMSEYEQSQLENQ 352 (493)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHhH
Confidence 678888999999999999999666554
No 65
>smart00338 BRLZ basic region leucin zipper.
Probab=25.58 E-value=1.8e+02 Score=21.89 Aligned_cols=29 Identities=24% Similarity=0.318 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+..|+++++.-+.....|..+...|+.|+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~ 56 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRREL 56 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55567776666666666666666666665
No 66
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=25.37 E-value=1.6e+02 Score=24.55 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=36.3
Q ss_pred hhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 018828 257 HTSTYQASMCKLIEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 257 h~sty~~slc~l~e~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
.+-+|-.-=-=||+.-..=++..|.+|++.-+.+++.|++..+.|+.++.
T Consensus 49 d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~ 98 (110)
T TIGR02338 49 DTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLK 98 (110)
T ss_pred cchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455444344556556667888999999999999999888888887763
No 67
>PF14331 ImcF-related_N: ImcF-related N-terminal domain
Probab=24.89 E-value=5.5e+02 Score=24.57 Aligned_cols=100 Identities=22% Similarity=0.287 Sum_probs=68.2
Q ss_pred eeeeeeeecCCCcccCCCcchhHHHHhHHHHHHHHHHHHHHHHhhcCCCCCCccceeehhhH---HHHHHHHHHHHHHhH
Q 018828 199 KEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQAIMQNMSDGKVHPLTYIHHTST---YQASMCKLIEYCLSP 275 (350)
Q Consensus 199 kEvpl~v~p~~~~~~~~~~l~s~~~Lq~iL~~EE~~ay~qa~~q~~~~~~~hpLt~iHh~st---y~~slc~l~e~~l~P 275 (350)
..+|++|+ +.|+| -|..|...-+-|-+||++ |++ |-.-|......... +...+-.|++.+-.=
T Consensus 68 ~~~PVYvv----~Tk~D-~l~GF~ef~~~L~~~~r~---q~l------G~t~~~~~~~~~~~~~~~~~~~~~l~~~L~~~ 133 (266)
T PF14331_consen 68 VRLPVYVV----FTKCD-LLPGFDEFFSDLSEEERE---QVL------GFTFPYDEDADGDAWAWFDEEFDELVARLNAR 133 (266)
T ss_pred CCCCeEee----eECCC-cccCHHHHHHhCCHHHHh---CCc------ccccCCccccccchHHHHHHHHHHHHHHHHHH
Confidence 46899998 44665 578999999999999876 334 66666666555554 777777776666555
Q ss_pred HHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 018828 276 AISALQDR--------LKENEIRLAMLTDEAKSLESEAFKGSDSS 312 (350)
Q Consensus 276 ~~~~l~dr--------l~~n~~rl~~L~~e~~~L~~e~~~~~~~~ 312 (350)
++..|.+- +-.==.+++.|++-...+..++|..+.-.
T Consensus 134 ~~~~l~~~~~~~~r~~l~~FP~ql~~L~~~L~~fl~~~f~~~~~~ 178 (266)
T PF14331_consen 134 VLERLAQERDAERRAALFSFPRQLAALRPPLREFLEELFRPNPYQ 178 (266)
T ss_pred HHHHHHhhcCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 55544421 12223567888888888889998776544
No 68
>PRK04325 hypothetical protein; Provisional
Probab=24.33 E-value=1.4e+02 Score=23.78 Aligned_cols=20 Identities=15% Similarity=0.248 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 018828 285 KENEIRLAMLTDEAKSLESE 304 (350)
Q Consensus 285 ~~n~~rl~~L~~e~~~L~~e 304 (350)
-+.+..+..|+.+.+.|-..
T Consensus 33 ~~Qq~~I~~L~~ql~~L~~r 52 (74)
T PRK04325 33 ARQQQTLDLLQAQLRLLYQQ 52 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33334444444444444333
No 69
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=24.04 E-value=1.9e+02 Score=23.15 Aligned_cols=29 Identities=28% Similarity=0.265 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
|..|+-++++-+.+-..|.++.++|..|.
T Consensus 20 i~~Lq~e~eeLke~n~~L~~e~~~L~~en 48 (72)
T PF06005_consen 20 IALLQMENEELKEKNNELKEENEELKEEN 48 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 45566666666666555555566666555
No 70
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=23.63 E-value=2.9e+02 Score=27.61 Aligned_cols=54 Identities=19% Similarity=0.324 Sum_probs=40.8
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCCC--CCCCCcCCC
Q 018828 269 IEYCLSPAISALQDRLKENEIRLAMLTDEAKSLESEAF--KGSDSSL--SSPHHSPSH 322 (350)
Q Consensus 269 ~e~~l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~~--~~~~~~~--~~p~~~~~~ 322 (350)
++.+..=+...+..|+++|+.||+.|.+....+++.+. +|+.... -||.+.+..
T Consensus 30 L~~v~~diF~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs~kAi~vfs~akyP~~ 87 (297)
T PF11945_consen 30 LDKVSNDIFSRISARVERNRERLQAIQQRIEVAQAKIEKLQGSKKAITVFSPAKYPAP 87 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccEEEeCcccCCCc
Confidence 34455567788999999999999999999998888775 5665543 567666543
No 71
>TIGR02376 Cu_nitrite_red nitrite reductase, copper-containing. This family consists of copper-type nitrite reductase. It reduces nitrite to nitric oxide, the first step in denitrification.
Probab=23.41 E-value=66 Score=31.59 Aligned_cols=29 Identities=10% Similarity=-0.017 Sum_probs=16.9
Q ss_pred eeeeccCCCCCCCCChHHHHhHHHhhhhCcCceEEEeccc
Q 018828 12 IGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCF 51 (350)
Q Consensus 12 VGWYHSHP~~~~~PS~vDV~TQ~~yQ~~~~pfVaLIvSP~ 51 (350)
.=|||+|++-. ...|...--+-+|||.|-
T Consensus 119 ty~YH~H~~~~-----------~~~q~~~Gl~G~liV~~~ 147 (311)
T TIGR02376 119 AFVYHCAPPGM-----------VPWHVVSGMNGAIMVLPR 147 (311)
T ss_pred EEEEEcCCCCc-----------hhHHhhcCcceEEEeecc
Confidence 35999997622 122333345667777763
No 72
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=22.69 E-value=2.8e+02 Score=23.50 Aligned_cols=33 Identities=27% Similarity=0.414 Sum_probs=22.4
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 273 LSPAISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 273 l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
|.--+..|++++++-....+.|+.+.+.+.+++
T Consensus 78 L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~ 110 (118)
T PF13815_consen 78 LSSQLEQLEERLQELQQEIEKLKQKLKKQKEEI 110 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566777777777777777776666666665
No 73
>PRK10965 multicopper oxidase; Provisional
Probab=22.65 E-value=36 Score=35.96 Aligned_cols=9 Identities=44% Similarity=1.291 Sum_probs=7.1
Q ss_pred eeeeccCCC
Q 018828 12 IGWYHSHPH 20 (350)
Q Consensus 12 VGWYHSHP~ 20 (350)
-=|||+|++
T Consensus 138 T~WYH~H~~ 146 (523)
T PRK10965 138 TCWFHPHQH 146 (523)
T ss_pred eEEEecCCC
Confidence 349999974
No 74
>PRK10883 FtsI repressor; Provisional
Probab=22.05 E-value=38 Score=35.19 Aligned_cols=9 Identities=33% Similarity=0.907 Sum_probs=7.1
Q ss_pred eeeccCCCC
Q 018828 13 GWYHSHPHI 21 (350)
Q Consensus 13 GWYHSHP~~ 21 (350)
=|||+|.+-
T Consensus 139 ~WYH~H~~~ 147 (471)
T PRK10883 139 CWYHANTPN 147 (471)
T ss_pred eEEccCCCC
Confidence 499999753
No 75
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=21.83 E-value=2.2e+02 Score=22.75 Aligned_cols=29 Identities=21% Similarity=0.249 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+++|++|+.+--.+...|++|...|.++.
T Consensus 2 L~~Le~kle~Li~~~~~L~~EN~~Lr~q~ 30 (65)
T TIGR02449 2 LQALAAQVEHLLEYLERLKSENRLLRAQE 30 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46677777777777777777777776665
No 76
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=21.52 E-value=3.2e+02 Score=26.50 Aligned_cols=35 Identities=29% Similarity=0.290 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEAFKGSDS 311 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~~~~~~~ 311 (350)
++.||.++.+-+.+++.+++=.+.||..+.+....
T Consensus 1 l~~lq~~l~~l~~~~~~~~~L~~kLE~DL~~~~~~ 35 (248)
T PF08172_consen 1 LEELQKELSELEAKLEEQKELNAKLENDLAKVQAS 35 (248)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 35688889999999999998899999888755543
No 77
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=21.37 E-value=4.8e+02 Score=26.55 Aligned_cols=68 Identities=16% Similarity=0.200 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHhhc--------CCCCCCccceeehh------hHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 018828 226 RVLYEEERAAYNQAIMQNM--------SDGKVHPLTYIHHT------STYQASMCKLIEYCLSPAISALQDRLKENEIRL 291 (350)
Q Consensus 226 ~iL~~EE~~ay~qa~~q~~--------~~~~~hpLt~iHh~------sty~~slc~l~e~~l~P~~~~l~drl~~n~~rl 291 (350)
|.++.+|-++|+||+..-+ ..++.-|+++---. +---.+.|-.+.-..+-++..|..|+.....+-
T Consensus 113 R~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKR 192 (334)
T KOG0774|consen 113 RQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKR 192 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5678899999999985332 25778888752111 111123444444445566777877776654443
Q ss_pred HH
Q 018828 292 AM 293 (350)
Q Consensus 292 ~~ 293 (350)
..
T Consensus 193 RN 194 (334)
T KOG0774|consen 193 RN 194 (334)
T ss_pred cc
Confidence 33
No 78
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=20.86 E-value=6.6e+02 Score=25.57 Aligned_cols=84 Identities=25% Similarity=0.289 Sum_probs=54.8
Q ss_pred chhHHHHhHHHHHHHHH-------HHHHHHHhhcCCCCCCccceeehhhHHHHHHHHHHHHHHhHHHHHHHH--------
Q 018828 218 LTSFTDLQRVLYEEERA-------AYNQAIMQNMSDGKVHPLTYIHHTSTYQASMCKLIEYCLSPAISALQD-------- 282 (350)
Q Consensus 218 l~s~~~Lq~iL~~EE~~-------ay~qa~~q~~~~~~~hpLt~iHh~sty~~slc~l~e~~l~P~~~~l~d-------- 282 (350)
|..|-+|-+.- +||. +|-+.+..+..++ ..-+-+-.+...|.+.+-+.++.+.. -|..|++
T Consensus 196 l~~F~~l~~~T--~~R~~f~~r~~~Yf~~l~~~f~d~-a~~~~A~l~~~~~~~~l~~~~~~~~~-~i~~l~~~l~~~~k~ 271 (406)
T PF02388_consen 196 LDDFYDLYKET--AERKGFSIRSLEYFENLYDAFGDK-AKFFLAELNGKEYLESLQEKLEKLEK-EIEKLEEKLEKNPKK 271 (406)
T ss_dssp HHHHHHHHHHH--HHHTT-----HHHHHHHHHHCCCC-EEEEEEEECCHHHHHHHHHHHHHHHH-HHHHHHHHHHH-THH
T ss_pred HHHHHHHHHHH--HhhCCCcccCHHHHHHHHHhcCCC-eEEEEEEEcHHHHHHHHHHHHHHHHH-HHHHHHHHHHhCcch
Confidence 55666655443 2332 6777888888555 67777777889999999888777644 3333443
Q ss_pred --HHHHHHHHHHHHHHHHHHHHHHH
Q 018828 283 --RLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 283 --rl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
++++.+.+++.+..+.+++++.+
T Consensus 272 ~~k~~~~~~q~~~~~k~~~~~~~~~ 296 (406)
T PF02388_consen 272 KNKLKELEEQLASLEKRIEEAEELI 296 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56666666777766666666644
No 79
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=20.62 E-value=1.7e+02 Score=30.53 Aligned_cols=34 Identities=24% Similarity=0.297 Sum_probs=30.9
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 018828 273 LSPAISALQDRLKENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 273 l~P~~~~l~drl~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
.+|.+..|++++++.+.+++.++++++.+++++.
T Consensus 69 ~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~ 102 (525)
T TIGR02231 69 DPERLAELRKQIRELEAELRDLEDRGDALKALAK 102 (525)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999999999999999999988764
No 80
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=20.60 E-value=2.4e+02 Score=21.80 Aligned_cols=31 Identities=19% Similarity=0.323 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEAFK 307 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~~~ 307 (350)
+..++..++..+.+++.|+.|..+|+.|..+
T Consensus 26 ~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~ 56 (85)
T TIGR02209 26 TRQLNNELQKLQLEIDKLQKEWRDLQLEVAE 56 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446667777888888889999999998854
No 81
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=20.54 E-value=2.2e+02 Score=22.16 Aligned_cols=30 Identities=20% Similarity=0.277 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSLESEAF 306 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L~~e~~ 306 (350)
|..|-+-+-+.+.++..|+++.+.|...+.
T Consensus 20 ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~ 49 (69)
T PF04102_consen 20 IEELNDVVTEQQRQIDRLQRQLRLLRERLR 49 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHT--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555556666666667777666666663
No 82
>PLN02168 copper ion binding / pectinesterase
Probab=20.46 E-value=64 Score=34.44 Aligned_cols=8 Identities=13% Similarity=0.139 Sum_probs=6.3
Q ss_pred eeeccCCC
Q 018828 13 GWYHSHPH 20 (350)
Q Consensus 13 GWYHSHP~ 20 (350)
=|||||.+
T Consensus 123 ~WYHsH~~ 130 (545)
T PLN02168 123 YFYFPSLL 130 (545)
T ss_pred EEEecChh
Confidence 39999953
No 83
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.23 E-value=2.8e+02 Score=20.59 Aligned_cols=25 Identities=24% Similarity=0.279 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 277 ISALQDRLKENEIRLAMLTDEAKSL 301 (350)
Q Consensus 277 ~~~l~drl~~n~~rl~~L~~e~~~L 301 (350)
.-.+..+++.-+.+++.++.|.++|
T Consensus 43 ~~~~r~~~~~~~k~l~~le~e~~~l 67 (68)
T PF06305_consen 43 RLRLRRRIRRLRKELKKLEKELEQL 67 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3446678888888888888888776
No 84
>PRK04406 hypothetical protein; Provisional
Probab=20.21 E-value=2.3e+02 Score=22.75 Aligned_cols=22 Identities=14% Similarity=0.338 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 018828 284 LKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 284 l~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+-+.+..+..|+.+.+.|-..+
T Consensus 34 v~~Qq~~I~~L~~ql~~L~~rl 55 (75)
T PRK04406 34 LSQQQLLITKMQDQMKYVVGKV 55 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444555555444444
No 85
>PRK02119 hypothetical protein; Provisional
Probab=20.08 E-value=2.3e+02 Score=22.55 Aligned_cols=24 Identities=8% Similarity=0.185 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 018828 282 DRLKENEIRLAMLTDEAKSLESEA 305 (350)
Q Consensus 282 drl~~n~~rl~~L~~e~~~L~~e~ 305 (350)
+-+-+.+..+..|+.+.+.|-..+
T Consensus 30 ~~v~~Qq~~id~L~~ql~~L~~rl 53 (73)
T PRK02119 30 QALIEQQFVIDKMQVQLRYMANKL 53 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444455555555554444
Done!