Query 014747
Match_columns 419
No_of_seqs 165 out of 249
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:07:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014747.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014747hhsearch_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 1.3E-68 2.7E-73 527.5 23.3 327 1-414 1-333 (424)
2 PF08969 USP8_dimer: USP8 dime 99.9 9.8E-24 2.1E-28 182.2 10.4 103 5-108 10-115 (115)
3 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.7 4.2E-17 9.1E-22 158.4 5.6 76 333-414 36-114 (252)
4 cd08066 MPN_AMSH_like Mov34/MP 99.6 6E-16 1.3E-20 143.2 8.2 83 332-414 1-83 (173)
5 cd08067 MPN_2A_DUB Mov34/MPN/P 98.4 4E-07 8.6E-12 85.6 6.8 78 334-414 6-87 (187)
6 cd08058 MPN_euk_mb Mpr1p, Pad1 98.4 3.3E-07 7.1E-12 79.4 4.9 72 341-414 2-73 (119)
7 cd07767 MPN Mpr1p, Pad1p N-ter 98.3 7.9E-07 1.7E-11 75.1 4.9 70 343-414 2-71 (116)
8 cd08069 MPN_RPN11_CSN5 Mov34/M 98.2 6E-06 1.3E-10 81.6 8.4 81 332-414 9-95 (268)
9 PF01398 JAB: JAB1/Mov34/MPN/P 98.1 5.3E-06 1.2E-10 70.8 5.6 81 332-414 3-89 (114)
10 smart00232 JAB_MPN JAB/MPN dom 98.0 2.3E-05 5E-10 67.7 7.1 77 335-414 2-84 (135)
11 cd08061 MPN_NPL4 Mov34/MPN/PAD 97.6 0.00011 2.5E-09 73.0 6.3 78 335-414 14-101 (274)
12 cd08068 MPN_BRCC36 Mov34/MPN/P 97.4 0.00034 7.3E-09 68.6 7.1 80 333-414 2-97 (244)
13 cd08070 MPN_like Mpr1p, Pad1p 97.3 0.00042 9E-09 60.7 6.1 73 340-414 2-78 (128)
14 PF04212 MIT: MIT (microtubule 97.1 0.0035 7.7E-08 49.2 8.3 69 28-101 1-69 (69)
15 cd02684 MIT_2 MIT: domain cont 97.1 0.0047 1E-07 50.0 8.8 71 29-104 3-73 (75)
16 cd02678 MIT_VPS4 MIT: domain c 97.0 0.0043 9.3E-08 49.9 8.4 71 28-103 2-72 (75)
17 smart00745 MIT Microtubule Int 97.0 0.0065 1.4E-07 48.5 9.2 73 26-103 2-74 (77)
18 cd02683 MIT_1 MIT: domain cont 96.9 0.0066 1.4E-07 49.4 8.4 69 30-103 4-72 (77)
19 cd02681 MIT_calpain7_1 MIT: do 96.8 0.008 1.7E-07 49.0 8.1 71 29-103 3-73 (76)
20 cd02656 MIT MIT: domain contai 96.6 0.022 4.7E-07 45.4 9.2 70 29-103 3-72 (75)
21 cd02677 MIT_SNX15 MIT: domain 96.5 0.023 5E-07 46.1 8.9 68 28-100 2-69 (75)
22 PF14464 Prok-JAB: Prokaryotic 96.4 0.0054 1.2E-07 51.0 4.7 62 339-414 2-67 (104)
23 cd02680 MIT_calpain7_2 MIT: do 95.3 0.12 2.6E-06 42.1 8.1 64 30-102 4-71 (75)
24 cd02682 MIT_AAA_Arch MIT: doma 94.8 0.18 3.9E-06 41.1 7.9 68 29-101 3-70 (75)
25 cd08065 MPN_eIF3h Mpr1p, Pad1p 94.5 0.068 1.5E-06 52.9 5.7 80 334-415 2-88 (266)
26 COG1310 Predicted metal-depend 94.1 0.072 1.6E-06 47.0 4.6 75 335-414 2-77 (134)
27 KOG0739 AAA+-type ATPase [Post 91.2 0.85 1.8E-05 46.8 8.0 73 28-104 6-78 (439)
28 TIGR02256 ICE_VC0181 integrati 90.8 0.41 8.9E-06 43.0 4.9 65 350-414 10-81 (131)
29 cd08060 MPN_UPF0172 Mov34/MPN/ 85.9 2.4 5.2E-05 39.9 6.7 70 338-414 2-78 (182)
30 cd08072 MPN_archaeal Mov34/MPN 84.8 2.3 5E-05 37.0 5.7 66 337-414 1-67 (117)
31 PF13374 TPR_10: Tetratricopep 84.4 2.7 5.8E-05 28.2 4.8 41 31-71 1-42 (42)
32 PF05021 NPL4: NPL4 family; I 83.9 1.5 3.2E-05 44.7 4.6 55 360-414 2-66 (306)
33 KOG1924 RhoA GTPase effector D 82.0 15 0.00032 42.0 11.6 28 54-81 423-450 (1102)
34 TIGR03735 PRTRC_A PRTRC system 81.3 2.9 6.2E-05 40.0 5.2 73 332-414 70-142 (192)
35 cd08057 MPN_euk_non_mb Mpr1p, 74.6 8.9 0.00019 34.7 6.2 60 356-416 22-86 (157)
36 PF13181 TPR_8: Tetratricopept 73.5 9.6 0.00021 24.7 4.7 30 32-61 1-30 (34)
37 PF05168 HEPN: HEPN domain; I 72.7 10 0.00022 31.2 5.7 41 26-66 2-42 (118)
38 PF07719 TPR_2: Tetratricopept 65.5 19 0.00041 23.0 4.7 30 32-61 1-30 (34)
39 KOG1795 U5 snRNP spliceosome s 65.4 3.9 8.4E-05 48.5 2.2 74 335-414 2097-2173(2321)
40 PF13424 TPR_12: Tetratricopep 62.7 23 0.00049 27.2 5.5 40 31-71 4-44 (78)
41 PF00515 TPR_1: Tetratricopept 60.4 26 0.00057 22.6 4.7 30 32-61 1-30 (34)
42 cd08062 MPN_RPN7_8 Mpr1p, Pad1 59.3 12 0.00026 37.5 4.2 58 356-414 25-90 (280)
43 PF13174 TPR_6: Tetratricopept 58.6 18 0.00039 22.8 3.7 28 34-61 2-29 (33)
44 cd08059 MPN_prok_mb Mpr1p, Pad 58.6 13 0.00028 30.8 3.7 50 356-414 15-64 (101)
45 COG5178 PRP8 U5 snRNP spliceos 56.3 8.1 0.00018 45.7 2.6 73 335-414 2136-2213(2365)
46 cd02679 MIT_spastin MIT: domai 56.3 1.1E+02 0.0025 25.1 8.9 44 25-68 1-44 (79)
47 PF13176 TPR_7: Tetratricopept 55.6 28 0.0006 23.5 4.3 28 35-62 2-29 (36)
48 PF10516 SHNi-TPR: SHNi-TPR; 54.7 31 0.00067 24.5 4.5 38 32-69 1-38 (38)
49 PF13414 TPR_11: TPR repeat; P 49.7 30 0.00066 25.7 4.2 30 32-61 3-32 (69)
50 PF02561 FliS: Flagellar prote 48.2 1.3E+02 0.0029 25.9 8.5 87 27-113 24-120 (122)
51 KOG4509 Uncharacterized conser 46.4 61 0.0013 31.1 6.3 74 28-105 11-84 (247)
52 KOG1556 26S proteasome regulat 46.3 18 0.00038 36.2 2.9 69 343-414 23-98 (309)
53 cd08073 MPN_NLPC_P60 Mpr1p, Pa 45.2 24 0.00052 30.3 3.3 63 342-414 3-67 (108)
54 PRK05685 fliS flagellar protei 42.9 2.2E+02 0.0049 25.2 9.2 84 28-112 31-125 (132)
55 PF13428 TPR_14: Tetratricopep 39.2 71 0.0015 22.2 4.5 28 34-61 3-30 (44)
56 cd08064 MPN_eIF3f Mpr1p, Pad1p 38.9 42 0.00092 33.1 4.4 58 357-415 23-85 (265)
57 PF13424 TPR_12: Tetratricopep 38.3 64 0.0014 24.6 4.5 35 28-62 42-76 (78)
58 COG2250 Uncharacterized conser 37.9 1.2E+02 0.0027 26.9 6.8 40 25-64 6-45 (132)
59 PF14220 DUF4329: Domain of un 37.5 39 0.00086 30.0 3.5 56 348-414 9-67 (123)
60 TIGR00208 fliS flagellar biosy 34.4 3.2E+02 0.0069 24.0 9.2 84 27-111 26-120 (124)
61 PRK15490 Vi polysaccharide bio 33.7 95 0.0021 34.6 6.3 69 30-106 40-109 (578)
62 KOG2834 Nuclear pore complex, 31.9 57 0.0012 35.2 4.1 76 336-414 179-264 (510)
63 KOG4253 Tryptophan-rich basic 30.7 1.1E+02 0.0025 28.6 5.4 59 51-111 10-75 (175)
64 smart00028 TPR Tetratricopepti 29.8 86 0.0019 17.8 3.2 27 34-60 3-29 (34)
65 PF08255 Leader_Trp: Trp-opero 28.9 31 0.00066 19.7 0.9 8 408-415 7-14 (14)
66 PF14346 DUF4398: Domain of un 28.6 1.2E+02 0.0025 25.4 4.8 36 26-61 39-74 (103)
67 TIGR01597 PYST-B Plasmodium yo 25.3 1.8E+02 0.0038 29.0 5.9 82 18-105 50-133 (255)
68 KOG2148 Exocyst protein Sec3 [ 22.4 3.4E+02 0.0073 31.1 7.9 80 33-112 652-739 (867)
69 PF13815 Dzip-like_N: Iguana/D 22.3 2E+02 0.0042 25.0 5.2 61 48-111 53-113 (118)
70 PTZ00453 cyclin-dependent kina 22.2 74 0.0016 27.3 2.4 48 366-416 33-81 (96)
71 PF13512 TPR_18: Tetratricopep 22.1 1.3E+02 0.0029 27.4 4.2 49 19-73 36-84 (142)
72 PF14938 SNAP: Soluble NSF att 22.0 1.2E+02 0.0025 29.8 4.2 36 28-63 110-146 (282)
73 KOG1554 COP9 signalosome, subu 21.6 1.1E+02 0.0023 31.4 3.7 79 332-414 52-139 (347)
74 KOG1924 RhoA GTPase effector D 20.7 2.1E+02 0.0044 33.4 6.0 19 48-70 301-319 (1102)
No 1
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=100.00 E-value=1.3e-68 Score=527.53 Aligned_cols=327 Identities=34% Similarity=0.502 Sum_probs=203.9
Q ss_pred CCCchhhhhHHHhh---cccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccH
Q 014747 1 MRSSSEGINIAASA---QRLDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFK 77 (419)
Q Consensus 1 ~~~~~~~~eL~~~A---~~~e~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~ 77 (419)
|-+|....+.+..+ .+++||.+||+++|||+|++|+|||.||++|||+++|||||+||++||++|||+||||++..
T Consensus 1 ~~~S~~p~er~~~lsr~G~i~~n~~IplkryfRsg~ei~rmA~VY~~EgN~enafvLy~ry~tLfiEkipkHrDy~s~k- 79 (424)
T KOG2880|consen 1 MDGSLEPEERVRALSRLGAIEVNKNIPLKRYFRSGTEILRMANVYLEEGNVENAFVLYLRYITLFIEKIPKHRDYRSVK- 79 (424)
T ss_pred CCCCcChHHHHHHHHhcCceeecCCCCHHHhhhhhHHHHHHHHHHHhcCCcchhhhHHHHHHHHHHHhcccCcchhhhc-
Confidence 44666666665544 45899999999999999999999999999999999999999999999999999999999554
Q ss_pred HHHHHHHHHHHHH-HHHHHhhcHHHHHHHHHHHHhhhhhcccccccCCCCCccccccccccccchh-hhhhcccchhhhh
Q 014747 78 SQKLYLKKKLLNA-LSELEELQPAVQQKINELNRKKTNQVTGWSHASQNSTLEWPSLKKQTLTNYD-VTKALRLPSRELA 155 (419)
Q Consensus 78 ~~k~~l~k~l~~v-l~~lE~LK~~I~~~Y~e~~~~~~~~~~~~~~~~~~s~~~~~~~~dp~l~~~~-~~~av~laq~e~~ 155 (419)
.++..++++|+.+ ++.+++||++|.++|+.++..+...++... .+ .+.+ .-|++.+
T Consensus 80 ~ek~d~~~klk~~~~p~~deL~~~ll~rY~~eyn~y~~~K~k~~--------------------~E~~k~l--e~~~~~E 137 (424)
T KOG2880|consen 80 PEKEDIRKKLKEEAFPRIDELKAKLLKRYNVEYNEYDHSKKKNL--------------------AERFKKL--EVQREEE 137 (424)
T ss_pred hhHHHHHHHHHHHhhhhHHHHHHHHHHHHhhHHHHHHHHHhhhH--------------------HHHHHHh--hcchhhH
Confidence 6777777777665 899999999999999988775433111000 00 0000 0122222
Q ss_pred hcCCchhhhhccchHHHHHhhhccCCCCCcchhhccccccCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCcc
Q 014747 156 YQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSES 235 (419)
Q Consensus 156 ~~~~r~~~~~rr~~~~~~~r~~~~~~~~~~ee~l~r~~~~~~~g~~~~~~~~~~~~~~~y~~~~d~~~~~l~~~~~~~~~ 235 (419)
.+++|.++..+++....+| ...+.+++.|....
T Consensus 138 ~e~kr~aq~k~Q~l~~~~f-----------------------------------------------~~~~~~~~~q~~~s 170 (424)
T KOG2880|consen 138 TERKRSAQTKQQQLESSQF-----------------------------------------------SPLEPPSFKQLLDS 170 (424)
T ss_pred HHHHHHHHHhhhcCCcccC-----------------------------------------------CccCchHHHhhhcc
Confidence 2223323332222222222 22222222222111
Q ss_pred cccccCCCCCCCCCcCcccccCCCCCccccCCCCCCCCCCCccCCCCCCCccccCCCCCCCccchhhhhhhccCCCcccc
Q 014747 236 SIKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTET 315 (419)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~s~l~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~p~PPpv~~~~~~~~~~~~p~~~~~ 315 (419)
+.....+. .+-+..+...+.++....+...-+....+.++|++...-..+..+ .+|++++...+ .+.+
T Consensus 171 ~~m~s~~~-~gl~e~~~~~~~~p~~~~~~~~~s~~l~~~~s~ep~~s~~~n~~~---k~p~~~r~l~p-------~a~~- 238 (424)
T KOG2880|consen 171 GPMPSNQS-NGLPEQPIGEPLVPSNESRSLNYSELLSVLSSPEPSDSCTTNVTI---KSPSVDRVLKP-------GATD- 238 (424)
T ss_pred cCCCcCCC-CCCcCCCcCCCCcccccccccCCchhhhhccCCCccccccccccc---cCCCCCccccc-------cccc-
Confidence 11110000 000001111111110000000001011122222222211122212 23333322211 1100
Q ss_pred ccccCCCCCCCCCCCC-CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccCh
Q 014747 316 ECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE 394 (419)
Q Consensus 316 ~p~~~~~~~~~~~~~~-l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~e 394 (419)
.........+. +|+|+||.+||+.||+||.+||.||+||||||||+|++|.|+|||||||||++|||+|.|+||
T Consensus 239 -----n~~~~~~~~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~ne 313 (424)
T KOG2880|consen 239 -----NSNHGESSEGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNE 313 (424)
T ss_pred -----ccccccccCCccceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCH
Confidence 00001111122 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCceeeeeeee
Q 014747 395 EEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 395 e~~f~~~~~~~l~~lgwiHT 414 (419)
||||++||+++|+|||||||
T Consensus 314 eelF~vQdq~~L~tlGWIHT 333 (424)
T KOG2880|consen 314 EELFEVQDQHELLTLGWIHT 333 (424)
T ss_pred HHHheecccccceeeeeeec
Confidence 99999999999999999999
No 2
>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=9.8e-24 Score=182.17 Aligned_cols=103 Identities=35% Similarity=0.534 Sum_probs=87.1
Q ss_pred hhhhhHHHhhccc-ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHH-H
Q 014747 5 SEGINIAASAQRL-DVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKL-Y 82 (419)
Q Consensus 5 ~~~~eL~~~A~~~-e~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~-~ 82 (419)
....+|.++|..+ +||+++|+++|+|+|.+|+++|.+|+++||+|+|||+|+||++|| ++||+||||+........ .
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 3457899999998 999999999999999999999999999999999999999999999 999999999976654444 2
Q ss_pred HHHHHHHH-HHHHHhhcHHHHHHHHHH
Q 014747 83 LKKKLLNA-LSELEELQPAVQQKINEL 108 (419)
Q Consensus 83 l~k~l~~v-l~~lE~LK~~I~~~Y~e~ 108 (419)
..+++..+ |+++|.||++|+++|+++
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 3
>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=99.67 E-value=4.2e-17 Score=158.44 Aligned_cols=76 Identities=20% Similarity=0.350 Sum_probs=72.9
Q ss_pred eEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccC---CeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceee
Q 014747 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPL 409 (419)
Q Consensus 333 ~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~---~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~l 409 (419)
.+++||.+|+.+|+.+|..|| ++||+|+|+... |.+.|++++||.|.||.|+|++.++. +++++.+||.+|
T Consensus 36 ~t~vlPknllkkFi~iaD~rt----Q~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~--~~~~~l~~Le~L 109 (252)
T cd08056 36 YTYILPKNLLKKFISISDLRT----QIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL--PQHEYLEDLEPL 109 (252)
T ss_pred CEEEeCHHHHHHHHHHhhhcc----eEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccC--ccchhhCCCEee
Confidence 479999999999999999999 899999999987 89999999999999999999999874 999999999999
Q ss_pred eeeee
Q 014747 410 GWIHV 414 (419)
Q Consensus 410 gwiHT 414 (419)
|||||
T Consensus 110 GWIHT 114 (252)
T cd08056 110 GWIHT 114 (252)
T ss_pred EEEEc
Confidence 99999
No 4
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=99.63 E-value=6e-16 Score=143.20 Aligned_cols=83 Identities=58% Similarity=0.997 Sum_probs=80.8
Q ss_pred CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeee
Q 014747 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW 411 (419)
Q Consensus 332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgw 411 (419)
+|.|+||.+++++|+.+|..||.+++|+||+|+|+...+.+.|+++++|.|.+++++|...+++++|.+++.+||-+|||
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 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eee
Q 014747 412 IHV 414 (419)
Q Consensus 412 iHT 414 (419)
|||
T Consensus 81 yHS 83 (173)
T cd08066 81 IHT 83 (173)
T ss_pred Eec
Confidence 999
No 5
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=98.44 E-value=4e-07 Score=85.62 Aligned_cols=78 Identities=23% Similarity=0.327 Sum_probs=67.0
Q ss_pred EeeeCHHHHHHHHHHHhhhcccccchhhhhccccc--CCeeEEEEEeeccCCCCCCCccc--cChHHHHHHhhcCCceee
Q 014747 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK--NRKFYITALIIPKQESTSDSCQA--TNEEEIFEVQDKRSLFPL 409 (419)
Q Consensus 334 ~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~--~~~~~it~liiP~q~~t~d~C~~--~~ee~~f~~~~~~~l~~l 409 (419)
.|.|.....=+-+..|...+ .|.||+|+|+.. .+.+.|+..+...+..+++.|++ ..+.+++++.++.|+.++
T Consensus 6 ~V~Is~~all~m~~Ha~~~~---~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~gl~vV 82 (187)
T cd08067 6 KVTVSSNALLLMDFHCHLTT---SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRGLSVV 82 (187)
T ss_pred EEEECHHHHHHHHHHhcCCC---cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcCCEEE
Confidence 47788777777777888755 999999999975 46899999998899999999986 457788999999999999
Q ss_pred eeeee
Q 014747 410 GWIHV 414 (419)
Q Consensus 410 gwiHT 414 (419)
||+|+
T Consensus 83 GwYHS 87 (187)
T cd08067 83 GWYHS 87 (187)
T ss_pred EEEec
Confidence 99998
No 6
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=98.40 E-value=3.3e-07 Score=79.41 Aligned_cols=72 Identities=39% Similarity=0.703 Sum_probs=61.8
Q ss_pred HHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 341 l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT 414 (419)
.+.+++..|..++ ..|+||+|+|+...+.+.+.++-|+.+...++++...++.+.+....+.|+..+||.|+
T Consensus 2 ~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~~~~~~~~~~~~~~g~~~vG~YHS 73 (119)
T cd08058 2 ALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYHS 73 (119)
T ss_pred HHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCCchhHHHHHHHHHHhCCCCeEEEEEec
Confidence 4678888999866 78999999999988777777788888888888887766667788889999999999998
No 7
>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=98.30 E-value=7.9e-07 Score=75.14 Aligned_cols=70 Identities=20% Similarity=0.190 Sum_probs=57.9
Q ss_pred HHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747 343 DNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 343 ~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT 414 (419)
..|+..|..++ ..|.||+|.|+...+.+.|++++...+..+.+.|.......+...+...|+-.+||+||
T Consensus 2 k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhs 71 (116)
T cd07767 2 KMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHT 71 (116)
T ss_pred HhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEc
Confidence 46888898874 56899999999999999999998888888777765543335677888899999999999
No 8
>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=98.16 E-value=6e-06 Score=81.63 Aligned_cols=81 Identities=20% Similarity=0.332 Sum_probs=69.2
Q ss_pred CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccCh--HHHHH--Hh--hcCC
Q 014747 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE--EEIFE--VQ--DKRS 405 (419)
Q Consensus 332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~e--e~~f~--~~--~~~~ 405 (419)
+..|.|+...+.+++..|.. ....|.||+|+|+...+.+.||+.+...+.++++.|+...| +.+++ .. ...+
T Consensus 9 ~~~V~Is~~allkil~Ha~~--~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~ 86 (268)
T cd08069 9 FEKVYISSLALLKMLKHARA--GGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRP 86 (268)
T ss_pred ccEEEECHHHHHHHHHHHhc--cCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCC
Confidence 67899999999999999988 56789999999999899999999998889999999998764 33444 22 3488
Q ss_pred ceeeeeeee
Q 014747 406 LFPLGWIHV 414 (419)
Q Consensus 406 l~~lgwiHT 414 (419)
+.++||.||
T Consensus 87 ~~vVGWYHS 95 (268)
T cd08069 87 ENVVGWYHS 95 (268)
T ss_pred ceeEeeecc
Confidence 999999999
No 9
>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=98.09 E-value=5.3e-06 Score=70.77 Aligned_cols=81 Identities=21% Similarity=0.371 Sum_probs=70.0
Q ss_pred CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCC-eeEEEEEeeccCCCCCCCccccChHH---HHHHhhc--CC
Q 014747 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KFYITALIIPKQESTSDSCQATNEEE---IFEVQDK--RS 405 (419)
Q Consensus 332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~-~~~it~liiP~q~~t~d~C~~~~ee~---~f~~~~~--~~ 405 (419)
..+|.|.+..+-+++..|..++.. |.||+|.|+...+ .+.||..+.-.+.++.+.|....++. .++...+ .+
T Consensus 3 ~~~V~i~p~vll~i~~h~~r~~~~--~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (114)
T PF01398_consen 3 VQTVQIHPLVLLKIIDHATRSSPN--EVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPN 80 (114)
T ss_dssp CEEEEEEHHHHHHHHHHHHHHHCT--EEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTT
T ss_pred cEEEEECHHHHHHHHHHHhcCCCC--EEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccccc
Confidence 478999999999999999887777 9999999999999 99999999999999999999987763 3444332 56
Q ss_pred ceeeeeeee
Q 014747 406 LFPLGWIHV 414 (419)
Q Consensus 406 l~~lgwiHT 414 (419)
+..+||.||
T Consensus 81 ~~iVGWY~s 89 (114)
T PF01398_consen 81 LEIVGWYHS 89 (114)
T ss_dssp SEEEEEEEE
T ss_pred ceEEEEEEc
Confidence 999999999
No 10
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=97.96 E-value=2.3e-05 Score=67.67 Aligned_cols=77 Identities=22% Similarity=0.373 Sum_probs=59.5
Q ss_pred eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHH------hhcCCcee
Q 014747 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV------QDKRSLFP 408 (419)
Q Consensus 335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~------~~~~~l~~ 408 (419)
|.|...++.+.++.|..+ ...|.||+|.|+...+.+.|++.+...+....+++... +.+.++. +...++-.
T Consensus 2 v~i~~~v~~~i~~h~~~~--~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 78 (135)
T smart00232 2 VKVHPLVPLNILKHAIRD--GPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEY-DEDYSHLMDEELKKVNKDLEI 78 (135)
T ss_pred EEEcHHHHHHHHHHHhcC--CCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhh-hhhHHHHHHHHHHhhCCCceE
Confidence 678888999999999876 67899999999998889999987775666677776322 3233322 23689999
Q ss_pred eeeeee
Q 014747 409 LGWIHV 414 (419)
Q Consensus 409 lgwiHT 414 (419)
+||+||
T Consensus 79 vGwyhs 84 (135)
T smart00232 79 VGWYHS 84 (135)
T ss_pred EEEEEc
Confidence 999999
No 11
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=97.59 E-value=0.00011 Score=72.98 Aligned_cols=78 Identities=21% Similarity=0.335 Sum_probs=66.4
Q ss_pred eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCC-------eeEEEEEeeccCCCCCCCccccCh---HHHHHHhhcC
Q 014747 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-------KFYITALIIPKQESTSDSCQATNE---EEIFEVQDKR 404 (419)
Q Consensus 335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~-------~~~it~liiP~q~~t~d~C~~~~e---e~~f~~~~~~ 404 (419)
-+--..++..|+.++-.+| +...||+|-|+.... .-.|....-|.|.|++|.++...+ +.+..++..-
T Consensus 14 ef~~~~~~~~f~~~~w~~~--~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~~l 91 (274)
T cd08061 14 EFDNPSIVEFFLYVFWRKT--GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAAAL 91 (274)
T ss_pred EEecHHHHHHHHHHHHHhh--cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHHHc
Confidence 4566789999999855544 689999999998754 799999999999999999998653 6677888889
Q ss_pred Cceeeeeeee
Q 014747 405 SLFPLGWIHV 414 (419)
Q Consensus 405 ~l~~lgwiHT 414 (419)
||..+|||+|
T Consensus 92 GL~~VG~IfT 101 (274)
T cd08061 92 GLERVGWIFT 101 (274)
T ss_pred CCeEEEEEEe
Confidence 9999999999
No 12
>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=97.43 E-value=0.00034 Score=68.58 Aligned_cols=80 Identities=21% Similarity=0.363 Sum_probs=57.7
Q ss_pred eEeeeCHHHHHHHHHHHhhhcccccchhhhhccccc-------CCeeEEEEEeec-cCCCCCCCccccChHHHH--HHhh
Q 014747 333 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-------NRKFYITALIIP-KQESTSDSCQATNEEEIF--EVQD 402 (419)
Q Consensus 333 ~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~-------~~~~~it~liiP-~q~~t~d~C~~~~ee~~f--~~~~ 402 (419)
..|.|+.+.+.+-+..|. +.--.|.||+|+|+.. .....|+..+.+ .....+|.|++.-|+.+- ...+
T Consensus 2 ~~V~Is~~~l~~il~HA~--~~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~ 79 (244)
T cd08068 2 SKVHLSADVYLVCLTHAL--STEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE 79 (244)
T ss_pred cEEEECHHHHHHHHHHHH--hCCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence 468999999999887765 4567899999999985 334455565554 445677878776665432 2233
Q ss_pred c------CCceeeeeeee
Q 014747 403 K------RSLFPLGWIHV 414 (419)
Q Consensus 403 ~------~~l~~lgwiHT 414 (419)
. +++.++||.|+
T Consensus 80 ~~~~~~~rgl~vVGwYHS 97 (244)
T cd08068 80 RLTEETGRPMRVVGWYHS 97 (244)
T ss_pred HHHhhccCCceEEEEEec
Confidence 4 99999999998
No 13
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=97.35 E-value=0.00042 Score=60.69 Aligned_cols=73 Identities=19% Similarity=0.269 Sum_probs=52.1
Q ss_pred HHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCC-CccccChHHHHHHh---hcCCceeeeeeee
Q 014747 340 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSD-SCQATNEEEIFEVQ---DKRSLFPLGWIHV 414 (419)
Q Consensus 340 ~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d-~C~~~~ee~~f~~~---~~~~l~~lgwiHT 414 (419)
+++.++|..|.. .-..|.||+|.|+-......|+.++-.....++. .+...+-++++... .+.++-.+||.||
T Consensus 2 ~~~~~il~ha~~--~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g~~~vG~~HS 78 (128)
T cd08070 2 ELLEAILAHAEA--EYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVVGIYHS 78 (128)
T ss_pred HHHHHHHHHHHh--CCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCCCeEEEEEeC
Confidence 467788888877 5589999999999888777787655333333333 45556666555444 4689999999999
No 14
>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=97.09 E-value=0.0035 Score=49.20 Aligned_cols=69 Identities=16% Similarity=0.174 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 014747 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (419)
Q Consensus 28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I 101 (419)
|+..|..++++|-.+.+.|+++.|+-+|..-+.+++.-+..-+ ....+..++.++..-+.++|.||..|
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 7889999999999999999999999999999999987766542 33566778899999999999999865
No 15
>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=97.05 E-value=0.0047 Score=50.02 Aligned_cols=71 Identities=15% Similarity=0.110 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 014747 29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK 104 (419)
Q Consensus 29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~ 104 (419)
+..|..++++|--.-..|+++.||-+|..-+++|+..+..-+ .+..+..++.++...+.++|.||..|+..
T Consensus 3 l~~Ai~lv~~Av~~D~~g~y~eA~~lY~~ale~~~~~~k~e~-----~~~~k~~lr~k~~eyl~RAE~LK~~l~~~ 73 (75)
T cd02684 3 LEKAIALVVQAVKKDQRGDAAAALSLYCSALQYFVPALHYET-----DAQRKEALRQKVLQYVSRAEELKALIASD 73 (75)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 346889999998899999999999999999999987774422 34567789999999999999999988753
No 16
>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=97.03 E-value=0.0043 Score=49.86 Aligned_cols=71 Identities=13% Similarity=0.127 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (419)
Q Consensus 28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~ 103 (419)
|+..|..++++|--.-..|+++.|+-+|..-+++++..+..-|+ ...+..++.++..-+.++|.||..|++
T Consensus 2 ~~~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~~k~e~~-----~~~k~~~~~k~~eyl~RaE~LK~~l~~ 72 (75)
T cd02678 2 FLQKAIELVKKAIEEDNAGNYEEALRLYQHALEYFMHALKYEKN-----PKSKESIRAKCTEYLDRAEKLKEYLAK 72 (75)
T ss_pred hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 67889999999999999999999999999999999877766443 356778889999999999999998853
No 17
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=97.00 E-value=0.0065 Score=48.51 Aligned_cols=73 Identities=16% Similarity=0.165 Sum_probs=63.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (419)
Q Consensus 26 r~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~ 103 (419)
+.|+..|.+++.+|--+.+.|+++.|+-+|..-+.+++..+..-| .+..+..+..++..-+.++|.||..|..
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 357889999999999999999999999999999999988776533 3456778889999999999999998864
No 18
>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=96.88 E-value=0.0066 Score=49.41 Aligned_cols=69 Identities=19% Similarity=0.244 Sum_probs=59.7
Q ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (419)
Q Consensus 30 Rsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~ 103 (419)
..|..+++.|--+-+.|+++.|+.+|..-+++|+..|..-||- ..+..++.++..-+.++|.||..|++
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 LAAKEVLKRAVELDQEGRFQEALVCYQEGIDLLMQVLKGTKDE-----AKKKNLRQKISEYMDRAEAIKKRLDQ 72 (77)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhCCCH-----HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5688999999999999999999999999999998777664433 45778889999999999999999864
No 19
>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=96.78 E-value=0.008 Score=49.00 Aligned_cols=71 Identities=15% Similarity=0.002 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747 29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (419)
Q Consensus 29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~ 103 (419)
-+.|..+++.|--+-+.|+++.|+.+|..-+++++..+-.+ ..+...+..++.++..-+.++|.||..|..
T Consensus 3 e~~Ai~~a~~Ave~D~~g~y~eA~~~Y~~aie~l~~~~~~~----~~n~~~k~~ir~K~~eYl~RAE~Lk~~l~~ 73 (76)
T cd02681 3 ERDAVQFARLAVQRDQEGRYSEAVFYYKEAAQLLIYAEMAG----TLNDSHLKTIQEKSNEYLDRAQALHQLVQG 73 (76)
T ss_pred HHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHhc----CCChHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 47899999999999999999999999999999998754332 113344566788999999999999998854
No 20
>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=96.56 E-value=0.022 Score=45.43 Aligned_cols=70 Identities=17% Similarity=0.179 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHH
Q 014747 29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQ 103 (419)
Q Consensus 29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~ 103 (419)
+..|..+++.|--+-..|+++.|+-+|..-+.+++..+..-+ ....+..++.++..-+.++|.||..|..
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 567889999999999999999999999999999987774433 2466778889999999999999998854
No 21
>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=96.49 E-value=0.023 Score=46.11 Aligned_cols=68 Identities=16% Similarity=0.154 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHH
Q 014747 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPA 100 (419)
Q Consensus 28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~ 100 (419)
|+..|..++++|--.-.+|+++.||-+|..-+++++..++.-+ ....|..++.++.+-+.++|+|+..
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 6778999999999999999999999999999999988877643 3466788999999999999999864
No 22
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=96.36 E-value=0.0054 Score=51.00 Aligned_cols=62 Identities=19% Similarity=0.412 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHH----HhhcCCceeeeeeee
Q 014747 339 TTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFE----VQDKRSLFPLGWIHV 414 (419)
Q Consensus 339 ~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~----~~~~~~l~~lgwiHT 414 (419)
.++.++++..+..+ ...|+||+|.|.-....+.|+..+- ....+.|. ...+.++-.+|+.||
T Consensus 2 ~~~~~~i~~~~~~~--~p~E~~G~L~g~~~~~~~~~~~~~~------------~~p~~~~~~~~~~~~~~~~~~vg~~HS 67 (104)
T PF14464_consen 2 EEVLEQIIAHARAA--YPNEACGLLLGRRDDQRFIVVPNVN------------PDPRDSFRRERFEARERGLEIVGIWHS 67 (104)
T ss_dssp -HHHHHHHHHHHHH--TTS-EEEEEEEEEECCEEEEEEEEE--------------HHCHHHHHH-HHHHHT-EEEEEEEE
T ss_pred HHHHHHHHHHHhhC--CCCeEEEEEEEEecCCEEEEEeCCC------------CCcHHHHHHHhhhhhcccceeeEEEEc
Confidence 45778888888777 6789999999999777887777654 22222222 567899999999999
No 23
>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=95.27 E-value=0.12 Score=42.11 Aligned_cols=64 Identities=20% Similarity=0.123 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHH----HHHHHHHhhcHHHH
Q 014747 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLL----NALSELEELQPAVQ 102 (419)
Q Consensus 30 Rsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~----~vl~~lE~LK~~I~ 102 (419)
.-|..++++|----..||++.||-+|+-.+++|+. + + ...-+..++.++. ..+.++|+||..|.
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 45788999998888889999999999999999975 2 2 3344566777775 88999999998875
No 24
>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=94.82 E-value=0.18 Score=41.13 Aligned_cols=68 Identities=13% Similarity=0.061 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHH
Q 014747 29 YRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAV 101 (419)
Q Consensus 29 lRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I 101 (419)
-++|..+++.|--+.++|+++.|.++|..-+++++.-+..-||-. .+..++.+|.+-+.++|.||..+
T Consensus 3 ~~~A~~~a~~AVe~D~~gr~~eAi~~Y~~aIe~L~q~~~~~pD~~-----~k~~yr~ki~eY~~Rae~Lk~~v 70 (75)
T cd02682 3 EEMARKYAINAVKAEKEGNAEDAITNYKKAIEVLSQIVKNYPDSP-----TRLIYEQMINEYKRRIEVLEKQN 70 (75)
T ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHhCCChH-----HHHHHHHHHHHHHHHHHHHHHHc
Confidence 467889999999999999999999999999999998888777664 35567788999999999999876
No 25
>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=94.47 E-value=0.068 Score=52.87 Aligned_cols=80 Identities=15% Similarity=0.177 Sum_probs=56.6
Q ss_pred EeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCcc--c---cChHHHHHHhhcCCc--
Q 014747 334 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQ--A---TNEEEIFEVQDKRSL-- 406 (419)
Q Consensus 334 ~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~--~---~~ee~~f~~~~~~~l-- 406 (419)
.|.|..-..-+-+..+..+- ..|.||.|.|...++.+-||..+--....+.+.+. . .--.++++...+.|+
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 47777777777777777655 78999999999999999999864433344434321 1 112455666667777
Q ss_pred eeeeeeeec
Q 014747 407 FPLGWIHVS 415 (419)
Q Consensus 407 ~~lgwiHT~ 415 (419)
.++||-||.
T Consensus 80 ~iVGWY~S~ 88 (266)
T cd08065 80 NHVGWYQST 88 (266)
T ss_pred cEEEeEeec
Confidence 899999994
No 26
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=94.15 E-value=0.072 Score=46.99 Aligned_cols=75 Identities=20% Similarity=0.440 Sum_probs=46.3
Q ss_pred eeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHH-HHHhhcCCceeeeeee
Q 014747 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEI-FEVQDKRSLFPLGWIH 413 (419)
Q Consensus 335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~-f~~~~~~~l~~lgwiH 413 (419)
+.|+.+++..-|..|..... .|.||+|+|+-....++ -+..+..+. .+.-....+-.+ .......|+.++||.|
T Consensus 2 ~~i~~~~l~~il~~a~~~~p--~E~~g~l~~~~~~~~~~--~~~n~~~~~-~~~~~~~~~~~~~~~~~~~~g~~vvg~yH 76 (134)
T COG1310 2 LVIPKEVLGAILEHARREHP--REVCGLLAGTREGERYF--PLKNVSVEP-VEYFEIDPEYSLFYLAAEDAGEVVVGWYH 76 (134)
T ss_pred ceecHHHHHHHHHHHHhcCC--hheEEEEEeecccceee--ccccccCCc-ceeEeeCHHHHHHHHHHhhCCCEEEEEEc
Confidence 56888899988888887755 99999999997662222 112222222 222222233333 2333345699999999
Q ss_pred e
Q 014747 414 V 414 (419)
Q Consensus 414 T 414 (419)
|
T Consensus 77 S 77 (134)
T COG1310 77 S 77 (134)
T ss_pred C
Confidence 8
No 27
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=91.20 E-value=0.85 Score=46.81 Aligned_cols=73 Identities=18% Similarity=0.156 Sum_probs=60.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHH
Q 014747 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQK 104 (419)
Q Consensus 28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~ 104 (419)
.+.-|.+++++|----..+|++.||-+|+-.++-|+..|.. .....+-|..++.++-+-|.++|+||.-|++.
T Consensus 6 ~l~kaI~lv~kA~~eD~a~nY~eA~~lY~~aleYF~~~lKY----E~~~~kaKd~IraK~~EYLdRAEkLK~yL~~~ 78 (439)
T KOG0739|consen 6 FLQKAIDLVKKAIDEDNAKNYEEALRLYQNALEYFLHALKY----EANNKKAKDSIRAKFTEYLDRAEKLKAYLKEK 78 (439)
T ss_pred HHHHHHHHHHHHhhhcchhchHHHHHHHHHHHHHHHHHHHh----hhcChhHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 67788999999998888999999999999999999877653 32233567788899999999999999977744
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=90.79 E-value=0.41 Score=42.96 Aligned_cols=65 Identities=22% Similarity=0.172 Sum_probs=43.1
Q ss_pred hhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccc----cC-hHHHHHHhhc--CCceeeeeeee
Q 014747 350 KSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQA----TN-EEEIFEVQDK--RSLFPLGWIHV 414 (419)
Q Consensus 350 ~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~----~~-ee~~f~~~~~--~~l~~lgwiHT 414 (419)
..+....-||||||.|.-..+.++|+.+..|.-......|.- .. .+.|=++..+ ..+..||==||
T Consensus 10 ~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWHt 81 (131)
T TIGR02256 10 RQWHDLSTETGGVLIGERRGAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHT 81 (131)
T ss_pred HhCcCCCCccceEEEEEEcCCcEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecCc
Confidence 344455669999999999888999999888764333222222 11 3444445444 34889998898
No 29
>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=85.90 E-value=2.4 Score=39.94 Aligned_cols=70 Identities=20% Similarity=0.198 Sum_probs=49.2
Q ss_pred CHHHHHHHHHHHhhhcccccchhhhhccccc-CCeeEEEEEeeccCCCCCCCccccChH------HHHHHhhcCCceeee
Q 014747 338 STTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKFYITALIIPKQESTSDSCQATNEE------EIFEVQDKRSLFPLG 410 (419)
Q Consensus 338 p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~-~~~~~it~liiP~q~~t~d~C~~~~ee------~~f~~~~~~~l~~lg 410 (419)
+.....+.+..|.. ---.|-||+|.|+.. .+...|+. +||-.. +|....-. .+-.++.++||-.+|
T Consensus 2 s~~ay~ki~~HA~k--~p~~evcGlLlG~~~~~~~~~V~d-~vPl~h----~~~~l~P~~Eval~~ve~~~~~~gl~IvG 74 (182)
T cd08060 2 STLAYVKMLLHAAK--YPHCAVNGLLLGKKSSGGSVEITD-AVPLFH----SCLALAPMLEVALALVDAYCKSSGLVIVG 74 (182)
T ss_pred CHHHHHHHHHHHHH--cCCchheEEEEeeecCCCCEEEEE-EEEcCC----CccccCHHHHHHHHHHHHHHHHCCCEEEE
Confidence 34455566666766 335699999999987 66788887 488554 34444322 345677889999999
Q ss_pred eeee
Q 014747 411 WIHV 414 (419)
Q Consensus 411 wiHT 414 (419)
+-|.
T Consensus 75 ~Yhs 78 (182)
T cd08060 75 YYQA 78 (182)
T ss_pred EEec
Confidence 9996
No 30
>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=84.84 E-value=2.3 Score=36.97 Aligned_cols=66 Identities=27% Similarity=0.346 Sum_probs=41.4
Q ss_pred eCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEee-ccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747 337 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALII-PKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 337 ~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~lii-P~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT 414 (419)
|+.++.+..++.|.. .--.|.||+|+|+-. .|+.++. |.... ++... ...+ .....++-.+|=.|+
T Consensus 1 i~~~~~~~i~~ha~~--~~P~E~CGlL~G~~~----~v~~~~~~~n~~~-~~~~~---~f~~--~~~~~g~~ivgi~HS 67 (117)
T cd08072 1 ISRDLLDSILEAAKS--SHPNEFAALLRGKDG----VITELLILPGTES-GEVSA---VFPL--LMLPLDMSIVGSVHS 67 (117)
T ss_pred CCHHHHHHHHHHHhh--cCCceEEEEEEeecc----EEEEEEECCCCCC-CCcce---eech--HHhcCCCeEEEEEEc
Confidence 467788877777754 445799999999764 5666554 42222 11111 1111 245688999999998
No 31
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=84.40 E-value=2.7 Score=28.19 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccC-CCcC
Q 014747 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP-CHRD 71 (419)
Q Consensus 31 sa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLp-kHPd 71 (419)
+|..+...|.+|...|+++.|--++-+-..+.-..+. .|||
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 3567788899999999999999999999999855543 4775
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=83.90 E-value=1.5 Score=44.71 Aligned_cols=55 Identities=29% Similarity=0.457 Sum_probs=45.2
Q ss_pred hhhhcccccC-C------eeEEEEEeeccCCCCCCCccc---cChHHHHHHhhcCCceeeeeeee
Q 014747 360 CGILAGSLKN-R------KFYITALIIPKQESTSDSCQA---TNEEEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 360 Cgil~g~l~~-~------~~~it~liiP~q~~t~d~C~~---~~ee~~f~~~~~~~l~~lgwiHT 414 (419)
||+|=|+-.. . .-.|-...-|.|+|+.|+-+- .+|+.+=.++..-||.-+|||-|
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~IfT 66 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWIFT 66 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEEEe
Confidence 6788887653 3 577778888999999998765 46777888888999999999998
No 33
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=81.98 E-value=15 Score=42.03 Aligned_cols=28 Identities=11% Similarity=0.056 Sum_probs=15.1
Q ss_pred HHHHHHHHHhhccCCCcCcccccHHHHH
Q 014747 54 MLLRFSSLVTETIPCHRDYLASFKSQKL 81 (419)
Q Consensus 54 ly~Ry~~LvvekLpkHPdyk~~~~~~k~ 81 (419)
-|++-++=|+..|--|+.+....-++|.
T Consensus 423 qYykLIEecISqIvlHr~~~DPdf~yr~ 450 (1102)
T KOG1924|consen 423 QYYKLIEECISQIVLHRTGMDPDFKYRF 450 (1102)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCcchhh
Confidence 3566666666666666666533333333
No 34
>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=81.29 E-value=2.9 Score=39.98 Aligned_cols=73 Identities=10% Similarity=0.069 Sum_probs=49.6
Q ss_pred CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeee
Q 014747 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW 411 (419)
Q Consensus 332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgw 411 (419)
++.=.||.+|.++|+..|... --.|+||+++|.-..+.+.+ .-+......++.-..... .+++|+..++=
T Consensus 70 ~~~g~Ip~~l~~~ii~hAr~~--~P~EacG~Iag~~~~~~~r~--~p~~N~~~Sp~~~~~d~~------~~~~ge~lV~i 139 (192)
T TIGR03735 70 FLCGPIPASLLEEFAEAARAA--LPNEVAAWIVWNSETGSLRL--AALESIEASPGHIDYRRP------RLDDGEHLVVD 139 (192)
T ss_pred EecCCCCHHHHHHHHHHHHhc--CCcceEEEEEEcCCCCEEEE--EeccccccCCceEEEcch------HHhCCCeEEEE
Confidence 455689999999999998875 46899999999855556533 222333444444444222 22777888888
Q ss_pred eee
Q 014747 412 IHV 414 (419)
Q Consensus 412 iHT 414 (419)
+|.
T Consensus 140 yHS 142 (192)
T TIGR03735 140 LHS 142 (192)
T ss_pred EcC
Confidence 886
No 35
>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=74.60 E-value=8.9 Score=34.67 Aligned_cols=60 Identities=15% Similarity=0.243 Sum_probs=37.4
Q ss_pred ccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccCh---HHHHHHhh--cCCceeeeeeeecc
Q 014747 356 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE---EEIFEVQD--KRSLFPLGWIHVSA 416 (419)
Q Consensus 356 ~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~e---e~~f~~~~--~~~l~~lgwiHT~~ 416 (419)
.-+-+|+|-|.-..+.+.||+-+-=.++.+.+. ...+- +++++... ..++..+||-||..
T Consensus 22 ~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~-~~~d~~y~~~m~~~~~~v~~~~~vVGWY~~~~ 86 (157)
T cd08057 22 IKRVIGVLLGYVDGDKIEVTNSFELPFDEEEES-IFIDTEYLEKRYNLHKKVYPQEKIVGWYSIGS 86 (157)
T ss_pred CCeEEEEEEeEEeCCEEEEEEeEEccccCCCcc-hhhhHHHHHHHHHHHHHhCCCCCEEEEEeecC
Confidence 467899999999999999988664334544443 11111 11111111 26778999999943
No 36
>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=73.50 E-value=9.6 Score=24.66 Aligned_cols=30 Identities=10% Similarity=0.130 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Q 014747 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (419)
Q Consensus 32 a~~llreA~iy~~egn~e~AYily~Ry~~L 61 (419)
|..++..|.+|.+.||++.|.-.|.+.+++
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 456788899999999999999999988776
No 37
>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=72.69 E-value=10 Score=31.22 Aligned_cols=41 Identities=17% Similarity=0.114 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhcc
Q 014747 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETI 66 (419)
Q Consensus 26 r~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekL 66 (419)
+.|++.|..-++.|+..+++|++..|..+..-.+.+.+..|
T Consensus 2 ~~~~~~A~~~l~~A~~~~~~~~~~~a~~~a~~a~e~~lkAl 42 (118)
T PF05168_consen 2 QDWLEKAEEDLKAAEILLEEGDYNWAVFHAYQAVEKALKAL 42 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67999999999999999999999999888877776665443
No 38
>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=65.53 E-value=19 Score=23.02 Aligned_cols=30 Identities=10% Similarity=0.022 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Q 014747 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (419)
Q Consensus 32 a~~llreA~iy~~egn~e~AYily~Ry~~L 61 (419)
|.-+...|.+|++.|+++.|--.|-+.+.|
T Consensus 1 a~~~~~lg~~~~~~~~~~~A~~~~~~al~l 30 (34)
T PF07719_consen 1 AEAWYYLGQAYYQLGNYEEAIEYFEKALEL 30 (34)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 345678899999999999999999988776
No 39
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=65.42 E-value=3.9 Score=48.51 Aligned_cols=74 Identities=19% Similarity=0.291 Sum_probs=49.1
Q ss_pred eeeCHHHHHHHHHHHhhhcccccchhhhhcccc-cCC--eeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeee
Q 014747 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSL-KNR--KFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW 411 (419)
Q Consensus 335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l-~~~--~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgw 411 (419)
.++|..|..+|+.++..-|. +-|.+-|.- .+| .=-|.+.+.+-|-|+-...+--+-- =+...-.||-.|||
T Consensus 2097 yilPkNllkkFi~isD~r~q----iag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~l--P~~~~l~d~e~Lgw 2170 (2321)
T KOG1795|consen 2097 YILPKNLLKKFITISDLRTQ----IAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFL--PIHGVLEDLEPLGW 2170 (2321)
T ss_pred eeccHHHHhhheeecchhhh----hheeeeccCCCCCCccceEEEEEeccccccccccccCccC--CcchhccCCcccch
Confidence 68999999999999988764 456666632 222 3356666777777765554432111 13344577889999
Q ss_pred eee
Q 014747 412 IHV 414 (419)
Q Consensus 412 iHT 414 (419)
|||
T Consensus 2171 ~hT 2173 (2321)
T KOG1795|consen 2171 IHT 2173 (2321)
T ss_pred hhc
Confidence 999
No 40
>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=62.66 E-value=23 Score=27.21 Aligned_cols=40 Identities=18% Similarity=0.154 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccC-CCcC
Q 014747 31 IADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIP-CHRD 71 (419)
Q Consensus 31 sa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLp-kHPd 71 (419)
+|..+...|.+|...|++++|--+|-+.+++ .+.+. .|++
T Consensus 4 ~a~~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~ 44 (78)
T PF13424_consen 4 TANAYNNLARVYRELGRYDEALDYYEKALDI-EEQLGDDHPD 44 (78)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTTTHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHCCCCHH
Confidence 4667788899999999999999999999999 56654 3444
No 41
>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=60.42 E-value=26 Score=22.65 Aligned_cols=30 Identities=10% Similarity=0.069 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Q 014747 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (419)
Q Consensus 32 a~~llreA~iy~~egn~e~AYily~Ry~~L 61 (419)
|...+..|.+|..-|+++.|...|-|.+.|
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 456778899999999999999999998766
No 42
>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=59.34 E-value=12 Score=37.51 Aligned_cols=58 Identities=17% Similarity=0.303 Sum_probs=36.8
Q ss_pred ccchhhhhcccccCCeeEEEEEe-eccCCCCCCCc-----cccChHHHHHHhh--cCCceeeeeeee
Q 014747 356 NLETCGILAGSLKNRKFYITALI-IPKQESTSDSC-----QATNEEEIFEVQD--KRSLFPLGWIHV 414 (419)
Q Consensus 356 ~~etCgil~g~l~~~~~~it~li-iP~q~~t~d~C-----~~~~ee~~f~~~~--~~~l~~lgwiHT 414 (419)
+.+-.|+|-|....+.+.||+-+ +|.. .+.|.. +..--+++++... ..+...+||-||
T Consensus 25 ~~~ViG~LLG~~~~~~veItnsF~~p~~-~~~~~~~~~~~d~~y~~~m~~~~kkv~~~e~vVGWY~t 90 (280)
T cd08062 25 SKRVVGVLLGSWKKGVLDVTNSFAVPFE-EDEKDPSVWFLDHNYLENMYGMFKKVNAKEKIVGWYST 90 (280)
T ss_pred CceEEEEEEEEEeCCEEEEEEeeecCcc-CCCCCcchhhhhHHHHHHHHHHHHHhCCCCCeEEEecC
Confidence 45788999999999999998765 4543 333321 1111122333322 267889999999
No 43
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=58.57 E-value=18 Score=22.85 Aligned_cols=28 Identities=7% Similarity=0.059 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Q 014747 34 NILKQADIFREEKNIIDLYVMLLRFSSL 61 (419)
Q Consensus 34 ~llreA~iy~~egn~e~AYily~Ry~~L 61 (419)
.+++.|.+|.+.|+.++|=-.|-+++.-
T Consensus 2 a~~~~a~~~~~~g~~~~A~~~~~~~~~~ 29 (33)
T PF13174_consen 2 ALYRLARCYYKLGDYDEAIEYFQRLIKR 29 (33)
T ss_dssp HHHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence 5789999999999999998888776543
No 44
>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=58.55 E-value=13 Score=30.83 Aligned_cols=50 Identities=20% Similarity=0.244 Sum_probs=32.3
Q ss_pred ccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747 356 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 356 ~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT 414 (419)
..|.||+|+|+-.+ ..+....+|. ++.+.+.. + +....+.+.-.+|-.|+
T Consensus 15 p~E~~gll~~~~~~--~~~~~~~~~~--~~~~~~~~----~-~~~a~~~~~~~v~i~Hs 64 (101)
T cd08059 15 PDEFCGFLSGSKDN--VMDELIFLPF--VSGSVSAV----I-DLAALEIGMKVVGLVHS 64 (101)
T ss_pred ChhhheeeecCCCC--eEEEEEeCCC--cCCccChH----H-HHHHhhCCCcEEEEEec
Confidence 57999999998543 3334444553 44333322 1 66777888888999997
No 45
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=56.34 E-value=8.1 Score=45.70 Aligned_cols=73 Identities=18% Similarity=0.446 Sum_probs=43.4
Q ss_pred eeeCHHHHHHHHHHHhhhcccccchhhhhccccc-CC---eeEEEEEeeccCCCCCCCccc-cChHHHHHHhhcCCceee
Q 014747 335 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-NR---KFYITALIIPKQESTSDSCQA-TNEEEIFEVQDKRSLFPL 409 (419)
Q Consensus 335 v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~-~~---~~~it~liiP~q~~t~d~C~~-~~ee~~f~~~~~~~l~~l 409 (419)
-.||..|.++|+.|...-+ -+.|..-|+-. +| +=+.+-.+||.- |.-...+. .+-- -|.-+-+||-.|
T Consensus 2136 y~lP~NLl~kF~~isD~~v----qvag~vyG~s~~d~p~ikeI~~~~lVPQl-gs~~~vq~~s~vP--~dlp~~e~le~l 2208 (2365)
T COG5178 2136 YRLPLNLLEKFMRISDPHV----QVAGLVYGKSGSDNPQIKEILSFGLVPQL-GSLSGVQSSSFVP--HDLPGDEDLEIL 2208 (2365)
T ss_pred ccccHHHHHhhheecccce----eeEEEEeccCCccCcchhheeEEEeeccc-cccccccccccCC--CCCCCcccceee
Confidence 6799999999999998765 45566666432 22 223344556643 33222222 1111 123345788999
Q ss_pred eeeee
Q 014747 410 GWIHV 414 (419)
Q Consensus 410 gwiHT 414 (419)
|||||
T Consensus 2209 Gwiht 2213 (2365)
T COG5178 2209 GWIHT 2213 (2365)
T ss_pred EEEec
Confidence 99999
No 46
>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=56.27 E-value=1.1e+02 Score=25.10 Aligned_cols=44 Identities=18% Similarity=0.052 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCC
Q 014747 25 LRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC 68 (419)
Q Consensus 25 lr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpk 68 (419)
++.||.-|-+.|..|=-+.+.|+.++|-.+|-+-....++.+.-
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 46799999999999999999999999999999999998877654
No 47
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=55.58 E-value=28 Score=23.48 Aligned_cols=28 Identities=11% Similarity=0.122 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHH
Q 014747 35 ILKQADIFREEKNIIDLYVMLLRFSSLV 62 (419)
Q Consensus 35 llreA~iy~~egn~e~AYily~Ry~~Lv 62 (419)
+...|.+|.+.|++++|--+|-+.+.|.
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 5677999999999999999999977654
No 48
>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=54.67 E-value=31 Score=24.47 Aligned_cols=38 Identities=18% Similarity=0.068 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCC
Q 014747 32 ADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCH 69 (419)
Q Consensus 32 a~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkH 69 (419)
|+.+.+-+.|.+..+|+++|.--|.+...|--+.+|-|
T Consensus 1 Adv~~~Lgeisle~e~f~qA~~D~~~aL~i~~~l~~~~ 38 (38)
T PF10516_consen 1 ADVYDLLGEISLENENFEQAIEDYEKALEIQEELLPPE 38 (38)
T ss_pred CcHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCC
Confidence 34577889999999999999999999999987766643
No 49
>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=49.65 E-value=30 Score=25.73 Aligned_cols=30 Identities=10% Similarity=0.128 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Q 014747 32 ADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (419)
Q Consensus 32 a~~llreA~iy~~egn~e~AYily~Ry~~L 61 (419)
|..+...|.+|++.|+++.|-..|.+.+.+
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~ 32 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIEL 32 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 567889999999999999999999998776
No 50
>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=48.18 E-value=1.3e+02 Score=25.90 Aligned_cols=87 Identities=17% Similarity=0.134 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCC-CcCcccccH----HHHHH-----HHHHHHHHHHHHHh
Q 014747 27 YYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPC-HRDYLASFK----SQKLY-----LKKKLLNALSELEE 96 (419)
Q Consensus 27 ~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpk-HPdyk~~~~----~~k~~-----l~k~l~~vl~~lE~ 96 (419)
..|--+..-++.|..+.+.||++.+-..+.|..+++.+.+.. .++-...-+ .-+.. +...+.+-.+.+++
T Consensus 24 ~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 24 MLYDGAIEFLKQAKEAIEQGDIEEKNEALQKAQDIITELQSSLDFEKGGEIADNLFRLYDYMIRQLVQANLKKDPERLDE 103 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 467888999999999999999999999999999999655544 333111111 11222 22344445677888
Q ss_pred hcHHHHHHHHHHHHhhh
Q 014747 97 LQPAVQQKINELNRKKT 113 (419)
Q Consensus 97 LK~~I~~~Y~e~~~~~~ 113 (419)
+...|..-.+.|.+..+
T Consensus 104 v~~~l~~l~~aW~e~~k 120 (122)
T PF02561_consen 104 VIRILEELRDAWEEIAK 120 (122)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 88888888888877543
No 51
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.42 E-value=61 Score=31.11 Aligned_cols=74 Identities=12% Similarity=0.100 Sum_probs=62.2
Q ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHHH
Q 014747 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKI 105 (419)
Q Consensus 28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~Y 105 (419)
.+..|..++..|---.++|.+.+|.+-|--=++|+++.|..-|- ....|..++.++-+-+.+++.|+.-|++.-
T Consensus 11 ~~~aAa~iL~~AVe~d~e~k~pqALl~YkeGIdLi~e~lk~~~l----dna~R~~i~~k~s~Ym~ka~diekYLdqek 84 (247)
T KOG4509|consen 11 LLKAAAPILCDAVEDDKEGKVPQALLCYKEGIDLIAEALKGMKL----DNADRCKIMAKFSDYMDKAADIEKYLDQEK 84 (247)
T ss_pred hhhhhhhHHHHHhcccccccccHHHHHHhhhHHHHHHHHccCCC----cchHHHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 46778889999999999999999999999999999999988662 225667788889899999999998887543
No 52
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=46.27 E-value=18 Score=36.16 Aligned_cols=69 Identities=26% Similarity=0.446 Sum_probs=46.8
Q ss_pred HHHHHHHhhhcccccchhhhhcccccCCeeEEEEE-eeccCCCCCCC----ccccChHHHHHHhhc--CCceeeeeeee
Q 014747 343 DNFMKLAKSNTDKNLETCGILAGSLKNRKFYITAL-IIPKQESTSDS----CQATNEEEIFEVQDK--RSLFPLGWIHV 414 (419)
Q Consensus 343 ~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~l-iiP~q~~t~d~----C~~~~ee~~f~~~~~--~~l~~lgwiHT 414 (419)
+.|=+.+. ..+----|||.|.-....+-||.- -+|+-+-..|+ -.+.-=|-+|+.+-+ ...-.+||-||
T Consensus 23 DhynR~~k---~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkKvNakekivGWYhT 98 (309)
T KOG1556|consen 23 DHYNRVGK---DTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKKVNAKEKVVGWYHT 98 (309)
T ss_pred HHHhhhcc---CcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHHhcchhheeeeecc
Confidence 44544443 223445799999999988888865 47887777763 223334567776654 66779999999
No 53
>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=45.24 E-value=24 Score=30.27 Aligned_cols=63 Identities=17% Similarity=0.258 Sum_probs=38.3
Q ss_pred HHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCC--CCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747 342 MDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQE--STSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 342 ~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~--~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT 414 (419)
.+.-++.|. ..--.|.||+|+|+-. ++ .++|-.. ..+-.....+-+|++...+.. -.+|-.|+
T Consensus 3 ~~~i~~ha~--~~~P~E~CGll~g~~~-----~~-~~~p~~N~~~~p~~~F~idp~e~~~a~~~~--~ivgi~HS 67 (108)
T cd08073 3 EDAILAHAK--AEYPREACGLVVRKGR-----KL-RYIPCRNIAADPEEHFEISPEDYAAAEDEG--EIVAVVHS 67 (108)
T ss_pred HHHHHHHHh--HCCCCcceEEEEecCC-----ce-EEEECccCCCCccceEEeCHHHHHHHhcCC--CEEEEEEc
Confidence 344445554 3445799999999762 22 2455332 223245556777888877654 47888887
No 54
>PRK05685 fliS flagellar protein FliS; Validated
Probab=42.92 E-value=2.2e+02 Score=25.16 Aligned_cols=84 Identities=15% Similarity=0.134 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCccc--ccHHH----HHHHH-----HHHHHHHHHHHh
Q 014747 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLA--SFKSQ----KLYLK-----KKLLNALSELEE 96 (419)
Q Consensus 28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~--~~~~~----k~~l~-----k~l~~vl~~lE~ 96 (419)
.|.-|..-++.|..+.++||++.+...+.|...++.+.... =|+.. .-+.. +.++. ..+.+-.+.+++
T Consensus 31 Lydgai~~l~~A~~ai~~~~~~~~~~~l~ka~~Ii~eL~~s-Ld~e~ggeiA~~L~~LY~y~~~~L~~A~~~~d~~~l~e 109 (132)
T PRK05685 31 LYEGALSFLAQAKLAIEQGDIEAKGEYLSKAINIINGLRNS-LDMEKGGEVAKNLSALYDYMIRRLLEANLRNDVQAIDE 109 (132)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhh-cCCccccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 67778888899999999999999999999999999554443 33332 11111 22232 333333566777
Q ss_pred hcHHHHHHHHHHHHhh
Q 014747 97 LQPAVQQKINELNRKK 112 (419)
Q Consensus 97 LK~~I~~~Y~e~~~~~ 112 (419)
+.+.|..-.+.|.+..
T Consensus 110 v~~il~~LreaW~~i~ 125 (132)
T PRK05685 110 VEGLLREIKEAWKQIP 125 (132)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 7777777777777643
No 55
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=39.23 E-value=71 Score=22.25 Aligned_cols=28 Identities=21% Similarity=0.105 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Q 014747 34 NILKQADIFREEKNIIDLYVMLLRFSSL 61 (419)
Q Consensus 34 ~llreA~iy~~egn~e~AYily~Ry~~L 61 (419)
..+..|..|.+.|++++|--+|-|.+.+
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~ 30 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRALAL 30 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4567799999999999999999996654
No 56
>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=38.91 E-value=42 Score=33.12 Aligned_cols=58 Identities=16% Similarity=0.305 Sum_probs=37.1
Q ss_pred cchhhhhcccccCCeeEEEEEeeccCCCCCCCccccCh---HHHHHHhh--cCCceeeeeeeec
Q 014747 357 LETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE---EEIFEVQD--KRSLFPLGWIHVS 415 (419)
Q Consensus 357 ~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~e---e~~f~~~~--~~~l~~lgwiHT~ 415 (419)
-.-+|.|-|....+.+.||+-+-=....+.|... .+. +++++..- ..+...+||-||.
T Consensus 23 ~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~-~d~~y~~~m~~~~kkv~~~~~vVGWY~tg 85 (265)
T cd08064 23 ERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVA-VDMEYHRTMYELHQKVNPKEVIVGWYATG 85 (265)
T ss_pred cEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEE-EcHHHHHHHHHHHHHhCCCCcEEeeeeCC
Confidence 4568999999999999998865322333333221 111 33444333 4788899999994
No 57
>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=38.28 E-value=64 Score=24.63 Aligned_cols=35 Identities=3% Similarity=-0.016 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Q 014747 28 YYRIADNILKQADIFREEKNIIDLYVMLLRFSSLV 62 (419)
Q Consensus 28 YlRsa~~llreA~iy~~egn~e~AYily~Ry~~Lv 62 (419)
...++..+...|.+|..-|+++.|--+|.+..+++
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 45568889999999999999999999999988876
No 58
>COG2250 Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown]
Probab=37.90 E-value=1.2e+02 Score=26.86 Aligned_cols=40 Identities=18% Similarity=-0.042 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhh
Q 014747 25 LRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTE 64 (419)
Q Consensus 25 lr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~Lvve 64 (419)
...|++-|...++.|..-++.|++.-|...-.-.+.+.+.
T Consensus 6 ~~~~~~rA~~~l~~A~~~le~G~y~~a~f~aqQAvel~lK 45 (132)
T COG2250 6 AEKWLRRAERDLKLAKRDLELGDYDLACFHAQQAVELALK 45 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 3569999999999999999999999998886666666544
No 59
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=37.50 E-value=39 Score=30.01 Aligned_cols=56 Identities=23% Similarity=0.336 Sum_probs=40.7
Q ss_pred HHhhhcc---cccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHHhhcCCceeeeeeee
Q 014747 348 LAKSNTD---KNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHV 414 (419)
Q Consensus 348 ~a~~Nt~---~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~~~~~~l~~lgwiHT 414 (419)
|+..|.. +|.|-||+. |+..+|.|+-|+ .+ .|+.++|...+=. .-.+.-.++-+||
T Consensus 9 l~~~n~~SI~~nrEy~G~I-~~~~~G~y~~t~-p~---~G~~~~~~~~~~~------~p~g~~~vA~yHT 67 (123)
T PF14220_consen 9 LQMYNPRSIRENREYCGYI-GKDEDGKYFATE-PR---RGENASCYPSNPP------CPNGSTIVASYHT 67 (123)
T ss_pred HHHhccccccCCcEEEEEE-EEcCCCcEEeec-Cc---cCCCCCcCCCCcc------cccccceeeEeec
Confidence 4556666 899999999 678899998774 22 3488888875533 1246668899999
No 60
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=34.43 E-value=3.2e+02 Score=23.97 Aligned_cols=84 Identities=14% Similarity=0.143 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccH--H----HHHHHH-----HHHHHHHHHHH
Q 014747 27 YYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFK--S----QKLYLK-----KKLLNALSELE 95 (419)
Q Consensus 27 ~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~--~----~k~~l~-----k~l~~vl~~lE 95 (419)
-.|.-+..-++.|..+.++||++.+-..+.|...++. -|...=|+..... . -+.++. ..+++-.+.++
T Consensus 26 mLydg~i~~l~~a~~ai~~~d~~~~~~~i~ka~~Ii~-eL~~~Ld~e~ggeiA~nL~~LY~y~~~~L~~An~~~d~~~l~ 104 (124)
T TIGR00208 26 MLYNGCLKFIRLAAQAIENDDIERKNENLIKAQNIIQ-ELNFTLDREKNIELSASLGALYDYMYRRLVQANIKNDTSKLA 104 (124)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-HHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHhhCCHHHHH
Confidence 3677788889999999999999999999999999984 4444445542211 1 122222 33333355666
Q ss_pred hhcHHHHHHHHHHHHh
Q 014747 96 ELQPAVQQKINELNRK 111 (419)
Q Consensus 96 ~LK~~I~~~Y~e~~~~ 111 (419)
++...|..=.+-|.+.
T Consensus 105 ev~~~l~~Lr~aW~e~ 120 (124)
T TIGR00208 105 EVEGYVRDFRDAWKEA 120 (124)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 6666666666777654
No 61
>PRK15490 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=33.69 E-value=95 Score=34.57 Aligned_cols=69 Identities=20% Similarity=0.237 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccHHHHH-HHHHHHHHHHHHHHhhcHHHHHHHH
Q 014747 30 RIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKL-YLKKKLLNALSELEELQPAVQQKIN 106 (419)
Q Consensus 30 Rsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~-~l~k~l~~vl~~lE~LK~~I~~~Y~ 106 (419)
.+|..|+.+|+..-+-|..|+||-+|-| .|..||| +....-.+. .....+.++...+-++-+-..++|+
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (578)
T PRK15490 40 LTSLAMLKKAEFLHDVNETERAYALYET-------LIAQNND-EARYEYARRLYNTGLAKDAQLILKKVSNGVQKKYN 109 (578)
T ss_pred hhHHHHHHHhhhhhhhhhhHhHHHHHHH-------HHHhCCc-chHHHHHHHHHhhhhhhHHHHHHHHhCccHhHHHH
Confidence 4789999999999999999999998877 3567998 311111111 1112344555555566666666665
No 62
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.89 E-value=57 Score=35.24 Aligned_cols=76 Identities=17% Similarity=0.381 Sum_probs=56.1
Q ss_pred eeCHHHHHHHHHHHhhhcccccchhhhhccccc-CCee------EEEEEeeccCCCCCCCcccc--ChHH-HHHHhhcCC
Q 014747 336 HISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKF------YITALIIPKQESTSDSCQAT--NEEE-IFEVQDKRS 405 (419)
Q Consensus 336 ~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~-~~~~------~it~liiP~q~~t~d~C~~~--~ee~-~f~~~~~~~ 405 (419)
|=-..+.+.||+--..- |.---|.|=|+.+ ++.. .|.-..=|.|.|+.|.-+.+ +|+. |=+....-|
T Consensus 179 Fd~~~~v~~Fl~~wr~s---g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lG 255 (510)
T KOG2834|consen 179 FDNAELVNHFLNEWRAS---GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLG 255 (510)
T ss_pred ecchHHHHHHHHHHHHh---hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcC
Confidence 44789999999765543 3344577778765 3444 67777779999999999876 3444 445666799
Q ss_pred ceeeeeeee
Q 014747 406 LFPLGWIHV 414 (419)
Q Consensus 406 l~~lgwiHT 414 (419)
|.-+|||-|
T Consensus 256 LrRVG~IFT 264 (510)
T KOG2834|consen 256 LRRVGWIFT 264 (510)
T ss_pred ceeeEEEEe
Confidence 999999999
No 63
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=30.66 E-value=1.1e+02 Score=28.56 Aligned_cols=59 Identities=10% Similarity=0.216 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhhccCC-CcCccc-ccHHHHHHHHHHHHHHHHHHHhhcHHHH-----HHHHHHHHh
Q 014747 51 LYVMLLRFSSLVTETIPC-HRDYLA-SFKSQKLYLKKKLLNALSELEELQPAVQ-----QKINELNRK 111 (419)
Q Consensus 51 AYily~Ry~~LvvekLpk-HPdyk~-~~~~~k~~l~k~l~~vl~~lE~LK~~I~-----~~Y~e~~~~ 111 (419)
|+++.++|..=| +++.. ||.|.. +.....+..+++ .+...++-++|++++ .+|.+|.+.
T Consensus 10 ~~llvl~Fl~~~-nk~r~l~~s~~i~~s~~~nkdakk~-~q~~~ei~dmKqelnavs~qD~fAkwaRl 75 (175)
T KOG4253|consen 10 AWLLVLKFLFGC-NKLRILLPSFSIFMSRVGNKDAKKE-SQKVAEIQDMKQELNAVSMQDNFAKWARL 75 (175)
T ss_pred HHHHHHHHHHhh-hHhheecchhhhhhhcccchhHHHH-HHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence 688889998888 56554 888873 222223333332 233556666777775 356666653
No 64
>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=29.80 E-value=86 Score=17.76 Aligned_cols=27 Identities=0% Similarity=-0.039 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHH
Q 014747 34 NILKQADIFREEKNIIDLYVMLLRFSS 60 (419)
Q Consensus 34 ~llreA~iy~~egn~e~AYily~Ry~~ 60 (419)
...+.|..|...|+++.|-..|.+.+.
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~ 29 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKALE 29 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence 346778899999999999888866543
No 65
>PF08255 Leader_Trp: Trp-operon Leader Peptide; InterPro: IPR013205 The tryptophan operon regulatory region of Citrobacter freundii (leader transcript) encodes a 14-residue peptide containing characteristic tandem tryptophan residues. It is about 10 nucleotides shorter than those of Escherichia coli and Salmonella typhimurium [].
Probab=28.89 E-value=31 Score=19.66 Aligned_cols=8 Identities=38% Similarity=0.734 Sum_probs=6.5
Q ss_pred eeeeeeec
Q 014747 408 PLGWIHVS 415 (419)
Q Consensus 408 ~lgwiHT~ 415 (419)
.+||-|||
T Consensus 7 L~~WWrtS 14 (14)
T PF08255_consen 7 LHGWWRTS 14 (14)
T ss_pred EeeEEEcC
Confidence 46999986
No 66
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=28.62 E-value=1.2e+02 Score=25.41 Aligned_cols=36 Identities=8% Similarity=-0.054 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Q 014747 26 RYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSL 61 (419)
Q Consensus 26 r~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~L 61 (419)
-..|+.|...|..|+..+.+||+.+|+.+....-..
T Consensus 39 p~el~~A~~~L~~A~~a~~~~~y~~A~~~A~~A~~~ 74 (103)
T PF14346_consen 39 PVELKEAREKLQRAKAALDDGDYERARRLAEQAQAD 74 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 458999999999999999999999998887765444
No 67
>TIGR01597 PYST-B Plasmodium yoelii subtelomeric family PYST-B. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism.
Probab=25.26 E-value=1.8e+02 Score=29.00 Aligned_cols=82 Identities=18% Similarity=0.205 Sum_probs=55.5
Q ss_pred ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcccccH--HHHHHHHHHHHHHHHHHH
Q 014747 18 DVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYLASFK--SQKLYLKKKLLNALSELE 95 (419)
Q Consensus 18 e~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk~~~~--~~k~~l~k~l~~vl~~lE 95 (419)
+.|....|..+|.|...+..|-.-|- +||.|-+|+.-. .=.+|.+|.+=.+.+. .--+..++-|.+...++|
T Consensus 50 d~dnqfdLn~FY~Stlsla~q~nd~~-~ddeEi~~lrni-----idShikkhkenntl~dLnnvd~ktkklI~el~keLe 123 (255)
T TIGR01597 50 DADNQFDLNEFYQSTLSLANQFNDCN-DDDKEIAHLRNI-----IDSHIKKHKERNTLPDLNNVDKKTKKLINKLQKELE 123 (255)
T ss_pred ccCccccHHHHHHHHHHHHHHhcccc-CchHHHHHHHHh-----HHHHHHhhhccccCcccccccHHHHHHHHHHHHHHH
Confidence 45667889999999999977766664 577777665432 2256777876654331 111244566777789999
Q ss_pred hhcHHHHHHH
Q 014747 96 ELQPAVQQKI 105 (419)
Q Consensus 96 ~LK~~I~~~Y 105 (419)
++|.+|+..-
T Consensus 124 e~kKeldnk~ 133 (255)
T TIGR01597 124 ELKKELDNEM 133 (255)
T ss_pred HHHHHhcccc
Confidence 9999887544
No 68
>KOG2148 consensus Exocyst protein Sec3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.36 E-value=3.4e+02 Score=31.09 Aligned_cols=80 Identities=15% Similarity=0.123 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHH----hCCHHHHHHHHHHHHHHHhhccCC-CcC-ccccc-HHHHHHHHHHHHHH-HHHHHhhcHHHHHH
Q 014747 33 DNILKQADIFRE----EKNIIDLYVMLLRFSSLVTETIPC-HRD-YLASF-KSQKLYLKKKLLNA-LSELEELQPAVQQK 104 (419)
Q Consensus 33 ~~llreA~iy~~----egn~e~AYily~Ry~~LvvekLpk-HPd-yk~~~-~~~k~~l~k~l~~v-l~~lE~LK~~I~~~ 104 (419)
.+..+.|+++++ -+|+|+||.-+.|.+=.-++|+.. ||- +.... -..+..+...+-+. +.-++..|..-++.
T Consensus 652 enfa~raE~if~naerRtdlekaYtklvravfvgiek~Aqq~pKtp~dVv~mENyh~~y~tLs~Lkis~lda~kkeaka~ 731 (867)
T KOG2148|consen 652 ENFARRAEIIFENAERRTDLEKAYTKLVRAVFVGIEKIAQQDPKTPADVVLMENYHHFYATLSDLKISCLDAAKKEAKAL 731 (867)
T ss_pred HHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhhHHHHHHHHHHHhccchhHHHHHHHHH
Confidence 344455555555 489999999999977766777554 332 11111 13344444433332 45667777777777
Q ss_pred HHHHHHhh
Q 014747 105 INELNRKK 112 (419)
Q Consensus 105 Y~e~~~~~ 112 (419)
|+.+.+.+
T Consensus 732 ~~dhl~ay 739 (867)
T KOG2148|consen 732 YADHLAAY 739 (867)
T ss_pred HHHHHHHH
Confidence 87766544
No 69
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=22.25 E-value=2e+02 Score=24.99 Aligned_cols=61 Identities=23% Similarity=0.391 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHhhccCCCcCcccccHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHh
Q 014747 48 IIDLYVMLLRFSSLVTETIPCHRDYLASFKSQKLYLKKKLLNALSELEELQPAVQQKINELNRK 111 (419)
Q Consensus 48 ~e~AYily~Ry~~LvvekLpkHPdyk~~~~~~k~~l~k~l~~vl~~lE~LK~~I~~~Y~e~~~~ 111 (419)
.+-.++-++|=+.|.+++|-...+|-. ..-..++.++.....+.++++..+.+.-++....
T Consensus 53 ~dp~~~klfrLaQl~ieYLl~~q~~L~---~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~l 113 (118)
T PF13815_consen 53 VDPNFLKLFRLAQLSIEYLLHCQEYLS---SQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKL 113 (118)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677888999999988877666532 3345666778888888888888888777665554
No 70
>PTZ00453 cyclin-dependent kinase; Provisional
Probab=22.23 E-value=74 Score=27.26 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=31.0
Q ss_pred cccCCeeEEEEEeeccCCCCCCCcc-ccChHHHHHHhhcCCceeeeeeeecc
Q 014747 366 SLKNRKFYITALIIPKQESTSDSCQ-ATNEEEIFEVQDKRSLFPLGWIHVSA 416 (419)
Q Consensus 366 ~l~~~~~~it~liiP~q~~t~d~C~-~~~ee~~f~~~~~~~l~~lgwiHT~~ 416 (419)
+-.++.|.-.|+|+||.-..--.+. -..|+|.-.+-.++ ..||+|=.+
T Consensus 33 kY~DD~yEYRHViLPk~~~k~ipk~~LL~E~EWR~LGIqq---S~GW~HY~~ 81 (96)
T PTZ00453 33 KYYDDEYEYRHVILPKDFARLVPRSRLMSESEWRQLGVQQ---SVGWRHYMI 81 (96)
T ss_pred ceeCCCcEEEEEEeCHHHHHhCCCCccccHHHHHHhhhcc---CCCcEEeee
Confidence 3446789999999998744333322 35577665554444 579999643
No 71
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=22.13 E-value=1.3e+02 Score=27.41 Aligned_cols=49 Identities=22% Similarity=0.252 Sum_probs=36.2
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhhccCCCcCcc
Q 014747 19 VDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDYL 73 (419)
Q Consensus 19 ~n~~iplr~YlRsa~~llreA~iy~~egn~e~AYily~Ry~~LvvekLpkHPdyk 73 (419)
++.+.|...|-..| -+.-+..|++.|+++.|.--|-||+.| =|+||+..
T Consensus 36 L~~ryP~g~ya~qA--qL~l~yayy~~~~y~~A~a~~~rFirL----hP~hp~vd 84 (142)
T PF13512_consen 36 LDTRYPFGEYAEQA--QLDLAYAYYKQGDYEEAIAAYDRFIRL----HPTHPNVD 84 (142)
T ss_pred HHhcCCCCcccHHH--HHHHHHHHHHccCHHHHHHHHHHHHHh----CCCCCCcc
Confidence 34455555565543 355688899999999999999998877 48888654
No 72
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=22.00 E-value=1.2e+02 Score=29.83 Aligned_cols=36 Identities=14% Similarity=0.208 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHh
Q 014747 28 YYRIADNILKQADIFREE-KNIIDLYVMLLRFSSLVT 63 (419)
Q Consensus 28 YlRsa~~llreA~iy~~e-gn~e~AYily~Ry~~Lvv 63 (419)
+-+.|..+.+.|.+|.+. ||+++|.-+|.+.++++-
T Consensus 110 ~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~ 146 (282)
T PF14938_consen 110 FSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYE 146 (282)
T ss_dssp HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 445566667778888888 899999999999888883
No 73
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=21.56 E-value=1.1e+02 Score=31.41 Aligned_cols=79 Identities=22% Similarity=0.308 Sum_probs=59.4
Q ss_pred CeEeeeCHHHHHHHHHHHhhhcccccchhhhhcccccCCeeEEEEEeeccCCCCCCCccccChHHHHHH-------hhcC
Q 014747 332 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV-------QDKR 404 (419)
Q Consensus 332 l~~v~~p~~l~~~fl~~a~~Nt~~~~etCgil~g~l~~~~~~it~liiP~q~~t~d~C~~~~ee~~f~~-------~~~~ 404 (419)
|+.|.|+.=-+-+.+..|..- -|||--|++-|+...+.++|....-=-=+||.--..+..|. .|| |.+.
T Consensus 52 fk~vkISalAllKm~~hA~~G--gnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~A--yEYmv~Y~e~~k~~ 127 (347)
T KOG1554|consen 52 FKHVKISALALLKMVMHARSG--GNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEA--YEYMVQYIEEAKNV 127 (347)
T ss_pred hhhhhhHHHHHHHHHHHHhcC--CCeEEEeeecccccCCeEEEEeccccccccccceechHHHH--HHHHHHHHHHHHHh
Confidence 788999998888888888753 58999999999999999999887655567777666664443 333 2232
Q ss_pred --Cceeeeeeee
Q 014747 405 --SLFPLGWIHV 414 (419)
Q Consensus 405 --~l~~lgwiHT 414 (419)
-.-++||-|.
T Consensus 128 gr~envVGWyHS 139 (347)
T KOG1554|consen 128 GRLENVVGWYHS 139 (347)
T ss_pred hhhhceeeeeec
Confidence 2348999997
No 74
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=20.65 E-value=2.1e+02 Score=33.36 Aligned_cols=19 Identities=11% Similarity=0.092 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHhhccCCCc
Q 014747 48 IIDLYVMLLRFSSLVTETIPCHR 70 (419)
Q Consensus 48 ~e~AYily~Ry~~LvvekLpkHP 70 (419)
-.+.||..|- ++|.|-+.|
T Consensus 301 ~~~l~vacmq----~INal~t~p 319 (1102)
T KOG1924|consen 301 KQQLQVACMQ----FINALVTSP 319 (1102)
T ss_pred hHHHHHHHHH----HHHHhcCCH
Confidence 4455555555 334444444
Done!