Query psy17875
Match_columns 107
No_of_seqs 144 out of 1046
Neff 8.6
Searched_HMMs 46136
Date Sat Aug 17 01:13:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17875.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17875hhsearch_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 8.5E-32 1.8E-36 186.8 12.5 103 3-107 1-108 (244)
2 cd08067 MPN_2A_DUB Mov34/MPN/P 99.9 6.3E-26 1.4E-30 152.8 12.1 92 5-106 6-97 (187)
3 cd08070 MPN_like Mpr1p, Pad1p 99.9 2E-25 4.2E-30 142.4 10.3 86 11-106 2-88 (128)
4 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 4.8E-25 1E-29 155.7 12.0 97 3-106 9-105 (268)
5 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 1.5E-23 3.3E-28 132.2 8.5 82 11-106 1-83 (119)
6 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 7.7E-23 1.7E-27 127.9 9.6 98 2-106 2-99 (114)
7 KOG1554|consensus 99.9 6.9E-23 1.5E-27 143.2 8.1 99 3-107 52-150 (347)
8 cd08066 MPN_AMSH_like Mov34/MP 99.9 1.1E-21 2.3E-26 130.9 10.6 90 3-106 1-93 (173)
9 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.9 5.2E-22 1.1E-26 123.4 8.5 75 12-106 2-77 (108)
10 smart00232 JAB_MPN JAB/MPN dom 99.9 1.7E-21 3.8E-26 124.1 10.3 92 5-106 1-94 (135)
11 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 6.4E-21 1.4E-25 134.7 10.1 92 4-103 1-93 (266)
12 cd08072 MPN_archaeal Mov34/MPN 99.8 5.5E-20 1.2E-24 115.8 8.7 77 8-106 1-77 (117)
13 cd08060 MPN_UPF0172 Mov34/MPN/ 99.8 1.2E-19 2.5E-24 121.9 9.4 80 8-101 1-83 (182)
14 COG1310 Predicted metal-depend 99.8 2.9E-19 6.3E-24 114.8 8.7 86 6-106 2-87 (134)
15 cd07767 MPN Mpr1p, Pad1p N-ter 99.8 1.3E-18 2.9E-23 108.4 8.8 80 14-106 2-81 (116)
16 PF14464 Prok-JAB: Prokaryotic 99.8 5.6E-18 1.2E-22 104.0 7.7 75 10-106 2-77 (104)
17 TIGR03735 PRTRC_A PRTRC system 99.7 1.1E-17 2.4E-22 112.5 9.0 79 7-106 74-152 (192)
18 KOG1555|consensus 99.7 1.7E-17 3.6E-22 118.2 6.5 97 3-107 30-134 (316)
19 cd08057 MPN_euk_non_mb Mpr1p, 99.7 1.7E-15 3.8E-20 99.6 9.9 87 6-101 1-89 (157)
20 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.6 1.8E-14 3.8E-19 102.6 10.9 89 4-101 1-95 (280)
21 cd08059 MPN_prok_mb Mpr1p, Pad 99.6 5.7E-15 1.2E-19 90.5 6.0 74 11-106 1-74 (101)
22 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.5 9.4E-14 2E-18 98.2 10.9 87 6-101 1-89 (265)
23 TIGR02256 ICE_VC0181 integrati 99.5 1.9E-13 4.2E-18 87.3 9.9 88 12-106 2-91 (131)
24 PLN03246 26S proteasome regula 99.4 4E-12 8.7E-17 91.4 11.2 92 2-101 4-100 (303)
25 PF03665 UPF0172: Uncharacteri 99.4 6.1E-12 1.3E-16 85.5 9.7 86 4-99 2-87 (196)
26 KOG1556|consensus 99.3 9.9E-12 2.2E-16 86.1 8.9 92 2-100 7-102 (309)
27 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.3 8.9E-12 1.9E-16 89.1 8.8 87 5-99 2-94 (288)
28 KOG2880|consensus 99.2 1.2E-11 2.6E-16 89.4 4.3 92 2-107 250-344 (424)
29 KOG1560|consensus 99.1 6.3E-10 1.4E-14 78.4 7.7 94 2-100 11-110 (339)
30 KOG3289|consensus 98.9 1E-08 2.2E-13 68.1 8.8 87 4-100 2-88 (199)
31 KOG2975|consensus 98.8 1.1E-08 2.4E-13 71.6 4.8 92 3-103 20-113 (288)
32 cd08056 MPN_PRP8 Mpr1p, Pad1p 98.4 1.7E-06 3.6E-11 60.9 7.3 87 5-106 37-124 (252)
33 cd08061 MPN_NPL4 Mov34/MPN/PAD 97.5 0.0023 5E-08 45.8 10.4 93 5-106 12-115 (274)
34 cd08071 MPN_DUF2466 Mov34/MPN/ 96.8 0.032 6.9E-07 34.8 8.9 73 16-106 6-78 (113)
35 KOG3050|consensus 96.6 0.0025 5.5E-08 44.8 3.5 91 4-105 9-105 (299)
36 PF05021 NPL4: NPL4 family; I 95.4 0.15 3.3E-06 37.1 8.1 62 29-99 2-69 (306)
37 PF04002 RadC: RadC-like JAB d 95.2 0.18 4E-06 31.7 7.0 79 10-106 5-83 (123)
38 PRK00024 hypothetical protein; 94.4 0.91 2E-05 31.6 9.5 80 9-106 105-184 (224)
39 TIGR00608 radc DNA repair prot 94.3 1.2 2.6E-05 30.9 10.3 80 9-106 99-178 (218)
40 PF14778 ODR4-like: Olfactory 88.2 1.8 3.9E-05 32.2 5.7 32 65-99 43-74 (362)
41 PF15659 Toxin-JAB1: JAB-like 86.8 0.66 1.4E-05 30.8 2.4 20 86-106 114-133 (162)
42 PF14220 DUF4329: Domain of un 82.5 0.95 2.1E-05 28.7 1.7 16 86-101 57-72 (123)
43 KOG2834|consensus 77.3 10 0.00022 29.4 5.9 79 10-96 182-264 (510)
44 PF07454 SpoIIP: Stage II spor 71.5 3.7 8.1E-05 29.4 2.3 21 85-105 70-90 (268)
45 PF07732 Cu-oxidase_3: Multico 58.5 4.9 0.00011 25.0 0.8 10 91-100 92-101 (117)
46 COG2003 RadC DNA repair protei 56.5 13 0.00028 26.1 2.7 40 58-106 145-184 (224)
47 TIGR03099 dCO2ase_PEP1 pyridox 55.3 21 0.00046 26.5 3.9 35 60-101 163-197 (398)
48 COG3449 DNA gyrase inhibitor [ 54.0 50 0.0011 21.8 5.0 36 66-101 21-59 (154)
49 PF08255 Leader_Trp: Trp-opero 53.4 10 0.00022 14.8 1.0 8 89-96 6-13 (14)
50 cd06843 PLPDE_III_PvsE_like Ty 49.3 28 0.0006 25.7 3.7 35 61-101 142-176 (377)
51 PHA00442 host recBCD nuclease 47.9 4.8 0.0001 21.9 -0.4 19 2-20 4-22 (59)
52 PF06442 DHFR_2: R67 dihydrofo 47.7 13 0.00028 21.0 1.3 11 87-97 39-49 (78)
53 COG4424 Uncharacterized protei 43.9 12 0.00027 26.1 1.0 16 91-106 141-156 (250)
54 KOG0256|consensus 43.0 68 0.0015 24.9 4.8 36 59-100 202-237 (471)
55 PRK10883 FtsI repressor; Provi 42.8 12 0.00027 28.8 1.0 11 90-100 137-147 (471)
56 COG4778 PhnL ABC-type phosphon 42.7 43 0.00093 23.1 3.4 12 86-97 201-212 (235)
57 COG2132 SufI Putative multicop 41.7 13 0.00027 28.4 0.9 9 92-100 128-136 (451)
58 PRK10965 multicopper oxidase; 40.8 12 0.00027 29.3 0.7 9 91-99 138-146 (523)
59 PF06812 ImpA-rel_N: ImpA-rela 38.9 5.3 0.00011 21.9 -1.2 24 71-94 3-26 (62)
60 TIGR02652 conserved hypothetic 37.8 11 0.00025 24.6 0.1 10 92-101 60-71 (163)
61 PF09935 DUF2167: Protein of u 37.3 1.5E+02 0.0033 21.0 7.5 86 5-95 23-114 (239)
62 KOG3844|consensus 37.2 35 0.00077 26.2 2.6 32 60-96 186-217 (476)
63 PF09654 DUF2396: Protein of u 36.5 12 0.00027 24.4 0.1 9 93-101 58-68 (161)
64 PF00886 Ribosomal_S16: Riboso 36.0 29 0.00062 19.2 1.5 16 85-100 23-38 (62)
65 PLN00039 photosystem II reacti 35.8 1.1E+02 0.0024 19.1 7.1 61 23-85 44-105 (111)
66 PLN02168 copper ion binding / 35.0 16 0.00035 28.9 0.6 8 92-99 123-130 (545)
67 KOG1670|consensus 34.9 83 0.0018 21.9 3.9 27 16-43 134-160 (212)
68 TIGR03389 laccase laccase, pla 34.9 16 0.00036 28.6 0.6 9 91-99 100-108 (539)
69 cd06839 PLPDE_III_Btrk_like Ty 34.7 67 0.0014 23.6 3.8 35 60-100 146-180 (382)
70 PRK13612 photosystem II reacti 34.0 1.2E+02 0.0026 19.0 6.9 60 24-85 47-107 (113)
71 PF03912 Psb28: Psb28 protein; 33.8 1.2E+02 0.0026 18.9 5.2 58 26-85 46-104 (108)
72 CHL00128 psbW photosystem II p 32.3 1.3E+02 0.0028 18.8 7.1 61 23-85 46-107 (113)
73 PLN02991 oxidoreductase 31.9 20 0.00042 28.4 0.6 8 92-99 125-132 (543)
74 TIGR03390 ascorbOXfungal L-asc 31.7 20 0.00043 28.2 0.6 8 92-99 108-115 (538)
75 COG2172 RsbW Anti-sigma regula 31.5 1.5E+02 0.0032 19.1 5.1 38 11-50 47-84 (146)
76 TIGR03047 PS_II_psb28 photosys 30.7 1.4E+02 0.003 18.6 7.0 60 24-85 44-104 (109)
77 PLN02835 oxidoreductase 29.5 22 0.00048 28.0 0.5 9 91-99 125-133 (539)
78 COG1753 Predicted antotoxin, c 29.0 77 0.0017 18.2 2.5 20 1-20 1-20 (74)
79 PLN02792 oxidoreductase 28.5 24 0.00052 27.8 0.6 8 92-99 113-120 (536)
80 PRK13611 photosystem II reacti 28.2 1.5E+02 0.0033 18.3 6.7 59 24-84 40-99 (104)
81 PRK05270 galactose-1-phosphate 28.1 24 0.00051 27.6 0.4 59 22-100 332-390 (493)
82 TIGR02376 Cu_nitrite_red nitri 27.3 31 0.00068 25.1 0.9 9 91-99 119-127 (311)
83 TIGR01480 copper_res_A copper- 27.2 26 0.00056 28.0 0.5 9 91-99 139-147 (587)
84 PF15591 Imm17: Immunity prote 26.5 1.2E+02 0.0027 17.5 3.1 15 27-41 25-39 (74)
85 PLN02354 copper ion binding / 26.2 28 0.0006 27.6 0.5 8 92-99 124-131 (552)
86 PF12367 PFO_beta_C: Pyruvate 24.1 1.4E+02 0.0031 16.7 3.1 27 66-98 25-51 (67)
87 TIGR03884 sel_bind_Methan sele 23.9 1.4E+02 0.0031 17.2 3.1 27 10-36 28-54 (74)
88 PLN00044 multi-copper oxidase- 23.7 33 0.00071 27.5 0.5 8 92-99 126-133 (596)
89 PF04626 DEC-1_C: Dec-1 protei 23.5 61 0.0013 20.5 1.6 18 88-105 59-76 (132)
90 TIGR01239 galT_2 galactose-1-p 23.2 25 0.00054 27.4 -0.2 59 22-100 329-387 (489)
91 PRK13610 photosystem II reacti 22.9 2E+02 0.0044 18.0 7.0 59 24-84 51-110 (113)
92 PF10929 DUF2811: Protein of u 22.8 1.1E+02 0.0023 16.8 2.3 13 67-79 7-19 (57)
93 PF07289 DUF1448: Protein of u 22.7 1.2E+02 0.0026 22.7 3.2 30 62-101 231-261 (339)
94 PLN02191 L-ascorbate oxidase 22.7 36 0.00077 27.1 0.5 9 91-99 120-128 (574)
95 COG2144 Selenophosphate synthe 22.5 1.5E+02 0.0032 22.0 3.5 31 70-103 109-139 (324)
96 PF13636 Nol1_Nop2_Fmu_2: pre- 21.9 1.1E+02 0.0025 18.3 2.6 45 24-72 13-58 (102)
97 PF15603 Imm45: Immunity prote 21.3 1.9E+02 0.0041 17.0 5.4 26 58-83 49-74 (82)
98 PF06962 rRNA_methylase: Putat 20.7 50 0.0011 21.4 0.8 34 65-100 66-99 (140)
99 PF08055 Trp_leader1: Tryptoph 20.6 50 0.0011 13.4 0.5 7 93-99 10-16 (18)
100 PRK13696 hypothetical protein; 20.6 1.4E+02 0.003 16.6 2.5 17 1-17 1-17 (62)
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=99.98 E-value=8.5e-32 Score=186.83 Aligned_cols=103 Identities=49% Similarity=0.772 Sum_probs=88.3
Q ss_pred eeEEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeC-----CceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHH
Q psy17875 3 LDVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKE-----EKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEA 77 (107)
Q Consensus 3 ~~~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~-----~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (107)
+++|.|+++++.+|+.||++++|+||||+|+|..++ ....+. +...+++.+.+++.++|+|||+++.+++++|
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~~~~~~~v~--i~~~~~~~~~~~s~~r~eidPee~~~a~~ea 78 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVH--ISAVIILRRSDKRKDRVEISPEQLSAASTEA 78 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCCCcceeEEEEeecccccccccceeEE--EeeeccccccCCCCceEEeCHHHHHHHHHHH
Confidence 478999999999999999999999999999998753 122222 3344455566778899999999999999999
Q ss_pred HHHHhhcCCCceEEEEEccCCCCCcccCCC
Q psy17875 78 EKLSKLYNRELRVIGWFHSHPHITVWPSDV 107 (107)
Q Consensus 78 ~~~~~~~~~~~~ivG~yHSHP~~~~~pS~~ 107 (107)
+++.+.+++++.+||||||||+++|+||.+
T Consensus 79 ~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~ 108 (244)
T cd08068 79 ERLTEETGRPMRVVGWYHSHPHITVWPSHV 108 (244)
T ss_pred HHHHhhccCCceEEEEEecCCCCCCCCCHh
Confidence 999999999999999999999999999964
No 2
>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=99.94 E-value=6.3e-26 Score=152.81 Aligned_cols=92 Identities=23% Similarity=0.245 Sum_probs=77.0
Q ss_pred EEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhc
Q psy17875 5 VAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLY 84 (107)
Q Consensus 5 ~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (107)
+|.|+..++++|+.||+.+. .|+||+|+|..+.+..... |+.+++..+. .+.++|++||++..++++.+++
T Consensus 6 ~V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~~~l~--Vt~~~p~~~~-~~~~~~e~dp~~q~e~~~~l~~----- 76 (187)
T cd08067 6 KVTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNTQNLT--ILQAFPCRSR-LTGLDCEMDPVSETEIRESLES----- 76 (187)
T ss_pred EEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEE--EEEEEecCCC-CCCcccccCHHHHHHHHHHHHH-----
Confidence 79999999999999999987 9999999999765333334 7887665543 3468999999888887777766
Q ss_pred CCCceEEEEEccCCCCCcccCC
Q psy17875 85 NRELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 85 ~~~~~ivG~yHSHP~~~~~pS~ 106 (107)
+|+.+||||||||.++++||.
T Consensus 77 -~gl~vVGwYHSHP~~~~~pS~ 97 (187)
T cd08067 77 -RGLSVVGWYHSHPTFPPNPSL 97 (187)
T ss_pred -cCCEEEEEEecCCCCCcCCCH
Confidence 889999999999999999996
No 3
>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=99.93 E-value=2e-25 Score=142.43 Aligned_cols=86 Identities=24% Similarity=0.361 Sum_probs=71.1
Q ss_pred HHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCC-ceEEeCHHHHHHHHHHHHHHHhhcCCCce
Q psy17875 11 DVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKH-DRVEASPEQLFEAVTEAEKLSKLYNRELR 89 (107)
Q Consensus 11 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (107)
.++.+|++||++++|+|+||+|+|..+..... |+.+++..+....+ ++|++||+++.++.+.+++ ++++
T Consensus 2 ~~~~~il~ha~~~~P~E~cGlL~G~~~~~~~~----i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~------~g~~ 71 (128)
T cd08070 2 ELLEAILAHAEAEYPEECCGLLLGKGGGVTAI----VTEVYPVRNVAESPRRRFEIDPAEQLAAQREARE------RGLE 71 (128)
T ss_pred HHHHHHHHHHHhCCCCceEEEEEeecCCCCce----EEEEEEccCCCCCCCceEEECHHHHHHHHHHHHH------CCCe
Confidence 57889999999999999999999998755432 23444444544444 8999999999998888776 7899
Q ss_pred EEEEEccCCCCCcccCC
Q psy17875 90 VIGWFHSHPHITVWPSD 106 (107)
Q Consensus 90 ivG~yHSHP~~~~~pS~ 106 (107)
+||||||||+.+++||.
T Consensus 72 ~vG~~HSHP~~~~~PS~ 88 (128)
T cd08070 72 VVGIYHSHPDGPARPSE 88 (128)
T ss_pred EEEEEeCCCCCCCCCCH
Confidence 99999999999999996
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=99.93 E-value=4.8e-25 Score=155.74 Aligned_cols=97 Identities=25% Similarity=0.459 Sum_probs=79.4
Q ss_pred eeEEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHh
Q psy17875 3 LDVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSK 82 (107)
Q Consensus 3 ~~~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (107)
+++|.|++.++.+|++||.++.|.||||+|+|...++ .+. |+++|+.+ ..++++++++++ ++.+.+.++ ++.+
T Consensus 9 ~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~~~-~v~---Vt~~fp~p-~~~t~~~v~~~~-e~~~~m~~~-~~~~ 81 (268)
T cd08069 9 FEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDY-TII---VVDVFALP-VEGTETRVNAQD-EFQEYMVQY-EMLK 81 (268)
T ss_pred ccEEEECHHHHHHHHHHHhccCCceEEEEEEeeecCC-eEE---EEEEEECC-cCCCCCceeccH-HHHHHHHHH-HHHH
Confidence 6789999999999999999999999999999997544 332 68888775 445678899887 454433222 3788
Q ss_pred hcCCCceEEEEEccCCCCCcccCC
Q psy17875 83 LYNRELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 83 ~~~~~~~ivG~yHSHP~~~~~pS~ 106 (107)
+.++++.+||||||||+++||||+
T Consensus 82 ~~~~~~~vVGWYHSHP~~g~~~S~ 105 (268)
T cd08069 82 QTGRPENVVGWYHSHPGYGCWLSG 105 (268)
T ss_pred HhCCCceeEeeeccCCCcCCcCCH
Confidence 889999999999999999999996
No 5
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.90 E-value=1.5e-23 Score=132.24 Aligned_cols=82 Identities=32% Similarity=0.469 Sum_probs=58.4
Q ss_pred HHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEE-EEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCce
Q psy17875 11 DVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKS-VHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELR 89 (107)
Q Consensus 11 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~-~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (107)
+++++|++||+++.|+|+||+|+|...++..... .+|+++++. .+..++.+.++++++++ ++|++
T Consensus 1 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~--------~~~~~~~~~~~~~~~~~------~~g~~ 66 (119)
T cd08058 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAG--------PDSCTGENVEELFNVQT------GRPLL 66 (119)
T ss_pred CHHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCC--------CCCchhHHHHHHHHHHh------CCCCe
Confidence 4789999999999999999999998764322111 125554322 12345555444444443 59999
Q ss_pred EEEEEccCCCCCcccCC
Q psy17875 90 VIGWFHSHPHITVWPSD 106 (107)
Q Consensus 90 ivG~yHSHP~~~~~pS~ 106 (107)
+||||||||+++++||.
T Consensus 67 ~vG~YHSHP~~~~~pS~ 83 (119)
T cd08058 67 VVGWYHSHPTFTAWLSS 83 (119)
T ss_pred EEEEEecCCCCCCccCH
Confidence 99999999999999995
No 6
>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=99.89 E-value=7.7e-23 Score=127.86 Aligned_cols=98 Identities=23% Similarity=0.402 Sum_probs=74.1
Q ss_pred ceeEEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHH
Q psy17875 2 SLDVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLS 81 (107)
Q Consensus 2 ~~~~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (107)
|.++|.|++.++.+|++|+.+..+.|+||+|+|..+++.. +. |+++|+.+... ....+.+++.++. +.+.+++
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~~-v~--I~~~f~~p~~~-~~~~~~~~~~~~~---~~~~~~~ 74 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDNT-VE--ITNSFPVPHSE-SEDDCDMDDEDFQ---KKMIELL 74 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT-E-EE--EEEEEEESEEE-ESSEEEEECCHHH---HHHHHHH
T ss_pred CcEEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCceE-EE--EEEEEEeeEec-CccccccchhhHH---HHHHhhh
Confidence 6789999999999999999998888999999999986633 33 78888765443 3445555443433 3456777
Q ss_pred hhcCCCceEEEEEccCCCCCcccCC
Q psy17875 82 KLYNRELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 82 ~~~~~~~~ivG~yHSHP~~~~~pS~ 106 (107)
++....+.+||||||||+.+++||.
T Consensus 75 ~~~~~~~~iVGWY~s~p~~~~~~S~ 99 (114)
T PF01398_consen 75 KKVNPNLEIVGWYHSHPNISCFPSP 99 (114)
T ss_dssp HHCSTTSEEEEEEEEESSS-SS--H
T ss_pred ccccccceEEEEEEccCCccccCCH
Confidence 7777779999999999999999985
No 7
>KOG1554|consensus
Probab=99.88 E-value=6.9e-23 Score=143.24 Aligned_cols=99 Identities=24% Similarity=0.372 Sum_probs=82.9
Q ss_pred eeEEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHh
Q psy17875 3 LDVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSK 82 (107)
Q Consensus 3 ~~~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (107)
++.|.|+..++++|+.||+++.+.|++|+|.|+..++..+ |.++|.. +.+++++|+....+.|. ++.+..+..+
T Consensus 52 fk~vkISalAllKm~~hA~~GgnlEiMGlm~Gkv~g~t~I----vmD~FaL-PVeGTETRVNAq~~AyE-Ymv~Y~e~~k 125 (347)
T KOG1554|consen 52 FKHVKISALALLKMVMHARSGGNLEIMGLMQGKVDGDTII----VMDSFAL-PVEGTETRVNAQAEAYE-YMVQYIEEAK 125 (347)
T ss_pred hhhhhhHHHHHHHHHHHHhcCCCeEEEeeecccccCCeEE----EEecccc-ccccccceechHHHHHH-HHHHHHHHHH
Confidence 5679999999999999999999999999999999766544 5788655 47889999988765443 3444556678
Q ss_pred hcCCCceEEEEEccCCCCCcccCCC
Q psy17875 83 LYNRELRVIGWFHSHPHITVWPSDV 107 (107)
Q Consensus 83 ~~~~~~~ivG~yHSHP~~~~~pS~~ 107 (107)
..|+.+++||||||||+.+||+|++
T Consensus 126 ~~gr~envVGWyHSHPgYgCWLSgI 150 (347)
T KOG1554|consen 126 NVGRLENVVGWYHSHPGYGCWLSGI 150 (347)
T ss_pred HhhhhhceeeeeecCCCCCccccCc
Confidence 8899999999999999999999984
No 8
>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=99.87 E-value=1.1e-21 Score=130.93 Aligned_cols=90 Identities=23% Similarity=0.421 Sum_probs=65.3
Q ss_pred eeEEEECHHHHHHHHHhhhcCC--CeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHHH
Q psy17875 3 LDVAYISEDVYFSMFYLALSND--KLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAEK 79 (107)
Q Consensus 3 ~~~v~i~~~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 79 (107)
++++.|+++++++|+.||.... |+|+||+|+|+..++. .. |..++.+.+. ++..++.+ ++.+ +++.++.
T Consensus 1 ~~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~--~~--I~~i~~~~q~-~~~~~~~~~~~~e---~~~~~~~ 72 (173)
T cd08066 1 LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNA--FF--ITHLIIPKQS-GTSDSCQTTNEEE---LFDFQDQ 72 (173)
T ss_pred CeEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCe--EE--EEEEEecccc-CCCceecCCCHHH---HHHHHHh
Confidence 4689999999999999999984 6999999999875432 22 4444333333 23344443 4433 3444554
Q ss_pred HHhhcCCCceEEEEEccCCCCCcccCC
Q psy17875 80 LSKLYNRELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 80 ~~~~~~~~~~ivG~yHSHP~~~~~pS~ 106 (107)
+|++++|||||||+.+++||.
T Consensus 73 ------~gle~vGwyHSHP~~~~~pS~ 93 (173)
T cd08066 73 ------HDLITLGWIHTHPTQTCFLSS 93 (173)
T ss_pred ------CCCeeEEEEeccCCCCCccCH
Confidence 899999999999999999996
No 9
>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=99.87 E-value=5.2e-22 Score=123.43 Aligned_cols=75 Identities=19% Similarity=0.212 Sum_probs=58.3
Q ss_pred HHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCC-CCCceEEeCHHHHHHHHHHHHHHHhhcCCCceE
Q psy17875 12 VYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLT-SKHDRVEASPEQLFEAVTEAEKLSKLYNRELRV 90 (107)
Q Consensus 12 ~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i 90 (107)
++.+|++||++++|+|+||||+|+.. +.. +.+ ..|.. .+.++|+|||+++.+++ + ..++
T Consensus 2 i~~~i~~ha~~~~P~E~CGll~g~~~----~~~--~~p---~~N~~~~p~~~F~idp~e~~~a~----~-------~~~i 61 (108)
T cd08073 2 LEDAILAHAKAEYPREACGLVVRKGR----KLR--YIP---CRNIAADPEEHFEISPEDYAAAE----D-------EGEI 61 (108)
T ss_pred HHHHHHHHHhHCCCCcceEEEEecCC----ceE--EEE---CccCCCCccceEEeCHHHHHHHh----c-------CCCE
Confidence 57899999999999999999999762 111 233 33333 35589999999988764 2 2389
Q ss_pred EEEEccCCCCCcccCC
Q psy17875 91 IGWFHSHPHITVWPSD 106 (107)
Q Consensus 91 vG~yHSHP~~~~~pS~ 106 (107)
+|+|||||+++++||.
T Consensus 62 vgi~HSHP~~~a~PS~ 77 (108)
T cd08073 62 VAVVHSHPDGSPAPSE 77 (108)
T ss_pred EEEEEcCCCCCCCCCH
Confidence 9999999999999995
No 10
>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=99.87 E-value=1.7e-21 Score=124.13 Aligned_cols=92 Identities=20% Similarity=0.389 Sum_probs=68.1
Q ss_pred EEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCc--eEEeCHHHHHHHHHHHHHHHh
Q psy17875 5 VAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHD--RVEASPEQLFEAVTEAEKLSK 82 (107)
Q Consensus 5 ~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 82 (107)
+|.|.+.++++|++|+.+..|.|+||+|+|...++. +. |+++++.++...... .+.+++.+ .+.+..+
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~p~e~~G~L~G~~~~~~-~~---i~~~~~~p~~~~~~~~~~~~~~~~~------~~~~~~~ 70 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKDR-PE---VKEVFAVPNEPQDDSVQEYDEDYSH------LMDEELK 70 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCCCcEEEEEEEEEEcCCE-EE---EEEEEecCcCCCCcchhhhhhhHHH------HHHHHHH
Confidence 378999999999999999999999999999986553 32 566665544332222 23333322 3444556
Q ss_pred hcCCCceEEEEEccCCCCCcccCC
Q psy17875 83 LYNRELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 83 ~~~~~~~ivG~yHSHP~~~~~pS~ 106 (107)
+.+.++++||||||||..+++||.
T Consensus 71 ~~~~~~~~vGwyhshp~~~~~pS~ 94 (135)
T smart00232 71 KVNKDLEIVGWYHSHPDESPFPSE 94 (135)
T ss_pred hhCCCceEEEEEEcCCCCCCCcCH
Confidence 667899999999999999999994
No 11
>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=99.85 E-value=6.4e-21 Score=134.72 Aligned_cols=92 Identities=15% Similarity=0.137 Sum_probs=73.2
Q ss_pred eEEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCC-CCceEEeCHHHHHHHHHHHHHHHh
Q psy17875 4 DVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTS-KHDRVEASPEQLFEAVTEAEKLSK 82 (107)
Q Consensus 4 ~~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 82 (107)
++|.|++.++.+|++|+.+..|.||||+|+|...++ .+. |++||+.++.+. ...++.+++.++ +..|.++++
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~p~~v~G~LLG~~~~~--~le--Vtn~Fp~P~~~~~~~~~~~~~~~~y---q~~m~~~~r 73 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLGLDVGG--TLE--VTNCFPFPKSEEDDSDRADEDIADY---QLEMMRLLR 73 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCCCcEEEEEEeeeEcCC--EEE--EEeccCCCCCCCCCcchhhhhHHHH---HHHHHHHHH
Confidence 479999999999999999999999999999999643 333 789987665432 222456666444 346888999
Q ss_pred hcCCCceEEEEEccCCCCCcc
Q psy17875 83 LYNRELRVIGWFHSHPHITVW 103 (107)
Q Consensus 83 ~~~~~~~ivG~yHSHP~~~~~ 103 (107)
+.|.+..+|||||||| .+++
T Consensus 74 ~v~~~e~iVGWY~S~p-~~~~ 93 (266)
T cd08065 74 EVNVDHNHVGWYQSTY-LGSF 93 (266)
T ss_pred HhCCCCcEEEeEeecC-CCCc
Confidence 9999999999999999 7777
No 12
>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=99.82 E-value=5.5e-20 Score=115.82 Aligned_cols=77 Identities=25% Similarity=0.239 Sum_probs=55.9
Q ss_pred ECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCC
Q psy17875 8 ISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRE 87 (107)
Q Consensus 8 i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (107)
|++.++.+|++||++++|+|+||+|+|+.+ .+ +.+++..+.......+.++. + +.+ .+
T Consensus 1 i~~~~~~~i~~ha~~~~P~E~CGlL~G~~~---~v-----~~~~~~~n~~~~~~~~~f~~-~-------~~~------~g 58 (117)
T cd08072 1 ISRDLLDSILEAAKSSHPNEFAALLRGKDG---VI-----TELLILPGTESGEVSAVFPL-L-------MLP------LD 58 (117)
T ss_pred CCHHHHHHHHHHHhhcCCceEEEEEEeecc---EE-----EEEEECCCCCCCCcceeech-H-------Hhc------CC
Confidence 578899999999999999999999999764 22 33333333333223333333 1 223 68
Q ss_pred ceEEEEEccCCCCCcccCC
Q psy17875 88 LRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 88 ~~ivG~yHSHP~~~~~pS~ 106 (107)
++++|+|||||+.+++||.
T Consensus 59 ~~ivgi~HSHP~~~~~PS~ 77 (117)
T cd08072 59 MSIVGSVHSHPSGSPRPSD 77 (117)
T ss_pred CeEEEEEEcCCCCCCCCCH
Confidence 9999999999999999995
No 13
>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=99.82 E-value=1.2e-19 Score=121.94 Aligned_cols=80 Identities=16% Similarity=0.269 Sum_probs=63.8
Q ss_pred ECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHH---HHHHHHHHHHHHhhc
Q psy17875 8 ISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQ---LFEAVTEAEKLSKLY 84 (107)
Q Consensus 8 i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 84 (107)
|++.++.+|+.||.+.+|.||||+|+|+...+..+. |++++|.++ .+|.++|.. +.++++.+++
T Consensus 1 is~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~~~~---V~d~vPl~h-----~~~~l~P~~Eval~~ve~~~~~----- 67 (182)
T cd08060 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVE---ITDAVPLFH-----SCLALAPMLEVALALVDAYCKS----- 67 (182)
T ss_pred CCHHHHHHHHHHHHHcCCchheEEEEeeecCCCCEE---EEEEEEcCC-----CccccCHHHHHHHHHHHHHHHH-----
Confidence 578999999999999999999999999986232232 567766654 369999974 7777766666
Q ss_pred CCCceEEEEEccCCCCC
Q psy17875 85 NRELRVIGWFHSHPHIT 101 (107)
Q Consensus 85 ~~~~~ivG~yHSHP~~~ 101 (107)
+|+.|||+|||||...
T Consensus 68 -~gl~IvG~Yhsh~~~~ 83 (182)
T cd08060 68 -SGLVIVGYYQANERLD 83 (182)
T ss_pred -CCCEEEEEEecCCccc
Confidence 8899999999999864
No 14
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.80 E-value=2.9e-19 Score=114.75 Aligned_cols=86 Identities=24% Similarity=0.374 Sum_probs=65.7
Q ss_pred EEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcC
Q psy17875 6 AYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYN 85 (107)
Q Consensus 6 v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (107)
+.|++.++..|+.||.+.+|.|+||+|+|.... .. ..++ .+. ...+...+.++++... ....+++
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~-~~-----~~~~-~n~-~~~~~~~~~~~~~~~~-~~~~~~~------ 66 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREG-ER-----YFPL-KNV-SVEPVEYFEIDPEYSL-FYLAAED------ 66 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeeccc-ce-----eecc-ccc-cCCcceeEeeCHHHHH-HHHHHhh------
Confidence 568999999999999999999999999998754 11 1222 222 2234567888886444 5555665
Q ss_pred CCceEEEEEccCCCCCcccCC
Q psy17875 86 RELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 86 ~~~~ivG~yHSHP~~~~~pS~ 106 (107)
+++.+||||||||+++++||.
T Consensus 67 ~g~~vvg~yHSHP~~~~~pS~ 87 (134)
T COG1310 67 AGEVVVGWYHSHPGGPPYPSE 87 (134)
T ss_pred CCCEEEEEEcCCCCCCCCcCH
Confidence 789999999999999999996
No 15
>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=99.78 E-value=1.3e-18 Score=108.39 Aligned_cols=80 Identities=23% Similarity=0.286 Sum_probs=54.5
Q ss_pred HHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEE
Q psy17875 14 FSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGW 93 (107)
Q Consensus 14 ~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~ 93 (107)
.+|++||+...|.|+||+|+|...++ +.. |..+++.++... ....+..++..+.+.+. +.++++|||
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~--~~~--i~~~~~~~~~~~---~~~~~~~~~~~~~~~~~------~~~~~iVGw 68 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKK--VLD--VDEVIAVPFDEG---DKDDNVWFLMYLDFKKL------NAGLRIVGW 68 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCC--EEE--EEEEEecccCCC---CCccHHHHHHHHHHHHh------cCCCeEEEE
Confidence 57899999999999999999998755 222 556554433221 11222223333332222 488999999
Q ss_pred EccCCCCCcccCC
Q psy17875 94 FHSHPHITVWPSD 106 (107)
Q Consensus 94 yHSHP~~~~~pS~ 106 (107)
|||||..+++||.
T Consensus 69 yhshp~~~~~~s~ 81 (116)
T cd07767 69 YHTHPKPSCFLSP 81 (116)
T ss_pred EEcCCCCCCccCH
Confidence 9999999999985
No 16
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.75 E-value=5.6e-18 Score=104.02 Aligned_cols=75 Identities=28% Similarity=0.443 Sum_probs=51.8
Q ss_pred HHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHH-HHHHHHhhcCCCc
Q psy17875 10 EDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVT-EAEKLSKLYNREL 88 (107)
Q Consensus 10 ~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 88 (107)
+.++.+|+.|+++..|+|+||+|+|....+. +. +++... ++|.+.++... .+.+ +++
T Consensus 2 ~~~~~~i~~~~~~~~p~E~~G~L~g~~~~~~-~~---~~~~~~------------~~p~~~~~~~~~~~~~------~~~ 59 (104)
T PF14464_consen 2 EEVLEQIIAHARAAYPNEACGLLLGRRDDQR-FI---VVPNVN------------PDPRDSFRRERFEARE------RGL 59 (104)
T ss_dssp -HHHHHHHHHHHHHTTS-EEEEEEEEEECCE-EE---EEEEEE--------------HHCHHHHHH-HHHH------HT-
T ss_pred HHHHHHHHHHHhhCCCCeEEEEEEEEecCCE-EE---EEeCCC------------CCcHHHHHHHhhhhhc------ccc
Confidence 5789999999999999999999999984332 22 233211 56766666654 4444 789
Q ss_pred eEEEEEccCCCCCcccCC
Q psy17875 89 RVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 89 ~ivG~yHSHP~~~~~pS~ 106 (107)
.++|+|||||+++++||.
T Consensus 60 ~~vg~~HSHP~~~a~pS~ 77 (104)
T PF14464_consen 60 EIVGIWHSHPSGPAFPSS 77 (104)
T ss_dssp EEEEEEEEESSSSSS--H
T ss_pred eeeEEEEcCCCCCCCCCH
Confidence 999999999999999995
No 17
>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=99.75 E-value=1.1e-17 Score=112.51 Aligned_cols=79 Identities=11% Similarity=0.070 Sum_probs=65.7
Q ss_pred EECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCC
Q psy17875 7 YISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNR 86 (107)
Q Consensus 7 ~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (107)
.|+..++.+|+.||++..|+|+||+|.|..+ + .. ..+++..+.+.+.+.|.+|+.+ .+ +
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~-~-~~-----~r~~p~~N~~~Sp~~~~~d~~~--------~~------~ 132 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNSE-T-GS-----LRLAALESIEASPGHIDYRRPR--------LD------D 132 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcCC-C-CE-----EEEEeccccccCCceEEEcchH--------Hh------C
Confidence 5899999999999999999999999999643 2 22 2345666777888999999852 22 7
Q ss_pred CceEEEEEccCCCCCcccCC
Q psy17875 87 ELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 87 ~~~ivG~yHSHP~~~~~pS~ 106 (107)
|+.+|+.|||||..+|+||.
T Consensus 133 ge~lV~iyHSH~~spA~PS~ 152 (192)
T TIGR03735 133 GEHLVVDLHSHGTGSAFFSE 152 (192)
T ss_pred CCeEEEEEcCCCCCCCCCCc
Confidence 89999999999999999996
No 18
>KOG1555|consensus
Probab=99.71 E-value=1.7e-17 Score=118.23 Aligned_cols=97 Identities=28% Similarity=0.462 Sum_probs=70.7
Q ss_pred eeEEEECHHHHHHHHHhhhcCCCee-EEEEe-ee---eEeCCceEEEEEeeeeeecccCCCCCce---EEeCHHHHHHHH
Q psy17875 3 LDVAYISEDVYFSMFYLALSNDKLE-VLSML-IG---ETKEEKGVKSVHVYTMVIPLRLTSKHDR---VEASPEQLFEAV 74 (107)
Q Consensus 3 ~~~v~i~~~~~~~i~~ha~~~~p~E-~cGlL-~G---~~~~~~~~~~~~i~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 74 (107)
-++++|+..++.+|++|.+...|.| +.|++ +| ...++..+. +.+.|..... +...+ -..|| ..+
T Consensus 30 ~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~---vv~v~am~~s-g~~is~~~e~~d~--V~q-- 101 (316)
T KOG1555|consen 30 KETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVR---VVDVFAMPQS-GTGISKFVEAVDP--VFQ-- 101 (316)
T ss_pred cceeeeehhhhhhcccccccCCchhhccceeecccccceeeeccee---eeeeeccccc-cceecccchhccH--HHH--
Confidence 4689999999999999999999999 99999 88 443333332 4454433222 11111 12333 222
Q ss_pred HHHHHHHhhcCCCceEEEEEccCCCCCcccCCC
Q psy17875 75 TEAEKLSKLYNRELRVIGWFHSHPHITVWPSDV 107 (107)
Q Consensus 75 ~~~~~~~~~~~~~~~ivG~yHSHP~~~~~pS~~ 107 (107)
.++.++++.+|+.+.+||||||||+++||||.|
T Consensus 102 ~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~v 134 (316)
T KOG1555|consen 102 TQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLV 134 (316)
T ss_pred HHHHHHHHhcCCcceEEeeccCCCCCCCCcccc
Confidence 467789999999999999999999999999975
No 19
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.65 E-value=1.7e-15 Score=99.56 Aligned_cols=87 Identities=10% Similarity=0.156 Sum_probs=68.4
Q ss_pred EEECHHHHHHHHHhhhcCC--CeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhh
Q psy17875 6 AYISEDVYFSMFYLALSND--KLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKL 83 (107)
Q Consensus 6 v~i~~~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (107)
|.|.+.++.+|++|+.+.. +.+++|+|+|...++ .+ . |+++|+.+. +...+...+|. + .++.|.+++++
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~-~v-e--V~nsF~lp~-~~~~~~~~~d~-~---y~~~m~~~~~~ 71 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGD-KI-E--VTNSFELPF-DEEEESIFIDT-E---YLEKRYNLHKK 71 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCC-EE-E--EEEeEEccc-cCCCcchhhhH-H---HHHHHHHHHHH
Confidence 5789999999999998877 899999999999744 33 2 789987654 33344455554 3 34467889999
Q ss_pred cCCCceEEEEEccCCCCC
Q psy17875 84 YNRELRVIGWFHSHPHIT 101 (107)
Q Consensus 84 ~~~~~~ivG~yHSHP~~~ 101 (107)
.+.++.+||||||+|...
T Consensus 72 v~~~~~vVGWY~~~~~~~ 89 (157)
T cd08057 72 VYPQEKIVGWYSIGSNNS 89 (157)
T ss_pred hCCCCCEEEEEeecCCCC
Confidence 999999999999999865
No 20
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.59 E-value=1.8e-14 Score=102.60 Aligned_cols=89 Identities=13% Similarity=0.137 Sum_probs=67.8
Q ss_pred eEEEECHHHHHHHHHhhhcC---CCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCce---EEeCHHHHHHHHHHH
Q psy17875 4 DVAYISEDVYFSMFYLALSN---DKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDR---VEASPEQLFEAVTEA 77 (107)
Q Consensus 4 ~~v~i~~~~~~~i~~ha~~~---~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 77 (107)
++|.|.+.++.+|++|+.+. .+.+++|.|+|...++ . +. |+++|+.+..+ ..+. +.+|. +| ++.|
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~-~-ve--ItnsF~~p~~~-~~~~~~~~~~d~-~y---~~~m 71 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKG-V-LD--VTNSFAVPFEE-DEKDPSVWFLDH-NY---LENM 71 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCC-E-EE--EEEeeecCccC-CCCCcchhhhhH-HH---HHHH
Confidence 47999999999999998764 3678999999999653 3 33 78998765432 2222 34554 44 4468
Q ss_pred HHHHhhcCCCceEEEEEccCCCCC
Q psy17875 78 EKLSKLYNRELRVIGWFHSHPHIT 101 (107)
Q Consensus 78 ~~~~~~~~~~~~ivG~yHSHP~~~ 101 (107)
.+++|+.+.++.+||||||+|...
T Consensus 72 ~~~~kkv~~~e~vVGWY~tg~~~~ 95 (280)
T cd08062 72 YGMFKKVNAKEKIVGWYSTGPKLR 95 (280)
T ss_pred HHHHHHhCCCCCeEEEecCCCCCC
Confidence 899999999999999999999854
No 21
>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=99.57 E-value=5.7e-15 Score=90.48 Aligned_cols=74 Identities=20% Similarity=0.219 Sum_probs=54.6
Q ss_pred HHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCceE
Q psy17875 11 DVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRV 90 (107)
Q Consensus 11 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i 90 (107)
+++..|..|++..+|+|+||+|+|..+. .+ ....+.. ...|++++.. .+++.+ .+..+
T Consensus 1 ~~~~~i~~~~~~~~p~E~~gll~~~~~~--~~-----~~~~~~~-----~~~~~~~~~~----~~~a~~------~~~~~ 58 (101)
T cd08059 1 DLLKTILVHAKDAHPDEFCGFLSGSKDN--VM-----DELIFLP-----FVSGSVSAVI----DLAALE------IGMKV 58 (101)
T ss_pred CHHHHHHHHHHhcCChhhheeeecCCCC--eE-----EEEEeCC-----CcCCccChHH----HHHHhh------CCCcE
Confidence 3678899999999999999999997642 33 2332221 2356777754 334454 78899
Q ss_pred EEEEccCCCCCcccCC
Q psy17875 91 IGWFHSHPHITVWPSD 106 (107)
Q Consensus 91 vG~yHSHP~~~~~pS~ 106 (107)
||.|||||++++.||.
T Consensus 59 v~i~HsHP~g~~~PS~ 74 (101)
T cd08059 59 VGLVHSHPSGSCRPSE 74 (101)
T ss_pred EEEEecCcCCCCCCCH
Confidence 9999999999999995
No 22
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=99.54 E-value=9.4e-14 Score=98.22 Aligned_cols=87 Identities=17% Similarity=0.268 Sum_probs=68.9
Q ss_pred EEECHHHHHHHHHhhhc--CCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhh
Q psy17875 6 AYISEDVYFSMFYLALS--NDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKL 83 (107)
Q Consensus 6 v~i~~~~~~~i~~ha~~--~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (107)
|.|.+.++.+|++|+.+ ..+.+++|.|+|...++ . +. |+++|+.+. +.+.+.+.+|. +|. +.|.+++|+
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~-~-ve--ItnsF~~p~-~~~~~~~~~d~-~y~---~~m~~~~kk 71 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEG-E-VE--ITNCFAVPH-NESEDQVAVDM-EYH---RTMYELHQK 71 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCC-E-EE--EEeCeecce-eCCCCeEEEcH-HHH---HHHHHHHHH
Confidence 57899999999999876 67789999999999753 3 33 789987654 33455778875 343 468889999
Q ss_pred cCCCceEEEEEccCCCCC
Q psy17875 84 YNRELRVIGWFHSHPHIT 101 (107)
Q Consensus 84 ~~~~~~ivG~yHSHP~~~ 101 (107)
.+.++.+||||||+|...
T Consensus 72 v~~~~~vVGWY~tg~~~~ 89 (265)
T cd08064 72 VNPKEVIVGWYATGSEIT 89 (265)
T ss_pred hCCCCcEEeeeeCCCCCC
Confidence 999999999999998643
No 23
>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=99.52 E-value=1.9e-13 Score=87.29 Aligned_cols=88 Identities=18% Similarity=0.131 Sum_probs=60.2
Q ss_pred HHHHHHHhhhc-CCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCC-CCCceEEeCHHHHHHHHHHHHHHHhhcCCCce
Q psy17875 12 VYFSMFYLALS-NDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLT-SKHDRVEASPEQLFEAVTEAEKLSKLYNRELR 89 (107)
Q Consensus 12 ~~~~i~~ha~~-~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (107)
++..|..|.+. ..|+|.||+|+|...++ .++ |+++..+...+ ++..+|..+... .++...+.+++++....
T Consensus 2 v~~~~~~~~Q~~~~~~EtGGiLiG~~~~~-~~i---i~~~t~P~p~d~~tr~~F~r~~~~---~q~~i~~~~~~s~g~~~ 74 (131)
T TIGR02256 2 VVAMLKSYRQWHDLSTETGGVLIGERRGA-HAV---ITKISEPGSGDIRTRKRFSRDGEH---HQSEVDEHFEVSGGVDT 74 (131)
T ss_pred HHHHHHHHHhCcCCCCccceEEEEEEcCC-cEE---EEEEEcCCCCcccCceEEEeCcHH---HHHHHHHHHHHhCCceE
Confidence 34556666664 46899999999998754 333 45554333222 344556665543 23356677777777799
Q ss_pred EEEEEccCCCCCcccCC
Q psy17875 90 VIGWFHSHPHITVWPSD 106 (107)
Q Consensus 90 ivG~yHSHP~~~~~pS~ 106 (107)
.+|-|||||...+.||.
T Consensus 75 ylGeWHtHP~~~p~PS~ 91 (131)
T TIGR02256 75 YLGEWHTHPEDQPEPSW 91 (131)
T ss_pred EEEecCcCCCCCCCCCH
Confidence 99999999999999996
No 24
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.41 E-value=4e-12 Score=91.41 Aligned_cols=92 Identities=15% Similarity=0.161 Sum_probs=70.1
Q ss_pred ceeEEEECHHHHHHHHHhhhcCCC---eeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCc--eEEeCHHHHHHHHHH
Q psy17875 2 SLDVAYISEDVYFSMFYLALSNDK---LEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHD--RVEASPEQLFEAVTE 76 (107)
Q Consensus 2 ~~~~v~i~~~~~~~i~~ha~~~~p---~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 76 (107)
+..+|.|.+.++.+|++|+.+..+ ..+.|.|+|...++ .+. |+++|+.+..+...+ .+.+|. +| ++.
T Consensus 4 ~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~--~ie--ItnsF~~p~~e~~~~~~~~~~D~-~y---~~~ 75 (303)
T PLN03246 4 GIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRG--RVD--VTNSFAVPFEEDDKDPSIWFLDH-NY---LES 75 (303)
T ss_pred CCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCC--EEE--EEeccccCcccCCCCccceeecH-HH---HHH
Confidence 467899999999999999987664 45999999998643 333 899987654332222 266764 44 446
Q ss_pred HHHHHhhcCCCceEEEEEccCCCCC
Q psy17875 77 AEKLSKLYNRELRVIGWFHSHPHIT 101 (107)
Q Consensus 77 ~~~~~~~~~~~~~ivG~yHSHP~~~ 101 (107)
|.+++|+.+.+..+||||+|-|...
T Consensus 76 m~~~~k~V~~~~~vVGWY~tg~~i~ 100 (303)
T PLN03246 76 MFGMFKRINAKEHVVGWYSTGPKLR 100 (303)
T ss_pred HHHHHHHhCCCCcEEeeecCCCCCC
Confidence 8899999999999999999998754
No 25
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=99.38 E-value=6.1e-12 Score=85.51 Aligned_cols=86 Identities=19% Similarity=0.282 Sum_probs=67.1
Q ss_pred eEEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhh
Q psy17875 4 DVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKL 83 (107)
Q Consensus 4 ~~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (107)
..|.|+..++.||+.||.+.+-.-|+|+|+|+...+...+. |++++|.++. ...+.| .+.-|+..++.+++.
T Consensus 2 ~~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~--i~DaVPLfH~-----~~~L~P-mlEvAL~qvd~~~~~ 73 (196)
T PF03665_consen 2 SSVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVE--IVDAVPLFHH-----WLSLSP-MLEVALAQVDAYAKS 73 (196)
T ss_pred ceEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEE--Eeeceecccc-----ccCcch-HHHHHHHHHHHHHhh
Confidence 47999999999999999999889999999999876654233 7888777653 223556 455566677777765
Q ss_pred cCCCceEEEEEccCCC
Q psy17875 84 YNRELRVIGWFHSHPH 99 (107)
Q Consensus 84 ~~~~~~ivG~yHSHP~ 99 (107)
.|+.||||||....
T Consensus 74 --~gl~IvGyY~Ane~ 87 (196)
T PF03665_consen 74 --NGLVIVGYYQANER 87 (196)
T ss_pred --CCCEEEEEEEeccc
Confidence 67999999999875
No 26
>KOG1556|consensus
Probab=99.34 E-value=9.9e-12 Score=86.11 Aligned_cols=92 Identities=20% Similarity=0.256 Sum_probs=68.9
Q ss_pred ceeEEEECHHHHHHHHHhhhcCCC---eeEEEEeeeeEeCCceEEEEEeeeeeec-ccCCCCCceEEeCHHHHHHHHHHH
Q psy17875 2 SLDVAYISEDVYFSMFYLALSNDK---LEVLSMLIGETKEEKGVKSVHVYTMVIP-LRLTSKHDRVEASPEQLFEAVTEA 77 (107)
Q Consensus 2 ~~~~v~i~~~~~~~i~~ha~~~~p---~E~cGlL~G~~~~~~~~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 77 (107)
+.++|.+.|.+++..++|-.+... ..|.|+|+|..+.+ ++. |++.|.. +..+....++++-...|++ .|
T Consensus 7 ~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~--~i~--vtnSfAvpFeEDdk~~svWFlDh~Y~e---sM 79 (309)
T KOG1556|consen 7 TVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGD--VID--VTNSFAVPFEEDDKDKSVWFLDHNYIE---SM 79 (309)
T ss_pred ccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCC--eEE--eecceeccccccCCCCceEEeccHHHH---HH
Confidence 467899999999999999986544 89999999999755 332 5666543 3333334455554446766 46
Q ss_pred HHHHhhcCCCceEEEEEccCCCC
Q psy17875 78 EKLSKLYNRELRVIGWFHSHPHI 100 (107)
Q Consensus 78 ~~~~~~~~~~~~ivG~yHSHP~~ 100 (107)
-.++++.+..+.+||||||-|..
T Consensus 80 ~~mfkKvNakekivGWYhTGPkl 102 (309)
T KOG1556|consen 80 FGMFKKVNAKEKVVGWYHTGPKL 102 (309)
T ss_pred HHHHHHhcchhheeeeeccCCcc
Confidence 78899999999999999999863
No 27
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.33 E-value=8.9e-12 Score=89.14 Aligned_cols=87 Identities=11% Similarity=0.167 Sum_probs=67.4
Q ss_pred EEEECHHHHHHHHHhhhcC----C--CeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHH
Q psy17875 5 VAYISEDVYFSMFYLALSN----D--KLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAE 78 (107)
Q Consensus 5 ~v~i~~~~~~~i~~ha~~~----~--p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (107)
+|.|.|.++.+|++|+.+. . |..++|.|+|..+++ . +. |+++|+.+..+.......+|. +|. +.|.
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~-~-ve--ItnsF~~p~~~~~~~~~~id~-~y~---~~m~ 73 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGR-E-IE--IENSFELKYDTNEDGEIVLDK-EFL---ETRL 73 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCC-E-EE--EEEEEecccccCCCCceeeCH-HHH---HHHH
Confidence 6899999999999999873 3 688999999987543 3 33 889987654332224566775 444 4678
Q ss_pred HHHhhcCCCceEEEEEccCCC
Q psy17875 79 KLSKLYNRELRVIGWFHSHPH 99 (107)
Q Consensus 79 ~~~~~~~~~~~ivG~yHSHP~ 99 (107)
+++|+.+.++.+||||++.|.
T Consensus 74 ~~~kkV~~~~~vVGWY~tg~~ 94 (288)
T cd08063 74 EQFKQVFKDLDFVGWYTTGPG 94 (288)
T ss_pred HHHHHhccCCceEEEEecCCC
Confidence 899999999999999999988
No 28
>KOG2880|consensus
Probab=99.22 E-value=1.2e-11 Score=89.42 Aligned_cols=92 Identities=29% Similarity=0.470 Sum_probs=69.4
Q ss_pred ceeEEEECHHHHHHHHHhhhc--CCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHH
Q psy17875 2 SLDVAYISEDVYFSMFYLALS--NDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAE 78 (107)
Q Consensus 2 ~~~~v~i~~~~~~~i~~ha~~--~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 78 (107)
++..|.|+.+.....++-|+. ....|.||+|.|+...+. .+ |+.++.+.+.. +++.+.. +.++++..+.
T Consensus 250 ~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~--f~--IThliiPkQea-tsd~C~t~neeelF~vQd--- 321 (424)
T KOG2880|consen 250 ILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNE--FY--ITHLIIPKQEA-TSDSCNTMNEEELFEVQD--- 321 (424)
T ss_pred cceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCc--EE--EEEEEeecccC-CCccccccCHHHHheecc---
Confidence 367899999999999988874 467899999999886443 23 67776666544 4565544 5566666542
Q ss_pred HHHhhcCCCceEEEEEccCCCCCcccCCC
Q psy17875 79 KLSKLYNRELRVIGWFHSHPHITVWPSDV 107 (107)
Q Consensus 79 ~~~~~~~~~~~ivG~yHSHP~~~~~pS~~ 107 (107)
.+++--+||.|+||+.+||.|.|
T Consensus 322 ------q~~L~tlGWIHTHPTQt~FmSSV 344 (424)
T KOG2880|consen 322 ------QHELLTLGWIHTHPTQTCFMSSV 344 (424)
T ss_pred ------cccceeeeeeecCCccchhheec
Confidence 26788999999999999999986
No 29
>KOG1560|consensus
Probab=99.08 E-value=6.3e-10 Score=78.42 Aligned_cols=94 Identities=11% Similarity=0.071 Sum_probs=67.5
Q ss_pred ceeEEEECHHHHHHHHHhhhcCCCe-e-EEEEeeeeEeCCceEEEEEeeeeeecccCCCCCc-eE---EeCHHHHHHHHH
Q psy17875 2 SLDVAYISEDVYFSMFYLALSNDKL-E-VLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHD-RV---EASPEQLFEAVT 75 (107)
Q Consensus 2 ~~~~v~i~~~~~~~i~~ha~~~~p~-E-~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~-~~---~~~~~~~~~~~~ 75 (107)
++++|.|+..++.+|++|++...|+ + +.|+|+|-.-++ +.. |++|||.++...-.+ .. .+| ++-...+-
T Consensus 11 ~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~-~Le---ITncFp~p~~~~~edda~~~~~~d-e~rq~~~l 85 (339)
T KOG1560|consen 11 PVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDG-RLE---ITNCFPFPSVLENEDDAVNKSVSD-EARQAYQL 85 (339)
T ss_pred ccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecc-eeE---eecccCCCccCCCccchhhhhhhH-HHHHHHHH
Confidence 5689999999999999999998887 3 789999988744 332 799987655321111 11 122 22223455
Q ss_pred HHHHHHhhcCCCceEEEEEccCCCC
Q psy17875 76 EAEKLSKLYNRELRVIGWFHSHPHI 100 (107)
Q Consensus 76 ~~~~~~~~~~~~~~ivG~yHSHP~~ 100 (107)
+|.+.++..|-+...||||.||--+
T Consensus 86 ~mlrrlr~vnid~~hVGwYqs~~vg 110 (339)
T KOG1560|consen 86 AMLRRLRYVNIDHLHVGWYQSAYVG 110 (339)
T ss_pred HHHHHhhhcCccceeeeeeeeehhc
Confidence 6778889999999999999999543
No 30
>KOG3289|consensus
Probab=98.94 E-value=1e-08 Score=68.07 Aligned_cols=87 Identities=16% Similarity=0.203 Sum_probs=62.0
Q ss_pred eEEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhh
Q psy17875 4 DVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKL 83 (107)
Q Consensus 4 ~~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (107)
-.+.|+..++.+|+.|+.+....-+.|+|+|.....+..+. |++|+|.++. ...+.| .+.-|...++.-.++
T Consensus 2 ~~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~--itdcVPLfH~-----~laLaP-mlEvAl~lId~~~~~ 73 (199)
T KOG3289|consen 2 GEVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVE--ITDCVPLFHS-----HLALAP-MLEVALNLIDVWGAQ 73 (199)
T ss_pred CceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEE--EEecchhhcc-----cccccc-HHHHHHHHHHHHHHh
Confidence 36899999999999999999889999999996654333443 7888877653 334444 233343334443333
Q ss_pred cCCCceEEEEEccCCCC
Q psy17875 84 YNRELRVIGWFHSHPHI 100 (107)
Q Consensus 84 ~~~~~~ivG~yHSHP~~ 100 (107)
.|+.|+|+||+..+.
T Consensus 74 --~GlviaGyy~Ane~~ 88 (199)
T KOG3289|consen 74 --AGLVIAGYYHANERV 88 (199)
T ss_pred --cCeEEEEEeecCCCc
Confidence 789999999988653
No 31
>KOG2975|consensus
Probab=98.77 E-value=1.1e-08 Score=71.57 Aligned_cols=92 Identities=18% Similarity=0.208 Sum_probs=71.1
Q ss_pred eeEEEECHHHHHHHHHhhhc--CCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHH
Q psy17875 3 LDVAYISEDVYFSMFYLALS--NDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKL 80 (107)
Q Consensus 3 ~~~v~i~~~~~~~i~~ha~~--~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (107)
.-+|.|.|.++.+|+++-.+ ...+.|+|-|+|..+++ .+. |++||.-++ .++.+++++|- +|.+ +|.++
T Consensus 20 ~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g--~ie--itNCFaVPh-nEssdqvevdm-~y~~---~M~~l 90 (288)
T KOG2975|consen 20 NLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKG--SVE--VTNCFAVPH-NESSDQVEVDM-EYAK---NMYEL 90 (288)
T ss_pred CceEEEcceEEeEeehhhhcCCccchhhhhheeecccCC--eEE--EEEeeeccC-ccccccceeeH-HHHH---HHHHH
Confidence 34799999999999997664 34567999999999743 333 899986654 34578999976 4443 67888
Q ss_pred HhhcCCCceEEEEEccCCCCCcc
Q psy17875 81 SKLYNRELRVIGWFHSHPHITVW 103 (107)
Q Consensus 81 ~~~~~~~~~ivG~yHSHP~~~~~ 103 (107)
.++++.++.+||||-+-++....
T Consensus 91 ~~k~npnE~vvGWyaTg~dvt~~ 113 (288)
T KOG2975|consen 91 HKKVNPNELVVGWYATGHDVTEH 113 (288)
T ss_pred hcccCCCceeEEEEecCCCcccc
Confidence 99999999999999888876554
No 32
>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=98.39 E-value=1.7e-06 Score=60.92 Aligned_cols=87 Identities=17% Similarity=0.315 Sum_probs=60.1
Q ss_pred EEEECHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCc-eEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhh
Q psy17875 5 VAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEK-GVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKL 83 (107)
Q Consensus 5 ~v~i~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (107)
++.|+++++.+.+.-|.. ..++||+|-|+.-.+. .+.+ |.-++.+++ .++.+.+.+..+ ..+. +..
T Consensus 37 t~vlPknllkkFi~iaD~--rtQ~~GyLyG~~~~d~~~vke--I~cIvipPQ-~gt~~sv~l~~~-~~~~--~~l----- 103 (252)
T cd08056 37 TYILPKNLLKKFISISDL--RTQIAGYLYGKSPPDNPQVKE--IRCIVLVPQ-LGTHQTVTLPQQ-LPQH--EYL----- 103 (252)
T ss_pred EEEeCHHHHHHHHHHhhh--cceEEEEEeccCCCCCCCeEE--EEEEEECCE-eCCcCcEECCcc-Cccc--hhh-----
Confidence 688999999999987764 4599999999875432 2332 333333433 456778888543 2221 111
Q ss_pred cCCCceEEEEEccCCCCCcccCC
Q psy17875 84 YNRELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 84 ~~~~~~ivG~yHSHP~~~~~pS~ 106 (107)
.+++.+||.|+||.-.++.|.
T Consensus 104 --~~Le~LGWIHTqp~e~~~Lss 124 (252)
T cd08056 104 --EDLEPLGWIHTQPNELPQLSP 124 (252)
T ss_pred --CCCEeeEEEEcCCCCccccCH
Confidence 679999999999999888775
No 33
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=97.52 E-value=0.0023 Score=45.81 Aligned_cols=93 Identities=13% Similarity=0.184 Sum_probs=55.0
Q ss_pred EEEECHHHHHHHHHh-hhcCCCeeEEEEeeeeEeCCc------eEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHH
Q psy17875 5 VAYISEDVYFSMFYL-ALSNDKLEVLSMLIGETKEEK------GVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEA 77 (107)
Q Consensus 5 ~v~i~~~~~~~i~~h-a~~~~p~E~cGlL~G~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (107)
.|.+.......-... ..+.....-||+|.|+..... +++ |...+.|++. +..+.+++.++..... .
T Consensus 12 ~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~---VeaIYEPPQ~-~~~d~~~~l~d~~~~~---v 84 (274)
T cd08061 12 HVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAV---VEAIYEPPQE-GTPDGFELLEDPNADT---V 84 (274)
T ss_pred EEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEE---EEEEECCCcc-CCCCCeEEccchhhhH---H
Confidence 344444444433333 455566889999999997552 332 3444555544 4567888865432221 2
Q ss_pred HHHHhhcCCCceEEEEEccCCCC----CcccCC
Q psy17875 78 EKLSKLYNRELRVIGWFHSHPHI----TVWPSD 106 (107)
Q Consensus 78 ~~~~~~~~~~~~ivG~yHSHP~~----~~~pS~ 106 (107)
++..+. .|++.|||..||+.. ..++|+
T Consensus 85 d~iA~~--lGL~~VG~IfT~l~~~~~d~~~LSs 115 (274)
T cd08061 85 DAIAAA--LGLERVGWIFTDLPREDKDGYFLSA 115 (274)
T ss_pred HHHHHH--cCCeEEEEEEecCCCCCCCceeECH
Confidence 222222 789999999999975 445553
No 34
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains 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. However, to date, the name RadC has been misleading and no function has been determined.
Probab=96.77 E-value=0.032 Score=34.77 Aligned_cols=73 Identities=21% Similarity=0.239 Sum_probs=46.3
Q ss_pred HHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEc
Q psy17875 16 MFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFH 95 (107)
Q Consensus 16 i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yH 95 (107)
.++......+.|.+.++.=.. ..++.. ...+ ..++.++..++|.++++. +.. .+..-+...|
T Consensus 6 ~~~~~~~~~~~E~~~vl~Ld~--~~~li~--~~~l-----~~G~~~~~~v~~R~i~~~---aL~------~~A~~vil~H 67 (113)
T cd08071 6 YLREELGDLDQEEFVVLLLDT--KNRLIA--VETI-----SVGTLNSSLVHPREIFKE---ALR------HNAAAIILAH 67 (113)
T ss_pred HHHHHhCCCCceEEEEEEecC--CCCEEE--EEEE-----eecCCcceecCHHHHHHH---HHH------HhhheEEEEe
Confidence 344444455788877775333 223332 1111 234567888999876652 333 4677889999
Q ss_pred cCCCCCcccCC
Q psy17875 96 SHPHITVWPSD 106 (107)
Q Consensus 96 SHP~~~~~pS~ 106 (107)
.||.+.+.||.
T Consensus 68 NHPsG~~~PS~ 78 (113)
T cd08071 68 NHPSGDPTPSR 78 (113)
T ss_pred eCCCCCCCCCH
Confidence 99999999994
No 35
>KOG3050|consensus
Probab=96.62 E-value=0.0025 Score=44.77 Aligned_cols=91 Identities=19% Similarity=0.230 Sum_probs=57.2
Q ss_pred eEEEECHHHHHHHHHhhh-----cCCCe-eEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHH
Q psy17875 4 DVAYISEDVYFSMFYLAL-----SNDKL-EVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEA 77 (107)
Q Consensus 4 ~~v~i~~~~~~~i~~ha~-----~~~p~-E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (107)
-+|.+.|.+...|-+|-- .+.|. .+.|-|+|+..+. .+ . |.+.|... .+...+.-.+|.+-+.+ .
T Consensus 9 ~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR-~v-E--i~NSFeL~-~d~~~~~~~~dke~l~k---k- 79 (299)
T KOG3050|consen 9 VTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGR-NV-E--IMNSFELK-MDTEEDTETIDKEYLEK---K- 79 (299)
T ss_pred eeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCc-eE-E--EeeeeEEE-ecchhhhhhccHHHHHH---H-
Confidence 378889999999998854 45676 8999999998632 33 2 56666543 22222222455533332 2
Q ss_pred HHHHhhcCCCceEEEEEccCCCCCcccC
Q psy17875 78 EKLSKLYNRELRVIGWFHSHPHITVWPS 105 (107)
Q Consensus 78 ~~~~~~~~~~~~ivG~yHSHP~~~~~pS 105 (107)
++.+|+.=.++.++|||-+-.+ +-||
T Consensus 80 ~eqykqVFpdl~vlGwYttG~d--~t~s 105 (299)
T KOG3050|consen 80 EEQYKQVFPDLYVLGWYTTGSD--PTPS 105 (299)
T ss_pred HHHHHHhcccceEEEEeecCCC--CChh
Confidence 2446666678999999986533 3454
No 36
>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=95.42 E-value=0.15 Score=37.15 Aligned_cols=62 Identities=18% Similarity=0.312 Sum_probs=39.6
Q ss_pred EEEeeeeEeCCc------eEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCC
Q psy17875 29 LSMLIGETKEEK------GVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPH 99 (107)
Q Consensus 29 cGlL~G~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~ 99 (107)
+|+|.|++.... +.+ |...+.|++ .+..+.+.+.+++..+ .++++.+. .|++.|||.=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~---VeaIYEPpQ-~~~~d~~~l~~d~~~~---~vd~iA~~--lGL~rVG~IfTdl~ 69 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAV---VEAIYEPPQ-EGEPDGFTLLPDENEE---RVDAIASA--LGLERVGWIFTDLT 69 (306)
T ss_pred eEEEEEEEeccCCCCCceEEE---EEEEECCCc-CCCCCCEEEcCCccHH---HHHHHHHH--CCCEEEEEEEecCc
Confidence 799999997554 332 344455555 3567788885433222 23333333 78999999999986
No 37
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=95.16 E-value=0.18 Score=31.72 Aligned_cols=79 Identities=16% Similarity=0.149 Sum_probs=39.1
Q ss_pred HHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCce
Q psy17875 10 EDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELR 89 (107)
Q Consensus 10 ~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (107)
++.+...++......+.|..-++.= +...++.. ...+ ..++.++..++|.++.+ .+.+ .+..
T Consensus 5 ~~~v~~~l~~~l~~~~~E~~~~l~L--d~~~~li~--~~~v-----~~G~~~~~~v~~R~I~~---~al~------~~A~ 66 (123)
T PF04002_consen 5 PEDVADYLRPKLQGLDQEQFRVLYL--DSKNRLIG--DEVV-----SEGTIDSAPVDPREIFR---RALR------LNAS 66 (123)
T ss_dssp HHHHHHHHTTTSS-TTS-EEEEEEE---TTSBEEE--EEEE-----EESTT-GGGCSHHHHHH---HHHH------TT-S
T ss_pred HHHHHHHHHHHhCCCCCeEEEEEEE--CCCCcEEE--EEEe-----cccCCCcccccHHHHHH---HHHh------hCCc
Confidence 4444555654555666777766652 22233432 1111 23445566788877654 3443 4556
Q ss_pred EEEEEccCCCCCcccCC
Q psy17875 90 VIGWFHSHPHITVWPSD 106 (107)
Q Consensus 90 ivG~yHSHP~~~~~pS~ 106 (107)
-+-..|=||.+.+.||.
T Consensus 67 ~vIl~HNHPsG~~~PS~ 83 (123)
T PF04002_consen 67 SVILAHNHPSGDPEPSD 83 (123)
T ss_dssp EEEEEEE-TTS--S--H
T ss_pred eEEEEEEcCCCCCCCCH
Confidence 67779999999999994
No 38
>PRK00024 hypothetical protein; Reviewed
Probab=94.40 E-value=0.91 Score=31.60 Aligned_cols=80 Identities=18% Similarity=0.188 Sum_probs=50.4
Q ss_pred CHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCc
Q psy17875 9 SEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNREL 88 (107)
Q Consensus 9 ~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (107)
++..+.+.+.......+.|...+|.=.. ..++.. ...+ ..++-++..++|.++++. +.+ .+-
T Consensus 105 ~~~~~~~~l~~~l~~~~~E~f~vl~Ld~--~~~li~--~~~i-----~~Gt~~~~~v~pRei~~~---Al~------~~A 166 (224)
T PRK00024 105 SPEDVADYLMAELRDEEQEHFVVLFLDT--KNRVIA--DEEL-----FIGTLNSSIVHPREIVKR---ALK------LNA 166 (224)
T ss_pred CHHHHHHHHHHHccCCCceEEEEEEECC--CCCEee--EEEe-----eeecCCeEEEcHHHHHHH---HHH------hhc
Confidence 4445555665555667788877775322 223332 1111 346677889999886653 333 345
Q ss_pred eEEEEEccCCCCCcccCC
Q psy17875 89 RVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 89 ~ivG~yHSHP~~~~~pS~ 106 (107)
.-|-.-|=||.+.+.||.
T Consensus 167 ~~iIl~HNHPSG~~~PS~ 184 (224)
T PRK00024 167 AALILAHNHPSGDPEPSQ 184 (224)
T ss_pred cceEEEecCCCCCCCCCH
Confidence 566678999999999995
No 39
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.28 E-value=1.2 Score=30.92 Aligned_cols=80 Identities=19% Similarity=0.240 Sum_probs=50.3
Q ss_pred CHHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCc
Q psy17875 9 SEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNREL 88 (107)
Q Consensus 9 ~~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (107)
++......+.......+.|.+-++.= +...++.. ...+ ..++-+...++|.++++ .+.+ .+-
T Consensus 99 s~~~v~~~l~~~l~~~~~E~f~vl~L--d~~n~li~--~~~i-----~~Gt~~~~~v~pReI~~---~Al~------~~A 160 (218)
T TIGR00608 99 SPEAAAEFLHTDLAHETREHFMVLFL--DRKNRLIA--KEVV-----FIGTVNHVPVHPREIFK---EALK------LSA 160 (218)
T ss_pred CHHHHHHHHHHHhcCCCceEEEEEEE--CCCCcEEE--EEEe-----ecCCCCeEEEcHHHHHH---HHHH------hhC
Confidence 44555566666566677887777652 22223332 1111 34667889999988665 3333 345
Q ss_pred eEEEEEccCCCCCcccCC
Q psy17875 89 RVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 89 ~ivG~yHSHP~~~~~pS~ 106 (107)
.-|-.-|=||.+.+.||.
T Consensus 161 ~~vIlaHNHPSG~~~PS~ 178 (218)
T TIGR00608 161 SALILAHNHPSGEPSPSQ 178 (218)
T ss_pred CeEEEEeecCCCCCCCCH
Confidence 566678999999999995
No 40
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=88.17 E-value=1.8 Score=32.18 Aligned_cols=32 Identities=19% Similarity=0.382 Sum_probs=22.1
Q ss_pred eCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCC
Q psy17875 65 ASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPH 99 (107)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~ 99 (107)
+|. +|..- .|++..|..-.|..|+|+|=..|.
T Consensus 43 id~-~WVae--HA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 43 IDE-EWVAE--HARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred cCH-HHHHH--HHHHHHhhCCCCcEEEEEEEEcCH
Confidence 444 56542 466667777789999999976653
No 41
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=86.77 E-value=0.66 Score=30.84 Aligned_cols=20 Identities=35% Similarity=0.534 Sum_probs=16.3
Q ss_pred CCceEEEEEccCCCCCcccCC
Q psy17875 86 RELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 86 ~~~~ivG~yHSHP~~~~~pS~ 106 (107)
.+..++. .||||..++.||.
T Consensus 114 ~~~~iid-iHSHP~~~~~~S~ 133 (162)
T PF15659_consen 114 NGNKIID-IHSHPENSNGPSG 133 (162)
T ss_pred CCceEEE-eccCCCCCCCCCc
Confidence 5566667 9999999989985
No 42
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=82.45 E-value=0.95 Score=28.71 Aligned_cols=16 Identities=13% Similarity=0.368 Sum_probs=13.3
Q ss_pred CCceEEEEEccCCCCC
Q psy17875 86 RELRVIGWFHSHPHIT 101 (107)
Q Consensus 86 ~~~~ivG~yHSHP~~~ 101 (107)
.+..+|+.||||....
T Consensus 57 ~g~~~vA~yHTHG~~~ 72 (123)
T PF14220_consen 57 NGSTIVASYHTHGAYS 72 (123)
T ss_pred cccceeeEeecccccC
Confidence 4689999999998754
No 43
>KOG2834|consensus
Probab=77.32 E-value=10 Score=29.44 Aligned_cols=79 Identities=18% Similarity=0.236 Sum_probs=43.6
Q ss_pred HHHHHHHHHhhhcCCCeeEEEEeeeeEeCCceE---EEEEeeeeeecccCCCCCceEEeCH-HHHHHHHHHHHHHHhhcC
Q psy17875 10 EDVYFSMFYLALSNDKLEVLSMLIGETKEEKGV---KSVHVYTMVIPLRLTSKHDRVEASP-EQLFEAVTEAEKLSKLYN 85 (107)
Q Consensus 10 ~~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~---~~~~i~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 85 (107)
+.+++..++.-+. ...--.|+|.|++.+...+ +.+.|...+.|++. +.++.+++.. ++..+..+.+. +
T Consensus 182 ~~~v~~Fl~~wr~-sg~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~-~~~dgl~l~~~~e~~~vD~~a~------~ 253 (510)
T KOG2834|consen 182 AELVNHFLNEWRA-SGVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQH-GEEDGLELLEDDEAKRVDAIAE------G 253 (510)
T ss_pred hHHHHHHHHHHHH-hhhhhcceEEEeecccccccccceeeEEEEecCCcc-CCcCCeEEeccchhhhHHHHHH------h
Confidence 4555555555443 3456679999999754433 00113334445444 4577888752 22222222233 3
Q ss_pred CCceEEEEEcc
Q psy17875 86 RELRVIGWFHS 96 (107)
Q Consensus 86 ~~~~ivG~yHS 96 (107)
.|++.|||.-+
T Consensus 254 lGLrRVG~IFT 264 (510)
T KOG2834|consen 254 LGLRRVGWIFT 264 (510)
T ss_pred cCceeeEEEEe
Confidence 88999999754
No 44
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=71.47 E-value=3.7 Score=29.44 Aligned_cols=21 Identities=19% Similarity=0.278 Sum_probs=15.9
Q ss_pred CCCceEEEEEccCCCCCcccC
Q psy17875 85 NRELRVIGWFHSHPHITVWPS 105 (107)
Q Consensus 85 ~~~~~ivG~yHSHP~~~~~pS 105 (107)
..+...|++||||.+-.=.|+
T Consensus 70 ~~~~~~V~IYhTH~~EsY~p~ 90 (268)
T PF07454_consen 70 TSGKPQVLIYHTHSTESYLPS 90 (268)
T ss_pred CCCCCEEEEEeCCCccccccc
Confidence 356789999999987655554
No 45
>PF07732 Cu-oxidase_3: Multicopper oxidase; InterPro: IPR011707 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 3 (or coupled binuclear) domains. ; GO: 0005507 copper ion binding; PDB: 2QT6_B 3KW7_B 2R7E_A 3CDZ_A 1SDD_A 3G5W_D 3UAC_A 2YXV_A 3OD3_A 3NSY_A ....
Probab=58.51 E-value=4.9 Score=24.96 Aligned_cols=10 Identities=50% Similarity=0.953 Sum_probs=7.7
Q ss_pred EEEEccCCCC
Q psy17875 91 IGWFHSHPHI 100 (107)
Q Consensus 91 vG~yHSHP~~ 100 (107)
.=|||+|...
T Consensus 92 t~wYH~H~~~ 101 (117)
T PF07732_consen 92 TYWYHSHVHG 101 (117)
T ss_dssp EEEEEECSTT
T ss_pred ceeEeeCCCc
Confidence 4499999765
No 46
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=56.49 E-value=13 Score=26.07 Aligned_cols=40 Identities=28% Similarity=0.346 Sum_probs=26.9
Q ss_pred CCCceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCCCcccCC
Q psy17875 58 SKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWPSD 106 (107)
Q Consensus 58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~~~~pS~ 106 (107)
++-+.-+.-|.++.+ .|.+ .+..=|-..|=||.+.+-||.
T Consensus 145 GTi~~s~V~PREI~k---~Al~------~nAaavIlaHNHPSGd~~PS~ 184 (224)
T COG2003 145 GTLNVSEVHPREIFK---EALK------YNAAAVILAHNHPSGDPTPSR 184 (224)
T ss_pred eecccceecHHHHHH---HHHH------hcchhhheeccCCCCCCCcCH
Confidence 445566777877654 3443 333444558999999999995
No 47
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated. The sequences in this family contain the pyridoxal binding domain (pfam02784) and C-terminal sheet domain (pfam00278) of a family of Pyridoxal-dependent decarboxylases. Characterized enzymes in this family decarboxylate substrates such as ornithine, diaminopimelate and arginine. The genes of the family modeled here, with the exception of those observed in certain Burkholderia species, are all found in the context of exopolysaccharide biosynthesis loci containing the exosortase/PEP-CTERM protein sorting system. More specifically, these are characteristic of the type 1 exosortase system represented by the Genome Property GenProp0652. The substrate of these enzymes may be a precursor of the carrier or linker which is hypothesized to release the PEP-CTERM protein from the exosortase enzyme. These enzymes are apparently most closely related to the diaminopimelate decarboxylase modeled by TIGR01048
Probab=55.28 E-value=21 Score=26.50 Aligned_cols=35 Identities=20% Similarity=0.214 Sum_probs=23.9
Q ss_pred CceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCCC
Q psy17875 60 HDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHIT 101 (107)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~~ 101 (107)
..+|=++++++.++.+.+ ++ .+.++.|+ |.|.++.
T Consensus 163 ~srFGi~~~e~~~~~~~~----~~--~~l~l~Gl-h~h~gs~ 197 (398)
T TIGR03099 163 AKQFGIDAEQVPAALAFI----KA--ADLDFQGF-HIFAGSQ 197 (398)
T ss_pred CCcCCCCHHHHHHHHHHH----Hh--CCCeEEEE-Eeccccc
Confidence 467888887766554333 33 37899998 8888654
No 48
>COG3449 DNA gyrase inhibitor [DNA replication, recombination, and repair]
Probab=53.98 E-value=50 Score=21.82 Aligned_cols=36 Identities=14% Similarity=0.294 Sum_probs=22.1
Q ss_pred CHHHHHHHHHHHHHHHhhcC---CCceEEEEEccCCCCC
Q psy17875 66 SPEQLFEAVTEAEKLSKLYN---RELRVIGWFHSHPHIT 101 (107)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~---~~~~ivG~yHSHP~~~ 101 (107)
++.++-+.++++....+..+ ..-..+|+||++|+.+
T Consensus 21 ~~~~~~~~~~~l~~W~~~~~l~p~~S~~~gI~~ddP~~T 59 (154)
T COG3449 21 DPATLKQTFEQLIAWRRENGLLPEQSETLGIYQDDPDTT 59 (154)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCCCCceEEEEecCCCCCC
Confidence 44455555555555444433 2256899999999854
No 49
>PF08255 Leader_Trp: Trp-operon Leader Peptide; InterPro: IPR013205 The tryptophan operon regulatory region of Citrobacter freundii (leader transcript) encodes a 14-residue peptide containing characteristic tandem tryptophan residues. It is about 10 nucleotides shorter than those of Escherichia coli and Salmonella typhimurium [].
Probab=53.42 E-value=10 Score=14.75 Aligned_cols=8 Identities=25% Similarity=1.078 Sum_probs=6.1
Q ss_pred eEEEEEcc
Q psy17875 89 RVIGWFHS 96 (107)
Q Consensus 89 ~ivG~yHS 96 (107)
.+.||||+
T Consensus 6 ~L~~WWrt 13 (14)
T PF08255_consen 6 SLHGWWRT 13 (14)
T ss_pred EEeeEEEc
Confidence 46799985
No 50
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=49.31 E-value=28 Score=25.73 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=23.0
Q ss_pred ceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCCC
Q psy17875 61 DRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHIT 101 (107)
Q Consensus 61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~~ 101 (107)
.+|=++++++.++.+.+.+ ..+.++.|+ |+|....
T Consensus 142 srfG~~~~~~~~~~~~~~~-----~~~l~~~Gl-h~H~gs~ 176 (377)
T cd06843 142 TPFGIDEADLPDALELLRD-----LPNIRLRGF-HFHLMSH 176 (377)
T ss_pred CCCCcCHHHHHHHHHHHHh-----CCCccEEEE-EEEcCcC
Confidence 4788888766555433322 136899998 9998754
No 51
>PHA00442 host recBCD nuclease inhibitor
Probab=47.91 E-value=4.8 Score=21.85 Aligned_cols=19 Identities=26% Similarity=0.244 Sum_probs=13.6
Q ss_pred ceeEEEECHHHHHHHHHhh
Q psy17875 2 SLDVAYISEDVYFSMFYLA 20 (107)
Q Consensus 2 ~~~~v~i~~~~~~~i~~ha 20 (107)
+-..|.|+++++..|-...
T Consensus 4 ~~d~VtitRd~wnd~q~yi 22 (59)
T PHA00442 4 SRDLVTITRDAWNDMQGYI 22 (59)
T ss_pred cccceeecHHHHHHHHHHH
Confidence 4457999999996665443
No 52
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=47.69 E-value=13 Score=21.01 Aligned_cols=11 Identities=27% Similarity=0.969 Sum_probs=7.4
Q ss_pred CceEEEEEccC
Q psy17875 87 ELRVIGWFHSH 97 (107)
Q Consensus 87 ~~~ivG~yHSH 97 (107)
..++||||-+.
T Consensus 39 qg~vvgwy~t~ 49 (78)
T PF06442_consen 39 QGQVVGWYCTK 49 (78)
T ss_dssp EEEEEEEE--S
T ss_pred cceEeEEEecc
Confidence 37899999754
No 53
>COG4424 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.92 E-value=12 Score=26.11 Aligned_cols=16 Identities=31% Similarity=0.482 Sum_probs=12.7
Q ss_pred EEEEccCCCCCcccCC
Q psy17875 91 IGWFHSHPHITVWPSD 106 (107)
Q Consensus 91 vG~yHSHP~~~~~pS~ 106 (107)
.|.||-||++++-+|.
T Consensus 141 TglwhahpdG~ap~s~ 156 (250)
T COG4424 141 TGLWHAHPDGPAPDSQ 156 (250)
T ss_pred hcceeccCCCCCCccc
Confidence 4679999999777664
No 54
>KOG0256|consensus
Probab=43.01 E-value=68 Score=24.87 Aligned_cols=36 Identities=25% Similarity=0.314 Sum_probs=29.4
Q ss_pred CCceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCC
Q psy17875 59 KHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHI 100 (107)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~ 100 (107)
+++.|.++.+.+.+|.++|++ .+..|=|+.=+.|..
T Consensus 202 Ss~~f~itv~alE~A~~~A~~------~~~kVkGvlitNPsN 237 (471)
T KOG0256|consen 202 SSNGFQITVEALEAALNQARK------LGLKVKGVLITNPSN 237 (471)
T ss_pred cCCCccccHHHHHHHHHHHHH------hCCceeEEEEeCCCC
Confidence 456799999889988888887 788899998888764
No 55
>PRK10883 FtsI repressor; Provisional
Probab=42.77 E-value=12 Score=28.82 Aligned_cols=11 Identities=18% Similarity=0.646 Sum_probs=8.0
Q ss_pred EEEEEccCCCC
Q psy17875 90 VIGWFHSHPHI 100 (107)
Q Consensus 90 ivG~yHSHP~~ 100 (107)
=.=|||+|...
T Consensus 137 GT~WYH~H~~~ 147 (471)
T PRK10883 137 ATCWYHANTPN 147 (471)
T ss_pred eeeEEccCCCC
Confidence 34699999753
No 56
>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=42.75 E-value=43 Score=23.13 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=10.6
Q ss_pred CCceEEEEEccC
Q psy17875 86 RELRVIGWFHSH 97 (107)
Q Consensus 86 ~~~~ivG~yHSH 97 (107)
+|..+||+||-+
T Consensus 201 ~GaAlvGIFHDe 212 (235)
T COG4778 201 RGAALVGIFHDE 212 (235)
T ss_pred cCceEEEeeccH
Confidence 889999999954
No 57
>COG2132 SufI Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=41.72 E-value=13 Score=28.37 Aligned_cols=9 Identities=44% Similarity=1.084 Sum_probs=7.4
Q ss_pred EEEccCCCC
Q psy17875 92 GWFHSHPHI 100 (107)
Q Consensus 92 G~yHSHP~~ 100 (107)
=|||||+..
T Consensus 128 ~wyh~H~~~ 136 (451)
T COG2132 128 YWYHPHTHG 136 (451)
T ss_pred eEeccCCCc
Confidence 399999974
No 58
>PRK10965 multicopper oxidase; Provisional
Probab=40.79 E-value=12 Score=29.29 Aligned_cols=9 Identities=56% Similarity=1.361 Sum_probs=7.1
Q ss_pred EEEEccCCC
Q psy17875 91 IGWFHSHPH 99 (107)
Q Consensus 91 vG~yHSHP~ 99 (107)
.=|||+|+.
T Consensus 138 T~WYH~H~~ 146 (523)
T PRK10965 138 TCWFHPHQH 146 (523)
T ss_pred eEEEecCCC
Confidence 459999973
No 59
>PF06812 ImpA-rel_N: ImpA-related N-terminal; InterPro: IPR010657 This entry represents a conserved region located towards the N-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans []. Note that many members are hypothetical proteins.
Probab=38.91 E-value=5.3 Score=21.89 Aligned_cols=24 Identities=25% Similarity=0.290 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHhhcCCCceEEEEE
Q psy17875 71 FEAVTEAEKLSKLYNRELRVIGWF 94 (107)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~ivG~y 94 (107)
..+.+.+.++++..++++++++||
T Consensus 3 ~~v~~~~~~lL~~~sKDlrv~~~l 26 (62)
T PF06812_consen 3 DKVEELALELLSEQSKDLRVAVWL 26 (62)
T ss_pred HHHHHHHHHHHHHcCchHHHHHHH
Confidence 334445666666666777776665
No 60
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=37.77 E-value=11 Score=24.56 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=7.4
Q ss_pred EEE--ccCCCCC
Q psy17875 92 GWF--HSHPHIT 101 (107)
Q Consensus 92 G~y--HSHP~~~ 101 (107)
-|| |+||++-
T Consensus 60 ~WYRQHthpDGi 71 (163)
T TIGR02652 60 QWYRQHTHPDGI 71 (163)
T ss_pred hhhhhccCCCce
Confidence 367 9999863
No 61
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=37.34 E-value=1.5e+02 Score=21.04 Aligned_cols=86 Identities=13% Similarity=0.223 Sum_probs=44.1
Q ss_pred EEEECHHHHHHHHHhhhcCCCe-eEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHh-
Q psy17875 5 VAYISEDVYFSMFYLALSNDKL-EVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSK- 82 (107)
Q Consensus 5 ~v~i~~~~~~~i~~ha~~~~p~-E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 82 (107)
-+.|++.--.++++. ....|. ..+|+++....++. +.. +... ...=.-...+-=++|++++.+.+++-.+...
T Consensus 23 ~~fL~~~~a~~~l~~-~GN~~~~~~~Gli~P~~~~~~-W~v--~~~y-~~~GyVkDdda~~id~d~LL~~~k~~t~e~N~ 97 (239)
T PF09935_consen 23 FRFLNPEDARKVLEE-WGNPPSPAELGLIFPDDDDED-WFV--VFEY-EDSGYVKDDDAKNIDYDELLKSMKEGTEESNK 97 (239)
T ss_pred cEEcCHHHHHHHHHH-hCCCCCcceEEEEeccCCCCC-EEE--EEEE-cCCCceecchhhhCCHHHHHHHHHHhHHhhhH
Confidence 356788888888844 333332 34899997763332 221 2221 1111111223345788777765544333221
Q ss_pred ---hcC-CCceEEEEEc
Q psy17875 83 ---LYN-RELRVIGWFH 95 (107)
Q Consensus 83 ---~~~-~~~~ivG~yH 95 (107)
+.| ..+.++||.-
T Consensus 98 eR~~~G~~~l~l~GW~~ 114 (239)
T PF09935_consen 98 ERKKRGYPPLHLVGWAE 114 (239)
T ss_pred HHHhcCCCceEEecccc
Confidence 111 3388999974
No 62
>KOG3844|consensus
Probab=37.23 E-value=35 Score=26.22 Aligned_cols=32 Identities=28% Similarity=0.469 Sum_probs=21.1
Q ss_pred CceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEcc
Q psy17875 60 HDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHS 96 (107)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHS 96 (107)
-..|+.+|..+.++ ++.+.. .+.+.|-||||+
T Consensus 186 l~fFeVsp~SFH~V----~Ev~sd-e~RlSIsGWfH~ 217 (476)
T KOG3844|consen 186 LVFFEVSPISFHDV----EEVLSD-EPRLSISGWFHF 217 (476)
T ss_pred EEEEEecccchhhH----HHHhcc-CcceeEeeeecC
Confidence 45688888666554 333322 356999999995
No 63
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=36.49 E-value=12 Score=24.36 Aligned_cols=9 Identities=44% Similarity=1.320 Sum_probs=7.0
Q ss_pred EE--ccCCCCC
Q psy17875 93 WF--HSHPHIT 101 (107)
Q Consensus 93 ~y--HSHP~~~ 101 (107)
|| |+||++-
T Consensus 58 WyrQHthpDGi 68 (161)
T PF09654_consen 58 WYRQHTHPDGI 68 (161)
T ss_pred hhhhccCCCce
Confidence 66 9999863
No 64
>PF00886 Ribosomal_S16: Ribosomal protein S16; InterPro: IPR000307 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups: Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2Y14_P 3UZ6_S 2J02_P 1HNZ_P 3V26_P 3KNL_P 1N34_P 2J00_P 1HNW_P 3OHC_P ....
Probab=36.03 E-value=29 Score=19.19 Aligned_cols=16 Identities=13% Similarity=0.488 Sum_probs=12.8
Q ss_pred CCCceEEEEEccCCCC
Q psy17875 85 NRELRVIGWFHSHPHI 100 (107)
Q Consensus 85 ~~~~~ivG~yHSHP~~ 100 (107)
|+-.+.||+|.-+++.
T Consensus 23 Gk~iE~lG~YdP~~~~ 38 (62)
T PF00886_consen 23 GKFIEELGFYDPIPNP 38 (62)
T ss_dssp SSESEEEEEEETTSSS
T ss_pred cchhhccceEcCCCCC
Confidence 4558999999988763
No 65
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=35.77 E-value=1.1e+02 Score=19.08 Aligned_cols=61 Identities=11% Similarity=0.120 Sum_probs=34.6
Q ss_pred CCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHHHHHhhcC
Q psy17875 23 NDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAEKLSKLYN 85 (107)
Q Consensus 23 ~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 85 (107)
....++.|+.+ .+++..+...++..=|.+-...+-+..|.+ ++++|.+-++-|++|.+.-|
T Consensus 44 ~~~~~itgm~l--iDeEGei~tr~v~~KFvnGkp~~iEa~y~m~s~~~WdRFMRFMeRYA~~ng 105 (111)
T PLN00039 44 GELGDITGLYM--IDEEGVLQTVDVSAKFVNGKPAGIEAKYVMRSPREWDRFMRFMERYAEENG 105 (111)
T ss_pred cccCceeeEEE--EccCccEEEEecceEEECCCccEEEEEEEECCHHHHHHHHHHHHHHHHhcC
Confidence 34678888766 333333332122222333222222345666 67899999999999887633
No 66
>PLN02168 copper ion binding / pectinesterase
Probab=35.03 E-value=16 Score=28.85 Aligned_cols=8 Identities=0% Similarity=0.027 Sum_probs=6.7
Q ss_pred EEEccCCC
Q psy17875 92 GWFHSHPH 99 (107)
Q Consensus 92 G~yHSHP~ 99 (107)
=|||||..
T Consensus 123 ~WYHsH~~ 130 (545)
T PLN02168 123 YFYFPSLL 130 (545)
T ss_pred EEEecChh
Confidence 59999975
No 67
>KOG1670|consensus
Probab=34.92 E-value=83 Score=21.93 Aligned_cols=27 Identities=4% Similarity=0.064 Sum_probs=18.0
Q ss_pred HHHhhhcCCCeeEEEEeeeeEeCCceEE
Q psy17875 16 MFYLALSNDKLEVLSMLIGETKEEKGVK 43 (107)
Q Consensus 16 i~~ha~~~~p~E~cGlL~G~~~~~~~~~ 43 (107)
++-.... +..|+||+++-......++.
T Consensus 134 lIGE~fd-~~deICGaV~NiR~k~~KIS 160 (212)
T KOG1670|consen 134 LIGEQFD-HSDEICGAVVNIRGKGDKIS 160 (212)
T ss_pred HHhhhcc-ccccceeEEEEeccCCceEE
Confidence 3334444 67899999998776555553
No 68
>TIGR03389 laccase laccase, plant. Members of this protein family include the copper-containing enzyme laccase (EC 1.10.3.2), often several from a single plant species, and additional, uncharacterized, closely related plant proteins termed laccase-like multicopper oxidases. This protein family shows considerable sequence similarity to the L-ascorbate oxidase (EC 1.10.3.3) family. Laccases are enzymes of rather broad specificity, and classification of all proteins scoring about the trusted cutoff of this model as laccases may be appropriate.
Probab=34.90 E-value=16 Score=28.59 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=7.1
Q ss_pred EEEEccCCC
Q psy17875 91 IGWFHSHPH 99 (107)
Q Consensus 91 vG~yHSHP~ 99 (107)
.=|||||..
T Consensus 100 T~WYHsH~~ 108 (539)
T TIGR03389 100 TLWWHAHIS 108 (539)
T ss_pred eEEEecCch
Confidence 469999964
No 69
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Probab=34.75 E-value=67 Score=23.60 Aligned_cols=35 Identities=20% Similarity=0.254 Sum_probs=22.7
Q ss_pred CceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCC
Q psy17875 60 HDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHI 100 (107)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~ 100 (107)
..+|=++++++.++.+.+ ++ ..+.++.|+ |.|..+
T Consensus 146 ~sKfG~~~~~~~~~~~~~----~~-~~~l~l~Gl-h~h~gs 180 (382)
T cd06839 146 PSQFGIDVEELPAVLARI----AA-LPNLRFVGL-HIYPGT 180 (382)
T ss_pred CCCcCCCHHHHHHHHHHH----Hh-CCCCcEEEE-EEecCc
Confidence 356778887765554333 22 145889998 999764
No 70
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=34.05 E-value=1.2e+02 Score=18.98 Aligned_cols=60 Identities=13% Similarity=0.048 Sum_probs=33.7
Q ss_pred CCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHHHHHhhcC
Q psy17875 24 DKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAEKLSKLYN 85 (107)
Q Consensus 24 ~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 85 (107)
...++.|+.+ .+++..+...++..=|.+-....-+..|.+ ++++|.+-++-|++|.+.-|
T Consensus 47 ~~~~itgm~L--iDeEGei~tr~v~~KFvnGkp~~iEa~y~m~s~~~WdRFMRFMeRYA~~ng 107 (113)
T PRK13612 47 TTGEITGMYM--IDEEGEIVTREVKAKFVNGKPSALEATYIWKSEQEWDRFMRFMERYAKENG 107 (113)
T ss_pred ccCceeeEEE--EccCccEEEEecceEEECCCccEEEEEEEECCHHHHHHHHHHHHHHHHhcC
Confidence 4568888766 333333332122222333222222345666 67899999999999887633
No 71
>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.
Probab=33.82 E-value=1.2e+02 Score=18.85 Aligned_cols=58 Identities=12% Similarity=0.070 Sum_probs=26.8
Q ss_pred eeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeC-HHHHHHHHHHHHHHHhhcC
Q psy17875 26 LEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEAS-PEQLFEAVTEAEKLSKLYN 85 (107)
Q Consensus 26 ~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 85 (107)
.++.|+.+ .++++.+...++..-|.+-....-+..|.|. +++|.+-++-|++|.+.-|
T Consensus 46 ~~itgm~l--iDeEGei~t~~v~~kFvnG~p~~iEa~y~m~s~~~WdRFMRFMeRYA~~Ng 104 (108)
T PF03912_consen 46 GEITGMYL--IDEEGEISTRDVNAKFVNGKPQAIEATYIMKSEEEWDRFMRFMERYAEANG 104 (108)
T ss_dssp -G---EEE--E-SS-EEEE--EEEEEETTEEEEEEEEEEE-SSHHHHHHHHHHHHHHHH--
T ss_pred cccceEEE--EccCccEEEEecceEEECCceEEEEEEEEECCHHHHHHHHHHHHHHHHhcC
Confidence 47778776 3333333321222223322111222356664 7899999999999887643
No 72
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=32.33 E-value=1.3e+02 Score=18.84 Aligned_cols=61 Identities=15% Similarity=0.084 Sum_probs=34.4
Q ss_pred CCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHHHHHhhcC
Q psy17875 23 NDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAEKLSKLYN 85 (107)
Q Consensus 23 ~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 85 (107)
....++.|+.+ .++++.+...++..=|.+-....-+..|.+ ++++|.+-++-|++|.+.-|
T Consensus 46 ~~~~~itgm~L--iDeEGei~tr~v~~KFvnGkp~~iEa~y~m~s~~~WdRFMRFMeRYA~~ng 107 (113)
T CHL00128 46 AKQGEITGMYL--IDEEGELSTRDVNAKFINGKPQAIEAIYIMKNPEAWDRFMRFMERYAEDNG 107 (113)
T ss_pred ccccceeeEEE--EccCccEEEEecceEEECCCccEEEEEEEECCHHHHHHHHHHHHHHHHhcC
Confidence 35678889766 333333332112222333222222345666 67899999999999887633
No 73
>PLN02991 oxidoreductase
Probab=31.94 E-value=20 Score=28.40 Aligned_cols=8 Identities=0% Similarity=0.019 Sum_probs=6.6
Q ss_pred EEEccCCC
Q psy17875 92 GWFHSHPH 99 (107)
Q Consensus 92 G~yHSHP~ 99 (107)
-|||||..
T Consensus 125 ~WYHsH~~ 132 (543)
T PLN02991 125 FYYFPSLG 132 (543)
T ss_pred eEEecCcc
Confidence 59999974
No 74
>TIGR03390 ascorbOXfungal L-ascorbate oxidase, fungal type. This model describes a family of fungal ascorbate oxidases, within a larger family of multicopper oxidases that also includes plant ascorbate oxidases (TIGR03388), plant laccases and laccase-like proteins (TIGR03389), and related proteins. The member from Acremonium sp. HI-25 is characterized.
Probab=31.73 E-value=20 Score=28.18 Aligned_cols=8 Identities=38% Similarity=0.654 Sum_probs=6.5
Q ss_pred EEEccCCC
Q psy17875 92 GWFHSHPH 99 (107)
Q Consensus 92 G~yHSHP~ 99 (107)
=|||||..
T Consensus 108 ~WYHsH~~ 115 (538)
T TIGR03390 108 YFYHSHVG 115 (538)
T ss_pred eEEecCCc
Confidence 49999974
No 75
>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]
Probab=31.49 E-value=1.5e+02 Score=19.14 Aligned_cols=38 Identities=11% Similarity=-0.074 Sum_probs=25.3
Q ss_pred HHHHHHHHhhhcCCCeeEEEEeeeeEeCCceEEEEEeeee
Q psy17875 11 DVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTM 50 (107)
Q Consensus 11 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~i~~~ 50 (107)
+++..++.|+.+..|.|.|-.+--...++...+. |+|-
T Consensus 47 E~~~N~v~Ha~~~~~~~g~I~i~~~~~~~~~~i~--i~D~ 84 (146)
T COG2172 47 EALTNAVKHAYKLDPSEGEIRIEVSLDDGKLEIR--IWDQ 84 (146)
T ss_pred HHHHHHHHHHhhcCCCCceEEEEEEEcCCeEEEE--EEeC
Confidence 4566788999999998777776655555543222 5653
No 76
>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.
Probab=30.71 E-value=1.4e+02 Score=18.61 Aligned_cols=60 Identities=13% Similarity=0.077 Sum_probs=33.7
Q ss_pred CCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHHHHHhhcC
Q psy17875 24 DKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAEKLSKLYN 85 (107)
Q Consensus 24 ~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 85 (107)
...++.|+.+ .+++..+...++..=|.+-....-+..|.+ ++++|.+-++-|+++.+.-|
T Consensus 44 ~~~~itGm~L--iDeEGei~tr~v~~KFvnGkp~~iEa~y~m~s~~~WdRFMRFmeRYA~~ng 104 (109)
T TIGR03047 44 DTGEITGMYL--IDEEGEIVTREVKAKFVNGKPKALEAVYIMKSEDEWDRFMRFMERYAEANG 104 (109)
T ss_pred cccceeeEEE--EccCccEEEEecceEEECCCccEEEEEEEECCHHHHHHHHHHHHHHHHhcC
Confidence 4568889766 333333332112222333222222335666 67899999999999877633
No 77
>PLN02835 oxidoreductase
Probab=29.52 E-value=22 Score=28.03 Aligned_cols=9 Identities=0% Similarity=-0.215 Sum_probs=6.9
Q ss_pred EEEEccCCC
Q psy17875 91 IGWFHSHPH 99 (107)
Q Consensus 91 vG~yHSHP~ 99 (107)
.=|||||..
T Consensus 125 T~WYHsH~~ 133 (539)
T PLN02835 125 TFTYFPSTL 133 (539)
T ss_pred eEEEEeCcc
Confidence 359999964
No 78
>COG1753 Predicted antotoxin, copG family [Signal transduction mechanisms]
Probab=28.97 E-value=77 Score=18.23 Aligned_cols=20 Identities=30% Similarity=0.424 Sum_probs=16.8
Q ss_pred CceeEEEECHHHHHHHHHhh
Q psy17875 1 MSLDVAYISEDVYFSMFYLA 20 (107)
Q Consensus 1 ~~~~~v~i~~~~~~~i~~ha 20 (107)
|...++.|+.+++.++++--
T Consensus 1 ~~~kTItI~ddvYe~L~kmK 20 (74)
T COG1753 1 MPTKTITISDDVYEKLVKMK 20 (74)
T ss_pred CCcceeeecHHHHHHHHHHH
Confidence 66789999999999988653
No 79
>PLN02792 oxidoreductase
Probab=28.50 E-value=24 Score=27.83 Aligned_cols=8 Identities=0% Similarity=0.073 Sum_probs=6.6
Q ss_pred EEEccCCC
Q psy17875 92 GWFHSHPH 99 (107)
Q Consensus 92 G~yHSHP~ 99 (107)
=|||||..
T Consensus 113 ~WYHsH~~ 120 (536)
T PLN02792 113 YFYFPSLA 120 (536)
T ss_pred eEEecCcc
Confidence 59999974
No 80
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=28.19 E-value=1.5e+02 Score=18.27 Aligned_cols=59 Identities=12% Similarity=0.090 Sum_probs=32.3
Q ss_pred CCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHHHHHhhc
Q psy17875 24 DKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAEKLSKLY 84 (107)
Q Consensus 24 ~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 84 (107)
...++.|+.+= +++..+...++..-|.+-....-+..|.+ ++++|.+-++-|+++.+.-
T Consensus 40 ~~~~itgm~li--DeEGei~tr~v~~KFvnGkp~~iEa~y~m~s~~~wdRFMRFmeRYA~~N 99 (104)
T PRK13611 40 DTQNILGMRMI--DEEGELTTRNIKAKFLNGEFKALEVIYDMETEAEWDRFLRFMERFSAAN 99 (104)
T ss_pred cccceeeEEEE--ccCCcEEEEecceEEECCCccEEEEEEEECCHHHHHHHHHHHHHHHHhc
Confidence 34678886652 23333332112222332222222335566 6789999999999987763
No 81
>PRK05270 galactose-1-phosphate uridylyltransferase; Provisional
Probab=28.06 E-value=24 Score=27.61 Aligned_cols=59 Identities=15% Similarity=0.218 Sum_probs=34.4
Q ss_pred cCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCC
Q psy17875 22 SNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHI 100 (107)
Q Consensus 22 ~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~ 100 (107)
+.+..|.++++.-. ++...-+ |++... .....|++|- ..+ + .+| -..--.|+||-|++.
T Consensus 332 r~YsDe~~~I~a~t--dg~pHnT--ITPIaR-----~~~~~yElDL--VLR------n--N~T-see~P~GIFHPH~e~ 390 (493)
T PRK05270 332 RGYSDESVDILAYT--DGTPHNT--ITPIAR-----RRGGKYELDL--VLR------N--NRT-SEEHPDGIFHPHPEV 390 (493)
T ss_pred hCCCccccceeecC--CCCcccC--CCceEE-----ecCCeeEEEE--Eee------c--CCC-ccccCCccccCchhh
Confidence 56889999999833 3333323 566422 2346889974 111 1 001 125578999999874
No 82
>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=27.30 E-value=31 Score=25.11 Aligned_cols=9 Identities=22% Similarity=0.309 Sum_probs=7.1
Q ss_pred EEEEccCCC
Q psy17875 91 IGWFHSHPH 99 (107)
Q Consensus 91 vG~yHSHP~ 99 (107)
.=|||+|+.
T Consensus 119 ty~YH~H~~ 127 (311)
T TIGR02376 119 AFVYHCAPP 127 (311)
T ss_pred EEEEEcCCC
Confidence 568999975
No 83
>TIGR01480 copper_res_A copper-resistance protein, CopA family. This model represents the CopA copper resistance protein family. CopA is related to laccase (benzenediol:oxygen oxidoreductase) and L-ascorbate oxidase, both copper-containing enzymes. Most members have a typical TAT (twin-arginine translocation) signal sequence with an Arg-Arg pair. Twin-arginine translocation is observed for a large number of periplasmic proteins that cross the inner membrane with metal-containing cofactors already bound. The combination of copper-binding sites and TAT translocation motif suggests a mechansism of resistance by packaging and export.
Probab=27.22 E-value=26 Score=28.01 Aligned_cols=9 Identities=44% Similarity=1.032 Sum_probs=7.0
Q ss_pred EEEEccCCC
Q psy17875 91 IGWFHSHPH 99 (107)
Q Consensus 91 vG~yHSHP~ 99 (107)
.=|||||..
T Consensus 139 TyWYHsH~~ 147 (587)
T TIGR01480 139 TYWYHSHSG 147 (587)
T ss_pred eEEEecCch
Confidence 459999964
No 84
>PF15591 Imm17: Immunity protein 17
Probab=26.52 E-value=1.2e+02 Score=17.45 Aligned_cols=15 Identities=20% Similarity=0.452 Sum_probs=11.6
Q ss_pred eEEEEeeeeEeCCce
Q psy17875 27 EVLSMLIGETKEEKG 41 (107)
Q Consensus 27 E~cGlL~G~~~~~~~ 41 (107)
-.||+++|...+|..
T Consensus 25 Gk~GVVlG~SeeD~~ 39 (74)
T PF15591_consen 25 GKRGVVLGISEEDGG 39 (74)
T ss_pred CceeEEEEEecCCCc
Confidence 468999999876653
No 85
>PLN02354 copper ion binding / oxidoreductase
Probab=26.18 E-value=28 Score=27.57 Aligned_cols=8 Identities=0% Similarity=0.060 Sum_probs=6.4
Q ss_pred EEEccCCC
Q psy17875 92 GWFHSHPH 99 (107)
Q Consensus 92 G~yHSHP~ 99 (107)
=|||||-.
T Consensus 124 ~WYHsH~~ 131 (552)
T PLN02354 124 YFYYPSTG 131 (552)
T ss_pred eEEecCcc
Confidence 59999964
No 86
>PF12367 PFO_beta_C: Pyruvate ferredoxin oxidoreductase beta subunit C terminal
Probab=24.07 E-value=1.4e+02 Score=16.69 Aligned_cols=27 Identities=19% Similarity=0.255 Sum_probs=17.7
Q ss_pred CHHHHHHHHHHHHHHHhhcCCCceEEEEEccCC
Q psy17875 66 SPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHP 98 (107)
Q Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP 98 (107)
||.++.+|++.+.+ .+.-.+|++--.+
T Consensus 25 Dp~d~~~A~~~a~e------~d~iplGIfY~~~ 51 (67)
T PF12367_consen 25 DPSDREAAMEKARE------GDKIPLGIFYRNE 51 (67)
T ss_pred CchhHHHHHHHHHh------cCCceEEEEEeCC
Confidence 56777887766655 4456778875444
No 87
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=23.86 E-value=1.4e+02 Score=17.19 Aligned_cols=27 Identities=4% Similarity=0.073 Sum_probs=22.9
Q ss_pred HHHHHHHHHhhhcCCCeeEEEEeeeeE
Q psy17875 10 EDVYFSMFYLALSNDKLEVLSMLIGET 36 (107)
Q Consensus 10 ~~~~~~i~~ha~~~~p~E~cGlL~G~~ 36 (107)
.+++.+|..+|++-.-+-+.|+=+-..
T Consensus 28 d~Al~eM~e~A~~lGAnAVVGvr~d~s 54 (74)
T TIGR03884 28 DEIVENLREKVKAKGGMGLIAFRITCA 54 (74)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEEEcC
Confidence 578999999999988888988877654
No 88
>PLN00044 multi-copper oxidase-related protein; Provisional
Probab=23.67 E-value=33 Score=27.54 Aligned_cols=8 Identities=0% Similarity=0.094 Sum_probs=6.5
Q ss_pred EEEccCCC
Q psy17875 92 GWFHSHPH 99 (107)
Q Consensus 92 G~yHSHP~ 99 (107)
=|||||-.
T Consensus 126 ~WYHsH~~ 133 (596)
T PLN00044 126 FFYAPSTA 133 (596)
T ss_pred eEeeccch
Confidence 49999964
No 89
>PF04626 DEC-1_C: Dec-1 protein, C terminal region; InterPro: IPR006720 The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing []. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). Alternative splicing generates different carboxy terminal ends in different protein isoforms. This domain is the most C-terminal region that is present in the main isoforms.; GO: 0005213 structural constituent of chorion, 0007304 chorion-containing eggshell formation, 0005576 extracellular region, 0042600 chorion
Probab=23.45 E-value=61 Score=20.51 Aligned_cols=18 Identities=22% Similarity=0.324 Sum_probs=15.0
Q ss_pred ceEEEEEccCCCCCcccC
Q psy17875 88 LRVIGWFHSHPHITVWPS 105 (107)
Q Consensus 88 ~~ivG~yHSHP~~~~~pS 105 (107)
-.||-+||+-|..+.+||
T Consensus 59 ptVINYY~~ap~~p~~~s 76 (132)
T PF04626_consen 59 PTVINYYYAAPQRPYVQS 76 (132)
T ss_pred CceeeeeccCCCCceecc
Confidence 689999999998766665
No 90
>TIGR01239 galT_2 galactose-1-phosphate uridylyltransferase, family 2. This enzyme is involved in glucose and galactose interconversion. This model describes one of two extremely distantly related branches of the model pfam01087 from PFAM.
Probab=23.23 E-value=25 Score=27.45 Aligned_cols=59 Identities=14% Similarity=0.126 Sum_probs=34.3
Q ss_pred cCCCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEeCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCC
Q psy17875 22 SNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHI 100 (107)
Q Consensus 22 ~~~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~ 100 (107)
+.+..|.++++.-. ++...-+ |++... .....|++|- +.+ + .+| -...-.|+||-|++.
T Consensus 329 r~YsDe~~~I~A~t--~g~pHnT--ITPIaR-----~~~~~yElDL--VLR------n--N~T-see~P~GIFHPH~ev 387 (489)
T TIGR01239 329 QTYSDEKAGIAAYS--DGTPHHT--VTPIAR-----RRDGKYELDL--VLR------D--NQT-SEEYPDGIFHPHQDV 387 (489)
T ss_pred hCCCccccceEecC--CCCcccc--CCceEE-----ecCCceEEEE--Eee------c--CCC-ccccCCccccCcHhh
Confidence 56889999999855 2333323 566422 2345788864 111 1 011 125678999999864
No 91
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=22.88 E-value=2e+02 Score=17.96 Aligned_cols=59 Identities=10% Similarity=0.041 Sum_probs=32.5
Q ss_pred CCeeEEEEeeeeEeCCceEEEEEeeeeeecccCCCCCceEEe-CHHHHHHHHHHHHHHHhhc
Q psy17875 24 DKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA-SPEQLFEAVTEAEKLSKLY 84 (107)
Q Consensus 24 ~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 84 (107)
...++.|+.+ .++++.+...++..=|.+-....-+..|.+ ++++|.+-++-|++|.+..
T Consensus 51 ~~~~ItGM~L--iDeEGei~tr~v~aKFvnGkp~~iEa~y~m~s~~~WdRFMRFMeRYA~~~ 110 (113)
T PRK13610 51 NYKSVQRMFL--IDSEGVLSTKKIDLSISEDHVKEVKSTYNWNSEEAFERFMRFASRYANSL 110 (113)
T ss_pred cccceeeeEE--EccCceEEEEeeeEEEEcCCccEEEEEEEECCHHHHHHHHHHHHHHHHHh
Confidence 4578888665 333333332112222322222222335666 5789999999999877654
No 92
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=22.83 E-value=1.1e+02 Score=16.78 Aligned_cols=13 Identities=31% Similarity=0.531 Sum_probs=7.5
Q ss_pred HHHHHHHHHHHHH
Q psy17875 67 PEQLFEAVTEAEK 79 (107)
Q Consensus 67 ~~~~~~~~~~~~~ 79 (107)
|+.+.++++.+.+
T Consensus 7 Pe~L~~~m~~fie 19 (57)
T PF10929_consen 7 PEDLHQAMKDFIE 19 (57)
T ss_pred cHHHHHHHHHHHH
Confidence 5666666555443
No 93
>PF07289 DUF1448: Protein of unknown function (DUF1448); InterPro: IPR006606 This entry represents the Bardet-Biedl syndrome 5 protein (BBL5). It consists of eukaryotic proteins of around 375 residues in length.
Probab=22.70 E-value=1.2e+02 Score=22.69 Aligned_cols=30 Identities=27% Similarity=0.475 Sum_probs=18.8
Q ss_pred eEEeCHH-HHHHHHHHHHHHHhhcCCCceEEEEEccCCCCC
Q psy17875 62 RVEASPE-QLFEAVTEAEKLSKLYNRELRVIGWFHSHPHIT 101 (107)
Q Consensus 62 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~~ 101 (107)
.|-+||. .+.+..+++..+.+. |+.||.++
T Consensus 231 GFRvDP~ErL~~l~KEi~sLh~v----------y~~~PifG 261 (339)
T PF07289_consen 231 GFRVDPEERLQELFKEIQSLHKV----------YSANPIFG 261 (339)
T ss_pred EEEcCHHHHHHHHHHHHHHHHHH----------HHhCCCcC
Confidence 4788984 455666677665553 56666554
No 94
>PLN02191 L-ascorbate oxidase
Probab=22.67 E-value=36 Score=27.10 Aligned_cols=9 Identities=22% Similarity=0.541 Sum_probs=6.9
Q ss_pred EEEEccCCC
Q psy17875 91 IGWFHSHPH 99 (107)
Q Consensus 91 vG~yHSHP~ 99 (107)
.=|||||..
T Consensus 120 T~wYHsH~~ 128 (574)
T PLN02191 120 THFYHGHYG 128 (574)
T ss_pred EEEEeeCcH
Confidence 459999964
No 95
>COG2144 Selenophosphate synthetase-related proteins [General function prediction only]
Probab=22.48 E-value=1.5e+02 Score=22.03 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHhhcCCCceEEEEEccCCCCCcc
Q psy17875 70 LFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVW 103 (107)
Q Consensus 70 ~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~~~~ 103 (107)
-.++++-+++-.++ -+-.+||= |+||+.+.-
T Consensus 109 ~~ei~eglr~~a~k--fgvpivGG-hthpd~~y~ 139 (324)
T COG2144 109 AREILEGLRKGARK--FGVPIVGG-HTHPDTPYC 139 (324)
T ss_pred HHHHHHHHHHHHHh--cCCceecC-ccCCCCCCc
Confidence 33444444443444 44678876 999997654
No 96
>PF13636 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome biogenesis; PDB: 3M4X_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A.
Probab=21.89 E-value=1.1e+02 Score=18.26 Aligned_cols=45 Identities=18% Similarity=0.234 Sum_probs=23.5
Q ss_pred CCeeEEEEeeeeEeCCceEEEEEeeeeeec-ccCCCCCceEEeCHHHHHH
Q psy17875 24 DKLEVLSMLIGETKEEKGVKSVHVYTMVIP-LRLTSKHDRVEASPEQLFE 72 (107)
Q Consensus 24 ~p~E~cGlL~G~~~~~~~~~~~~i~~~~~~-~~~~~~~~~~~~~~~~~~~ 72 (107)
......|+.+|+...+. +.- ...+.. .........++++.++..+
T Consensus 13 l~v~r~Gl~lg~~~k~~-f~P---s~~la~~~~~~~~~~~iel~~e~a~~ 58 (102)
T PF13636_consen 13 LKVLRAGLYLGEIKKNR-FEP---SHALAMALGPEATKNVIELDDEQALR 58 (102)
T ss_dssp SEECECSEEEEEEETTE-EEE---BHHHHHCB--GCCS-EEEETCHHHHH
T ss_pred CeEEecCcEeeeEeCCc-EEE---CHHHHHhhCccccceEEECCHHHHHH
Confidence 45678899999987543 221 111111 1112234578998865444
No 97
>PF15603 Imm45: Immunity protein 45
Probab=21.30 E-value=1.9e+02 Score=16.95 Aligned_cols=26 Identities=12% Similarity=0.070 Sum_probs=18.1
Q ss_pred CCCceEEeCHHHHHHHHHHHHHHHhh
Q psy17875 58 SKHDRVEASPEQLFEAVTEAEKLSKL 83 (107)
Q Consensus 58 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (107)
.|.+.-.++..+..+..+++.+.+..
T Consensus 49 ~P~e~~~it~~e~q~II~aI~~~~~~ 74 (82)
T PF15603_consen 49 PPHENEPITIAERQKIIEAIEKYFSE 74 (82)
T ss_pred CCCCCcccCHHHHHHHHHHHHHHHhc
Confidence 34556678888888887777775553
No 98
>PF06962 rRNA_methylase: Putative rRNA methylase; InterPro: IPR010719 This family contains a number of putative rRNA methylases.; PDB: 3EEY_H 3LBY_A 3MTI_A.
Probab=20.67 E-value=50 Score=21.39 Aligned_cols=34 Identities=26% Similarity=0.299 Sum_probs=22.2
Q ss_pred eCHHHHHHHHHHHHHHHhhcCCCceEEEEEccCCCC
Q psy17875 65 ASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHI 100 (107)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~~~~~~~~ivG~yHSHP~~ 100 (107)
-.|+.-..|.+.+.++++. .|.-++-.|.-||++
T Consensus 66 T~~~TTl~Al~~al~lL~~--gG~i~iv~Y~GH~gG 99 (140)
T PF06962_consen 66 TKPETTLKALEAALELLKP--GGIITIVVYPGHPGG 99 (140)
T ss_dssp --HHHHHHHHHHHHHHEEE--EEEEEEEE--STCHH
T ss_pred cCcHHHHHHHHHHHHhhcc--CCEEEEEEeCCCCCC
Confidence 3466777787777777775 556777889999864
No 99
>PF08055 Trp_leader1: Tryptophan leader peptide; InterPro: IPR012638 This family consists of the tryptophan (trp) leader peptides. Tryptophan accumulation is the principal event resulting in down regulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either result in the termination of transcription of the trp operon when tryptophan is in plentiful supply or vice versa [].
Probab=20.59 E-value=50 Score=13.45 Aligned_cols=7 Identities=43% Similarity=1.493 Sum_probs=4.7
Q ss_pred EEccCCC
Q psy17875 93 WFHSHPH 99 (107)
Q Consensus 93 ~yHSHP~ 99 (107)
||-.||.
T Consensus 10 wwtahpa 16 (18)
T PF08055_consen 10 WWTAHPA 16 (18)
T ss_pred eeecccc
Confidence 5677775
No 100
>PRK13696 hypothetical protein; Provisional
Probab=20.55 E-value=1.4e+02 Score=16.61 Aligned_cols=17 Identities=35% Similarity=0.575 Sum_probs=14.4
Q ss_pred CceeEEEECHHHHHHHH
Q psy17875 1 MSLDVAYISEDVYFSMF 17 (107)
Q Consensus 1 ~~~~~v~i~~~~~~~i~ 17 (107)
|...+|.|+.+++..+.
T Consensus 1 ~m~K~ItI~dd~Y~~L~ 17 (62)
T PRK13696 1 MMMKTITISDDVYEKLL 17 (62)
T ss_pred CCcceEEeCHHHHHHHH
Confidence 45578999999998888
Done!