Query 010474
Match_columns 509
No_of_seqs 260 out of 707
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 00:57:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010474.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010474hhsearch_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 3.2E-89 6.8E-94 684.8 23.9 418 2-509 2-424 (424)
2 cd08066 MPN_AMSH_like Mov34/MP 100.0 8.1E-43 1.7E-47 329.7 20.0 173 332-509 1-173 (173)
3 cd08067 MPN_2A_DUB Mov34/MPN/P 99.9 1E-26 2.2E-31 222.5 16.0 127 333-463 5-148 (187)
4 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 2.2E-26 4.9E-31 231.6 16.3 132 332-466 9-150 (268)
5 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 1.4E-26 3.1E-31 205.9 12.2 114 340-460 1-119 (119)
6 cd08068 MPN_BRCC36 Mov34/MPN/P 99.9 1.2E-24 2.5E-29 215.2 14.9 126 333-461 2-151 (244)
7 PF08969 USP8_dimer: USP8 dime 99.9 1.1E-23 2.4E-28 186.6 10.1 103 5-108 10-115 (115)
8 KOG1554 COP9 signalosome, subu 99.9 1.8E-23 3.9E-28 206.0 9.8 131 332-465 52-193 (347)
9 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.9 3.2E-21 7E-26 191.1 12.6 135 333-474 36-178 (252)
10 cd07767 MPN Mpr1p, Pad1p N-ter 99.8 8.8E-21 1.9E-25 165.7 11.8 106 343-450 2-107 (116)
11 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.8 1.9E-20 4.1E-25 188.6 13.4 138 334-478 2-149 (266)
12 smart00232 JAB_MPN JAB/MPN dom 99.8 8.4E-20 1.8E-24 163.2 15.4 126 334-461 1-134 (135)
13 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 1.8E-20 3.9E-25 164.7 8.5 106 332-439 3-114 (114)
14 cd08070 MPN_like Mpr1p, Pad1p 99.8 7.2E-19 1.6E-23 158.2 13.5 115 340-461 2-120 (128)
15 KOG1560 Translation initiation 99.8 3.7E-19 8E-24 175.3 9.0 143 332-479 12-169 (339)
16 KOG1555 26S proteasome regulat 99.7 1.8E-17 3.9E-22 167.8 6.9 132 332-465 30-177 (316)
17 cd08072 MPN_archaeal Mov34/MPN 99.7 2.4E-16 5.1E-21 140.4 12.6 108 337-460 1-108 (117)
18 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.6 1.4E-14 3.1E-19 127.4 11.2 102 341-458 2-104 (108)
19 COG1310 Predicted metal-depend 99.5 4.3E-14 9.3E-19 128.3 12.0 113 335-461 2-117 (134)
20 cd08057 MPN_euk_non_mb Mpr1p, 99.5 2.9E-13 6.4E-18 126.1 14.3 126 335-461 1-136 (157)
21 PF14464 Prok-JAB: Prokaryotic 99.5 2.6E-13 5.7E-18 116.8 9.3 90 339-447 2-96 (104)
22 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.3 1.4E-11 3.1E-16 124.2 13.7 127 335-465 1-134 (265)
23 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.3 1.9E-11 4.1E-16 124.3 14.5 123 334-460 2-134 (280)
24 TIGR03735 PRTRC_A PRTRC system 99.2 5.2E-11 1.1E-15 114.2 10.8 113 333-460 71-183 (192)
25 cd08059 MPN_prok_mb Mpr1p, Pad 99.2 2.3E-10 4.9E-15 98.8 10.2 101 340-457 1-101 (101)
26 cd08060 MPN_UPF0172 Mov34/MPN/ 99.1 6.2E-10 1.4E-14 106.6 12.4 107 337-450 1-115 (182)
27 cd08061 MPN_NPL4 Mov34/MPN/PAD 98.9 1.2E-08 2.5E-13 103.6 12.5 133 332-467 10-164 (274)
28 TIGR02256 ICE_VC0181 integrati 98.8 4.2E-08 9E-13 89.3 11.2 105 341-446 2-113 (131)
29 cd08063 MPN_CSN6 Mpr1p, Pad1p 98.8 4.7E-08 1E-12 100.0 12.1 128 334-465 2-142 (288)
30 PLN03246 26S proteasome regula 98.7 1.4E-07 3.1E-12 97.1 14.2 125 332-460 5-139 (303)
31 KOG1556 26S proteasome regulat 98.0 3.4E-05 7.4E-10 76.2 10.8 115 332-450 8-130 (309)
32 PF05021 NPL4: NPL4 family; I 97.9 4.9E-05 1.1E-09 78.5 10.5 107 360-467 2-147 (306)
33 PF03665 UPF0172: Uncharacteri 97.6 0.00047 1E-08 67.1 11.4 113 334-449 3-120 (196)
34 KOG2975 Translation initiation 97.6 0.00026 5.6E-09 70.8 8.5 129 332-465 20-154 (288)
35 KOG1795 U5 snRNP spliceosome s 97.2 0.00047 1E-08 80.2 5.9 149 334-492 2096-2248(2321)
36 PF04212 MIT: MIT (microtubule 96.5 0.012 2.5E-07 47.4 7.4 69 28-101 1-69 (69)
37 cd02684 MIT_2 MIT: domain cont 96.4 0.022 4.7E-07 47.1 8.3 69 30-103 4-72 (75)
38 cd02678 MIT_VPS4 MIT: domain c 96.4 0.018 3.9E-07 47.3 7.7 70 28-102 2-71 (75)
39 smart00745 MIT Microtubule Int 96.3 0.026 5.5E-07 46.2 8.5 73 26-103 2-74 (77)
40 cd02683 MIT_1 MIT: domain cont 96.3 0.019 4.2E-07 47.7 7.7 69 30-103 4-72 (77)
41 cd02681 MIT_calpain7_1 MIT: do 96.3 0.018 3.8E-07 47.9 7.3 69 30-102 4-72 (76)
42 cd02677 MIT_SNX15 MIT: domain 95.7 0.068 1.5E-06 44.2 8.2 68 28-100 2-69 (75)
43 cd02656 MIT MIT: domain contai 95.6 0.09 1.9E-06 42.9 8.4 70 29-103 3-72 (75)
44 COG5178 PRP8 U5 snRNP spliceos 95.1 0.052 1.1E-06 63.6 7.3 127 333-468 2134-2267(2365)
45 KOG3289 Uncharacterized conser 95.1 0.09 1.9E-06 50.3 7.7 107 334-448 3-119 (199)
46 cd02680 MIT_calpain7_2 MIT: do 94.4 0.18 3.9E-06 41.9 7.1 64 30-102 4-71 (75)
47 cd02682 MIT_AAA_Arch MIT: doma 93.2 0.41 9E-06 39.8 7.2 67 30-101 4-70 (75)
48 cd08071 MPN_DUF2466 Mov34/MPN/ 92.8 1.1 2.4E-05 39.8 9.9 70 356-430 15-84 (113)
49 KOG2834 Nuclear pore complex, 92.0 0.8 1.7E-05 49.6 9.3 129 334-466 176-344 (510)
50 KOG0739 AAA+-type ATPase [Post 91.2 0.65 1.4E-05 48.4 7.3 71 28-102 6-76 (439)
51 PF14220 DUF4329: Domain of un 90.2 1.5 3.2E-05 39.8 8.0 98 354-473 18-120 (123)
52 PF04002 RadC: RadC-like JAB d 86.5 3.4 7.4E-05 37.1 7.8 69 356-429 20-88 (123)
53 KOG3050 COP9 signalosome, subu 86.5 1.5 3.3E-05 44.0 5.9 108 335-449 11-129 (299)
54 PRK00024 hypothetical protein; 79.6 13 0.00028 37.0 9.5 85 338-429 105-189 (224)
55 TIGR00608 radc DNA repair prot 77.8 20 0.00043 35.6 10.1 85 338-429 99-183 (218)
56 PF13174 TPR_6: Tetratricopept 69.8 8.8 0.00019 25.0 3.9 29 34-62 2-30 (33)
57 PF13374 TPR_10: Tetratricopep 68.4 13 0.00028 25.4 4.6 41 31-71 1-42 (42)
58 PF15659 Toxin-JAB1: JAB-like 67.9 27 0.00058 33.3 8.0 41 401-443 111-151 (162)
59 PF13512 TPR_18: Tetratricopep 67.4 50 0.0011 30.8 9.5 47 21-73 38-84 (142)
60 PF13181 TPR_8: Tetratricopept 59.3 24 0.00052 23.3 4.5 30 32-61 1-30 (34)
61 PF05168 HEPN: HEPN domain; I 56.1 26 0.00056 29.7 5.3 38 26-63 2-39 (118)
62 PF07719 TPR_2: Tetratricopept 54.9 33 0.00072 22.3 4.6 31 32-62 1-31 (34)
63 KOG1924 RhoA GTPase effector D 46.5 2E+02 0.0043 34.1 11.4 28 408-435 767-794 (1102)
64 PF13428 TPR_14: Tetratricopep 46.3 35 0.00076 24.4 3.9 35 34-72 3-37 (44)
65 PF13176 TPR_7: Tetratricopept 41.2 57 0.0012 22.4 4.1 28 35-62 2-29 (36)
66 PF13424 TPR_12: Tetratricopep 38.7 79 0.0017 24.8 5.2 36 31-67 4-39 (78)
67 PF14778 ODR4-like: Olfactory 37.6 49 0.0011 35.2 4.9 57 361-417 1-74 (362)
68 PF00515 TPR_1: Tetratricopept 35.9 97 0.0021 20.3 4.6 30 32-61 1-30 (34)
69 PRK15490 Vi polysaccharide bio 35.0 1E+02 0.0023 35.0 7.1 69 30-106 40-109 (578)
70 KOG4253 Tryptophan-rich basic 32.5 89 0.0019 29.7 5.1 59 51-111 10-75 (175)
71 KOG4509 Uncharacterized conser 32.0 1.2E+02 0.0025 29.7 5.8 72 28-103 11-82 (247)
72 PF13414 TPR_11: TPR repeat; P 31.6 77 0.0017 24.1 4.0 36 32-71 3-38 (69)
73 COG2003 RadC DNA repair protei 31.2 55 0.0012 32.8 3.7 39 391-429 151-189 (224)
74 COG5100 NPL4 Nuclear pore prot 29.8 72 0.0016 34.7 4.5 130 334-467 235-404 (571)
75 PF09935 DUF2167: Protein of u 25.3 2.8E+02 0.0061 28.2 7.6 79 334-414 23-115 (239)
76 PF13525 YfiO: Outer membrane 25.2 1.3E+02 0.0028 28.8 5.2 36 33-72 43-78 (203)
77 PF10516 SHNi-TPR: SHNi-TPR; 23.8 1.7E+02 0.0036 21.1 4.2 37 32-68 1-37 (38)
78 PRK05685 fliS flagellar protei 23.3 5.3E+02 0.012 23.3 8.5 84 28-112 31-125 (132)
79 PF02561 FliS: Flagellar prote 22.5 5.1E+02 0.011 22.9 8.1 84 28-112 25-119 (122)
80 PF14346 DUF4398: Domain of un 22.5 1.6E+02 0.0035 25.2 4.7 32 26-57 39-70 (103)
81 cd02679 MIT_spastin MIT: domai 21.9 4.8E+02 0.01 21.9 8.1 44 25-68 1-44 (79)
82 PF13424 TPR_12: Tetratricopep 21.6 1.7E+02 0.0036 22.9 4.3 35 28-62 42-76 (78)
83 smart00028 TPR Tetratricopepti 20.7 1.5E+02 0.0032 17.2 3.1 26 34-59 3-28 (34)
No 1
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=100.00 E-value=3.2e-89 Score=684.76 Aligned_cols=418 Identities=39% Similarity=0.601 Sum_probs=290.4
Q ss_pred CCcccchhHHH---hhcCccccCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHH
Q 010474 2 RSSSEGINIAA---SAQRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKS 78 (509)
Q Consensus 2 ~~~~~~~~l~~---~a~~~e~n~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~ 78 (509)
-+|.+.++.+. .+..|+||.|||+|+|||+|++|+|||.||++|||+|+|||||+||++||+||||+||||++.. .
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 34555555443 3345899999999999999999999999999999999999999999999999999999999544 6
Q ss_pred HHHHHHHHHHHH-HHHHHhhCHHHHHHHHHHHHhhhhccccCcccCCCCCccccchhcccccchhhhhhccccchhhhhc
Q 010474 79 QKLYLKKKLLNA-LSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYDVTKALRLPSRELAYQ 157 (509)
Q Consensus 79 ~k~~~~~~l~~v-l~~lE~LK~~l~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 157 (509)
+++.+.++|+.+ ++.+++||++|.++|+.+++.+-..++... .+. .+.+ +.+++.+.+
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 788888887665 899999999999999988765422110000 000 0112 123333333
Q ss_pred CCchhhhhcccchHHHHhhhccCCCCCcchhhcccccCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCcccc
Q 010474 158 GSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSI 237 (509)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (509)
++|.++..+++....+|..+ +......+...++....+.+|+.++-
T Consensus 140 ~kr~aq~k~Q~l~~~~f~~~-~~~~~~q~~~s~~m~s~~~~gl~e~~--------------------------------- 185 (424)
T KOG2880|consen 140 RKRSAQTKQQQLESSQFSPL-EPPSFKQLLDSGPMPSNQSNGLPEQP--------------------------------- 185 (424)
T ss_pred HHHHHHHhhhcCCcccCCcc-CchHHHhhhcccCCCcCCCCCCcCCC---------------------------------
Confidence 44333443333333333321 10000011111111111111111110
Q ss_pred cccCCCCCCCCCcccccccCCCCCcccccCCCCCCCCCCccCCCCCCCccccCCCCCCCcchhhhhhhhccCCCcccccc
Q 010474 238 KIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETEC 317 (509)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ppp~~~~~~~~~~~~~~~~~~~~~ 317 (509)
. ..+.++....+...-+....+..+|++......+..+ .+|++++...+ .+.+
T Consensus 186 ----~----------~~~~~p~~~~~~~~~s~~l~~~~s~ep~~s~~~n~~~---k~p~~~r~l~p-------~a~~--- 238 (424)
T KOG2880|consen 186 ----I----------GEPLVPSNESRSLNYSELLSVLSSPEPSDSCTTNVTI---KSPSVDRVLKP-------GATD--- 238 (424)
T ss_pred ----c----------CCCCcccccccccCCchhhhhccCCCccccccccccc---cCCCCCccccc-------cccc---
Confidence 0 0000000000000000001111122221111111112 23333332211 1000
Q ss_pred ccCCCCCCCCCCCC-ceEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHH
Q 010474 318 QVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEE 396 (509)
Q Consensus 318 ~~~~~~~~~~~~~~-~~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e 396 (509)
. ........+. ++.|+||..++..|++.|.+||.+++|+||+|||++..+.|+||++++|+|++|+|+|.++|+++
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 0000111112 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEEEcCCCCchhhhccccCCC
Q 010474 397 IFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGF 476 (509)
Q Consensus 397 ~~~~~~~~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt~p~g~~~i~~c~~~~F 476 (509)
+|++|+.++|.+||||||||+|+||||++||||||+||.|+||+|||||+|+.. .+|+||||+|+||.+|.+|+++||
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 999999999999999999999999999999999999999999999999999976 589999999999999999999999
Q ss_pred ccCCCCCCCCCCcccCCceeecCCCceEEeeCC
Q 010474 477 HPHDPPPDGGPIYKPCTDVYMNPNLKFDVIDLR 509 (509)
Q Consensus 477 hph~~~~~~~~ly~~~~hV~~~~~~~f~vvDLR 509 (509)
|||+. +|+|||+.|+||||..+.+++|+|||
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 68999999999999999999999998
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=8.1e-43 Score=329.68 Aligned_cols=173 Identities=57% Similarity=1.016 Sum_probs=162.5
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEE
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW 411 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGW 411 (509)
++++.||++++.+|+.||+.++..|+|+||+|+|...++...|++++.++|.+++++|++.++++++++++.+|+.+|||
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 47899999999999999999864579999999999888889999998999999999999999888889999999999999
Q ss_pred EcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEEEcCCCCchhhhccccCCCccCCCCCCCCCCccc
Q 010474 412 IHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGFHPHDPPPDGGPIYKP 491 (509)
Q Consensus 412 yHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt~p~g~~~i~~c~~~~Fhph~~~~~~~~ly~~ 491 (509)
|||||..+||||.+|++||++||++.|++++|||||.. ..+++|||++++||+++.+|+++|||||+.+ ++||++
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 4799999997799999999999999999874 799999
Q ss_pred CCceeecCCCceEEeeCC
Q 010474 492 CTDVYMNPNLKFDVIDLR 509 (509)
Q Consensus 492 ~~hV~~~~~~~f~vvDLR 509 (509)
|+||+...++.|+++|||
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=99.94 E-value=1e-26 Score=222.46 Aligned_cols=127 Identities=24% Similarity=0.362 Sum_probs=110.4
Q ss_pred eEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceec--CCEEEEEEEEecCCCCCCcccccCChHH---HHHHHhhCCCc
Q 010474 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK--NRKFYITALIIPKQESTSDSCQATNEEE---IFEVQDKRSLF 407 (509)
Q Consensus 333 ~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~--~~~l~Vt~~~~p~q~~t~~~~~~~de~e---~~~~~~~~gl~ 407 (509)
..|.|+..++++|++||+... .|+||+|+|..+ .+.+.|+.+||+++..+++.|++ |+++ +++.++.+|+.
T Consensus 5 f~V~Is~~all~m~~Ha~~~~---~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~-dp~~q~e~~~~l~~~gl~ 80 (187)
T cd08067 5 FKVTVSSNALLLMDFHCHLTT---SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEM-DPVSETEIRESLESRGLS 80 (187)
T ss_pred EEEEECHHHHHHHHHHhcCCC---cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCccccc-CHHHHHHHHHHHHHcCCE
Confidence 569999999999999999943 999999999975 46899999999999877788875 4443 45567899999
Q ss_pred ceEEEcCCCCCCCCCCHHHHHhHHHhhhhCC-------CeEEEEEcCCCCC-----CcccEEEEcCCC
Q 010474 408 PLGWIHTHPTQSCFMSSIDVHTHYSYQIMLP-------ESVAIVMAPQDAT-----RKHGIFRLTSPG 463 (509)
Q Consensus 408 ~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~p-------e~IaIV~sP~~~~-----~~~gaFRLt~p~ 463 (509)
+||||||||.++|+||.+|++||+.||.|++ ++|||||||+++. ..+++|++.++.
T Consensus 81 vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~ 148 (187)
T cd08067 81 VVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPP 148 (187)
T ss_pred EEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCC
Confidence 9999999999999999999999999999988 7999999999853 247999999653
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=2.2e-26 Score=231.57 Aligned_cols=132 Identities=25% Similarity=0.408 Sum_probs=115.0
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChH--HHHH--H--HhhCC
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEE--EIFE--V--QDKRS 405 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~--e~~~--~--~~~~g 405 (509)
++.|.|++.++.+|++||.+. .|.|+||+|+|...++.+.|+++|++++.++++.|+..++. ++++ . ...++
T Consensus 9 ~~~V~Is~~allkil~Ha~~~--~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~ 86 (268)
T cd08069 9 FEKVYISSLALLKMLKHARAG--GPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRP 86 (268)
T ss_pred ccEEEECHHHHHHHHHHHhcc--CCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCC
Confidence 688999999999999999995 49999999999988899999999999998888888875532 2333 2 24688
Q ss_pred CcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCC-CC---cccEEEEcCCCCch
Q 010474 406 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA-TR---KHGIFRLTSPGGMS 466 (509)
Q Consensus 406 l~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~-~~---~~gaFRLt~p~g~~ 466 (509)
+.+||||||||.++||||.+|++||..||.+.+++|+|||||..+ .. .+||||+++ .|+.
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 32 479999995 5664
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=99.94 E-value=1.4e-26 Score=205.88 Aligned_cols=114 Identities=39% Similarity=0.727 Sum_probs=93.4
Q ss_pred HHHHHHHHHHhcCCCCCcceEEEeeceecC-----CEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcC
Q 010474 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKN-----RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHT 414 (509)
Q Consensus 340 ~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~-----~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHS 414 (509)
+++++|++||++++ |+|+||+|+|.... ..+.|+++++.+... +..+..+.+..+.++|+.+||||||
T Consensus 1 ~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~-----~~~~~~~~~~~~~~~g~~~vG~YHS 73 (119)
T cd08058 1 DALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSC-----TGENVEELFNVQTGRPLLVVGWYHS 73 (119)
T ss_pred CHHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCCc-----hhHHHHHHHHHHhCCCCeEEEEEec
Confidence 47899999999976 99999999998763 456777777654422 1111122344467999999999999
Q ss_pred CCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEEEc
Q 010474 415 HPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLT 460 (509)
Q Consensus 415 HP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt 460 (509)
||.+++|||.+|+++|++||++.|++++||+||.++...+|+|||+
T Consensus 74 HP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~~~~~~a~rl~ 119 (119)
T cd08058 74 HPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRNKDTGIFRLT 119 (119)
T ss_pred CCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCCCcccceEEeC
Confidence 9999999999999999999999999999999999865679999996
No 6
>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=99.92 E-value=1.2e-24 Score=215.20 Aligned_cols=126 Identities=23% Similarity=0.387 Sum_probs=103.1
Q ss_pred eEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceec-------CCEEEEEEEEecCCC-CCCcccccCChHHHHHH---H
Q 010474 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-------NRKFYITALIIPKQE-STSDSCQATNEEEIFEV---Q 401 (509)
Q Consensus 333 ~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~-------~~~l~Vt~~~~p~q~-~t~~~~~~~de~e~~~~---~ 401 (509)
..|.|+.+++++|+.||.+.. |+|+||+|+|..+ ...+.|+..+++.+. .+.+.++ +|+++++.+ +
T Consensus 2 ~~V~Is~~~l~~il~HA~~~~--P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~e-idPee~~~a~~ea 78 (244)
T cd08068 2 SKVHLSADVYLVCLTHALSTE--KEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVE-ISPEQLSAASTEA 78 (244)
T ss_pred cEEEECHHHHHHHHHHHHhCC--CcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEE-eCHHHHHHHHHHH
Confidence 579999999999999999955 9999999999874 334555566665554 4455554 677877654 2
Q ss_pred hh------CCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCC-------CcccEEEEcC
Q 010474 402 DK------RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT-------RKHGIFRLTS 461 (509)
Q Consensus 402 ~~------~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~-------~~~gaFRLt~ 461 (509)
+. +|+.+||||||||.++|+||.+|+.+|.+||++.|++++||+|+.... ..++|||+.+
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 2479999985
No 7
>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=1.1e-23 Score=186.62 Aligned_cols=103 Identities=35% Similarity=0.534 Sum_probs=87.0
Q ss_pred ccchhHHHhhcCc-cccCCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHH-H
Q 010474 5 SEGINIAASAQRL-DVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKL-Y 82 (509)
Q Consensus 5 ~~~~~l~~~a~~~-e~n~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~-~ 82 (509)
+..-+|.+.|..+ +||+++|+++|+|+|.+|+++|++|+++||+|+|||+|+||++|| ++||+||||+........ .
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 010474 83 LKKKLLNA-LSELEELQPAVQQKINEL 108 (509)
Q Consensus 83 ~~~~l~~v-l~~lE~LK~~l~~~Y~~~ 108 (509)
..+++..+ |++||+||++|+++|+++
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 23555444 899999999999999874
No 8
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.89 E-value=1.8e-23 Score=206.03 Aligned_cols=131 Identities=27% Similarity=0.389 Sum_probs=113.8
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHH--HHHH---h--hC
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEI--FEVQ---D--KR 404 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~--~~~~---~--~~ 404 (509)
++.|.|+..++++|+.||++ ++++|+||+|.|+..++.+.|.++|.+|.+||..++.+..++.- .+|. . .+
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 78999999999999999999 55999999999999999999999999999999998877554322 2222 2 56
Q ss_pred CCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCC----cccEEEEcCCCCc
Q 010474 405 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR----KHGIFRLTSPGGM 465 (509)
Q Consensus 405 gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~----~~gaFRLt~p~g~ 465 (509)
-+.+||||||||+.+|++|.+|+.||.-.|....++||||+||.++-. .+||||.- |.|.
T Consensus 130 ~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTy-p~gy 193 (347)
T KOG1554|consen 130 LENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTY-PKGY 193 (347)
T ss_pred hhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecc-cCCC
Confidence 678999999999999999999999999999999999999999998742 36999976 6674
No 9
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=99.85 E-value=3.2e-21 Score=191.13 Aligned_cols=135 Identities=21% Similarity=0.326 Sum_probs=119.8
Q ss_pred eEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecC---CEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcce
Q 010474 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPL 409 (509)
Q Consensus 333 ~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~---~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~v 409 (509)
..+.||.+++.+||..|..+| |+||+|.|+... ++.+|+++++|+|.++.++|.+.++ +.+.+...||+.|
T Consensus 36 ~t~vlPknllkkFi~iaD~rt----Q~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~--~~~~~~l~~Le~L 109 (252)
T cd08056 36 YTYILPKNLLKKFISISDLRT----QIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQ--LPQHEYLEDLEPL 109 (252)
T ss_pred CEEEeCHHHHHHHHHHhhhcc----eEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCcc--CccchhhCCCEee
Confidence 479999999999999999865 999999999865 7899999999999999999998664 4667778999999
Q ss_pred EEEcCCCCCCCCCCHHHHHhHHHhhhhCC-----CeEEEEEcCCCCCCcccEEEEcCCCCchhhhccccC
Q 010474 410 GWIHTHPTQSCFMSSIDVHTHYSYQIMLP-----ESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQR 474 (509)
Q Consensus 410 GWyHSHP~~~afpSs~DL~tq~sYQ~~~p-----e~IaIV~sP~~~~~~~gaFRLt~p~g~~~i~~c~~~ 474 (509)
|||||||+.++|||+.|+++|+.||.+.| .+|+|+|+++...-+++||+|| +.|+++.++=++.
T Consensus 110 GWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~SftpGs~sl~ay~LT-~~G~~wg~~n~d~ 178 (252)
T cd08056 110 GWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFTPGSCSLTAYKLT-PEGYEWGKQNKDL 178 (252)
T ss_pred EEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCCCCceEEEEEecC-HHHHHHHHhCccc
Confidence 99999999999999999999999999998 7999999998333358999999 5799988776653
No 10
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.84 E-value=8.8e-21 Score=165.72 Aligned_cols=106 Identities=27% Similarity=0.367 Sum_probs=88.0
Q ss_pred HHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCCCCCCCC
Q 010474 343 DNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFM 422 (509)
Q Consensus 343 ~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~~~afp 422 (509)
.+|++||+.++ +.|+||+|+|+..++.+.|++++++++..+...+...........+...|+.+||||||||..+++|
T Consensus 2 k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~~ 79 (116)
T cd07767 2 KMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCFL 79 (116)
T ss_pred HhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCcc
Confidence 57999999966 9999999999998889999999999886554433221111122345689999999999999999999
Q ss_pred CHHHHHhHHHhhhhCCCeEEEEEcCCCC
Q 010474 423 SSIDVHTHYSYQIMLPESVAIVMAPQDA 450 (509)
Q Consensus 423 Ss~DL~tq~sYQ~~~pe~IaIV~sP~~~ 450 (509)
|..|+.+|..||.+.|++++|||++...
T Consensus 80 s~~dv~~~~~~q~~~~~~v~li~~~~~~ 107 (116)
T cd07767 80 SPNDLATHELFQRYFPEKVMIIVDVKPK 107 (116)
T ss_pred CHHHHHHHHHHHHhCCCCEEEEEECCCc
Confidence 9999999999999999999999999875
No 11
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.84 E-value=1.9e-20 Score=188.56 Aligned_cols=138 Identities=18% Similarity=0.251 Sum_probs=111.3
Q ss_pred EEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCccc--ccCChHH---HHHHHhhCCC--
Q 010474 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSC--QATNEEE---IFEVQDKRSL-- 406 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~--~~~de~e---~~~~~~~~gl-- 406 (509)
.|.|++.++.+|++||.++. |.|+||+|+|...++.+.||++|+.+...+.+.. ...+... +++...+.|.
T Consensus 2 ~V~I~~~vllkIv~H~~~~~--p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e 79 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEEL--PELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDH 79 (266)
T ss_pred EEEEeHHHHHHHHHHHhcCC--CcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCC
Confidence 59999999999999999965 9999999999999999999999999886554432 2222233 3333445555
Q ss_pred cceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCC---CcccEEEEcCCCCchhhhccccCCCcc
Q 010474 407 FPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT---RKHGIFRLTSPGGMSVIRQCQQRGFHP 478 (509)
Q Consensus 407 ~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~---~~~gaFRLt~p~g~~~i~~c~~~~Fhp 478 (509)
.+|||||||| .++|.|..+++++++||...+++|+||+||..+. ..++|||++ +.||.. +++..|.+
T Consensus 80 ~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~-~~~~~~---~~~~~~~~ 149 (266)
T cd08065 80 NHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLS-EKFMEL---YKEGKFST 149 (266)
T ss_pred cEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEc-HHHHHH---hhcCCcCH
Confidence 9999999999 9999999999999999999999999999998532 357999998 578854 45555765
No 12
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.83 E-value=8.4e-20 Score=163.23 Aligned_cols=126 Identities=29% Similarity=0.446 Sum_probs=103.2
Q ss_pred EEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccC--ChHHH-HHH--HhhCCCcc
Q 010474 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQAT--NEEEI-FEV--QDKRSLFP 408 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~--de~e~-~~~--~~~~gl~~ 408 (509)
+|.|...++.+|++||.++. +.|+||+|+|...++.+.|+++|+.++....+.+... ++.+. .+. +...++.+
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~--p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDG--PEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEI 78 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCC--CcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceE
Confidence 37899999999999999965 9999999999998889999999998776554443222 22222 221 34789999
Q ss_pred eEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCC---cccEEEEcC
Q 010474 409 LGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR---KHGIFRLTS 461 (509)
Q Consensus 409 vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~---~~gaFRLt~ 461 (509)
||||||||..+++||..|+.+|..||.+++.++.+++++..+.. .+++|++++
T Consensus 79 vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 79 VGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 99999999999999999999999999999999999999988642 369999874
No 13
>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=99.82 E-value=1.8e-20 Score=164.74 Aligned_cols=106 Identities=26% Similarity=0.448 Sum_probs=87.5
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCC-EEEEEEEEecCCCCCCcccccCChHHH---HHHHh--hCC
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KFYITALIIPKQESTSDSCQATNEEEI---FEVQD--KRS 405 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~-~l~Vt~~~~p~q~~t~~~~~~~de~e~---~~~~~--~~g 405 (509)
+.+|.|.+.++.+|++||.++. +.|+||+|+|...++ .+.|+++|+.+...+.+.|...+.... ++... ...
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 6789999999999999999965 679999999999998 999999999998877777766554433 23322 245
Q ss_pred CcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCC
Q 010474 406 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPE 439 (509)
Q Consensus 406 l~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe 439 (509)
+.+||||||||.++||||..||++|+.||.|.|.
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 8999999999999999999999999999999874
No 14
>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=99.80 E-value=7.2e-19 Score=158.22 Aligned_cols=115 Identities=17% Similarity=0.254 Sum_probs=95.4
Q ss_pred HHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCc-ccccCChHHHHHH---HhhCCCcceEEEcCC
Q 010474 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSD-SCQATNEEEIFEV---QDKRSLFPLGWIHTH 415 (509)
Q Consensus 340 ~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~-~~~~~de~e~~~~---~~~~gl~~vGWyHSH 415 (509)
.++.+|++||+... |.|+||+|+|........|+.++++++...+. ..+.+|+++++++ .+..|+.+|||||||
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 57889999999965 99999999999887666788899888865544 5566788776655 457899999999999
Q ss_pred CCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEEEcC
Q 010474 416 PTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 461 (509)
Q Consensus 416 P~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt~ 461 (509)
|+.+++||.+|+.++ ..++.++||+++......+++|++.+
T Consensus 80 P~~~~~PS~~D~~~~-----~~~~~~~lIv~~~~~~~~~~~~~~~~ 120 (128)
T cd08070 80 PDGPARPSETDLRLA-----WPPGVSYLIVSLAGGAPELRAWRLEG 120 (128)
T ss_pred CCCCCCCCHHHHHhc-----cCCCCeEEEEECCCCCcEEEEEEEcC
Confidence 999999999999863 34578999999877655799999985
No 15
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=3.7e-19 Score=175.29 Aligned_cols=143 Identities=20% Similarity=0.385 Sum_probs=114.2
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCC--CCcccc--cCChH-HHHH--HH---
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQES--TSDSCQ--ATNEE-EIFE--VQ--- 401 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~--t~~~~~--~~de~-e~~~--~~--- 401 (509)
+.+|.|.+.++++|++||++..-+..=+.|+|+|...++++.||+|||.++.. ..|.+. ..+++ +.++ ++
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 78999999999999999999863323356999999999999999999987732 112111 12232 1222 22
Q ss_pred --hhCCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCc---ccEEEEcCCCCchhhhccccCCC
Q 010474 402 --DKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRK---HGIFRLTSPGGMSVIRQCQQRGF 476 (509)
Q Consensus 402 --~~~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~---~gaFRLt~p~g~~~i~~c~~~~F 476 (509)
.+.+-..||||.|| ..+.|+|..-+++|++||.+.|++|++|+||..+.++ ++||||| |..| ..|++++|
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 15666899999999 7899999888999999999999999999999998765 5999999 5666 67999999
Q ss_pred ccC
Q 010474 477 HPH 479 (509)
Q Consensus 477 hph 479 (509)
.|.
T Consensus 167 tpe 169 (339)
T KOG1560|consen 167 TPE 169 (339)
T ss_pred CHH
Confidence 987
No 16
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.70 E-value=1.8e-17 Score=167.81 Aligned_cols=132 Identities=22% Similarity=0.377 Sum_probs=106.1
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCCCcc-eEEEe-ec---ee-cCCEEEEEEEEecCCCCCCcccc--cCChHH---HHHH
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDKNLE-TCGIL-AG---SL-KNRKFYITALIIPKQESTSDSCQ--ATNEEE---IFEV 400 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~~~E-vcGlL-~G---~~-~~~~l~Vt~~~~p~q~~t~~~~~--~~de~e---~~~~ 400 (509)
-++|+|...++.++++|++... +.| ++|++ +| .+ ...+..|.++|..++.++..+|+ ..|+.- .+++
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 5789999999999999999965 999 99999 89 33 23577888899999999888844 344432 2222
Q ss_pred --HhhCCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCC---cccEEEEcCCCCc
Q 010474 401 --QDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR---KHGIFRLTSPGGM 465 (509)
Q Consensus 401 --~~~~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~---~~gaFRLt~p~g~ 465 (509)
++.+.+.+||||||||.++|+||++|+.||.+||++.+.+++.+++|..+.. ...+|++.++..+
T Consensus 108 l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~~~~ 177 (316)
T KOG1555|consen 108 LKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINPQWI 177 (316)
T ss_pred HHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCcccc
Confidence 4577788999999999999999999999999999998888888888877643 2588888876443
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=99.69 E-value=2.4e-16 Score=140.43 Aligned_cols=108 Identities=20% Similarity=0.209 Sum_probs=85.4
Q ss_pred ECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCC
Q 010474 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHP 416 (509)
Q Consensus 337 I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP 416 (509)
|+.+++..|++||++.. |+|+||+|+|+.. .|++++++++...++....++. .+...|+.+||.|||||
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 57889999999999965 9999999999764 6888888766543333222221 24578999999999999
Q ss_pred CCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEEEc
Q 010474 417 TQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLT 460 (509)
Q Consensus 417 ~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt 460 (509)
+.+++||.+|+.. +.+|++++||+++-+....+++|++.
T Consensus 70 ~~~~~PS~~D~~~-----~~~~~~~~lIvs~~~~~~~~~a~~~~ 108 (117)
T cd08072 70 SGSPRPSDADLSF-----FSKTGLVHIIVGYPYDEDDWRAYDSD 108 (117)
T ss_pred CCCCCCCHHHHHh-----hhcCCCEEEEEECcCCCCCEEEEecC
Confidence 9999999999864 35699999999975544579999976
No 18
>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=99.58 E-value=1.4e-14 Score=127.38 Aligned_cols=102 Identities=18% Similarity=0.190 Sum_probs=79.8
Q ss_pred HHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCC-CcccccCChHHHHHHHhhCCCcceEEEcCCCCCC
Q 010474 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQEST-SDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQS 419 (509)
Q Consensus 341 ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t-~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~~~ 419 (509)
++..|++||+... |.|+||+|+|+. .++.+++.++... +...+.+|+++++++++. + .+||.|||||+..
T Consensus 2 i~~~i~~ha~~~~--P~E~CGll~g~~-----~~~~~~p~~N~~~~p~~~F~idp~e~~~a~~~-~-~ivgi~HSHP~~~ 72 (108)
T cd08073 2 LEDAILAHAKAEY--PREACGLVVRKG-----RKLRYIPCRNIAADPEEHFEISPEDYAAAEDE-G-EIVAVVHSHPDGS 72 (108)
T ss_pred HHHHHHHHHhHCC--CCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHHHhcC-C-CEEEEEEcCCCCC
Confidence 5789999999955 999999999976 2456677776543 335566799998887643 3 8999999999999
Q ss_pred CCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEE
Q 010474 420 CFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFR 458 (509)
Q Consensus 420 afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFR 458 (509)
+.||..|+.. +.+|+..+||++.... .+++|+
T Consensus 73 a~PS~~D~~~-----~~~~~~~~iIvs~~~~--~~~~~~ 104 (108)
T cd08073 73 PAPSEADRAQ-----QEATGLPWIIVSWPEG--DLRVFR 104 (108)
T ss_pred CCCCHHHHHH-----hhcCCCcEEEEEcCCC--CEEEEe
Confidence 9999999853 3568999999997533 467775
No 19
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.55 E-value=4.3e-14 Score=128.28 Aligned_cols=113 Identities=21% Similarity=0.303 Sum_probs=78.2
Q ss_pred EEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCC-CCcccccCChHH--HHHHHhhCCCcceEE
Q 010474 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQES-TSDSCQATNEEE--IFEVQDKRSLFPLGW 411 (509)
Q Consensus 335 V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~-t~~~~~~~de~e--~~~~~~~~gl~~vGW 411 (509)
+.|+..++..||.||..++ |.|+||+|+|...+ ...+..++.. .+......+++. .+..+...|+.+|||
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 5789999999999999966 99999999998765 2223333322 212223333332 233356778999999
Q ss_pred EcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEEEcC
Q 010474 412 IHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 461 (509)
Q Consensus 412 yHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt~ 461 (509)
|||||..+|+||..|+. +|.+.+--+.||+.+... ...|+..+
T Consensus 75 yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~~~---~~~~~~~~ 117 (134)
T COG1310 75 YHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPGR---VHKGRAVD 117 (134)
T ss_pred EcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCCCc---eeEEeeec
Confidence 99999999999999997 455666656677776544 34444443
No 20
>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=99.51 E-value=2.9e-13 Score=126.05 Aligned_cols=126 Identities=13% Similarity=0.176 Sum_probs=94.8
Q ss_pred EEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHH---HHHH--hhCCCcce
Q 010474 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEI---FEVQ--DKRSLFPL 409 (509)
Q Consensus 335 V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~---~~~~--~~~gl~~v 409 (509)
|.|.+.++.+|++|+.+....+.+++|+|+|...++.+.|+++|+.+...+.+. ...|.+.+ ++.. -..+..+|
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~-~~~d~~y~~~m~~~~~~v~~~~~vV 79 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEES-IFIDTEYLEKRYNLHKKVYPQEKIV 79 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcc-hhhhHHHHHHHHHHHHHhCCCCCEE
Confidence 568889999999999875434789999999999999999999999988655443 22333322 2221 25678999
Q ss_pred EEEcCCCCCCCCCCHHHHHhHHHhhhh-CCCeEEEEEcCCCC----CCcccEEEEcC
Q 010474 410 GWIHTHPTQSCFMSSIDVHTHYSYQIM-LPESVAIVMAPQDA----TRKHGIFRLTS 461 (509)
Q Consensus 410 GWyHSHP~~~afpSs~DL~tq~sYQ~~-~pe~IaIV~sP~~~----~~~~gaFRLt~ 461 (509)
||||||+..++.++..|...|..|... .+..|+|++||... .-.+++|++..
T Consensus 80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~ 136 (157)
T cd08057 80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQ 136 (157)
T ss_pred EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEec
Confidence 999999988877777776666555544 67789999999751 12479999984
No 21
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.46 E-value=2.6e-13 Score=116.80 Aligned_cols=90 Identities=21% Similarity=0.401 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHH---H-HHhhCCCcceEEEcC
Q 010474 339 TTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIF---E-VQDKRSLFPLGWIHT 414 (509)
Q Consensus 339 ~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~---~-~~~~~gl~~vGWyHS 414 (509)
..++.+|+.||..+. +.|+||+|+|......+.|+..+. .++.+.+ . .+...++.+||+|||
T Consensus 2 ~~~~~~i~~~~~~~~--p~E~~G~L~g~~~~~~~~~~~~~~------------~~p~~~~~~~~~~~~~~~~~~vg~~HS 67 (104)
T PF14464_consen 2 EEVLEQIIAHARAAY--PNEACGLLLGRRDDQRFIVVPNVN------------PDPRDSFRRERFEARERGLEIVGIWHS 67 (104)
T ss_dssp -HHHHHHHHHHHHHT--TS-EEEEEEEEEECCEEEEEEEEE--------------HHCHHHHHH-HHHHHT-EEEEEEEE
T ss_pred HHHHHHHHHHHhhCC--CCeEEEEEEEEecCCEEEEEeCCC------------CCcHHHHHHHhhhhhcccceeeEEEEc
Confidence 468999999999966 999999999998666777766554 2222222 2 457899999999999
Q ss_pred CCCCCCCCCHHHHHhHHHhhhhCC-CeEEEEEcC
Q 010474 415 HPTQSCFMSSIDVHTHYSYQIMLP-ESVAIVMAP 447 (509)
Q Consensus 415 HP~~~afpSs~DL~tq~sYQ~~~p-e~IaIV~sP 447 (509)
||+..++||.+|+.+.. .. ..++||++.
T Consensus 68 HP~~~a~pS~~D~~~~~-----~~~~~~~iI~~~ 96 (104)
T PF14464_consen 68 HPSGPAFPSSTDIRSMR-----DLAPPSYIIVGN 96 (104)
T ss_dssp ESSSSSS--HHHHHTHC-----CS-SCEEEEEEE
T ss_pred CCCCCCCCCHHHHHhhh-----ccCCeEEEEEeC
Confidence 99999999999998632 22 788888887
No 22
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=99.33 E-value=1.4e-11 Score=124.23 Aligned_cols=127 Identities=13% Similarity=0.189 Sum_probs=94.5
Q ss_pred EEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHH---HHHHHh--hCCCcce
Q 010474 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEE---IFEVQD--KRSLFPL 409 (509)
Q Consensus 335 V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e---~~~~~~--~~gl~~v 409 (509)
|.|.+.++.+|++|+.+....+..++|.|+|...++.+.||++|+.+...+.+... .|.+. +++... ..+..+|
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~-~d~~y~~~m~~~~kkv~~~~~vV 79 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVA-VDMEYHRTMYELHQKVNPKEVIV 79 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEE-EcHHHHHHHHHHHHHhCCCCcEE
Confidence 46788999999999887544567899999999999999999999998765555433 33322 233322 6788999
Q ss_pred EEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCC--cccEEEEcCCCCc
Q 010474 410 GWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR--KHGIFRLTSPGGM 465 (509)
Q Consensus 410 GWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~--~~gaFRLt~p~g~ 465 (509)
|||||+|.. -.+...||.++++|...+..|.|++||..+.. .++||++.+ .|+
T Consensus 80 GWY~tg~~~--~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~-~~~ 134 (265)
T cd08064 80 GWYATGSEI--TEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSP-LGV 134 (265)
T ss_pred eeeeCCCCC--CccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEe-ccc
Confidence 999999832 23466678877777655578999999976542 579999984 454
No 23
>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=1.9e-11 Score=124.28 Aligned_cols=123 Identities=11% Similarity=0.170 Sum_probs=93.6
Q ss_pred EEEECHHHHHHHHHHHhcCC-CCCcceEEEeeceecCCEEEEEEEEecCCCCCCccc--ccCChHH---HHHHH--hhCC
Q 010474 334 QLHISTTMMDNFMKLAKSNT-DKNLETCGILAGSLKNRKFYITALIIPKQESTSDSC--QATNEEE---IFEVQ--DKRS 405 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt-~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~--~~~de~e---~~~~~--~~~g 405 (509)
.|.|.+.++.+|++|+.+.. +.+.+++|.|+|...++.+.|+++|+.+...+.+.. ...|.+. +++.. -..+
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~~ 81 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNAK 81 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCCC
Confidence 58999999999999987633 226789999999999999999999998876544432 1233222 22222 2677
Q ss_pred CcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCC--cccEEEEc
Q 010474 406 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR--KHGIFRLT 460 (509)
Q Consensus 406 l~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~--~~gaFRLt 460 (509)
..+||||||||. ++..|+..|..|+...+..|+|+++|..... .+++|.-.
T Consensus 82 e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~ 134 (280)
T cd08062 82 EKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAV 134 (280)
T ss_pred CCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEe
Confidence 899999999987 5677888888899888889999999976432 46888765
No 24
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=99.23 E-value=5.2e-11 Score=114.21 Aligned_cols=113 Identities=17% Similarity=0.150 Sum_probs=81.9
Q ss_pred eEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEE
Q 010474 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWI 412 (509)
Q Consensus 333 ~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWy 412 (509)
..=.||..++.+|+.||+++. |+|+||+|+|...++.+ .++++.+...+.....+++. ...+|+.+|+.|
T Consensus 71 ~~g~Ip~~l~~~ii~hAr~~~--P~EacG~Iag~~~~~~~---r~~p~~N~~~Sp~~~~~d~~-----~~~~ge~lV~iy 140 (192)
T TIGR03735 71 LCGPIPASLLEEFAEAARAAL--PNEVAAWIVWNSETGSL---RLAALESIEASPGHIDYRRP-----RLDDGEHLVVDL 140 (192)
T ss_pred ecCCCCHHHHHHHHHHHHhcC--CcceEEEEEEcCCCCEE---EEEeccccccCCceEEEcch-----HHhCCCeEEEEE
Confidence 344789999999999999966 99999999996444443 45777665444444445544 348999999999
Q ss_pred cCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEEEEc
Q 010474 413 HTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLT 460 (509)
Q Consensus 413 HSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt 460 (509)
||||..++|||.+|+.--. -.-.++.|+.-.+.....=+|||-
T Consensus 141 HSH~~spA~PS~tD~~Dd~-----~~~k~~~ViG~~~~~~p~~~~Rl~ 183 (192)
T TIGR03735 141 HSHGTGSAFFSETDDADDK-----GEVKISGVLGCLDQGTPQAVFRLC 183 (192)
T ss_pred cCCCCCCCCCCcccchhhc-----CceEEEEEEEecCCCCceEEEEEE
Confidence 9999999999999985311 113466676665553335677875
No 25
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.15 E-value=2.3e-10 Score=98.75 Aligned_cols=101 Identities=20% Similarity=0.231 Sum_probs=71.3
Q ss_pred HHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCCCCC
Q 010474 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQS 419 (509)
Q Consensus 340 ~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~~~ 419 (509)
+++..|+.|+.... |.|+||+|+|...+ .|.++.+.++.. .+ .++.. +..+...|...||.|||||+..
T Consensus 1 ~~~~~i~~~~~~~~--p~E~~gll~~~~~~---~~~~~~~~~~~~----~~-~~~~~-~~~a~~~~~~~v~i~HsHP~g~ 69 (101)
T cd08059 1 DLLKTILVHAKDAH--PDEFCGFLSGSKDN---VMDELIFLPFVS----GS-VSAVI-DLAALEIGMKVVGLVHSHPSGS 69 (101)
T ss_pred CHHHHHHHHHHhcC--ChhhheeeecCCCC---eEEEEEeCCCcC----Cc-cChHH-HHHHhhCCCcEEEEEecCcCCC
Confidence 36788999999955 99999999997644 455555444321 11 23333 5667788999999999999999
Q ss_pred CCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCCCcccEE
Q 010474 420 CFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIF 457 (509)
Q Consensus 420 afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~~~~gaF 457 (509)
+.||..|+... ..+...+||++..+ ...+++|
T Consensus 70 ~~PS~~D~~~~-----~~~~~~~iIv~~~~-~~~~~~~ 101 (101)
T cd08059 70 CRPSEADLSLF-----TRFGLYHVIVCYPY-ENSWKCY 101 (101)
T ss_pred CCCCHHHHHHH-----HhcCCeEEEEECCC-cccEEEC
Confidence 99999999642 23466777776554 3345655
No 26
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=99.12 E-value=6.2e-10 Score=106.59 Aligned_cols=107 Identities=12% Similarity=0.098 Sum_probs=76.8
Q ss_pred ECHHHHHHHHHHHhcCCCCCcceEEEeeceec-CCEEEEEEEEecCCCCCCcccccCChHH---HHH---HHhhCCCcce
Q 010474 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKFYITALIIPKQESTSDSCQATNEEE---IFE---VQDKRSLFPL 409 (509)
Q Consensus 337 I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~-~~~l~Vt~~~~p~q~~t~~~~~~~de~e---~~~---~~~~~gl~~v 409 (509)
|+..++.+|+.||.... +.|+||+|+|+.. ++...|++++|.... +...+|.. ++. ++...|+.+|
T Consensus 1 is~~ay~ki~~HA~k~p--~~evcGlLlG~~~~~~~~~V~d~vPl~h~-----~~~l~P~~Eval~~ve~~~~~~gl~Iv 73 (182)
T cd08060 1 LSTLAYVKMLLHAAKYP--HCAVNGLLLGKKSSGGSVEITDAVPLFHS-----CLALAPMLEVALALVDAYCKSSGLVIV 73 (182)
T ss_pred CCHHHHHHHHHHHHHcC--CchheEEEEeeecCCCCEEEEEEEEcCCC-----ccccCHHHHHHHHHHHHHHHHCCCEEE
Confidence 56789999999999954 8899999999987 677899999998763 24455542 333 3568999999
Q ss_pred EEEcCCCCCC-CCCCHHHHHhHHHhhhhCCCeEEEEEcCCCC
Q 010474 410 GWIHTHPTQS-CFMSSIDVHTHYSYQIMLPESVAIVMAPQDA 450 (509)
Q Consensus 410 GWyHSHP~~~-afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~ 450 (509)
|+|||||... ..|+.+=..---.-+...+.++.++++-..-
T Consensus 74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l 115 (182)
T cd08060 74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKL 115 (182)
T ss_pred EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccc
Confidence 9999999763 2444432221122334567888888886543
No 27
>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=103.58 Aligned_cols=133 Identities=18% Similarity=0.321 Sum_probs=103.5
Q ss_pred ceEEEECH-HHHHHHHHHHhcCCCCCcceEEEeeceecCC-------EEEEEEEEecCCCCCCcccccCCh---HHHHHH
Q 010474 332 PLQLHIST-TMMDNFMKLAKSNTDKNLETCGILAGSLKNR-------KFYITALIIPKQESTSDSCQATNE---EEIFEV 400 (509)
Q Consensus 332 ~~~V~I~~-~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~-------~l~Vt~~~~p~q~~t~~~~~~~de---~e~~~~ 400 (509)
+.+|.+.. .++..|+..+...+ ....||+|.|+.... ...|..++.|+|.++.+.++.... ..+-++
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 34566555 44555555466666 688999999998653 688888899999999998887643 234455
Q ss_pred HhhCCCcceEEEcCCCCC----CCCCCHHHHHhHHHhhh------hCCCeEEEEEcCCCCC-CcccEEEEcCCCCchh
Q 010474 401 QDKRSLFPLGWIHTHPTQ----SCFMSSIDVHTHYSYQI------MLPESVAIVMAPQDAT-RKHGIFRLTSPGGMSV 467 (509)
Q Consensus 401 ~~~~gl~~vGWyHSHP~~----~afpSs~DL~tq~sYQ~------~~pe~IaIV~sP~~~~-~~~gaFRLt~p~g~~~ 467 (509)
+..-||..||||+||+.. +.|||+.++.+...||. .-..+|.+|++|..+. ..+.+|++++. +|..
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 778999999999999987 89999999999999996 4468899999997553 34799999974 7744
No 28
>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=98.80 E-value=4.2e-08 Score=89.26 Aligned_cols=105 Identities=18% Similarity=0.149 Sum_probs=66.2
Q ss_pred HHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCC--CCCcccccCCh--HHHHH-HHh-h-CCCcceEEEc
Q 010474 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQE--STSDSCQATNE--EEIFE-VQD-K-RSLFPLGWIH 413 (509)
Q Consensus 341 ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~--~t~~~~~~~de--~e~~~-~~~-~-~gl~~vGWyH 413 (509)
++..|..+.+.. ..+.|+||+|+|...+..+.|+.+..|... .++..+....+ .+.++ +.. . ..+..||-+|
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 345555555554 468899999999998888899988765432 23333332222 22222 222 2 3378999999
Q ss_pred CCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEc
Q 010474 414 THPTQSCFMSSIDVHTHYSYQIMLPESVAIVMA 446 (509)
Q Consensus 414 SHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~s 446 (509)
|||...+.||.+|+.+....=...-..+.||+.
T Consensus 81 tHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG 113 (131)
T TIGR02256 81 THPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG 113 (131)
T ss_pred cCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence 999999999999998765332211224445544
No 29
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=98.78 E-value=4.7e-08 Score=99.97 Aligned_cols=128 Identities=16% Similarity=0.198 Sum_probs=87.7
Q ss_pred EEEECHHHHHHHHHHHhcCCCC----CcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHH---HHHH--hhC
Q 010474 334 QLHISTTMMDNFMKLAKSNTDK----NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEI---FEVQ--DKR 404 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt~~----~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~---~~~~--~~~ 404 (509)
.|.|-+.++.+|++|+...... +.-++|.|+|...++.+.|+++|+.+...+.+.-...|.+.+ ++.. -..
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 4788889999999999884321 456899999999999999999998877543311122343322 2222 256
Q ss_pred CCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCC--CC--cccEEEEcCCCCc
Q 010474 405 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA--TR--KHGIFRLTSPGGM 465 (509)
Q Consensus 405 gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~--~~--~~gaFRLt~p~g~ 465 (509)
++.+||||+|.+. +.+.+...||. .|....+..|++++||... .. .+++|+-.. .|.
T Consensus 82 ~~~vVGWY~tg~~-~~~~~~~~Ih~--~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~-~~~ 142 (288)
T cd08063 82 DLDFVGWYTTGPG-GPTESDLPIHK--QILEINESPVLLLLDPEANASGKDLPVTIYESVL-ELV 142 (288)
T ss_pred CCceEEEEecCCC-CCCHHHHHHHH--HHHhhCCCcEEEEEccccccCCCCCceeEEEEEE-ecc
Confidence 7899999999876 44444444554 4555566679999999773 22 369998652 344
No 30
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=98.75 E-value=1.4e-07 Score=97.10 Aligned_cols=125 Identities=13% Similarity=0.186 Sum_probs=88.2
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCC-CcceEEEeeceecCCEEEEEEEEecCCCCCCcc--cccCChH---HHHHHH--hh
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDK-NLETCGILAGSLKNRKFYITALIIPKQESTSDS--CQATNEE---EIFEVQ--DK 403 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~-~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~--~~~~de~---e~~~~~--~~ 403 (509)
+..|.|-+.++.+|++|+.+.... ..-+.|.|+|...++.+.||++|+.+.....+. .-..|.+ ++++.. -.
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 567999999999999999885421 233899999999999999999998876433221 0113322 223322 26
Q ss_pred CCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCC--CcccEEEEc
Q 010474 404 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIFRLT 460 (509)
Q Consensus 404 ~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~--~~~gaFRLt 460 (509)
.+..+||||+|.|. ++..|+.-|..|....+..|.+++++.... -.+++|...
T Consensus 85 ~~~~vVGWY~tg~~----i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~ 139 (303)
T PLN03246 85 AKEHVVGWYSTGPK----LRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAV 139 (303)
T ss_pred CCCcEEeeecCCCC----CCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEE
Confidence 77799999999765 445566667777777888888999976532 246888755
No 31
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=98.04 E-value=3.4e-05 Score=76.23 Aligned_cols=115 Identities=17% Similarity=0.230 Sum_probs=81.4
Q ss_pred ceEEEECHHHHHHHHHHHhcCC-CCCcceEEEeeceecCCEEEEEEEEecCCCCCC--cccccCC---hHHHHHHHh--h
Q 010474 332 PLQLHISTTMMDNFMKLAKSNT-DKNLETCGILAGSLKNRKFYITALIIPKQESTS--DSCQATN---EEEIFEVQD--K 403 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt-~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~--~~~~~~d---e~e~~~~~~--~ 403 (509)
...|.|-+.+++..+.|...-. ..+--+.|+|+|.+.++++.||+.|..+.+... .++-..| -+.+|.++. +
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 5679999999999999976632 233568899999999999999999977664221 1122222 244566664 5
Q ss_pred CCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCC
Q 010474 404 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA 450 (509)
Q Consensus 404 ~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~ 450 (509)
....+||||||-|. +-.-||.-...+-.+.|..+.+|++.+-.
T Consensus 88 akekivGWYhTGPk----l~~nDl~In~l~k~y~pnpvLvIIdvkpk 130 (309)
T KOG1556|consen 88 AKEKVVGWYHTGPK----LRENDLDINELLKRYVPNPVLVIIDVKPK 130 (309)
T ss_pred chhheeeeeccCCc----cccchhhHHHHHhhcCCCceEEEEecccc
Confidence 66689999999764 44455555556667789999899887544
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=97.94 E-value=4.9e-05 Score=78.51 Aligned_cols=107 Identities=22% Similarity=0.342 Sum_probs=83.8
Q ss_pred EEEeeceecCC-------EEEEEEEEecCCCCCCcccccCCh---HHHHHHHhhCCCcceEEEcCCCC------------
Q 010474 360 CGILAGSLKNR-------KFYITALIIPKQESTSDSCQATNE---EEIFEVQDKRSLFPLGWIHTHPT------------ 417 (509)
Q Consensus 360 cGlL~G~~~~~-------~l~Vt~~~~p~q~~t~~~~~~~de---~e~~~~~~~~gl~~vGWyHSHP~------------ 417 (509)
+|+|.|..... ...|..++.|+|.++.+.....+. +.+=+++..-||..||||=||+.
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 79999998642 578888889999998887765432 22334567889999999999998
Q ss_pred ---CCCCCCHHHHHhHHHhhhhCC-------------CeEEEEEcCCCCC-CcccEEEEcCCCCchh
Q 010474 418 ---QSCFMSSIDVHTHYSYQIMLP-------------ESVAIVMAPQDAT-RKHGIFRLTSPGGMSV 467 (509)
Q Consensus 418 ---~~afpSs~DL~tq~sYQ~~~p-------------e~IaIV~sP~~~~-~~~gaFRLt~p~g~~~ 467 (509)
.+.|+|+..+-+-..+|...| .+|.+|+++..+. ..+.+|.+++ -+|..
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 889999999999999998763 4799999996552 2469999996 46643
No 33
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.65 E-value=0.00047 Score=67.06 Aligned_cols=113 Identities=11% Similarity=0.090 Sum_probs=74.0
Q ss_pred EEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCE--EEEEEEEecCCCCCCcccccCCh--HHHHHHHhhCCCcce
Q 010474 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRK--FYITALIIPKQESTSDSCQATNE--EEIFEVQDKRSLFPL 409 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~--l~Vt~~~~p~q~~t~~~~~~~de--~e~~~~~~~~gl~~v 409 (509)
.|.|+..++.||+-||.... -.-|+|+|+|...++. +.|++++|.--...+-. -|... ..+-.++...|+.+|
T Consensus 3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L~-PmlEvAL~qvd~~~~~~gl~Iv 79 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSLS-PMLEVALAQVDAYAKSNGLVIV 79 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeeceeccccccCcc-hHHHHHHHHHHHHHhhCCCEEE
Confidence 58899999999999999854 5778999999987543 99999998844221110 01100 122334678999999
Q ss_pred EEEcCCCCC-CCCCCHHHHHhHHHhhhhCCCeEEEEEcCCC
Q 010474 410 GWIHTHPTQ-SCFMSSIDVHTHYSYQIMLPESVAIVMAPQD 449 (509)
Q Consensus 410 GWyHSHP~~-~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~ 449 (509)
|+||..... ..-||..=..---.-+...+.++.|+++-..
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 2345554221111122356899999988544
No 34
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=97.58 E-value=0.00026 Score=70.80 Aligned_cols=129 Identities=14% Similarity=0.236 Sum_probs=88.1
Q ss_pred ceEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCCh--HHHHHHHh--hCCCc
Q 010474 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE--EEIFEVQD--KRSLF 407 (509)
Q Consensus 332 ~~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de--~e~~~~~~--~~gl~ 407 (509)
-..|.|-+.++..|+.+......+..-++|-|+|...++.+.||+||..|-..+++.++...+ .++++.-. ..+..
T Consensus 20 ~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~npnE~ 99 (288)
T KOG2975|consen 20 NLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVNPNEL 99 (288)
T ss_pred CceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccCCCce
Confidence 467888888888888887776555556899999999999999999997665444455543221 22333322 55668
Q ss_pred ceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCC--CcccEEEEcCCCCc
Q 010474 408 PLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIFRLTSPGGM 465 (509)
Q Consensus 408 ~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~--~~~gaFRLt~p~g~ 465 (509)
+||||-|-+..+.+-|- ||. -|-.-.|+.|-+-+|-..+. -.+|+|--+ +-|+
T Consensus 100 vvGWyaTg~dvt~~ssl--ihd--yYare~~~pvhLtVDT~~~n~rm~ikaYvss-~~Gv 154 (288)
T KOG2975|consen 100 VVGWYATGHDVTEHSSL--IHD--YYAREAPNPVHLTVDTSLQNGRMSIKAYVSS-LMGV 154 (288)
T ss_pred eEEEEecCCCcccchhH--HHH--HhhccCCCCeEEEEeccccCCccceeEEEEe-ccCC
Confidence 99999987776654333 444 34455688899998876552 146888655 3454
No 35
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=97.19 E-value=0.00047 Score=80.20 Aligned_cols=149 Identities=19% Similarity=0.262 Sum_probs=105.0
Q ss_pred EEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecC---CEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceE
Q 010474 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLG 410 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~---~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vG 410 (509)
...||..++.+|+..+.. ..-+.|++.|.... .+-.|.++.-++|-++-..+.... .+=....-.|++.+|
T Consensus 2096 tyilPkNllkkFi~isD~----r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~--~lP~~~~l~d~e~Lg 2169 (2321)
T KOG1795|consen 2096 TYILPKNLLKKFITISDL----RTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPS--FLPIHGVLEDLEPLG 2169 (2321)
T ss_pred eeeccHHHHhhheeecch----hhhhheeeeccCCCCCCccceEEEEEeccccccccccccCc--cCCcchhccCCcccc
Confidence 468899999999988876 45889999996642 345677777778866533332211 011223467889999
Q ss_pred EEcCCCCCCCCCCHHHHHhHHHhhhhC-CCeEEEEEcCCCCCCcccEEEEcCCCCchhhhccccCCCccCCCCCCCCCCc
Q 010474 411 WIHTHPTQSCFMSSIDVHTHYSYQIML-PESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGFHPHDPPPDGGPIY 489 (509)
Q Consensus 411 WyHSHP~~~afpSs~DL~tq~sYQ~~~-pe~IaIV~sP~~~~~~~gaFRLt~p~g~~~i~~c~~~~Fhph~~~~~~~~ly 489 (509)
|+||.|.--.++|+.|+.||..--... ..+|.|-|+-.-.+-++.+|.|| |.|.++...-+..|=.|+.- .|.-|
T Consensus 2170 w~hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~~tpgs~sl~ay~lt-~~G~eWg~~n~d~g~~~~gy---~pt~~ 2245 (2321)
T KOG1795|consen 2170 WIHTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCSFTPGSCSLTAYKLT-PSGYEWGEVNKDKGNNPKGY---LPTHY 2245 (2321)
T ss_pred hhhcCccccccCCHHHhhhhhhhhhcCccceEEEEeeccCCcceeeeeccC-ccccccchhcccccCCcccc---CccHH
Confidence 999999999999999999997543333 46787877754333357999999 57999887777777667653 24455
Q ss_pred ccC
Q 010474 490 KPC 492 (509)
Q Consensus 490 ~~~ 492 (509)
++|
T Consensus 2246 e~~ 2248 (2321)
T KOG1795|consen 2246 EKV 2248 (2321)
T ss_pred HHH
Confidence 554
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=96.53 E-value=0.012 Score=47.40 Aligned_cols=69 Identities=16% Similarity=0.174 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHH
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l 101 (509)
|+..|..++++|-.+.+.||++.|+-+|..=+.+++.-+..-+ ....+..++.++..-+.++|.||..|
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 7889999999999999999999999999998888876655542 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=96.38 E-value=0.022 Score=47.15 Aligned_cols=69 Identities=16% Similarity=0.118 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010474 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (509)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (509)
.-|..|+++|--.-..|+++.||-+|+.=+.+|+.-+..- ..+..|..++.++...+.++|+||..|+.
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=61.0
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHH
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQ 102 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~ 102 (509)
|+..|..++++|--....|+++.|+-+|..=+.+++.-+..-++ +..+..++.++..-+.++|.||..|+
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=96.34 E-value=0.026 Score=46.22 Aligned_cols=73 Identities=16% Similarity=0.165 Sum_probs=63.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010474 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (509)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (509)
+.|+..|.+++.+|--+.+.|+++.|+-+|..=+.+++.-+..=| .+..+..++.++..-+.++|.||..|..
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 458899999999999999999999999999999999987775532 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=96.32 E-value=0.019 Score=47.70 Aligned_cols=69 Identities=19% Similarity=0.263 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010474 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (509)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (509)
..|.++++.|--+-+.|+++.|+.+|..=+.+|+.-|..-|| ...|..++.++..-+.++|.||..|++
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 568899999999999999999999999999999876665432 245778889999999999999998864
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=96.30 E-value=0.018 Score=47.93 Aligned_cols=69 Identities=16% Similarity=0.020 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHH
Q 010474 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQ 102 (509)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~ 102 (509)
|.|..+++.|--+-++|+++.|+.+|..=+.+|+..+..+ ..+...+..++.++..-+.++|.||..|.
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 6899999999999999999999999999999998643332 11334466778999999999999999875
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=95.70 E-value=0.068 Score=44.25 Aligned_cols=68 Identities=16% Similarity=0.154 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHH
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPA 100 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~ 100 (509)
|+--|..++++|--.-.+||++.|+-+|..=+++|+.-++.-+ ....|..++.++.+-+.++|+|+..
T Consensus 2 ~l~~A~~l~~~Ave~d~~~~y~eA~~~Y~~~i~~~~~~~k~e~-----~~~~k~~ir~K~~eYl~RAE~i~~~ 69 (75)
T cd02677 2 YLEQAAELIRLALEKEEEGDYEAAFEFYRAGVDLLLKGVQGDS-----SPERREAVKRKIAEYLKRAEEILRL 69 (75)
T ss_pred hHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhccCC-----CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6678899999999999999999999999999999987776632 2466889999999999999998764
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=95.56 E-value=0.09 Score=42.92 Aligned_cols=70 Identities=17% Similarity=0.179 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010474 29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (509)
Q Consensus 29 ~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (509)
+..|..+++.|--+.+.||++.|+-+|..=+.+++.-+..-+ .+..+..++.++...+.++|.||..|..
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 567889999999999999999999999999999987674432 2466788889999999999999998854
No 44
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=95.07 E-value=0.052 Score=63.61 Aligned_cols=127 Identities=17% Similarity=0.272 Sum_probs=81.7
Q ss_pred eEEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCC---EEEEEEEEecCCCCCCcccccC--ChHHHHHHHhhCCCc
Q 010474 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR---KFYITALIIPKQESTSDSCQAT--NEEEIFEVQDKRSLF 407 (509)
Q Consensus 333 ~~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~---~l~Vt~~~~p~q~~t~~~~~~~--de~e~~~~~~~~gl~ 407 (509)
.+-.||..++.+|+..... ..-|.|++.|+...+ .-.|..+...+|-++-..+... -+. +.-...||+
T Consensus 2134 ~~y~lP~NLl~kF~~isD~----~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~---dlp~~e~le 2206 (2365)
T COG5178 2134 QMYRLPLNLLEKFMRISDP----HVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPH---DLPGDEDLE 2206 (2365)
T ss_pred ccccccHHHHHhhheeccc----ceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCC---CCCCcccce
Confidence 3577899999999998766 568999999976532 3344444445665432222110 010 112347899
Q ss_pred ceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCCCC--CcccEEEEcCCCCchhh
Q 010474 408 PLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIFRLTSPGGMSVI 468 (509)
Q Consensus 408 ~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~~~--~~~gaFRLt~p~g~~~i 468 (509)
+|||+|+.-.--.|++..++.||. |-...|++=||-.+..+.+ -+.+++.+++ +|.++.
T Consensus 2207 ~lGwihtq~~el~~l~~~~v~th~-k~~~d~~~d~v~ltv~~~pgsiSl~ay~v~k-eG~~Wg 2267 (2365)
T COG5178 2207 ILGWIHTQDDELPYLEVAGVLTHR-KKIVDPEWDAVTLTVSYLPGSISLRAYVVKK-EGCNWG 2267 (2365)
T ss_pred eeEEEecCCcccchhhhhhhhhhh-hcccCccccceeeeeeeccceeeeeeeeehh-cccccc
Confidence 999999988888999999999985 3334454444433333332 2468998886 677664
No 45
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=95.06 E-value=0.09 Score=50.27 Aligned_cols=107 Identities=13% Similarity=0.164 Sum_probs=69.8
Q ss_pred EEEECHHHHHHHHHHHhcCCCCCcceEEEeecee--cCCEEEEEEEEecCCCCCCcccccCChHHHHHH-----HhhCCC
Q 010474 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSL--KNRKFYITALIIPKQESTSDSCQATNEEEIFEV-----QDKRSL 406 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~--~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~-----~~~~gl 406 (509)
.+.|+..++.+|+-||..-- ---|-|+|+|.. .++.+.||+++|.--+... ...+.|+.-+ ....|+
T Consensus 3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~~kg~~v~itdcVPLfH~~la----LaPmlEvAl~lId~~~~~~Gl 76 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPATGKGECVEITDCVPLFHSHLA----LAPMLEVALNLIDVWGAQAGL 76 (199)
T ss_pred ceeehhhHHHHHHHHhccCc--ccceeeEEEeccCCCCCeEEEEecchhhccccc----cccHHHHHHHHHHHHHHhcCe
Confidence 47899999999999998843 455789999954 4589999999988554321 1223343221 348999
Q ss_pred cceEEEcCCCCCC-CCCCH--HHHHhHHHhhhhCCCeEEEEEcCC
Q 010474 407 FPLGWIHTHPTQS-CFMSS--IDVHTHYSYQIMLPESVAIVMAPQ 448 (509)
Q Consensus 407 ~~vGWyHSHP~~~-afpSs--~DL~tq~sYQ~~~pe~IaIV~sP~ 448 (509)
.++|+||+--++. ..+.. .-|..+ -+...|.+..||.+-+
T Consensus 77 viaGyy~Ane~~~D~s~~~~A~kiadr--Ise~f~~A~ilv~dn~ 119 (199)
T KOG3289|consen 77 VIAGYYHANERVNDQSLNPVALKIADR--ISEFFPDAAILVLDNK 119 (199)
T ss_pred EEEEEeecCCCccccCccHHHHHHHHH--HHhhCCCCeEEEEecc
Confidence 9999999864322 11222 222222 2345788887877754
No 46
>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=94.40 E-value=0.18 Score=41.91 Aligned_cols=64 Identities=20% Similarity=0.123 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHH----HHHHHHHhhCHHHH
Q 010474 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLL----NALSELEELQPAVQ 102 (509)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~----~vl~~lE~LK~~l~ 102 (509)
.-|..|+++|----..||++.||=||+-=+.+|+. + + ...-+..++.++. ..+.++|+||..|.
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 2345667778885 88999999999875
No 47
>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=93.21 E-value=0.41 Score=39.76 Aligned_cols=67 Identities=13% Similarity=0.075 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHH
Q 010474 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (509)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l 101 (509)
++|.++++.|--|.++|+++.|.++|..=+.+++.-+..-||-. .+..++.++.+-++++|.||..+
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 67899999999999999999999999999999988887777654 35667888999999999999876
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=92.77 E-value=1.1 Score=39.77 Aligned_cols=70 Identities=21% Similarity=0.210 Sum_probs=49.7
Q ss_pred CcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCCCCCCCCCHHHHHhH
Q 010474 356 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTH 430 (509)
Q Consensus 356 ~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~~~afpSs~DL~tq 430 (509)
+.|.+.+|+=...++.+....++ .|+-+.| ..++.++|......+..-++.-|.||++.+.||..|++.-
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----VGTLNSS-LVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELT 84 (113)
T ss_pred CceEEEEEEecCCCCEEEEEEEe----ecCCcce-ecCHHHHHHHHHHHhhheEEEEeeCCCCCCCCCHHHHHHH
Confidence 67888777644333433333222 2333333 3568899998888888999999999999999999999753
No 49
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=92.01 E-value=0.8 Score=49.61 Aligned_cols=129 Identities=19% Similarity=0.337 Sum_probs=92.2
Q ss_pred EEEE-CHHHHHHHHHHHhcCCCCCcceEEEeeceecC-CEE------EEEEEEecCCCCCCcccccCC--hHHHHH-HHh
Q 010474 334 QLHI-STTMMDNFMKLAKSNTDKNLETCGILAGSLKN-RKF------YITALIIPKQESTSDSCQATN--EEEIFE-VQD 402 (509)
Q Consensus 334 ~V~I-~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~-~~l------~Vt~~~~p~q~~t~~~~~~~d--e~e~~~-~~~ 402 (509)
+|.+ ...+++.||.--+.. +.--.|+|.|.... +.+ .|..++-|+|.++.|....++ ++..++ .+.
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 57789999999864 333 777888899999988877653 333344 367
Q ss_pred hCCCcceEEEcCCC---------------CCCCCCCHHHHHhHHHhhhhCCC-------------eEEEEEcCCCCC-Cc
Q 010474 403 KRSLFPLGWIHTHP---------------TQSCFMSSIDVHTHYSYQIMLPE-------------SVAIVMAPQDAT-RK 453 (509)
Q Consensus 403 ~~gl~~vGWyHSHP---------------~~~afpSs~DL~tq~sYQ~~~pe-------------~IaIV~sP~~~~-~~ 453 (509)
.-||.-||||-|-- ..+.|+|+.++.+-..+|.+-|. +|-+|++-.... -+
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 34679999999998999988774 455665543332 13
Q ss_pred ccEEEEcCCCCch
Q 010474 454 HGIFRLTSPGGMS 466 (509)
Q Consensus 454 ~gaFRLt~p~g~~ 466 (509)
+-.|.+++ -+|.
T Consensus 333 f~~YQVSn-qc~a 344 (510)
T KOG2834|consen 333 FEGYQVSN-QCMA 344 (510)
T ss_pred eeeeehhH-HHHH
Confidence 57788776 4665
No 50
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=91.24 E-value=0.65 Score=48.41 Aligned_cols=71 Identities=17% Similarity=0.138 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHH
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQ 102 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~ 102 (509)
.+.-|..++++|----..+|++.||-||+--+.-|+..|.. .....+-|..++.++-+-|.++|+||.-|+
T Consensus 6 ~l~kaI~lv~kA~~eD~a~nY~eA~~lY~~aleYF~~~lKY----E~~~~kaKd~IraK~~EYLdRAEkLK~yL~ 76 (439)
T KOG0739|consen 6 FLQKAIDLVKKAIDEDNAKNYEEALRLYQNALEYFLHALKY----EANNKKAKDSIRAKFTEYLDRAEKLKAYLK 76 (439)
T ss_pred HHHHHHHHHHHHhhhcchhchHHHHHHHHHHHHHHHHHHHh----hhcChhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67789999999999999999999999999988888777653 323445678999999999999999999776
No 51
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=90.15 E-value=1.5 Score=39.80 Aligned_cols=98 Identities=18% Similarity=0.316 Sum_probs=57.7
Q ss_pred CCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCCC-----CCCCCCHHHHH
Q 010474 354 DKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT-----QSCFMSSIDVH 428 (509)
Q Consensus 354 ~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~-----~~afpSs~DL~ 428 (509)
..+.|.||+++ +..++.+.-|. +..+..+.|...+. -...+...|+-||||.. ..-.+|..|+.
T Consensus 18 ~~nrEy~G~I~-~~~~G~y~~t~----p~~G~~~~~~~~~~------~~p~g~~~vA~yHTHG~~~~~y~~evfS~~D~~ 86 (123)
T PF14220_consen 18 RENREYCGYIG-KDEDGKYFATE----PRRGENASCYPSNP------PCPNGSTIVASYHTHGAYSDGYDNEVFSPQDIR 86 (123)
T ss_pred cCCcEEEEEEE-EcCCCcEEeec----CccCCCCCcCCCCc------ccccccceeeEeecccccCCCccccCCCHHHhh
Confidence 36899999986 44455555442 23345566655432 12457789999999985 45679999997
Q ss_pred hHHHhhhhCCCeEEEEEcCCCCCCcccEEEEcCCCCchhhhcccc
Q 010474 429 THYSYQIMLPESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQ 473 (509)
Q Consensus 429 tq~sYQ~~~pe~IaIV~sP~~~~~~~gaFRLt~p~g~~~i~~c~~ 473 (509)
.- ....++.+ |-.| +-+.|+.. +.++..-..|.+
T Consensus 87 ~~--~~~~~~gY---l~TP-----~Grl~~~~-~~~~~~~q~~~~ 120 (123)
T PF14220_consen 87 GD--KNNGINGY---LGTP-----GGRLWKYD-PSTKTIRQICGQ 120 (123)
T ss_pred hh--hhcCccce---EeCC-----CCcEEEEc-CchhHHHHHHhc
Confidence 64 12222333 2222 33455544 566655566654
No 52
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=86.51 E-value=3.4 Score=37.10 Aligned_cols=69 Identities=25% Similarity=0.194 Sum_probs=40.1
Q ss_pred CcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCCCCCCCCCHHHHHh
Q 010474 356 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHT 429 (509)
Q Consensus 356 ~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~~~afpSs~DL~t 429 (509)
..|.+.+++=...++.+.+..++ .|+.+.|. .++.++|...-..+..-|-..|-||++.+.||..|+..
T Consensus 20 ~~E~~~~l~Ld~~~~li~~~~v~----~G~~~~~~-v~~R~I~~~al~~~A~~vIl~HNHPsG~~~PS~~D~~~ 88 (123)
T PF04002_consen 20 DQEQFRVLYLDSKNRLIGDEVVS----EGTIDSAP-VDPREIFRRALRLNASSVILAHNHPSGDPEPSDADIAL 88 (123)
T ss_dssp TS-EEEEEEE-TTSBEEEEEEEE----ESTT-GGG-CSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHH
T ss_pred CCeEEEEEEECCCCcEEEEEEec----ccCCCccc-ccHHHHHHHHHhhCCceEEEEEEcCCCCCCCCHhHHHH
Confidence 56776666533333333333322 24444444 57899999888888888888999999999999999854
No 53
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=86.47 E-value=1.5 Score=44.02 Aligned_cols=108 Identities=17% Similarity=0.267 Sum_probs=63.6
Q ss_pred EEECHHHHHHHHHH-----HhcCCCCCc-ceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHH-----hh
Q 010474 335 LHISTTMMDNFMKL-----AKSNTDKNL-ETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQ-----DK 403 (509)
Q Consensus 335 V~I~~~ll~~~l~h-----A~~nt~~~~-EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~-----~~ 403 (509)
|.+-+.+++.|-.| ++. +.|. -|.|-|+|+..++.+.|.+.|..+-....+. +.+|-+.+..-+ -=
T Consensus 11 v~LHPLVImniSdH~tR~k~Q~--gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~-~~~dke~l~kk~eqykqVF 87 (299)
T KOG3050|consen 11 VKLHPLVIMNISDHYTRVKTQL--GPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDT-ETIDKEYLEKKEEQYKQVF 87 (299)
T ss_pred EEeccEEEEehhHHHHHHHhhc--CCcHHHhhhhheecccCceEEEeeeeEEEecchhhh-hhccHHHHHHHHHHHHHhc
Confidence 44444445555555 333 3466 7899999999999999999998755322221 123333222211 24
Q ss_pred CCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEEEEcCCC
Q 010474 404 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQD 449 (509)
Q Consensus 404 ~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaIV~sP~~ 449 (509)
.++.++|||-+- .-+...|+|.|..--....--+.+-..|..
T Consensus 88 pdl~vlGwYttG----~d~t~sd~~i~k~l~~i~esplflkLNp~t 129 (299)
T KOG3050|consen 88 PDLYVLGWYTTG----SDPTPSDIHIHKQLMDINESPLFLKLNPAT 129 (299)
T ss_pred ccceEEEEeecC----CCCChhhhHHHHHHHhhhcCceEEEecchh
Confidence 688999999873 334667777776433333333555555543
No 54
>PRK00024 hypothetical protein; Reviewed
Probab=79.64 E-value=13 Score=37.05 Aligned_cols=85 Identities=21% Similarity=0.151 Sum_probs=55.6
Q ss_pred CHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCCC
Q 010474 338 STTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT 417 (509)
Q Consensus 338 ~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~ 417 (509)
.+..+.+++...-.+ ...|...+|+=...+..+....++ .|+-+.| ..++.++|..+-..+..-|-.-|=||+
T Consensus 105 ~~~~~~~~l~~~l~~--~~~E~f~vl~Ld~~~~li~~~~i~----~Gt~~~~-~v~pRei~~~Al~~~A~~iIl~HNHPS 177 (224)
T PRK00024 105 SPEDVADYLMAELRD--EEQEHFVVLFLDTKNRVIADEELF----IGTLNSS-IVHPREIVKRALKLNAAALILAHNHPS 177 (224)
T ss_pred CHHHHHHHHHHHccC--CCceEEEEEEECCCCCEeeEEEee----eecCCeE-EEcHHHHHHHHHHhhccceEEEecCCC
Confidence 334444555544443 367888877643333333332222 2444444 357899999888777777888899999
Q ss_pred CCCCCCHHHHHh
Q 010474 418 QSCFMSSIDVHT 429 (509)
Q Consensus 418 ~~afpSs~DL~t 429 (509)
+.+.||..|+..
T Consensus 178 G~~~PS~~D~~~ 189 (224)
T PRK00024 178 GDPEPSQADILI 189 (224)
T ss_pred CCCCCCHHHHHH
Confidence 999999999854
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=77.77 E-value=20 Score=35.63 Aligned_cols=85 Identities=22% Similarity=0.174 Sum_probs=55.0
Q ss_pred CHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHHhhCCCcceEEEcCCCC
Q 010474 338 STTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT 417 (509)
Q Consensus 338 ~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~~~~gl~~vGWyHSHP~ 417 (509)
+++.+..++...-.+ ...|.+.+|+=...+..+....++ .|+-+.| ..++.++|...-..+..-|=.-|=||+
T Consensus 99 s~~~v~~~l~~~l~~--~~~E~f~vl~Ld~~n~li~~~~i~----~Gt~~~~-~v~pReI~~~Al~~~A~~vIlaHNHPS 171 (218)
T TIGR00608 99 SPEAAAEFLHTDLAH--ETREHFMVLFLDRKNRLIAKEVVF----IGTVNHV-PVHPREIFKEALKLSASALILAHNHPS 171 (218)
T ss_pred CHHHHHHHHHHHhcC--CCceEEEEEEECCCCcEEEEEEee----cCCCCeE-EEcHHHHHHHHHHhhCCeEEEEeecCC
Confidence 344555566555553 367887777522222332222221 2444444 357899999887777777777899999
Q ss_pred CCCCCCHHHHHh
Q 010474 418 QSCFMSSIDVHT 429 (509)
Q Consensus 418 ~~afpSs~DL~t 429 (509)
+.+.||..|+..
T Consensus 172 G~~~PS~~Di~~ 183 (218)
T TIGR00608 172 GEPSPSQEDILI 183 (218)
T ss_pred CCCCCCHHHHHH
Confidence 999999999854
No 56
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=69.77 E-value=8.8 Score=25.01 Aligned_cols=29 Identities=7% Similarity=0.045 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010474 34 NILKQADIFREEKNIIDLYVMLLRFSSLV 62 (509)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (509)
.+++.|.+|.+.||.++|=-.|-+++..+
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 57899999999999999999888877654
No 57
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=68.40 E-value=13 Score=25.43 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCC-CCcc
Q 010474 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP-CHRD 71 (509)
Q Consensus 31 sa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp-~Hpd 71 (509)
+|..+...|.+|..-|+++.|=-++-+=+.+.-..+. .|||
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 3567778899999999999999999998888744433 3775
No 58
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=67.92 E-value=27 Score=33.30 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=28.0
Q ss_pred HhhCCCcceEEEcCCCCCCCCCCHHHHHhHHHhhhhCCCeEEE
Q 010474 401 QDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAI 443 (509)
Q Consensus 401 ~~~~gl~~vGWyHSHP~~~afpSs~DL~tq~sYQ~~~pe~IaI 443 (509)
+...+-.++. |||||..+.++|..|..+-..+. .+|-++++
T Consensus 111 l~~~~~~iid-iHSHP~~~~~~S~~D~~~~~~~~-~i~~a~y~ 151 (162)
T PF15659_consen 111 LKNNGNKIID-IHSHPENSNGPSGNDMKNAKPRK-NIPYAIYS 151 (162)
T ss_pred hccCCceEEE-eccCCCCCCCCCcchhhhhhhcc-cccceeeE
Confidence 3456667777 99999999899999987643222 24444443
No 59
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=67.44 E-value=50 Score=30.80 Aligned_cols=47 Identities=21% Similarity=0.218 Sum_probs=35.3
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccc
Q 010474 21 NRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYL 73 (509)
Q Consensus 21 ~~iplr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk 73 (509)
.+.|...|-.-| -|.-|..|++.|+++.|.--+-||+.|- |+||+.-
T Consensus 38 ~ryP~g~ya~qA--qL~l~yayy~~~~y~~A~a~~~rFirLh----P~hp~vd 84 (142)
T PF13512_consen 38 TRYPFGEYAEQA--QLDLAYAYYKQGDYEEAIAAYDRFIRLH----PTHPNVD 84 (142)
T ss_pred hcCCCCcccHHH--HHHHHHHHHHccCHHHHHHHHHHHHHhC----CCCCCcc
Confidence 334444443322 3445889999999999999999999998 9999753
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=59.27 E-value=24 Score=23.25 Aligned_cols=30 Identities=10% Similarity=0.130 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 010474 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (509)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (509)
|..++..|.+|.+.||++.|.-.|.+-+.+
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=56.11 E-value=26 Score=29.69 Aligned_cols=38 Identities=18% Similarity=0.083 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHh
Q 010474 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVT 63 (509)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ 63 (509)
+.|++-|..-++.|+..+++|++..|..+..--+-+.+
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 68999999999999999999999988877765555443
No 62
>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=54.89 E-value=33 Score=22.35 Aligned_cols=31 Identities=10% Similarity=-0.009 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010474 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (509)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (509)
|.-++..|.+|++.|++++|--.+-|-+.|.
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 3456788999999999999999988877664
No 63
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=46.54 E-value=2e+02 Score=34.06 Aligned_cols=28 Identities=14% Similarity=-0.008 Sum_probs=15.5
Q ss_pred ceEEEcCCCCCCCCCCHHHHHhHHHhhh
Q 010474 408 PLGWIHTHPTQSCFMSSIDVHTHYSYQI 435 (509)
Q Consensus 408 ~vGWyHSHP~~~afpSs~DL~tq~sYQ~ 435 (509)
++...-+-+....++|.+-...+++-|.
T Consensus 767 F~vvm~~vkrL~pRL~~ilFKl~fse~v 794 (1102)
T KOG1924|consen 767 FVVVMSQVKRLRPRLSAILFKLTFSEQV 794 (1102)
T ss_pred HhHHHhhccccChhHHHHHHHhhHHHHH
Confidence 3333334455667777776655555554
No 64
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=46.34 E-value=35 Score=24.43 Aligned_cols=35 Identities=20% Similarity=0.098 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCccc
Q 010474 34 NILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY 72 (509)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdy 72 (509)
..+..|..|.+.|++++|--+|-|.+.+. |.+++.
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~----P~~~~a 37 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRALALD----PDDPEA 37 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHC----cCCHHH
Confidence 35677999999999999999999977765 666544
No 65
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=41.20 E-value=57 Score=22.39 Aligned_cols=28 Identities=11% Similarity=0.122 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010474 35 ILKQADIFREEKNIIDLYVMLLRFSSLV 62 (509)
Q Consensus 35 llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (509)
+...|.+|++.||+++|--+|-+-+.|-
T Consensus 2 l~~Lg~~~~~~g~~~~Ai~~y~~aL~l~ 29 (36)
T PF13176_consen 2 LNNLGRIYRQQGDYEKAIEYYEQALALA 29 (36)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence 5677999999999999999999865443
No 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=38.65 E-value=79 Score=24.80 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCC
Q 010474 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP 67 (509)
Q Consensus 31 sa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp 67 (509)
+|..+...|.+|++.|++++|--+|-+-+.+ .+.+.
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 56664
No 67
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=37.56 E-value=49 Score=35.23 Aligned_cols=57 Identities=26% Similarity=0.324 Sum_probs=36.2
Q ss_pred EEeecee-cCCEEEEEEEEecCCCCC-Cc---------ccccCChHHHHHHH------hhCCCcceEEEcCCCC
Q 010474 361 GILAGSL-KNRKFYITALIIPKQEST-SD---------SCQATNEEEIFEVQ------DKRSLFPLGWIHTHPT 417 (509)
Q Consensus 361 GlL~G~~-~~~~l~Vt~~~~p~q~~t-~~---------~~~~~de~e~~~~~------~~~gl~~vGWyHSHP~ 417 (509)
|||+|.. ..+.-+|-++++.|...+ .+ .....|++.+.+.+ -..|+.+||+|=.+|.
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 8999998 555567777775544322 11 12235666665543 3689999999976653
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=35.93 E-value=97 Score=20.31 Aligned_cols=30 Identities=10% Similarity=0.069 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Q 010474 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (509)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~L 61 (509)
|...+..|.+|..-|+++.|...|.|=+.+
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 455678899999999999999998886655
No 69
>PRK15490 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=35.02 E-value=1e+02 Score=35.05 Aligned_cols=69 Identities=19% Similarity=0.238 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHH-HHHHHHHHHHHhhCHHHHHHHH
Q 010474 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLK-KKLLNALSELEELQPAVQQKIN 106 (509)
Q Consensus 30 Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~-~~l~~vl~~lE~LK~~l~~~Y~ 106 (509)
.||.+|+.+|+..-+-|..|+||-+|-| |. ..|+| +....-.+.+.+ .-+.++...+-++.+-.+++|+
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~----~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (578)
T PRK15490 40 LTSLAMLKKAEFLHDVNETERAYALYET---LI----AQNND-EARYEYARRLYNTGLAKDAQLILKKVSNGVQKKYN 109 (578)
T ss_pred hhHHHHHHHhhhhhhhhhhHhHHHHHHH---HH----HhCCc-chHHHHHHHHHhhhhhhHHHHHHHHhCccHhHHHH
Confidence 5789999999999999999999998876 43 68998 322211122222 2345566666677777777776
No 70
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=32.51 E-value=89 Score=29.73 Aligned_cols=59 Identities=10% Similarity=0.233 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhccCCC-Cccccccc-HHHHHHHHHHHHHHHHHHHhhCHHHH-----HHHHHHHHh
Q 010474 51 LYVMLLRFSSLVTETIPC-HRDYLASF-KSQKLYLKKKLLNALSELEELQPAVQ-----QKINELNRK 111 (509)
Q Consensus 51 AYily~Ry~~Lv~ekLp~-Hpdyk~~~-~~~k~~~~~~l~~vl~~lE~LK~~l~-----~~Y~~~~~~ 111 (509)
|++|.++|..=| ++++. ||.|.... ....+..+++. ..+.++-++|.+|+ ..|.+|.+.
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 688999999888 56654 88886322 12233333333 33566667777774 456666653
No 71
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.95 E-value=1.2e+02 Score=29.73 Aligned_cols=72 Identities=13% Similarity=0.115 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccccHHHHHHHHHHHHHHHHHHHhhCHHHHH
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~~~~~k~~~~~~l~~vl~~lE~LK~~l~~ 103 (509)
-+..|..++..|---.++|.+.+|.+-|--=++|+++-|..-|-= ...|..++.++-+-+.+++.|++-|++
T Consensus 11 ~~~aAa~iL~~AVe~d~e~k~pqALl~YkeGIdLi~e~lk~~~ld----na~R~~i~~k~s~Ym~ka~diekYLdq 82 (247)
T KOG4509|consen 11 LLKAAAPILCDAVEDDKEGKVPQALLCYKEGIDLIAEALKGMKLD----NADRCKIMAKFSDYMDKAADIEKYLDQ 82 (247)
T ss_pred hhhhhhhHHHHHhcccccccccHHHHHHhhhHHHHHHHHccCCCc----chHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 356788899999999999999999999999999999999886622 235667778888889999999887764
No 72
>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=31.59 E-value=77 Score=24.13 Aligned_cols=36 Identities=11% Similarity=0.164 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcc
Q 010474 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRD 71 (509)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpd 71 (509)
|..+...|.+|++.|++++|-..|.+-+.+- |.|++
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~----p~~~~ 38 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD----PNNAE 38 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS----TTHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC----CCCHH
Confidence 5678889999999999999999999877763 55544
No 73
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=31.18 E-value=55 Score=32.82 Aligned_cols=39 Identities=23% Similarity=0.220 Sum_probs=31.9
Q ss_pred cCChHHHHHHHhhCCCcceEEEcCCCCCCCCCCHHHHHh
Q 010474 391 ATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHT 429 (509)
Q Consensus 391 ~~de~e~~~~~~~~gl~~vGWyHSHP~~~afpSs~DL~t 429 (509)
...|.|++..+-..+..-|=..|=||+..+-||..|+.-
T Consensus 151 ~V~PREI~k~Al~~nAaavIlaHNHPSGd~~PS~aD~~i 189 (224)
T COG2003 151 EVHPREIFKEALKYNAAAVILAHNHPSGDPTPSRADILI 189 (224)
T ss_pred eecHHHHHHHHHHhcchhhheeccCCCCCCCcCHHHHHH
Confidence 456899999877666666666899999999999999853
No 74
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=29.76 E-value=72 Score=34.65 Aligned_cols=130 Identities=22% Similarity=0.322 Sum_probs=87.5
Q ss_pred EEEE-CHHHHHHHHHHHhcCCCCCcceEEEeeceecC--C-----EEEEEEEEecCCCCCCcccccCCh--HHHHHH-Hh
Q 010474 334 QLHI-STTMMDNFMKLAKSNTDKNLETCGILAGSLKN--R-----KFYITALIIPKQESTSDSCQATNE--EEIFEV-QD 402 (509)
Q Consensus 334 ~V~I-~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~--~-----~l~Vt~~~~p~q~~t~~~~~~~de--~e~~~~-~~ 402 (509)
+|.. .+.+++.||..=+.. +....|.|.|...+ + .-.|..++-|+|...+|-+.+... +.+++. +.
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 4444 457899999877663 56789999998853 1 234556667889877776655211 112222 34
Q ss_pred hCCCcceEEEcCCC---------------CCCCCCCHHHHHhHHHhhhhCC-------------CeEEEEEcCCCCC-Cc
Q 010474 403 KRSLFPLGWIHTHP---------------TQSCFMSSIDVHTHYSYQIMLP-------------ESVAIVMAPQDAT-RK 453 (509)
Q Consensus 403 ~~gl~~vGWyHSHP---------------~~~afpSs~DL~tq~sYQ~~~p-------------e~IaIV~sP~~~~-~~ 453 (509)
.-||..+|.|-|-- .-+-|+|+..+..-..+|.|.| .+|.+|++-.-+. -+
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 77889999987632 2356999999999999999886 4678888865542 24
Q ss_pred ccEEEEcCCCCchh
Q 010474 454 HGIFRLTSPGGMSV 467 (509)
Q Consensus 454 ~gaFRLt~p~g~~~ 467 (509)
+-.|.+++ .+|.-
T Consensus 392 ~~sYQVSn-~~~AL 404 (571)
T COG5100 392 LQSYQVSN-QCMAL 404 (571)
T ss_pred eeEEeehh-hhhHH
Confidence 67788885 46633
No 75
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=25.34 E-value=2.8e+02 Score=28.16 Aligned_cols=79 Identities=11% Similarity=0.206 Sum_probs=46.7
Q ss_pred EEEECHHHHHHHHHHHhcCCCCCcceEEEeeceecCCEEEEEEEEecCCCCCCcccccCChHHHHHHH-h----------
Q 010474 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQ-D---------- 402 (509)
Q Consensus 334 ~V~I~~~ll~~~l~hA~~nt~~~~EvcGlL~G~~~~~~l~Vt~~~~p~q~~t~~~~~~~de~e~~~~~-~---------- 402 (509)
.++|++.--.+++ ..--|...+.+ +|+++....+..+.|+--+...-.-..+.-...|..++++-+ +
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 4899999999999 44455433344 999998775556665443433222222333455666665432 1
Q ss_pred h---CCCcceEEEcC
Q 010474 403 K---RSLFPLGWIHT 414 (509)
Q Consensus 403 ~---~gl~~vGWyHS 414 (509)
+ ..+.++||.--
T Consensus 101 ~~G~~~l~l~GW~~~ 115 (239)
T PF09935_consen 101 KRGYPPLHLVGWAEP 115 (239)
T ss_pred hcCCCceEEeccccC
Confidence 2 34478999653
No 76
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=25.22 E-value=1.3e+02 Score=28.81 Aligned_cols=36 Identities=17% Similarity=0.147 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCccc
Q 010474 33 DNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY 72 (509)
Q Consensus 33 ~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdy 72 (509)
.-++..|..|.+.||++.|-..+-+|+.++ |.||..
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 345777999999999999999999999888 999854
No 77
>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=23.83 E-value=1.7e+02 Score=21.09 Aligned_cols=37 Identities=19% Similarity=0.066 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCC
Q 010474 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68 (509)
Q Consensus 32 a~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~ 68 (509)
|+.+.+.|+|.+..+|+++|.-=|.+-+.|--+.+|-
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 3456788999999999999999998888887665554
No 78
>PRK05685 fliS flagellar protein FliS; Validated
Probab=23.30 E-value=5.3e+02 Score=23.30 Aligned_cols=84 Identities=15% Similarity=0.171 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCccccc--ccHHH----HHHHHHH-----HHHHHHHHHh
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLA--SFKSQ----KLYLKKK-----LLNALSELEE 96 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~--~~~~~----k~~~~~~-----l~~vl~~lE~ 96 (509)
=|.-|..-++.|..+.++||++.+..-+.|-..++.+ |...=|+.. .-+.. +..+..+ +.+-.+.+++
T Consensus 31 Lydgai~~l~~A~~ai~~~~~~~~~~~l~ka~~Ii~e-L~~sLd~e~ggeiA~~L~~LY~y~~~~L~~A~~~~d~~~l~e 109 (132)
T PRK05685 31 LYEGALSFLAQAKLAIEQGDIEAKGEYLSKAINIING-LRNSLDMEKGGEVAKNLSALYDYMIRRLLEANLRNDVQAIDE 109 (132)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH-HHhhcCCccccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 4556677778899999999999999999999988854 444334432 11111 2233333 3333466666
Q ss_pred hCHHHHHHHHHHHHhh
Q 010474 97 LQPAVQQKINELNRKK 112 (509)
Q Consensus 97 LK~~l~~~Y~~~~~~~ 112 (509)
..+.|..-.+.|.+..
T Consensus 110 v~~il~~LreaW~~i~ 125 (132)
T PRK05685 110 VEGLLREIKEAWKQIP 125 (132)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 6666766677776643
No 79
>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=22.48 E-value=5.1e+02 Score=22.86 Aligned_cols=84 Identities=19% Similarity=0.197 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCCCcccccc--cHHH----HHHH-----HHHHHHHHHHHHh
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLAS--FKSQ----KLYL-----KKKLLNALSELEE 96 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~Hpdyk~~--~~~~----k~~~-----~~~l~~vl~~lE~ 96 (509)
=|--+..-++.|..+.++||++.+-.-+.|-..++.+-... =|+... -+.. +..+ ...+.+-.+.+++
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 45667788899999999999999999999999888644433 233211 1111 2222 2334444577777
Q ss_pred hCHHHHHHHHHHHHhh
Q 010474 97 LQPAVQQKINELNRKK 112 (509)
Q Consensus 97 LK~~l~~~Y~~~~~~~ 112 (509)
+...|..-.+.|.+..
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 7777777777887644
No 80
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=22.46 E-value=1.6e+02 Score=25.19 Aligned_cols=32 Identities=9% Similarity=-0.009 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcChhhHHHHHHH
Q 010474 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLR 57 (509)
Q Consensus 26 r~Y~Rsa~~llr~A~iy~~egn~e~AYily~R 57 (509)
-..|+.|...|..|...+.+||+.+|+.+...
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 81
>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=21.90 E-value=4.8e+02 Score=21.86 Aligned_cols=44 Identities=18% Similarity=0.052 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHHhccCCC
Q 010474 25 LRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68 (509)
Q Consensus 25 lr~Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv~ekLp~ 68 (509)
+|-||.-|-+-+..|=-+.+.|+.++|-.+|-+=+...++.+.-
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 46799999999999999999999999999999888888776654
No 82
>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=21.64 E-value=1.7e+02 Score=22.89 Aligned_cols=35 Identities=3% Similarity=-0.016 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHH
Q 010474 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (509)
Q Consensus 28 Y~Rsa~~llr~A~iy~~egn~e~AYily~Ry~~Lv 62 (509)
...+|..+...|.+|..-||++.|--++.+=++++
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 35568888999999999999999999998877775
No 83
>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=20.70 E-value=1.5e+02 Score=17.21 Aligned_cols=26 Identities=0% Similarity=-0.043 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhcChhhHHHHHHHHH
Q 010474 34 NILKQADIFREEKNIIDLYVMLLRFS 59 (509)
Q Consensus 34 ~llr~A~iy~~egn~e~AYily~Ry~ 59 (509)
...+.|..|...|+++.|-..+.+-+
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~ 28 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKAL 28 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 34677889999999999988776544
Done!