Query psy5853
Match_columns 217
No_of_seqs 159 out of 651
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 19:44:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5853.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5853hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00167 VPS9 Domain present 100.0 2.1E-36 4.7E-41 230.0 10.6 103 114-216 1-105 (117)
2 PF02204 VPS9: Vacuolar sortin 100.0 7.5E-29 1.6E-33 184.4 11.1 101 115-215 1-104 (104)
3 KOG2320|consensus 99.8 2.5E-19 5.5E-24 164.2 13.8 198 17-215 297-506 (651)
4 KOG2319|consensus 99.2 1E-10 2.3E-15 108.5 10.5 159 52-213 176-340 (477)
5 KOG2319|consensus 99.2 9.7E-12 2.1E-16 115.4 2.1 180 36-216 294-476 (477)
6 cd06859 PX_SNX1_2_like The pho 63.8 6.1 0.00013 29.2 2.3 43 2-46 62-104 (114)
7 PF04558 tRNA_synt_1c_R1: Glut 56.6 41 0.0009 27.0 6.1 66 144-214 32-98 (164)
8 cd08798 Death_NFkB2_p100 Death 48.7 12 0.00027 26.2 1.6 30 3-32 37-66 (76)
9 cd06861 PX_Vps5p The phosphoin 43.2 29 0.00063 25.7 3.1 42 2-47 62-103 (112)
10 cd07288 PX_SNX15 The phosphoin 41.1 29 0.00063 26.2 2.8 42 2-47 68-109 (118)
11 cd07292 PX_SNX6 The phosphoino 38.0 45 0.00098 26.1 3.5 11 1-11 61-71 (141)
12 cd07284 PX_SNX7 The phosphoino 36.9 35 0.00076 25.6 2.7 43 2-46 62-106 (116)
13 cd08797 Death_NFkB1_p105 Death 34.7 25 0.00055 24.6 1.5 30 3-32 37-66 (76)
14 cd07281 PX_SNX1 The phosphoino 34.6 42 0.00092 25.3 2.8 44 2-47 64-115 (124)
15 PLN02859 glutamine-tRNA ligase 34.0 3.8E+02 0.0082 27.1 9.9 67 143-214 33-100 (788)
16 cd07283 PX_SNX30 The phosphoin 31.3 61 0.0013 24.3 3.2 43 2-46 62-106 (116)
17 cd07291 PX_SNX5 The phosphoino 31.1 64 0.0014 25.3 3.3 10 2-11 62-71 (141)
18 PHA02698 hypothetical protein; 28.7 1.1E+02 0.0023 21.5 3.7 51 3-60 30-80 (89)
19 PF15393 DUF4615: Domain of un 26.1 36 0.00077 26.2 1.1 50 91-142 6-55 (124)
20 cd07285 PX_SNX9 The phosphoino 24.6 99 0.0021 23.7 3.3 41 2-46 58-98 (126)
21 cd07293 PX_SNX3 The phosphoino 24.6 69 0.0015 24.2 2.5 43 2-46 62-111 (123)
22 cd06865 PX_SNX_like The phosph 24.2 87 0.0019 23.4 2.9 43 2-46 67-110 (120)
23 cd06863 PX_Atg24p The phosphoi 23.3 1.6E+02 0.0035 21.7 4.3 43 2-46 63-108 (118)
24 cd07282 PX_SNX2 The phosphoino 23.1 78 0.0017 23.9 2.5 43 2-46 64-114 (124)
25 cd06867 PX_SNX41_42 The phosph 21.8 89 0.0019 22.9 2.6 43 2-46 53-102 (112)
26 cd06892 PX_SNX5_like The phosp 21.0 1.5E+02 0.0033 23.2 3.8 10 2-11 62-71 (141)
27 PF08038 Tom7: TOM7 family; I 21.0 74 0.0016 19.6 1.6 19 160-178 18-39 (42)
28 cd08310 Death_NFkB-like Death 21.0 45 0.00097 22.9 0.7 26 3-28 34-59 (72)
29 KOG2527|consensus 20.9 1E+02 0.0023 24.0 2.7 41 1-44 78-118 (144)
30 PF00010 HLH: Helix-loop-helix 20.7 74 0.0016 20.0 1.7 14 200-213 41-54 (55)
31 cd06898 PX_SNX10 The phosphoin 20.2 97 0.0021 23.0 2.5 41 2-45 62-102 (113)
No 1
>smart00167 VPS9 Domain present in VPS9. Domain present in yeast vacuolar sorting protein 9 and other proteins.
Probab=100.00 E-value=2.1e-36 Score=230.01 Aligned_cols=103 Identities=33% Similarity=0.595 Sum_probs=97.7
Q ss_pred ChHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhhcCC-CCCCchhhhHHHHHHHHhcCCCChhhHHHHHHhhcc-Cc
Q psy5853 114 PWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSLTS-AVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSFYA-NK 191 (217)
Q Consensus 114 ~~~~a~~~L~~i~~~~sP~dKl~~i~~~~k~I~~~i~~~~-~~~~ADd~LPiliyviika~~~~l~s~i~yI~~f~~-~~ 191 (217)
+|+.|+.+|++||.++||+|||.||++||+.|++.++... .++|||||||+||||||||+||+++||++||++|++ +.
T Consensus 1 ~~~~a~~eL~~i~~~~sP~dKL~~il~~~~~I~~~l~~~~~~~~~ADdfLPilIYviika~~~~l~sn~~yI~~f~~~~~ 80 (117)
T smart00167 1 FVEIEQIELKFLQLYKSPSDKIKCLLRACKLIYTLLETQSGEVAGADDFLPVLIYVIIKCDPRDLLLNAEYMEEFLEPSL 80 (117)
T ss_pred CccHHHHHHHHccccCCHHHHHHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHHHHhccChhhHHHHHHHHHHHCCccc
Confidence 6999999999999999999999999999999999998654 679999999999999999999999999999999997 67
Q ss_pred cCChhHHHHHHHHHHHHHHhccCCC
Q psy5853 192 MEGEIQYWWVQFCSAIEFIKTMDYK 216 (217)
Q Consensus 192 ~~gE~~Y~lt~l~aAv~fI~~l~~~ 216 (217)
+.||.|||||||+||++||++++.+
T Consensus 81 l~gE~gY~lT~l~aAv~fi~~l~~~ 105 (117)
T smart00167 81 LTGEGGYYLTSLSAALALIKGLTEA 105 (117)
T ss_pred cccHHHHHHHHHHHHHHHHHHCCHH
Confidence 8999999999999999999999864
No 2
>PF02204 VPS9: Vacuolar sorting protein 9 (VPS9) domain; InterPro: IPR003123 This domain is present in yeast vacuolar sorting protein 9 and other proteins.; PDB: 1TXU_A 2OT3_A 2EFD_A 2EFE_C 2EFC_C 2EFH_A.
Probab=99.96 E-value=7.5e-29 Score=184.37 Aligned_cols=101 Identities=35% Similarity=0.749 Sum_probs=85.8
Q ss_pred hHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhh--cCCCCCCchhhhHHHHHHHHhcCCCChhhHHHHHHhhcc-Cc
Q psy5853 115 WPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLS--LTSAVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSFYA-NK 191 (217)
Q Consensus 115 ~~~a~~~L~~i~~~~sP~dKl~~i~~~~k~I~~~i~--~~~~~~~ADd~LPiliyviika~~~~l~s~i~yI~~f~~-~~ 191 (217)
|++|+++|++|+..+||.+|+.||.++++.|.+.+. ..+..+||||+||+++||++||++++++|+++||+.|+. +.
T Consensus 1 ~~~a~~~L~~i~~~~sP~~Kl~~l~~~~~~I~~~~~~~~~~~~~~aDdllpiliyvli~s~~~~l~s~i~~i~~f~~~~~ 80 (104)
T PF02204_consen 1 WEKAIEELKKINSVKSPLEKLKCLVKAFKEIQNAIKTSKSPSEISADDLLPILIYVLIKSNPPNLYSNIKYIEDFIDSSL 80 (104)
T ss_dssp -HHHHHHHHHGGG--SHHHHHHHHHHHHHHHHHHHHHHCCTS-B-HHHHHHHHHHHHHHH--TTHHHHHHHHHHHSCCCT
T ss_pred CHHHHHHHHHccccCCHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHhcCcccHHHHHHHHHHHccccc
Confidence 789999999999999999999999999999999992 223789999999999999999999999999999999986 66
Q ss_pred cCChhHHHHHHHHHHHHHHhccCC
Q psy5853 192 MEGEIQYWWVQFCSAIEFIKTMDY 215 (217)
Q Consensus 192 ~~gE~~Y~lt~l~aAv~fI~~l~~ 215 (217)
+.||.||++|||++|++||++++.
T Consensus 81 ~~~e~~y~ltt~~aA~~~i~~~~~ 104 (104)
T PF02204_consen 81 LSGEEGYYLTTFEAAVEYIQNLEF 104 (104)
T ss_dssp TSCHHHHHHHHHHHHHHHHHC---
T ss_pred cCCHHHHHHHHHHHHHHHHHHccC
Confidence 799999999999999999999873
No 3
>KOG2320|consensus
Probab=99.81 E-value=2.5e-19 Score=164.19 Aligned_cols=198 Identities=16% Similarity=0.187 Sum_probs=153.3
Q ss_pred CCCCcHHHHHHHHHHhhHh--HhhcCc------ccCCCCHHHHHHHHH-HHHHHHHHHhHHhhcCCCCCCCchhhHHHHH
Q psy5853 17 QGGGTAEYRRRTYEFVDNN--RRDYRS------GYSDSNSVQLSLAKI-AIDRAVISRCYMYAMYPNGDGDISRDQVLHE 87 (217)
Q Consensus 17 ~~~~~~~~~~~~~~f~~~~--~~~~~~------~~~~~~~~~~~~~~~-~lE~~V~~~iy~~if~~~~~~~~~~D~~l~~ 87 (217)
+....+.+.+.|++||+.. -+..++ .-...++.++|.+.| ++.+.|+..+-..+...... ...+|..|++
T Consensus 297 ~~td~a~mL~~iRq~lt~~k~yL~qs~e~~~~v~~~~~s~~~leavlEs~Lhk~vLkPlkp~l~~~l~~-~h~~dGsl~~ 375 (651)
T KOG2320|consen 297 RPTDSASMLQSIRQALTRRKNYLSQSPELDTPVQPSLLSETPLEAVLESALHKSVLKPLKPNLSAQLPP-VHSKDGSLQQ 375 (651)
T ss_pred CCCcHHHHHHHHHHHHHHhHHHHhhcCCCCCCccccccCcchHHHHHHHHHHHhhccccchhHhhhcch-hhhhccHHHH
Confidence 3344577888999999874 122222 222346677887766 77888888777666655442 4578888887
Q ss_pred HHHHhhcccCCCCcccccCCCCCCCCChHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhhcCC--CCCCchhhhHHH
Q psy5853 88 HVKNLAKIITPNHKYLRIPKMFHSECPWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSLTS--AVPAADDLIPVL 165 (217)
Q Consensus 88 ~i~~L~~~i~p~~l~l~I~~~~~~~~~~~~a~~~L~~i~~~~sP~dKl~~i~~~~k~I~~~i~~~~--~~~~ADd~LPil 165 (217)
.-+++.-+.+..--++|+--.......+++....+.+|.+.++|..|+..++++||.|+..+...+ ...|||||+|+|
T Consensus 376 l~en~~vvr~~~~~~lG~~~~~Ps~~~mEqvk~k~~~m~r~YSP~kkl~~Llk~ckLly~~~~~~~~g~~~gaDdflP~l 455 (651)
T KOG2320|consen 376 LKENQDVVRAANPTALGVFLSTPSDVLMEQVKQKFTAMQRRYSPSKKLHALLKACKLLYAGMGGDNEGLAYGADDFLPVL 455 (651)
T ss_pred HhcccceecccCccccceeccCCcHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHHHhccCCCCCCCCchhhHHHH
Confidence 777766553323334666333333445788888999999999999999999999999999987433 789999999999
Q ss_pred HHHHHhcCCCChhhHHHHHHhhcc-CccCChhHHHHHHHHHHHHHHhccCC
Q psy5853 166 VYVLIKANPPSLLSTVQYVNSFYA-NKMEGEIQYWWVQFCSAIEFIKTMDY 215 (217)
Q Consensus 166 iyviika~~~~l~s~i~yI~~f~~-~~~~gE~~Y~lt~l~aAv~fI~~l~~ 215 (217)
.||+.|++.+.+..+++||++|.+ +.+.||.|||+|++.+|++.|++++.
T Consensus 456 syvla~s~~~e~~~e~eYM~ELLdP~l~~geggYYLTs~~~al~~iks~~~ 506 (651)
T KOG2320|consen 456 SYVLARSDLQELLTEAEYMMELLDPDLLSGEGGYYLTSLYGALEHIKSLGR 506 (651)
T ss_pred HHHHHhcchhcchHHHHHHHHhcChhhhcCccchhHHHHHHHHHHHhcccc
Confidence 999999999999999999999996 77799999999999999999998863
No 4
>KOG2319|consensus
Probab=99.19 E-value=1e-10 Score=108.53 Aligned_cols=159 Identities=23% Similarity=0.349 Sum_probs=134.5
Q ss_pred HHHHHHHHHHHHHHhHHhhcCCCCCCCchhhHHHHHHHHHhhcccCCCCcccccCCCCC---CCCChHHHHHHHhcccCC
Q psy5853 52 SLAKIAIDRAVISRCYMYAMYPNGDGDISRDQVLHEHVKNLAKIITPNHKYLRIPKMFH---SECPWPAAQAEISSISSY 128 (217)
Q Consensus 52 ~~~~~~lE~~V~~~iy~~if~~~~~~~~~~D~~l~~~i~~L~~~i~p~~l~l~I~~~~~---~~~~~~~a~~~L~~i~~~ 128 (217)
......++......++..++.+....+.++|..++..++.++++ +++. ++|+..-. .+.....+...+..|+..
T Consensus 176 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~d~~~~~~~~~~~~l-~~~~--~~i~~~~~~~~~~~~~~~~~~~~~~i~~~ 252 (477)
T KOG2319|consen 176 NKLYFTCEDSAEAFISNILLDSETSDDAEFDLALSKAIRRLQGL-TSQM--LDIPVLEQIPELSKRVALASQRLALIREL 252 (477)
T ss_pred HHHHHHHhhHHHHHHhccccCcccCCHHHHhHHHHHHHHhhccc-chhh--ccccccccccchhHHHHHHHHHHHHHHHh
Confidence 34455677778888888888887777889999999999999999 7776 45553222 122467888899999999
Q ss_pred CCHHH-HHHHHHHHHHHHHHHhhcCC-CCCCchhhhHHHHHHHHhcCCCChhhHHHHHHhhcc-CccCChhHHHHHHHHH
Q psy5853 129 KTAHD-KVQCVYRTLNTILNLLSLTS-AVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSFYA-NKMEGEIQYWWVQFCS 205 (217)
Q Consensus 129 ~sP~d-Kl~~i~~~~k~I~~~i~~~~-~~~~ADd~LPiliyviika~~~~l~s~i~yI~~f~~-~~~~gE~~Y~lt~l~a 205 (217)
..|++ |..|.++|++.|+..++... ...++|.|+|.++|.+++++++++.++++|+.+|+. ..+.|+.+|++.++.+
T Consensus 253 ~~~~~~~~~~~~~~~~~~f~~l~~~~~e~~~~~~~l~~~~~~~~~~~~~~~~s~~~~~~~~~~~e~~~~~~~~~~~~~~~ 332 (477)
T KOG2319|consen 253 LTPRDKKEACALNCEKPIFSALKITDDENAGADKFLPSLIYCLLKAQGPHLVSNIQYILRFRAPERLSGEEKYYLFTYAC 332 (477)
T ss_pred hcchhhhHHHHHHHHHHHHhhhhccchhhhhHHhhhHHHHHHHHhcCCcccccHHHHHHhcccHHhhhccchhhhhhhhh
Confidence 99999 79999999999999999877 789999999999999999999999999999999997 7889999999999988
Q ss_pred HHHHHhcc
Q psy5853 206 AIEFIKTM 213 (217)
Q Consensus 206 Av~fI~~l 213 (217)
+-.++...
T Consensus 333 ~~~~~~~~ 340 (477)
T KOG2319|consen 333 ASSDIFDA 340 (477)
T ss_pred hhhhhhhh
Confidence 88777543
No 5
>KOG2319|consensus
Probab=99.16 E-value=9.7e-12 Score=115.40 Aligned_cols=180 Identities=26% Similarity=0.224 Sum_probs=153.8
Q ss_pred HhhcCcccCCCCHHHHHHHHHHHHHHHHHHhHHhhcCCCCCCCchhhHHHHHHHHHhhcccCCCCcccccCCCCCCCCCh
Q psy5853 36 RRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQVLHEHVKNLAKIITPNHKYLRIPKMFHSECPW 115 (217)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~lE~~V~~~iy~~if~~~~~~~~~~D~~l~~~i~~L~~~i~p~~l~l~I~~~~~~~~~~ 115 (217)
.+.....|...++.+......++|+......|...+.++...+...+..++..+..++.+.+ .|....++.....+.+|
T Consensus 294 ~~~~~~~~~~~s~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~q~~~~-~~~~~~~~~~~~~e~~~ 372 (477)
T KOG2319|consen 294 CLLKAQGPHLVSNIQYILRFRAPERLSGEEKYYLFTYACASSDIFDATLLSLTISSLQDFAR-EHTAYESEEVSLREEEV 372 (477)
T ss_pred HHHhcCCcccccHHHHHHhcccHHhhhccchhhhhhhhhhhhhhhhhhhhhcccchhhhhhh-hccchhhhhhhhccCcc
Confidence 45555677777788888888899999999999998888766666777777777777777644 55555666656667789
Q ss_pred HHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhhcCC--CCCCchhhhHHHHHHHHhcCCCChhhHHHHHHhhccCcc-
Q psy5853 116 PAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSLTS--AVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSFYANKM- 192 (217)
Q Consensus 116 ~~a~~~L~~i~~~~sP~dKl~~i~~~~k~I~~~i~~~~--~~~~ADd~LPiliyviika~~~~l~s~i~yI~~f~~~~~- 192 (217)
..+..++..++.+.+|.+|+.|.+++++.|.+....+. ...++||+.|+..+|.++++|+.+.++++|++.|..+..
T Consensus 373 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~i~~~~~~s~~~~v~~~~d~~~~~~~v~ik~~p~~~~sl~q~~~~~~~s~~~ 452 (477)
T KOG2319|consen 373 PSASPDLRSLDDEFTKNLKLLCDVRLRSAINNLLYASLSSPVADADDPSAVEGSVSIKPNPLEILSLVQKIEEFDGSSLE 452 (477)
T ss_pred cccchhhhccchhhcCCcccccchhhhhhhccchhhcccCcccccccccchheeecccCCchhhhhhhhhhccccccccc
Confidence 99999999999999999999999999999998877654 678999999999999999999999999999999987655
Q ss_pred CChhHHHHHHHHHHHHHHhccCCC
Q psy5853 193 EGEIQYWWVQFCSAIEFIKTMDYK 216 (217)
Q Consensus 193 ~gE~~Y~lt~l~aAv~fI~~l~~~ 216 (217)
.|+..|++..+.+|+++|++++.+
T Consensus 453 ~g~~~~~~~~~~~a~~~~k~~~~~ 476 (477)
T KOG2319|consen 453 PGEDSLLPSLFKRAAENIKTFNKS 476 (477)
T ss_pred ccchhhccccchhHHHhccccccC
Confidence 699999999999999999999875
No 6
>cd06859 PX_SNX1_2_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 1 and 2. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. This subfamily consists of SNX1, SNX2, and similar proteins. They harbor a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. Both domains have been shown to determine the specific membrane-targeting of SNX1. SNX1 and SNX2 are components of the retromer complex,
Probab=63.82 E-value=6.1 Score=29.20 Aligned_cols=43 Identities=16% Similarity=0.126 Sum_probs=30.8
Q ss_pred CCCCCCcccccccccCCCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVTGQGGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
+||.|-|..+.++.+.+...++=++.++.||.. +..|+.|...
T Consensus 62 ~P~lP~k~~~~~~~~~~~~ie~Rr~~L~~fL~~--i~~~p~l~~s 104 (114)
T cd06859 62 VPPPPEKQAVGRFKVKFEFIEKRRAALERFLRR--IAAHPVLRKD 104 (114)
T ss_pred eCCCCCCcccCccCccHHHHHHHHHHHHHHHHH--HhcChhhccC
Confidence 678888888776654444566777788888854 6778877764
No 7
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.
Probab=56.65 E-value=41 Score=26.96 Aligned_cols=66 Identities=15% Similarity=0.313 Sum_probs=40.8
Q ss_pred HHHHHhhcCCCCCCchhhhHHHHHHHHhcCCCChhhHHHHHHhhc-cCccCChhHHHHHHHHHHHHHHhccC
Q psy5853 144 TILNLLSLTSAVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSFY-ANKMEGEIQYWWVQFCSAIEFIKTMD 214 (217)
Q Consensus 144 ~I~~~i~~~~~~~~ADd~LPiliyviika~~~~l~s~i~yI~~f~-~~~~~gE~~Y~lt~l~aAv~fI~~l~ 214 (217)
.+...+.......+.|.=.-.|+|.+.-.-+++-..+..||-.|. +.++.+.. ++.+|+.|++.-.
T Consensus 32 ~L~~iI~ea~~~~~~dk~~g~LLy~lAtk~k~~~~~~r~~iv~~I~~gklkt~~-----Ql~AA~~Yl~~~~ 98 (164)
T PF04558_consen 32 SLKAIINEAGVDSGCDKKQGNLLYQLATKLKPQALPHRPFIVKYIVDGKLKTNL-----QLDAALKYLKSNP 98 (164)
T ss_dssp HHHHHHHTS-TT----HHHHHHHHHHHHHHTT---TTHHHHHHHHHTTS--SHH-----HHHHHHHHHHHHG
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHhCCCCCHH-----HHHHHHHHHHHCC
Confidence 344455554455788888889999998876667777888888887 46665544 7889999998643
No 8
>cd08798 Death_NFkB2_p100 Death domain of the Nuclear Factor-KappaB2 precursor protein p100. Death Domain (DD) of the Nuclear Factor-KappaB2 (NF-kB2) precursor protein p100. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB2 (or p52) is produced from the processing of the precursor protein p100, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the non-canonical NF-kB pathway. The p100 precursor is cytosolic and interacts with RelB. Upon phosphorylation by IKKalpha, p100 is processed to its 52kDa active, DNA binding form and the p52/RelB complex is translocated into the nucleus. The non-canonical pathway plays a role in adaptive immunity and lymphorganogenesis. In general, DDs are protein-protein interaction domains found i
Probab=48.70 E-value=12 Score=26.19 Aligned_cols=30 Identities=10% Similarity=0.020 Sum_probs=26.1
Q ss_pred CCCCCcccccccccCCCCcHHHHHHHHHHh
Q psy5853 3 LPPPIKPDISNVTGQGGGTAEYRRRTYEFV 32 (217)
Q Consensus 3 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~ 32 (217)
.|||++.=+.+.+.+++..+.+.+.++++=
T Consensus 37 ~~SPt~~LLd~yE~~~G~l~~L~~aL~~mG 66 (76)
T cd08798 37 TQSPPGSLLRSYELAGGPLQGLIEALQDMG 66 (76)
T ss_pred CCCchHHHHHHhhccCCCHHHHHHHHHHhC
Confidence 589999999999999999999998877653
No 9
>cd06861 PX_Vps5p The phosphoinositide binding Phox Homology domain of yeast sorting nexin Vps5p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. The PX domain of Vps5p binds phosphatidylinositol-3-phosphate (PI3P
Probab=43.20 E-value=29 Score=25.65 Aligned_cols=42 Identities=14% Similarity=0.179 Sum_probs=26.8
Q ss_pred CCCCCCcccccccccCCCCcHHHHHHHHHHhhHhHhhcCcccCCCC
Q psy5853 2 VLPPPIKPDISNVTGQGGGTAEYRRRTYEFVDNNRRDYRSGYSDSN 47 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~ 47 (217)
++|.|-|..+.++. .+-.++=++.++.||.. +..|+.|.+..
T Consensus 62 iP~lP~K~~~~~~~--~~fie~Rr~~Le~fL~~--i~~~p~l~~s~ 103 (112)
T cd06861 62 VPPPPEKQSVGRFD--DNFVEQRRAALEKMLRK--IANHPVLQKDP 103 (112)
T ss_pred cCCCCCcccccCCC--HHHHHHHHHHHHHHHHH--HHCCcccccCc
Confidence 67888888776543 12234445667778754 77888887643
No 10
>cd07288 PX_SNX15 The phosphoinositide binding Phox Homology domain of Sorting Nexin 15. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX15 contains an N-terminal PX domain and a C-terminal Microtubule Interacting and Trafficking (MIT) domain. It plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of t
Probab=41.05 E-value=29 Score=26.16 Aligned_cols=42 Identities=12% Similarity=-0.013 Sum_probs=29.9
Q ss_pred CCCCCCcccccccccCCCCcHHHHHHHHHHhhHhHhhcCcccCCCC
Q psy5853 2 VLPPPIKPDISNVTGQGGGTAEYRRRTYEFVDNNRRDYRSGYSDSN 47 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~ 47 (217)
++|.|-|+-+.++. ...+++=++.+++|+. .+..|+.|++..
T Consensus 68 ~Pp~P~K~~~g~f~--~~fIeeRR~~Le~fL~--~i~~~p~l~~s~ 109 (118)
T cd07288 68 FPPFPRAQVFGRFE--AAVIEERRNAAEAMLL--FTVNIPALYNSP 109 (118)
T ss_pred cCCCCCceeeccCC--HHHHHHHHHHHHHHHH--HHhCChhhcCCh
Confidence 67888777777653 3345666667788884 478999999753
No 11
>cd07292 PX_SNX6 The phosphoinositide binding Phox Homology domain of Sorting Nexin 6. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transfo
Probab=38.00 E-value=45 Score=26.15 Aligned_cols=11 Identities=36% Similarity=0.975 Sum_probs=9.8
Q ss_pred CCCCCCCcccc
Q psy5853 1 MVLPPPIKPDI 11 (217)
Q Consensus 1 ~~~~~p~~~~~ 11 (217)
.|||.|-||.+
T Consensus 61 IVPPlP~K~~~ 71 (141)
T cd07292 61 IIPPAPPRPDF 71 (141)
T ss_pred EECCCCCCccc
Confidence 38999999988
No 12
>cd07284 PX_SNX7 The phosphoinositide binding Phox Homology domain of Sorting Nexin 7. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX7 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-6, SNX8, SNX30,
Probab=36.91 E-value=35 Score=25.62 Aligned_cols=43 Identities=12% Similarity=0.093 Sum_probs=27.6
Q ss_pred CCCCCCccccccccc--CCCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVTG--QGGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~--~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
|+|-|-|..+.+..+ .++-.++=++.++.||.. +..|+..+..
T Consensus 62 iPplP~K~~~~~~~~~~~~~fie~Rr~~Le~FL~r--i~~hp~L~~s 106 (116)
T cd07284 62 IPPLPEKFVMKGMVERFNEDFIETRRKALHKFLNR--IADHPTLTFN 106 (116)
T ss_pred eCCCCCcchhhhccccCCHHHHHHHHHHHHHHHHH--HHcCcccccC
Confidence 688888876644332 233445555667888854 7888877764
No 13
>cd08797 Death_NFkB1_p105 Death domain of the Nuclear Factor-KappaB1 precursor protein p105. Death Domain (DD) of the Nuclear Factor-KappaB1 (NF-kB1) precursor protein p105. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB1 (or p50) is produced from the processing of the precursor protein p105, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the classical (or canonical) NF-kB pathway. In the cytosol, p50 forms an inactive complex with RelA (or p65) and the Inhibitor of NF-kB (IkB). Activation is triggered by the phosphorylation and degradation of IkB, resulting in the active DNA-binding p50-RelA dimer to migrate to the nucleus. The classical pathway regulates the majority of genes activated by NF-kB including those encod
Probab=34.74 E-value=25 Score=24.61 Aligned_cols=30 Identities=23% Similarity=0.233 Sum_probs=25.6
Q ss_pred CCCCCcccccccccCCCCcHHHHHHHHHHh
Q psy5853 3 LPPPIKPDISNVTGQGGGTAEYRRRTYEFV 32 (217)
Q Consensus 3 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~ 32 (217)
.|||+.-=++++|..++..+++++.++++=
T Consensus 37 ~pSPt~~LLd~~E~~~G~l~~L~~aL~~mG 66 (76)
T cd08797 37 SPSPSKTLLDNYEVSGGTVRELLAALKRMG 66 (76)
T ss_pred CCCcHHHHHHHHhcCCCCHHHHHHHHHHhC
Confidence 599999999999999988899998776653
No 14
>cd07281 PX_SNX1 The phosphoinositide binding Phox Homology domain of Sorting Nexin 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX1 is both membrane associated and a cytosolic protein that exists as a tetramer in protein complexes. It can associate reversibly with membranes of the endosomal compartment, thereby coating these vesicles. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval
Probab=34.60 E-value=42 Score=25.28 Aligned_cols=44 Identities=18% Similarity=0.145 Sum_probs=26.4
Q ss_pred CCCCCCccccccc----ccCC----CCcHHHHHHHHHHhhHhHhhcCcccCCCC
Q psy5853 2 VLPPPIKPDISNV----TGQG----GGTAEYRRRTYEFVDNNRRDYRSGYSDSN 47 (217)
Q Consensus 2 ~~~~p~~~~~~~~----~~~~----~~~~~~~~~~~~f~~~~~~~~~~~~~~~~ 47 (217)
+||.|-|..+... ++.+ +-.++=++.++.||. .+..|+.|.+..
T Consensus 64 iPp~P~K~~~~~~~~~~~~~~~~~~~fie~Rr~~Le~FL~--~l~~~p~l~~s~ 115 (124)
T cd07281 64 VPPPPEKSLIGMTKVKVGKEDSSSAEFLERRRAALERYLQ--RIVSHPSLLQDP 115 (124)
T ss_pred eCCCCCccccccchhhccccccccHHHHHHHHHHHHHHHH--HHhcCcccccCh
Confidence 5788888877543 2212 223444455677774 478889888743
No 15
>PLN02859 glutamine-tRNA ligase
Probab=34.01 E-value=3.8e+02 Score=27.11 Aligned_cols=67 Identities=15% Similarity=0.271 Sum_probs=46.4
Q ss_pred HHHHHHhhcCCCCCCchhhhHHHHHHHHhcCCCChhhHHHHHHhhcc-CccCChhHHHHHHHHHHHHHHhccC
Q psy5853 143 NTILNLLSLTSAVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSFYA-NKMEGEIQYWWVQFCSAIEFIKTMD 214 (217)
Q Consensus 143 k~I~~~i~~~~~~~~ADd~LPiliyviika~~~~l~s~i~yI~~f~~-~~~~gE~~Y~lt~l~aAv~fI~~l~ 214 (217)
+.+..++...+...++|.=.-.|+|.+.-.-+++...+..+|-.+.. +.+.+.. ++.||+.|+++-.
T Consensus 33 ~~L~~iI~ea~~~~~~dk~~g~LLy~LAtk~~~~~~~~r~~lv~~I~~gkIkT~~-----Ql~AA~kYl~~~~ 100 (788)
T PLN02859 33 SNLTAVIHEAGVTNGCDKTVGNLLYTVATKYPANALVHRPTLLSYIVSSKIKTPA-----QLEAAFSFFSSTG 100 (788)
T ss_pred HHHHHHHHhcCCccCCChHHHHHHHHHHHhcCCccchhHHHHHHHHHhCCCCCHH-----HHHHHHHHHHhCC
Confidence 33444555444334578778888998887767778888888888874 5665544 7889999997643
No 16
>cd07283 PX_SNX30 The phosphoinositide binding Phox Homology domain of Sorting Nexin 30. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX30 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-8, and SNX32
Probab=31.34 E-value=61 Score=24.27 Aligned_cols=43 Identities=16% Similarity=0.083 Sum_probs=25.8
Q ss_pred CCCCCCccccccccc--CCCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVTG--QGGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~--~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
|||-|-|+.+....+ .++-.++=++.++.||.. +..|+.....
T Consensus 62 iPpLP~K~~~~~~~~~~~~~fie~Rr~~Le~FL~~--i~~hp~L~~s 106 (116)
T cd07283 62 IPPLPEKFVVKGVVDRFSEEFVETRRKALDKFLKR--IADHPVLSFN 106 (116)
T ss_pred cCCCCCcccccccccCCCHHHHHHHHHHHHHHHHH--HHcCcccccC
Confidence 688888877643322 122334444566788854 6788777653
No 17
>cd07291 PX_SNX5 The phosphoinositide binding Phox Homology domain of Sorting Nexin 5. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting
Probab=31.11 E-value=64 Score=25.31 Aligned_cols=10 Identities=50% Similarity=1.006 Sum_probs=9.3
Q ss_pred CCCCCCcccc
Q psy5853 2 VLPPPIKPDI 11 (217)
Q Consensus 2 ~~~~p~~~~~ 11 (217)
|||.|-|+.+
T Consensus 62 IPPlPeK~~~ 71 (141)
T cd07291 62 IPPAPPKPDF 71 (141)
T ss_pred ECCCCCCccc
Confidence 7999999988
No 18
>PHA02698 hypothetical protein; Provisional
Probab=28.70 E-value=1.1e+02 Score=21.52 Aligned_cols=51 Identities=10% Similarity=0.273 Sum_probs=31.1
Q ss_pred CCCCCcccccccccCCCCcHHHHHHHHHHhhHhHhhcCcccCCCCHHHHHHHHHHHHH
Q psy5853 3 LPPPIKPDISNVTGQGGGTAEYRRRTYEFVDNNRRDYRSGYSDSNSVQLSLAKIAIDR 60 (217)
Q Consensus 3 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lE~ 60 (217)
-|-|+-....+|. .++++..+-+|++.. ...+..+-++.++++.+...+|.
T Consensus 30 tp~p~peeV~~Cs-----PEdMs~mLD~FLedi--q~ksElqLLsqEEMdELl~Eled 80 (89)
T PHA02698 30 TPEPTPEEVPQCS-----PEDMSDMLDNFLEDI--QYKSELQLLSQEEMDELLVELED 80 (89)
T ss_pred CCCCChhhhccCC-----HHHHHHHHHHHHHHH--HHHHHHHHhhHHHHHHHHHHHHH
Confidence 3455555555554 688899899999863 22222233456677777666654
No 19
>PF15393 DUF4615: Domain of unknown function (DUF4615)
Probab=26.08 E-value=36 Score=26.16 Aligned_cols=50 Identities=18% Similarity=0.112 Sum_probs=35.6
Q ss_pred HhhcccCCCCcccccCCCCCCCCChHHHHHHHhcccCCCCHHHHHHHHHHHH
Q psy5853 91 NLAKIITPNHKYLRIPKMFHSECPWPAAQAEISSISSYKTAHDKVQCVYRTL 142 (217)
Q Consensus 91 ~L~~~i~p~~l~l~I~~~~~~~~~~~~a~~~L~~i~~~~sP~dKl~~i~~~~ 142 (217)
.|.|.| +.|++|+...-....-++.|...|+.+.+-++|.=|=.+|+++.
T Consensus 6 EL~WCI--~QLelgl~~~k~t~kq~ee~~k~i~~L~S~k~plvkKRqlMr~~ 55 (124)
T PF15393_consen 6 ELDWCI--QQLELGLQRQKLTPKQIEEASKAIRTLKSNKAPLVKKRQLMRST 55 (124)
T ss_pred HHHHHH--HHHHHHhhcCCCCHHHHHHHHHHHHHhhCCCCccHHHHHHHHHH
Confidence 345543 45556665433333457899999999999999998888888764
No 20
>cd07285 PX_SNX9 The phosphoinositide binding Phox Homology domain of Sorting Nexin 9. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX9, also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). It contains an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature. T
Probab=24.61 E-value=99 Score=23.71 Aligned_cols=41 Identities=15% Similarity=-0.006 Sum_probs=25.4
Q ss_pred CCCCCCcccccccccCCCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVTGQGGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
|||-|-|..+.++.. +-.++=++.++.||. .+..|+.....
T Consensus 58 vPplP~K~~~g~f~~--~FIe~Rr~~Le~FL~--ri~~hP~L~~~ 98 (126)
T cd07285 58 IPSLPDKQVTGRFEE--EFIKMRMERLQAWMT--RMCRHPVISES 98 (126)
T ss_pred cCCCCCccccCCCCH--HHHHHHHHHHHHHHH--HHHcCcCcCCC
Confidence 788888877765531 223344445667774 47788877653
No 21
>cd07293 PX_SNX3 The phosphoinositide binding Phox Homology domain of Sorting Nexin 3. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX3 associates with early endosomes through a PX domain-mediated interaction with phosphatidylinositol-3-phosphate (PI3P). It associates with the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, and functions as a cargo-specific adaptor f
Probab=24.60 E-value=69 Score=24.25 Aligned_cols=43 Identities=14% Similarity=0.079 Sum_probs=26.9
Q ss_pred CCCCCCccccccccc-------CCCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVTG-------QGGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~-------~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
|+|-|-|..+..+.. ..+-.++=++.++.|+. .+..||.+++.
T Consensus 62 iPpLP~K~~~~~~~~~~~~~~~~~~fie~Rr~~Le~FL~--~i~~hP~l~~~ 111 (123)
T cd07293 62 VPPLPGKALFRQLPFRGDDGIFDDSFIEERKQGLEQFLN--KVAGHPLAQNE 111 (123)
T ss_pred cCCCCCCchhhhcccccccCCCCHHHHHHHHHHHHHHHH--HHHcCcccccC
Confidence 688888888754311 11123444556677884 47888988874
No 22
>cd06865 PX_SNX_like The phosphoinositide binding Phox Homology domain of SNX-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. This subfamily is composed of uncharacterized proteins, predominantly from plants, with similarity to sorting nexins. A few members show a similar domain architectu
Probab=24.15 E-value=87 Score=23.44 Aligned_cols=43 Identities=14% Similarity=0.061 Sum_probs=26.0
Q ss_pred CCCCCCcccccccc-cCCCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVT-GQGGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~-~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
+||-|-|+-+.... ...+-.++=++.++.||.. +..|+.|++.
T Consensus 67 iPplP~K~~~~~~~~~~~~fie~Rr~~Le~fL~~--i~~~p~l~~s 110 (120)
T cd06865 67 VPPRPDKSVVESQVMQSAEFIEQRRVALEKYLNR--LAAHPVIGLS 110 (120)
T ss_pred eCCCcCCccccccccCCHHHHHHHHHHHHHHHHH--HHcCceeecC
Confidence 56777776664322 2233345555667778854 7788888764
No 23
>cd06863 PX_Atg24p The phosphoinositide binding Phox Homology domain of yeast Atg24p, an autophagic degradation protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The yeast Atg24p is a sorting nexin (SNX) which is involved in membrane fusion events at the vacuolar surface during pexophagy. This is facilitated via binding of Atg24p to phosphatidylinositol 3-phosphate (PI3P) through its PX domain. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway.
Probab=23.27 E-value=1.6e+02 Score=21.68 Aligned_cols=43 Identities=21% Similarity=0.206 Sum_probs=26.7
Q ss_pred CCCCCCcccccccccCC---CCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVTGQG---GGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~~---~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
+||-|-|..+..+.+.. .-.++=++.++.||.. +..|+.|.+.
T Consensus 63 iPplP~K~~~~~~~~~~~~~~~ie~Rr~~Le~fL~~--i~~~p~l~~s 108 (118)
T cd06863 63 VPPLPDKHRLEYITGDRFSPEFITRRAQSLQRFLRR--ISLHPVLSQS 108 (118)
T ss_pred CCCCCCccccccccccCCCHHHHHHHHHHHHHHHHH--HhcCcccccC
Confidence 67888888765543322 2234456666777754 7788877764
No 24
>cd07282 PX_SNX2 The phosphoinositide binding Phox Homology domain of Sorting Nexin 2. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX2 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures efficient cargo sort
Probab=23.12 E-value=78 Score=23.94 Aligned_cols=43 Identities=12% Similarity=0.061 Sum_probs=26.6
Q ss_pred CCCCCCccccccccc---C-----CCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVTG---Q-----GGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~---~-----~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
|||-|-|..+...+. . .+-.++=++.++.||.. +..|+.|.+.
T Consensus 64 iPplP~K~~~~~~~~~~~~~~~~~~~fie~Rr~~Le~fL~~--i~~~p~l~~s 114 (124)
T cd07282 64 VPPAPEKSIVGMTKVKVGKEDSSSTEFVEKRRAALERYLQR--TVKHPTLLQD 114 (124)
T ss_pred eCCCCCCccccccccccccccccCHHHHHHHHHHHHHHHHH--HhcCcccccC
Confidence 688888887764421 1 12234444566788854 7888888764
No 25
>cd06867 PX_SNX41_42 The phosphoinositide binding Phox Homology domain of fungal Sorting Nexins 41 and 42. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX41 and SNX42 (also called Atg20p) form dimers with SNX4, and are required in protein recycling from the sorting endosome (post-Golgi endosome) back
Probab=21.81 E-value=89 Score=22.93 Aligned_cols=43 Identities=12% Similarity=0.138 Sum_probs=25.7
Q ss_pred CCCCCCcccccccc-------cCCCCcHHHHHHHHHHhhHhHhhcCcccCCC
Q psy5853 2 VLPPPIKPDISNVT-------GQGGGTAEYRRRTYEFVDNNRRDYRSGYSDS 46 (217)
Q Consensus 2 ~~~~p~~~~~~~~~-------~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~ 46 (217)
++|-|-|..+.+.. ...+-.++=++.++.||.. +..|+.+...
T Consensus 53 iPplP~K~~~~~~~~~~~~~~~~~~~ie~Rr~~Le~fL~~--l~~~p~l~~s 102 (112)
T cd06867 53 IPPIPEKHSLKDYAKKPSKAKNDAKIIERRKRMLQRFLNR--CLQHPILRND 102 (112)
T ss_pred cCCCCCcchhhhhccccccccCcHHHHHHHHHHHHHHHHH--HhcChhhccC
Confidence 57778887765431 1112234445567788854 6788888764
No 26
>cd06892 PX_SNX5_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 5 and 6. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Members of this subfamily include SNX5, SNX6, and similar proteins. They contain a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to other sorting nexins including SNX1-2. The PX-BAR structural unit helps determine the specific membrane-targeting of som
Probab=20.97 E-value=1.5e+02 Score=23.22 Aligned_cols=10 Identities=50% Similarity=1.006 Sum_probs=9.1
Q ss_pred CCCCCCcccc
Q psy5853 2 VLPPPIKPDI 11 (217)
Q Consensus 2 ~~~~p~~~~~ 11 (217)
|||.|-|+.+
T Consensus 62 VPP~P~K~~~ 71 (141)
T cd06892 62 IPPAPPKPDF 71 (141)
T ss_pred ECCCCCCccc
Confidence 8999999977
No 27
>PF08038 Tom7: TOM7 family; InterPro: IPR012621 This family consists of TOM7 family of mitochondrial import receptors. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=20.97 E-value=74 Score=19.63 Aligned_cols=19 Identities=37% Similarity=0.990 Sum_probs=14.3
Q ss_pred hhhHHHHHHHHhc--CC-CChh
Q psy5853 160 DLIPVLVYVLIKA--NP-PSLL 178 (217)
Q Consensus 160 d~LPiliyviika--~~-~~l~ 178 (217)
-|+|+.+|+=.++ ++ |.+.
T Consensus 18 GfIP~IlylG~~~~~~p~Psl~ 39 (42)
T PF08038_consen 18 GFIPLILYLGFRSGADPMPSLI 39 (42)
T ss_pred eehHHHHHHhhccCCCCCCcHH
Confidence 4899999998887 55 5443
No 28
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=20.95 E-value=45 Score=22.87 Aligned_cols=26 Identities=27% Similarity=0.316 Sum_probs=19.6
Q ss_pred CCCCCcccccccccCCCCcHHHHHHH
Q psy5853 3 LPPPIKPDISNVTGQGGGTAEYRRRT 28 (217)
Q Consensus 3 ~~~p~~~~~~~~~~~~~~~~~~~~~~ 28 (217)
.|||++.=++.++.++.....+...+
T Consensus 34 ~~sPt~~LL~~we~~~~tv~~L~~~L 59 (72)
T cd08310 34 SPSPTKMLLDYFEMQGGTLERLRDAL 59 (72)
T ss_pred CCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence 69999999999998885555555544
No 29
>KOG2527|consensus
Probab=20.86 E-value=1e+02 Score=24.03 Aligned_cols=41 Identities=15% Similarity=-0.026 Sum_probs=30.8
Q ss_pred CCCCCCCcccccccccCCCCcHHHHHHHHHHhhHhHhhcCcccC
Q psy5853 1 MVLPPPIKPDISNVTGQGGGTAEYRRRTYEFVDNNRRDYRSGYS 44 (217)
Q Consensus 1 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~ 44 (217)
+|||=|-|+.+.+.-.+ +.+++=++.+..||.. +..|++-+
T Consensus 78 vvP~LPgK~~~~~~~fr-e~IEeRrqgLe~fl~k--VaghpL~q 118 (144)
T KOG2527|consen 78 VVPELPGKALFRQLPFR-EFIEERRQGLEVFLRK--VAGHPLLQ 118 (144)
T ss_pred cCCCCCcHHHHhcCchH-HHHHHHHHHHHHHHHH--HhCchhhh
Confidence 47888999888775544 6778888888888854 77777665
No 30
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=20.75 E-value=74 Score=19.99 Aligned_cols=14 Identities=29% Similarity=0.415 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHhcc
Q psy5853 200 WVQFCSAIEFIKTM 213 (217)
Q Consensus 200 lt~l~aAv~fI~~l 213 (217)
.+.|+.|++||+.|
T Consensus 41 ~~iL~~ai~yI~~L 54 (55)
T PF00010_consen 41 ASILQKAIDYIKQL 54 (55)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHh
Confidence 56788888888765
No 31
>cd06898 PX_SNX10 The phosphoinositide binding Phox Homology domain of Sorting Nexin 10. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX10 may be involved in the regulation of endosome homeostasis. Its expression induces the formation of giant vacuoles in mammalian cells.
Probab=20.21 E-value=97 Score=22.96 Aligned_cols=41 Identities=12% Similarity=0.050 Sum_probs=24.5
Q ss_pred CCCCCCcccccccccCCCCcHHHHHHHHHHhhHhHhhcCcccCC
Q psy5853 2 VLPPPIKPDISNVTGQGGGTAEYRRRTYEFVDNNRRDYRSGYSD 45 (217)
Q Consensus 2 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 45 (217)
++|-|-|..+.++.+ ..-.++=++.++.||.. +..|+.+.+
T Consensus 62 ~p~lP~K~~~~~~~~-~~fie~Rr~~L~~fL~~--i~~~p~l~~ 102 (113)
T cd06898 62 LPSLPPKNLFGRFNN-EGFIEERQQGLQDFLEK--VLQTPLLLS 102 (113)
T ss_pred CCCCCCCccccCCCC-HHHHHHHHHHHHHHHHH--HHcChhhcc
Confidence 567777777766531 33444445556667743 667776655
Done!