Query 010576
Match_columns 507
No_of_seqs 245 out of 628
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 02:08:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010576.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010576hhsearch_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 3.3E-90 7.1E-95 692.4 24.8 416 2-507 2-424 (424)
2 cd08066 MPN_AMSH_like Mov34/MP 100.0 2.9E-41 6.2E-46 319.1 19.6 171 332-507 1-173 (173)
3 cd08067 MPN_2A_DUB Mov34/MPN/P 99.9 7.7E-27 1.7E-31 223.3 16.1 126 333-461 5-148 (187)
4 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 2.7E-26 5.8E-31 230.9 16.1 130 332-464 9-150 (268)
5 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 4.3E-26 9.3E-31 202.7 12.0 114 340-458 1-119 (119)
6 KOG1554 COP9 signalosome, subu 99.9 1.3E-25 2.7E-30 221.4 9.9 128 332-462 52-192 (347)
7 cd08068 MPN_BRCC36 Mov34/MPN/P 99.9 8.3E-24 1.8E-28 209.2 14.7 126 332-459 1-151 (244)
8 PF08969 USP8_dimer: USP8 dime 99.9 8.6E-24 1.9E-28 187.2 10.0 103 5-108 10-115 (115)
9 KOG1560 Translation initiation 99.8 2.1E-21 4.5E-26 191.3 9.0 142 332-478 12-170 (339)
10 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.8 1.3E-20 2.8E-25 189.6 13.6 135 334-476 2-149 (266)
11 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.8 7.9E-21 1.7E-25 188.4 10.8 133 333-471 36-177 (252)
12 cd07767 MPN Mpr1p, Pad1p N-ter 99.8 2E-20 4.4E-25 163.2 11.7 103 343-448 2-107 (116)
13 smart00232 JAB_MPN JAB/MPN dom 99.8 4.4E-19 9.5E-24 158.3 15.4 123 335-459 2-134 (135)
14 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 7.4E-20 1.6E-24 160.7 8.3 104 332-437 3-114 (114)
15 KOG1555 26S proteasome regulat 99.7 5.1E-18 1.1E-22 171.9 5.7 128 332-461 30-175 (316)
16 cd08070 MPN_like Mpr1p, Pad1p 99.7 1.4E-16 3E-21 143.3 13.0 113 340-459 2-120 (128)
17 cd08072 MPN_archaeal Mov34/MPN 99.5 1.2E-13 2.6E-18 123.0 12.6 107 337-459 1-109 (117)
18 cd08057 MPN_euk_non_mb Mpr1p, 99.5 2.1E-13 4.5E-18 127.0 14.4 125 335-459 1-136 (157)
19 COG1310 Predicted metal-depend 99.5 5.2E-13 1.1E-17 121.1 12.0 111 335-459 2-117 (134)
20 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.4 7.1E-12 1.5E-16 126.3 13.7 125 335-463 1-134 (265)
21 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.3 1.5E-11 3.2E-16 125.1 14.2 120 334-458 2-134 (280)
22 PF14464 Prok-JAB: Prokaryotic 99.3 5.7E-12 1.2E-16 108.4 9.6 94 339-445 2-96 (104)
23 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.3 2.7E-11 5.8E-16 106.6 11.3 99 341-456 2-104 (108)
24 cd08060 MPN_UPF0172 Mov34/MPN/ 99.0 4.9E-09 1.1E-13 100.4 11.2 107 337-448 1-115 (182)
25 cd08061 MPN_NPL4 Mov34/MPN/PAD 98.9 1.2E-08 2.5E-13 103.5 12.7 131 332-465 10-164 (274)
26 cd08059 MPN_prok_mb Mpr1p, Pad 98.8 1.6E-08 3.4E-13 87.2 9.2 78 340-427 1-79 (101)
27 cd08063 MPN_CSN6 Mpr1p, Pad1p 98.8 2.7E-08 5.8E-13 101.7 11.7 137 334-477 2-153 (288)
28 PLN03246 26S proteasome regula 98.8 8.2E-08 1.8E-12 98.8 14.0 123 332-458 5-139 (303)
29 TIGR03735 PRTRC_A PRTRC system 98.8 3.8E-08 8.2E-13 94.7 9.8 110 333-458 71-183 (192)
30 TIGR02256 ICE_VC0181 integrati 98.7 1.2E-07 2.6E-12 86.3 10.4 90 341-431 2-100 (131)
31 KOG1556 26S proteasome regulat 98.1 3E-05 6.5E-10 76.7 10.9 113 332-448 8-130 (309)
32 PF05021 NPL4: NPL4 family; I 98.0 4.6E-05 1E-09 78.7 10.5 105 360-465 2-147 (306)
33 KOG2975 Translation initiation 97.8 0.00011 2.4E-09 73.4 9.5 127 332-464 20-155 (288)
34 PF03665 UPF0172: Uncharacteri 97.7 0.00027 5.7E-09 68.8 11.0 111 334-447 3-120 (196)
35 KOG1795 U5 snRNP spliceosome s 96.6 0.0021 4.7E-08 75.0 5.2 149 334-490 2096-2248(2321)
36 PF04212 MIT: MIT (microtubule 96.6 0.011 2.4E-07 47.6 7.5 69 28-101 1-69 (69)
37 cd02684 MIT_2 MIT: domain cont 96.4 0.021 4.5E-07 47.3 8.3 69 30-103 4-72 (75)
38 cd02678 MIT_VPS4 MIT: domain c 96.4 0.018 3.9E-07 47.4 7.8 70 28-102 2-71 (75)
39 smart00745 MIT Microtubule Int 96.3 0.025 5.5E-07 46.3 8.5 73 26-103 2-74 (77)
40 cd02683 MIT_1 MIT: domain cont 96.3 0.019 4E-07 47.8 7.7 69 30-103 4-72 (77)
41 cd02681 MIT_calpain7_1 MIT: do 96.3 0.017 3.7E-07 48.1 7.4 69 30-102 4-72 (76)
42 cd02677 MIT_SNX15 MIT: domain 95.7 0.067 1.5E-06 44.3 8.2 68 28-100 2-69 (75)
43 cd02656 MIT MIT: domain contai 95.6 0.088 1.9E-06 43.0 8.5 70 29-103 3-72 (75)
44 KOG3289 Uncharacterized conser 94.8 0.24 5.1E-06 47.5 9.8 109 334-446 3-119 (199)
45 cd02680 MIT_calpain7_2 MIT: do 94.4 0.17 3.8E-06 42.0 7.1 64 30-102 4-71 (75)
46 cd02682 MIT_AAA_Arch MIT: doma 93.3 0.39 8.5E-06 40.0 7.2 67 30-101 4-70 (75)
47 KOG2834 Nuclear pore complex, 92.9 0.69 1.5E-05 50.1 10.0 128 334-465 176-345 (510)
48 cd08071 MPN_DUF2466 Mov34/MPN/ 92.4 1.1 2.4E-05 39.8 9.4 69 356-428 15-84 (113)
49 KOG0739 AAA+-type ATPase [Post 91.0 0.7 1.5E-05 48.2 7.4 72 28-103 6-77 (439)
50 COG5178 PRP8 U5 snRNP spliceos 91.0 0.27 5.9E-06 58.1 4.8 121 334-463 2135-2264(2365)
51 PF04002 RadC: RadC-like JAB d 85.9 3.5 7.5E-05 37.1 7.5 82 340-427 6-88 (123)
52 KOG3050 COP9 signalosome, subu 82.9 1.9 4.2E-05 43.4 4.9 109 334-446 10-128 (299)
53 PF14220 DUF4329: Domain of un 79.8 8.9 0.00019 34.9 7.7 65 354-428 18-88 (123)
54 PRK00024 hypothetical protein; 79.6 11 0.00024 37.5 9.0 84 338-427 105-189 (224)
55 TIGR00608 radc DNA repair prot 76.5 19 0.00041 35.8 9.6 84 338-427 99-183 (218)
56 PF13374 TPR_10: Tetratricopep 69.0 12 0.00026 25.5 4.6 41 31-71 1-42 (42)
57 PF13174 TPR_6: Tetratricopept 64.9 13 0.00027 24.3 3.9 29 34-62 2-30 (33)
58 PF13512 TPR_18: Tetratricopep 63.4 66 0.0014 30.0 9.5 48 20-73 37-84 (142)
59 PF15659 Toxin-JAB1: JAB-like 61.6 37 0.00081 32.4 7.6 40 399-440 111-150 (162)
60 PF13181 TPR_8: Tetratricopept 59.8 23 0.00051 23.3 4.5 30 32-61 1-30 (34)
61 PF05168 HEPN: HEPN domain; I 57.1 25 0.00053 29.8 5.3 38 26-63 2-39 (118)
62 KOG1924 RhoA GTPase effector D 56.4 88 0.0019 36.8 10.6 27 55-81 424-450 (1102)
63 PF07719 TPR_2: Tetratricopept 50.4 43 0.00093 21.8 4.6 31 32-62 1-31 (34)
64 PF13176 TPR_7: Tetratricopept 41.8 55 0.0012 22.5 4.1 28 35-62 2-29 (36)
65 PF13428 TPR_14: Tetratricopep 40.7 48 0.001 23.7 3.9 29 34-62 3-31 (44)
66 PF13424 TPR_12: Tetratricopep 39.6 76 0.0016 24.9 5.3 36 31-67 4-39 (78)
67 COG5100 NPL4 Nuclear pore prot 38.3 38 0.00083 36.7 4.1 128 334-465 235-404 (571)
68 PF00515 TPR_1: Tetratricopept 36.5 94 0.002 20.4 4.6 30 32-61 1-30 (34)
69 KOG4253 Tryptophan-rich basic 33.2 83 0.0018 30.0 5.0 59 51-111 10-75 (175)
70 PF13414 TPR_11: TPR repeat; P 32.0 75 0.0016 24.2 4.0 30 32-61 3-32 (69)
71 KOG4509 Uncharacterized conser 31.0 1.2E+02 0.0027 29.6 5.9 73 28-104 11-83 (247)
72 PF14778 ODR4-like: Olfactory 30.2 70 0.0015 34.1 4.6 55 361-415 1-74 (362)
73 PRK15490 Vi polysaccharide bio 27.8 1.9E+02 0.0041 33.1 7.6 69 30-106 40-109 (578)
74 COG2003 RadC DNA repair protei 27.7 66 0.0014 32.3 3.6 89 335-429 102-192 (224)
75 PF14346 DUF4398: Domain of un 22.6 1.6E+02 0.0034 25.2 4.7 32 26-57 39-70 (103)
76 PF10516 SHNi-TPR: SHNi-TPR; 22.5 1.9E+02 0.004 20.9 4.2 37 32-68 1-37 (38)
77 cd02679 MIT_spastin MIT: domai 22.1 4.8E+02 0.01 21.9 8.1 44 25-68 1-44 (79)
78 PF13424 TPR_12: Tetratricopep 21.9 1.6E+02 0.0035 22.9 4.3 35 28-62 42-76 (78)
79 PF13525 YfiO: Outer membrane 21.8 1.7E+02 0.0036 28.1 5.2 36 33-72 43-78 (203)
80 smart00028 TPR Tetratricopepti 21.4 1.4E+02 0.003 17.3 3.1 26 34-59 3-28 (34)
81 PF09935 DUF2167: Protein of u 20.6 4.7E+02 0.01 26.6 8.1 80 334-416 23-118 (239)
82 PF02561 FliS: Flagellar prote 20.1 6.1E+02 0.013 22.4 8.1 84 28-112 25-119 (122)
No 1
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=100.00 E-value=3.3e-90 Score=692.43 Aligned_cols=416 Identities=39% Similarity=0.598 Sum_probs=293.6
Q ss_pred CCcccchhHHHh---hcCccccCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHH
Q 010576 2 RSSSEGINIAAS---AQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKS 78 (507)
Q Consensus 2 ~~~~~~~~l~~~---a~~~e~n~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~ 78 (507)
-+|.+.++.+.. +..|+||.|||+|+|||+|++|+|||.||++|||+++|||||+||++||+||||+||||++.. .
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 455555554443 345899999999999999999999999999999999999999999999999999999999544 6
Q ss_pred HHHHHHHHHHHH-HHHHHhhCHHHHHHHHHHHHhhhhccccCcccCCCCCccccchhccccCchhhhhhhccchhhhhhc
Q 010576 79 QKLYLKKKLLNA-LSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQ 157 (507)
Q Consensus 79 ~k~~~~~~l~~v-l~~lE~LK~~l~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~v~~~~~~~~~~ 157 (507)
+++.+.++|+.+ ++.+|+||++|.++|+.+++.+-..++... .+. .+.+ +.|++.+.+
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 778888787665 899999999999999988775522110000 000 0111 224555555
Q ss_pred CCchhhhhccchhHHHHhhhccCCCCCcchhhccccccCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCcccc
Q 010576 158 GSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSI 237 (507)
Q Consensus 158 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~e~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (507)
++|.++..+++....+|..+ +......+...++....+.+|+.++-. .+
T Consensus 140 ~kr~aq~k~Q~l~~~~f~~~-~~~~~~q~~~s~~m~s~~~~gl~e~~~-----------------------------~~- 188 (424)
T KOG2880|consen 140 RKRSAQTKQQQLESSQFSPL-EPPSFKQLLDSGPMPSNQSNGLPEQPI-----------------------------GE- 188 (424)
T ss_pred HHHHHHHhhhcCCcccCCcc-CchHHHhhhcccCCCcCCCCCCcCCCc-----------------------------CC-
Confidence 66666665555555554431 111111111111111111111111100 00
Q ss_pred cccCCCCCCCCCcccccccCCCCCcccccCCCCCCCCCCccCCCCCCCccccCCCCCCCcchhhhhhhhccCCCcccccc
Q 010576 238 KIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETEC 317 (507)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~pPp~~~~~~~~~~~~~~~~~~~~~ 317 (507)
+.++....+...-+....+..+|++......+..+ .+|++++...+ .+.+
T Consensus 189 -----------------~~~p~~~~~~~~~s~~l~~~~s~ep~~s~~~n~~~---k~p~~~r~l~p-------~a~~--- 238 (424)
T KOG2880|consen 189 -----------------PLVPSNESRSLNYSELLSVLSSPEPSDSCTTNVTI---KSPSVDRVLKP-------GATD--- 238 (424)
T ss_pred -----------------CCcccccccccCCchhhhhccCCCccccccccccc---cCCCCCccccc-------cccc---
Confidence 00000000000000000111111211111111112 23333332211 1000
Q ss_pred ccCCCCCCCCCCCC-CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC--cCCHHH
Q 010576 318 QVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS--ATNEEE 394 (507)
Q Consensus 318 ~~~~~~~~~~~~~~-~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~--~~~eee 394 (507)
. ........+. ++.|+||.+++..|+++|.+||.+++|+||+|||++..|.|+|||++||+|++|+|+ ++||++
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 899999999999999999999999999999999999999999999999999999997 899999
Q ss_pred HHHHhhhCCCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEEecCCCCchhhhccccCCC
Q 010576 395 IFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGF 474 (507)
Q Consensus 395 i~~~~~~~~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFrLt~p~gm~~i~~c~~~gF 474 (507)
+|++|++++|.+||||||||||||||||+||||||+||+|+||+|||||+|+.. .+|+||||+|.||.+|.+|+++||
T Consensus 316 lF~vQdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~--~tGiFrLt~~~Gm~~i~~C~~~GF 393 (424)
T KOG2880|consen 316 LFEVQDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSK--TTGIFRLTDPGGMEVIRGCRKKGF 393 (424)
T ss_pred HheecccccceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccC--CcceEEecCCcchHHHhhcccCCC
Confidence 999999999999999999999999999999999999999999999999999975 499999999999999999999999
Q ss_pred cCCCCCCCCCCCcccCCceeecCCCceEEeeCC
Q 010576 475 HPHDPPPDGGPIYKPCTDVYMNPNLKFDVIDLR 507 (507)
Q Consensus 475 hph~~~~~~~~~y~~~~hv~~~~~~~~~v~DLR 507 (507)
|||+. +++|+|+.|+||||..+.++.|+|||
T Consensus 394 HpH~~--~~~pl~~~~~~v~~~~~~k~~v~dLR 424 (424)
T KOG2880|consen 394 HPHSE--KGPPLFEHCSHVYMHHNNKLCVIDLR 424 (424)
T ss_pred CCCCC--CCCCceeecceeEEcCCcceeeeeCC
Confidence 99974 58999999999999999999999998
No 2
>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=100.00 E-value=2.9e-41 Score=319.08 Aligned_cols=171 Identities=56% Similarity=1.000 Sum_probs=159.0
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC--cCCHHHHHHHhhhCCCcceEE
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS--ATNEEEIFEVQDKRSLFPLGW 409 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~--~~~eeei~~~~~~~~l~~VGW 409 (507)
++++.||..++.+|+.||..++..++|+||+|+|+..++.+.|+++++|.|.+++++ ..++++++++++.+|+.+|||
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 478999999999999999998756799999999999888899999999999887776 567888999999999999999
Q ss_pred EcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEEecCCCCchhhhccccCCCcCCCCCCCCCCCccc
Q 010576 410 IHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGFHPHDPPPDGGPIYKP 489 (507)
Q Consensus 410 yHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFrLt~p~gm~~i~~c~~~gFhph~~~~~~~~~y~~ 489 (507)
|||||..+||||.+|++||++||.+.|++++|||||.. ..+++|||++++||..+.+|+++|||||+.+ ++||++
T Consensus 81 yHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~~--~~l~afrl~~~~g~~~~~~~~~~~~h~~~~~---~~~~~~ 155 (173)
T cd08066 81 IHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPKY--NEFGIFRLTDPPGLDEILNCKKTGFHPHPKD---PPLYED 155 (173)
T ss_pred EeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCCC--cEEeEEEeecCCcceecccCCcCccCCCCCC---CCccee
Confidence 99999999999999999999999999999999999963 4699999997789999999999999999874 799999
Q ss_pred CCceeecCCCceEEeeCC
Q 010576 490 CTDVYMNPNLKFDVIDLR 507 (507)
Q Consensus 490 ~~hv~~~~~~~~~v~DLR 507 (507)
|+||++.+++.|+++|||
T Consensus 156 ~~~~~~~~~~~~~~~~~~ 173 (173)
T cd08066 156 CGHVIWKDQLKVTVVDLR 173 (173)
T ss_pred eeEEEEcCCCceEEEeCC
Confidence 999999999999999998
No 3
>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=7.7e-27 Score=223.32 Aligned_cols=126 Identities=25% Similarity=0.342 Sum_probs=107.4
Q ss_pred eEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeC--CEEEEEEEEecCCCCCCCC-cCCH---HHHHHHhhhCCCcc
Q 010576 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN--RKFYITALIIPKQESTSDS-ATNE---EEIFEVQDKRSLFP 406 (507)
Q Consensus 333 ~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~--~~l~It~~~iP~q~~t~d~-~~~e---eei~~~~~~~~l~~ 406 (507)
-.|.|++.++++|++||+... .|+||+|+|.++. +.+.|+++|..++..+++. .+++ .+++++++.+|+.+
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 FKVTVSSNALLLMDFHCHLTT---SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRGLSV 81 (187)
T ss_pred EEEEECHHHHHHHHHHhcCCC---cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcCCEE
Confidence 369999999999999999843 9999999999864 6899999996666555454 5555 34667788999999
Q ss_pred eEEEcCCCCCCCCCCHHHHHhhhhhhccCC-------CeEEEEEcCCCCCC-----ceeEEEecCCC
Q 010576 407 LGWIHTHPTQSCFMSSIDVHTHYSYQIMLP-------ESVAIVMAPQDATR-----KHGIFRLTSPG 461 (507)
Q Consensus 407 VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~p-------e~IaIV~dP~~~~~-----~~gaFrLt~p~ 461 (507)
||||||||.++|+||.+|++||+.||.|++ ++|||||||+++.. .+++|++.+++
T Consensus 82 VGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~ 148 (187)
T cd08067 82 VGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPP 148 (187)
T ss_pred EEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCC
Confidence 999999999999999999999999999998 79999999998532 47999999653
No 4
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.94 E-value=2.7e-26 Score=230.91 Aligned_cols=130 Identities=25% Similarity=0.420 Sum_probs=110.9
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCH---HHHHH--H--hhhCC
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNE---EEIFE--V--QDKRS 403 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~e---eei~~--~--~~~~~ 403 (507)
++.|.|++.++++|++||.... +.|+||+|+|...++++.|+++|..++.+++++ ..++ +.+++ . +.+++
T Consensus 9 ~~~V~Is~~allkil~Ha~~~~--p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~ 86 (268)
T cd08069 9 FEKVYISSLALLKMLKHARAGG--PIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRP 86 (268)
T ss_pred ccEEEECHHHHHHHHHHHhccC--CceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCC
Confidence 7899999999999999999954 999999999999999999999996667666665 3232 23444 3 34689
Q ss_pred CcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCC-CC---ceeEEEecCCCCch
Q 010576 404 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA-TR---KHGIFRLTSPGGMS 464 (507)
Q Consensus 404 l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~-~~---~~gaFrLt~p~gm~ 464 (507)
+.+||||||||+++||||..|++||..||.+.+++|+|||||..+ .. ++||||+++ +|+.
T Consensus 87 ~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~-~~~~ 150 (268)
T cd08069 87 ENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIP-PGYK 150 (268)
T ss_pred ceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEEC-cccc
Confidence 999999999999999999999999999999999999999999887 33 479999995 5764
No 5
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.93 E-value=4.3e-26 Score=202.66 Aligned_cols=114 Identities=39% Similarity=0.727 Sum_probs=91.9
Q ss_pred HHHHHHHHHHhhcCCCCcceEEEecceeeC-----CEEEEEEEEecCCCCCCCCcCCHHHHHHHhhhCCCcceEEEcCCC
Q 010576 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKN-----RKFYITALIIPKQESTSDSATNEEEIFEVQDKRSLFPLGWIHTHP 414 (507)
Q Consensus 340 ~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~-----~~l~It~~~iP~q~~t~d~~~~eeei~~~~~~~~l~~VGWyHSHP 414 (507)
+++++|++||++++ |.|+||+|+|.... ..+.|++++..... .+ ..+..+.+..+.++|+++||||||||
T Consensus 1 ~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~--~~-~~~~~~~~~~~~~~g~~~vG~YHSHP 75 (119)
T cd08058 1 DALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDS--CT-GENVEELFNVQTGRPLLVVGWYHSHP 75 (119)
T ss_pred CHHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCC--ch-hHHHHHHHHHHhCCCCeEEEEEecCC
Confidence 47899999999976 99999999999874 44667776621111 01 11112234456799999999999999
Q ss_pred CCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEEec
Q 010576 415 TQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLT 458 (507)
Q Consensus 415 t~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFrLt 458 (507)
++++|||..|+++|+.||.+.|++|+||+||.++...+|+||||
T Consensus 76 ~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~~~~~~a~rl~ 119 (119)
T cd08058 76 TFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRNKDTGIFRLT 119 (119)
T ss_pred CCCCccCHHHHHHHHHHhccCCCeEEEEECcCCCCcccceEEeC
Confidence 99999999999999999999999999999999865678999996
No 6
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.92 E-value=1.3e-25 Score=221.42 Aligned_cols=128 Identities=27% Similarity=0.420 Sum_probs=112.5
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCCcCCHHHHHHHh---------hhC
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSATNEEEIFEVQ---------DKR 402 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~~~~eeei~~~~---------~~~ 402 (507)
++.|.|++.+++||+.||+. ++++|+||+|.|++.++++.|.++|..+.+||+.+....++.++|+ .++
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 79999999999999999999 5599999999999999999999999777888888754455555553 257
Q ss_pred CCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCC----ceeEEEecCCCC
Q 010576 403 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR----KHGIFRLTSPGG 462 (507)
Q Consensus 403 ~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~----~~gaFrLt~p~g 462 (507)
-.++||||||||+.+||||++|+.||.-.|....++||||+||.++-. .+||||.. |.|
T Consensus 130 ~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTy-p~g 192 (347)
T KOG1554|consen 130 LENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTY-PKG 192 (347)
T ss_pred hhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecc-cCC
Confidence 889999999999999999999999999999999999999999998743 26999988 556
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=8.3e-24 Score=209.18 Aligned_cols=126 Identities=23% Similarity=0.383 Sum_probs=103.2
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceee-------CCEEEEEEEEecCC-CCCCCC-cCCHHHHHHH---h
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-------NRKFYITALIIPKQ-ESTSDS-ATNEEEIFEV---Q 399 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~-------~~~l~It~~~iP~q-~~t~d~-~~~eeei~~~---~ 399 (507)
+..|.|+.+++++|+.||.... |.|+||+|+|.++ ...+.|+..+.+.. ..+.++ .+|++++++. +
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~--P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea 78 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTE--KEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEA 78 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCC--CcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHH
Confidence 3579999999999999999965 9999999999985 23455556554433 334555 8899887654 3
Q ss_pred hh------CCCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCC-------CceeEEEecC
Q 010576 400 DK------RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT-------RKHGIFRLTS 459 (507)
Q Consensus 400 ~~------~~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~-------~~~gaFrLt~ 459 (507)
+. +++.+||||||||.++|+||.+|+.||.+||++.|++++||+|++... ..++|||+.+
T Consensus 79 ~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~ 151 (244)
T cd08068 79 ERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQ 151 (244)
T ss_pred HHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecC
Confidence 34 999999999999999999999999999999999999999999987642 2469999985
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=8.6e-24 Score=187.24 Aligned_cols=103 Identities=35% Similarity=0.534 Sum_probs=87.0
Q ss_pred ccchhHHHhhcCc-cccCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHH-H
Q 010576 5 SEGINIAASAQRL-DVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKL-Y 82 (507)
Q Consensus 5 ~~~~~l~~~a~~~-e~n~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~-~ 82 (507)
+..-+|.+.|..+ +||+++|+++|+|+|.+|+++|++|+++||+|+|||+|+||++|| ++||+||||+........ .
T Consensus 10 ~s~~~L~~~a~~~~~~~~~~~l~~y~rsa~~l~~~A~~~~~egd~E~AYvl~~R~~~L~-~ki~~Hpdy~~~~~~~~~~~ 88 (115)
T PF08969_consen 10 SSLEELNKLADVFPEFDKNIPLKRYLRSANKLLREAEEYRQEGDEEQAYVLYMRYLTLV-EKIPKHPDYKKDKNSYKKLL 88 (115)
T ss_dssp CCHHHHHHCCCT-GGGSTTS-HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH-CCHCCSCCCCCTHHCCHHHH
T ss_pred hhHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HHhhcCccccccchHHHHHH
Confidence 3456899999998 999999999999999999999999999999999999999999999 999999999976654444 2
Q ss_pred HHHHHHHH-HHHHHhhCHHHHHHHHHH
Q 010576 83 LKKKLLNA-LSELEELQPAVQQKINEL 108 (507)
Q Consensus 83 ~~~~l~~v-l~~lE~LK~~l~~~Y~~~ 108 (507)
..+++..+ |++||+||++|+++|+++
T Consensus 89 ~~~~~~~~il~~lE~Lk~~L~~rY~~e 115 (115)
T PF08969_consen 89 GKKKLNEVILEELEKLKPSLKERYEEE 115 (115)
T ss_dssp HHHHHHHCHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 33555444 899999999999999874
No 9
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=2.1e-21 Score=191.27 Aligned_cols=142 Identities=21% Similarity=0.426 Sum_probs=116.2
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEE-ecCCCCCCCCc-----CCHH-HHHHH--h---
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI-IPKQESTSDSA-----TNEE-EIFEV--Q--- 399 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~~-----~~ee-ei~~~--~--- 399 (507)
+++|.|++.++++|++||++...++.-+.|+|+|.+.++++.||+|| +|.....+|.+ .+++ +.++. +
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 89999999999999999999873333456999999999999999999 66654333332 2222 12222 1
Q ss_pred --hhCCCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCc---eeEEEecCCCCchhhhccccCCC
Q 010576 400 --DKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRK---HGIFRLTSPGGMSVIRQCQQRGF 474 (507)
Q Consensus 400 --~~~~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~---~gaFrLt~p~gm~~i~~c~~~gF 474 (507)
.+.|...||||.|| .+|.|+|..-+++|+.||.+.|++|++|+||.++.+| .+||||| |..| ..|++++|
T Consensus 92 r~vnid~~hVGwYqs~-~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLT-p~am---~~~kekdw 166 (339)
T KOG1560|consen 92 RYVNIDHLHVGWYQSA-YVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLT-PEAM---AAHKEKDW 166 (339)
T ss_pred hhcCccceeeeeeeee-hhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcC-HHHH---HHHhcCCC
Confidence 26799999999998 8999999888999999999999999999999999887 4999999 5666 67999999
Q ss_pred cCCC
Q 010576 475 HPHD 478 (507)
Q Consensus 475 hph~ 478 (507)
.|+.
T Consensus 167 tpea 170 (339)
T KOG1560|consen 167 TPEA 170 (339)
T ss_pred CHHH
Confidence 9873
No 10
>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=99.84 E-value=1.3e-20 Score=189.62 Aligned_cols=135 Identities=21% Similarity=0.318 Sum_probs=108.1
Q ss_pred EEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEE-ecCCCCCCCC---cCCH----HHHHHHhhhC--C
Q 010576 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI-IPKQESTSDS---ATNE----EEIFEVQDKR--S 403 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~---~~~e----eei~~~~~~~--~ 403 (507)
.|.|++.++++|++||..+. +.|+||+|+|...++++.||+|| +|... +.+. .... .+|++...+. +
T Consensus 2 ~V~I~~~vllkIv~H~~~~~--p~~v~G~LLG~~~~~~leVtn~Fp~P~~~-~~~~~~~~~~~~~yq~~m~~~~r~v~~~ 78 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEEL--PELVQGQLLGLDVGGTLEVTNCFPFPKSE-EDDSDRADEDIADYQLEMMRLLREVNVD 78 (266)
T ss_pred EEEEeHHHHHHHHHHHhcCC--CcEEEEEEeeeEcCCEEEEEeccCCCCCC-CCCcchhhhhHHHHHHHHHHHHHHhCCC
Confidence 69999999999999999966 99999999999999999999999 55433 2222 1222 2344444444 5
Q ss_pred CcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCC---ceeEEEecCCCCchhhhccccCCCcC
Q 010576 404 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR---KHGIFRLTSPGGMSVIRQCQQRGFHP 476 (507)
Q Consensus 404 l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~---~~gaFrLt~p~gm~~i~~c~~~gFhp 476 (507)
..+|||||||| .++|.|..++++++.||...+++|+||+||..+.. .++|||++ +.||.. ++++.|.+
T Consensus 79 e~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~-~~~~~~---~~~~~~~~ 149 (266)
T cd08065 79 HNHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLS-EKFMEL---YKEGKFST 149 (266)
T ss_pred CcEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEc-HHHHHH---hhcCCcCH
Confidence 59999999999 99999999999999999999999999999985322 47999999 468844 56666765
No 11
>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=99.84 E-value=7.9e-21 Score=188.44 Aligned_cols=133 Identities=22% Similarity=0.337 Sum_probs=115.6
Q ss_pred eEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeC---CEEEEEEEEecCCCCCCCC-cCCHHHHHHHhhhCCCcceE
Q 010576 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDS-ATNEEEIFEVQDKRSLFPLG 408 (507)
Q Consensus 333 ~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~---~~l~It~~~iP~q~~t~d~-~~~eeei~~~~~~~~l~~VG 408 (507)
..+.||.+++.+|+..|..+| |+||+|.|+... +..+|+++++|+|.++.++ .+.. ++.+++...||+.||
T Consensus 36 ~t~vlPknllkkFi~iaD~rt----Q~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~-~~~~~~~l~~Le~LG 110 (252)
T cd08056 36 YTYILPKNLLKKFISISDLRT----QIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQ-QLPQHEYLEDLEPLG 110 (252)
T ss_pred CEEEeCHHHHHHHHHHhhhcc----eEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCc-cCccchhhCCCEeeE
Confidence 479999999999999999865 999999999876 7889999999999999998 3322 257788889999999
Q ss_pred EEcCCCCCCCCCCHHHHHhhhhhhccCC-----CeEEEEEcCCCCCCceeEEEecCCCCchhhhcccc
Q 010576 409 WIHTHPTQSCFMSSIDVHTHYSYQIMLP-----ESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQ 471 (507)
Q Consensus 409 WyHSHPt~t~fpSs~DL~tq~~YQ~m~p-----e~IaIV~dP~~~~~~~gaFrLt~p~gm~~i~~c~~ 471 (507)
||||||+.++|||+.|++||+.||.|.| ++|+|+|++....-+++||+|| +.|++-..+=+.
T Consensus 111 WIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~SftpGs~sl~ay~LT-~~G~~wg~~n~d 177 (252)
T cd08056 111 WIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFTPGSCSLTAYKLT-PEGYEWGKQNKD 177 (252)
T ss_pred EEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCCCCceEEEEEecC-HHHHHHHHhCcc
Confidence 9999999999999999999999999999 7999999998544468999999 479876555443
No 12
>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=99.83 E-value=2e-20 Score=163.23 Aligned_cols=103 Identities=29% Similarity=0.415 Sum_probs=86.2
Q ss_pred HHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCCcCCHH---HHHHHhhhCCCcceEEEcCCCCCCCC
Q 010576 343 DNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSATNEE---EIFEVQDKRSLFPLGWIHTHPTQSCF 419 (507)
Q Consensus 343 ~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~~~~ee---ei~~~~~~~~l~~VGWyHSHPt~t~f 419 (507)
.+|++||+.++ +.|+||+|+|+..++.+.|+++|..++..+... .++. .+..++...|+.+||||||||..++|
T Consensus 2 k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~ 78 (116)
T cd07767 2 KMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKD-DNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCF 78 (116)
T ss_pred HhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCc-cHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCc
Confidence 57999999976 899999999999999999999996555433222 2222 22345678999999999999999999
Q ss_pred CCHHHHHhhhhhhccCCCeEEEEEcCCCC
Q 010576 420 MSSIDVHTHYSYQIMLPESVAIVMAPQDA 448 (507)
Q Consensus 420 pSs~DL~tq~~YQ~m~pe~IaIV~dP~~~ 448 (507)
+|..|+.+|..||.+.+++|+||||+...
T Consensus 79 ~s~~dv~~~~~~q~~~~~~v~li~~~~~~ 107 (116)
T cd07767 79 LSPNDLATHELFQRYFPEKVMIIVDVKPK 107 (116)
T ss_pred cCHHHHHHHHHHHHhCCCCEEEEEECCCc
Confidence 99999999999999999999999999875
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=99.81 E-value=4.4e-19 Score=158.33 Aligned_cols=123 Identities=29% Similarity=0.436 Sum_probs=99.5
Q ss_pred EEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC--cC--CHH-HHHH--HhhhCCCcce
Q 010576 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS--AT--NEE-EIFE--VQDKRSLFPL 407 (507)
Q Consensus 335 V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~--~~--~ee-ei~~--~~~~~~l~~V 407 (507)
|.|...++.+|++||.++. +.|+||+|+|+..++.+.|+++|..+....+++ .. +.. ++.+ .+...++.+|
T Consensus 2 v~i~~~v~~~i~~h~~~~~--p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 79 (135)
T smart00232 2 VKVHPLVPLNILKHAIRDG--PEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIV 79 (135)
T ss_pred EEEcHHHHHHHHHHHhcCC--CcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEE
Confidence 7899999999999999965 999999999999888999999994434332222 12 221 1222 1347899999
Q ss_pred EEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCC---ceeEEEecC
Q 010576 408 GWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR---KHGIFRLTS 459 (507)
Q Consensus 408 GWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~---~~gaFrLt~ 459 (507)
|||||||..+++||..|+.+|..||.+++.++.++++|..+.. ..++|++++
T Consensus 80 Gwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 80 GWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 9999999999999999999999999999999999999988642 358999874
No 14
>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=99.80 E-value=7.4e-20 Score=160.70 Aligned_cols=104 Identities=26% Similarity=0.447 Sum_probs=80.9
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCC-EEEEEEEEecCCCCCCCC--cCCHH---HHHHHhh--hCC
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KFYITALIIPKQESTSDS--ATNEE---EIFEVQD--KRS 403 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~-~l~It~~~iP~q~~t~d~--~~~ee---ei~~~~~--~~~ 403 (507)
+++|.|.+.++++|++||.... +.|+||+|+|...++ .+.|+++|..+...+.+. ..+.+ ++++... ..+
T Consensus 3 ~~~V~i~p~vll~i~~h~~r~~--~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (114)
T PF01398_consen 3 VQTVQIHPLVLLKIIDHATRSS--PNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPN 80 (114)
T ss_dssp CEEEEEEHHHHHHHHHHHHHHH--CTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTT
T ss_pred cEEEEECHHHHHHHHHHHhcCC--CCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccccc
Confidence 6889999999999999999865 669999999999999 999999995444433333 22221 3444432 356
Q ss_pred CcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCC
Q 010576 404 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPE 437 (507)
Q Consensus 404 l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe 437 (507)
+.+||||||||.++||||..|+++|+.||.|.|.
T Consensus 81 ~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 81 LEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp SEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred ceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 9999999999999999999999999999998873
No 15
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=5.1e-18 Score=171.86 Aligned_cols=128 Identities=22% Similarity=0.406 Sum_probs=101.8
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcc-eEEEe-cc---eee-CCEEEEEEEEecCCCCCCCC--c--CCH---HHHHH-
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLE-TCGIL-AG---SLK-NRKFYITALIIPKQESTSDS--A--TNE---EEIFE- 397 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~E-vcGlL-~G---~~~-~~~l~It~~~iP~q~~t~d~--~--~~e---eei~~- 397 (507)
-++|+|...+++++++|++... +.| ++|++ +| .+. ..++.|.++|...+.++.-+ . .|+ .++++
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 KETVYISSLALLKMLRHDRAGS--PEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQMMDL 107 (316)
T ss_pred cceeeeehhhhhhcccccccCC--chhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHHHHH
Confidence 4789999999999999999955 999 89999 89 333 36778888887777776655 1 222 12222
Q ss_pred -HhhhCCCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCc---eeEEEecCCC
Q 010576 398 -VQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRK---HGIFRLTSPG 461 (507)
Q Consensus 398 -~~~~~~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~---~gaFrLt~p~ 461 (507)
.++++.+++||||||||.|+||||++|+.||.+||.+.+.++|.+++|..+..+ .++|++-++.
T Consensus 108 l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~~ 175 (316)
T KOG1555|consen 108 LKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINPQ 175 (316)
T ss_pred HHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCcc
Confidence 356788999999999999999999999999999999988888888888765432 4889888753
No 16
>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=99.70 E-value=1.4e-16 Score=143.25 Aligned_cols=113 Identities=17% Similarity=0.286 Sum_probs=88.6
Q ss_pred HHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCC-CCC-CC-cCCHHHHHHH---hhhCCCcceEEEcCC
Q 010576 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQE-STS-DS-ATNEEEIFEV---QDKRSLFPLGWIHTH 413 (507)
Q Consensus 340 ~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~-~t~-d~-~~~eeei~~~---~~~~~l~~VGWyHSH 413 (507)
.++.+|++||+.+. |.|+||+|+|........|+.++..++. ..+ +. .+|+++..+. ....++.+|||||||
T Consensus 2 ~~~~~il~ha~~~~--P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g~~~vG~~HSH 79 (128)
T cd08070 2 ELLEAILAHAEAEY--PEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVVGIYHSH 79 (128)
T ss_pred HHHHHHHHHHHhCC--CCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCCCeEEEEEeCC
Confidence 57889999999966 9999999999998776677777633333 323 23 6788765544 457899999999999
Q ss_pred CCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEEecC
Q 010576 414 PTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 459 (507)
Q Consensus 414 Pt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFrLt~ 459 (507)
|+.+++||..|+.++. .+..+.||++...+...+++|++.+
T Consensus 80 P~~~~~PS~~D~~~~~-----~~~~~~lIv~~~~~~~~~~~~~~~~ 120 (128)
T cd08070 80 PDGPARPSETDLRLAW-----PPGVSYLIVSLAGGAPELRAWRLEG 120 (128)
T ss_pred CCCCCCCCHHHHHhcc-----CCCCeEEEEECCCCCcEEEEEEEcC
Confidence 9999999999998754 3467788888776545689999985
No 17
>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=99.52 E-value=1.2e-13 Score=123.04 Aligned_cols=107 Identities=24% Similarity=0.243 Sum_probs=80.9
Q ss_pred eCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEe-cCCCCCCCC-cCCHHHHHHHhhhCCCcceEEEcCCC
Q 010576 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALII-PKQESTSDS-ATNEEEIFEVQDKRSLFPLGWIHTHP 414 (507)
Q Consensus 337 I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~i-P~q~~t~d~-~~~eeei~~~~~~~~l~~VGWyHSHP 414 (507)
|+.+++..|++||++.. |.|+||+|+|+.. .|++++. ++....+.. .+.. .+...|+.+||.|||||
T Consensus 1 i~~~~~~~i~~ha~~~~--P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~~~f~~-----~~~~~g~~ivgi~HSHP 69 (117)
T cd08072 1 ISRDLLDSILEAAKSSH--PNEFAALLRGKDG----VITELLILPGTESGEVSAVFPL-----LMLPLDMSIVGSVHSHP 69 (117)
T ss_pred CCHHHHHHHHHHHhhcC--CceEEEEEEeecc----EEEEEEECCCCCCCCcceeech-----HHhcCCCeEEEEEEcCC
Confidence 57889999999999966 9999999999764 6888774 433322111 1112 25577999999999999
Q ss_pred CCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEEecC
Q 010576 415 TQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 459 (507)
Q Consensus 415 t~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFrLt~ 459 (507)
+.++.||..|+... ..|+.+.||+++-.....+++|++.+
T Consensus 70 ~~~~~PS~~D~~~~-----~~~~~~~lIvs~~~~~~~~~a~~~~g 109 (117)
T cd08072 70 SGSPRPSDADLSFF-----SKTGLVHIIVGYPYDEDDWRAYDSDG 109 (117)
T ss_pred CCCCCCCHHHHHhh-----hcCCCEEEEEECcCCCCCEEEEecCC
Confidence 99999999998632 35888899998544334689998774
No 18
>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=99.52 E-value=2.1e-13 Score=126.97 Aligned_cols=125 Identities=13% Similarity=0.180 Sum_probs=90.8
Q ss_pred EEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHH---HHHHH--hhhCCCcceE
Q 010576 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEE---EIFEV--QDKRSLFPLG 408 (507)
Q Consensus 335 V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~ee---ei~~~--~~~~~l~~VG 408 (507)
|.|.+.++++|++|+......+.+++|+|+|...++.+.|+++|..+...+.+. ..+.+ ++++. ....++.+||
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 578899999999999875434788999999999999999999993333433333 33332 23332 2256899999
Q ss_pred EEcCCCCCCCCCCHHHHHhhhhhhcc-CCCeEEEEEcCCCC----CCceeEEEecC
Q 010576 409 WIHTHPTQSCFMSSIDVHTHYSYQIM-LPESVAIVMAPQDA----TRKHGIFRLTS 459 (507)
Q Consensus 409 WyHSHPt~t~fpSs~DL~tq~~YQ~m-~pe~IaIV~dP~~~----~~~~gaFrLt~ 459 (507)
|||||+..+++++..|...|..|... .+..|+|++||... .-.+++|++++
T Consensus 81 WY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~ 136 (157)
T cd08057 81 WYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQ 136 (157)
T ss_pred EEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEec
Confidence 99999988766777775444444433 67789999999751 22479999994
No 19
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.46 E-value=5.2e-13 Score=121.12 Aligned_cols=111 Identities=20% Similarity=0.329 Sum_probs=75.1
Q ss_pred EEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEE-ecCCCC-CCCC-cCCHHH--HHHHhhhCCCcceEE
Q 010576 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI-IPKQES-TSDS-ATNEEE--IFEVQDKRSLFPLGW 409 (507)
Q Consensus 335 V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~-t~d~-~~~eee--i~~~~~~~~l~~VGW 409 (507)
+.|+.+++..||.||..++ +.|+||+|+|...+ ...+ ++.-.. ..+. ..+++- .+..+...|+.+|||
T Consensus 2 ~~i~~~~l~~il~~a~~~~--p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~g~~vvg~ 74 (134)
T COG1310 2 LVIPKEVLGAILEHARREH--PREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEYSLFYLAAEDAGEVVVGW 74 (134)
T ss_pred ceecHHHHHHHHHHHHhcC--ChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHHHHHHHHHhhCCCEEEEE
Confidence 5789999999999999976 89999999999875 2222 111111 1122 233322 233456778999999
Q ss_pred EcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEEecC
Q 010576 410 IHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 459 (507)
Q Consensus 410 yHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFrLt~ 459 (507)
|||||+..|+||..|+. +|.+.+-.+.||+.+... ...|+..+
T Consensus 75 yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~~~---~~~~~~~~ 117 (134)
T COG1310 75 YHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPGR---VHKGRAVD 117 (134)
T ss_pred EcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCCCc---eeEEeeec
Confidence 99999999999999998 444455545666665443 34444443
No 20
>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=99.36 E-value=7.1e-12 Score=126.32 Aligned_cols=125 Identities=15% Similarity=0.249 Sum_probs=93.5
Q ss_pred EEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEE-ecCCCCCCCC-cCCHH---HHHHHh--hhCCCcce
Q 010576 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI-IPKQESTSDS-ATNEE---EIFEVQ--DKRSLFPL 407 (507)
Q Consensus 335 V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~-~~~ee---ei~~~~--~~~~l~~V 407 (507)
|.|.+.++++|++|+......+..++|.|+|...++.+.||++| +|..+ +.+. ..|.+ ++++.. ...+..+|
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~-~~~~~~~d~~y~~~m~~~~kkv~~~~~vV 79 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNE-SEDQVAVDMEYHRTMYELHQKVNPKEVIV 79 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeC-CCCeEEEcHHHHHHHHHHHHHhCCCCcEE
Confidence 57889999999999877444567899999999999999999999 55433 3333 44432 344432 36799999
Q ss_pred EEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCC--ceeEEEecCCCCc
Q 010576 408 GWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR--KHGIFRLTSPGGM 463 (507)
Q Consensus 408 GWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~--~~gaFrLt~p~gm 463 (507)
|||||+|..+ .+...+|.|+.+|...+..|.|++||..+.. .++||++++ .|+
T Consensus 80 GWY~tg~~~~--~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~-~~~ 134 (265)
T cd08064 80 GWYATGSEIT--EHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSP-LGV 134 (265)
T ss_pred eeeeCCCCCC--ccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEe-ccc
Confidence 9999998433 3466788888888765688999999986532 479999984 464
No 21
>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=99.33 E-value=1.5e-11 Score=125.08 Aligned_cols=120 Identities=13% Similarity=0.241 Sum_probs=90.7
Q ss_pred EEEeCHHHHHHHHHHHhhcC-CCCcceEEEecceeeCCEEEEEEEE-ecCCCCCCCC----cCCHH---HHHHHh--hhC
Q 010576 334 QLHISTTMMDNFMKLAKSNT-DKNLETCGILAGSLKNRKFYITALI-IPKQESTSDS----ATNEE---EIFEVQ--DKR 402 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt-~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~----~~~ee---ei~~~~--~~~ 402 (507)
.|.|.+.++++|++|+.... +.+.+++|.|+|...++.+.|+++| +|..+ +.+. ..|.+ ++++.. ...
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~-~~~~~~~~~~d~~y~~~m~~~~kkv~~ 80 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEE-DEKDPSVWFLDHNYLENMYGMFKKVNA 80 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccC-CCCCcchhhhhHHHHHHHHHHHHHhCC
Confidence 58999999999999987633 2267899999999999999999999 55533 2222 23332 233332 367
Q ss_pred CCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCC--ceeEEEec
Q 010576 403 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR--KHGIFRLT 458 (507)
Q Consensus 403 ~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~--~~gaFrLt 458 (507)
+..+||||||||. ++..|+..|..|+...+..|.|++||..... .+++|.-.
T Consensus 81 ~e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~ 134 (280)
T cd08062 81 KEKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAV 134 (280)
T ss_pred CCCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEe
Confidence 8999999999987 4667888888899888889999999986422 36888766
No 22
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.33 E-value=5.7e-12 Score=108.41 Aligned_cols=94 Identities=21% Similarity=0.390 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCCcCCHHHHHH-HhhhCCCcceEEEcCCCCCC
Q 010576 339 TTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSATNEEEIFE-VQDKRSLFPLGWIHTHPTQS 417 (507)
Q Consensus 339 ~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~~~~eeei~~-~~~~~~l~~VGWyHSHPt~t 417 (507)
..++..|+.||..+. +.|+||+|+|......+.|+..+.+ +. .+.-.... .+...++.+||+|||||+..
T Consensus 2 ~~~~~~i~~~~~~~~--p~E~~G~L~g~~~~~~~~~~~~~~~------~p-~~~~~~~~~~~~~~~~~~vg~~HSHP~~~ 72 (104)
T PF14464_consen 2 EEVLEQIIAHARAAY--PNEACGLLLGRRDDQRFIVVPNVNP------DP-RDSFRRERFEARERGLEIVGIWHSHPSGP 72 (104)
T ss_dssp -HHHHHHHHHHHHHT--TS-EEEEEEEEEECCEEEEEEEEE--------H-HCHHHHHH-HHHHHT-EEEEEEEEESSSS
T ss_pred HHHHHHHHHHHhhCC--CCeEEEEEEEEecCCEEEEEeCCCC------Cc-HHHHHHHhhhhhcccceeeEEEEcCCCCC
Confidence 468899999999976 9999999999997777777776531 00 11112333 56788999999999999999
Q ss_pred CCCCHHHHHhhhhhhccCCCeEEEEEcC
Q 010576 418 CFMSSIDVHTHYSYQIMLPESVAIVMAP 445 (507)
Q Consensus 418 ~fpSs~DL~tq~~YQ~m~pe~IaIV~dP 445 (507)
++||.+|+.+..... ..++||+..
T Consensus 73 a~pS~~D~~~~~~~~----~~~~iI~~~ 96 (104)
T PF14464_consen 73 AFPSSTDIRSMRDLA----PPSYIIVGN 96 (104)
T ss_dssp SS--HHHHHTHCCS-----SCEEEEEEE
T ss_pred CCCCHHHHHhhhccC----CeEEEEEeC
Confidence 999999998654221 677788876
No 23
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.29 E-value=2.7e-11 Score=106.64 Aligned_cols=99 Identities=19% Similarity=0.262 Sum_probs=71.8
Q ss_pred HHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCC--CCC-CC-cCCHHHHHHHhhhCCCcceEEEcCCCCC
Q 010576 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQE--STS-DS-ATNEEEIFEVQDKRSLFPLGWIHTHPTQ 416 (507)
Q Consensus 341 ~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~--~t~-d~-~~~eeei~~~~~~~~l~~VGWyHSHPt~ 416 (507)
++..|+.||+... |.|.||+|+|+.. ++.++ |..+ ..+ +. .++++++++.+.. + .+||.|||||+.
T Consensus 2 i~~~i~~ha~~~~--P~E~CGll~g~~~-----~~~~~-p~~N~~~~p~~~F~idp~e~~~a~~~-~-~ivgi~HSHP~~ 71 (108)
T cd08073 2 LEDAILAHAKAEY--PREACGLVVRKGR-----KLRYI-PCRNIAADPEEHFEISPEDYAAAEDE-G-EIVAVVHSHPDG 71 (108)
T ss_pred HHHHHHHHHhHCC--CCcceEEEEecCC-----ceEEE-ECccCCCCccceEEeCHHHHHHHhcC-C-CEEEEEEcCCCC
Confidence 5778999999966 9999999999762 33333 3332 222 22 7899888887643 2 899999999999
Q ss_pred CCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEE
Q 010576 417 SCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFR 456 (507)
Q Consensus 417 t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFr 456 (507)
.+.||..|+.. ...++...||++-... .+.+|+
T Consensus 72 ~a~PS~~D~~~-----~~~~~~~~iIvs~~~~--~~~~~~ 104 (108)
T cd08073 72 SPAPSEADRAQ-----QEATGLPWIIVSWPEG--DLRVFR 104 (108)
T ss_pred CCCCCHHHHHH-----hhcCCCcEEEEEcCCC--CEEEEe
Confidence 99999999952 2357777888876432 256665
No 24
>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=98.95 E-value=4.9e-09 Score=100.45 Aligned_cols=107 Identities=11% Similarity=0.053 Sum_probs=74.0
Q ss_pred eCHHHHHHHHHHHhhcCCCCcceEEEecceee-CCEEEEEEEEecCCCCCCCCcCCHHH------HHHHhhhCCCcceEE
Q 010576 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKFYITALIIPKQESTSDSATNEEE------IFEVQDKRSLFPLGW 409 (507)
Q Consensus 337 I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~-~~~l~It~~~iP~q~~t~d~~~~eee------i~~~~~~~~l~~VGW 409 (507)
|+..++.+|+.||.... +.|+||+|+|+.. ++.+.|++++..... -..+++.. +-.++...|+.+||+
T Consensus 1 is~~ay~ki~~HA~k~p--~~evcGlLlG~~~~~~~~~V~d~vPl~h~---~~~l~P~~Eval~~ve~~~~~~gl~IvG~ 75 (182)
T cd08060 1 LSTLAYVKMLLHAAKYP--HCAVNGLLLGKKSSGGSVEITDAVPLFHS---CLALAPMLEVALALVDAYCKSSGLVIVGY 75 (182)
T ss_pred CCHHHHHHHHHHHHHcC--CchheEEEEeeecCCCCEEEEEEEEcCCC---ccccCHHHHHHHHHHHHHHHHCCCEEEEE
Confidence 56789999999999954 7899999999987 677899998733221 12445432 234567899999999
Q ss_pred EcCCCCCC-CCCCHHHHHhhhhhhccCCCeEEEEEcCCCC
Q 010576 410 IHTHPTQS-CFMSSIDVHTHYSYQIMLPESVAIVMAPQDA 448 (507)
Q Consensus 410 yHSHPt~t-~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~ 448 (507)
|||||... .-|+.+=..---.-+...+.++.+++|=.+-
T Consensus 76 Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l 115 (182)
T cd08060 76 YQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKL 115 (182)
T ss_pred EecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccc
Confidence 99999764 2344332211112334467888888877654
No 25
>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=98.91 E-value=1.2e-08 Score=103.53 Aligned_cols=131 Identities=19% Similarity=0.317 Sum_probs=100.3
Q ss_pred CeEEEeCHHH-HHHHHHHHhhcCCCCcceEEEecceeeCC-------EEEEEEEEecCCCCCCCC-cC----CHHHHHHH
Q 010576 332 PLQLHISTTM-MDNFMKLAKSNTDKNLETCGILAGSLKNR-------KFYITALIIPKQESTSDS-AT----NEEEIFEV 398 (507)
Q Consensus 332 ~~~V~I~~~~-l~k~L~hA~~nt~~~~EvcGlL~G~~~~~-------~l~It~~~iP~q~~t~d~-~~----~eeei~~~ 398 (507)
+..|.+.... +..|+..+..++ ....||+|.|+.... ...|..++-|+|.++.+. ++ +++.+-+.
T Consensus 10 Vd~vef~~~~~~~~f~~~~w~~~--~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~i 87 (274)
T cd08061 10 VDHVEFDNPSIVEFFLYVFWRKT--GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAI 87 (274)
T ss_pred cCEEEEecHHHHHHHHHHHHHhh--cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHH
Confidence 3456666544 445554366655 678899999999864 577777779999999887 32 22335556
Q ss_pred hhhCCCcceEEEcCCCCC----CCCCCHHHHHhhhhhhc------cCCCeEEEEEcCCCC-CCceeEEEecCCCCchh
Q 010576 399 QDKRSLFPLGWIHTHPTQ----SCFMSSIDVHTHYSYQI------MLPESVAIVMAPQDA-TRKHGIFRLTSPGGMSV 465 (507)
Q Consensus 399 ~~~~~l~~VGWyHSHPt~----t~fpSs~DL~tq~~YQ~------m~pe~IaIV~dP~~~-~~~~gaFrLt~p~gm~~ 465 (507)
+...||..||||+||+.. ++|||+.++.+...||. .-..+|.+|++|..+ .....+|++++. +|..
T Consensus 88 A~~lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~g~i~~~ayQvSdq-~~~l 164 (274)
T cd08061 88 AAALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKDGQIHFEAYQVSDQ-AMAL 164 (274)
T ss_pred HHHcCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCCCceeeeeeeecHH-HHHH
Confidence 788999999999999988 89999999999999996 457899999999744 224799999974 7754
No 26
>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=98.84 E-value=1.6e-08 Score=87.25 Aligned_cols=78 Identities=26% Similarity=0.390 Sum_probs=58.4
Q ss_pred HHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEE-ecCCCCCCCCcCCHHHHHHHhhhCCCcceEEEcCCCCCCC
Q 010576 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI-IPKQESTSDSATNEEEIFEVQDKRSLFPLGWIHTHPTQSC 418 (507)
Q Consensus 340 ~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~~~~eeei~~~~~~~~l~~VGWyHSHPt~t~ 418 (507)
+++..|+.|+.... +.|.||+|+|...+ .|+++. ++.. + ...++.+ +..+...+...||.|||||+..+
T Consensus 1 ~~~~~i~~~~~~~~--p~E~~gll~~~~~~---~~~~~~~~~~~--~--~~~~~~~-~~~a~~~~~~~v~i~HsHP~g~~ 70 (101)
T cd08059 1 DLLKTILVHAKDAH--PDEFCGFLSGSKDN---VMDELIFLPFV--S--GSVSAVI-DLAALEIGMKVVGLVHSHPSGSC 70 (101)
T ss_pred CHHHHHHHHHHhcC--ChhhheeeecCCCC---eEEEEEeCCCc--C--CccChHH-HHHHhhCCCcEEEEEecCcCCCC
Confidence 36778899999865 99999999998643 344544 3321 1 1233333 66778889999999999999999
Q ss_pred CCCHHHHHh
Q 010576 419 FMSSIDVHT 427 (507)
Q Consensus 419 fpSs~DL~t 427 (507)
.||..|+..
T Consensus 71 ~PS~~D~~~ 79 (101)
T cd08059 71 RPSEADLSL 79 (101)
T ss_pred CCCHHHHHH
Confidence 999999963
No 27
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=98.82 E-value=2.7e-08 Score=101.67 Aligned_cols=137 Identities=14% Similarity=0.176 Sum_probs=92.4
Q ss_pred EEEeCHHHHHHHHHHHhhcCCC----CcceEEEecceeeCCEEEEEEEE-ecCCCCCCCC-cCCHH---HHHHHh--hhC
Q 010576 334 QLHISTTMMDNFMKLAKSNTDK----NLETCGILAGSLKNRKFYITALI-IPKQESTSDS-ATNEE---EIFEVQ--DKR 402 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt~~----~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~-~~~ee---ei~~~~--~~~ 402 (507)
.|.|-+.++++|++|+...... +.-++|.|+|...++.+.|+++| +|......+. ..|.+ ++++.. ...
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV~~ 81 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQVFK 81 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHhcc
Confidence 5889999999999999874321 45689999999999999999999 6654332122 44432 233332 357
Q ss_pred CCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCC--CC--ceeEEEecCCCCchhhhccccCCCcCC
Q 010576 403 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA--TR--KHGIFRLTSPGGMSVIRQCQQRGFHPH 477 (507)
Q Consensus 403 ~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~--~~--~~gaFrLt~p~gm~~i~~c~~~gFhph 477 (507)
++.+||||+|.+. +.+.+...||.++ ....+..|.+++||..+ .. .+++|+-.. .|... ....-|.|.
T Consensus 82 ~~~vVGWY~tg~~-~~~~~~~~Ih~~~--~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~-~~~~~---~~~~~F~~i 153 (288)
T cd08063 82 DLDFVGWYTTGPG-GPTESDLPIHKQI--LEINESPVLLLLDPEANASGKDLPVTIYESVL-ELVDG---EATLRFREL 153 (288)
T ss_pred CCceEEEEecCCC-CCCHHHHHHHHHH--HhhCCCcEEEEEccccccCCCCCceeEEEEEE-eccCC---ccccEEEee
Confidence 8999999999876 5555555566554 45556679999999773 21 368998763 45432 122237665
No 28
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=98.78 E-value=8.2e-08 Score=98.81 Aligned_cols=123 Identities=15% Similarity=0.245 Sum_probs=87.4
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCC-CcceEEEecceeeCCEEEEEEEE-ecCCCCCCCC---cCCH---HHHHHHh--hh
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDK-NLETCGILAGSLKNRKFYITALI-IPKQESTSDS---ATNE---EEIFEVQ--DK 401 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~-~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~---~~~e---eei~~~~--~~ 401 (507)
+..|.|.+.++++|++|+...... +.-++|.|+|...++.+.||++| +|..+...+. ..|. +++++.. ..
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 577999999999999999875422 23489999999999999999999 6654332221 2343 2344432 36
Q ss_pred CCCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCC--CceeEEEec
Q 010576 402 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIFRLT 458 (507)
Q Consensus 402 ~~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~--~~~gaFrLt 458 (507)
.+..+||||+|.|.. +..|+.-|..|....+..|-+++|+.... -.+++|...
T Consensus 85 ~~~~vVGWY~tg~~i----~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~ 139 (303)
T PLN03246 85 AKEHVVGWYSTGPKL----RENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAV 139 (303)
T ss_pred CCCcEEeeecCCCCC----CcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEE
Confidence 788999999998764 34556666667777777888899876432 246888765
No 29
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=98.76 E-value=3.8e-08 Score=94.70 Aligned_cols=110 Identities=17% Similarity=0.203 Sum_probs=74.2
Q ss_pred eEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCC--CCCCCC-cCCHHHHHHHhhhCCCcceEE
Q 010576 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQ--ESTSDS-ATNEEEIFEVQDKRSLFPLGW 409 (507)
Q Consensus 333 ~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q--~~t~d~-~~~eeei~~~~~~~~l~~VGW 409 (507)
+.=.||..++.+|+.||+... |+|+||++.|.-.+..+ .++ |.+ ..+++. .+++. +..+|+..|+-
T Consensus 71 ~~g~Ip~~l~~~ii~hAr~~~--P~EacG~Iag~~~~~~~---r~~-p~~N~~~Sp~~~~~d~~-----~~~~ge~lV~i 139 (192)
T TIGR03735 71 LCGPIPASLLEEFAEAARAAL--PNEVAAWIVWNSETGSL---RLA-ALESIEASPGHIDYRRP-----RLDDGEHLVVD 139 (192)
T ss_pred ecCCCCHHHHHHHHHHHHhcC--CcceEEEEEEcCCCCEE---EEE-eccccccCCceEEEcch-----HHhCCCeEEEE
Confidence 444899999999999999966 99999999997443433 333 333 233333 55554 44889999999
Q ss_pred EcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCCCceeEEEec
Q 010576 410 IHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLT 458 (507)
Q Consensus 410 yHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~~~~gaFrLt 458 (507)
|||||...+|||.+|+.-=.+ .--|+.|+--.+...-.=+|||-
T Consensus 140 yHSH~~spA~PS~tD~~Dd~~-----~~k~~~ViG~~~~~~p~~~~Rl~ 183 (192)
T TIGR03735 140 LHSHGTGSAFFSETDDADDKG-----EVKISGVLGCLDQGTPQAVFRLC 183 (192)
T ss_pred EcCCCCCCCCCCcccchhhcC-----ceEEEEEEEecCCCCceEEEEEE
Confidence 999999999999999953221 11234443333321224677776
No 30
>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=98.69 E-value=1.2e-07 Score=86.29 Aligned_cols=90 Identities=20% Similarity=0.178 Sum_probs=61.1
Q ss_pred HHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC---cCC---HHH-HHHHhh-h-CCCcceEEEc
Q 010576 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS---ATN---EEE-IFEVQD-K-RSLFPLGWIH 411 (507)
Q Consensus 341 ~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~---~~~---eee-i~~~~~-~-~~l~~VGWyH 411 (507)
++..|..+.+.. ..+.|+||+|+|...+..+.|+++..|........ .-+ ..+ +-++.. . ..+..||-+|
T Consensus 2 v~~~~~~~~Q~~-~~~~EtGGiLiG~~~~~~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWH 80 (131)
T TIGR02256 2 VVAMLKSYRQWH-DLSTETGGVLIGERRGAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWH 80 (131)
T ss_pred HHHHHHHHHhCc-CCCCccceEEEEEEcCCcEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecC
Confidence 344455555543 46789999999999888899999876654322211 111 122 223332 2 3488999999
Q ss_pred CCCCCCCCCCHHHHHhhhhh
Q 010576 412 THPTQSCFMSSIDVHTHYSY 431 (507)
Q Consensus 412 SHPt~t~fpSs~DL~tq~~Y 431 (507)
|||...+-||.+|+.+....
T Consensus 81 tHP~~~p~PS~~D~~~~~~~ 100 (131)
T TIGR02256 81 THPEDQPEPSWTDRRSWRTI 100 (131)
T ss_pred cCCCCCCCCCHHHHHHHHHH
Confidence 99999999999999887644
No 31
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=3e-05 Score=76.70 Aligned_cols=113 Identities=18% Similarity=0.288 Sum_probs=80.0
Q ss_pred CeEEEeCHHHHHHHHHHHhhcC-CCCcceEEEecceeeCCEEEEEEEE-ecCCCCCCCC---cCC---HHHHHHHhh--h
Q 010576 332 PLQLHISTTMMDNFMKLAKSNT-DKNLETCGILAGSLKNRKFYITALI-IPKQESTSDS---ATN---EEEIFEVQD--K 401 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt-~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~---~~~---eeei~~~~~--~ 401 (507)
...|.|-+.+++..+.|...-. ..+--+.|+|+|.+.++++.||+.| +|-.+...+. -+| -+.||.++. +
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 5779999999999999976532 2345678999999999999999999 4544433332 122 245777664 5
Q ss_pred CCCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCC
Q 010576 402 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA 448 (507)
Q Consensus 402 ~~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~ 448 (507)
....+||||||-|.. ..|-.|++ ..+-...|..+.+|+|-+-.
T Consensus 88 akekivGWYhTGPkl--~~nDl~In--~l~k~y~pnpvLvIIdvkpk 130 (309)
T KOG1556|consen 88 AKEKVVGWYHTGPKL--RENDLDIN--ELLKRYVPNPVLVIIDVKPK 130 (309)
T ss_pred chhheeeeeccCCcc--ccchhhHH--HHHhhcCCCceEEEEecccc
Confidence 677899999998754 34555554 44556678888888887644
No 32
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=97.95 E-value=4.6e-05 Score=78.69 Aligned_cols=105 Identities=25% Similarity=0.375 Sum_probs=82.0
Q ss_pred EEEecceeeCC-------EEEEEEEEecCCCCCCCC-cC----CHHHHHHHhhhCCCcceEEEcCCCC------------
Q 010576 360 CGILAGSLKNR-------KFYITALIIPKQESTSDS-AT----NEEEIFEVQDKRSLFPLGWIHTHPT------------ 415 (507)
Q Consensus 360 cGlL~G~~~~~-------~l~It~~~iP~q~~t~d~-~~----~eeei~~~~~~~~l~~VGWyHSHPt------------ 415 (507)
+|+|.|..... ...|..++-|+|+++.|. ++ +++.+=+.+..-||..||||=||+.
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 79999999852 467777779999999888 32 2333445677889999999999998
Q ss_pred ---CCCCCCHHHHHhhhhhhccCC-------------CeEEEEEcCCCCC-CceeEEEecCCCCchh
Q 010576 416 ---QSCFMSSIDVHTHYSYQIMLP-------------ESVAIVMAPQDAT-RKHGIFRLTSPGGMSV 465 (507)
Q Consensus 416 ---~t~fpSs~DL~tq~~YQ~m~p-------------e~IaIV~dP~~~~-~~~gaFrLt~p~gm~~ 465 (507)
.+.|||+..+-+-..+|...| .+|.+|+++..+. ...-+|.+++ .+|..
T Consensus 82 r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~~g~i~~~ayQvS~-q~~~L 147 (306)
T PF05021_consen 82 RHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDEEGEIHFEAYQVSN-QCVAL 147 (306)
T ss_pred cccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCCCCceeeEEeeehH-HHHHH
Confidence 889999999999999998653 5899999996441 1369999997 46644
No 33
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=97.79 E-value=0.00011 Score=73.43 Aligned_cols=127 Identities=16% Similarity=0.273 Sum_probs=87.5
Q ss_pred CeEEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEE-ecCCCCCCCC-cCCHH---HHHHHh--hhCCC
Q 010576 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALI-IPKQESTSDS-ATNEE---EIFEVQ--DKRSL 404 (507)
Q Consensus 332 ~~~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~-iP~q~~t~d~-~~~ee---ei~~~~--~~~~l 404 (507)
-..|.|-+.++..++.+...-..+..-++|-|+|...++.+.||+|| +|-.++. |. +.+.+ +|++.- .+.+.
T Consensus 20 ~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEss-dqvevdm~y~~~M~~l~~k~npnE 98 (288)
T KOG2975|consen 20 NLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESS-DQVEVDMEYAKNMYELHKKVNPNE 98 (288)
T ss_pred CceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCcccc-ccceeeHHHHHHHHHHhcccCCCc
Confidence 46788888888888877665444455579999999999999999999 7766543 44 44432 233332 35688
Q ss_pred cceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCCCCC--CceeEEEecCCCCch
Q 010576 405 FPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIFRLTSPGGMS 464 (507)
Q Consensus 405 ~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~~~--~~~gaFrLt~p~gm~ 464 (507)
.+||||-|-+..+.+-|. +|. -|-.-.++.|-+-+|-..+. -++++|--+ +-|+.
T Consensus 99 ~vvGWyaTg~dvt~~ssl--ihd--yYare~~~pvhLtVDT~~~n~rm~ikaYvss-~~Gvp 155 (288)
T KOG2975|consen 99 LVVGWYATGHDVTEHSSL--IHD--YYAREAPNPVHLTVDTSLQNGRMSIKAYVSS-LMGVP 155 (288)
T ss_pred eeEEEEecCCCcccchhH--HHH--HhhccCCCCeEEEEeccccCCccceeEEEEe-ccCCC
Confidence 899999987777765433 444 45566788888888876542 146888666 34653
No 34
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.73 E-value=0.00027 Score=68.80 Aligned_cols=111 Identities=12% Similarity=0.121 Sum_probs=74.8
Q ss_pred EEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCE--EEEEEEEecCCC-CCCCCcC---CHHHHHHHhhhCCCcce
Q 010576 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRK--FYITALIIPKQE-STSDSAT---NEEEIFEVQDKRSLFPL 407 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~--l~It~~~iP~q~-~t~d~~~---~eeei~~~~~~~~l~~V 407 (507)
.|.|+..+..||+-||..-- -.-|+|+|+|.-.++. +.|++++ |-.+ .+.-+.+ .-..+-.|+...|+.+|
T Consensus 3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaV-PLfH~~~~L~PmlEvAL~qvd~~~~~~gl~Iv 79 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAV-PLFHHWLSLSPMLEVALAQVDAYAKSNGLVIV 79 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeece-eccccccCcchHHHHHHHHHHHHHhhCCCEEE
Confidence 58999999999999999843 5778999999987644 9999987 3333 2222211 12234457788999999
Q ss_pred EEEcCCCCC-CCCCCHHHHHhhhhhhccCCCeEEEEEcCCC
Q 010576 408 GWIHTHPTQ-SCFMSSIDVHTHYSYQIMLPESVAIVMAPQD 447 (507)
Q Consensus 408 GWyHSHPt~-t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~~ 447 (507)
||||..... ..-|+.+=..-----+...+.++.|++|-.+
T Consensus 80 GyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~k 120 (196)
T PF03665_consen 80 GYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKK 120 (196)
T ss_pred EEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcc
Confidence 999986532 2335554221111122346889999988764
No 35
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=96.64 E-value=0.0021 Score=75.04 Aligned_cols=149 Identities=19% Similarity=0.252 Sum_probs=99.7
Q ss_pred EEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeC---CEEEEEEEEecCCCCCCCCcCCHHHHHHHhhhCCCcceEEE
Q 010576 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSATNEEEIFEVQDKRSLFPLGWI 410 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~---~~l~It~~~iP~q~~t~d~~~~eeei~~~~~~~~l~~VGWy 410 (507)
.-.||..++.+|+..+.. ..-+.|++.|.--. ..-.|..+...+|-++-....-+..+=....-.|+..+||+
T Consensus 2096 tyilPkNllkkFi~isD~----r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~lP~~~~l~d~e~Lgw~ 2171 (2321)
T KOG1795|consen 2096 TYILPKNLLKKFITISDL----RTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFLPIHGVLEDLEPLGWI 2171 (2321)
T ss_pred eeeccHHHHhhheeecch----hhhhheeeeccCCCCCCccceEEEEEeccccccccccccCccCCcchhccCCcccchh
Confidence 347899999999988776 45789999996543 23366666666665433221111001123446789999999
Q ss_pred cCCCCCCCCCCHHHHHhhhhhhccC-CCeEEEEEcCCCCCCceeEEEecCCCCchhhhccccCCCcCCCCCCCCCCCccc
Q 010576 411 HTHPTQSCFMSSIDVHTHYSYQIML-PESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGFHPHDPPPDGGPIYKP 489 (507)
Q Consensus 411 HSHPt~t~fpSs~DL~tq~~YQ~m~-pe~IaIV~dP~~~~~~~gaFrLt~p~gm~~i~~c~~~gFhph~~~~~~~~~y~~ 489 (507)
||-|.--.++|..|+-||.---.-. ..+|.|-|+-.-.+-+..+|.|| +.|.+-...-+..|=.|+.. .|.-|++
T Consensus 2172 hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~~tpgs~sl~ay~lt-~~G~eWg~~n~d~g~~~~gy---~pt~~e~ 2247 (2321)
T KOG1795|consen 2172 HTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCSFTPGSCSLTAYKLT-PSGYEWGEVNKDKGNNPKGY---LPTHYEK 2247 (2321)
T ss_pred hcCccccccCCHHHhhhhhhhhhcCccceEEEEeeccCCcceeeeeccC-ccccccchhcccccCCcccc---CccHHHH
Confidence 9999999999999999998543333 46888888766544457999999 47876555555555556654 3455665
Q ss_pred C
Q 010576 490 C 490 (507)
Q Consensus 490 ~ 490 (507)
|
T Consensus 2248 ~ 2248 (2321)
T KOG1795|consen 2248 V 2248 (2321)
T ss_pred H
Confidence 5
No 36
>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=96.56 E-value=0.011 Score=47.58 Aligned_cols=69 Identities=16% Similarity=0.174 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHH
Q 010576 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (507)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l 101 (507)
|+..|..++++|-.+.+.||++.|+-+|..=+.+++.-+..-+ .+..+..++.++..-+.++|.||..|
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 7889999999999999999999999999998888866655432 34567788899999999999999865
No 37
>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=96.40 E-value=0.021 Score=47.29 Aligned_cols=69 Identities=16% Similarity=0.118 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010576 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (507)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (507)
.-|..|+++|--.-..|+++.||-+|+.=+.+|+.-+..- ..+..|..++.++...+.++|+||..|+.
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 4688999999999999999999999999999998766442 13456778999999999999999998864
No 38
>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=96.36 E-value=0.018 Score=47.35 Aligned_cols=70 Identities=13% Similarity=0.122 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHH
Q 010576 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQ 102 (507)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~ 102 (507)
|+..|..++++|--....|+++.|+-+|..=+.+++.-+..-++ +..+..++.++..-+.++|.||..|+
T Consensus 2 ~~~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~~k~e~~-----~~~k~~~~~k~~eyl~RaE~LK~~l~ 71 (75)
T cd02678 2 FLQKAIELVKKAIEEDNAGNYEEALRLYQHALEYFMHALKYEKN-----PKSKESIRAKCTEYLDRAEKLKEYLA 71 (75)
T ss_pred hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 67889999999999999999999999999999999876655432 35677888999999999999999885
No 39
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=96.35 E-value=0.025 Score=46.26 Aligned_cols=73 Identities=16% Similarity=0.165 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010576 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (507)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (507)
+.|+..|.+++.+|--+.+.|+++.|+-+|..=+.+++.-+..-| .+..+..++.++..-+.++|.||..|..
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 40
>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=96.34 E-value=0.019 Score=47.84 Aligned_cols=69 Identities=19% Similarity=0.263 Sum_probs=59.3
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010576 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (507)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (507)
..|.++++.|--+-+.|+++.|+.+|..=+.+|+.-|..-|| ...|..++.++..-+.++|.||..|++
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 568999999999999999999999999999999877655432 345778889999999999999998864
No 41
>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=96.32 E-value=0.017 Score=48.08 Aligned_cols=69 Identities=16% Similarity=0.020 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHH
Q 010576 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQ 102 (507)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~ 102 (507)
|.|..+++.|--+-++|+++.|+.+|..=+.+|+..+..+ ..+...+..++.++.+-+.++|.||..|.
T Consensus 4 ~~Ai~~a~~Ave~D~~g~y~eA~~~Y~~aie~l~~~~~~~----~~n~~~k~~ir~K~~eYl~RAE~Lk~~l~ 72 (76)
T cd02681 4 RDAVQFARLAVQRDQEGRYSEAVFYYKEAAQLLIYAEMAG----TLNDSHLKTIQEKSNEYLDRAQALHQLVQ 72 (76)
T ss_pred HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHhc----CCChHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 6899999999999999999999999999999997643332 11334566778999999999999999875
No 42
>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=95.71 E-value=0.067 Score=44.33 Aligned_cols=68 Identities=16% Similarity=0.154 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHH
Q 010576 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPA 100 (507)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~ 100 (507)
|+--|..++++|--.-.+||++.|+-+|..=+++|+.-++.-+ .+..|..++.++.+-+.++|+|+..
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 6678999999999999999999999999999999987776632 2466789999999999999998764
No 43
>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=95.58 E-value=0.088 Score=42.99 Aligned_cols=70 Identities=17% Similarity=0.179 Sum_probs=59.7
Q ss_pred HHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010576 29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (507)
Q Consensus 29 ~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (507)
+..|..+++.|--+.+.||++.|+-+|..=+.+++.-+..-+ .+..+..++.++...+.++|.||..|..
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 2466788889999999999999998854
No 44
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=94.79 E-value=0.24 Score=47.54 Aligned_cols=109 Identities=12% Similarity=0.123 Sum_probs=68.7
Q ss_pred EEEeCHHHHHHHHHHHhhcCCCCcceEEEecceee--CCEEEEEEEEecCCCCCCCCcCCHHHH-----HHHhhhCCCcc
Q 010576 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK--NRKFYITALIIPKQESTSDSATNEEEI-----FEVQDKRSLFP 406 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~--~~~l~It~~~iP~q~~t~d~~~~eeei-----~~~~~~~~l~~ 406 (507)
.|.|+..+..||+-||..-- ---|-|+|+|... ++.+.||+|+...-+...-. -+-|+ -......|+.+
T Consensus 3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~~kg~~v~itdcVPLfH~~laLa--PmlEvAl~lId~~~~~~Glvi 78 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPATGKGECVEITDCVPLFHSHLALA--PMLEVALNLIDVWGAQAGLVI 78 (199)
T ss_pred ceeehhhHHHHHHHHhccCc--ccceeeEEEeccCCCCCeEEEEecchhhccccccc--cHHHHHHHHHHHHHHhcCeEE
Confidence 47899999999999998732 4456899999665 47899999983332222211 12222 12356889999
Q ss_pred eEEEcCCCCCC-CCCCHHHHHhhhhhhccCCCeEEEEEcCC
Q 010576 407 LGWIHTHPTQS-CFMSSIDVHTHYSYQIMLPESVAIVMAPQ 446 (507)
Q Consensus 407 VGWyHSHPt~t-~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~ 446 (507)
+|+||+--.+. .-+..+=..---.-+..+|.+..||.+-+
T Consensus 79 aGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~ 119 (199)
T KOG3289|consen 79 AGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNK 119 (199)
T ss_pred EEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEecc
Confidence 99999854322 22222222222234456788777777665
No 45
>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=94.42 E-value=0.17 Score=42.03 Aligned_cols=64 Identities=20% Similarity=0.123 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHH----HHHHHHHhhCHHHH
Q 010576 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLL----NALSELEELQPAVQ 102 (507)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~----~vl~~lE~LK~~l~ 102 (507)
.-|..|+++|----..||++.||=||+-=+.+|+. + + ...-+..++.++. ..+.++|+||..|.
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 2 2 3345667778885 88999999999875
No 46
>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=93.31 E-value=0.39 Score=39.95 Aligned_cols=67 Identities=13% Similarity=0.075 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHH
Q 010576 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (507)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l 101 (507)
++|..+++.|--|.++|+++.|..+|..=+.+++.-+..-||-. .+..++.++.+-++++|.||..+
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 67899999999999999999999999999999988887767654 35667888999999999999876
No 47
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=92.86 E-value=0.69 Score=50.14 Aligned_cols=128 Identities=19% Similarity=0.344 Sum_probs=91.8
Q ss_pred EEEe-CHHHHHHHHHHHhhcCCCCcceEEEecceeeC-CEE------EEEEEEecCCCCCCCC-cC--C-HHHHH-HHhh
Q 010576 334 QLHI-STTMMDNFMKLAKSNTDKNLETCGILAGSLKN-RKF------YITALIIPKQESTSDS-AT--N-EEEIF-EVQD 400 (507)
Q Consensus 334 ~V~I-~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~-~~l------~It~~~iP~q~~t~d~-~~--~-eeei~-~~~~ 400 (507)
.|.+ ...++..||.--+.. +.--.|+|.|.... +.+ .|..++-|+|.++.|. ++ + ++..+ +.+.
T Consensus 176 ~VeFd~~~~v~~Fl~~wr~s---g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~ 252 (510)
T KOG2834|consen 176 HVEFDNAELVNHFLNEWRAS---GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAE 252 (510)
T ss_pred eEeecchHHHHHHHHHHHHh---hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHH
Confidence 3444 468999999887763 47778999999975 333 6666668999999998 22 2 33223 4567
Q ss_pred hCCCcceEEEcCCC---------------CCCCCCCHHHHHhhhhhhccCCC-------------eEEEEEcCCCCC-Cc
Q 010576 401 KRSLFPLGWIHTHP---------------TQSCFMSSIDVHTHYSYQIMLPE-------------SVAIVMAPQDAT-RK 451 (507)
Q Consensus 401 ~~~l~~VGWyHSHP---------------t~t~fpSs~DL~tq~~YQ~m~pe-------------~IaIV~dP~~~~-~~ 451 (507)
+-||..||||-|-- ..+.|||+..+.+-..+|.+.|. +|-+|++-.... -+
T Consensus 253 ~lGLrRVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~s~~~~fgSkfVT~visg~~~~~V~ 332 (510)
T KOG2834|consen 253 GLGLRRVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEWSRDGHFGSKFVTLVISGDLDGEVH 332 (510)
T ss_pred hcCceeeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchheeeccccccceeEEEEEecCCCccee
Confidence 89999999997632 35679999999999999998773 566676654331 13
Q ss_pred eeEEEecCCCCchh
Q 010576 452 HGIFRLTSPGGMSV 465 (507)
Q Consensus 452 ~gaFrLt~p~gm~~ 465 (507)
+-.|..++ .+|..
T Consensus 333 f~~YQVSn-qc~al 345 (510)
T KOG2834|consen 333 FEGYQVSN-QCMAL 345 (510)
T ss_pred eeeeehhH-HHHHH
Confidence 57788886 46653
No 48
>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=92.44 E-value=1.1 Score=39.82 Aligned_cols=69 Identities=22% Similarity=0.213 Sum_probs=49.5
Q ss_pred CcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHHHHHHHhhhCCCcceEEEcCCCCCCCCCCHHHHHhh
Q 010576 356 NLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTH 428 (507)
Q Consensus 356 ~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~eeei~~~~~~~~l~~VGWyHSHPt~t~fpSs~DL~tq 428 (507)
+.|.+.+|+=.-.++.+....++ .|+-++ ..++.++|..+...+..-|+..|.||+..+.||..|++.-
T Consensus 15 ~~E~~~vl~Ld~~~~li~~~~l~----~G~~~~~~v~~R~i~~~aL~~~A~~vil~HNHPsG~~~PS~~D~~~T 84 (113)
T cd08071 15 DQEEFVVLLLDTKNRLIAVETIS----VGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELT 84 (113)
T ss_pred CceEEEEEEecCCCCEEEEEEEe----ecCCcceecCHHHHHHHHHHHhhheEEEEeeCCCCCCCCCHHHHHHH
Confidence 67887776433323333332222 234344 6788999999999999999999999999999999999654
No 49
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=91.04 E-value=0.7 Score=48.24 Aligned_cols=72 Identities=17% Similarity=0.144 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010576 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (507)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (507)
.+.-|..|+++|----..+|++.||-||+--+.-|+..|.. .....+-|..++.++-+-|.++|+||.-|++
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 67789999999999999999999999999988888776653 3223456788999999999999999997763
No 50
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=91.03 E-value=0.27 Score=58.07 Aligned_cols=121 Identities=17% Similarity=0.317 Sum_probs=74.4
Q ss_pred EEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCC---EEEEEEEEecCCCCCCCC----cCCHHHHHHHhhhCCCcc
Q 010576 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR---KFYITALIIPKQESTSDS----ATNEEEIFEVQDKRSLFP 406 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~---~l~It~~~iP~q~~t~d~----~~~eeei~~~~~~~~l~~ 406 (507)
.-.||..++.+|+..... .+-|.|++.|+-..+ .-.|......+|-+.-.. ..-+. +.-...||.+
T Consensus 2135 ~y~lP~NLl~kF~~isD~----~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~---dlp~~e~le~ 2207 (2365)
T COG5178 2135 MYRLPLNLLEKFMRISDP----HVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPH---DLPGDEDLEI 2207 (2365)
T ss_pred cccccHHHHHhhheeccc----ceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCC---CCCCccccee
Confidence 456899999999988766 568899999976532 223443333334321111 10010 1122478999
Q ss_pred eEEEcCCCCCCCCCCHHHHHhhhhhhccCCC--eEEEEEcCCCCCCceeEEEecCCCCc
Q 010576 407 LGWIHTHPTQSCFMSSIDVHTHYSYQIMLPE--SVAIVMAPQDATRKHGIFRLTSPGGM 463 (507)
Q Consensus 407 VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe--~IaIV~dP~~~~~~~gaFrLt~p~gm 463 (507)
|||+|+--.--.||+..++-||. |-...|+ +|.|-++-.-..-+..+|.+++ +|.
T Consensus 2208 lGwihtq~~el~~l~~~~v~th~-k~~~d~~~d~v~ltv~~~pgsiSl~ay~v~k-eG~ 2264 (2365)
T COG5178 2208 LGWIHTQDDELPYLEVAGVLTHR-KKIVDPEWDAVTLTVSYLPGSISLRAYVVKK-EGC 2264 (2365)
T ss_pred eEEEecCCcccchhhhhhhhhhh-hcccCccccceeeeeeeccceeeeeeeeehh-ccc
Confidence 99999987777899999999996 4444554 4444433222222358888885 564
No 51
>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=85.86 E-value=3.5 Score=37.07 Aligned_cols=82 Identities=21% Similarity=0.183 Sum_probs=45.0
Q ss_pred HHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHHHHHHHhhhCCCcceEEEcCCCCCCC
Q 010576 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEEEIFEVQDKRSLFPLGWIHTHPTQSC 418 (507)
Q Consensus 340 ~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~eeei~~~~~~~~l~~VGWyHSHPt~t~ 418 (507)
+.+..+++..-.+ ...|.+.+++=.-.+..+.+..++ .|+.+. ..++.++|+.+-..+..-|-..|-||+..+
T Consensus 6 ~~v~~~l~~~l~~--~~~E~~~~l~Ld~~~~li~~~~v~----~G~~~~~~v~~R~I~~~al~~~A~~vIl~HNHPsG~~ 79 (123)
T PF04002_consen 6 EDVADYLRPKLQG--LDQEQFRVLYLDSKNRLIGDEVVS----EGTIDSAPVDPREIFRRALRLNASSVILAHNHPSGDP 79 (123)
T ss_dssp HHHHHHHTTTSS---TTS-EEEEEEE-TTSBEEEEEEEE----ESTT-GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--
T ss_pred HHHHHHHHHHhCC--CCCeEEEEEEECCCCcEEEEEEec----ccCCCcccccHHHHHHHHHhhCCceEEEEEEcCCCCC
Confidence 3344444433332 355776655322222333333332 244455 678999999988888888888999999999
Q ss_pred CCCHHHHHh
Q 010576 419 FMSSIDVHT 427 (507)
Q Consensus 419 fpSs~DL~t 427 (507)
.||..|+..
T Consensus 80 ~PS~~D~~~ 88 (123)
T PF04002_consen 80 EPSDADIAL 88 (123)
T ss_dssp S--HHHHHH
T ss_pred CCCHhHHHH
Confidence 999999854
No 52
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=82.93 E-value=1.9 Score=43.37 Aligned_cols=109 Identities=17% Similarity=0.266 Sum_probs=61.3
Q ss_pred EEEeCHHHHHHHHHHHhh---cCCCCc-ceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHHHHHHHh-----hhCC
Q 010576 334 QLHISTTMMDNFMKLAKS---NTDKNL-ETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEEEIFEVQ-----DKRS 403 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~---nt~~~~-EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~eeei~~~~-----~~~~ 403 (507)
+|.+-+.+++.|-.|-.. -.+.+. -|.|-|+|+-.++.++|.+.|..+-.-..+. ++|-+-+.+-+ .=.+
T Consensus 10 tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk~eqykqVFpd 89 (299)
T KOG3050|consen 10 TVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTETIDKEYLEKKEEQYKQVFPD 89 (299)
T ss_pred eEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhhhccHHHHHHHHHHHHHhccc
Confidence 344445555555555221 113466 6889999999999999999995543322222 34433222222 2359
Q ss_pred CcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEEEEEcCC
Q 010576 404 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQ 446 (507)
Q Consensus 404 l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~IaIV~dP~ 446 (507)
+.++|||-|- .. +...|+|-|..--....--+.+-..|.
T Consensus 90 l~vlGwYttG--~d--~t~sd~~i~k~l~~i~esplflkLNp~ 128 (299)
T KOG3050|consen 90 LYVLGWYTTG--SD--PTPSDIHIHKQLMDINESPLFLKLNPA 128 (299)
T ss_pred ceEEEEeecC--CC--CChhhhHHHHHHHhhhcCceEEEecch
Confidence 9999999873 33 356677666532221222344444443
No 53
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=79.85 E-value=8.9 Score=34.86 Aligned_cols=65 Identities=20% Similarity=0.318 Sum_probs=40.1
Q ss_pred CCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHHHHHHHhhhCCCcceEEEcCCCC-----CCCCCCHHHHHh
Q 010576 354 DKNLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEEEIFEVQDKRSLFPLGWIHTHPT-----QSCFMSSIDVHT 427 (507)
Q Consensus 354 ~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~eeei~~~~~~~~l~~VGWyHSHPt-----~t~fpSs~DL~t 427 (507)
.++.|.||+.+ +..++.+.-|. |.. +..++ ... ..-...+...|+-||||.. .+-.+|..|+..
T Consensus 18 ~~nrEy~G~I~-~~~~G~y~~t~---p~~-G~~~~~~~~-----~~~~p~g~~~vA~yHTHG~~~~~y~~evfS~~D~~~ 87 (123)
T PF14220_consen 18 RENREYCGYIG-KDEDGKYFATE---PRR-GENASCYPS-----NPPCPNGSTIVASYHTHGAYSDGYDNEVFSPQDIRG 87 (123)
T ss_pred cCCcEEEEEEE-EcCCCcEEeec---Ccc-CCCCCcCCC-----CcccccccceeeEeecccccCCCccccCCCHHHhhh
Confidence 46899999874 45556655443 222 22222 100 0112357889999999985 456799999976
Q ss_pred h
Q 010576 428 H 428 (507)
Q Consensus 428 q 428 (507)
-
T Consensus 88 ~ 88 (123)
T PF14220_consen 88 D 88 (123)
T ss_pred h
Confidence 5
No 54
>PRK00024 hypothetical protein; Reviewed
Probab=79.64 E-value=11 Score=37.48 Aligned_cols=84 Identities=21% Similarity=0.152 Sum_probs=57.1
Q ss_pred CHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHHHHHHHhhhCCCcceEEEcCCCCC
Q 010576 338 STTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEEEIFEVQDKRSLFPLGWIHTHPTQ 416 (507)
Q Consensus 338 ~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~eeei~~~~~~~~l~~VGWyHSHPt~ 416 (507)
+++.+.++++..-.+ ...|...+|+=.-.+..+....++ .||-+. ..++.++|..+-..+..-|-.-|=||+.
T Consensus 105 ~~~~~~~~l~~~l~~--~~~E~f~vl~Ld~~~~li~~~~i~----~Gt~~~~~v~pRei~~~Al~~~A~~iIl~HNHPSG 178 (224)
T PRK00024 105 SPEDVADYLMAELRD--EEQEHFVVLFLDTKNRVIADEELF----IGTLNSSIVHPREIVKRALKLNAAALILAHNHPSG 178 (224)
T ss_pred CHHHHHHHHHHHccC--CCceEEEEEEECCCCCEeeEEEee----eecCCeEEEcHHHHHHHHHHhhccceEEEecCCCC
Confidence 445555666554443 367887776533333333333322 355555 6789999999888888888889999999
Q ss_pred CCCCCHHHHHh
Q 010576 417 SCFMSSIDVHT 427 (507)
Q Consensus 417 t~fpSs~DL~t 427 (507)
.+.||..|+..
T Consensus 179 ~~~PS~~D~~~ 189 (224)
T PRK00024 179 DPEPSQADILI 189 (224)
T ss_pred CCCCCHHHHHH
Confidence 99999999853
No 55
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.55 E-value=19 Score=35.76 Aligned_cols=84 Identities=23% Similarity=0.176 Sum_probs=56.2
Q ss_pred CHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHHHHHHHhhhCCCcceEEEcCCCCC
Q 010576 338 STTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEEEIFEVQDKRSLFPLGWIHTHPTQ 416 (507)
Q Consensus 338 ~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~eeei~~~~~~~~l~~VGWyHSHPt~ 416 (507)
+++.+..+++....+ ...|.+.+|+=...+..+....++ .||-+. ...+.++|..+-..+..-|=.-|=||+.
T Consensus 99 s~~~v~~~l~~~l~~--~~~E~f~vl~Ld~~n~li~~~~i~----~Gt~~~~~v~pReI~~~Al~~~A~~vIlaHNHPSG 172 (218)
T TIGR00608 99 SPEAAAEFLHTDLAH--ETREHFMVLFLDRKNRLIAKEVVF----IGTVNHVPVHPREIFKEALKLSASALILAHNHPSG 172 (218)
T ss_pred CHHHHHHHHHHHhcC--CCceEEEEEEECCCCcEEEEEEee----cCCCCeEEEcHHHHHHHHHHhhCCeEEEEeecCCC
Confidence 455666666655553 367877666322222222222222 355555 6789999999888888888888999999
Q ss_pred CCCCCHHHHHh
Q 010576 417 SCFMSSIDVHT 427 (507)
Q Consensus 417 t~fpSs~DL~t 427 (507)
.+.||..|+..
T Consensus 173 ~~~PS~~Di~~ 183 (218)
T TIGR00608 173 EPSPSQEDILI 183 (218)
T ss_pred CCCCCHHHHHH
Confidence 99999999853
No 56
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=69.02 E-value=12 Score=25.54 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCC-CCcc
Q 010576 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP-CHRD 71 (507)
Q Consensus 31 sa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp-~Hpd 71 (507)
+|..+...|.+|..-|+++.|=-++-+=+.+....+. .|||
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 3567778899999999999999999998877744433 3775
No 57
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=64.94 E-value=13 Score=24.25 Aligned_cols=29 Identities=7% Similarity=0.045 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010576 34 NILKQADIFREEKNIIDLYVMLLRFSSLV 62 (507)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (507)
.+++.|.+|.+.||.++|=-.|-+++..+
T Consensus 2 a~~~~a~~~~~~g~~~~A~~~~~~~~~~~ 30 (33)
T PF13174_consen 2 ALYRLARCYYKLGDYDEAIEYFQRLIKRY 30 (33)
T ss_dssp HHHHHHHHHHHHCHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHHHHC
Confidence 57899999999999999998888877653
No 58
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=63.38 E-value=66 Score=30.02 Aligned_cols=48 Identities=23% Similarity=0.246 Sum_probs=35.2
Q ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccc
Q 010576 20 DNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYL 73 (507)
Q Consensus 20 n~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk 73 (507)
+.+.|...|-.-| -|.-|..|++.|+++.|.--+-||+.|- |+||+.-
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 3334444444322 3445889999999999999999999997 8998653
No 59
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=61.58 E-value=37 Score=32.38 Aligned_cols=40 Identities=20% Similarity=0.203 Sum_probs=28.0
Q ss_pred hhhCCCcceEEEcCCCCCCCCCCHHHHHhhhhhhccCCCeEE
Q 010576 399 QDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVA 440 (507)
Q Consensus 399 ~~~~~l~~VGWyHSHPt~t~fpSs~DL~tq~~YQ~m~pe~Ia 440 (507)
+...+-.++. |||||..+.++|..|..+-..+.. +|-+|+
T Consensus 111 l~~~~~~iid-iHSHP~~~~~~S~~D~~~~~~~~~-i~~a~y 150 (162)
T PF15659_consen 111 LKNNGNKIID-IHSHPENSNGPSGNDMKNAKPRKN-IPYAIY 150 (162)
T ss_pred hccCCceEEE-eccCCCCCCCCCcchhhhhhhccc-ccceee
Confidence 3446777778 999999999999999876543332 444443
No 60
>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=59.80 E-value=23 Score=23.35 Aligned_cols=30 Identities=10% Similarity=0.130 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 010576 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (507)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (507)
|..++..|.+|.+.||++.|.-.|.+-+.+
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 455678899999999999999999887765
No 61
>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=57.08 E-value=25 Score=29.79 Aligned_cols=38 Identities=18% Similarity=0.083 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHh
Q 010576 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVT 63 (507)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ 63 (507)
+.|++-|..-++.|+..+++|++..|..+..--+-+.+
T Consensus 2 ~~~~~~A~~~l~~A~~~~~~~~~~~a~~~a~~a~e~~l 39 (118)
T PF05168_consen 2 QDWLEKAEEDLKAAEILLEEGDYNWAVFHAYQAVEKAL 39 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999988877765555543
No 62
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=56.41 E-value=88 Score=36.82 Aligned_cols=27 Identities=11% Similarity=0.070 Sum_probs=14.9
Q ss_pred HHHHHHHHhccCCCCcccccccHHHHH
Q 010576 55 LLRFSSLVTETIPCHRDYLASFKSQKL 81 (507)
Q Consensus 55 y~Ry~~Lv~ekLp~Hpdyk~~~~~~k~ 81 (507)
||+-+.=|+..|--|+.+....-++|.
T Consensus 424 YykLIEecISqIvlHr~~~DPdf~yr~ 450 (1102)
T KOG1924|consen 424 YYKLIEECISQIVLHRTGMDPDFKYRF 450 (1102)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCcchhh
Confidence 555555556666667666543334444
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=50.43 E-value=43 Score=21.83 Aligned_cols=31 Identities=10% Similarity=-0.009 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010576 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (507)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (507)
|.-++..|.+|++.|++++|--.+-|-+.|.
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 3456788999999999999999988877663
No 64
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=41.82 E-value=55 Score=22.50 Aligned_cols=28 Identities=11% Similarity=0.122 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010576 35 ILKQADIFREEKNIIDLYVMLLRFSSLV 62 (507)
Q Consensus 35 llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (507)
+...|.+|++.||+++|--+|-+-+.|-
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 5678999999999999999999865543
No 65
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=40.70 E-value=48 Score=23.71 Aligned_cols=29 Identities=21% Similarity=0.068 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010576 34 NILKQADIFREEKNIIDLYVMLLRFSSLV 62 (507)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (507)
..+..|..|.+.|++++|--+|-|.+.+.
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~ 31 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRALALD 31 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 35677999999999999999999977663
No 66
>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=39.56 E-value=76 Score=24.90 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCC
Q 010576 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP 67 (507)
Q Consensus 31 sa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp 67 (507)
+|..+...|.+|++.|++++|--+|-+-+.+ .+.+.
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 67
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=38.30 E-value=38 Score=36.70 Aligned_cols=128 Identities=22% Similarity=0.347 Sum_probs=87.0
Q ss_pred EEEe-CHHHHHHHHHHHhhcCCCCcceEEEecceeeC--CE-E----EEEEEEecCCCCCCCC-cCCH---HHHHH-Hhh
Q 010576 334 QLHI-STTMMDNFMKLAKSNTDKNLETCGILAGSLKN--RK-F----YITALIIPKQESTSDS-ATNE---EEIFE-VQD 400 (507)
Q Consensus 334 ~V~I-~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~--~~-l----~It~~~iP~q~~t~d~-~~~e---eei~~-~~~ 400 (507)
.|.. .+.++..|+..=+.. +.--.|.|.|...+ +. | .|..++-|+|....|. ++.+ +.+.+ .+.
T Consensus 235 HvEF~~~~iv~~Fi~~WR~s---G~QRfGy~yG~y~~y~n~PLGiKaVveaIyEPpQ~de~DG~t~ee~~de~l~d~~a~ 311 (571)
T COG5100 235 HVEFDGKHIVENFIRNWRES---GRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPAS 311 (571)
T ss_pred eeeecCchHHHHHHHHHHHh---hhhhheeeeeehhhccCCcchhHHHhhhhcCCccccCCCceEeeeeccccccccccc
Confidence 3443 457899999887763 56778999999864 21 2 3444457889877776 4421 11222 234
Q ss_pred hCCCcceEEEcCCC---------------CCCCCCCHHHHHhhhhhhccCC-------------CeEEEEEcCCCC-CCc
Q 010576 401 KRSLFPLGWIHTHP---------------TQSCFMSSIDVHTHYSYQIMLP-------------ESVAIVMAPQDA-TRK 451 (507)
Q Consensus 401 ~~~l~~VGWyHSHP---------------t~t~fpSs~DL~tq~~YQ~m~p-------------e~IaIV~dP~~~-~~~ 451 (507)
.-||..||.|-|-- .-+-|+|+..+..-..+|.|.| .+|.+|++-..+ +.+
T Consensus 312 ~~GL~riG~IfTDl~d~gs~~GsV~ckrh~dsyFLSSLEv~~~A~~Qt~hpn~~k~sr~g~FgSkfvT~Visgnl~GeI~ 391 (571)
T COG5100 312 GTGLERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIG 391 (571)
T ss_pred ccCceeeeeeeeehhhccCCCCceeeeccccceehhhhhhHHHhhhhhcCCCcccccccccccceeEEEEEecccCceee
Confidence 67899999987632 2356999999999999999986 478888877643 234
Q ss_pred eeEEEecCCCCchh
Q 010576 452 HGIFRLTSPGGMSV 465 (507)
Q Consensus 452 ~gaFrLt~p~gm~~ 465 (507)
+-.|.+++ .+|..
T Consensus 392 ~~sYQVSn-~~~AL 404 (571)
T COG5100 392 LQSYQVSN-QCMAL 404 (571)
T ss_pred eeEEeehh-hhhHH
Confidence 57788886 46644
No 68
>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=36.46 E-value=94 Score=20.40 Aligned_cols=30 Identities=10% Similarity=0.069 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 010576 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (507)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (507)
|...+..|.+|..-|+++.|...|.|=+.+
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 455778899999999999999998886655
No 69
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=33.22 E-value=83 Score=29.98 Aligned_cols=59 Identities=10% Similarity=0.233 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhccCCC-Cccccccc-HHHHHHHHHHHHHHHHHHHhhCHHHH-----HHHHHHHHh
Q 010576 51 LYVMLLRFSSLVTETIPC-HRDYLASF-KSQKLYLKKKLLNALSELEELQPAVQ-----QKINELNRK 111 (507)
Q Consensus 51 AYily~Ry~~Lv~ekLp~-Hpdyk~~~-~~~k~~~~~~l~~vl~~lE~LK~~l~-----~~Y~~~~~~ 111 (507)
|+++.++|..=| ++++. ||.|.... ....+..+++. +.+.++-++|.+|+ ..|.+|.+.
T Consensus 10 ~~llvl~Fl~~~-nk~r~l~~s~~i~~s~~~nkdakk~~-q~~~ei~dmKqelnavs~qD~fAkwaRl 75 (175)
T KOG4253|consen 10 AWLLVLKFLFGC-NKLRILLPSFSIFMSRVGNKDAKKES-QKVAEIQDMKQELNAVSMQDNFAKWARL 75 (175)
T ss_pred HHHHHHHHHHhh-hHhheecchhhhhhhcccchhHHHHH-HHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence 688899999888 55544 88876322 12233333333 33566667777774 356666653
No 70
>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=32.04 E-value=75 Score=24.19 Aligned_cols=30 Identities=10% Similarity=0.128 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 010576 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (507)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (507)
|..+...|.+|++.|++++|--.|.+-+.+
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 567888999999999999999999987776
No 71
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.00 E-value=1.2e+02 Score=29.60 Aligned_cols=73 Identities=12% Similarity=0.119 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHHH
Q 010576 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK 104 (507)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~~ 104 (507)
-+..|..++..|---.++|.+.+|.+-|--=++|+++-|..-|-= ...|..++.++-+-+.+++.|++-|++.
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 2356677788888899999998887743
No 72
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=30.20 E-value=70 Score=34.06 Aligned_cols=55 Identities=25% Similarity=0.408 Sum_probs=36.8
Q ss_pred EEeccee-eCCEEEEEEEE-ecCCCCCCC--------C---cCCHHHHHHHhh------hCCCcceEEEcCCCC
Q 010576 361 GILAGSL-KNRKFYITALI-IPKQESTSD--------S---ATNEEEIFEVQD------KRSLFPLGWIHTHPT 415 (507)
Q Consensus 361 GlL~G~~-~~~~l~It~~~-iP~q~~t~d--------~---~~~eeei~~~~~------~~~l~~VGWyHSHPt 415 (507)
|||+|.. ..+.-+|-+++ .|......+ . .+|++-+.+++. .-|+.+||.|=.+|.
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 55556777777 666543333 1 355655666643 569999999876653
No 73
>PRK15490 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=27.77 E-value=1.9e+02 Score=33.09 Aligned_cols=69 Identities=19% Similarity=0.233 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHH-HHHHHHHHHHHhhCHHHHHHHH
Q 010576 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLK-KKLLNALSELEELQPAVQQKIN 106 (507)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~-~~l~~vl~~lE~LK~~l~~~Y~ 106 (507)
.||.+|+.+|+..-+-|..|+||-+|-|- +..|+| +....-.+.+.+ .-+.++...+-++.+-.+++|+
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (578)
T PRK15490 40 LTSLAMLKKAEFLHDVNETERAYALYETL-------IAQNND-EARYEYARRLYNTGLAKDAQLILKKVSNGVQKKYN 109 (578)
T ss_pred hhHHHHHHHhhhhhhhhhhHhHHHHHHHH-------HHhCCc-chHHHHHHHHHhhhhhhHHHHHHHHhCccHhHHHH
Confidence 57899999999999999999999988773 356998 322211122222 2345556666677777777776
No 74
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=27.65 E-value=66 Score=32.28 Aligned_cols=89 Identities=20% Similarity=0.198 Sum_probs=54.0
Q ss_pred EEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC-cCCHHHHHHHhhhCCCcceEEEcCC
Q 010576 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS-ATNEEEIFEVQDKRSLFPLGWIHTH 413 (507)
Q Consensus 335 V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~-~~~eeei~~~~~~~~l~~VGWyHSH 413 (507)
+.-+++.+.++++-...+. ..|.--+|+=...+..+....+|+ ||-+. ..-+.|+|.++-..+..-|=..|=|
T Consensus 102 ~i~sp~~~~~~l~~~l~~~--~~E~f~vL~Ld~qnrlI~~e~lf~----GTi~~s~V~PREI~k~Al~~nAaavIlaHNH 175 (224)
T COG2003 102 VITSPEAVAEYLRAELGGE--EREHFVVLYLDSQNRLIATETLFI----GTLNVSEVHPREIFKEALKYNAAAVILAHNH 175 (224)
T ss_pred ccCCHHHHHHHHHHHhhhh--HHHHHHHHHhcCcCceecceeEEe----eecccceecHHHHHHHHHHhcchhhheeccC
Confidence 4456666666666554433 344432222111122223333332 34444 5668899999887777777778999
Q ss_pred CCCCCCCCHHHHH-hhh
Q 010576 414 PTQSCFMSSIDVH-THY 429 (507)
Q Consensus 414 Pt~t~fpSs~DL~-tq~ 429 (507)
|+..+-||..|+. |+.
T Consensus 176 PSGd~~PS~aD~~iT~r 192 (224)
T COG2003 176 PSGDPTPSRADILITER 192 (224)
T ss_pred CCCCCCcCHHHHHHHHH
Confidence 9999999999985 443
No 75
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=22.57 E-value=1.6e+02 Score=25.23 Aligned_cols=32 Identities=9% Similarity=-0.009 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHH
Q 010576 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLR 57 (507)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~R 57 (507)
-..|+.|...|..|...+.+||+.+|+.+...
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 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=22.48 E-value=1.9e+02 Score=20.92 Aligned_cols=37 Identities=19% Similarity=0.066 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCC
Q 010576 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68 (507)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~ 68 (507)
|+.+.+.|+|.+..+|+++|.-=|.+-+.|--+.+|-
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 3456788999999999999999888888887655553
No 77
>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=22.11 E-value=4.8e+02 Score=21.91 Aligned_cols=44 Identities=18% Similarity=0.052 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCC
Q 010576 25 LRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68 (507)
Q Consensus 25 lr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~ 68 (507)
+|-||.-|-+-+..|=-+.+.|+.++|-.+|-+=+...++.+.-
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 46799999999999999999999999999999988888776554
No 78
>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=21.88 E-value=1.6e+02 Score=22.93 Aligned_cols=35 Identities=3% Similarity=-0.016 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010576 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (507)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (507)
...+|..+...|.+|..-||++.|--++.+=++++
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 35568888999999999999999999988877765
No 79
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=21.78 E-value=1.7e+02 Score=28.06 Aligned_cols=36 Identities=17% Similarity=0.147 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCccc
Q 010576 33 DNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY 72 (507)
Q Consensus 33 ~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdy 72 (507)
.-++..|..|.+.||++.|-..+-+|+.++ |.||..
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 345777999999999999999999998877 888754
No 80
>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=21.40 E-value=1.4e+02 Score=17.32 Aligned_cols=26 Identities=0% Similarity=-0.043 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHH
Q 010576 34 NILKQADIFREEKNIIDLYVMLLRFS 59 (507)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~ 59 (507)
...+.|..|...|+++.|-..+.+-+
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~ 28 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKAL 28 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 34677899999999999988776544
No 81
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=20.60 E-value=4.7e+02 Score=26.59 Aligned_cols=80 Identities=11% Similarity=0.187 Sum_probs=51.2
Q ss_pred EEEeCHHHHHHHHHHHhhcCCCCcceEEEecceeeCCEEEEEEEEecCCCCCCCC--cCCHHHHHHHhh-----------
Q 010576 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDS--ATNEEEIFEVQD----------- 400 (507)
Q Consensus 334 ~V~I~~~~l~k~L~hA~~nt~~~~EvcGlL~G~~~~~~l~It~~~iP~q~~t~d~--~~~eeei~~~~~----------- 400 (507)
.++|++.--.+++ ..--|...+.+ +|+++....+..+.|+--|...-.-..|. ..|.+++++-+.
T Consensus 23 ~~fL~~~~a~~~l-~~~GN~~~~~~-~Gli~P~~~~~~W~v~~~y~~~GyVkDdda~~id~d~LL~~~k~~t~e~N~eR~ 100 (239)
T PF09935_consen 23 FRFLNPEDARKVL-EEWGNPPSPAE-LGLIFPDDDDEDWFVVFEYEDSGYVKDDDAKNIDYDELLKSMKEGTEESNKERK 100 (239)
T ss_pred cEEcCHHHHHHHH-HHhCCCCCcce-EEEEeccCCCCCEEEEEEEcCCCceecchhhhCCHHHHHHHHHHhHHhhhHHHH
Confidence 3899999999999 44445533444 99999877666666666564443322222 677777765421
Q ss_pred ---hCCCcceEEEcCCCCC
Q 010576 401 ---KRSLFPLGWIHTHPTQ 416 (507)
Q Consensus 401 ---~~~l~~VGWyHSHPt~ 416 (507)
-..+.++||.-- |+.
T Consensus 101 ~~G~~~l~l~GW~~~-P~Y 118 (239)
T PF09935_consen 101 KRGYPPLHLVGWAEP-PHY 118 (239)
T ss_pred hcCCCceEEeccccC-Ccc
Confidence 136778999764 544
No 82
>PF02561 FliS: Flagellar protein FliS; InterPro: IPR003713 The fliD operon of several bacteria consists of three flagellar genes, fliD, fliS, and fliT, and is transcribed in this order []. In Bacillus subtilis the operon encoding the flagellar proteins FliD, FliS, and FliT is sigma D-dependent [].; GO: 0009296 flagellum assembly, 0009288 bacterial-type flagellum; PDB: 1VH6_A 3IQC_B 3K1I_B 1ORJ_B 1ORY_A.
Probab=20.11 E-value=6.1e+02 Score=22.36 Aligned_cols=84 Identities=19% Similarity=0.174 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccc--cHH----HHHHHH-----HHHHHHHHHHHh
Q 010576 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLAS--FKS----QKLYLK-----KKLLNALSELEE 96 (507)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~--~~~----~k~~~~-----~~l~~vl~~lE~ 96 (507)
=|--+..-++.|..+.++||++.+-.-+.|-..++.+-... =|+... -+. -+..+. ..+.+-.+.+++
T Consensus 25 Lyd~ai~~l~~a~~a~~~~~~~~~~~~l~ka~~Ii~~L~~~-Ld~e~g~eia~~L~~lY~y~~~~L~~A~~~~d~~~l~~ 103 (122)
T PF02561_consen 25 LYDGAIEFLKQAKEAIEQGDIEEKNEALQKAQDIITELQSS-LDFEKGGEIADNLFRLYDYMIRQLVQANLKKDPERLDE 103 (122)
T ss_dssp HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHT-CCTTTTHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhh-cCCCCCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 45667788899999999999999999999999888543333 223211 111 122222 333334577777
Q ss_pred hCHHHHHHHHHHHHhh
Q 010576 97 LQPAVQQKINELNRKK 112 (507)
Q Consensus 97 LK~~l~~~Y~~~~~~~ 112 (507)
+...|..-.+.|.+..
T Consensus 104 v~~~l~~l~~aW~e~~ 119 (122)
T PF02561_consen 104 VIRILEELRDAWEEIA 119 (122)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 7777777777777644
Done!