Query 041688
Match_columns 277
No_of_seqs 111 out of 312
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 09:39:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041688.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041688hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03087 DUF241: Arabidopsis p 100.0 2.7E-68 5.9E-73 479.1 23.9 226 41-274 1-231 (231)
2 PF05633 DUF793: Protein of un 99.9 4.1E-21 8.8E-26 183.0 19.5 248 19-275 38-389 (389)
3 PF05055 DUF677: Protein of un 89.7 20 0.00043 34.5 18.9 42 73-114 66-107 (336)
4 cd07665 BAR_SNX1 The Bin/Amphi 83.2 23 0.0005 32.2 11.7 72 36-114 75-146 (234)
5 cd07664 BAR_SNX2 The Bin/Amphi 82.1 27 0.00058 31.8 11.6 69 36-114 75-146 (234)
6 PF05600 DUF773: Protein of un 62.7 1.1E+02 0.0023 31.2 11.6 95 42-143 398-495 (507)
7 PF14389 Lzipper-MIP1: Leucine 57.0 23 0.0005 27.3 4.5 36 233-268 53-88 (88)
8 KOG2911 Uncharacterized conser 47.0 2.7E+02 0.0058 27.8 11.1 27 124-150 275-301 (439)
9 PF02609 Exonuc_VII_S: Exonucl 45.8 62 0.0013 22.2 4.9 45 101-149 3-47 (53)
10 cd07597 BAR_SNX8 The Bin/Amphi 43.3 1.2E+02 0.0027 27.4 7.8 64 39-112 89-153 (246)
11 COG3352 FlaC Putative archaeal 39.7 44 0.00095 28.6 3.9 35 234-268 72-106 (157)
12 PF12325 TMF_TATA_bd: TATA ele 38.0 52 0.0011 26.9 4.0 41 102-142 17-57 (120)
13 cd07627 BAR_Vps5p The Bin/Amph 35.3 3.1E+02 0.0068 24.1 13.2 62 37-108 58-119 (216)
14 PF03670 UPF0184: Uncharacteri 35.2 93 0.002 24.0 4.7 33 233-265 25-57 (83)
15 TIGR02338 gimC_beta prefoldin, 34.6 93 0.002 24.6 5.0 41 234-274 67-107 (110)
16 PF03087 DUF241: Arabidopsis p 33.5 3.6E+02 0.0078 24.2 14.5 31 38-68 36-71 (231)
17 cd07623 BAR_SNX1_2 The Bin/Amp 32.3 3.6E+02 0.0078 23.9 12.2 64 36-109 65-128 (224)
18 PRK09343 prefoldin subunit bet 31.6 99 0.0021 25.0 4.7 38 234-271 71-108 (121)
19 KOG3229 Vacuolar sorting prote 31.3 1E+02 0.0022 27.9 5.0 41 99-142 12-52 (227)
20 KOG0994 Extracellular matrix g 30.4 8.8E+02 0.019 27.8 15.1 34 239-273 1722-1755(1758)
21 PF00429 TLV_coat: ENV polypro 30.4 1E+02 0.0022 31.7 5.6 35 237-271 431-465 (561)
22 PF05615 THOC7: Tho complex su 30.0 3E+02 0.0066 22.3 7.5 69 46-114 44-115 (139)
23 KOG3681 Alpha-catenin [Extrace 29.3 5.3E+02 0.012 27.9 10.5 85 54-142 275-369 (835)
24 COG1382 GimC Prefoldin, chaper 27.2 1.6E+02 0.0035 24.1 5.2 38 232-269 68-105 (119)
25 COG5124 Protein predicted to b 26.9 3.2E+02 0.0069 24.3 7.2 66 84-149 79-150 (209)
26 cd07662 BAR_SNX6 The Bin/Amphi 26.1 5E+02 0.011 23.5 11.9 69 36-114 75-146 (218)
27 cd00823 TopoIIB_Trans TopoIIB_ 25.9 83 0.0018 26.9 3.4 41 91-138 109-149 (151)
28 PF10018 Med4: Vitamin-D-recep 24.4 1.8E+02 0.0038 25.3 5.3 42 234-275 22-63 (188)
29 PF03866 HAP: Hydrophobic abun 24.3 2.1E+02 0.0046 24.1 5.4 56 37-97 95-150 (164)
30 cd07663 BAR_SNX5 The Bin/Amphi 23.7 5.5E+02 0.012 23.2 12.6 68 36-113 75-145 (218)
31 PRK14066 exodeoxyribonuclease 22.6 2.5E+02 0.0054 21.0 5.1 45 101-149 8-52 (75)
32 PF06657 Cep57_MT_bd: Centroso 21.7 3.5E+02 0.0077 20.3 7.1 56 84-151 14-69 (79)
33 KOG4427 E3 ubiquitin protein l 21.5 4.6E+02 0.01 28.5 8.3 54 91-145 7-60 (1096)
34 PF10393 Matrilin_ccoil: Trime 21.0 1.7E+02 0.0036 20.1 3.5 23 235-257 24-46 (47)
35 cd07626 BAR_SNX9_like The Bin/ 20.9 4.6E+02 0.0099 23.2 7.3 51 36-96 64-114 (199)
No 1
>PF03087 DUF241: Arabidopsis protein of unknown function; InterPro: IPR004320 This family represents plant proteins of unknown function.
Probab=100.00 E-value=2.7e-68 Score=479.13 Aligned_cols=226 Identities=50% Similarity=0.694 Sum_probs=208.3
Q ss_pred HHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHHHHHHHHHhcCCCCchh
Q 041688 41 HIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQSVQGLQSALRRRKGDETEL 120 (277)
Q Consensus 41 ~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~eLqsalRRr~~~~~~~ 120 (277)
+||++|.|||+|++|||++|+|||+|++++ +||||++|||||+|||+||+|||+|++||||++|||++||||++|+ +
T Consensus 1 dgL~~L~~Ly~~~~ell~lp~tq~al~~~~-~k~ve~lLd~sL~LLD~c~~~rd~ll~lKe~v~eLqsalRRr~~~~--~ 77 (231)
T PF03087_consen 1 DGLSGLKDLYECLEELLQLPSTQQALSHHQ-EKWVEELLDGSLRLLDACGTFRDALLQLKEHVQELQSALRRRDDGS--I 77 (231)
T ss_pred CchhHHHHHHHHHHHHHcCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchh--H
Confidence 589999999999999999999999999999 9999999999999999999999999999999999999999998443 9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCCCC-CchH----HHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCchh
Q 041688 121 TSEIKKYLASRKAVKKTIHKASGNLEGMENKCLSP-LNEK----HVSMLKEVEEVTFTAFESLLSLVAGRRTGSMLSGFS 195 (277)
Q Consensus 121 ~~~v~~y~~~rkk~kK~i~k~l~~LK~~~~k~~~~-~~~d----~v~~l~ev~~iti~vf~sll~~~s~~~~~~~~~~Ws 195 (277)
+++|++|+++|||++|+|+|+++++|+++++..++ .+.+ ++++++||+++|+++|+++++|+|+|..++++++|+
T Consensus 78 ~~~i~sy~~~rKk~kK~i~K~~~~lk~~~~~~~~~~~~~~~~~~vv~~l~ea~~~t~si~~sll~~ls~~~~~~~~~~ws 157 (231)
T PF03087_consen 78 ESEIASYIRSRKKAKKEIAKLLRSLKRMSNKSSSSNDDDEHLSAVVRVLREAREITVSIFESLLSFLSSPSKKSKSSKWS 157 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccchh
Confidence 99999999999999999999999999999984222 2222 499999999999999999999999998999999999
Q ss_pred HHHHhhcCCccccccccccccchhhhhhHHhhccccccchHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHhhhc
Q 041688 196 LVSKLIRPKRIACREDKNDINEFGKVDAALIDHKTIKSYNIFCLQNQLKELESSIQYLEEGLESLSRRLIKARVSLLNI 274 (277)
Q Consensus 196 lvskl~~~~~v~~~~~~~~~nE~~~vDaal~~~~~~~~~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tRVsLLNi 274 (277)
+|++++++++. |...+...||++++|+++.. +.+++++++++||+||.||++||+|+|+|||+|||||||||||
T Consensus 158 lvsk~~~~~~~-~~~~~~~~~e~~~~d~~~~~----~~e~~~~~~~~Le~LE~~Ie~lE~glE~vFR~LIktRVSLLNI 231 (231)
T PF03087_consen 158 LVSKLMQKKRS-CDSSEENRNEFEKVDAALKS----DEEEVQNAQKRLEELEECIEELEEGLECVFRRLIKTRVSLLNI 231 (231)
T ss_pred HHHHHHhcccc-cchhHHHHHHHHHHHHHhhh----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999864 66666689999999988731 4688999999999999999999999999999999999999998
No 2
>PF05633 DUF793: Protein of unknown function (DUF793); InterPro: IPR008511 This entry includes Protein BYPASS 1 which is required for normal root and shoot development. Prevents constitutive production of a root mobile carotenoid-derived signaling compound that is capable of arresting shoot and leaf development [, ].
Probab=99.87 E-value=4.1e-21 Score=183.03 Aligned_cols=248 Identities=16% Similarity=0.194 Sum_probs=180.1
Q ss_pred ChhhHHHHH----Hhhhhccc-------cccHHHHHHhhHHHHHhHHHHHcCchhHH-HHhhhhhhhhHHhhhhhhhHHH
Q 041688 19 FTSEVEETL----SRLRSSQA-------ASNIGHIINGLQDLHDCVDKILQLPLTQQ-ALSQVSNRKFVDELVNGSLRIL 86 (277)
Q Consensus 19 ~~~~~e~~L----~~L~~~~~-------sss~~~~L~~L~~l~~~v~~Ll~lP~~q~-aL~~~~~~k~vee~LD~Sl~LL 86 (277)
.+..||.++ ..|.+... .+||...|..+...|+.+..|| |..+. +++..+.+||+++|||+||++|
T Consensus 38 ~L~~Fq~~va~rl~~L~~~~~~~~~~LSL~W~~~~ld~~l~~~~efr~li--~~~~~~~~s~~~~dk~v~eylD~sVKlL 115 (389)
T PF05633_consen 38 ELEAFQRHVAERLSDLSPSSKDSDDFLSLSWMRKALDSFLCCHEEFRALI--TNLRDLPLSKPPDDKWVDEYLDRSVKLL 115 (389)
T ss_pred hHHHHHHHHHHHHHHhccCcCcccccccHHHHHHHHHHHHHHHHHHHHHH--hcccccccCCchHHHHHHHHHHHHHHHH
Confidence 456677555 55655431 5899999999999999999998 33322 4566788999999999999999
Q ss_pred HhhhhHHHHHHHhHHHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhh----------ccC----
Q 041688 87 DICSIAQNALLQSKQSVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTIHKASGNLEGME----------NKC---- 152 (277)
Q Consensus 87 DvC~~~~d~l~~lke~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l~~LK~~~----------~k~---- 152 (277)
||||+++|.|.+++++..-+|.|++-.+..++ ..-..|.|+|| .+..+...++.-. +++
T Consensus 116 DvCNA~~~gi~~lr~~~~ll~~al~~L~~~~~---~~~~~~rRAr~----aL~dl~~~~~~~~~~~~~~~~~rnrs~~r~ 188 (389)
T PF05633_consen 116 DVCNAIRDGISQLRQWQLLLQIALHALDSSRP---LGEGQLRRARK----ALSDLKIAMLDDKDSGSSGGSHRNRSFGRS 188 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC---CcHHHHHHHHH----HHHHHHHHHhcccccCcccccccccccccc
Confidence 99999999999999999999999999875422 12235656655 5555554442211 000
Q ss_pred --CC---CC--------c------------------------------------hHHHHHHHHHHHHHHHHHHHHHHHhh
Q 041688 153 --LS---PL--------N------------------------------------EKHVSMLKEVEEVTFTAFESLLSLVA 183 (277)
Q Consensus 153 --~~---~~--------~------------------------------------~d~v~~l~ev~~iti~vf~sll~~~s 183 (277)
++ ++ . ...++.+|.+..+|++|.-.+...++
T Consensus 189 ~~~~~~~~~s~~~~~~~~~rsls~~vsr~wsa~~~Lq~m~~nL~~Pk~~esak~~gL~~A~Y~m~~vtvFV~~vlVAA~p 268 (389)
T PF05633_consen 189 NSSGRRSSSSSGSRSAGHFRSLSWSVSRNWSAARQLQAMGENLVLPKGKESAKGRGLLRAMYGMKSVTVFVCWVLVAAFP 268 (389)
T ss_pred cCCCCCCCCccccCCcccchhhhhhhhhhhhhHHHHHHHHhcCCCCCCccccccchHHHHHHHHHHHHHHHHHHHHHeee
Confidence 00 00 0 01277899999999999888888776
Q ss_pred ccc-------C-CCCCCchhHHHHhhcCCcc------ccccccccccchhhhhhHH-----hhcc---ccc-------cc
Q 041688 184 GRR-------T-GSMLSGFSLVSKLIRPKRI------ACREDKNDINEFGKVDAAL-----IDHK---TIK-------SY 234 (277)
Q Consensus 184 ~~~-------~-~~~~~~Wslvskl~~~~~v------~~~~~~~~~nE~~~vDaal-----~~~~---~~~-------~~ 234 (277)
.+. . .|+...|+.-...+|.+.. ...+.-..++|++.||++. +... ... .+
T Consensus 269 c~~rgL~~~l~~vP~~~~WA~s~~~LQ~rI~eEikkk~~kgs~gLLkEl~~ve~~vr~L~el~d~~~~p~~~e~~~ev~~ 348 (389)
T PF05633_consen 269 CQDRGLQVHLSAVPRQFSWAPSFISLQERINEEIKKKERKGSCGLLKELQQVEASVRELHELIDSFQFPLEEEKEEEVRE 348 (389)
T ss_pred cCCccccCCCCCCccccccchHHHHHHHHHHHHHhhccccCcchHHHHHHHHHHHHHHHHHHHHhccCCcchhHHHHHHH
Confidence 642 2 4677899987788886531 1111234689999999876 1111 111 13
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHhhhcc
Q 041688 235 NIFCLQNQLKELESSIQYLEEGLESLSRRLIKARVSLLNIL 275 (277)
Q Consensus 235 ~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tRVsLLNil 275 (277)
.|+++.+-.+.|++++++||.+++.+|++++.+|..+|+.|
T Consensus 349 ~V~EL~~~~~~L~~GLdpLerqVre~Fh~IV~sR~elLd~l 389 (389)
T PF05633_consen 349 AVEELARVCEALSQGLDPLERQVREVFHRIVRSRTELLDSL 389 (389)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhhHHHHhcC
Confidence 48999999999999999999999999999999999999875
No 3
>PF05055 DUF677: Protein of unknown function (DUF677); InterPro: IPR007749 This entry contains proteins belonging to the UPF0496 family, found in plants. This family includes AT14A like proteins from Arabidopsis thaliana. At14a contains a small domain that has sequence similarities to integrins from fungi, insects and humans. Transcripts of At14a are found in all Arabidopsis tissues and the protein localises partly to the plasma membrane [].
Probab=89.68 E-value=20 Score=34.46 Aligned_cols=42 Identities=17% Similarity=0.392 Sum_probs=39.5
Q ss_pred hhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHHHHHHHHHhcC
Q 041688 73 KFVDELVNGSLRILDICSIAQNALLQSKQSVQGLQSALRRRK 114 (277)
Q Consensus 73 k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~eLqsalRRr~ 114 (277)
..|++|.|.|..=+|+|++...++-+.+.+.+-++.+|.+-+
T Consensus 66 ~Lv~~YFd~S~~a~~~C~~L~k~I~~aR~~~~~I~~al~~~~ 107 (336)
T PF05055_consen 66 RLVSDYFDSSLEASDFCEALLKCIHRARDNYLPIRRALKQFE 107 (336)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhh
Confidence 589999999999999999999999999999999999998854
No 4
>cd07665 BAR_SNX1 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX1 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 effcient cargo sorting by facilitating proper membrane localization
Probab=83.21 E-value=23 Score=32.24 Aligned_cols=72 Identities=15% Similarity=0.278 Sum_probs=50.6
Q ss_pred cccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHHHHHHHHHhcC
Q 041688 36 ASNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQSVQGLQSALRRRK 114 (277)
Q Consensus 36 sss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~eLqsalRRr~ 114 (277)
+.+++..|+.|.+++..+.++.+- +++ ++--.+.+.||+-+|++..+-.+=+.=..+-++.+.++.-|.+++
T Consensus 75 ~~~Ls~als~laev~~~i~~~~~~-qa~------qd~~~f~e~l~eYiRli~SVK~~f~~R~k~~~~~~~~~~~l~kKr 146 (234)
T cd07665 75 NTALSRALSQLAEVEEKIEQLHQE-QAN------NDFFLLAELLADYIRLLSAVRGAFDQRMKTWQRWQDAQAMLQKKR 146 (234)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHH-HHH------HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455888999999999999998854 222 334568999999999887664444444445556666776676654
No 5
>cd07664 BAR_SNX2 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. 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 effcient cargo sorting by facilitating proper membrane localization
Probab=82.09 E-value=27 Score=31.79 Aligned_cols=69 Identities=16% Similarity=0.283 Sum_probs=45.4
Q ss_pred cccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhH---HHHHHHHHHHHh
Q 041688 36 ASNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSK---QSVQGLQSALRR 112 (277)
Q Consensus 36 sss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lk---e~v~eLqsalRR 112 (277)
+.+++..|+.|.+++.-+.++.+--..| +--...+.|++-+|++.. .|++|.+-. ++.+.++..|.+
T Consensus 75 ~~~ls~~l~~laev~~ki~~~~~~qa~~-------d~~~l~e~L~eYiR~i~s---vK~~f~~R~k~~~~~~~a~~~L~k 144 (234)
T cd07664 75 HTALSRALSQLAEVEEKIDQLHQDQAFA-------DFYLFSELLGDYIRLIAA---VKGVFDQRMKCWQKWQDAQVTLQK 144 (234)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHH-------hHHHHHhhHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568889999999999999986443332 233567889999987654 455554443 344455555666
Q ss_pred cC
Q 041688 113 RK 114 (277)
Q Consensus 113 r~ 114 (277)
++
T Consensus 145 kr 146 (234)
T cd07664 145 KR 146 (234)
T ss_pred HH
Confidence 54
No 6
>PF05600 DUF773: Protein of unknown function (DUF773); InterPro: IPR008491 This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown.
Probab=62.69 E-value=1.1e+02 Score=31.17 Aligned_cols=95 Identities=16% Similarity=0.220 Sum_probs=76.5
Q ss_pred HHHhhHHHHHhHHHHH---cCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHHHHHHHHHhcCCCCc
Q 041688 42 IINGLQDLHDCVDKIL---QLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQSVQGLQSALRRRKGDET 118 (277)
Q Consensus 42 ~L~~L~~l~~~v~~Ll---~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~eLqsalRRr~~~~~ 118 (277)
.-..+.+....|++++ .-|.+|+-+.=....+.||.+-+..-.-+..+.-++.....+.+-.++++..+..-
T Consensus 398 t~~~i~~ml~~V~~ii~~Lt~~~~~~L~~Ik~SprYvdrl~~~L~qk~~~~~k~~~~~~~l~~kr~e~~~e~~~l----- 472 (507)
T PF05600_consen 398 TAESIEEMLSAVEEIISQLTNPRTQHLFMIKSSPRYVDRLVESLQQKLKQEEKLRRKREDLEEKRQEAQEEQQEL----- 472 (507)
T ss_pred CHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----
Confidence 4445555666666655 55777777666667899999999999999999999999999999999999988774
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHh
Q 041688 119 ELTSEIKKYLASRKAVKKTIHKASG 143 (277)
Q Consensus 119 ~~~~~v~~y~~~rkk~kK~i~k~l~ 143 (277)
+.++...+...|.++|.|.+-+.
T Consensus 473 --~pkL~~l~~~Tr~Lq~~iE~~IS 495 (507)
T PF05600_consen 473 --EPKLDALVERTRELQKQIEADIS 495 (507)
T ss_pred --HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35888999999999999988654
No 7
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=57.04 E-value=23 Score=27.29 Aligned_cols=36 Identities=28% Similarity=0.326 Sum_probs=31.7
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHH
Q 041688 233 SYNIFCLQNQLKELESSIQYLEEGLESLSRRLIKAR 268 (277)
Q Consensus 233 ~~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tR 268 (277)
+..++.+...+..||..|--||..+..|||.+.+-|
T Consensus 53 p~~~keLL~EIA~lE~eV~~LE~~v~~L~~~l~~q~ 88 (88)
T PF14389_consen 53 PKKAKELLEEIALLEAEVAKLEQKVLSLYRQLFQQR 88 (88)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 456788888999999999999999999999997654
No 8
>KOG2911 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.04 E-value=2.7e+02 Score=27.82 Aligned_cols=27 Identities=26% Similarity=0.500 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 041688 124 IKKYLASRKAVKKTIHKASGNLEGMEN 150 (277)
Q Consensus 124 v~~y~~~rkk~kK~i~k~l~~LK~~~~ 150 (277)
-..|+|.||.+.|.+.++...+-+.+.
T Consensus 275 A~~ylr~rk~~eK~~er~~~~l~~l~~ 301 (439)
T KOG2911|consen 275 AITYLRARKLLEKDLERKVSSLNNLET 301 (439)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 457999999999999999877766553
No 9
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=45.79 E-value=62 Score=22.25 Aligned_cols=45 Identities=22% Similarity=0.350 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 041688 101 QSVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTIHKASGNLEGME 149 (277)
Q Consensus 101 e~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l~~LK~~~ 149 (277)
+.+..|+.++++-.+|+.+++..+..|-+. -+-+++|-..|...+
T Consensus 3 e~~~~Le~Iv~~Le~~~~sLdes~~lyeeg----~~l~~~c~~~L~~~e 47 (53)
T PF02609_consen 3 EAMERLEEIVEKLESGELSLDESLKLYEEG----MELIKKCQERLEEAE 47 (53)
T ss_dssp HHHHHHHHHHHHHHTT-S-HHHHHHHHHHH----HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 445666666777666788999999998444 445666655555544
No 10
>cd07597 BAR_SNX8 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 8. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX8 and the yeast counterpart Mvp1p are involved in sorting and delivery of late-Golgi proteins, such as carboxypeptidase Y, to vacuoles. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=43.31 E-value=1.2e+02 Score=27.42 Aligned_cols=64 Identities=16% Similarity=0.186 Sum_probs=40.9
Q ss_pred HHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhH-HHHHHHHHHHHh
Q 041688 39 IGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSK-QSVQGLQSALRR 112 (277)
Q Consensus 39 ~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lk-e~v~eLqsalRR 112 (277)
+..||..+..-+..+.++. ..+...|-+..+|..=.++|+|.++||.+-.-+ ..+.+.+.+.+|
T Consensus 89 l~~~l~~~s~~~~~~s~~~----------~~~a~~~~~~vlE~Lk~~~d~l~S~r~lf~R~~k~~~~~i~~l~~r 153 (246)
T cd07597 89 INEGLSSLSKHFQLLSDLS----------EDEARAEEDGVLEKLKLQLDLLVSLRDLFERHEKLSLNNIQRLLKR 153 (246)
T ss_pred HHHHHHHHHHHHHHHHHHH----------HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHH
Confidence 4555555555555544443 123356889999999999999999999887555 333333333333
No 11
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=39.66 E-value=44 Score=28.63 Aligned_cols=35 Identities=23% Similarity=0.210 Sum_probs=29.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHH
Q 041688 234 YNIFCLQNQLKELESSIQYLEEGLESLSRRLIKAR 268 (277)
Q Consensus 234 ~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tR 268 (277)
...+...+.+|.||..|.+|+.-+|-|.|-++--|
T Consensus 72 k~~~~~~eelerLe~~iKdl~~lye~Vs~d~Npf~ 106 (157)
T COG3352 72 KQLQDIKEELERLEENIKDLVSLYELVSRDFNPFM 106 (157)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Confidence 45788999999999999999999999988765443
No 12
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=37.97 E-value=52 Score=26.91 Aligned_cols=41 Identities=34% Similarity=0.460 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 041688 102 SVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTIHKAS 142 (277)
Q Consensus 102 ~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l 142 (277)
-+--|++.|||++|--..+..+++..-..|+.+..+|-++.
T Consensus 17 ~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~ 57 (120)
T PF12325_consen 17 LVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLM 57 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46678999999986445677788888888888888877764
No 13
>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. 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. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=35.32 E-value=3.1e+02 Score=24.12 Aligned_cols=62 Identities=13% Similarity=0.161 Sum_probs=36.5
Q ss_pred ccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHHHHHH
Q 041688 37 SNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQSVQGLQS 108 (277)
Q Consensus 37 ss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~eLqs 108 (277)
.+++..|+.+++++..+..+..--.. ++-.-+.+.|+.-+++ |++.|++|.+--...++.|.
T Consensus 58 ~~l~~~l~~~a~~~~~~~~~~~~~a~-------~e~~~l~~~L~ey~r~---~~Svk~~~~~R~~~~~~~~~ 119 (216)
T cd07627 58 KSLSDLLAALAEVQKRIKESLERQAL-------QDVLTLGVTLDEYIRS---IGSVRAAFAQRQKLWQYWQS 119 (216)
T ss_pred hHhHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
Confidence 45666777777777777777643122 2234455666666664 55666666665555544443
No 14
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=35.19 E-value=93 Score=23.97 Aligned_cols=33 Identities=21% Similarity=0.292 Sum_probs=26.6
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhHhHHHHHHH
Q 041688 233 SYNIFCLQNQLKELESSIQYLEEGLESLSRRLI 265 (277)
Q Consensus 233 ~~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI 265 (277)
.+++..+-..|..|..|++-||...+.|+-+|.
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE~rnD~l~~~L~ 57 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLEQRNDHLHAQLQ 57 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 345667778899999999999999998887765
No 15
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=34.61 E-value=93 Score=24.57 Aligned_cols=41 Identities=20% Similarity=0.202 Sum_probs=28.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHhhhc
Q 041688 234 YNIFCLQNQLKELESSIQYLEEGLESLSRRLIKARVSLLNI 274 (277)
Q Consensus 234 ~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tRVsLLNi 274 (277)
+-..++.++.+.+|..|..+|...+.+-..+-..+-.|=-+
T Consensus 67 e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~~ 107 (110)
T TIGR02338 67 EAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQEA 107 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567777777888888888777777777776666554333
No 16
>PF03087 DUF241: Arabidopsis protein of unknown function; InterPro: IPR004320 This family represents plant proteins of unknown function.
Probab=33.48 E-value=3.6e+02 Score=24.24 Aligned_cols=31 Identities=19% Similarity=0.071 Sum_probs=22.1
Q ss_pred cHHHHHHhhHHHHHhHHHHH-----cCchhHHHHhh
Q 041688 38 NIGHIINGLQDLHDCVDKIL-----QLPLTQQALSQ 68 (277)
Q Consensus 38 s~~~~L~~L~~l~~~v~~Ll-----~lP~~q~aL~~ 68 (277)
-..+|.-.|.|+|+++.|.+ +.-..|-+|++
T Consensus 36 ~lLd~sL~LLD~c~~~rd~ll~lKe~v~eLqsalRR 71 (231)
T PF03087_consen 36 ELLDGSLRLLDACGTFRDALLQLKEHVQELQSALRR 71 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35678888999999999976 33344556654
No 17
>cd07623 BAR_SNX1_2 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 1 and 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX1, SNX2, and similar proteins. SNX1 and SNX2 are components 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), wh
Probab=32.27 E-value=3.6e+02 Score=23.93 Aligned_cols=64 Identities=9% Similarity=0.205 Sum_probs=41.9
Q ss_pred cccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHHHHHHH
Q 041688 36 ASNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQSVQGLQSA 109 (277)
Q Consensus 36 sss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~eLqsa 109 (277)
+.++...|+.++++|.-+.++..=-..| +---+.+.|+.-++ +|++++++|.+-....+..|.+
T Consensus 65 ~~~Ls~al~~la~~~~ki~~~~~~qa~~-------d~~~l~e~L~eY~r---~i~svk~~f~~R~~a~~~~q~a 128 (224)
T cd07623 65 HTSLSRALSQLAEVEEKIEQLHGEQADT-------DFYILAELLKDYIG---LIGAIKDVFHERVKVWQNWQNA 128 (224)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 3457788888999999988887331222 22334566666665 4678888888777666555544
No 18
>PRK09343 prefoldin subunit beta; Provisional
Probab=31.60 E-value=99 Score=25.04 Aligned_cols=38 Identities=18% Similarity=0.121 Sum_probs=25.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHh
Q 041688 234 YNIFCLQNQLKELESSIQYLEEGLESLSRRLIKARVSL 271 (277)
Q Consensus 234 ~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tRVsL 271 (277)
+-..++.+++|.++..|..||...+.+=..+...+-.|
T Consensus 71 e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l 108 (121)
T PRK09343 71 KVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKI 108 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34466667777777777777777777766666655554
No 19
>KOG3229 consensus Vacuolar sorting protein VPS24 [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.32 E-value=1e+02 Score=27.88 Aligned_cols=41 Identities=27% Similarity=0.447 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 041688 99 SKQSVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTIHKAS 142 (277)
Q Consensus 99 lke~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l 142 (277)
-||.+++.|+.||.-. -.+...|...=+-++|++|.|++++
T Consensus 12 PKEq~r~wq~kiRke~---r~ldrqir~iqree~kv~~~iK~aA 52 (227)
T KOG3229|consen 12 PKEQVREWQSKIRKEG---RQLDRQIRDIQREEEKVQKSIKQAA 52 (227)
T ss_pred hHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3789999999998742 3567778888888888888888764
No 20
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=30.42 E-value=8.8e+02 Score=27.84 Aligned_cols=34 Identities=24% Similarity=0.304 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHhhh
Q 041688 239 LQNQLKELESSIQYLEEGLESLSRRLIKARVSLLN 273 (277)
Q Consensus 239 ~~~~Le~LE~~I~~lE~gle~lFR~LI~tRVsLLN 273 (277)
-..+|+..+.-|.+||..++.+-+. |+-||+.-+
T Consensus 1722 ~~~~L~~~~aeL~~Le~r~~~vl~~-I~~rv~~y~ 1755 (1758)
T KOG0994|consen 1722 NEQALEDKAAELAGLEKRVESVLDH-INERVLYYA 1755 (1758)
T ss_pred hhHHHHHHHHHhhhHHHHHHHHHHH-Hhhhhhhhh
Confidence 3457777888889999999988654 778887654
No 21
>PF00429 TLV_coat: ENV polyprotein (coat polyprotein); InterPro: IPR018154 Enveloped viruses such as Human immunodeficiency virus 1, influenza virus, and Ebola virus sp. express a surface glycoprotein that mediates both cell attachment and fusion of viral and cellular membranes. The ENV polyprotein (coat polyprotein) usually contains two coat proteins which differ depending on the source. The structure of a number of the ENV polyprotein domains have been determined: The crystal structure of an extraviral segment of the Moloney murine leukemia virus (MoMuLV) transmembrane (TM) subunit has been determined to 1.7-A resolution. This segment contains a trimeric coiled coil, with a hydrophobic cluster at its base and a strand that packs in an antiparallel orientation against the coiled coil. This structure serves as a model for a wide range of viral fusion proteins; key residues in this structure are conserved among C- and D-type retroviruses and the filovirus ebola []. An essential step in retrovirus infection is the binding of the virus to its receptor on a target cell. The structure of the receptor-binding domain of the envelope glycoprotein from Friend murine leukemia virus (F-MuLV) has been determined determined to 2.0-A resolution. The core of the domain is an antiparallel beta sandwich, with two interstrand loops forming a helical subdomain atop the sandwich. The residues in the helical region, but not in the beta sandwich, are highly variable among mammalian C-type retroviruses with distinct tropisms, indicating that the helical subdomain determines the receptor specificity of the virus []. ; PDB: 1LCS_B 1MOF_A 1XNL_A 2XZ3_A 1AOL_A 1Y4M_C.
Probab=30.41 E-value=1e+02 Score=31.73 Aligned_cols=35 Identities=37% Similarity=0.517 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHh
Q 041688 237 FCLQNQLKELESSIQYLEEGLESLSRRLIKARVSL 271 (277)
Q Consensus 237 ~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tRVsL 271 (277)
..+.+-+++++.+|..|++.+..+--..+|+|.+|
T Consensus 431 ~~~~~d~~~~~~~i~~l~~~~~sl~~~v~qnr~~l 465 (561)
T PF00429_consen 431 NALEEDLQALEDSISALQEQLTSLAEVVLQNRRAL 465 (561)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchhh
Confidence 45667888999999999999999999999999986
No 22
>PF05615 THOC7: Tho complex subunit 7; InterPro: IPR008501 The Tho complex (THOC) is involved in transcription elongation and mRNA export from the nucleus []. This entry represents the subunit THOC7, which is found in higher eukaryotes, and the non-homologous subunit Mft1p found in yeast. The funtions of these subunits are unknown, and it is not known if these subunits are functionally equivalent.
Probab=29.97 E-value=3e+02 Score=22.35 Aligned_cols=69 Identities=13% Similarity=0.086 Sum_probs=48.7
Q ss_pred hHHHHHhHHHHH---cCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHHHHHHHHHhcC
Q 041688 46 LQDLHDCVDKIL---QLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQSVQGLQSALRRRK 114 (277)
Q Consensus 46 L~~l~~~v~~Ll---~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~eLqsalRRr~ 114 (277)
...+|..+-..+ .++.....+...-+..-.+.|=+..-.+.+-|..+++-+..+|..+.+.+-..++|.
T Consensus 44 ~~~~~e~~l~~l~~~e~~~~k~q~~~~~n~~e~e~Y~~~~~~i~~~i~~~k~~ie~lk~~L~~ak~~r~~k~ 115 (139)
T PF05615_consen 44 SQFLYERLLKELAQFEFSILKSQLILEMNKRERENYEQLNEEIEQEIEQAKKEIEELKEELEEAKRVRQNKE 115 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444433 344443334445677888999999999999999999999999999999888766653
No 23
>KOG3681 consensus Alpha-catenin [Extracellular structures]
Probab=29.34 E-value=5.3e+02 Score=27.91 Aligned_cols=85 Identities=21% Similarity=0.306 Sum_probs=55.1
Q ss_pred HHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhh--hHHHHH--------HHhHHHHHHHHHHHHhcCCCCchhhHH
Q 041688 54 DKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICS--IAQNAL--------LQSKQSVQGLQSALRRRKGDETELTSE 123 (277)
Q Consensus 54 ~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~--~~~d~l--------~~lke~v~eLqsalRRr~~~~~~~~~~ 123 (277)
.+.+..|..+ ....-++..+.++|+...+.|.|. -.|+.+ -++.+.+.|+++.-.+ +|+.+.+...
T Consensus 275 ~~~l~~~~~~---~r~~le~~le~Iis~aa~~aDs~~~d~rreri~a~~~al~q~l~d~l~E~~~~~~~-k~~~~~l~~a 350 (835)
T KOG3681|consen 275 IDPLTNPEAR---SRPSLEVRLEQIISGAALMADSCCRDLRRERIVAECNALRQALQDLLSEYQSNAGR-KGRSPALELA 350 (835)
T ss_pred hhhhhchhhc---cCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhc-cccChhHHHH
Confidence 3344555543 445567889999999999999985 122222 2345566667776444 4556677777
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041688 124 IKKYLASRKAVKKTIHKAS 142 (277)
Q Consensus 124 v~~y~~~rkk~kK~i~k~l 142 (277)
+...-..-|.++|.+.+.+
T Consensus 351 i~~l~kkl~dLrrqLr~a~ 369 (835)
T KOG3681|consen 351 IDQLTKKLKDLKRQLRKAA 369 (835)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7777677777777777664
No 24
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=27.23 E-value=1.6e+02 Score=24.12 Aligned_cols=38 Identities=29% Similarity=0.281 Sum_probs=23.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHH
Q 041688 232 KSYNIFCLQNQLKELESSIQYLEEGLESLSRRLIKARV 269 (277)
Q Consensus 232 ~~~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tRV 269 (277)
+++-+.++.++.|.||..|.-||..-+.+=-++=.-+.
T Consensus 68 k~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~ 105 (119)
T COG1382 68 KEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQS 105 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556777777777777777777666665554443333
No 25
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=26.94 E-value=3.2e+02 Score=24.25 Aligned_cols=66 Identities=23% Similarity=0.325 Sum_probs=43.3
Q ss_pred HHHHhhhhHHHHHHHhHHHHHHHH------HHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 041688 84 RILDICSIAQNALLQSKQSVQGLQ------SALRRRKGDETELTSEIKKYLASRKAVKKTIHKASGNLEGME 149 (277)
Q Consensus 84 ~LLDvC~~~~d~l~~lke~v~eLq------salRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l~~LK~~~ 149 (277)
.+=|.|+..+.-+-.||+.+..+. -+-||+.+-+..-.-.-.+.+..||+-.+++++-+.+|...+
T Consensus 79 k~~~~~~~l~~~~~~~kqdi~t~~e~i~~ek~~r~k~~Te~~~n~~~~~Ll~~~k~eqd~~k~~l~~l~~~~ 150 (209)
T COG5124 79 KLYDSSELLKKKIQEVKQDIATYKEEIDKEKATRRKKFTEGQKNYNREALLEKRKKEQDEIKKKLNSLQKIE 150 (209)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHhccccccC
Confidence 456777777777777776665443 223777664433334455677888888888888877776554
No 26
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. 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 transforming growth factor-beta family. It also plays
Probab=26.09 E-value=5e+02 Score=23.53 Aligned_cols=69 Identities=19% Similarity=0.223 Sum_probs=43.9
Q ss_pred cccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHHHHH---HHHHHHHh
Q 041688 36 ASNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQSVQ---GLQSALRR 112 (277)
Q Consensus 36 sss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke~v~---eLqsalRR 112 (277)
++.+...|++|.|+++.+..+-.--.. .+.--..++|+.-+++++ +.||.|-+-=.+.+ ..+.+|.+
T Consensus 75 ~t~L~~~l~~laev~eki~~l~~~~A~-------~e~l~L~e~L~~Y~r~~~---A~Kdll~rR~r~l~~~enA~k~L~K 144 (218)
T cd07662 75 STDICKFFLKVSELFDKTRKIEARVAA-------DEDLKLSDLLKYYLRESQ---AAKDLLYRRSRSLVDYENANKALDK 144 (218)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHhh-------hhhhhHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456888999999999999998744222 122245677777777655 55666655444433 44455655
Q ss_pred cC
Q 041688 113 RK 114 (277)
Q Consensus 113 r~ 114 (277)
++
T Consensus 145 aR 146 (218)
T cd07662 145 AR 146 (218)
T ss_pred HH
Confidence 54
No 27
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=25.89 E-value=83 Score=26.89 Aligned_cols=41 Identities=15% Similarity=0.304 Sum_probs=32.5
Q ss_pred hHHHHHHHhHHHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHH
Q 041688 91 IAQNALLQSKQSVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTI 138 (277)
Q Consensus 91 ~~~d~l~~lke~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i 138 (277)
+.||++...-|-..|++.||+-- -.+++.|+.-+++.++.-
T Consensus 109 ~~KeaIadvpEI~~EIrlAl~~~-------~R~L~~~l~kk~~~~e~~ 149 (151)
T cd00823 109 EGKEAIADIPEIEEEIKLALQEV-------ARKLKRYLSKKRKERELQ 149 (151)
T ss_pred cchhhhcCCHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHh
Confidence 47899999999999999999864 157889998888776543
No 28
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=24.43 E-value=1.8e+02 Score=25.28 Aligned_cols=42 Identities=21% Similarity=0.290 Sum_probs=37.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHhhhcc
Q 041688 234 YNIFCLQNQLKELESSIQYLEEGLESLSRRLIKARVSLLNIL 275 (277)
Q Consensus 234 ~~~~~~~~~Le~LE~~I~~lE~gle~lFR~LI~tRVsLLNil 275 (277)
..-+..+.++..|...+..++..+..+-+.|..+|..|-+++
T Consensus 22 ~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 22 QEHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445788899999999999999999999999999999998765
No 29
>PF03866 HAP: Hydrophobic abundant protein (HAP) ; InterPro: IPR005566 Expression of Hydrophobic Abundant protein is thought to be developmentally regulated and possibly involved in spherule cell wall formation [].
Probab=24.26 E-value=2.1e+02 Score=24.08 Aligned_cols=56 Identities=23% Similarity=0.349 Sum_probs=46.8
Q ss_pred ccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHH
Q 041688 37 SNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALL 97 (277)
Q Consensus 37 ss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~ 97 (277)
++|++.|-++....+.+||-++...+|.-|. ..|+.++--.+-+|=+-.+.-|++.
T Consensus 95 tgIln~ll~fd~~~~~vee~l~~~~aq~lla-----glv~ai~alplavlval~~lt~ala 150 (164)
T PF03866_consen 95 TGILNSLLGFDAILELVEEVLHVLLAQSLLA-----GLVNAILALPLAVLVALSTLTDALA 150 (164)
T ss_pred HHHHHHHhcccHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 5688999999999999999999988875554 6888888888888887777777664
No 30
>cd07663 BAR_SNX5 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. 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 as a mammalian equivalent of yeast Vsp17p. It
Probab=23.70 E-value=5.5e+02 Score=23.20 Aligned_cols=68 Identities=13% Similarity=0.172 Sum_probs=42.6
Q ss_pred cccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHHHHhHH---HHHHHHHHHHh
Q 041688 36 ASNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNALLQSKQ---SVQGLQSALRR 112 (277)
Q Consensus 36 sss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l~~lke---~v~eLqsalRR 112 (277)
++++...|+.|.|+++.+..+.+--.. .+.--..+.|+.-+++..+ .||.|-+-=. .-++.|.+|.+
T Consensus 75 ~t~L~kals~lae~~Ek~~~l~~r~A~-------~d~~~L~e~L~~Y~r~~~A---~K~ll~rR~ral~~~e~A~~~L~K 144 (218)
T cd07663 75 PTVIKKYLLKVAELFEKLRKVEDRVAS-------DQDLKLTELLRYYMLNIEA---AKDLLYRRARALADYENSNKALDK 144 (218)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHH-------hHHhhHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556888999999999999998743222 2334567888888887654 4454443222 23344444544
Q ss_pred c
Q 041688 113 R 113 (277)
Q Consensus 113 r 113 (277)
.
T Consensus 145 a 145 (218)
T cd07663 145 A 145 (218)
T ss_pred H
Confidence 3
No 31
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=22.56 E-value=2.5e+02 Score=21.01 Aligned_cols=45 Identities=20% Similarity=0.336 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 041688 101 QSVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTIHKASGNLEGME 149 (277)
Q Consensus 101 e~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l~~LK~~~ 149 (277)
+.+..|+..+++-..|+.+++..++.|=+- -+-++.|-..|...+
T Consensus 8 eal~~LE~IV~~LE~g~l~Leesl~lyeeG----~~L~k~C~~~L~~ae 52 (75)
T PRK14066 8 TALKKLEEVVKKLEGGELSLDDSLKAFEEG----VKHAAFCSKKLDEAE 52 (75)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 445566666666666889999999999444 333444444444443
No 32
>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein). It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].
Probab=21.68 E-value=3.5e+02 Score=20.27 Aligned_cols=56 Identities=16% Similarity=0.206 Sum_probs=42.0
Q ss_pred HHHHhhhhHHHHHHHhHHHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhcc
Q 041688 84 RILDICSIAQNALLQSKQSVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTIHKASGNLEGMENK 151 (277)
Q Consensus 84 ~LLDvC~~~~d~l~~lke~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l~~LK~~~~k 151 (277)
.|-++--+.+|-|.+|+--.++|+..++.-+..-. .+-|+.+..++.+++ +.|+.|
T Consensus 14 ~Ls~vl~~LqDE~~hm~~e~~~L~~~~~~~d~s~~---------~~~R~~L~~~l~~lv---~~mE~K 69 (79)
T PF06657_consen 14 ALSEVLKALQDEFGHMKMEHQELQDEYKQMDPSLG---------RRKRRDLEQELEELV---KRMEAK 69 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccC---------hHHHHHHHHHHHHHH---HHHHHH
Confidence 45677788999999999999999999988763211 356777777787774 455555
No 33
>KOG4427 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.52 E-value=4.6e+02 Score=28.47 Aligned_cols=54 Identities=26% Similarity=0.341 Sum_probs=39.5
Q ss_pred hHHHHHHHhHHHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 041688 91 IAQNALLQSKQSVQGLQSALRRRKGDETELTSEIKKYLASRKAVKKTIHKASGNL 145 (277)
Q Consensus 91 ~~~d~l~~lke~v~eLqsalRRr~~~~~~~~~~v~~y~~~rkk~kK~i~k~l~~L 145 (277)
+.|+++++--...+|.++.-|||....--++.-+..|+ .|||+.++|..-..++
T Consensus 7 ~sra~fl~k~~qeREer~~qrrr~~aa~~iq~~lrsyl-~Rkk~~~~I~~e~d~~ 60 (1096)
T KOG4427|consen 7 ISRAAFLAKVSQEREERSYQRRREAAALFIQRVLRSYL-VRKKAQIEIQEEFDNL 60 (1096)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHh
Confidence 45788888888889999999998643344666677774 5788888888655444
No 34
>PF10393 Matrilin_ccoil: Trimeric coiled-coil oligomerisation domain of matrilin; InterPro: IPR019466 This entry represents a short domain found the matrilin (cartilage matrix) proteins. It forms a coiled coil structure and contains a single cysteine residue at its start which is likely to form a di-sulphide bridge with a corresponding cysteine in an upstream EGF domain (IPR006209 from INTERPRO), thereby spanning the VWA domain of the protein (IPR002035 from INTERPRO).This domain is likely to be responsible for protein trimerisation []. ; PDB: 1AQ5_C.
Probab=20.98 E-value=1.7e+02 Score=20.11 Aligned_cols=23 Identities=22% Similarity=0.384 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhH
Q 041688 235 NIFCLQNQLKELESSIQYLEEGL 257 (277)
Q Consensus 235 ~~~~~~~~Le~LE~~I~~lE~gl 257 (277)
.++.+..+|+++..-++.||.++
T Consensus 24 ~lq~Lt~kL~~vs~RLe~LEn~~ 46 (47)
T PF10393_consen 24 ALQSLTQKLDAVSKRLEALENRL 46 (47)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 35566667777777777777653
No 35
>cd07626 BAR_SNX9_like The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9 and Similar Proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX9, SNX18, SNX33, and similar proteins. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis, while SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. BAR domains for
Probab=20.88 E-value=4.6e+02 Score=23.23 Aligned_cols=51 Identities=6% Similarity=0.007 Sum_probs=32.6
Q ss_pred cccHHHHHHhhHHHHHhHHHHHcCchhHHHHhhhhhhhhHHhhhhhhhHHHHhhhhHHHHH
Q 041688 36 ASNIGHIINGLQDLHDCVDKILQLPLTQQALSQVSNRKFVDELVNGSLRILDICSIAQNAL 96 (277)
Q Consensus 36 sss~~~~L~~L~~l~~~v~~Ll~lP~~q~aL~~~~~~k~vee~LD~Sl~LLDvC~~~~d~l 96 (277)
++.+...|+.++++|+.|++|..--.- .+---+-|.|..-.+|| ++++|.|
T Consensus 64 ~t~Ls~Al~~~g~~~e~Ig~l~~eQa~-------~D~~~l~E~L~eY~gll---~~~pdi~ 114 (199)
T cd07626 64 SVPLTQAIKHTGQAYEEIGELFAEQPK-------HDLIPLLDGLHEYKGLL---STFPDII 114 (199)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhH-------hhHHHHHHHHHHHHhHH---HhhhHHH
Confidence 566889999999999999999843111 11122345555555554 4555555
Done!