Query 048208
Match_columns 290
No_of_seqs 113 out of 314
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 07:25:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048208.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048208hhsearch_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 3.6E-67 7.8E-72 475.5 24.6 226 49-287 1-231 (231)
2 PF05633 DUF793: Protein of un 99.9 4.7E-23 1E-27 197.8 21.8 255 24-288 36-389 (389)
3 PF05055 DUF677: Protein of un 93.2 8.6 0.00019 37.2 19.5 42 81-122 66-107 (336)
4 cd07665 BAR_SNX1 The Bin/Amphi 78.3 23 0.00051 32.5 10.1 72 44-122 75-146 (234)
5 cd07664 BAR_SNX2 The Bin/Amphi 76.3 28 0.00061 31.9 10.0 68 45-122 76-146 (234)
6 PF05600 DUF773: Protein of un 60.9 1.1E+02 0.0023 31.4 11.3 95 50-151 398-495 (507)
7 KOG3229 Vacuolar sorting prote 47.7 1.2E+02 0.0026 27.6 8.1 40 108-150 13-52 (227)
8 PF10018 Med4: Vitamin-D-recep 46.5 42 0.0009 29.5 5.1 60 223-288 4-63 (188)
9 PF14389 Lzipper-MIP1: Leucine 43.6 33 0.00071 26.6 3.5 36 246-281 53-88 (88)
10 cd07597 BAR_SNX8 The Bin/Amphi 42.0 96 0.0021 28.4 6.9 64 47-120 89-153 (246)
11 TIGR02338 gimC_beta prefoldin, 33.7 1E+02 0.0022 24.5 5.1 42 246-287 66-107 (110)
12 PF05615 THOC7: Tho complex su 32.9 2.4E+02 0.0052 23.2 7.4 57 66-122 59-115 (139)
13 TIGR01834 PHA_synth_III_E poly 31.5 3.4E+02 0.0074 26.2 9.0 30 244-273 286-315 (320)
14 PRK09343 prefoldin subunit bet 29.3 1.3E+02 0.0028 24.6 5.1 41 246-286 70-110 (121)
15 PF12325 TMF_TATA_bd: TATA ele 28.6 74 0.0016 26.2 3.5 40 110-149 17-56 (120)
16 cd07626 BAR_SNX9_like The Bin/ 28.4 3.6E+02 0.0078 24.1 8.1 52 43-104 63-114 (199)
17 PF02609 Exonuc_VII_S: Exonucl 28.2 1.9E+02 0.0041 19.9 5.1 41 109-153 3-43 (53)
18 COG5124 Protein predicted to b 26.6 3E+02 0.0065 24.6 7.0 65 92-156 79-149 (209)
19 cd00823 TopoIIB_Trans TopoIIB_ 25.5 67 0.0015 27.7 2.8 41 99-146 109-149 (151)
20 cd07623 BAR_SNX1_2 The Bin/Amp 24.5 5.1E+02 0.011 23.1 10.6 64 44-117 65-128 (224)
21 PF00429 TLV_coat: ENV polypro 23.9 1.2E+02 0.0025 31.6 4.7 34 251-284 432-465 (561)
22 COG1382 GimC Prefoldin, chaper 23.9 1.3E+02 0.0029 24.8 4.2 36 246-281 69-104 (119)
23 PF05377 FlaC_arch: Flagella a 23.5 1E+02 0.0023 22.1 3.0 20 251-270 18-37 (55)
24 COG3352 FlaC Putative archaeal 23.2 67 0.0015 27.8 2.3 36 246-281 71-106 (157)
25 KOG3681 Alpha-catenin [Extrace 22.5 7.5E+02 0.016 27.0 10.2 84 63-150 276-369 (835)
26 PF03866 HAP: Hydrophobic abun 21.9 2.9E+02 0.0063 23.5 5.8 60 42-106 92-151 (164)
27 PF10805 DUF2730: Protein of u 21.2 1.7E+02 0.0038 23.3 4.3 32 244-275 62-93 (106)
28 PF06785 UPF0242: Uncharacteri 21.2 7E+02 0.015 24.5 8.9 62 94-155 112-173 (401)
29 cd07627 BAR_Vps5p The Bin/Amph 21.0 5.9E+02 0.013 22.5 12.0 62 45-116 58-119 (216)
No 1
>PF03087 DUF241: Arabidopsis protein of unknown function; InterPro: IPR004320 This family represents plant proteins of unknown function.
Probab=100.00 E-value=3.6e-67 Score=475.52 Aligned_cols=226 Identities=50% Similarity=0.746 Sum_probs=209.9
Q ss_pred hHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhhHHHHHHHHHHhhcCCCCchh
Q 048208 49 NNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMKEDTQVLESTLRRRRGYEPRV 128 (290)
Q Consensus 49 ~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lke~~~eLqsaLRRr~g~~~~~ 128 (290)
+||++|.|||+|++|||++|+|||+|++++ +||||++|||||+|||+||+|||+|++||||++|||++||||++|+ +
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 9999999999999999999999999999999999999999998554 8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcC-C-C--CCCch-hhHHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcCCCchh
Q 048208 129 SNEVGAYLRSRKKANKAIHKSLRVLKTS-P-C--SSSEN-ETIAMIIILREVEGVTYTVFESLLSYLSGTKGQSYQSRWS 203 (290)
Q Consensus 129 ~~~v~~y~~~rkk~kK~i~K~l~~Lk~~-k-~--~~~d~-~~~~~v~~l~ev~~~tisvf~slls~~s~~~~~~~~~~Ws 203 (290)
+++|++|+++|||++|+|.|+++++|++ + . .+.++ +.+.++++++||+.+|+++|+++++|+|+|..++++++||
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 9999999999999999999999999999 3 1 23333 5899999999999999999999999999999999999999
Q ss_pred HHHHHhhhccccchhhhhhhhhhHHHHHHHHhhhccCCCCCCCCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHh
Q 048208 204 LVSKLIHTKRVTCEAEAIEINEFEKVDAALCSLIGNKSRKSTFLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTRVS 283 (290)
Q Consensus 204 ~vskl~~~~~v~~~~~~~~~nEl~~vDaal~~l~~~~~~~~~~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tRVs 283 (290)
+|++++++++ .|+..+...||++++|+++.. + .+.+++++++||+||.||++||+|+|+|||+|||||||
T Consensus 158 lvsk~~~~~~-~~~~~~~~~~e~~~~d~~~~~-------~--~e~~~~~~~~Le~LE~~Ie~lE~glE~vFR~LIktRVS 227 (231)
T PF03087_consen 158 LVSKLMQKKR-SCDSSEENRNEFEKVDAALKS-------D--EEEVQNAQKRLEELEECIEELEEGLECVFRRLIKTRVS 227 (231)
T ss_pred HHHHHHhccc-ccchhHHHHHHHHHHHHHhhh-------h--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999885 566666699999999999852 1 57899999999999999999999999999999999999
Q ss_pred hhhc
Q 048208 284 LLNF 287 (290)
Q Consensus 284 LLNi 287 (290)
||||
T Consensus 228 LLNI 231 (231)
T PF03087_consen 228 LLNI 231 (231)
T ss_pred HhcC
Confidence 9998
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=99.91 E-value=4.7e-23 Score=197.76 Aligned_cols=255 Identities=19% Similarity=0.248 Sum_probs=192.7
Q ss_pred CCChhhHHHHHH-hhhhcc---------CCchhHHhHHHhhHHHHHhHHHHHcCchhHH-HHHHhhhhhhHHHhhhhhhH
Q 048208 24 HPLASQIDECLS-RLRATE---------TTSSSICNNIIGLSDLYDLLNNLLLLPHTQQ-ALAQECNKKQVDDVLDRSLR 92 (290)
Q Consensus 24 hP~~~~~e~~L~-~Lr~~~---------sssssi~~~L~~L~~l~~~v~~Ll~lP~tQ~-aL~~~~~~k~vee~LD~Sl~ 92 (290)
.|.+..||.++. +|.... -|.+||...|..+...|+.+..|| |..+. +++..+.+|||++|||++|+
T Consensus 36 ~~~L~~Fq~~va~rl~~L~~~~~~~~~~LSL~W~~~~ld~~l~~~~efr~li--~~~~~~~~s~~~~dk~v~eylD~sVK 113 (389)
T PF05633_consen 36 EAELEAFQRHVAERLSDLSPSSKDSDDFLSLSWMRKALDSFLCCHEEFRALI--TNLRDLPLSKPPDDKWVDEYLDRSVK 113 (389)
T ss_pred hhhHHHHHHHHHHHHHHhccCcCcccccccHHHHHHHHHHHHHHHHHHHHHH--hcccccccCCchHHHHHHHHHHHHHH
Confidence 446788999888 677652 146899999999999999999998 33332 56667899999999999999
Q ss_pred HHHHhhhHHHHHHhhhHHHHHHHHHHhhcCCCCchhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC------------C--
Q 048208 93 LMDVCGTAKDALTQMKEDTQVLESTLRRRRGYEPRVSNEVGAYLRSRKKANKAIHKSLRVLKTSP------------C-- 158 (290)
Q Consensus 93 LLDvC~~~rd~l~~lke~~~eLqsaLRRr~g~~~~~~~~v~~y~~~rkk~kK~i~K~l~~Lk~~k------------~-- 158 (290)
+|||||+++|.|.+++++..-+|.|++-.+..++. .-+.|.|+|| .+..+...|+..+ +
T Consensus 114 lLDvCNA~~~gi~~lr~~~~ll~~al~~L~~~~~~---~~~~~rRAr~----aL~dl~~~~~~~~~~~~~~~~~rnrs~~ 186 (389)
T PF05633_consen 114 LLDVCNAIRDGISQLRQWQLLLQIALHALDSSRPL---GEGQLRRARK----ALSDLKIAMLDDKDSGSSGGSHRNRSFG 186 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC---cHHHHHHHHH----HHHHHHHHHhcccccCcccccccccccc
Confidence 99999999999999999999999999998754221 2235767766 5555554442210 0
Q ss_pred ---------CC-------------------------------------C---chhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 048208 159 ---------SS-------------------------------------S---ENETIAMIIILREVEGVTYTVFESLLSY 189 (290)
Q Consensus 159 ---------~~-------------------------------------~---d~~~~~~v~~l~ev~~~tisvf~slls~ 189 (290)
.+ + ...+..+++.+|.+..+|++|+-.+...
T Consensus 187 r~~~~~~~~~~s~~~~~~~~~rsls~~vsr~wsa~~~Lq~m~~nL~~Pk~~esak~~gL~~A~Y~m~~vtvFV~~vlVAA 266 (389)
T PF05633_consen 187 RSNSSGRRSSSSSGSRSAGHFRSLSWSVSRNWSAARQLQAMGENLVLPKGKESAKGRGLLRAMYGMKSVTVFVCWVLVAA 266 (389)
T ss_pred cccCCCCCCCCccccCCcccchhhhhhhhhhhhhHHHHHHHHhcCCCCCCccccccchHHHHHHHHHHHHHHHHHHHHHe
Confidence 00 0 0112357889999999999998888876
Q ss_pred hhcc-c------C-CcCCCchhHHHHHhhhccccch-------hhhhhhhhhHHHHHHHHhhhccC-CC-CC---C----
Q 048208 190 LSGT-K------G-QSYQSRWSLVSKLIHTKRVTCE-------AEAIEINEFEKVDAALCSLIGNK-SR-KS---T---- 245 (290)
Q Consensus 190 ~s~~-~------~-~~~~~~Ws~vskl~~~~~v~~~-------~~~~~~nEl~~vDaal~~l~~~~-~~-~~---~---- 245 (290)
++.+ . . .|++..|+.-...+|.+ |.-| +....++|++.||++.+.|++-. +. .| |
T Consensus 267 ~pc~~rgL~~~l~~vP~~~~WA~s~~~LQ~r-I~eEikkk~~kgs~gLLkEl~~ve~~vr~L~el~d~~~~p~~~e~~~e 345 (389)
T PF05633_consen 267 FPCQDRGLQVHLSAVPRQFSWAPSFISLQER-INEEIKKKERKGSCGLLKELQQVEASVRELHELIDSFQFPLEEEKEEE 345 (389)
T ss_pred eecCCccccCCCCCCccccccchHHHHHHHH-HHHHHhhccccCcchHHHHHHHHHHHHHHHHHHHHhccCCcchhHHHH
Confidence 6653 2 2 47788999888888865 3222 11256899999999999887621 11 11 1
Q ss_pred -CCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHhhhhcc
Q 048208 246 -FLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTRVSLLNFL 288 (290)
Q Consensus 246 -~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tRVsLLNil 288 (290)
.+.|+++.+..+.|++++++||.+++.||++++.+|..+|+.|
T Consensus 346 v~~~V~EL~~~~~~L~~GLdpLerqVre~Fh~IV~sR~elLd~l 389 (389)
T PF05633_consen 346 VREAVEELARVCEALSQGLDPLERQVREVFHRIVRSRTELLDSL 389 (389)
T ss_pred HHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhhHHHHhcC
Confidence 3468899999999999999999999999999999999999976
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=93.21 E-value=8.6 Score=37.21 Aligned_cols=42 Identities=19% Similarity=0.378 Sum_probs=39.3
Q ss_pred hhHHHhhhhhhHHHHHhhhHHHHHHhhhHHHHHHHHHHhhcC
Q 048208 81 KQVDDVLDRSLRLMDVCGTAKDALTQMKEDTQVLESTLRRRR 122 (290)
Q Consensus 81 k~vee~LD~Sl~LLDvC~~~rd~l~~lke~~~eLqsaLRRr~ 122 (290)
..|++|.|.|..=+|+|++....+-+.+.+.+-++.+|.+-+
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 479999999999999999999999999999999999998854
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=78.34 E-value=23 Score=32.49 Aligned_cols=72 Identities=14% Similarity=0.203 Sum_probs=49.0
Q ss_pred chhHHhHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhhHHHHHHHHHHhhcC
Q 048208 44 SSSICNNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMKEDTQVLESTLRRRR 122 (290)
Q Consensus 44 sssi~~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lke~~~eLqsaLRRr~ 122 (290)
+.+++.+|+.|.+++..+.++.+- +++ ++---..+.||+-+|++..+-.+-+.=..+-++.+.++.-|.+++
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 345778999999999999998854 222 333457899999999877664443333444455666666666654
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=76.34 E-value=28 Score=31.88 Aligned_cols=68 Identities=16% Similarity=0.240 Sum_probs=44.0
Q ss_pred hhHHhHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhhH---HHHHHHHHHhhc
Q 048208 45 SSICNNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMKE---DTQVLESTLRRR 121 (290)
Q Consensus 45 ssi~~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lke---~~~eLqsaLRRr 121 (290)
.+++..|+.|.+++..+.++.+--..| +---..+.||+-+|++.. .|++|.+-.. +.+.++..|.++
T Consensus 76 ~~ls~~l~~laev~~ki~~~~~~qa~~-------d~~~l~e~L~eYiR~i~s---vK~~f~~R~k~~~~~~~a~~~L~kk 145 (234)
T cd07664 76 TALSRALSQLAEVEEKIDQLHQDQAFA-------DFYLFSELLGDYIRLIAA---VKGVFDQRMKCWQKWQDAQVTLQKK 145 (234)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHH-------hHHHHHhhHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999987443222 223457889999987654 4555544433 344455556665
Q ss_pred C
Q 048208 122 R 122 (290)
Q Consensus 122 ~ 122 (290)
+
T Consensus 146 r 146 (234)
T cd07664 146 R 146 (234)
T ss_pred H
Confidence 4
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=60.89 E-value=1.1e+02 Score=31.42 Aligned_cols=95 Identities=11% Similarity=0.213 Sum_probs=76.8
Q ss_pred HHHhhHHHHHhHHHHH---cCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhhHHHHHHHHHHhhcCCCCc
Q 048208 50 NIIGLSDLYDLLNNLL---LLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMKEDTQVLESTLRRRRGYEP 126 (290)
Q Consensus 50 ~L~~L~~l~~~v~~Ll---~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lke~~~eLqsaLRRr~g~~~ 126 (290)
.-..+.+....|++++ .-|.+|+-+-=....+.||.+-+..-.-+..+.-++.....+.+-.++++..+..-
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 4445556666666655 45777887776677899999999999999999999999999999999999988764
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHH
Q 048208 127 RVSNEVGAYLRSRKKANKAIHKSLR 151 (290)
Q Consensus 127 ~~~~~v~~y~~~rkk~kK~i~K~l~ 151 (290)
+.++...+...|.++|.|.+.+.
T Consensus 473 --~pkL~~l~~~Tr~Lq~~iE~~IS 495 (507)
T PF05600_consen 473 --EPKLDALVERTRELQKQIEADIS 495 (507)
T ss_pred --HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34888899899999999988654
No 7
>KOG3229 consensus Vacuolar sorting protein VPS24 [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.68 E-value=1.2e+02 Score=27.57 Aligned_cols=40 Identities=20% Similarity=0.380 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHhhcCCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 048208 108 KEDTQVLESTLRRRRGYEPRVSNEVGAYLRSRKKANKAIHKSL 150 (290)
Q Consensus 108 ke~~~eLqsaLRRr~g~~~~~~~~v~~y~~~rkk~kK~i~K~l 150 (290)
||.+++.|+.||.-. -.+...|...=+-++|++|.|+++.
T Consensus 13 KEq~r~wq~kiRke~---r~ldrqir~iqree~kv~~~iK~aA 52 (227)
T KOG3229|consen 13 KEQVREWQSKIRKEG---RQLDRQIRDIQREEEKVQKSIKQAA 52 (227)
T ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 788999999998632 2366677777788888888888764
No 8
>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=46.47 E-value=42 Score=29.47 Aligned_cols=60 Identities=13% Similarity=0.270 Sum_probs=47.2
Q ss_pred hhhhHHHHHHHHhhhccCCCCCCCCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHhhhhcc
Q 048208 223 INEFEKVDAALCSLIGNKSRKSTFLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTRVSLLNFL 288 (290)
Q Consensus 223 ~nEl~~vDaal~~l~~~~~~~~~~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tRVsLLNil 288 (290)
+.+|-..|..|...+.. ...-+..+.++..|...+..++..+..+-+.|..+|..|-+++
T Consensus 4 ~~~L~~~d~~L~~~L~~------l~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 4 AEDLIEADDELSSALEE------LQEHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566667666655431 3345778899999999999999999999999999999997765
No 9
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=43.64 E-value=33 Score=26.64 Aligned_cols=36 Identities=25% Similarity=0.271 Sum_probs=31.0
Q ss_pred CCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHH
Q 048208 246 FLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTR 281 (290)
Q Consensus 246 ~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tR 281 (290)
+..++.+...+..||..|--||..+..|||.|.+-|
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 346778888899999999999999999999997654
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=42.02 E-value=96 Score=28.40 Aligned_cols=64 Identities=20% Similarity=0.340 Sum_probs=42.0
Q ss_pred HHhHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhh-HHHHHHHHHHhh
Q 048208 47 ICNNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMK-EDTQVLESTLRR 120 (290)
Q Consensus 47 i~~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lk-e~~~eLqsaLRR 120 (290)
+..||..+..-...+.++. ..+...|-+.+++..=.++|+|.++||.+-.-+ .-+.+.+.+.+|
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 5556666555555555544 123355889999999999999999999998655 333334444443
No 11
>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=33.66 E-value=1e+02 Score=24.52 Aligned_cols=42 Identities=14% Similarity=0.085 Sum_probs=33.0
Q ss_pred CCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHhhhhc
Q 048208 246 FLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTRVSLLNF 287 (290)
Q Consensus 246 ~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tRVsLLNi 287 (290)
.+...++.++.+.+|..|..+|...+.+-..+-..+-.|=-+
T Consensus 66 ~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~~ 107 (110)
T TIGR02338 66 EEAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQEA 107 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678889999999999999999998888887776655433
No 12
>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=32.86 E-value=2.4e+02 Score=23.17 Aligned_cols=57 Identities=14% Similarity=0.184 Sum_probs=44.8
Q ss_pred cCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhhHHHHHHHHHHhhcC
Q 048208 66 LLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMKEDTQVLESTLRRRR 122 (290)
Q Consensus 66 ~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lke~~~eLqsaLRRr~ 122 (290)
.++.....+...-+..-++.|=+..-.+.+-|..+++-+..+|..+.+.+-..++|.
T Consensus 59 e~~~~k~q~~~~~n~~e~e~Y~~~~~~i~~~i~~~k~~ie~lk~~L~~ak~~r~~k~ 115 (139)
T PF05615_consen 59 EFSILKSQLILEMNKRERENYEQLNEEIEQEIEQAKKEIEELKEELEEAKRVRQNKE 115 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334443334445677788999999999999999999999999999999988777654
No 13
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.
Probab=31.46 E-value=3.4e+02 Score=26.23 Aligned_cols=30 Identities=17% Similarity=0.248 Sum_probs=26.3
Q ss_pred CCCCChHHHHHHHHHHHHhhhhhhhhhhHH
Q 048208 244 STFLNPEDVHNMLGELESCTQDLEGGFESL 273 (290)
Q Consensus 244 ~~~~~~~~~~~~le~LE~~I~~lE~gle~l 273 (290)
|+..++++++++|.+||..+..|+.+++.+
T Consensus 286 PTRsElDe~~krL~ELrR~vr~L~k~l~~l 315 (320)
T TIGR01834 286 PTRSELDEAHQRIQQLRREVKSLKKRLGDL 315 (320)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 346789999999999999999999998765
No 14
>PRK09343 prefoldin subunit beta; Provisional
Probab=29.31 E-value=1.3e+02 Score=24.57 Aligned_cols=41 Identities=15% Similarity=0.122 Sum_probs=32.5
Q ss_pred CCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHhhhh
Q 048208 246 FLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTRVSLLN 286 (290)
Q Consensus 246 ~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tRVsLLN 286 (290)
.+...++.+++|.++..|..||...+.+=..+...+..|=.
T Consensus 70 ~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ 110 (121)
T PRK09343 70 TKVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKINE 110 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888999999999999999988888888777666543
No 15
>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=28.64 E-value=74 Score=26.24 Aligned_cols=40 Identities=25% Similarity=0.262 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhcCCCCchhhhhHHHHHHHHHHHHHHHHHH
Q 048208 110 DTQVLESTLRRRRGYEPRVSNEVGAYLRSRKKANKAIHKS 149 (290)
Q Consensus 110 ~~~eLqsaLRRr~g~~~~~~~~v~~y~~~rkk~kK~i~K~ 149 (290)
-+.-|++.|||++|--..+..++...-..|+.+..+|-+.
T Consensus 17 ~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l 56 (120)
T PF12325_consen 17 LVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKL 56 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999998532345666666666666666666554
No 16
>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=28.45 E-value=3.6e+02 Score=24.11 Aligned_cols=52 Identities=19% Similarity=0.152 Sum_probs=32.9
Q ss_pred CchhHHhHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHH
Q 048208 43 TSSSICNNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDAL 104 (290)
Q Consensus 43 ssssi~~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l 104 (290)
.++.+..+|+.++++|+.|++|..-..- .+---+-|.|..-.+| |++++|.|
T Consensus 63 ~~t~Ls~Al~~~g~~~e~Ig~l~~eQa~-------~D~~~l~E~L~eY~gl---l~~~pdi~ 114 (199)
T cd07626 63 TSVPLTQAIKHTGQAYEEIGELFAEQPK-------HDLIPLLDGLHEYKGL---LSTFPDII 114 (199)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHhhH-------hhHHHHHHHHHHHHhH---HHhhhHHH
Confidence 3667899999999999999999833111 1111234455555554 44566666
No 17
>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=28.23 E-value=1.9e+02 Score=19.92 Aligned_cols=41 Identities=20% Similarity=0.212 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhcCCCCchhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 048208 109 EDTQVLESTLRRRRGYEPRVSNEVGAYLRSRKKANKAIHKSLRVL 153 (290)
Q Consensus 109 e~~~eLqsaLRRr~g~~~~~~~~v~~y~~~rkk~kK~i~K~l~~L 153 (290)
+.+..|+.++++-.+|+.++...+..|-+..+ -+++|-..|
T Consensus 3 e~~~~Le~Iv~~Le~~~~sLdes~~lyeeg~~----l~~~c~~~L 43 (53)
T PF02609_consen 3 EAMERLEEIVEKLESGELSLDESLKLYEEGME----LIKKCQERL 43 (53)
T ss_dssp HHHHHHHHHHHHHHTT-S-HHHHHHHHHHHHH----HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH----HHHHHHHHH
Confidence 45666777777777788999999998844443 455554444
No 18
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=26.55 E-value=3e+02 Score=24.60 Aligned_cols=65 Identities=26% Similarity=0.346 Sum_probs=44.1
Q ss_pred HHHHHhhhHHHHHHhhhHHHHHHH------HHHhhcCCCCchhhhhHHHHHHHHHHHHHHHHHHHHHhhcC
Q 048208 92 RLMDVCGTAKDALTQMKEDTQVLE------STLRRRRGYEPRVSNEVGAYLRSRKKANKAIHKSLRVLKTS 156 (290)
Q Consensus 92 ~LLDvC~~~rd~l~~lke~~~eLq------saLRRr~g~~~~~~~~v~~y~~~rkk~kK~i~K~l~~Lk~~ 156 (290)
.+=|.|+..+.-+-.||+.+..+. -+-||+.+.+..-.-.-.+.+..||+-.+.+++-+.+|...
T Consensus 79 k~~~~~~~l~~~~~~~kqdi~t~~e~i~~ek~~r~k~~Te~~~n~~~~~Ll~~~k~eqd~~k~~l~~l~~~ 149 (209)
T COG5124 79 KLYDSSELLKKKIQEVKQDIATYKEEIDKEKATRRKKFTEGQKNYNREALLEKRKKEQDEIKKKLNSLQKI 149 (209)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 466788888888877777665443 23377776443333334456788998889999888877765
No 19
>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=25.54 E-value=67 Score=27.69 Aligned_cols=41 Identities=17% Similarity=0.345 Sum_probs=32.0
Q ss_pred hHHHHHHhhhHHHHHHHHHHhhcCCCCchhhhhHHHHHHHHHHHHHHH
Q 048208 99 TAKDALTQMKEDTQVLESTLRRRRGYEPRVSNEVGAYLRSRKKANKAI 146 (290)
Q Consensus 99 ~~rd~l~~lke~~~eLqsaLRRr~g~~~~~~~~v~~y~~~rkk~kK~i 146 (290)
+.||++...-|-..|++.||+-- .-+++.|+.-+++.+...
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 46899999999999999999853 247888988887766543
No 20
>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=24.50 E-value=5.1e+02 Score=23.15 Aligned_cols=64 Identities=13% Similarity=0.159 Sum_probs=41.2
Q ss_pred chhHHhHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhhHHHHHHHHH
Q 048208 44 SSSICNNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMKEDTQVLEST 117 (290)
Q Consensus 44 sssi~~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lke~~~eLqsa 117 (290)
+.++...|+.++++|..+.++..=-..| +---+.+.|+.-++ +|++++++|.+-....+..|.+
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 3457788888999999988887331111 12234556666655 4678888888776666555544
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=23.92 E-value=1.2e+02 Score=31.56 Aligned_cols=34 Identities=24% Similarity=0.344 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHhh
Q 048208 251 DVHNMLGELESCTQDLEGGFESLQRRLIKTRVSL 284 (290)
Q Consensus 251 ~~~~~le~LE~~I~~lE~gle~lFR~LI~tRVsL 284 (290)
.+.+-+++++.+|..|++++..+--..+|+|.+|
T Consensus 432 ~~~~d~~~~~~~i~~l~~~~~sl~~~v~qnr~~l 465 (561)
T PF00429_consen 432 ALEEDLQALEDSISALQEQLTSLAEVVLQNRRAL 465 (561)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchhh
Confidence 4556788999999999999999999999999986
No 22
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=23.91 E-value=1.3e+02 Score=24.83 Aligned_cols=36 Identities=25% Similarity=0.178 Sum_probs=22.7
Q ss_pred CCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHH
Q 048208 246 FLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTR 281 (290)
Q Consensus 246 ~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tR 281 (290)
.+.++++.++.|.||..|.-||..-+.+=-++=.-+
T Consensus 69 ~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq 104 (119)
T COG1382 69 EEAVDELEERKETLELRIKTLEKQEEKLQERLEELQ 104 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777777777777777766666555444333
No 23
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=23.47 E-value=1e+02 Score=22.06 Aligned_cols=20 Identities=15% Similarity=0.239 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHhhhhhhhhh
Q 048208 251 DVHNMLGELESCTQDLEGGF 270 (290)
Q Consensus 251 ~~~~~le~LE~~I~~lE~gl 270 (290)
.+++..+.+-..|++++.-+
T Consensus 18 tvk~en~~i~~~ve~i~env 37 (55)
T PF05377_consen 18 TVKKENEEISESVEKIEENV 37 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555554444
No 24
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=23.19 E-value=67 Score=27.75 Aligned_cols=36 Identities=22% Similarity=0.215 Sum_probs=30.2
Q ss_pred CCChHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHH
Q 048208 246 FLNPEDVHNMLGELESCTQDLEGGFESLQRRLIKTR 281 (290)
Q Consensus 246 ~~~~~~~~~~le~LE~~I~~lE~gle~lFR~LI~tR 281 (290)
...++.+.+.+|.||..|.+|+..+|-|-|-++--|
T Consensus 71 kk~~~~~~eelerLe~~iKdl~~lye~Vs~d~Npf~ 106 (157)
T COG3352 71 KKQLQDIKEELERLEENIKDLVSLYELVSRDFNPFM 106 (157)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Confidence 457888999999999999999999999988765433
No 25
>KOG3681 consensus Alpha-catenin [Extracellular structures]
Probab=22.51 E-value=7.5e+02 Score=27.04 Aligned_cols=84 Identities=12% Similarity=0.297 Sum_probs=52.5
Q ss_pred HHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhh--hHHHHH--------HhhhHHHHHHHHHHhhcCCCCchhhhhH
Q 048208 63 NLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCG--TAKDAL--------TQMKEDTQVLESTLRRRRGYEPRVSNEV 132 (290)
Q Consensus 63 ~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~--~~rd~l--------~~lke~~~eLqsaLRRr~g~~~~~~~~v 132 (290)
+.+..|..+ ....-++..+.++|+...+.|.|. -.|+.+ -++.+.+.|+++.- +++|+...+...+
T Consensus 276 ~~l~~~~~~---~r~~le~~le~Iis~aa~~aDs~~~d~rreri~a~~~al~q~l~d~l~E~~~~~-~~k~~~~~l~~ai 351 (835)
T KOG3681|consen 276 DPLTNPEAR---SRPSLEVRLEQIISGAALMADSCCRDLRRERIVAECNALRQALQDLLSEYQSNA-GRKGRSPALELAI 351 (835)
T ss_pred hhhhchhhc---cCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhhHHHHHHHHHHHHHHHHHh-hccccChhHHHHH
Confidence 334444433 344457889999999999999885 122222 23445566666653 3445556677777
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 048208 133 GAYLRSRKKANKAIHKSL 150 (290)
Q Consensus 133 ~~y~~~rkk~kK~i~K~l 150 (290)
...-+.-|.++|+++++.
T Consensus 352 ~~l~kkl~dLrrqLr~a~ 369 (835)
T KOG3681|consen 352 DQLTKKLKDLKRQLRKAA 369 (835)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 766667777777777764
No 26
>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=21.95 E-value=2.9e+02 Score=23.50 Aligned_cols=60 Identities=27% Similarity=0.417 Sum_probs=48.7
Q ss_pred CCchhHHhHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHh
Q 048208 42 TTSSSICNNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQ 106 (290)
Q Consensus 42 sssssi~~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~ 106 (290)
++-++|++.|-++....+.+||.++...+|.-|. ..++.++--.+-+|=+-.+.-|++..
T Consensus 92 ~TVtgIln~ll~fd~~~~~vee~l~~~~aq~lla-----glv~ai~alplavlval~~lt~ala~ 151 (164)
T PF03866_consen 92 STVTGILNSLLGFDAILELVEEVLHVLLAQSLLA-----GLVNAILALPLAVLVALSTLTDALAS 151 (164)
T ss_pred chHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 4567799999999999999999999877775554 57888888888888877777777643
No 27
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=21.16 E-value=1.7e+02 Score=23.26 Aligned_cols=32 Identities=19% Similarity=0.235 Sum_probs=25.6
Q ss_pred CCCCChHHHHHHHHHHHHhhhhhhhhhhHHHH
Q 048208 244 STFLNPEDVHNMLGELESCTQDLEGGFESLQR 275 (290)
Q Consensus 244 ~~~~~~~~~~~~le~LE~~I~~lE~gle~lFR 275 (290)
|...++..++-.+.+++..+..++..++.+=|
T Consensus 62 Pt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~ 93 (106)
T PF10805_consen 62 PTRDDVHDLQLELAELRGELKELSARLQGVSH 93 (106)
T ss_pred CCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 34678888999999999999999888776644
No 28
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=21.15 E-value=7e+02 Score=24.52 Aligned_cols=62 Identities=16% Similarity=0.137 Sum_probs=45.8
Q ss_pred HHHhhhHHHHHHhhhHHHHHHHHHHhhcCCCCchhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 048208 94 MDVCGTAKDALTQMKEDTQVLESTLRRRRGYEPRVSNEVGAYLRSRKKANKAIHKSLRVLKT 155 (290)
Q Consensus 94 LDvC~~~rd~l~~lke~~~eLqsaLRRr~g~~~~~~~~v~~y~~~rkk~kK~i~K~l~~Lk~ 155 (290)
+.=-.-.+|+|..+|.+.+-|.-.+|+.+--...++..+++|.+-++...-+-....+.|+.
T Consensus 112 ~nqL~~~~~vf~k~k~~~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE 173 (401)
T PF06785_consen 112 KNQLFHVREVFMKTKGDIQHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAE 173 (401)
T ss_pred HHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHH
Confidence 33334578899999999999999999987545668999999998887665555554444444
No 29
>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=20.98 E-value=5.9e+02 Score=22.55 Aligned_cols=62 Identities=18% Similarity=0.192 Sum_probs=36.9
Q ss_pred hhHHhHHHhhHHHHHhHHHHHcCchhHHHHHHhhhhhhHHHhhhhhhHHHHHhhhHHHHHHhhhHHHHHHHH
Q 048208 45 SSICNNIIGLSDLYDLLNNLLLLPHTQQALAQECNKKQVDDVLDRSLRLMDVCGTAKDALTQMKEDTQVLES 116 (290)
Q Consensus 45 ssi~~~L~~L~~l~~~v~~Ll~lP~tQ~aL~~~~~~k~vee~LD~Sl~LLDvC~~~rd~l~~lke~~~eLqs 116 (290)
.+++..|+.+++++..+..+..--.. ++-.-+.+.|+.-+++ |++.|++|.+-....+..|.
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 34666777777777777777643111 2233455666766664 56677777666555555444
Done!