Query 012602
Match_columns 460
No_of_seqs 215 out of 540
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 04:21:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012602.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012602hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2880 SMAD6 interacting prot 100.0 9.6E-79 2.1E-83 604.2 22.3 369 2-459 2-375 (424)
2 KOG1554 COP9 signalosome, subu 100.0 3E-31 6.5E-36 258.6 8.6 125 332-459 52-183 (347)
3 cd08066 MPN_AMSH_like Mov34/MP 100.0 2.3E-28 5E-33 228.4 13.7 117 332-449 1-117 (173)
4 cd08067 MPN_2A_DUB Mov34/MPN/P 100.0 3.7E-28 8.1E-33 229.5 13.1 118 333-454 5-133 (187)
5 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 4.2E-27 9.1E-32 233.7 15.0 125 332-459 9-139 (268)
6 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 5.6E-25 1.2E-29 192.9 10.9 111 340-453 1-111 (119)
7 cd08068 MPN_BRCC36 Mov34/MPN/P 99.9 1.4E-24 3.1E-29 212.2 12.7 123 332-457 1-142 (244)
8 PF08969 USP8_dimer: USP8 dime 99.9 4E-24 8.7E-29 186.9 10.1 102 6-108 11-115 (115)
9 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.9 1.8E-21 3.8E-26 190.9 9.9 110 333-449 36-153 (252)
10 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 5.8E-21 1.2E-25 165.4 7.4 105 332-439 3-113 (114)
11 cd07767 MPN Mpr1p, Pad1p N-ter 99.8 5E-20 1.1E-24 158.4 10.8 107 343-452 2-108 (116)
12 KOG1555 26S proteasome regulat 99.8 8E-21 1.7E-25 190.1 6.4 126 332-460 30-168 (316)
13 smart00232 JAB_MPN JAB/MPN dom 99.8 1.6E-18 3.5E-23 152.4 13.3 120 334-457 1-125 (135)
14 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.7 4.5E-17 9.7E-22 161.9 11.9 115 334-452 2-123 (266)
15 cd08070 MPN_like Mpr1p, Pad1p 99.6 5.7E-15 1.2E-19 131.0 10.9 104 340-451 2-109 (128)
16 COG1310 Predicted metal-depend 99.5 1.4E-13 2.9E-18 123.3 9.7 108 335-454 2-112 (134)
17 cd08057 MPN_euk_non_mb Mpr1p, 99.4 5.7E-12 1.2E-16 115.7 12.7 123 335-457 1-127 (157)
18 cd08072 MPN_archaeal Mov34/MPN 99.3 1.4E-11 2.9E-16 108.6 11.1 95 337-449 1-96 (117)
19 PF14464 Prok-JAB: Prokaryotic 99.3 9.3E-12 2E-16 105.6 8.4 94 339-448 2-96 (104)
20 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.2 7E-11 1.5E-15 118.6 12.6 113 334-451 2-122 (280)
21 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.1 5.4E-10 1.2E-14 97.2 8.8 92 341-448 2-95 (108)
22 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.0 1.3E-09 2.9E-14 108.4 11.7 115 335-452 1-119 (265)
23 KOG1560 Translation initiation 99.0 2.7E-09 5.9E-14 105.3 10.0 121 332-454 12-144 (339)
24 cd08061 MPN_NPL4 Mov34/MPN/PAD 98.9 7.1E-09 1.5E-13 103.8 11.5 116 334-451 12-147 (274)
25 TIGR02256 ICE_VC0181 integrati 98.9 1.3E-08 2.9E-13 91.5 10.2 90 342-432 3-99 (131)
26 cd08060 MPN_UPF0172 Mov34/MPN/ 98.8 7.7E-09 1.7E-13 97.9 8.1 107 337-451 1-115 (182)
27 TIGR03735 PRTRC_A PRTRC system 98.7 2.4E-08 5.1E-13 95.0 7.4 88 333-431 71-159 (192)
28 cd08059 MPN_prok_mb Mpr1p, Pad 98.5 3E-07 6.5E-12 78.2 7.3 77 340-428 1-78 (101)
29 cd08063 MPN_CSN6 Mpr1p, Pad1p 98.4 1.3E-06 2.7E-11 88.2 10.0 117 334-455 2-128 (288)
30 PLN03246 26S proteasome regula 98.2 1.4E-05 3E-10 81.4 11.7 114 332-450 5-126 (303)
31 PF05021 NPL4: NPL4 family; I 97.9 4.9E-05 1.1E-09 77.6 9.3 91 360-450 2-129 (306)
32 KOG1556 26S proteasome regulat 97.5 0.0005 1.1E-08 67.7 9.8 111 332-447 8-126 (309)
33 PF03665 UPF0172: Uncharacteri 97.3 0.00045 9.8E-09 66.4 6.8 112 334-450 3-120 (196)
34 PF04212 MIT: MIT (microtubule 96.6 0.011 2.3E-07 47.1 7.6 69 28-101 1-69 (69)
35 cd02684 MIT_2 MIT: domain cont 96.5 0.019 4.1E-07 47.0 8.4 69 30-103 4-72 (75)
36 smart00745 MIT Microtubule Int 96.5 0.021 4.5E-07 46.1 8.6 73 26-103 2-74 (77)
37 cd02678 MIT_VPS4 MIT: domain c 96.5 0.016 3.5E-07 47.1 7.9 71 28-103 2-72 (75)
38 cd02683 MIT_1 MIT: domain cont 96.4 0.017 3.6E-07 47.6 7.8 69 30-103 4-72 (77)
39 cd02681 MIT_calpain7_1 MIT: do 96.4 0.017 3.6E-07 47.6 7.5 70 30-103 4-73 (76)
40 cd02677 MIT_SNX15 MIT: domain 95.9 0.056 1.2E-06 44.3 8.2 68 28-100 2-69 (75)
41 cd02656 MIT MIT: domain contai 95.7 0.079 1.7E-06 42.7 8.6 70 29-103 3-72 (75)
42 KOG2975 Translation initiation 95.7 0.031 6.7E-07 55.8 7.2 110 333-448 21-135 (288)
43 cd02680 MIT_calpain7_2 MIT: do 94.5 0.17 3.7E-06 41.6 7.2 64 30-102 4-71 (75)
44 KOG1795 U5 snRNP spliceosome s 93.6 0.073 1.6E-06 62.4 4.4 107 334-447 2096-2206(2321)
45 cd02682 MIT_AAA_Arch MIT: doma 93.5 0.38 8.3E-06 39.6 7.3 67 30-101 4-70 (75)
46 KOG2834 Nuclear pore complex, 93.4 0.28 6E-06 52.5 8.1 99 338-440 181-304 (510)
47 KOG0739 AAA+-type ATPase [Post 91.2 0.7 1.5E-05 47.8 7.5 72 28-103 6-77 (439)
48 KOG3289 Uncharacterized conser 91.1 0.55 1.2E-05 44.7 6.2 81 334-418 3-88 (199)
49 cd08071 MPN_DUF2466 Mov34/MPN/ 88.2 3 6.5E-05 36.6 8.3 71 354-429 13-83 (113)
50 PF14220 DUF4329: Domain of un 85.5 3 6.6E-05 37.4 6.9 66 354-430 18-88 (123)
51 COG5178 PRP8 U5 snRNP spliceos 85.4 0.7 1.5E-05 54.3 3.4 100 334-441 2135-2238(2365)
52 PF04002 RadC: RadC-like JAB d 78.7 7.5 0.00016 34.4 6.8 82 340-428 6-87 (123)
53 KOG1924 RhoA GTPase effector D 74.8 33 0.00071 39.8 11.7 27 55-81 424-450 (1102)
54 PF13374 TPR_10: Tetratricopep 71.3 11 0.00023 25.5 4.7 41 31-71 1-42 (42)
55 PF13174 TPR_6: Tetratricopept 66.7 11 0.00025 24.1 3.9 28 34-61 2-29 (33)
56 PF13512 TPR_18: Tetratricopep 65.6 59 0.0013 30.0 9.5 48 20-73 37-84 (142)
57 PF15659 Toxin-JAB1: JAB-like 64.9 18 0.0004 34.0 6.2 33 398-431 108-140 (162)
58 PF13181 TPR_8: Tetratricopept 60.9 22 0.00049 23.1 4.5 30 32-61 1-30 (34)
59 PF05168 HEPN: HEPN domain; I 59.3 22 0.00049 29.6 5.4 37 26-62 2-38 (118)
60 PRK00024 hypothetical protein; 58.2 50 0.0011 32.4 8.2 86 336-428 103-188 (224)
61 KOG3050 COP9 signalosome, subu 56.4 10 0.00022 38.1 3.0 73 354-431 33-111 (299)
62 TIGR00608 radc DNA repair prot 55.1 71 0.0015 31.4 8.7 87 335-428 96-182 (218)
63 PF07719 TPR_2: Tetratricopept 52.6 39 0.00084 21.7 4.6 31 32-62 1-31 (34)
64 COG5100 NPL4 Nuclear pore prot 43.3 19 0.00041 38.6 2.7 110 336-449 238-385 (571)
65 PF13428 TPR_14: Tetratricopep 42.7 44 0.00096 23.6 3.9 28 34-61 3-30 (44)
66 PF13176 TPR_7: Tetratricopept 42.6 54 0.0012 22.3 4.2 28 35-62 2-29 (36)
67 PF00515 TPR_1: Tetratricopept 36.9 95 0.0021 20.1 4.6 30 32-61 1-30 (34)
68 KOG4509 Uncharacterized conser 34.6 1E+02 0.0022 29.8 5.9 73 28-104 11-83 (247)
69 PF13414 TPR_11: TPR repeat; P 34.3 68 0.0015 24.1 4.0 30 32-61 3-32 (69)
70 PF14455 Metal_CEHH: Predicted 34.1 14 0.00031 34.5 0.2 64 340-423 86-152 (177)
71 PRK10548 flagellar biosynthesi 34.0 3.5E+02 0.0075 24.2 9.1 73 32-110 18-91 (121)
72 PRK15490 Vi polysaccharide bio 32.0 1.5E+02 0.0032 33.5 7.5 69 30-106 40-109 (578)
73 KOG1924 RhoA GTPase effector D 29.5 1.4E+02 0.003 35.0 6.8 14 46-59 299-312 (1102)
74 PF14778 ODR4-like: Olfactory 29.4 63 0.0014 34.0 4.0 57 361-417 1-74 (362)
75 PF13424 TPR_12: Tetratricopep 26.8 1.5E+02 0.0032 22.8 4.9 36 31-67 4-39 (78)
76 PF10516 SHNi-TPR: SHNi-TPR; 24.8 1.6E+02 0.0035 21.0 4.2 37 32-68 1-37 (38)
77 COG2003 RadC DNA repair protei 24.8 56 0.0012 32.4 2.5 96 334-436 101-197 (224)
78 PF14346 DUF4398: Domain of un 24.6 1.4E+02 0.0031 25.2 4.7 32 26-57 39-70 (103)
79 PF13525 YfiO: Outer membrane 24.4 1.4E+02 0.0031 28.1 5.2 36 33-72 43-78 (203)
80 PF13424 TPR_12: Tetratricopep 23.1 1.5E+02 0.0033 22.8 4.3 35 28-62 42-76 (78)
81 TIGR01597 PYST-B Plasmodium yo 22.9 3.3E+02 0.0073 27.4 7.4 82 18-105 50-133 (255)
82 smart00028 TPR Tetratricopepti 22.3 1.3E+02 0.0029 17.1 3.1 26 34-59 3-28 (34)
83 PF12895 Apc3: Anaphase-promot 20.4 84 0.0018 24.9 2.4 24 34-57 27-50 (84)
84 cd02679 MIT_spastin MIT: domai 20.4 5E+02 0.011 21.5 8.0 44 25-68 1-44 (79)
85 KOG4745 Metalloproteinase inhi 20.2 73 0.0016 29.3 2.1 57 354-426 24-95 (141)
No 1
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=100.00 E-value=9.6e-79 Score=604.23 Aligned_cols=369 Identities=35% Similarity=0.523 Sum_probs=242.9
Q ss_pred CCchhhhhHHH---hhcCcccCCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHH
Q 012602 2 RSSSEGINIAA---SAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKS 78 (460)
Q Consensus 2 ~~~~~~~~l~~---~a~~~evn~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~ 78 (460)
-+|.+.++.+. .+..++||.|||+|+|||+|++|+|||.||++|||+|+|||||+||++||+||||+||||++.. .
T Consensus 2 ~~S~~p~er~~~lsr~G~i~~n~~IplkryfRsg~ei~rmA~VY~~EgN~enafvLy~ry~tLfiEkipkHrDy~s~k-~ 80 (424)
T KOG2880|consen 2 DGSLEPEERVRALSRLGAIEVNKNIPLKRYFRSGTEILRMANVYLEEGNVENAFVLYLRYITLFIEKIPKHRDYRSVK-P 80 (424)
T ss_pred CCCcChHHHHHHHHhcCceeecCCCCHHHhhhhhHHHHHHHHHHHhcCCcchhhhHHHHHHHHHHHhcccCcchhhhc-h
Confidence 34555554443 4445899999999999999999999999999999999999999999999999999999999554 7
Q ss_pred HHHHHHHHHHHH-HHHHHhhcHHHHHHHHHHHHhhhhccccCcccCCCCCccccchhccccCchhhhhhhccchhhhhhc
Q 012602 79 QKLYLKKKLLNA-LSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQ 157 (460)
Q Consensus 79 ~k~~l~~~l~~v-l~~lE~LK~~L~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av~~~~~~~~~~ 157 (460)
+++++.++|+.+ ++.+|+||++|.++|+.+++.+-..+.... .+. .+.+ .-|++.+.+
T Consensus 81 ek~d~~~klk~~~~p~~deL~~~ll~rY~~eyn~y~~~K~k~~-------------~E~------~k~l--e~~~~~E~e 139 (424)
T KOG2880|consen 81 EKEDIRKKLKEEAFPRIDELKAKLLKRYNVEYNEYDHSKKKNL-------------AER------FKKL--EVQREEETE 139 (424)
T ss_pred hHHHHHHHHHHHhhhhHHHHHHHHHHHHhhHHHHHHHHHhhhH-------------HHH------HHHh--hcchhhHHH
Confidence 888888887765 899999999999999988764422110000 000 0111 113334444
Q ss_pred CCchhhhhccchhHHHHhhhccCCCCCcchhhccccccCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCcccc
Q 012602 158 GSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSI 237 (460)
Q Consensus 158 ~~~~~~~~~r~~~~~~~r~~~~~~~~~~e~~l~r~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (460)
++|.+|..+++....+|.. .+.+++.|....+.
T Consensus 140 ~kr~aq~k~Q~l~~~~f~~-----------------------------------------------~~~~~~~q~~~s~~ 172 (424)
T KOG2880|consen 140 RKRSAQTKQQQLESSQFSP-----------------------------------------------LEPPSFKQLLDSGP 172 (424)
T ss_pred HHHHHHHhhhcCCcccCCc-----------------------------------------------cCchHHHhhhcccC
Confidence 4444444443333333322 11111111111111
Q ss_pred cccCCCCCCCCCcCcccccCCCCCccccCCCCCCCCCCCccCCCCCCCccccCCCCCCCccchhhhhhhccCCCcccccc
Q 012602 238 KIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETEC 317 (460)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~p~pPpv~~~~~~~~~~~~p~~~~~~~ 317 (460)
... ..+.+........+.++....+...-+....+..+|++.+.......++ +|++++.. .|.+.+
T Consensus 173 m~s-~~~~gl~e~~~~~~~~p~~~~~~~~~s~~l~~~~s~ep~~s~~~n~~~k---~p~~~r~l-------~p~a~~--- 238 (424)
T KOG2880|consen 173 MPS-NQSNGLPEQPIGEPLVPSNESRSLNYSELLSVLSSPEPSDSCTTNVTIK---SPSVDRVL-------KPGATD--- 238 (424)
T ss_pred CCc-CCCCCCcCCCcCCCCcccccccccCCchhhhhccCCCcccccccccccc---CCCCCccc-------cccccc---
Confidence 100 0000000000000001000000000010111222222222222222222 23332222 111100
Q ss_pred ccCCCCCCCCCCCC-CeEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHH
Q 012602 318 QVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEE 396 (460)
Q Consensus 318 ~~~~~~~~~~~~~~-~~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~e 396 (460)
. ........+. ++.|+||.+++..||.+|.+||.+|+||||||||++..|.|+|||++||+|++|+|+|+++||++
T Consensus 239 n---~~~~~~~~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~neee 315 (424)
T KOG2880|consen 239 N---SNHGESSEGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNEEE 315 (424)
T ss_pred c---cccccccCCccceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCHHH
Confidence 0 0000111122 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCCCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCccceee
Q 012602 397 IFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRKRNAII 459 (460)
Q Consensus 397 i~~~~~~~~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~~~~~~ 459 (460)
+|++||+++|.+|||||||||||||||||||||||+||+| +||+|||||+|+ .++.+||.
T Consensus 316 lF~vQdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiM-lPEAiAIV~aPk--~~~tGiFr 375 (424)
T KOG2880|consen 316 LFEVQDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIM-LPEAIAIVCAPK--SKTTGIFR 375 (424)
T ss_pred HheecccccceeeeeeecCCccchhheeccccccceeeee-cchheeEEeccc--cCCcceEE
Confidence 9999999999999999999999999999999999999999 999999999999 56666663
No 2
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.97 E-value=3e-31 Score=258.64 Aligned_cols=125 Identities=23% Similarity=0.262 Sum_probs=117.1
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhh-------cC
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQD-------KR 404 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~-------~~ 404 (460)
|+.|.||+.+++||+.||++ ++++||||+|.|++++++++|.++|..+++||++++++..|++.+.++. ++
T Consensus 52 fk~vkISalAllKm~~hA~~--GgnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr 129 (347)
T KOG1554|consen 52 FKHVKISALALLKMVMHARS--GGNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGR 129 (347)
T ss_pred hhhhhhHHHHHHHHHHHHhc--CCCeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHhhh
Confidence 89999999999999999999 8999999999999999999999999999999999999999887654433 57
Q ss_pred CCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCccceee
Q 012602 405 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRKRNAII 459 (460)
Q Consensus 405 ~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~~~~~~ 459 (460)
-+++||||||||+++||||++|+.||...|.+ +.+|+|||+||.+|...|+|-|
T Consensus 130 ~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~f-QePfvAvViDP~Rtlsagkv~i 183 (347)
T KOG1554|consen 130 LENVVGWYHSHPGYGCWLSGIDVSTQMLNQRF-QEPFVAVVIDPTRTLSAGKVNI 183 (347)
T ss_pred hhceeeeeecCCCCCccccCcchhHHHHhhhh-cCCeEEEEecCccccccCceee
Confidence 78999999999999999999999999999998 9999999999999999998854
No 3
>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=99.95 E-value=2.3e-28 Score=228.38 Aligned_cols=117 Identities=56% Similarity=0.960 Sum_probs=111.7
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCcccee
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW 411 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGW 411 (460)
++++.||.+++.+|+.||..||..++|+||+|+|+..++.+.|+.+++|+|.+++++|++.++++++++++.+||.+|||
T Consensus 1 ~~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~~e~~~~~~~~gle~vGw 80 (173)
T cd08066 1 LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNEEELFDFQDQHDLITLGW 80 (173)
T ss_pred CeEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCHHHHHHHHHhCCCeeEEE
Confidence 57899999999999999999877889999999999988888999999999999999999999888999999999999999
Q ss_pred eccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCC
Q 012602 412 IHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRG 449 (460)
Q Consensus 412 yHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~ 449 (460)
|||||+.+||||.+|++||.+||.| .|++++|||||.
T Consensus 81 yHSHP~~~~~pS~~Dv~t~~~~~~~-~p~~~~lIvSp~ 117 (173)
T cd08066 81 IHTHPTQTCFLSSVDLHTHCSYQLM-LPEAIAIVCAPK 117 (173)
T ss_pred EeccCCCCCccCHHHHHHHHHHHhc-CCCeEEEEECCC
Confidence 9999999999999999999999999 999999999995
No 4
>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=99.95 E-value=3.7e-28 Score=229.54 Aligned_cols=118 Identities=20% Similarity=0.236 Sum_probs=106.3
Q ss_pred eEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeC--CeEEEEEEeecCCCCCCCccccCCH--HHHHHHhhcCCCcc
Q 012602 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN--RKFYITALIIPKQESTSDSCQATNE--EEIFEVQDKRSLFP 408 (460)
Q Consensus 333 ~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~--~~~~It~~~~p~q~~t~d~c~~~~E--~ei~~~~~~~~l~~ 408 (460)
.+|.|+..++++|+.||+.+ . .|+||+|+|.++. +.+.|+.+|..++..+++.|++..+ .++++.++++|+.+
T Consensus 5 f~V~Is~~all~m~~Ha~~~--~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~gl~v 81 (187)
T cd08067 5 FKVTVSSNALLLMDFHCHLT--T-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRGLSV 81 (187)
T ss_pred EEEEECHHHHHHHHHHhcCC--C-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcCCEE
Confidence 47999999999999999993 3 9999999999874 5789999998888888899988764 45688889999999
Q ss_pred ceeeccCCCCCCCCChhHHhhhhhhccccCC-------CceEEEecCCccCCc
Q 012602 409 LGWIHTHPTQSCFMSSIDVHTHYSYQVNVVP-------DARSCWKKRGEIGRK 454 (460)
Q Consensus 409 vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~p-------e~iAIV~sP~~t~~~ 454 (460)
||||||||+++||||.+|++||.+||.| ++ +||||||||+++.+.
T Consensus 82 VGwYHSHP~~~~~pS~~Di~tQ~~yQ~~-~~~~~~~~~p~v~~I~~P~~~~~~ 133 (187)
T cd08067 82 VGWYHSHPTFPPNPSLRDIDTQLDYQIM-FKGSDSGYEPCVGLICSPYDRRNS 133 (187)
T ss_pred EEEEecCCCCCcCCCHHHHHHHHHHHhh-ccccccCCCCeEEEEEccccCCCC
Confidence 9999999999999999999999999999 87 799999999988664
No 5
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.95 E-value=4.2e-27 Score=233.68 Aligned_cols=125 Identities=22% Similarity=0.302 Sum_probs=112.6
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHH--HHH--H--hhcCC
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEE--IFE--V--QDKRS 405 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~e--i~~--~--~~~~~ 405 (460)
++.|.|+..++.+|+.||.. +.+.|+||+|+|...++++.|+++|..++++++++|++..|.+ +++ . ..+++
T Consensus 9 ~~~V~Is~~allkil~Ha~~--~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~ 86 (268)
T cd08069 9 FEKVYISSLALLKMLKHARA--GGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRP 86 (268)
T ss_pred ccEEEECHHHHHHHHHHHhc--cCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCC
Confidence 78999999999999999999 7899999999999989999999999999999999999977543 333 2 23688
Q ss_pred CccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCccceee
Q 012602 406 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRKRNAII 459 (460)
Q Consensus 406 l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~~~~~~ 459 (460)
+.+||||||||+++||||++|+.||..||.+ .+++|||||||.++.+.|++.+
T Consensus 87 ~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~-~~~~V~lViDP~~t~~~g~~~i 139 (268)
T cd08069 87 ENVVGWYHSHPGYGCWLSGIDVNTQQLNQQL-QDPFVAVVVDPIRSLVKGKVVI 139 (268)
T ss_pred ceeEeeeccCCCcCCcCCHHHHHHHHHHHhc-CCCcEEEEEeCCccccCCccee
Confidence 9999999999999999999999999999999 8999999999999977776654
No 6
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.92 E-value=5.6e-25 Score=192.90 Aligned_cols=111 Identities=35% Similarity=0.644 Sum_probs=85.6
Q ss_pred HHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeeccCCCCC
Q 012602 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQS 419 (460)
Q Consensus 340 ~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~~t 419 (460)
+++++|+.||+. +.+.|+||+|+|.+..+.+.+..+-+..+...+..++...+...+..+.++|+.+||||||||+++
T Consensus 1 ~~~~~i~~ha~~--~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~~~~~~~~~~~~~~g~~~vG~YHSHP~~~ 78 (119)
T cd08058 1 DALLKMLQHAES--NTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYHSHPTFT 78 (119)
T ss_pred CHHHHHHHHhcC--CCCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchhHHHHHHHHHHhCCCCeEEEEEecCCCCC
Confidence 478999999999 569999999999997543323222222333333333332223446667799999999999999999
Q ss_pred CCCChhHHhhhhhhccccCCCceEEEecCCccCC
Q 012602 420 CFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGR 453 (460)
Q Consensus 420 ~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~ 453 (460)
+|||..|++||.+||.+ +|++++|||||.++..
T Consensus 79 ~~pS~~Di~~~~~~q~~-~p~~~~lI~s~~~~~~ 111 (119)
T cd08058 79 AWLSSVDIHTQASYQLM-LPEAIAIVVSPKHRNK 111 (119)
T ss_pred CccCHHHHHHHHHHhcc-CCCeEEEEECcCCCCc
Confidence 99999999999999999 9999999999988633
No 7
>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=99.91 E-value=1.4e-24 Score=212.15 Aligned_cols=123 Identities=21% Similarity=0.273 Sum_probs=99.7
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeC-------CeEEEEEEeecC-CCCCCCccccCCHHHH--HHHh
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN-------RKFYITALIIPK-QESTSDSCQATNEEEI--FEVQ 401 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~-------~~~~It~~~~p~-q~~t~d~c~~~~E~ei--~~~~ 401 (460)
+.+|.|+.+++.+|+.||.. +.+.|+||+|+|++++ ..+.|+..+.+. ...+++++++.+|+.+ ...+
T Consensus 1 l~~V~Is~~~l~~il~HA~~--~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea 78 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALS--TEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEA 78 (244)
T ss_pred CcEEEECHHHHHHHHHHHHh--CCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHH
Confidence 46799999999999999999 8899999999999853 234454555443 4567899999988753 2223
Q ss_pred h------cCCCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCc---cCCccce
Q 012602 402 D------KRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGE---IGRKRNA 457 (460)
Q Consensus 402 ~------~~~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~---t~~~~~~ 457 (460)
+ ++++.+||||||||+++||||++|++||.+||++ .|++++||||+.+ +...+++
T Consensus 79 ~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~-~p~~v~lIvS~~~~~~~~~~~~~ 142 (244)
T cd08068 79 ERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMM-DSGFVGLIFSCFNEDKSTKMGEV 142 (244)
T ss_pred HHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhh-CCCcEEEEEEecCCccccccCCE
Confidence 3 4999999999999999999999999999999987 9999999999765 4444443
No 8
>PF08969 USP8_dimer: USP8 dimerisation domain; InterPro: IPR015063 This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It has no known function. ; PDB: 2XZE_B 2A9U_A.
Probab=99.90 E-value=4e-24 Score=186.94 Aligned_cols=102 Identities=34% Similarity=0.532 Sum_probs=86.5
Q ss_pred hhhhHHHhhcCc-ccCCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHH-H
Q 012602 6 EGINIAASAQRL-DVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLY-L 83 (460)
Q Consensus 6 ~~~~l~~~a~~~-evn~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~-l 83 (460)
..-+|.+.|..+ +||+++|+++|+|+|.+|+++|++|+++||+|+|||+|+||++|| ++||+||||+......... .
T Consensus 11 s~~~L~~~a~~~~~~~~~~~l~~y~rsa~~l~~~A~~~~~egd~E~AYvl~~R~~~L~-~ki~~Hpdy~~~~~~~~~~~~ 89 (115)
T PF08969_consen 11 SLEELNKLADVFPEFDKNIPLKRYLRSANKLLREAEEYRQEGDEEQAYVLYMRYLTLV-EKIPKHPDYKKDKNSYKKLLG 89 (115)
T ss_dssp CHHHHHHCCCT-GGGSTTS-HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH-CCHCCSCCCCCTHHCCHHHHH
T ss_pred hHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HHhhcCccccccchHHHHHHH
Confidence 345799999998 999999999999999999999999999999999999999999999 9999999999766544442 2
Q ss_pred HHHHHHH-HHHHHhhcHHHHHHHHHH
Q 012602 84 KKKLLNA-LSELEELQPAVQQKINEL 108 (460)
Q Consensus 84 ~~~l~~v-l~~lE~LK~~L~~~Y~~~ 108 (460)
.+++..+ |+++|+||++|+++|+++
T Consensus 90 ~~~~~~~il~~lE~Lk~~L~~rY~~e 115 (115)
T PF08969_consen 90 KKKLNEVILEELEKLKPSLKERYEEE 115 (115)
T ss_dssp HHHHHHCHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3555444 899999999999999874
No 9
>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=99.85 E-value=1.8e-21 Score=190.92 Aligned_cols=110 Identities=21% Similarity=0.286 Sum_probs=102.1
Q ss_pred eEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeC---CeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccc
Q 012602 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPL 409 (460)
Q Consensus 333 ~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~---~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~v 409 (460)
.+++||.+++.+|+..|..|| |+||+|+|+... +...|+++++|+|.|+.++|++.++. ++.++..+|..|
T Consensus 36 ~t~vlPknllkkFi~iaD~rt----Q~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~--~~~~~l~~Le~L 109 (252)
T cd08056 36 YTYILPKNLLKKFISISDLRT----QIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL--PQHEYLEDLEPL 109 (252)
T ss_pred CEEEeCHHHHHHHHHHhhhcc----eEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccC--ccchhhCCCEee
Confidence 479999999999999998864 999999999865 67899999999999999999998874 677778999999
Q ss_pred eeeccCCCCCCCCChhHHhhhhhhccccCC-----CceEEEecCC
Q 012602 410 GWIHTHPTQSCFMSSIDVHTHYSYQVNVVP-----DARSCWKKRG 449 (460)
Q Consensus 410 GWyHSHP~~t~flSsvDl~Tq~~yQ~m~~p-----e~iAIV~sP~ 449 (460)
|||||||+.+||||++|++||+.||.| .| .+|.|||++.
T Consensus 110 GWIHTqp~e~~~Lss~Dv~tha~~~~~-~~~w~~~~~V~it~Sft 153 (252)
T cd08056 110 GWIHTQPNELPQLSPQDVTTHAKILAD-NPSWDGEKTVILTCSFT 153 (252)
T ss_pred EEEEcCCCCccccCHHHHHHHHHHHHh-ccccCCCcEEEEEEcCC
Confidence 999999999999999999999999999 88 7999999987
No 10
>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=99.83 E-value=5.8e-21 Score=165.41 Aligned_cols=105 Identities=26% Similarity=0.428 Sum_probs=87.2
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCC-eEEEEEEeecCCCCCCCccccCCHHHH---HHHhh--cCC
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KFYITALIIPKQESTSDSCQATNEEEI---FEVQD--KRS 405 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~-~~~It~~~~p~q~~t~d~c~~~~E~ei---~~~~~--~~~ 405 (460)
+++|.|.+.++.+|+.||..+ .+.|+||+|+|++.++ .+.|++.|..+..++.+.|.+..+... ++... ..+
T Consensus 3 ~~~V~i~p~vll~i~~h~~r~--~~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (114)
T PF01398_consen 3 VQTVQIHPLVLLKIIDHATRS--SPNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPN 80 (114)
T ss_dssp CEEEEEEHHHHHHHHHHHHHH--HCTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTT
T ss_pred cEEEEECHHHHHHHHHHHhcC--CCCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccccc
Confidence 688999999999999999884 3449999999999999 999999999888888888877665432 22222 256
Q ss_pred CccceeeccCCCCCCCCChhHHhhhhhhccccCC
Q 012602 406 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVP 439 (460)
Q Consensus 406 l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~p 439 (460)
+.+||||||||+++||||..|++||+.||.| .|
T Consensus 81 ~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~-~~ 113 (114)
T PF01398_consen 81 LEIVGWYHSHPNISCFPSPTDIETQKQYQRM-NP 113 (114)
T ss_dssp SEEEEEEEEESSS-SS--HHHHHHHHHHHHH-TT
T ss_pred ceEEEEEEccCCccccCCHHHHHHHHHHHHh-CC
Confidence 9999999999999999999999999999998 66
No 11
>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=99.82 E-value=5e-20 Score=158.39 Aligned_cols=107 Identities=24% Similarity=0.278 Sum_probs=89.4
Q ss_pred HHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeeccCCCCCCCC
Q 012602 343 DNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFM 422 (460)
Q Consensus 343 ~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~~t~fl 422 (460)
.+|+.||.. ..+.|+||+|+|+..++.+.|+.+|..++..+.+.+.......+...+...++.+||||||||...+|+
T Consensus 2 k~il~~a~~--~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~~ 79 (116)
T cd07767 2 KMFLDAAKS--INGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCFL 79 (116)
T ss_pred HhHHHHHhc--CCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCcc
Confidence 578999998 458999999999999888899999988876655443322112334556689999999999999999999
Q ss_pred ChhHHhhhhhhccccCCCceEEEecCCccC
Q 012602 423 SSIDVHTHYSYQVNVVPDARSCWKKRGEIG 452 (460)
Q Consensus 423 SsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~ 452 (460)
|..|+.+|..||.+ .+++++|||++....
T Consensus 80 s~~dv~~~~~~q~~-~~~~v~li~~~~~~~ 108 (116)
T cd07767 80 SPNDLATHELFQRY-FPEKVMIIVDVKPKD 108 (116)
T ss_pred CHHHHHHHHHHHHh-CCCCEEEEEECCCcc
Confidence 99999999999999 899999999998753
No 12
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.82 E-value=8e-21 Score=190.07 Aligned_cols=126 Identities=18% Similarity=0.255 Sum_probs=107.2
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCCCee-eEEEe-ee---eE-eCCeEEEEEEeecCCCCCCCccccC--C---HHHHH--
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDKNLE-TCGIL-AG---SL-KNRKFYITALIIPKQESTSDSCQAT--N---EEEIF-- 398 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~~~E-~cGiL-~G---~~-~~~~~~It~~~~p~q~~t~d~c~~~--~---E~ei~-- 398 (460)
=++|+|+..++.+|+.|++. +.+.| |+|+| +| .+ +..+..|.++|...+.++.-+|.-. + ..+++
T Consensus 30 ~e~v~i~slall~m~rh~r~--~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~q~~~~ 107 (316)
T KOG1555|consen 30 KETVYISSLALLKMLRHDRA--GSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQMMDL 107 (316)
T ss_pred cceeeeehhhhhhccccccc--CCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHHHHH
Confidence 46899999999999999999 88999 99999 99 43 3457788889999999988874332 2 12333
Q ss_pred HHhhcCCCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCccceeeC
Q 012602 399 EVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRKRNAIIC 460 (460)
Q Consensus 399 ~~~~~~~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~~~~~~~ 460 (460)
-.++++.++|||||||||+|+||||++|+.||.+||.+ -+..+|.|++|..+.+++++++|
T Consensus 108 l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~-~~r~~a~~v~~i~S~~g~vv~d~ 168 (316)
T KOG1555|consen 108 LKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQAL-SSRAVAVVVDPIQSPYGKVVPDA 168 (316)
T ss_pred HHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhh-ccCCcceeeecccCCCCCccCCh
Confidence 34557778999999999999999999999999999998 88999999999999999999876
No 13
>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=99.79 E-value=1.6e-18 Score=152.40 Aligned_cols=120 Identities=26% Similarity=0.328 Sum_probs=98.6
Q ss_pred EEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCC---HHHHHH--HhhcCCCcc
Q 012602 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATN---EEEIFE--VQDKRSLFP 408 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~---E~ei~~--~~~~~~l~~ 408 (460)
.|.|...++.+++.||.. ..+.|+||+|+|+..++.+.|+++|..+.....+.+...+ .+++.+ .+...++.+
T Consensus 1 ~v~i~~~v~~~i~~h~~~--~~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (135)
T smart00232 1 EVKVHPLVPLNILKHAIR--DGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEI 78 (135)
T ss_pred CEEEcHHHHHHHHHHHhc--CCCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceE
Confidence 378999999999999998 5799999999999988899999999866665555542222 122222 234789999
Q ss_pred ceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCccce
Q 012602 409 LGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRKRNA 457 (460)
Q Consensus 409 vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~~~~ 457 (460)
||||||||..+++||..|+.+|..||.+ ++.++.++++|..+.. +++
T Consensus 79 vGwyhshp~~~~~pS~~D~~~~~~~~~~-~~~~~~~~v~~~~s~~-g~~ 125 (135)
T smart00232 79 VGWYHSHPDESPFPSEVDVATHESYQAP-WPISVVLIVDPIKSFQ-GRL 125 (135)
T ss_pred EEEEEcCCCCCCCcCHHHHHHHHHHHhc-CCceEEEEECCCcccc-CcE
Confidence 9999999999999999999999999999 9999999999999865 443
No 14
>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=99.71 E-value=4.5e-17 Score=161.86 Aligned_cols=115 Identities=15% Similarity=0.176 Sum_probs=96.7
Q ss_pred EEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCcc--ccCCH---HHHHHHhhcCCC--
Q 012602 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSC--QATNE---EEIFEVQDKRSL-- 406 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c--~~~~E---~ei~~~~~~~~l-- 406 (460)
.|.|++.++.+|+.||.. +.+.|+||+|+|...++.+.||++|..+...+.+.+ ...+. .++++...+.|.
T Consensus 2 ~V~I~~~vllkIv~H~~~--~~p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e 79 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKE--ELPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDH 79 (266)
T ss_pred EEEEeHHHHHHHHHHHhc--CCCcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCC
Confidence 699999999999999999 669999999999999999999999987766655542 22221 234555556666
Q ss_pred ccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccC
Q 012602 407 FPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIG 452 (460)
Q Consensus 407 ~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~ 452 (460)
.+|||||||| .++|.|..+++++..||.. .+++|+||+||..+.
T Consensus 80 ~iVGWY~S~p-~~~~~~~s~id~~~~~q~~-~~~~v~Li~D~~~s~ 123 (266)
T cd08065 80 NHVGWYQSTY-LGSFFTRDLIETQYNYQEA-IEESVVLVYDPSKTS 123 (266)
T ss_pred cEEEeEeecC-CCCcCCHHHHHHHHHHhcc-CCCCEEEEECCCccc
Confidence 9999999999 9999999999999999998 899999999999863
No 15
>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=99.60 E-value=5.7e-15 Score=131.02 Aligned_cols=104 Identities=16% Similarity=0.195 Sum_probs=81.1
Q ss_pred HHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCC-CCC-CccccCCHHH--HHHHhhcCCCccceeeccC
Q 012602 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQE-STS-DSCQATNEEE--IFEVQDKRSLFPLGWIHTH 415 (460)
Q Consensus 340 ~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~-~t~-d~c~~~~E~e--i~~~~~~~~l~~vGWyHSH 415 (460)
.++..|+.||.. ..+.|+||+|+|+.......|+.++..+.. ..+ +...+..++. +.+...+.|+.+|||||||
T Consensus 2 ~~~~~il~ha~~--~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g~~~vG~~HSH 79 (128)
T cd08070 2 ELLEAILAHAEA--EYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVVGIYHSH 79 (128)
T ss_pred HHHHHHHHHHHh--CCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCCCeEEEEEeCC
Confidence 578899999999 789999999999998777778877754443 334 5556665543 3455568899999999999
Q ss_pred CCCCCCCChhHHhhhhhhccccCCCceEEEecCCcc
Q 012602 416 PTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEI 451 (460)
Q Consensus 416 P~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t 451 (460)
|+..++||.+|+.++ + .++.+.||++..++
T Consensus 80 P~~~~~PS~~D~~~~-----~-~~~~~~lIv~~~~~ 109 (128)
T cd08070 80 PDGPARPSETDLRLA-----W-PPGVSYLIVSLAGG 109 (128)
T ss_pred CCCCCCCCHHHHHhc-----c-CCCCeEEEEECCCC
Confidence 999999999999753 2 34678888887654
No 16
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.48 E-value=1.4e-13 Score=123.25 Aligned_cols=108 Identities=19% Similarity=0.273 Sum_probs=71.9
Q ss_pred EEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCC-C-CCccccCCHHHH-HHHhhcCCCcccee
Q 012602 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQES-T-SDSCQATNEEEI-FEVQDKRSLFPLGW 411 (460)
Q Consensus 335 V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~-t-~d~c~~~~E~ei-~~~~~~~~l~~vGW 411 (460)
+.|+.+++..+|.||.. ..+.|+||+|+|+... ...+..+... . .+......+-.+ .......|+.+|||
T Consensus 2 ~~i~~~~l~~il~~a~~--~~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~g~~vvg~ 74 (134)
T COG1310 2 LVIPKEVLGAILEHARR--EHPREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEYSLFYLAAEDAGEVVVGW 74 (134)
T ss_pred ceecHHHHHHHHHHHHh--cCChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHHHHHHHHHhhCCCEEEEE
Confidence 57899999999999998 6689999999999866 1122111111 1 122222223222 23344677999999
Q ss_pred eccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCc
Q 012602 412 IHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRK 454 (460)
Q Consensus 412 yHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~ 454 (460)
|||||+..||||..|+. .|.+ .+-...|||.+.....+
T Consensus 75 yHSHP~~~~~pS~~D~~----~~~~-~~~~~~iv~~~~~~~~~ 112 (134)
T COG1310 75 YHSHPGGPPYPSEADRR----LSKL-GPLPWLIVSVPPGRVHK 112 (134)
T ss_pred EcCCCCCCCCcCHHHHh----hccc-cCCCEEEEEcCCCceeE
Confidence 99999999999999998 4554 44434566665544433
No 17
>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=99.37 E-value=5.7e-12 Score=115.74 Aligned_cols=123 Identities=12% Similarity=0.091 Sum_probs=89.1
Q ss_pred EEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCH--HHHHHH--hhcCCCccce
Q 012602 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE--EEIFEV--QDKRSLFPLG 410 (460)
Q Consensus 335 V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E--~ei~~~--~~~~~l~~vG 410 (460)
|.|.+.++.+|+.|+..+...+.+++|+|+|...++.+.|++.|..+.+.+.+......+ +++++. ....++.+||
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vVG 80 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIVG 80 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEEE
Confidence 567888999999999874333789999999999999999999999777766654222111 112222 1257889999
Q ss_pred eeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCccce
Q 012602 411 WIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRKRNA 457 (460)
Q Consensus 411 WyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~~~~ 457 (460)
|||||+..+++++..|...|..|.....++.|+++++|..+...+++
T Consensus 81 WY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l 127 (157)
T cd08057 81 WYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKL 127 (157)
T ss_pred EEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcc
Confidence 99999998877877776555544331146789999999885444444
No 18
>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=99.32 E-value=1.4e-11 Score=108.56 Aligned_cols=95 Identities=24% Similarity=0.240 Sum_probs=71.3
Q ss_pred eCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEee-cCCCCCCCccccCCHHHHHHHhhcCCCccceeeccC
Q 012602 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALII-PKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTH 415 (460)
Q Consensus 337 is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~-p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSH 415 (460)
|+.+++..++.||.. ..+.|.||+|+|+-. .|+.++. ++.... +....- +- .+...|+.+||-||||
T Consensus 1 i~~~~~~~i~~ha~~--~~P~E~CGlL~G~~~----~v~~~~~~~n~~~~-~~~~~f-~~----~~~~~g~~ivgi~HSH 68 (117)
T cd08072 1 ISRDLLDSILEAAKS--SHPNEFAALLRGKDG----VITELLILPGTESG-EVSAVF-PL----LMLPLDMSIVGSVHSH 68 (117)
T ss_pred CCHHHHHHHHHHHhh--cCCceEEEEEEeecc----EEEEEEECCCCCCC-Ccceee-ch----HHhcCCCeEEEEEEcC
Confidence 578899999999999 789999999999763 5777765 433322 211110 11 1457899999999999
Q ss_pred CCCCCCCChhHHhhhhhhccccCCCceEEEecCC
Q 012602 416 PTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRG 449 (460)
Q Consensus 416 P~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~ 449 (460)
|+..+.||..|+.. .. .++.+.+|+++-
T Consensus 69 P~~~~~PS~~D~~~-----~~-~~~~~~lIvs~~ 96 (117)
T cd08072 69 PSGSPRPSDADLSF-----FS-KTGLVHIIVGYP 96 (117)
T ss_pred CCCCCCCCHHHHHh-----hh-cCCCEEEEEECc
Confidence 99999999999852 22 688999999953
No 19
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.29 E-value=9.3e-12 Score=105.56 Aligned_cols=94 Identities=19% Similarity=0.338 Sum_probs=66.2
Q ss_pred HHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHH-HhhcCCCccceeeccCCC
Q 012602 339 TTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFE-VQDKRSLFPLGWIHTHPT 417 (460)
Q Consensus 339 ~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~-~~~~~~l~~vGWyHSHP~ 417 (460)
..++..|+.||.. ..+.|+||+|+|......+.|+..+.+ .....-.... .....++.+||+|||||+
T Consensus 2 ~~~~~~i~~~~~~--~~p~E~~G~L~g~~~~~~~~~~~~~~~---------~p~~~~~~~~~~~~~~~~~~vg~~HSHP~ 70 (104)
T PF14464_consen 2 EEVLEQIIAHARA--AYPNEACGLLLGRRDDQRFIVVPNVNP---------DPRDSFRRERFEARERGLEIVGIWHSHPS 70 (104)
T ss_dssp -HHHHHHHHHHHH--HTTS-EEEEEEEEEECCEEEEEEEEE-----------HHCHHHHHH-HHHHHT-EEEEEEEEESS
T ss_pred HHHHHHHHHHHhh--CCCCeEEEEEEEEecCCEEEEEeCCCC---------CcHHHHHHHhhhhhcccceeeEEEEcCCC
Confidence 4688999999999 679999999999997777777776641 0011112223 567899999999999999
Q ss_pred CCCCCChhHHhhhhhhccccCCCceEEEecC
Q 012602 418 QSCFMSSIDVHTHYSYQVNVVPDARSCWKKR 448 (460)
Q Consensus 418 ~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP 448 (460)
..++||.+|+.+... ....++||++.
T Consensus 71 ~~a~pS~~D~~~~~~-----~~~~~~iI~~~ 96 (104)
T PF14464_consen 71 GPAFPSSTDIRSMRD-----LAPPSYIIVGN 96 (104)
T ss_dssp SSSS--HHHHHTHCC-----S-SCEEEEEEE
T ss_pred CCCCCCHHHHHhhhc-----cCCeEEEEEeC
Confidence 999999999965321 11678888875
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=99.23 E-value=7e-11 Score=118.60 Aligned_cols=113 Identities=12% Similarity=0.143 Sum_probs=88.0
Q ss_pred EEEeCHHHHHHHHHHhhccC-CCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccc--cCCHHH---HHHHh--hcCC
Q 012602 334 QLHISTTMMDNFMKLAKSNT-DKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQ--ATNEEE---IFEVQ--DKRS 405 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt-~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~--~~~E~e---i~~~~--~~~~ 405 (460)
.|.|.+-++.+++.|+..-. +.+.+++|.|+|...++.+.|+++|..+.+.+.+... ..+.++ +++.. ...+
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~~ 81 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNAK 81 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCCC
Confidence 58999999999999986522 3468999999999999999999999976665555432 122222 22222 2578
Q ss_pred CccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCcc
Q 012602 406 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEI 451 (460)
Q Consensus 406 l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t 451 (460)
..+||||||||. ++..|+..|..|+.. .+..|.++++|...
T Consensus 82 e~vVGWY~tg~~----~~~~d~~ih~~~~~~-~~~pv~l~vd~~~~ 122 (280)
T cd08062 82 EKIVGWYSTGPK----LRPNDLDINELFRRY-CPNPVLVIIDVRPK 122 (280)
T ss_pred CCeEEEecCCCC----CCcchHHHHHHHHHh-CCCCEEEEEecCCC
Confidence 999999999998 577889999999987 88899999999764
No 21
>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=99.07 E-value=5.4e-10 Score=97.19 Aligned_cols=92 Identities=17% Similarity=0.179 Sum_probs=65.8
Q ss_pred HHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecC-CCCCC-CccccCCHHHHHHHhhcCCCccceeeccCCCC
Q 012602 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPK-QESTS-DSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQ 418 (460)
Q Consensus 341 ~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~-q~~t~-d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~~ 418 (460)
++..++.||+. ..+.|.||+|+|+-. ++.++..+ ....+ +...+..++. ++..+ .+ .+||-|||||+.
T Consensus 2 i~~~i~~ha~~--~~P~E~CGll~g~~~-----~~~~~p~~N~~~~p~~~F~idp~e~-~~a~~-~~-~ivgi~HSHP~~ 71 (108)
T cd08073 2 LEDAILAHAKA--EYPREACGLVVRKGR-----KLRYIPCRNIAADPEEHFEISPEDY-AAAED-EG-EIVAVVHSHPDG 71 (108)
T ss_pred HHHHHHHHHhH--CCCCcceEEEEecCC-----ceEEEECccCCCCccceEEeCHHHH-HHHhc-CC-CEEEEEEcCCCC
Confidence 57789999999 889999999999761 33333323 23333 5556655554 44432 33 899999999999
Q ss_pred CCCCChhHHhhhhhhccccCCCceEEEecC
Q 012602 419 SCFMSSIDVHTHYSYQVNVVPDARSCWKKR 448 (460)
Q Consensus 419 t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP 448 (460)
.+.||..|+. +.+ .++...||++-
T Consensus 72 ~a~PS~~D~~-----~~~-~~~~~~iIvs~ 95 (108)
T cd08073 72 SPAPSEADRA-----QQE-ATGLPWIIVSW 95 (108)
T ss_pred CCCCCHHHHH-----Hhh-cCCCcEEEEEc
Confidence 9999999994 223 57888888884
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=99.04 E-value=1.3e-09 Score=108.38 Aligned_cols=115 Identities=13% Similarity=0.169 Sum_probs=85.6
Q ss_pred EEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHH--HHHHHhh--cCCCccce
Q 012602 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEE--EIFEVQD--KRSLFPLG 410 (460)
Q Consensus 335 V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~--ei~~~~~--~~~l~~vG 410 (460)
|.|.+-++.+++.|+.........++|.|+|...++.+.||+.|..+...+.+.+....+. ++++... ..+..+||
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d~~y~~~m~~~~kkv~~~~~vVG 80 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDMEYHRTMYELHQKVNPKEVIVG 80 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEcHHHHHHHHHHHHHhCCCCcEEe
Confidence 5678889999999987644556899999999999999999999997766666655544322 2333322 67889999
Q ss_pred eeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccC
Q 012602 411 WIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIG 452 (460)
Q Consensus 411 WyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~ 452 (460)
||||+|..+ .+...+|.|..+|.. .+..|.++++|..+.
T Consensus 81 WY~tg~~~~--~~~~~Ih~~~~~~~~-~~~pI~L~~D~~~~~ 119 (265)
T cd08064 81 WYATGSEIT--EHSALIHDYYSRECT-SYNPIHLTVDTSLDD 119 (265)
T ss_pred eeeCCCCCC--ccHHHHHHHHHhhCC-CCCCEEEEEeCCCCC
Confidence 999998432 235667777777755 458899999997654
No 23
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=98.96 E-value=2.7e-09 Score=105.27 Aligned_cols=121 Identities=16% Similarity=0.267 Sum_probs=92.8
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEee-cCCCCCCCc-ccc--CCHH---HHHHHhh--
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALII-PKQESTSDS-CQA--TNEE---EIFEVQD-- 402 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~-p~q~~t~d~-c~~--~~E~---ei~~~~~-- 402 (460)
++.|.|...+..+|+.|++.-.-.+-=+.|+|+|-+.++.+-||.+|. |....-+|. ++. .+|+ +..+.+.
T Consensus 12 vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~mlrrl 91 (339)
T KOG1560|consen 12 VKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAMLRRL 91 (339)
T ss_pred cceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHHHHHh
Confidence 789999999999999999985444466779999999999999999997 443322222 221 1222 1111111
Q ss_pred ---cCCCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCc
Q 012602 403 ---KRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRK 454 (460)
Q Consensus 403 ---~~~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~ 454 (460)
+-+-..||||-|| .++.|+|.-=|.+|+.||.| .|+.|++|.||.+|.++
T Consensus 92 r~vnid~~hVGwYqs~-~vgs~lS~~lveSqy~YQ~a-~pesVvliYD~~kssqG 144 (339)
T KOG1560|consen 92 RYVNIDHLHVGWYQSA-YVGSFLSPALVESQYAYQKA-IPESVVLIYDPIKSSQG 144 (339)
T ss_pred hhcCccceeeeeeeee-hhccccCHHHHHHHHHHHhc-CCccEEEEeccccccCc
Confidence 4566789999999 77899997779999999999 99999999999998775
No 24
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=98.92 E-value=7.1e-09 Score=103.83 Aligned_cols=116 Identities=18% Similarity=0.286 Sum_probs=91.6
Q ss_pred EEEeCH-HHHHHHHHHhhccCCCCeeeEEEeeeeEeCC-------eEEEEEEeecCCCCCCCccccCCH---HHHHHHhh
Q 012602 334 QLHIST-TMMDNFMKLAKSNTDKNLETCGILAGSLKNR-------KFYITALIIPKQESTSDSCQATNE---EEIFEVQD 402 (460)
Q Consensus 334 ~V~is~-~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~-------~~~It~~~~p~q~~t~d~c~~~~E---~ei~~~~~ 402 (460)
.|.+.. .++..|+..+-.+| +...||+|.|+.... +..|..++-|+|.++.|.+.+..+ +.+-.++.
T Consensus 12 ~vef~~~~~~~~f~~~~w~~~--~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~ 89 (274)
T cd08061 12 HVEFDNPSIVEFFLYVFWRKT--GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAA 89 (274)
T ss_pred EEEEecHHHHHHHHHHHHHhh--cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHH
Confidence 454444 44455554355543 699999999999764 577777788999999999988754 33556677
Q ss_pred cCCCccceeeccCCCC----CCCCChhHHhhhhhhccc-----cCCCceEEEecCCcc
Q 012602 403 KRSLFPLGWIHTHPTQ----SCFMSSIDVHTHYSYQVN-----VVPDARSCWKKRGEI 451 (460)
Q Consensus 403 ~~~l~~vGWyHSHP~~----t~flSsvDl~Tq~~yQ~m-----~~pe~iAIV~sP~~t 451 (460)
.-||..||||+||+.. ++|||+.++.+...||.+ +-..||-+|++|..+
T Consensus 90 ~lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~ 147 (274)
T cd08061 90 ALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKD 147 (274)
T ss_pred HcCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCC
Confidence 8999999999999987 999999999999999962 267899999999865
No 25
>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=98.87 E-value=1.3e-08 Score=91.55 Aligned_cols=90 Identities=21% Similarity=0.159 Sum_probs=62.5
Q ss_pred HHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccC--C---HHHHHHHhh--cCCCccceeecc
Q 012602 342 MDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQAT--N---EEEIFEVQD--KRSLFPLGWIHT 414 (460)
Q Consensus 342 ~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~--~---E~ei~~~~~--~~~l~~vGWyHS 414 (460)
+..|..+.+. ...+.|+||+|+|...++.++|+++..|.-......+... . .+.+-++.. +..+..||=+||
T Consensus 3 ~~~~~~~~Q~-~~~~~EtGGiLiG~~~~~~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWHt 81 (131)
T TIGR02256 3 VAMLKSYRQW-HDLSTETGGVLIGERRGAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHT 81 (131)
T ss_pred HHHHHHHHhC-cCCCCccceEEEEEEcCCcEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecCc
Confidence 4455555554 3667899999999998888999998765543333333332 2 223333333 244899999999
Q ss_pred CCCCCCCCChhHHhhhhh
Q 012602 415 HPTQSCFMSSIDVHTHYS 432 (460)
Q Consensus 415 HP~~t~flSsvDl~Tq~~ 432 (460)
||....-||.+|+.+-..
T Consensus 82 HP~~~p~PS~~D~~~~~~ 99 (131)
T TIGR02256 82 HPEDQPEPSWTDRRSWRT 99 (131)
T ss_pred CCCCCCCCCHHHHHHHHH
Confidence 999999999999987653
No 26
>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=98.84 E-value=7.7e-09 Score=97.92 Aligned_cols=107 Identities=11% Similarity=0.040 Sum_probs=73.4
Q ss_pred eCHHHHHHHHHHhhccCCCCeeeEEEeeeeEe-CCeEEEEEEeecCCCCCCCccccCCHH--H---HHHHhhcCCCccce
Q 012602 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKFYITALIIPKQESTSDSCQATNEE--E---IFEVQDKRSLFPLG 410 (460)
Q Consensus 337 is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~-~~~~~It~~~~p~q~~t~d~c~~~~E~--e---i~~~~~~~~l~~vG 410 (460)
|+..++.+|+.||.. .-..|+||+|+|+.. ++...|++++...-. ...+.+.. . +-.++..+|+.+||
T Consensus 1 is~~ay~ki~~HA~k--~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~----~~~l~P~~Eval~~ve~~~~~~gl~IvG 74 (182)
T cd08060 1 LSTLAYVKMLLHAAK--YPHCAVNGLLLGKKSSGGSVEITDAVPLFHS----CLALAPMLEVALALVDAYCKSSGLVIVG 74 (182)
T ss_pred CCHHHHHHHHHHHHH--cCCchheEEEEeeecCCCCEEEEEEEEcCCC----ccccCHHHHHHHHHHHHHHHHCCCEEEE
Confidence 578899999999999 668899999999997 667899999865542 12233332 2 34556689999999
Q ss_pred eeccCCCCC-CCCChhHHh-hhhhhccccCCCceEEEecCCcc
Q 012602 411 WIHTHPTQS-CFMSSIDVH-THYSYQVNVVPDARSCWKKRGEI 451 (460)
Q Consensus 411 WyHSHP~~t-~flSsvDl~-Tq~~yQ~m~~pe~iAIV~sP~~t 451 (460)
+|||||... .-|+.+=.. ...-.+. .+.++.++++=.+-
T Consensus 75 ~Yhsh~~~~d~~~~~~a~kIadki~~~--~~~a~ll~vdn~~l 115 (182)
T cd08060 75 YYQANERLDDSSPSPVAKKIADKIAEN--FSNACLLMVDNEKL 115 (182)
T ss_pred EEecCCcccCCCCcHHHHHHHHHHHHh--CCCCEEEEEeCccc
Confidence 999999874 233333211 1122222 46777787775544
No 27
>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=98.73 E-value=2.4e-08 Score=95.04 Aligned_cols=88 Identities=16% Similarity=0.151 Sum_probs=67.7
Q ss_pred eEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEee-cCCCCCCCccccCCHHHHHHHhhcCCCcccee
Q 012602 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALII-PKQESTSDSCQATNEEEIFEVQDKRSLFPLGW 411 (460)
Q Consensus 333 ~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~-p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGW 411 (460)
..=.||.+++.+|+.||+. +.+.|+||+++|.-.+..+ .++. .....++++..+... ...+|+.+|+-
T Consensus 71 ~~g~Ip~~l~~~ii~hAr~--~~P~EacG~Iag~~~~~~~---r~~p~~N~~~Sp~~~~~d~~------~~~~ge~lV~i 139 (192)
T TIGR03735 71 LCGPIPASLLEEFAEAARA--ALPNEVAAWIVWNSETGSL---RLAALESIEASPGHIDYRRP------RLDDGEHLVVD 139 (192)
T ss_pred ecCCCCHHHHHHHHHHHHh--cCCcceEEEEEEcCCCCEE---EEEeccccccCCceEEEcch------HHhCCCeEEEE
Confidence 3348999999999999999 8899999999997333332 3333 334556666666444 23889999999
Q ss_pred eccCCCCCCCCChhHHhhhh
Q 012602 412 IHTHPTQSCFMSSIDVHTHY 431 (460)
Q Consensus 412 yHSHP~~t~flSsvDl~Tq~ 431 (460)
|||||...+|+|.+|..--.
T Consensus 140 yHSH~~spA~PS~tD~~Dd~ 159 (192)
T TIGR03735 140 LHSHGTGSAFFSETDDADDK 159 (192)
T ss_pred EcCCCCCCCCCCcccchhhc
Confidence 99999999999999996543
No 28
>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=98.51 E-value=3e-07 Score=78.20 Aligned_cols=77 Identities=25% Similarity=0.389 Sum_probs=55.6
Q ss_pred HHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEE-eecCCCCCCCccccCCHHHHHHHhhcCCCccceeeccCCCC
Q 012602 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITAL-IIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQ 418 (460)
Q Consensus 340 ~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~-~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~~ 418 (460)
+++..++.|+.. ..+.|.||+|+|.-.+ .|+.+ .++.. +. ++.... +......+...||-|||||+.
T Consensus 1 ~~~~~i~~~~~~--~~p~E~~gll~~~~~~---~~~~~~~~~~~--~~---~~~~~~--~~~a~~~~~~~v~i~HsHP~g 68 (101)
T cd08059 1 DLLKTILVHAKD--AHPDEFCGFLSGSKDN---VMDELIFLPFV--SG---SVSAVI--DLAALEIGMKVVGLVHSHPSG 68 (101)
T ss_pred CHHHHHHHHHHh--cCChhhheeeecCCCC---eEEEEEeCCCc--CC---ccChHH--HHHHhhCCCcEEEEEecCcCC
Confidence 356778888887 5699999999998643 23333 33422 21 122222 566778899999999999999
Q ss_pred CCCCChhHHh
Q 012602 419 SCFMSSIDVH 428 (460)
Q Consensus 419 t~flSsvDl~ 428 (460)
.+.||..|+.
T Consensus 69 ~~~PS~~D~~ 78 (101)
T cd08059 69 SCRPSEADLS 78 (101)
T ss_pred CCCCCHHHHH
Confidence 9999999996
No 29
>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=98.40 E-value=1.3e-06 Score=88.24 Aligned_cols=117 Identities=15% Similarity=0.122 Sum_probs=79.0
Q ss_pred EEEeCHHHHHHHHHHhhccCCC----CeeeEEEeeeeEeCCeEEEEEEeecCCCCCC-CccccCCHHH---HHHH--hhc
Q 012602 334 QLHISTTMMDNFMKLAKSNTDK----NLETCGILAGSLKNRKFYITALIIPKQESTS-DSCQATNEEE---IFEV--QDK 403 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~----~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~-d~c~~~~E~e---i~~~--~~~ 403 (460)
.|.|-+-++..++.|+...... +--++|.|+|...++.+.|++.|..+...+. +... .+.+. +++. ...
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~-id~~y~~~m~~~~kkV~ 80 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIV-LDKEFLETRLEQFKQVF 80 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCcee-eCHHHHHHHHHHHHHhc
Confidence 4777888888898888763211 4679999999998899999999985554333 3222 22222 2222 225
Q ss_pred CCCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCccCCcc
Q 012602 404 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGEIGRKR 455 (460)
Q Consensus 404 ~~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~t~~~~ 455 (460)
.++.+||||+|.+. +.+.+...+|.| |... .+..|.++++|..+...+
T Consensus 81 ~~~~vVGWY~tg~~-~~~~~~~~Ih~~--~~~~-~~~pv~L~~D~~~~~~~~ 128 (288)
T cd08063 81 KDLDFVGWYTTGPG-GPTESDLPIHKQ--ILEI-NESPVLLLLDPEANASGK 128 (288)
T ss_pred cCCceEEEEecCCC-CCCHHHHHHHHH--HHhh-CCCcEEEEEccccccCCC
Confidence 77999999999988 455555445544 5554 566799999998853333
No 30
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=98.18 E-value=1.4e-05 Score=81.43 Aligned_cols=114 Identities=13% Similarity=0.161 Sum_probs=79.8
Q ss_pred CeEEEeCHHHHHHHHHHhhccCCC-CeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCc-c-ccCCHH---HHHHHhh--c
Q 012602 332 PLQLHISTTMMDNFMKLAKSNTDK-NLETCGILAGSLKNRKFYITALIIPKQESTSDS-C-QATNEE---EIFEVQD--K 403 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~nt~~-~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~-c-~~~~E~---ei~~~~~--~ 403 (460)
...|.|-+-++..++.|+...... +--+.|.|+|...++.+.||..|.-+.....+. . -..+.+ ++++... .
T Consensus 5 ~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k~V~ 84 (303)
T PLN03246 5 IEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMFKRIN 84 (303)
T ss_pred CcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHHHHhC
Confidence 567999999999999998763221 345999999999999999999998443322221 1 112222 2232222 5
Q ss_pred CCCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecCCc
Q 012602 404 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKRGE 450 (460)
Q Consensus 404 ~~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~ 450 (460)
.+..+||||+|-|.. +..|+.-|..|... .+..|-+++++.-
T Consensus 85 ~~~~vVGWY~tg~~i----~~~d~~IH~~~~~~-~~~Pv~L~vD~~~ 126 (303)
T PLN03246 85 AKEHVVGWYSTGPKL----RENDLDIHELFNDY-VPNPVLVIIDVQP 126 (303)
T ss_pred CCCcEEeeecCCCCC----CcchHHHHHHHHhh-CCCCeEEEEecCC
Confidence 778999999998774 44577777778776 7777778888754
No 31
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=97.90 E-value=4.9e-05 Score=77.59 Aligned_cols=91 Identities=26% Similarity=0.343 Sum_probs=73.8
Q ss_pred EEEeeeeEeCC-------eEEEEEEeecCCCCCCCccccCC---HHHHHHHhhcCCCccceeeccCCC------------
Q 012602 360 CGILAGSLKNR-------KFYITALIIPKQESTSDSCQATN---EEEIFEVQDKRSLFPLGWIHTHPT------------ 417 (460)
Q Consensus 360 cGiL~G~~~~~-------~~~It~~~~p~q~~t~d~c~~~~---E~ei~~~~~~~~l~~vGWyHSHP~------------ 417 (460)
+|+|.|+.+.. +..|..++-|+|+++.|.....+ |+.+-+++..-||..||||=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~IfTdl~~~~~~~g~v~~~ 81 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWIFTDLTDDGSGDGTVKCK 81 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEEEecCcccccCCCceeec
Confidence 79999999753 46777777799999999887743 334455666789999999999998
Q ss_pred ---CCCCCChhHHhhhhhhcccc------------CCCceEEEecCCc
Q 012602 418 ---QSCFMSSIDVHTHYSYQVNV------------VPDARSCWKKRGE 450 (460)
Q Consensus 418 ---~t~flSsvDl~Tq~~yQ~m~------------~pe~iAIV~sP~~ 450 (460)
.+.|||+..+-+=..+|... ...||-+|+++..
T Consensus 82 r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~ 129 (306)
T PF05021_consen 82 RHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDE 129 (306)
T ss_pred cccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCC
Confidence 89999999999888888862 2358999999953
No 32
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=97.54 E-value=0.0005 Score=67.66 Aligned_cols=111 Identities=18% Similarity=0.216 Sum_probs=73.7
Q ss_pred CeEEEeCHHHHHHHHHHhhc-cCCCCeeeEEEeeeeEeCCeEEEEEEeecCCC-CCCC-c-cccCC--HHHHHHHhh--c
Q 012602 332 PLQLHISTTMMDNFMKLAKS-NTDKNLETCGILAGSLKNRKFYITALIIPKQE-STSD-S-CQATN--EEEIFEVQD--K 403 (460)
Q Consensus 332 ~~~V~is~~~~~~fl~hA~~-nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~-~t~d-~-c~~~~--E~ei~~~~~--~ 403 (460)
...|.|-+.+++..+.|=.. .+..+--+.|+|+|.+.++++.|+..|..+.+ ...| + +.+.. -+-+|..+. .
T Consensus 8 ~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkKvN 87 (309)
T KOG1556|consen 8 VEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKKVN 87 (309)
T ss_pred cceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHHhc
Confidence 56788888888888887543 33456789999999999999999999985544 3222 2 22221 233555544 5
Q ss_pred CCCccceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEec
Q 012602 404 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKK 447 (460)
Q Consensus 404 ~~l~~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~s 447 (460)
....+||||||-|.- ..+-+|+ +..+-.+ .|..+-+|++
T Consensus 88 akekivGWYhTGPkl--~~nDl~I--n~l~k~y-~pnpvLvIId 126 (309)
T KOG1556|consen 88 AKEKVVGWYHTGPKL--RENDLDI--NELLKRY-VPNPVLVIID 126 (309)
T ss_pred chhheeeeeccCCcc--ccchhhH--HHHHhhc-CCCceEEEEe
Confidence 778999999998763 3344444 4555555 5655555555
No 33
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.34 E-value=0.00045 Score=66.38 Aligned_cols=112 Identities=13% Similarity=0.065 Sum_probs=73.9
Q ss_pred EEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCe--EEEEEEeecCCCCCCCccccCCHH---HHHHHhhcCCCcc
Q 012602 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRK--FYITALIIPKQESTSDSCQATNEE---EIFEVQDKRSLFP 408 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~--~~It~~~~p~q~~t~d~c~~~~E~---ei~~~~~~~~l~~ 408 (460)
.|.|+..++.||+.||.. =--.-|+|+|+|+-.++. +.|++++...=..+.- ...-|. .+-.++...|+.+
T Consensus 3 ~v~is~~AY~K~~LHaaK--yP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L--~PmlEvAL~qvd~~~~~~gl~I 78 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAK--YPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSL--SPMLEVALAQVDAYAKSNGLVI 78 (196)
T ss_pred eEEEcHHHHHHHHHHhcc--CCCCceeeEEEeccCCCCceEEEeeceeccccccCc--chHHHHHHHHHHHHHhhCCCEE
Confidence 589999999999999998 456899999999987654 9999998654322111 112232 3456777899999
Q ss_pred ceeeccCCCC-CCCCChhHHhhhhhhccccCCCceEEEecCCc
Q 012602 409 LGWIHTHPTQ-SCFMSSIDVHTHYSYQVNVVPDARSCWKKRGE 450 (460)
Q Consensus 409 vGWyHSHP~~-t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP~~ 450 (460)
||+||..... ..-||.+=...=..=..- .+.++.|+++=.+
T Consensus 79 vGyY~Ane~~~d~~~~~~a~kiad~I~~~-~~~a~ll~idn~k 120 (196)
T PF03665_consen 79 VGYYQANERLDDNSPSPVAEKIADKIAEN-FSDACLLMIDNKK 120 (196)
T ss_pred EEEEEeccccccCCCCHHHHHHHHHHHhh-CCCcEEEEEECcc
Confidence 9999987643 233444421100000112 4778888887544
No 34
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=96.61 E-value=0.011 Score=47.06 Aligned_cols=69 Identities=16% Similarity=0.174 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 012602 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (460)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L 101 (460)
|+..|..++++|-.+.+.||++.|+-+|..=+.+++.-+..-+ .+..+..++.++..-+.++|.||..|
T Consensus 1 y~~~A~~~~~~Av~~D~~g~~~~A~~~Y~~ai~~l~~~~~~~~-----~~~~~~~l~~k~~~yl~RAE~lk~~L 69 (69)
T PF04212_consen 1 YLDKAIELIKKAVEADEAGNYEEALELYKEAIEYLMQALKSES-----NPERRQALRQKMKEYLERAEKLKEYL 69 (69)
T ss_dssp -HHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHST-----THHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 7889999999999999999999999999998888866554432 34566778899999999999999865
No 35
>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.
Probab=96.49 E-value=0.019 Score=47.01 Aligned_cols=69 Identities=16% Similarity=0.118 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 012602 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (460)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~ 103 (460)
.-|..++++|--.-..|+++.||-+|+.=+.+|+..+..- ..+..|..++.++...+.++|+||..|+.
T Consensus 4 ~~Ai~lv~~Av~~D~~g~y~eA~~lY~~ale~~~~~~k~e-----~~~~~k~~lr~k~~eyl~RAE~LK~~l~~ 72 (75)
T cd02684 4 EKAIALVVQAVKKDQRGDAAAALSLYCSALQYFVPALHYE-----TDAQRKEALRQKVLQYVSRAEELKALIAS 72 (75)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4688999999999999999999999999999997766442 13456778999999999999999998864
No 36
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=96.47 E-value=0.021 Score=46.12 Aligned_cols=73 Identities=16% Similarity=0.165 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 012602 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (460)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~ 103 (460)
+.|+..|.+++.+|--+.+.|+++.|+-+|..=+.+++.-+..-| .+..+..++.++..-+.++|.||..|..
T Consensus 2 ~~~~~~A~~li~~Av~~d~~g~~~eAl~~Y~~a~e~l~~~~~~~~-----~~~~~~~~~~k~~eyl~raE~lk~~~~~ 74 (77)
T smart00745 2 RDYLSKAKELISKALKADEAGDYEEALELYKKAIEYLLEGIKVES-----DSKRREAVKAKAAEYLDRAEEIKKSLLE 74 (77)
T ss_pred ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 458899999999999999999999999999999999988775432 2456778889999999999999998864
No 37
>cd02678 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
Probab=96.46 E-value=0.016 Score=47.10 Aligned_cols=71 Identities=13% Similarity=0.127 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 012602 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (460)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~ 103 (460)
|+..|..++++|--....|+++.|+-+|..=+.+++.-+..-++ +..+..++.++..-+.++|.||..|++
T Consensus 2 ~~~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~~k~e~~-----~~~k~~~~~k~~eyl~RaE~LK~~l~~ 72 (75)
T cd02678 2 FLQKAIELVKKAIEEDNAGNYEEALRLYQHALEYFMHALKYEKN-----PKSKESIRAKCTEYLDRAEKLKEYLAK 72 (75)
T ss_pred hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 67889999999999999999999999999999999776655432 356778889999999999999998853
No 38
>cd02683 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear.
Probab=96.42 E-value=0.017 Score=47.56 Aligned_cols=69 Identities=19% Similarity=0.263 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 012602 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (460)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~ 103 (460)
..|.++++.|--+-+.|+++.|+.+|..=+.+|+.-|..-|| ...|..++.++..-+.++|.||..|++
T Consensus 4 ~~a~~l~~~Ave~D~~g~y~eAl~~Y~~aie~l~~~lk~e~d-----~~~k~~~r~ki~eY~~RAE~Lk~~l~~ 72 (77)
T cd02683 4 LAAKEVLKRAVELDQEGRFQEALVCYQEGIDLLMQVLKGTKD-----EAKKKNLRQKISEYMDRAEAIKKRLDQ 72 (77)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 568899999999999999999999999999999776655432 345778889999999999999998864
No 39
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=96.37 E-value=0.017 Score=47.62 Aligned_cols=70 Identities=16% Similarity=0.015 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 012602 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (460)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~ 103 (460)
|.|..+++.|--+-++|+++.|+.+|..=+.+|+..+..+ ..++..+..++.++..-+.++|.||..|..
T Consensus 4 ~~Ai~~a~~Ave~D~~g~y~eA~~~Y~~aie~l~~~~~~~----~~n~~~k~~ir~K~~eYl~RAE~Lk~~l~~ 73 (76)
T cd02681 4 RDAVQFARLAVQRDQEGRYSEAVFYYKEAAQLLIYAEMAG----TLNDSHLKTIQEKSNEYLDRAQALHQLVQG 73 (76)
T ss_pred HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHhc----CCChHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 6899999999999999999999999999999997643332 113344666789999999999999998753
No 40
>cd02677 MIT_SNX15 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
Probab=95.85 E-value=0.056 Score=44.33 Aligned_cols=68 Identities=16% Similarity=0.154 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHH
Q 012602 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPA 100 (460)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~ 100 (460)
|+--|..++++|--...+||++.||-+|..=+++|+.-++.-+ .+..|..++.++.+-+.++|+|+..
T Consensus 2 ~l~~A~~l~~~Ave~d~~~~y~eA~~~Y~~~i~~~~~~~k~e~-----~~~~k~~ir~K~~eYl~RAE~i~~~ 69 (75)
T cd02677 2 YLEQAAELIRLALEKEEEGDYEAAFEFYRAGVDLLLKGVQGDS-----SPERREAVKRKIAEYLKRAEEILRL 69 (75)
T ss_pred hHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6678899999999999999999999999999999987776632 2466788999999999999998763
No 41
>cd02656 MIT MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear.
Probab=95.72 E-value=0.079 Score=42.70 Aligned_cols=70 Identities=17% Similarity=0.179 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 012602 29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (460)
Q Consensus 29 ~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~ 103 (460)
+..|..+++.|--+.+.||++.|+-+|..=+.+++.-+..-+ .+..+..++.++...+.++|.||..|..
T Consensus 3 ~~~a~~l~~~Av~~D~~g~~~~Al~~Y~~a~e~l~~~~~~~~-----~~~~k~~l~~k~~~yl~RaE~Lk~~l~~ 72 (75)
T cd02656 3 LQQAKELIKQAVKEDEDGNYEEALELYKEALDYLLQALKAEK-----EPKLRKLLRKKVKEYLDRAEFLKELLKK 72 (75)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 567889999999999999999999999999999977764432 2466778889999999999999998854
No 42
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=95.69 E-value=0.031 Score=55.77 Aligned_cols=110 Identities=18% Similarity=0.297 Sum_probs=69.6
Q ss_pred eEEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEee-cCCCCCCCccccCCH--HHHHHHhh--cCCCc
Q 012602 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALII-PKQESTSDSCQATNE--EEIFEVQD--KRSLF 407 (460)
Q Consensus 333 ~~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~-p~q~~t~d~c~~~~E--~ei~~~~~--~~~l~ 407 (460)
.+|.|=+.++..++.+-..-+.+..-+||-|+|+.+++.+-||.+|. |..++ +|.++.+-| .++++.-. ..+..
T Consensus 21 ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEs-sdqvevdm~y~~~M~~l~~k~npnE~ 99 (288)
T KOG2975|consen 21 LTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNES-SDQVEVDMEYAKNMYELHKKVNPNEL 99 (288)
T ss_pred ceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccc-cccceeeHHHHHHHHHHhcccCCCce
Confidence 34555444444444443333367788999999999999999999998 55555 466655443 22333322 57788
Q ss_pred cceeeccCCCCCCCCChhHHhhhhhhccccCCCceEEEecC
Q 012602 408 PLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARSCWKKR 448 (460)
Q Consensus 408 ~vGWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~iAIV~sP 448 (460)
+||||-|-++.+.+=|-+ |--|=.- -++.|-+-+|-
T Consensus 100 vvGWyaTg~dvt~~ssli----hdyYare-~~~pvhLtVDT 135 (288)
T KOG2975|consen 100 VVGWYATGHDVTEHSSLI----HDYYARE-APNPVHLTVDT 135 (288)
T ss_pred eEEEEecCCCcccchhHH----HHHhhcc-CCCCeEEEEec
Confidence 999999988887776554 3334333 45555555543
No 43
>cd02680 MIT_calpain7_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=94.53 E-value=0.17 Score=41.62 Aligned_cols=64 Identities=20% Similarity=0.123 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHH----HHHHHHHhhcHHHH
Q 012602 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLL----NALSELEELQPAVQ 102 (460)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~----~vl~~lE~LK~~L~ 102 (460)
.-|..|+++|----..||++.||=||+-=+.+|+. + + ...-+..++.++. ..+.++|+||..|.
T Consensus 4 ~kai~Lv~~A~~eD~~gny~eA~~lY~~ale~~~~------e-k--n~~~k~~i~~K~~~~a~~yl~RAE~Lk~~l~ 71 (75)
T cd02680 4 ERAHFLVTQAFDEDEKGNAEEAIELYTEAVELCIN------T-S--NETMDQALQTKLKQLARQALDRAEALKESMS 71 (75)
T ss_pred HHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHH------h-c--ChhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35788999999999999999999999999999975 3 2 2345667778885 88999999999875
No 44
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=93.56 E-value=0.073 Score=62.37 Aligned_cols=107 Identities=20% Similarity=0.225 Sum_probs=75.6
Q ss_pred EEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeC-C--eEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccce
Q 012602 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN-R--KFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLG 410 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~-~--~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vG 410 (460)
+-.||.+++.+|+.++.. ..-|.|++.|.--. | .--|..+...+|-|+-..+....-- =....-.++..+|
T Consensus 2096 tyilPkNllkkFi~isD~----r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~l--P~~~~l~d~e~Lg 2169 (2321)
T KOG1795|consen 2096 TYILPKNLLKKFITISDL----RTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFL--PIHGVLEDLEPLG 2169 (2321)
T ss_pred eeeccHHHHhhheeecch----hhhhheeeeccCCCCCCccceEEEEEeccccccccccccCccC--CcchhccCCcccc
Confidence 457999999999998865 67889999996532 2 2356666667887765554432110 0223357899999
Q ss_pred eeccCCCCCCCCChhHHhhhhhhccccC-CCceEEEec
Q 012602 411 WIHTHPTQSCFMSSIDVHTHYSYQVNVV-PDARSCWKK 447 (460)
Q Consensus 411 WyHSHP~~t~flSsvDl~Tq~~yQ~m~~-pe~iAIV~s 447 (460)
|+||.|.--.+||..|+-||.---.- . ..+|-|-|+
T Consensus 2170 w~hTq~~el~~lsp~dV~th~ki~~~-~k~k~i~~t~~ 2206 (2321)
T KOG1795|consen 2170 WIHTQPNELPQLSPQDVTTHAKILVD-NKEKCIIITCS 2206 (2321)
T ss_pred hhhcCccccccCCHHHhhhhhhhhhc-CccceEEEEee
Confidence 99999999999999999999853222 2 346666665
No 45
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=93.48 E-value=0.38 Score=39.60 Aligned_cols=67 Identities=13% Similarity=0.075 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 012602 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (460)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L 101 (460)
++|..+++.|--|.++|+++.|..+|..=+.+++.-+..-||-. .+..++.++.+-++++|.||..+
T Consensus 4 ~~A~~~a~~AVe~D~~gr~~eAi~~Y~~aIe~L~q~~~~~pD~~-----~k~~yr~ki~eY~~Rae~Lk~~v 70 (75)
T cd02682 4 EMARKYAINAVKAEKEGNAEDAITNYKKAIEVLSQIVKNYPDSP-----TRLIYEQMINEYKRRIEVLEKQN 70 (75)
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHhCCChH-----HHHHHHHHHHHHHHHHHHHHHHc
Confidence 57899999999999999999999999999999988877767654 35667888999999999999876
No 46
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=93.43 E-value=0.28 Score=52.52 Aligned_cols=99 Identities=21% Similarity=0.401 Sum_probs=77.0
Q ss_pred CHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCC-eE------EEEEEeecCCCCCCCccccC--CHHH-HHHHhhcCCCc
Q 012602 338 STTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KF------YITALIIPKQESTSDSCQAT--NEEE-IFEVQDKRSLF 407 (460)
Q Consensus 338 s~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~-~~------~It~~~~p~q~~t~d~c~~~--~E~e-i~~~~~~~~l~ 407 (460)
.+.+...|+.--+. .+.-..|+|.|+.... .+ .|...+-|+|.+++|...+. +|+. +=+...+-||+
T Consensus 181 ~~~~v~~Fl~~wr~---sg~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLr 257 (510)
T KOG2834|consen 181 NAELVNHFLNEWRA---SGVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLR 257 (510)
T ss_pred chHHHHHHHHHHHH---hhhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCce
Confidence 78899999998886 4678899999999753 22 56666669999999988876 2333 33446689999
Q ss_pred cceeeccCC---------------CCCCCCChhHHhhhhhhccccCCC
Q 012602 408 PLGWIHTHP---------------TQSCFMSSIDVHTHYSYQVNVVPD 440 (460)
Q Consensus 408 ~vGWyHSHP---------------~~t~flSsvDl~Tq~~yQ~m~~pe 440 (460)
-||||-|-- -.+.|||+.++-|-..+|.+ .|.
T Consensus 258 RVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~-hpn 304 (510)
T KOG2834|consen 258 RVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNK-HPN 304 (510)
T ss_pred eeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhc-CCc
Confidence 999998632 24679999999999999988 763
No 47
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=91.20 E-value=0.7 Score=47.77 Aligned_cols=72 Identities=17% Similarity=0.144 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 012602 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (460)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~ 103 (460)
++.-|..++++|----..||++.||-||+--+.-|+..|.. .....+-|..++.++-+-|.++|+||.-|++
T Consensus 6 ~l~kaI~lv~kA~~eD~a~nY~eA~~lY~~aleYF~~~lKY----E~~~~kaKd~IraK~~EYLdRAEkLK~yL~~ 77 (439)
T KOG0739|consen 6 FLQKAIDLVKKAIDEDNAKNYEEALRLYQNALEYFLHALKY----EANNKKAKDSIRAKFTEYLDRAEKLKAYLKE 77 (439)
T ss_pred HHHHHHHHHHHHhhhcchhchHHHHHHHHHHHHHHHHHHHh----hhcChhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 67789999999999999999999999999988888766653 3233456788999999999999999998764
No 48
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=91.15 E-value=0.55 Score=44.67 Aligned_cols=81 Identities=14% Similarity=0.071 Sum_probs=56.8
Q ss_pred EEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEe--CCeEEEEEEeecCCCCCCCccccCCHHHHH---HHhhcCCCcc
Q 012602 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK--NRKFYITALIIPKQESTSDSCQATNEEEIF---EVQDKRSLFP 408 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~--~~~~~It~~~~p~q~~t~d~c~~~~E~ei~---~~~~~~~l~~ 408 (460)
.|.|+..++.+|..||.. -.---|-|+|+|... +++..|++.+...-....- ...-|-.+. .-..+.|+.+
T Consensus 3 ~veis~~aY~kmiLH~ak--yph~aVnGLLla~~~~kg~~v~itdcVPLfH~~laL--aPmlEvAl~lId~~~~~~Glvi 78 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAK--YPHAAVNGLLLAPATGKGECVEITDCVPLFHSHLAL--APMLEVALNLIDVWGAQAGLVI 78 (199)
T ss_pred ceeehhhHHHHHHHHhcc--CcccceeeEEEeccCCCCCeEEEEecchhhcccccc--ccHHHHHHHHHHHHHHhcCeEE
Confidence 478999999999999988 456677899999764 4678999988665433221 111132221 2244799999
Q ss_pred ceeeccCCCC
Q 012602 409 LGWIHTHPTQ 418 (460)
Q Consensus 409 vGWyHSHP~~ 418 (460)
+|.||.--++
T Consensus 79 aGyy~Ane~~ 88 (199)
T KOG3289|consen 79 AGYYHANERV 88 (199)
T ss_pred EEEeecCCCc
Confidence 9999987653
No 49
>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=88.20 E-value=3 Score=36.55 Aligned_cols=71 Identities=23% Similarity=0.211 Sum_probs=48.8
Q ss_pred CCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeeccCCCCCCCCChhHHhh
Q 012602 354 DKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHT 429 (460)
Q Consensus 354 ~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~~t~flSsvDl~T 429 (460)
+.+.|.+.+|+=.-.++-+....++ .|+-+.|.... -++|...-..+..-|.--|.||+..+.||.-|++.
T Consensus 13 ~~~~E~~~vl~Ld~~~~li~~~~l~----~G~~~~~~v~~-R~i~~~aL~~~A~~vil~HNHPsG~~~PS~~D~~~ 83 (113)
T cd08071 13 DLDQEEFVVLLLDTKNRLIAVETIS----VGTLNSSLVHP-REIFKEALRHNAAAIILAHNHPSGDPTPSREDIEL 83 (113)
T ss_pred CCCceEEEEEEecCCCCEEEEEEEe----ecCCcceecCH-HHHHHHHHHHhhheEEEEeeCCCCCCCCCHHHHHH
Confidence 4588998888433333322222222 34445544433 66788888889999999999999999999999873
No 50
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=85.47 E-value=3 Score=37.44 Aligned_cols=66 Identities=21% Similarity=0.345 Sum_probs=44.8
Q ss_pred CCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeeccCCC-----CCCCCChhHHh
Q 012602 354 DKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT-----QSCFMSSIDVH 428 (460)
Q Consensus 354 ~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~-----~t~flSsvDl~ 428 (460)
..+.|.||+.+ +..++.+.-|. ...++.+.|...+-. .-.+..+|+-||||.. ..-.+|..|+.
T Consensus 18 ~~nrEy~G~I~-~~~~G~y~~t~----p~~G~~~~~~~~~~~------~p~g~~~vA~yHTHG~~~~~y~~evfS~~D~~ 86 (123)
T PF14220_consen 18 RENREYCGYIG-KDEDGKYFATE----PRRGENASCYPSNPP------CPNGSTIVASYHTHGAYSDGYDNEVFSPQDIR 86 (123)
T ss_pred cCCcEEEEEEE-EcCCCcEEeec----CccCCCCCcCCCCcc------cccccceeeEeecccccCCCccccCCCHHHhh
Confidence 37999999985 44455555442 234455666664421 1357789999999996 45689999998
Q ss_pred hh
Q 012602 429 TH 430 (460)
Q Consensus 429 Tq 430 (460)
..
T Consensus 87 ~~ 88 (123)
T PF14220_consen 87 GD 88 (123)
T ss_pred hh
Confidence 76
No 51
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=85.36 E-value=0.7 Score=54.33 Aligned_cols=100 Identities=18% Similarity=0.376 Sum_probs=64.8
Q ss_pred EEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCC--eE-EEEEEeecCCCCCCCccccCC-HHHHHHHhhcCCCccc
Q 012602 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR--KF-YITALIIPKQESTSDSCQATN-EEEIFEVQDKRSLFPL 409 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~--~~-~It~~~~p~q~~t~d~c~~~~-E~ei~~~~~~~~l~~v 409 (460)
.-.||.+++.+|+.+... .+-|.|++.|+-..+ .+ -|......+|-|.-..+.... -- -+.-...+|.+|
T Consensus 2135 ~y~lP~NLl~kF~~isD~----~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP--~dlp~~e~le~l 2208 (2365)
T COG5178 2135 MYRLPLNLLEKFMRISDP----HVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVP--HDLPGDEDLEIL 2208 (2365)
T ss_pred cccccHHHHHhhheeccc----ceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCC--CCCCCcccceee
Confidence 457899999999998754 789999999976432 11 333333344544322222100 00 011224689999
Q ss_pred eeeccCCCCCCCCChhHHhhhhhhccccCCCc
Q 012602 410 GWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDA 441 (460)
Q Consensus 410 GWyHSHP~~t~flSsvDl~Tq~~yQ~m~~pe~ 441 (460)
||+||.-.--.||+..|+-||.- -.. .|++
T Consensus 2209 Gwihtq~~el~~l~~~~v~th~k-~~~-d~~~ 2238 (2365)
T COG5178 2209 GWIHTQDDELPYLEVAGVLTHRK-KIV-DPEW 2238 (2365)
T ss_pred EEEecCCcccchhhhhhhhhhhh-ccc-Cccc
Confidence 99999988889999999999964 333 5654
No 52
>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=78.69 E-value=7.5 Score=34.45 Aligned_cols=82 Identities=21% Similarity=0.178 Sum_probs=44.1
Q ss_pred HHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeeccCCCCC
Q 012602 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQS 419 (460)
Q Consensus 340 ~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~~t 419 (460)
+....++..... +.+.|.+.+++=.-.+.-+.+..++ .|+.+.|.+. -.++|...-..+-.-|=-.|-||+..
T Consensus 6 ~~v~~~l~~~l~--~~~~E~~~~l~Ld~~~~li~~~~v~----~G~~~~~~v~-~R~I~~~al~~~A~~vIl~HNHPsG~ 78 (123)
T PF04002_consen 6 EDVADYLRPKLQ--GLDQEQFRVLYLDSKNRLIGDEVVS----EGTIDSAPVD-PREIFRRALRLNASSVILAHNHPSGD 78 (123)
T ss_dssp HHHHHHHTTTSS---TTS-EEEEEEE-TTSBEEEEEEEE----ESTT-GGGCS-HHHHHHHHHHTT-SEEEEEEE-TTS-
T ss_pred HHHHHHHHHHhC--CCCCeEEEEEEECCCCcEEEEEEec----ccCCCccccc-HHHHHHHHHhhCCceEEEEEEcCCCC
Confidence 344445544444 4567888888332222223333333 4566666664 35577777677777677789999999
Q ss_pred CCCChhHHh
Q 012602 420 CFMSSIDVH 428 (460)
Q Consensus 420 ~flSsvDl~ 428 (460)
+.||.-|+.
T Consensus 79 ~~PS~~D~~ 87 (123)
T PF04002_consen 79 PEPSDADIA 87 (123)
T ss_dssp -S--HHHHH
T ss_pred CCCCHhHHH
Confidence 999999985
No 53
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=74.80 E-value=33 Score=39.76 Aligned_cols=27 Identities=11% Similarity=0.070 Sum_probs=14.1
Q ss_pred HHHHHHHHhccCCCCcccccccHHHHH
Q 012602 55 LLRFSSLVTETIPCHRDYLASFKSQKL 81 (460)
Q Consensus 55 y~Ry~~LvlekLpkHpdyk~~~~~~k~ 81 (460)
||+-+.=|+..|--|+.+....-++|.
T Consensus 424 YykLIEecISqIvlHr~~~DPdf~yr~ 450 (1102)
T KOG1924|consen 424 YYKLIEECISQIVLHRTGMDPDFKYRF 450 (1102)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCcchhh
Confidence 455555555556666666543334444
No 54
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=71.26 E-value=11 Score=25.50 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCC-CCcc
Q 012602 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP-CHRD 71 (460)
Q Consensus 31 sa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLp-kHpd 71 (460)
+|..+...|.+|..-|+++.|=-++-+=+.+.-..+. .|||
T Consensus 1 ta~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~G~~Hpd 42 (42)
T PF13374_consen 1 TASALNNLANAYRAQGRYEEALELLEEALEIRERLLGPDHPD 42 (42)
T ss_dssp -HHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH----------
T ss_pred CHHHHHHHHHHHHhhhhcchhhHHHHHHHHHHHHHhcccccC
Confidence 3567778899999999999999999998877643333 3775
No 55
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=66.66 E-value=11 Score=24.12 Aligned_cols=28 Identities=7% Similarity=0.059 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 012602 34 NILKQADIFREEKNIIDLYVMLLRFSSL 61 (460)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~~L 61 (460)
.+++.|.+|.+.||.++|=-.|-+++..
T Consensus 2 a~~~~a~~~~~~g~~~~A~~~~~~~~~~ 29 (33)
T PF13174_consen 2 ALYRLARCYYKLGDYDEAIEYFQRLIKR 29 (33)
T ss_dssp HHHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence 5789999999999999999888887664
No 56
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=65.60 E-value=59 Score=29.98 Aligned_cols=48 Identities=23% Similarity=0.246 Sum_probs=35.3
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccc
Q 012602 20 DNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYL 73 (460)
Q Consensus 20 n~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk 73 (460)
+.+.|...|-.-| -|.-|..|++.|+++.|.--+-||+.|- |+||+.-
T Consensus 37 ~~ryP~g~ya~qA--qL~l~yayy~~~~y~~A~a~~~rFirLh----P~hp~vd 84 (142)
T PF13512_consen 37 DTRYPFGEYAEQA--QLDLAYAYYKQGDYEEAIAAYDRFIRLH----PTHPNVD 84 (142)
T ss_pred HhcCCCCcccHHH--HHHHHHHHHHccCHHHHHHHHHHHHHhC----CCCCCcc
Confidence 3444444454433 3445888999999999999999999986 8998653
No 57
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=64.89 E-value=18 Score=34.04 Aligned_cols=33 Identities=24% Similarity=0.169 Sum_probs=25.5
Q ss_pred HHHhhcCCCccceeeccCCCCCCCCChhHHhhhh
Q 012602 398 FEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHY 431 (460)
Q Consensus 398 ~~~~~~~~l~~vGWyHSHP~~t~flSsvDl~Tq~ 431 (460)
+.-+...+-.++. |||||..+.++|..|...=.
T Consensus 108 ~~kl~~~~~~iid-iHSHP~~~~~~S~~D~~~~~ 140 (162)
T PF15659_consen 108 QEKLKNNGNKIID-IHSHPENSNGPSGNDMKNAK 140 (162)
T ss_pred hhhhccCCceEEE-eccCCCCCCCCCcchhhhhh
Confidence 3334457777888 99999999999999976543
No 58
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=60.90 E-value=22 Score=23.12 Aligned_cols=30 Identities=10% Similarity=0.130 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 012602 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (460)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (460)
|..++..|.+|.+.||++.|.-.|.+-+.+
T Consensus 1 a~~~~~lg~~y~~~~~~~~A~~~~~~a~~~ 30 (34)
T PF13181_consen 1 AEAYYNLGKIYEQLGDYEEALEYFEKALEL 30 (34)
T ss_dssp -HHHHHHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 455678899999999999999999887665
No 59
>PF05168 HEPN: HEPN domain; InterPro: IPR007842 The HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain is a region of 110 residues found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archeabacterial proteins. There are three classes of proteins with HEPN domain: Single-domain HEPN proteins found in many bacteria. Two-domain proteins with N-terminal nucleotidyltransferase (NT) and C- terminal HEPN domains. This N-terminal NT domain belongs to a large family of NTs, which includes several classes of enzymes that are responsible for some types of bacterial resistance to aminoglycosides. These enzymes deactivate various antibiotics by transferring a nucleotidyl group to the drug. A multidomain sacsin protein in genomes of fish and mammals. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain (see PDOC00553 from PROSITEDOC). The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C-terminal all- alpha-helical domain of kanamycin nucleotidyltransferases (KNTases). It is composed of five alpha helices, three of which form an up- and-down helical bundle, with a pair of short helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding [].; PDB: 1O3U_A 1WOL_A 3O10_D 2HSB_A 1UFB_A.
Probab=59.34 E-value=22 Score=29.57 Aligned_cols=37 Identities=19% Similarity=0.097 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 012602 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (460)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (460)
+.|++-|..-++.|+..+++|++..|..+..--+-+.
T Consensus 2 ~~~~~~A~~~l~~A~~~~~~~~~~~a~~~a~~a~e~~ 38 (118)
T PF05168_consen 2 QDWLEKAEEDLKAAEILLEEGDYNWAVFHAYQAVEKA 38 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 6899999999999999999999998887766555444
No 60
>PRK00024 hypothetical protein; Reviewed
Probab=58.18 E-value=50 Score=32.43 Aligned_cols=86 Identities=22% Similarity=0.154 Sum_probs=55.7
Q ss_pred EeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeeccC
Q 012602 336 HISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTH 415 (460)
Q Consensus 336 ~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSH 415 (460)
.-++....+++..... +...|.+.+|+=.-.+.-+....++ .||-+.|.... -++|...-..+-.-|=.-|=|
T Consensus 103 i~~~~~~~~~l~~~l~--~~~~E~f~vl~Ld~~~~li~~~~i~----~Gt~~~~~v~p-Rei~~~Al~~~A~~iIl~HNH 175 (224)
T PRK00024 103 LLSPEDVADYLMAELR--DEEQEHFVVLFLDTKNRVIADEELF----IGTLNSSIVHP-REIVKRALKLNAAALILAHNH 175 (224)
T ss_pred CCCHHHHHHHHHHHcc--CCCceEEEEEEECCCCCEeeEEEee----eecCCeEEEcH-HHHHHHHHHhhccceEEEecC
Confidence 3344455556555555 5689999998443333333333333 45556555443 667777776666666667999
Q ss_pred CCCCCCCChhHHh
Q 012602 416 PTQSCFMSSIDVH 428 (460)
Q Consensus 416 P~~t~flSsvDl~ 428 (460)
|+..+.||.-|+.
T Consensus 176 PSG~~~PS~~D~~ 188 (224)
T PRK00024 176 PSGDPEPSQADIL 188 (224)
T ss_pred CCCCCCCCHHHHH
Confidence 9999999999986
No 61
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=56.39 E-value=10 Score=38.09 Aligned_cols=73 Identities=22% Similarity=0.361 Sum_probs=45.0
Q ss_pred CCCe-eeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhh-----cCCCccceeeccCCCCCCCCChhHH
Q 012602 354 DKNL-ETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQD-----KRSLFPLGWIHTHPTQSCFMSSIDV 427 (460)
Q Consensus 354 ~~~~-E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~-----~~~l~~vGWyHSHP~~t~flSsvDl 427 (460)
+.+. -|.|-|+|+-.++.+-|...|..+-....+.- +.+-+.+...++ =.+|.++|||-|- ... .--|+
T Consensus 33 gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~-~~dke~l~kk~eqykqVFpdl~vlGwYttG--~d~--t~sd~ 107 (299)
T KOG3050|consen 33 GPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTE-TIDKEYLEKKEEQYKQVFPDLYVLGWYTTG--SDP--TPSDI 107 (299)
T ss_pred CCcHHHhhhhheecccCceEEEeeeeEEEecchhhhh-hccHHHHHHHHHHHHHhcccceEEEEeecC--CCC--Chhhh
Confidence 4566 89999999999988888888876543333321 222222221111 3789999999753 222 44566
Q ss_pred hhhh
Q 012602 428 HTHY 431 (460)
Q Consensus 428 ~Tq~ 431 (460)
|-|.
T Consensus 108 ~i~k 111 (299)
T KOG3050|consen 108 HIHK 111 (299)
T ss_pred HHHH
Confidence 6554
No 62
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.07 E-value=71 Score=31.37 Aligned_cols=87 Identities=21% Similarity=0.171 Sum_probs=56.8
Q ss_pred EEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeecc
Q 012602 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHT 414 (460)
Q Consensus 335 V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHS 414 (460)
+.-+++....++..... ....|.+.+| .++...-.|....+- .||-+.|.... -++|...-..+-.-|=.-|=
T Consensus 96 ~l~s~~~v~~~l~~~l~--~~~~E~f~vl--~Ld~~n~li~~~~i~--~Gt~~~~~v~p-ReI~~~Al~~~A~~vIlaHN 168 (218)
T TIGR00608 96 VIRSPEAAAEFLHTDLA--HETREHFMVL--FLDRKNRLIAKEVVF--IGTVNHVPVHP-REIFKEALKLSASALILAHN 168 (218)
T ss_pred CCCCHHHHHHHHHHHhc--CCCceEEEEE--EECCCCcEEEEEEee--cCCCCeEEEcH-HHHHHHHHHhhCCeEEEEee
Confidence 34455566667666666 5689998888 454433233332221 46666655544 66777766666555555699
Q ss_pred CCCCCCCCChhHHh
Q 012602 415 HPTQSCFMSSIDVH 428 (460)
Q Consensus 415 HP~~t~flSsvDl~ 428 (460)
||+..+.||.-|+.
T Consensus 169 HPSG~~~PS~~Di~ 182 (218)
T TIGR00608 169 HPSGEPSPSQEDIL 182 (218)
T ss_pred cCCCCCCCCHHHHH
Confidence 99999999999986
No 63
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=52.62 E-value=39 Score=21.74 Aligned_cols=31 Identities=10% Similarity=-0.009 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 012602 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (460)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (460)
|.-++..|.+|++.|++++|--.+-|-+.|.
T Consensus 1 a~~~~~lg~~~~~~~~~~~A~~~~~~al~l~ 31 (34)
T PF07719_consen 1 AEAWYYLGQAYYQLGNYEEAIEYFEKALELD 31 (34)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHHHC
Confidence 3456788999999999999999888876653
No 64
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=43.31 E-value=19 Score=38.59 Aligned_cols=110 Identities=20% Similarity=0.250 Sum_probs=78.7
Q ss_pred EeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeC--C-----eEEEEEEeecCCCCCCCccccCCHH--HHHHH-hhcCC
Q 012602 336 HISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN--R-----KFYITALIIPKQESTSDSCQATNEE--EIFEV-QDKRS 405 (460)
Q Consensus 336 ~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~--~-----~~~It~~~~p~q~~t~d~c~~~~E~--ei~~~-~~~~~ 405 (460)
+-.+.++..|+..=+. .+.-..|+|.|+..+ | +-+|...+-|+|+.-+|-+.+...+ .+++. ..+-|
T Consensus 238 F~~~~iv~~Fi~~WR~---sG~QRfGy~yG~y~~y~n~PLGiKaVveaIyEPpQ~de~DG~t~ee~~de~l~d~~a~~~G 314 (571)
T COG5100 238 FDGKHIVENFIRNWRE---SGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTG 314 (571)
T ss_pred ecCchHHHHHHHHHHH---hhhhhheeeeeehhhccCCcchhHHHhhhhcCCccccCCCceEeeeecccccccccccccC
Confidence 3467889999987775 467788999999964 2 2355666669999999887773322 22322 33679
Q ss_pred CccceeeccCCC---------------CCCCCChhHHhhhhhhccccCC-------------CceEEEecCC
Q 012602 406 LFPLGWIHTHPT---------------QSCFMSSIDVHTHYSYQVNVVP-------------DARSCWKKRG 449 (460)
Q Consensus 406 l~~vGWyHSHP~---------------~t~flSsvDl~Tq~~yQ~m~~p-------------e~iAIV~sP~ 449 (460)
|..||.|-|--+ -+-||||..+..-..+|.| .| .|+-+|++-.
T Consensus 315 L~riG~IfTDl~d~gs~~GsV~ckrh~dsyFLSSLEv~~~A~~Qt~-hpn~~k~sr~g~FgSkfvT~Visgn 385 (571)
T COG5100 315 LERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTM-HPNTVKDSREGEFGSKFVTIVISGN 385 (571)
T ss_pred ceeeeeeeeehhhccCCCCceeeeccccceehhhhhhHHHhhhhhc-CCCcccccccccccceeEEEEEecc
Confidence 999999986321 2369999999998999998 75 4677777653
No 65
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=42.68 E-value=44 Score=23.60 Aligned_cols=28 Identities=21% Similarity=0.105 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 012602 34 NILKQADIFREEKNIIDLYVMLLRFSSL 61 (460)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~~L 61 (460)
..+..|..|.+.|++++|--+|-|.+.+
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~ 30 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRALAL 30 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4567799999999999999999997665
No 66
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=42.57 E-value=54 Score=22.26 Aligned_cols=28 Identities=11% Similarity=0.122 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 012602 35 ILKQADIFREEKNIIDLYVMLLRFSSLV 62 (460)
Q Consensus 35 llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (460)
+...|.+|++.||+++|--+|-+-+.|-
T Consensus 2 l~~Lg~~~~~~g~~~~Ai~~y~~aL~l~ 29 (36)
T PF13176_consen 2 LNNLGRIYRQQGDYEKAIEYYEQALALA 29 (36)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence 5677999999999999999999865443
No 67
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=36.90 E-value=95 Score=20.12 Aligned_cols=30 Identities=10% Similarity=0.069 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 012602 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (460)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (460)
|...+..|.+|..-|+++.|...|.|=+.+
T Consensus 1 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~ 30 (34)
T PF00515_consen 1 AEAYYNLGNAYFQLGDYEEALEYYQRALEL 30 (34)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence 455678899999999999999998886654
No 68
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.59 E-value=1e+02 Score=29.82 Aligned_cols=73 Identities=12% Similarity=0.119 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 012602 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK 104 (460)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~~ 104 (460)
-+..|..++..|---.++|.+.+|.+-|--=++|+++-|..-|-= ...|..++.++-+-+.+++.|++-|++.
T Consensus 11 ~~~aAa~iL~~AVe~d~e~k~pqALl~YkeGIdLi~e~lk~~~ld----na~R~~i~~k~s~Ym~ka~diekYLdqe 83 (247)
T KOG4509|consen 11 LLKAAAPILCDAVEDDKEGKVPQALLCYKEGIDLIAEALKGMKLD----NADRCKIMAKFSDYMDKAADIEKYLDQE 83 (247)
T ss_pred hhhhhhhHHHHHhcccccccccHHHHHHhhhHHHHHHHHccCCCc----chHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 356788899999999999999999999999999999999886622 2456677788888899999999888754
No 69
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=34.32 E-value=68 Score=24.11 Aligned_cols=30 Identities=10% Similarity=0.128 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 012602 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (460)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (460)
|..+...|.+|++.||+++|--.|.+-+.+
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~ 32 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIEL 32 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 567888999999999999999999987665
No 70
>PF14455 Metal_CEHH: Predicted metal binding domain
Probab=34.10 E-value=14 Score=34.53 Aligned_cols=64 Identities=13% Similarity=0.201 Sum_probs=44.8
Q ss_pred HHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecC-CCCCCCccccCCHHHHHHHhhcCCCccceeeccCCC-
Q 012602 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPK-QESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT- 417 (460)
Q Consensus 340 ~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~-q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyHSHP~- 417 (460)
++..+||..-+.- +.+-|++++|.+.- .+.+++.+.+. .++++.-|-...-| ||+||.
T Consensus 86 ~l~~~mlr~~~L~-~app~~~~~l~qq~---~~s~~~~~~ah~~~~~pF~Cm~G~rE----------------YH~h~sH 145 (177)
T PF14455_consen 86 DLGLKMLRRPHLP-GAPPEMISVLMQQQ---ALSLQDFLSAHPNTGRPFLCMRGVRE----------------YHTHPSH 145 (177)
T ss_pred ccchhhhhcCCCC-CCCchhhhhccccc---chhhhhhccCCCCCCCcEEEeccchh----------------hcCCccc
Confidence 3566777766654 45788888887753 67888877654 57888888776666 999996
Q ss_pred -CCCCCC
Q 012602 418 -QSCFMS 423 (460)
Q Consensus 418 -~t~flS 423 (460)
...|++
T Consensus 146 ~gd~W~~ 152 (177)
T PF14455_consen 146 TGDLWLL 152 (177)
T ss_pred ccchHhh
Confidence 444554
No 71
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=33.95 E-value=3.5e+02 Score=24.23 Aligned_cols=73 Identities=22% Similarity=0.198 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCC-cccccccHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHH
Q 012602 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCH-RDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNR 110 (460)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkH-pdyk~~~~~~k~~l~~~l~~vl~~lE~LK~~L~~~Y~~~~~ 110 (460)
..+|+.-| ++||.+..=-+-..|+.+| +.|..- +... .....+.....-++++|..=-++|..+..+-++..+
T Consensus 18 S~~ML~aA----~~g~Wd~Li~lE~~y~~~V-e~l~~~~~~~~-l~~~~q~~~~~lL~~IL~nda~Ir~Llq~rl~eL~~ 91 (121)
T PRK10548 18 SQSMLRLA----TEGQWDELIEQEVAYVQAV-EEIAHLTIPPD-ISTVMQEQLRPMLRQILDNEAELKQLLQQRMDELSS 91 (121)
T ss_pred HHHHHHHH----HHCCHHHHHHHHHHHHHHH-HHHHhcCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566666 8999999999999999998 666332 2222 233444444445566664444456666666655554
No 72
>PRK15490 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=32.04 E-value=1.5e+02 Score=33.52 Aligned_cols=69 Identities=17% Similarity=0.205 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHH-HHHHHHHHHHHhhcHHHHHHHH
Q 012602 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLK-KKLLNALSELEELQPAVQQKIN 106 (460)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~~~k~~l~-~~l~~vl~~lE~LK~~L~~~Y~ 106 (460)
.|+.+|+.+|+..-+-|..|+||-+|-|-+ ..|+| +....-.+...+ .-+.++...+-++-+-.+++|+
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (578)
T PRK15490 40 LTSLAMLKKAEFLHDVNETERAYALYETLI-------AQNND-EARYEYARRLYNTGLAKDAQLILKKVSNGVQKKYN 109 (578)
T ss_pred hhHHHHHHHhhhhhhhhhhHhHHHHHHHHH-------HhCCc-chHHHHHHHHHhhhhhhHHHHHHHHhCccHhHHHH
Confidence 578999999999999999999999887733 46998 322211122222 2355566666677777777776
No 73
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=29.55 E-value=1.4e+02 Score=34.98 Aligned_cols=14 Identities=21% Similarity=0.209 Sum_probs=7.5
Q ss_pred cChhhHHHHHHHHH
Q 012602 46 KNIIDLYVMLLRFS 59 (460)
Q Consensus 46 gn~e~AYily~Ry~ 59 (460)
++..+.||..|-|+
T Consensus 299 ~e~~~l~vacmq~I 312 (1102)
T KOG1924|consen 299 LEKQQLQVACMQFI 312 (1102)
T ss_pred cchHHHHHHHHHHH
Confidence 33555666666543
No 74
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=29.39 E-value=63 Score=33.96 Aligned_cols=57 Identities=25% Similarity=0.386 Sum_probs=36.8
Q ss_pred EEeeeeE-eCCeEEEEEEee-cCCCCCCC---------ccccCCHHHHHHHhh------cCCCccceeeccCCC
Q 012602 361 GILAGSL-KNRKFYITALII-PKQESTSD---------SCQATNEEEIFEVQD------KRSLFPLGWIHTHPT 417 (460)
Q Consensus 361 GiL~G~~-~~~~~~It~~~~-p~q~~t~d---------~c~~~~E~ei~~~~~------~~~l~~vGWyHSHP~ 417 (460)
|+|+|.. ..+.-+|-+++. |..++..+ +....+++++.+.+. -.|+.|||-|=.+|.
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 8999999 555556666554 55543333 123356777765544 479999999976653
No 75
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=26.81 E-value=1.5e+02 Score=22.84 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCC
Q 012602 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP 67 (460)
Q Consensus 31 sa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLp 67 (460)
+|..+...|.+|++.|++++|--+|-+-+.+ .+.+.
T Consensus 4 ~a~~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~ 39 (78)
T PF13424_consen 4 TANAYNNLARVYRELGRYDEALDYYEKALDI-EEQLG 39 (78)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTT
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHC
Confidence 4667788899999999999999999999999 56654
No 76
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=24.83 E-value=1.6e+02 Score=20.97 Aligned_cols=37 Identities=19% Similarity=0.066 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCC
Q 012602 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68 (460)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpk 68 (460)
|+.+.+.|+|.+..+|+++|.-=|.+-+.|--+.+|-
T Consensus 1 Adv~~~Lgeisle~e~f~qA~~D~~~aL~i~~~l~~~ 37 (38)
T PF10516_consen 1 ADVYDLLGEISLENENFEQAIEDYEKALEIQEELLPP 37 (38)
T ss_pred CcHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCC
Confidence 3456788999999999999999998888877655553
No 77
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=24.82 E-value=56 Score=32.39 Aligned_cols=96 Identities=18% Similarity=0.163 Sum_probs=60.0
Q ss_pred EEEeCHHHHHHHHHHhhccCCCCeeeEEEeeeeEeCCeEEEEEEeecCCCCCCCccccCCHHHHHHHhhcCCCccceeec
Q 012602 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH 413 (460)
Q Consensus 334 ~V~is~~~~~~fl~hA~~nt~~~~E~cGiL~G~~~~~~~~It~~~~p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyH 413 (460)
.+.-++..+.+++.-... ....|+--+|+=.-.+.-+....+|+-....+. .--.|++...-..+..-|=.-|
T Consensus 101 ~~i~sp~~~~~~l~~~l~--~~~~E~f~vL~Ld~qnrlI~~e~lf~GTi~~s~-----V~PREI~k~Al~~nAaavIlaH 173 (224)
T COG2003 101 VVITSPEAVAEYLRAELG--GEEREHFVVLYLDSQNRLIATETLFIGTLNVSE-----VHPREIFKEALKYNAAAVILAH 173 (224)
T ss_pred CccCCHHHHHHHHHHHhh--hhHHHHHHHHHhcCcCceecceeEEeeecccce-----ecHHHHHHHHHHhcchhhheec
Confidence 466777888888876666 345555444422222333444555654333322 2246777776666666666679
Q ss_pred cCCCCCCCCChhHHh-hhhhhccc
Q 012602 414 THPTQSCFMSSIDVH-THYSYQVN 436 (460)
Q Consensus 414 SHP~~t~flSsvDl~-Tq~~yQ~m 436 (460)
=||+...-||.-|+. |+.-.|..
T Consensus 174 NHPSGd~~PS~aD~~iT~rl~~a~ 197 (224)
T COG2003 174 NHPSGDPTPSRADILITERLKEAG 197 (224)
T ss_pred cCCCCCCCcCHHHHHHHHHHHHHH
Confidence 999999999999976 65555544
No 78
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=24.62 E-value=1.4e+02 Score=25.20 Aligned_cols=32 Identities=9% Similarity=-0.009 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHH
Q 012602 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLR 57 (460)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~R 57 (460)
-..|+.|...|..|...+.+||+.+|+.+...
T Consensus 39 p~el~~A~~~L~~A~~a~~~~~y~~A~~~A~~ 70 (103)
T PF14346_consen 39 PVELKEAREKLQRAKAALDDGDYERARRLAEQ 70 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 45899999999999999999999999877654
No 79
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=24.39 E-value=1.4e+02 Score=28.12 Aligned_cols=36 Identities=17% Similarity=0.147 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCccc
Q 012602 33 DNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY 72 (460)
Q Consensus 33 ~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdy 72 (460)
..++..|..|.+.||++.|-..+-+|+.++ |.||..
T Consensus 43 ~A~l~la~a~y~~~~y~~A~~~~~~fi~~y----P~~~~~ 78 (203)
T PF13525_consen 43 QAQLMLAYAYYKQGDYEEAIAAYERFIKLY----PNSPKA 78 (203)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHH-----TT-TTH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC----CCCcch
Confidence 345777999999999999999999988876 888754
No 80
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=23.12 E-value=1.5e+02 Score=22.75 Aligned_cols=35 Identities=3% Similarity=-0.016 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 012602 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (460)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (460)
...+|..+...|.+|..-||++.|--++.+=++++
T Consensus 42 ~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~ 76 (78)
T PF13424_consen 42 HPDTANTLNNLGECYYRLGDYEEALEYYQKALDIF 76 (78)
T ss_dssp HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence 34568888899999999999999999988877765
No 81
>TIGR01597 PYST-B Plasmodium yoelii subtelomeric family PYST-B. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism.
Probab=22.92 E-value=3.3e+02 Score=27.36 Aligned_cols=82 Identities=18% Similarity=0.183 Sum_probs=54.7
Q ss_pred ccCCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccH--HHHHHHHHHHHHHHHHHH
Q 012602 18 DVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFK--SQKLYLKKKLLNALSELE 95 (460)
Q Consensus 18 evn~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpkHpdyk~~~~--~~k~~l~~~l~~vl~~lE 95 (460)
+.|+...|..+|.|..++..|-.-|- +||.|-+|+--.- =.++.+|-+=++.+- ..-+..++-+.+...+||
T Consensus 50 d~dnqfdLn~FY~Stlsla~q~nd~~-~ddeEi~~lrnii-----dShikkhkenntl~dLnnvd~ktkklI~el~keLe 123 (255)
T TIGR01597 50 DADNQFDLNEFYQSTLSLANQFNDCN-DDDKEIAHLRNII-----DSHIKKHKERNTLPDLNNVDKKTKKLINKLQKELE 123 (255)
T ss_pred ccCccccHHHHHHHHHHHHHHhcccc-CchHHHHHHHHhH-----HHHHHhhhccccCcccccccHHHHHHHHHHHHHHH
Confidence 56777889999999999988777664 6888877654332 246667765554321 111234455666778999
Q ss_pred hhcHHHHHHH
Q 012602 96 ELQPAVQQKI 105 (460)
Q Consensus 96 ~LK~~L~~~Y 105 (460)
++|++|+..-
T Consensus 124 e~kKeldnk~ 133 (255)
T TIGR01597 124 ELKKELDNEM 133 (255)
T ss_pred HHHHHhcccc
Confidence 9999887543
No 82
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=22.31 E-value=1.3e+02 Score=17.12 Aligned_cols=26 Identities=0% Similarity=-0.043 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHH
Q 012602 34 NILKQADIFREEKNIIDLYVMLLRFS 59 (460)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~ 59 (460)
...+.|..|...|+++.|-..+.+-+
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~ 28 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKAL 28 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 34677889999999999988776543
No 83
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=20.44 E-value=84 Score=24.90 Aligned_cols=24 Identities=8% Similarity=0.158 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHH
Q 012602 34 NILKQADIFREEKNIIDLYVMLLR 57 (460)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~R 57 (460)
-++..|.+|++.|++++|+-++-+
T Consensus 27 ~~~~la~~~~~~~~y~~A~~~~~~ 50 (84)
T PF12895_consen 27 YLYNLAQCYFQQGKYEEAIELLQK 50 (84)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHH
Confidence 355679999999999999888866
No 84
>cd02679 MIT_spastin MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
Probab=20.39 E-value=5e+02 Score=21.52 Aligned_cols=44 Identities=18% Similarity=0.052 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCC
Q 012602 25 LRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68 (460)
Q Consensus 25 lr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~LvlekLpk 68 (460)
+|-||.-|-+-+..|=-+.+.|+.++|-.+|-+=+....+.+.-
T Consensus 1 ik~~~~~A~~~I~kaL~~dE~g~~e~Al~~Y~~gi~~l~eg~ai 44 (79)
T cd02679 1 IRGYYKQAFEEISKALRADEWGDKEQALAHYRKGLRELEEGIAV 44 (79)
T ss_pred CchHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHHHHHHcCC
Confidence 46799999999999999999999999999999988888776654
No 85
>KOG4745 consensus Metalloproteinase inhibitor TIMP and related proteins [General function prediction only]
Probab=20.22 E-value=73 Score=29.34 Aligned_cols=57 Identities=30% Similarity=0.472 Sum_probs=32.6
Q ss_pred CCCeeeEE----EeeeeEe-CCeEEEEE-Eee-cCCCCCCCccccCCHHHHHHHhhcCCCccceeec--------cCCCC
Q 012602 354 DKNLETCG----ILAGSLK-NRKFYITA-LII-PKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIH--------THPTQ 418 (460)
Q Consensus 354 ~~~~E~cG----iL~G~~~-~~~~~It~-~~~-p~q~~t~d~c~~~~E~ei~~~~~~~~l~~vGWyH--------SHP~~ 418 (460)
+..+++.| ||+|++. ++.+.|+- -|+ |-- + . ...+--.+.+||| .=|+.
T Consensus 24 G~~l~~~~~keYLlaGrv~~dg~l~itlC~~v~pwd-----~---l--------s~~qre~~~~~y~~~c~C~vt~C~~i 87 (141)
T KOG4745|consen 24 GLKLDVGGKKEYLLAGRVEGDGKLLITLCDFVVPWD-----R---L--------SLTQREGLNHWYHVGCNCTVTPCPSI 87 (141)
T ss_pred ceeeecCCcEEEEEeeeecCCCcEEEEeeceEeech-----h---c--------chHHhccccceeeecccceeeecCCC
Confidence 34455555 8899997 55666642 232 210 0 0 0111234678998 35678
Q ss_pred CCCCChhH
Q 012602 419 SCFMSSID 426 (460)
Q Consensus 419 t~flSsvD 426 (460)
.||+|+-|
T Consensus 88 pC~lss~~ 95 (141)
T KOG4745|consen 88 PCFLSSPD 95 (141)
T ss_pred ccccCCCC
Confidence 99999965
Done!