Query 009270
Match_columns 538
No_of_seqs 347 out of 1415
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 22:30:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009270.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009270hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1471 Phosphatidylinositol t 100.0 2.8E-37 6.1E-42 319.0 21.0 216 203-424 35-260 (317)
2 KOG1470 Phosphatidylinositol t 100.0 3.7E-36 7.9E-41 305.3 16.3 198 209-423 46-245 (324)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 4.3E-28 9.4E-33 224.3 11.5 151 259-420 7-159 (159)
4 smart00516 SEC14 Domain in hom 99.9 2.8E-25 6E-30 205.3 13.6 144 265-421 14-157 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 3.1E-23 6.7E-28 189.0 13.0 146 262-420 12-157 (157)
6 PF13897 GOLD_2: Golgi-dynamic 99.9 1.1E-21 2.4E-26 174.8 10.0 92 442-534 1-134 (136)
7 KOG3878 Protein involved in ma 99.5 3.4E-14 7.3E-19 142.6 5.7 96 439-535 323-467 (469)
8 PF13716 CRAL_TRIO_2: Divergen 99.3 6.1E-13 1.3E-17 122.7 4.5 140 261-422 4-145 (149)
9 PF03765 CRAL_TRIO_N: CRAL/TRI 98.7 3.6E-08 7.8E-13 76.1 6.5 30 207-236 26-55 (55)
10 KOG4406 CDC42 Rho GTPase-activ 97.7 0.00012 2.6E-09 77.1 9.3 127 266-413 89-215 (467)
11 KOG3287 Membrane trafficking p 97.5 0.0013 2.8E-08 64.0 11.7 82 439-533 37-126 (236)
12 KOG1693 emp24/gp25L/p24 family 95.8 0.051 1.1E-06 52.5 8.9 75 445-531 31-111 (209)
13 KOG1692 Putative cargo transpo 95.0 0.064 1.4E-06 51.5 6.5 72 444-535 39-112 (201)
14 PF01105 EMP24_GP25L: emp24/gp 90.8 0.072 1.6E-06 49.8 0.0 88 440-535 4-98 (183)
15 PF09394 Inhibitor_I42: Chagas 72.7 28 0.00061 28.9 8.5 86 440-535 1-92 (92)
16 smart00110 C1Q Complement comp 63.8 14 0.0003 33.8 5.2 21 499-520 38-58 (135)
17 PF14555 UBA_4: UBA-like domai 51.2 21 0.00045 25.9 3.3 24 211-234 14-37 (43)
18 KOG1534 Putative transcription 48.3 33 0.00071 34.3 5.1 106 304-413 75-194 (273)
19 PF02845 CUE: CUE domain; Int 45.2 33 0.00072 24.6 3.6 28 208-235 13-40 (42)
20 PF00386 C1q: C1q domain; Int 44.4 17 0.00038 32.2 2.4 20 503-522 35-54 (127)
21 cd05860 Ig4_SCFR Fourth immuno 37.5 2.8E+02 0.006 24.3 8.7 81 438-536 11-100 (101)
22 smart00546 CUE Domain that may 36.7 56 0.0012 23.5 3.6 27 208-234 14-40 (43)
23 PF07462 MSP1_C: Merozoite sur 27.2 96 0.0021 34.8 5.0 27 214-243 391-417 (574)
24 PF08938 HBS1_N: HBS1 N-termin 27.2 24 0.00051 29.2 0.4 26 211-236 45-70 (79)
25 PF06394 Pepsin-I3: Pepsin inh 26.3 42 0.00091 27.9 1.7 25 109-133 34-58 (76)
26 PF14213 DUF4325: Domain of un 26.2 1.8E+02 0.0039 23.4 5.4 45 327-375 20-66 (74)
27 smart00165 UBA Ubiquitin assoc 23.8 1.1E+02 0.0025 20.8 3.3 24 210-233 13-36 (37)
28 cd00194 UBA Ubiquitin Associat 22.4 1.3E+02 0.0027 20.7 3.3 25 210-234 13-37 (38)
29 PF00627 UBA: UBA/TS-N domain; 21.9 1.3E+02 0.0029 20.7 3.3 23 211-233 15-37 (37)
30 PF03641 Lysine_decarbox: Poss 20.7 1.3E+02 0.0029 27.1 4.0 43 363-408 86-133 (133)
No 1
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=2.8e-37 Score=319.02 Aligned_cols=216 Identities=31% Similarity=0.522 Sum_probs=181.4
Q ss_pred CCCCCC-CCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHcCCCccCccccc-ccccc--eEEeeccCCCCCcEEEEec
Q 009270 203 VPLLKD-DRTDVILLKFLRARDFKVRDAFVMIKNTIQWRKDFGIEALLNEDLG-DDLEK--VVFMHGFDRDGHPVCYNVY 278 (538)
Q Consensus 203 ~pll~~-~~~D~~LLRFLRArkfdVekA~~mL~~~l~WRk~~~iD~i~~~~~~-~el~k--~~~l~G~Dk~GrPV~~~~~ 278 (538)
.|++++ ..+|.+||||||||+||+++|.+||.+++.||+++++|.|...... .++.+ ...++|.|++|+||++.+.
T Consensus 35 ~~~l~~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~ 114 (317)
T KOG1471|consen 35 KPHLPNKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKYYPQGLHGVDKEGRPVYIERL 114 (317)
T ss_pred ccCCCCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhhccccccccCCCCCEEEEecc
Confidence 345664 7899999999999999999999999999999999999998876221 33333 2468999999999999999
Q ss_pred CccChhhhhhccccCHHHHHHHHHHHHHHHHHHHHHh-----ccCCCCeeEEEEEEeCCCCCCCCch-hHHHHHHHHHHh
Q 009270 279 GEFQNKQLYAKTFSDEEKRMKFLRWRIQFLERSIRKL-----NFRPGGVSTIFQVNDLKNSPGPGKR-ELRIATKQALQL 352 (538)
Q Consensus 279 G~~d~~~l~~~~~~d~e~~~~~lr~~i~llE~~l~~l-----~~~~~~v~~iv~IiDl~g~sgl~~~-~l~~~~k~il~l 352 (538)
|..|.++++..+. ..+++++.+..+|+.++.+ .....+++++++|+||+|+++..+. ..+..++.++.+
T Consensus 115 g~~~~~~l~~~~~-----~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~ 189 (317)
T KOG1471|consen 115 GKIDPKGLLKRTG-----SLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKI 189 (317)
T ss_pred CCCCcccceeecc-----HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHH
Confidence 9999999988763 4677777777777765322 1124689999999999987544332 236778999999
Q ss_pred hccccccccceEEEEeCChHHHHHHHhhcccCChhhhcceEEcCCCCchHHHhcccCCCCccccCCCCcCCC
Q 009270 353 LQDNYPEFVAKQVFINVPWWYLAFHTMISPFMTQRTKSKFVFAGPSKSTETLFKYISPEHVPIQYGGLSVDY 424 (538)
Q Consensus 353 lq~~YPE~L~rI~IINaP~~f~~lw~lVKpfL~~~Tr~KI~~lg~~~~~e~L~k~Id~d~LP~~yGG~~~d~ 424 (538)
+|+|||++++++||||+|++|+++|++|||||+++|++||+++++ ++.++|+++|++++||.+|||++.+.
T Consensus 190 ~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~-~~~~~L~k~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 190 LQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHS-KDKESLLKYIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred HHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCC-CchhhhhhhCCHhhCccccCCCcccc
Confidence 999999999999999999999999999999999999999995543 69999999999999999999999863
No 2
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=3.7e-36 Score=305.27 Aligned_cols=198 Identities=31% Similarity=0.561 Sum_probs=169.3
Q ss_pred CCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHcCCCc-cCcccccccc-cceEEeeccCCCCCcEEEEecCccChhhh
Q 009270 209 DRTDVILLKFLRARDFKVRDAFVMIKNTIQWRKDFGIEA-LLNEDLGDDL-EKVVFMHGFDRDGHPVCYNVYGEFQNKQL 286 (538)
Q Consensus 209 ~~~D~~LLRFLRArkfdVekA~~mL~~~l~WRk~~~iD~-i~~~~~~~el-~k~~~l~G~Dk~GrPV~~~~~G~~d~~~l 286 (538)
.++|.+||||||||+|||.+|.+||.++|.||+.+++.. +..+.+..++ .+++|+.|+|++||||+|++... +.
T Consensus 46 ~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G~D~~gRPVl~~~~~~-~~--- 121 (324)
T KOG1470|consen 46 WCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILGHDKDGRPVLYLRPRP-HR--- 121 (324)
T ss_pred cCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEecccCCCCeEEEEecCC-CC---
Confidence 458999999999999999999999999999999999887 5444444344 46889999999999999985542 11
Q ss_pred hhccccCHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEEEEEEeCCCCCCCCchhHHHHHHHHHHhhccccccccceEEE
Q 009270 287 YAKTFSDEEKRMKFLRWRIQFLERSIRKLNFRPGGVSTIFQVNDLKNSPGPGKRELRIATKQALQLLQDNYPEFVAKQVF 366 (538)
Q Consensus 287 ~~~~~~d~e~~~~~lr~~i~llE~~l~~l~~~~~~v~~iv~IiDl~g~sgl~~~~l~~~~k~il~llq~~YPE~L~rI~I 366 (538)
+++. +...+.|+.+|+||.++..| +.+++++++++|++|++ +++.+ .++.+.++.+||+||||||++.+|
T Consensus 122 -qn~~----t~~~~~r~~Vy~mE~Ai~~l---p~~qe~~~~L~D~~~fs-~sN~d-~~~~k~~~~~lq~hYPErLg~a~l 191 (324)
T KOG1470|consen 122 -QNTK----TQKELERLLVYTLENAILFL---PPGQEQFVWLFDLTGFS-MSNPD-IKFLKELLHILQDHYPERLGKALL 191 (324)
T ss_pred -CCCC----CHHHHHHHHHHHHHHHHHhC---CCCcceEEEEEecccCc-ccCCC-cHHHHHHHHHHHHhChHHhhhhhh
Confidence 1121 35789999999999997655 77899999999999884 55555 678899999999999999999999
Q ss_pred EeCChHHHHHHHhhcccCChhhhcceEEcCCCCchHHHhcccCCCCccccCCCCcCC
Q 009270 367 INVPWWYLAFHTMISPFMTQRTKSKFVFAGPSKSTETLFKYISPEHVPIQYGGLSVD 423 (538)
Q Consensus 367 INaP~~f~~lw~lVKpfL~~~Tr~KI~~lg~~~~~e~L~k~Id~d~LP~~yGG~~~d 423 (538)
+|+||+|..+|++|||||++.|++||.|+.+ ...|.+|||+++||..|||+...
T Consensus 192 ~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~---~~~l~~~~d~~~l~s~~GG~~~~ 245 (324)
T KOG1470|consen 192 VNAPWIFQPFWKIIKPFLDPKTASKVKFVEP---KDDLSEYFDESQLPSLFGGKLLF 245 (324)
T ss_pred cCChHHHHHHHHHhhhccChhhhceeEEecC---hhHHHhhCCccccchhhCCCccc
Confidence 9999999999999999999999999999964 44599999999999999996553
No 3
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=99.95 E-value=4.3e-28 Score=224.26 Aligned_cols=151 Identities=33% Similarity=0.632 Sum_probs=121.7
Q ss_pred ceEEeeccCCCCCcEEEEecCccChhhhhhccccCHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEEEEEEeCCCCCCCC
Q 009270 259 KVVFMHGFDRDGHPVCYNVYGEFQNKQLYAKTFSDEEKRMKFLRWRIQFLERSIRKLNFRPGGVSTIFQVNDLKNSPGPG 338 (538)
Q Consensus 259 k~~~l~G~Dk~GrPV~~~~~G~~d~~~l~~~~~~d~e~~~~~lr~~i~llE~~l~~l~~~~~~v~~iv~IiDl~g~sgl~ 338 (538)
+..+++|+|++||||+|.++|++|.... ...+++++.++++|.+++.+.. .+.++++++|+|++|++ ++
T Consensus 7 ~~~~~~g~D~~gr~v~~~~~~~~~~~~~---------~~~~~~~~~~~~~E~~~~~~~~-~~~~~~~~~iiD~~g~~-~~ 75 (159)
T PF00650_consen 7 GPFYLHGRDKDGRPVIYIRLGRFDPKKF---------SPEDVIRFFVYLLERMLKRMPE-GGQVEGIVVIIDLSGFS-LS 75 (159)
T ss_dssp SCEEEEEE-TTS-EEEEEEGTT--HHTS----------HHHHHHHHHHHHHHHHHTHHH-TSHHH-EEEEEE-TT---HH
T ss_pred eeEEECCCCCCcCEEEEEEcccCCCCcC---------CHHHHHHHHHHHHHHHHhhhcc-cccceeEEEEEeCCCce-Ee
Confidence 3578999999999999999999998843 3578999999999999876543 46789999999999774 22
Q ss_pred chh--HHHHHHHHHHhhccccccccceEEEEeCChHHHHHHHhhcccCChhhhcceEEcCCCCchHHHhcccCCCCcccc
Q 009270 339 KRE--LRIATKQALQLLQDNYPEFVAKQVFINVPWWYLAFHTMISPFMTQRTKSKFVFAGPSKSTETLFKYISPEHVPIQ 416 (538)
Q Consensus 339 ~~~--l~~~~k~il~llq~~YPE~L~rI~IINaP~~f~~lw~lVKpfL~~~Tr~KI~~lg~~~~~e~L~k~Id~d~LP~~ 416 (538)
... ..+.++.+++++|++||++++++||||+|++|.++|+++++||+++|++||+|+++.++.+.|.+||++++||.+
T Consensus 76 ~~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~ 155 (159)
T PF00650_consen 76 NFDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVE 155 (159)
T ss_dssp HHHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGG
T ss_pred ccccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchh
Confidence 111 156789999999999999999999999999999999999999999999999999766677899999999999999
Q ss_pred CCCC
Q 009270 417 YGGL 420 (538)
Q Consensus 417 yGG~ 420 (538)
|||+
T Consensus 156 ~GG~ 159 (159)
T PF00650_consen 156 YGGT 159 (159)
T ss_dssp GTSS
T ss_pred cCCC
Confidence 9996
No 4
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.93 E-value=2.8e-25 Score=205.26 Aligned_cols=144 Identities=33% Similarity=0.653 Sum_probs=127.3
Q ss_pred ccCCCCCcEEEEecCccChhhhhhccccCHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEEEEEEeCCCCCCCCchhHHH
Q 009270 265 GFDRDGHPVCYNVYGEFQNKQLYAKTFSDEEKRMKFLRWRIQFLERSIRKLNFRPGGVSTIFQVNDLKNSPGPGKRELRI 344 (538)
Q Consensus 265 G~Dk~GrPV~~~~~G~~d~~~l~~~~~~d~e~~~~~lr~~i~llE~~l~~l~~~~~~v~~iv~IiDl~g~sgl~~~~l~~ 344 (538)
|+|++||||+|+++|+++.... +.+++++++++.+|.+++. ...+..++++++|+|++|++.. ... .+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~---------~~~~~~~~~~~~~e~~~~~-~~~~~~~~~~~~i~D~~~~~~~-~~~-~~ 81 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSV---------TLEELLRYLVYVLEKILQR-EKKTGGIEGFTVIFDLKGLSMS-NPD-LS 81 (158)
T ss_pred CCCCCcCEEEEEeccccccCcC---------CHHHHHHHHHHHHHHHHHH-HhcCCCeeeEEEEEECCCCCcc-ccc-HH
Confidence 6999999999999999886543 3689999999999999865 2236788999999999987533 222 57
Q ss_pred HHHHHHHhhccccccccceEEEEeCChHHHHHHHhhcccCChhhhcceEEcCCCCchHHHhcccCCCCccccCCCCc
Q 009270 345 ATKQALQLLQDNYPEFVAKQVFINVPWWYLAFHTMISPFMTQRTKSKFVFAGPSKSTETLFKYISPEHVPIQYGGLS 421 (538)
Q Consensus 345 ~~k~il~llq~~YPE~L~rI~IINaP~~f~~lw~lVKpfL~~~Tr~KI~~lg~~~~~e~L~k~Id~d~LP~~yGG~~ 421 (538)
.++.++.+++.+||++++++||||+|+++.++|+++++||++++++||+++++ ++.+.|.++|++++||.+|||++
T Consensus 82 ~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~-~~~~~L~~~i~~~~lP~~~GG~~ 157 (158)
T smart00516 82 VLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGN-DSKEELLEYIDPEQLPEELGGTL 157 (158)
T ss_pred HHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCC-CCHHHHHhhCCHhhCcHhhCCCC
Confidence 88999999999999999999999999999999999999999999999999986 57899999999999999999986
No 5
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.90 E-value=3.1e-23 Score=188.96 Aligned_cols=146 Identities=30% Similarity=0.534 Sum_probs=122.9
Q ss_pred EeeccCCCCCcEEEEecCccChhhhhhccccCHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEEEEEEeCCCCCCCCchh
Q 009270 262 FMHGFDRDGHPVCYNVYGEFQNKQLYAKTFSDEEKRMKFLRWRIQFLERSIRKLNFRPGGVSTIFQVNDLKNSPGPGKRE 341 (538)
Q Consensus 262 ~l~G~Dk~GrPV~~~~~G~~d~~~l~~~~~~d~e~~~~~lr~~i~llE~~l~~l~~~~~~v~~iv~IiDl~g~sgl~~~~ 341 (538)
+..|.|++||||++.++++.+....+ ..++++++.++.+|.+++.+.. ..+++++|+|++|++...+..
T Consensus 12 ~~~~~D~~gr~V~~~~~~~~~~~~~~--------~~~~~~~~~~~~~e~~~~~~~~---~~~~~~~i~D~~~~~~~~~~~ 80 (157)
T cd00170 12 YLGGRDKEGRPVLIIRAGNKDLSKSL--------DSEELLRYLVYTLEKLLQEDDE---QVEGFVVIIDLKGLSLSHLLP 80 (157)
T ss_pred ccCCCCCCcCEEEEEecCCcchhhcC--------CHHHHHHHHHHHHHHHHhhhhh---cccceEEEEECCCCChhccch
Confidence 34456999999999999976655432 1378999999999999876543 227899999999885332221
Q ss_pred HHHHHHHHHHhhccccccccceEEEEeCChHHHHHHHhhcccCChhhhcceEEcCCCCchHHHhcccCCCCccccCCCC
Q 009270 342 LRIATKQALQLLQDNYPEFVAKQVFINVPWWYLAFHTMISPFMTQRTKSKFVFAGPSKSTETLFKYISPEHVPIQYGGL 420 (538)
Q Consensus 342 l~~~~k~il~llq~~YPE~L~rI~IINaP~~f~~lw~lVKpfL~~~Tr~KI~~lg~~~~~e~L~k~Id~d~LP~~yGG~ 420 (538)
..+.++.++.+++++||++++++||||+|++|.++|+++++||++++++||++++++ .+.|.++|++++||.+|||+
T Consensus 81 ~~~~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~--~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 81 DPSLLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD--KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred hHHHHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC--HHHHHhhCChhhCcHhhCCC
Confidence 357789999999999999999999999999999999999999999999999999752 88999999999999999996
No 6
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=99.86 E-value=1.1e-21 Score=174.82 Aligned_cols=92 Identities=18% Similarity=0.213 Sum_probs=80.3
Q ss_pred ccCCCceeEEEEEec-CeeEEEEEEEecceeeEEEEEeecC----------------C-----------------C----
Q 009270 442 VKPATKQNVEIIIYE-KCTVVWEIRVVGWEVSYGAEFVPEA----------------K-----------------D---- 483 (538)
Q Consensus 442 V~~gs~~~v~i~V~~-g~~L~WeF~t~~~DI~Fgi~f~~~~----------------~-----------------g---- 483 (538)
|++|...+|.++..+ |..|+|+|.|+++|||||++|.-+. + |
T Consensus 1 v~~Ge~~tvrVpt~~~G~~l~WeFaTd~yDIgFG~~few~~~~s~~vsv~vses~de~~~~~~~~~~~~~~~ve~gs~~~ 80 (136)
T PF13897_consen 1 VGRGETVTVRVPTHPEGKCLFWEFATDSYDIGFGVYFEWTPPTSNQVSVHVSESSDEEDEEEEEEEDSESGDVEKGSERS 80 (136)
T ss_pred CCcCcEEEEEcccCCCCCEEEEEEeeCCCCceEEEEEEecCCCCCceeEecccCccccccccccccccCccchhcccccc
Confidence 678999999998886 9999999999999999999994210 0 0
Q ss_pred --ceEEEEecCcccCCCCcceecCeEEcCcCcEEEEEEECCCC--CceeEEEEEE
Q 009270 484 --KYTIIIQKPTKLSPTDEPVVCQRFKVDELGKILLTVDNPTS--KKKKLLYRFK 534 (538)
Q Consensus 484 --~~~~~V~~~~r~~~~~~pve~Gs~~~~epG~yvL~fDNs~S--~sKkv~Y~i~ 534 (538)
..+.+|+|..|++||..+ +.|++.|+.+|+|+|.|||||| |+|+|+|+|-
T Consensus 81 ~~~~~~eviPv~R~dsH~~~-~~Gs~~c~~~GvYvLkFDNSYS~~rsK~l~Y~V~ 134 (136)
T PF13897_consen 81 SRPEMDEVIPVYRRDSHLEV-EAGSHTCPGPGVYVLKFDNSYSWFRSKKLYYRVY 134 (136)
T ss_pred CCCCeeEEeEeeeeecCcce-eceEEECCCCeEEEEEeeCcceeEEeeEEEEEEE
Confidence 114689999999999999 8999999999999999999999 9999999985
No 7
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.47 E-value=3.4e-14 Score=142.62 Aligned_cols=96 Identities=23% Similarity=0.268 Sum_probs=82.0
Q ss_pred cccccCCCceeEEEEEec-CeeEEEEEEEecceeeEEEEEeec--------------CCCc-------------------
Q 009270 439 EITVKPATKQNVEIIIYE-KCTVVWEIRVVGWEVSYGAEFVPE--------------AKDK------------------- 484 (538)
Q Consensus 439 ~v~V~~gs~~~v~i~V~~-g~~L~WeF~t~~~DI~Fgi~f~~~--------------~~g~------------------- 484 (538)
.++|++|...+|.++..+ |+.|.|+|.|+++||||||+|.-. ++++
T Consensus 323 vItvGhGetVTVRVPThenGsclFWEFATD~YDIGFGvYFEWt~~~~n~VsVHVSeSddded~~~~~e~E~~e~G~~~~E 402 (469)
T KOG3878|consen 323 VITVGHGETVTVRVPTHENGSCLFWEFATDSYDIGFGVYFEWTKPVTNEVSVHVSESDDDEDCVYLSETEDLESGSLSQE 402 (469)
T ss_pred eEEecCCceEEEeccccCCCceEEEEeccccccccceEEEEeecCCCceeEEEecccccchhhhhhhhhhhhhcCCchhh
Confidence 688999999999999887 999999999999999999999421 1100
Q ss_pred -------------eEEEEecCcccCCCCcceecCeEEcCcCcEEEEEEECCCC--CceeEEEEEEe
Q 009270 485 -------------YTIIIQKPTKLSPTDEPVVCQRFKVDELGKILLTVDNPTS--KKKKLLYRFKV 535 (538)
Q Consensus 485 -------------~~~~V~~~~r~~~~~~pve~Gs~~~~epG~yvL~fDNs~S--~sKkv~Y~i~v 535 (538)
...+|+|.-|..||... -.||+..+.-|+|.|.|||||| |+|.|.||+--
T Consensus 403 ~gA~~n~~~anKp~~deIvPvYRRdCheEV-YaGSH~YPGrGvYLLKFDNSYSlWRsKtlYYRVYY 467 (469)
T KOG3878|consen 403 RGAVNNPTAANKPPIDEIVPVYRRDCHEEV-YAGSHSYPGRGVYLLKFDNSYSLWRSKTLYYRVYY 467 (469)
T ss_pred hhhhcCCCCCCCCCcccccchhhhhhhHHh-hcccccCCCCceEEEEecchhhhhcccceEEEEEe
Confidence 02467888889999887 7999999999999999999999 99999999853
No 8
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.34 E-value=6.1e-13 Score=122.70 Aligned_cols=140 Identities=21% Similarity=0.315 Sum_probs=92.0
Q ss_pred EEeeccCCCCCcEEEEecCccChhhhhhccccCHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEEEEEEeCCCCCCCCch
Q 009270 261 VFMHGFDRDGHPVCYNVYGEFQNKQLYAKTFSDEEKRMKFLRWRIQFLERSIRKLNFRPGGVSTIFQVNDLKNSPGPGKR 340 (538)
Q Consensus 261 ~~l~G~Dk~GrPV~~~~~G~~d~~~l~~~~~~d~e~~~~~lr~~i~llE~~l~~l~~~~~~v~~iv~IiDl~g~sgl~~~ 340 (538)
++..|+|++||||+++...++ ... ...+.++.+.+..+... -.-.++++|+|+.+.+. ...
T Consensus 4 ~~~gG~d~~g~pV~~~~~~~~-~~~---------~~~~~ll~yl~~~l~~~--------~~~~~f~vVid~~~~~~-~~~ 64 (149)
T PF13716_consen 4 FYPGGRDREGRPVVVFIASRL-PSS---------DDLERLLLYLLSTLSEE--------VVDKPFSVVIDHTGFSR-SSE 64 (149)
T ss_dssp -EEEEEBTTS-EEEEEEGGG--C-T---------THHHHHHHHHHHHH-TT--------TTTS-EEEEEE-TT--G-GG-
T ss_pred EEecccCCCcCEEEEEECCcC-cch---------hhHHHHHHHHHHhhhHH--------hcCCCEEEEEEcCCCcc-ccC
Confidence 466799999999999886655 211 13455666655554211 11235999999997642 222
Q ss_pred hHHHHHHHHHHhhccccccccceEEEEeCChHHHHHH-HhhcccCChhh-hcceEEcCCCCchHHHhcccCCCCccccCC
Q 009270 341 ELRIATKQALQLLQDNYPEFVAKQVFINVPWWYLAFH-TMISPFMTQRT-KSKFVFAGPSKSTETLFKYISPEHVPIQYG 418 (538)
Q Consensus 341 ~l~~~~k~il~llq~~YPE~L~rI~IINaP~~f~~lw-~lVKpfL~~~T-r~KI~~lg~~~~~e~L~k~Id~d~LP~~yG 418 (538)
.-+..++++..++...|+..|+++||||+.++++.++ .+.+++++.+. ..||.++. ....|.+|||+++||..+|
T Consensus 65 ~~~~~l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~---sl~~L~~~i~~~qL~~~lp 141 (149)
T PF13716_consen 65 PSLSWLKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVS---SLSELSKHIDPSQLPESLP 141 (149)
T ss_dssp --HHHHHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEES---STCGGGGTSGGGG------
T ss_pred CchHHHHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEEC---CHHHHHhhCCHHHhcccCC
Confidence 2377889999999999999999999999999999999 66677778888 99999985 5789999999999999999
Q ss_pred CCcC
Q 009270 419 GLSV 422 (538)
Q Consensus 419 G~~~ 422 (538)
|...
T Consensus 142 ~~~~ 145 (149)
T PF13716_consen 142 GVLQ 145 (149)
T ss_dssp HHH-
T ss_pred CEEe
Confidence 8764
No 9
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=98.71 E-value=3.6e-08 Score=76.13 Aligned_cols=30 Identities=57% Similarity=0.908 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhhhcCCCHHHHHHHHHHH
Q 009270 207 KDDRTDVILLKFLRARDFKVRDAFVMIKNT 236 (538)
Q Consensus 207 ~~~~~D~~LLRFLRArkfdVekA~~mL~~~ 236 (538)
....+|.+||||||||+|||++|.+||+++
T Consensus 26 ~~~~~d~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 26 KEDHDDNFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp TSS-SHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHHHccCCHHHHHHHHHhC
Confidence 356789999999999999999999999875
No 10
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=97.74 E-value=0.00012 Score=77.10 Aligned_cols=127 Identities=10% Similarity=0.239 Sum_probs=88.6
Q ss_pred cCCCCCcEEEEecCccChhhhhhccccCHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEEEEEEeCCCCCCCCchhHHHH
Q 009270 266 FDRDGHPVCYNVYGEFQNKQLYAKTFSDEEKRMKFLRWRIQFLERSIRKLNFRPGGVSTIFQVNDLKNSPGPGKRELRIA 345 (538)
Q Consensus 266 ~Dk~GrPV~~~~~G~~d~~~l~~~~~~d~e~~~~~lr~~i~llE~~l~~l~~~~~~v~~iv~IiDl~g~sgl~~~~l~~~ 345 (538)
.|+.||.|+++...++....-+ .-..++++.++.++..++. . .+.|+=-.|.+ ..++...+.
T Consensus 89 ~D~~gr~iivv~a~rlp~~~el--------d~~~li~~~v~~id~~Ve~------D---Yt~vYfh~gl~-s~nkp~l~~ 150 (467)
T KOG4406|consen 89 KDKQGRKIIVVYACRLPSSSEL--------DDIRLISYLVYTIDKYVEN------D---YTLVYFHHGLP-SDNKPYLQL 150 (467)
T ss_pred ccccCCeeEEEEEecCCchhhh--------hhHHHHHHHHHHHHHHHhc------c---ceeeehhcCCc-ccccchHHH
Confidence 6999999988887777544221 1234889999999988753 1 23332222221 123332333
Q ss_pred HHHHHHhhccccccccceEEEEeCChHHHHHHHhhcccCChhhhcceEEcCCCCchHHHhcccCCCCc
Q 009270 346 TKQALQLLQDNYPEFVAKQVFINVPWWYLAFHTMISPFMTQRTKSKFVFAGPSKSTETLFKYISPEHV 413 (538)
Q Consensus 346 ~k~il~llq~~YPE~L~rI~IINaP~~f~~lw~lVKpfL~~~Tr~KI~~lg~~~~~e~L~k~Id~d~L 413 (538)
+.....-+-.||=--++.+|+|..-|+..++|+++|||++.+..+||+.+ +...+|.++|.-++|
T Consensus 151 l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~---n~lseL~~~l~l~rL 215 (467)
T KOG4406|consen 151 LFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYF---NSLSELFEALKLNRL 215 (467)
T ss_pred HHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEe---ehHHHHHHhhhhhhh
Confidence 33334444456778899999999999999999999999999999999998 468899988864443
No 11
>KOG3287 consensus Membrane trafficking protein, emp24/gp25L/p24 family [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.49 E-value=0.0013 Score=63.95 Aligned_cols=82 Identities=16% Similarity=0.293 Sum_probs=57.8
Q ss_pred cccccCCCceeEEEEEecCeeEEEEEEEe-c---ceeeEEEEEeecCCCceEEEEecCcccCCCCcceecCeEE--cCcC
Q 009270 439 EITVKPATKQNVEIIIYEKCTVVWEIRVV-G---WEVSYGAEFVPEAKDKYTIIIQKPTKLSPTDEPVVCQRFK--VDEL 512 (538)
Q Consensus 439 ~v~V~~gs~~~v~i~V~~g~~L~WeF~t~-~---~DI~Fgi~f~~~~~g~~~~~V~~~~r~~~~~~pve~Gs~~--~~ep 512 (538)
.+.|.||++...-=.+..|.+|.-++.+. | .||+|.+. .| .| .+++.-.++. +|.++ ..++
T Consensus 37 tv~ipAGk~eCf~Q~v~~~~tle~eyQVi~G~GDl~i~Ftl~-~P--~G--~~lv~~q~k~--------dg~ht~e~~e~ 103 (236)
T KOG3287|consen 37 TVMIPAGKTECFYQPVPQGATLEVEYQVIDGAGDLDIDFTLL-NP--AG--EVLVSDQRKV--------DGVHTVEVTET 103 (236)
T ss_pred EEEecCCCceeeeeeccCCeEEEEEEEEEecCCccceeeEEe-CC--Cc--cEEeeccccc--------CceeEeeccCC
Confidence 67889998888777777788888888775 3 48999986 23 33 2333333332 44443 4689
Q ss_pred cEEEEEEECCCC--CceeEEEEE
Q 009270 513 GKILLTVDNPTS--KKKKLLYRF 533 (538)
Q Consensus 513 G~yvL~fDNs~S--~sKkv~Y~i 533 (538)
|-|.|+|||++| .+|.|.+.+
T Consensus 104 GdY~~CfDNsFS~fs~K~Vffel 126 (236)
T KOG3287|consen 104 GDYQVCFDNSFSTFSRKLVFFEL 126 (236)
T ss_pred cceEEEEcCccccccceEEEEEE
Confidence 999999999999 566677666
No 12
>KOG1693 consensus emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.79 E-value=0.051 Score=52.45 Aligned_cols=75 Identities=25% Similarity=0.370 Sum_probs=46.2
Q ss_pred CCceeEEEEEec-CeeEEEEEEEe---cceeeEEEEEeecCCCceEEEEe-cCcccCCCCcceecCeEEcCcCcEEEEEE
Q 009270 445 ATKQNVEIIIYE-KCTVVWEIRVV---GWEVSYGAEFVPEAKDKYTIIIQ-KPTKLSPTDEPVVCQRFKVDELGKILLTV 519 (538)
Q Consensus 445 gs~~~v~i~V~~-g~~L~WeF~t~---~~DI~Fgi~f~~~~~g~~~~~V~-~~~r~~~~~~pve~Gs~~~~epG~yvL~f 519 (538)
+.+..+-..+.. ++++..+|.|. +.||+|-|+ .|+ |. +++. ..+|+. +-.|+...-|+|.++|
T Consensus 31 ~aKqC~Y~d~~~~~~~~~~~fqV~tGG~fDVD~~I~-aPd--gk--vI~~~~kk~~~-------~~~f~ae~~G~Y~fCF 98 (209)
T KOG1693|consen 31 NAKQCFYEDLKKDDDTTSFEFQVQTGGHFDVDYDIE-APD--GK--VIYSEKKKRYD-------SFLFKAEGKGEYTFCF 98 (209)
T ss_pred cchhheeeecccCCceEEEEEEEEeCCceeeEEEEE-CCC--CC--EEeeccccccc-------cEEEEEecceEEEEEe
Confidence 333333334443 45555555554 348999986 343 32 3333 233332 4578899999999999
Q ss_pred ECCCC-CceeEEE
Q 009270 520 DNPTS-KKKKLLY 531 (538)
Q Consensus 520 DNs~S-~sKkv~Y 531 (538)
+|.+| .++|+-|
T Consensus 99 sN~fstf~~Kiv~ 111 (209)
T KOG1693|consen 99 SNEFSTFSHKIVY 111 (209)
T ss_pred cCccccccceEee
Confidence 99999 6666655
No 13
>KOG1692 consensus Putative cargo transport protein EMP24 (p24 protein family) [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.97 E-value=0.064 Score=51.54 Aligned_cols=72 Identities=19% Similarity=0.213 Sum_probs=49.1
Q ss_pred CCCceeEEEEEecCeeEEEEEEEecceeeEEEEEeecCCCceEEEEecCcccCCCCcceecCeEEcCcCcEEEEEEECCC
Q 009270 444 PATKQNVEIIIYEKCTVVWEIRVVGWEVSYGAEFVPEAKDKYTIIIQKPTKLSPTDEPVVCQRFKVDELGKILLTVDNPT 523 (538)
Q Consensus 444 ~gs~~~v~i~V~~g~~L~WeF~t~~~DI~Fgi~f~~~~~g~~~~~V~~~~r~~~~~~pve~Gs~~~~epG~yvL~fDNs~ 523 (538)
.|.+..+.|.|-+|. .-||+|.|. .|+ | .+|.+..|-++ -.=+|+++.+|+|.++|+|.+
T Consensus 39 ~gd~~~vsF~v~~gg---------~~~vd~~I~-gP~--~---~~i~~~~~~ss-----gk~tF~a~~~G~Y~fCF~N~~ 98 (201)
T KOG1692|consen 39 EGDKLSVSFEVIDGG---------FLGVDVEIT-GPD--G---KIIHKGKRESS-----GKYTFTAPKKGTYTFCFSNKM 98 (201)
T ss_pred cCCEEEEEEEEecCC---------ccceeEEEE-CCC--C---chhhhcccccC-----ceEEEEecCCceEEEEecCCC
Confidence 566666666664421 226777775 342 2 24555554333 234688999999999999999
Q ss_pred C--CceeEEEEEEe
Q 009270 524 S--KKKKLLYRFKV 535 (538)
Q Consensus 524 S--~sKkv~Y~i~v 535 (538)
| ..|.|.+.|.+
T Consensus 99 s~mtpk~V~F~ihv 112 (201)
T KOG1692|consen 99 STMTPKTVMFTIHV 112 (201)
T ss_pred CCCCceEEEEEEEE
Confidence 9 89999999986
No 14
>PF01105 EMP24_GP25L: emp24/gp25L/p24 family/GOLD; InterPro: IPR009038 The GOLD (for Golgi dynamics) domain is a protein module found in several eukaryotic Golgi and lipid-traffic proteins. It is typically between 90 and 150 amino acids long. Most of the size difference observed in the GOLD-domain superfamily is traceable to a single large low-complexity insert that is seen in some versions of the domain. With the exception of the p24 proteins, which have a simple architecture with the GOLD domain as their only globular domain, all other GOLD-domain proteins contain additional conserved globular domains. In these proteins, the GOLD domain co-occurs with lipid-, sterol- or fatty acid-binding domains such as PH, CRAL-TRIO, FYVE oxysterol binding- and acyl CoA-binding domains, suggesting that these proteins may interact with membranes. The GOLD domain can also be found associated with a RUN domain, which may have a role in the interaction of various proteins with cytoskeletal filaments. The GOLD domain is predicted to mediate diverse protein-protein interactions []. A secondary structure prediction for the GOLD domain reveals that it is likely to adopt a compact all-beta-fold structure with six to seven strands. Most of the sequence conservation is centred on the hydrophobic cores that support these predicted strands. The predicted secondary-structure elements and the size of the conserved core of the domain suggests that it may form a beta- sandwich fold with the strands arranged in two beta sheets stacked on each other []. Some proteins known to contain a GOLD domain are listed below: Eukaryotic proteins of the p24 family. Animal Sec14-like proteins. They are involved in secretion. Human Golgi resident protein GCP60. It interacts with the Golgi integral membrane protein Giantin. Yeast oxysterol-binding protein homologue 3 (OSH3). ; GO: 0006810 transport, 0016021 integral to membrane; PDB: 1P23_A 1M23_A.
Probab=90.75 E-value=0.072 Score=49.80 Aligned_cols=88 Identities=18% Similarity=0.287 Sum_probs=0.0
Q ss_pred ccccCCCceeEEEEEecCeeEEEEEEEecc----eeeEEEEEeecCCCceEEEEecCcccCCCCcceecCeEEcCcCcEE
Q 009270 440 ITVKPATKQNVEIIIYEKCTVVWEIRVVGW----EVSYGAEFVPEAKDKYTIIIQKPTKLSPTDEPVVCQRFKVDELGKI 515 (538)
Q Consensus 440 v~V~~gs~~~v~i~V~~g~~L~WeF~t~~~----DI~Fgi~f~~~~~g~~~~~V~~~~r~~~~~~pve~Gs~~~~epG~y 515 (538)
+.|.+|....+-..+..|..+...|.+.++ +|.|.|. .|++.| ..++.... ... . -.=+|.+.++|.|
T Consensus 4 f~l~~g~~~Cf~e~v~~~~~i~~~y~v~~~~~~~~v~~~i~-~~~~~~--~~i~~~~~-~~~-~---~~f~f~~~~~G~y 75 (183)
T PF01105_consen 4 FELEPGETECFYEEVPKGTTIRGSYRVTDGGGAYDVDFTIR-DPDPNG--EVIYSKSD-KES-E---GSFSFTAKESGEY 75 (183)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEECCCCcEEEEEEcCCCcEEEEEEEEeeccccceEEEEEE-ecccCC--ceeeeecc-ccc-C---CcEEEEeccCCCE
Confidence 456777777777777777777777777544 4666654 222222 22222211 111 0 0335678899999
Q ss_pred EEEEECCCCC--c-eeEEEEEEe
Q 009270 516 LLTVDNPTSK--K-KKLLYRFKV 535 (538)
Q Consensus 516 vL~fDNs~S~--s-Kkv~Y~i~v 535 (538)
.++|+|+.++ . +.|.+.+.+
T Consensus 76 ~iCf~n~~~~~~~~~~v~~~~~~ 98 (183)
T PF01105_consen 76 QICFDNSSSSFSPSKRVSFDIDV 98 (183)
T ss_dssp -----------------------
T ss_pred EEEEEcCCCCccccEEEEEEEEE
Confidence 9999999882 3 788777765
No 15
>PF09394 Inhibitor_I42: Chagasin family peptidase inhibitor I42; InterPro: IPR018990 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Chagasin reversible inhibitor of papain-like cysteine proteases []. Chagasin has a beta-barrel structure, which is a unique variant of the immunoglobulin fold with homology to human CD8alpha [, ].; PDB: 2NQD_A 2NNR_A 2H7W_B 3E1Z_A 3CBK_B 3CBJ_B 2OUL_B 2FO8_A 2WGN_B 2C34_A ....
Probab=72.65 E-value=28 Score=28.94 Aligned_cols=86 Identities=15% Similarity=0.197 Sum_probs=52.5
Q ss_pred ccccCCCceeEEEEEecCeeEEEEEEEecceeeE-EEEEeecCCCceEEEEecCcccCCCCcceecCeEEcCcCcEEEEE
Q 009270 440 ITVKPATKQNVEIIIYEKCTVVWEIRVVGWEVSY-GAEFVPEAKDKYTIIIQKPTKLSPTDEPVVCQRFKVDELGKILLT 518 (538)
Q Consensus 440 v~V~~gs~~~v~i~V~~g~~L~WeF~t~~~DI~F-gi~f~~~~~g~~~~~V~~~~r~~~~~~pve~Gs~~~~epG~yvL~ 518 (538)
++++.|....|.++-..+.-..|.+.....-+.+ +-.|.+...+. ..+.. .+. ..=.|.+..+|...|.
T Consensus 1 I~v~~g~~~~I~L~~npstGY~W~~~~~~~~l~l~~~~~~~~~~~~--------~~vG~-~g~-~~f~f~a~~~G~~~i~ 70 (92)
T PF09394_consen 1 ITVKVGDTFEIELPENPSTGYSWSLSSDSDGLQLVSEEYIPDNSPS--------GLVGA-PGT-RTFTFKALKPGTTTIK 70 (92)
T ss_dssp -EEETTSEEEEEEEEBCCGTBEEEECTSTTTEEEEEEEEEESSTSS--------TSSTS-SEE-EEEEEEESSSEEEEEE
T ss_pred CeecCCCEEEEEECCCCCCCeEEEEecCCCeEEEcCCcEEeCCCCc--------CCCCC-CcE-EEEEEEEecCeeEEEE
Confidence 4678888888877776656689988763333444 33333321111 02222 122 4567899999999999
Q ss_pred EECCCC-----CceeEEEEEEe
Q 009270 519 VDNPTS-----KKKKLLYRFKV 535 (538)
Q Consensus 519 fDNs~S-----~sKkv~Y~i~v 535 (538)
|....+ ..+++.|.+.|
T Consensus 71 ~~y~r~we~~~~~~~~~~~V~V 92 (92)
T PF09394_consen 71 FEYRRPWEKGSPIKTFTITVTV 92 (92)
T ss_dssp EEEEBTTTBSTTSEEEEEEEEE
T ss_pred EEEECcCCCCCccEEEEEEEEC
Confidence 987655 23567777765
No 16
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=63.79 E-value=14 Score=33.79 Aligned_cols=21 Identities=14% Similarity=0.254 Sum_probs=18.5
Q ss_pred CcceecCeEEcCcCcEEEEEEE
Q 009270 499 DEPVVCQRFKVDELGKILLTVD 520 (538)
Q Consensus 499 ~~pve~Gs~~~~epG~yvL~fD 520 (538)
-.+ ..|.|+|+-||+|.+.|.
T Consensus 38 yd~-~TG~Ftcpv~GvY~F~f~ 58 (135)
T smart00110 38 YDP-RTGKFTCPVPGVYYFSYH 58 (135)
T ss_pred ccC-CCCEEECeeceEEEEEEE
Confidence 345 699999999999999997
No 17
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=51.19 E-value=21 Score=25.89 Aligned_cols=24 Identities=13% Similarity=0.307 Sum_probs=20.5
Q ss_pred CHHHHHHHhhhcCCCHHHHHHHHH
Q 009270 211 TDVILLKFLRARDFKVRDAFVMIK 234 (538)
Q Consensus 211 ~D~~LLRFLRArkfdVekA~~mL~ 234 (538)
++.....||.+++||++.|...+-
T Consensus 14 ~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 14 DEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp SHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578889999999999999998874
No 18
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=48.29 E-value=33 Score=34.30 Aligned_cols=106 Identities=13% Similarity=0.190 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHhccC---CCCeeEEEEEEeCCCCCCCCchhHHHHHHHHHHhhccccccccceEEEEeCCh------HHH
Q 009270 304 RIQFLERSIRKLNFR---PGGVSTIFQVNDLKNSPGPGKRELRIATKQALQLLQDNYPEFVAKQVFINVPW------WYL 374 (538)
Q Consensus 304 ~i~llE~~l~~l~~~---~~~v~~iv~IiDl~g~sgl~~~~l~~~~k~il~llq~~YPE~L~rI~IINaP~------~f~ 374 (538)
.+++||+++..++.. .|..+.=.+|+||-|-- --..| ...+++++.-++. .=.++..+|++..++ ||+
T Consensus 75 Lv~cmEyl~~NldwL~~~~Gd~eddylifDcPGQI-ELytH-~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~KfiS 151 (273)
T KOG1534|consen 75 LVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQI-ELYTH-LPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFIS 151 (273)
T ss_pred chhHHHHHHHHHHHHHhhccCccCCEEEEeCCCee-EEeec-ChhHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHHH
Confidence 478888887766542 45667778899997531 11223 3456777777766 333555566655554 555
Q ss_pred HHHHhhccc----CCh-hhhcceEEcCCCCchHHHhcccCCCCc
Q 009270 375 AFHTMISPF----MTQ-RTKSKFVFAGPSKSTETLFKYISPEHV 413 (538)
Q Consensus 375 ~lw~lVKpf----L~~-~Tr~KI~~lg~~~~~e~L~k~Id~d~L 413 (538)
.+.+.+..+ ++. +..+|.-++.+ ..++.|.+|++++..
T Consensus 152 G~lsAlsAMi~lE~P~INvlsKMDLlk~-~~k~~l~~Fl~~d~~ 194 (273)
T KOG1534|consen 152 GCLSALSAMISLEVPHINVLSKMDLLKD-KNKKELERFLNPDEY 194 (273)
T ss_pred HHHHHHHHHHHhcCcchhhhhHHHHhhh-hhHHHHHHhcCCchh
Confidence 444433333 332 34667777764 578888888887643
No 19
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=45.16 E-value=33 Score=24.59 Aligned_cols=28 Identities=18% Similarity=0.157 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHhhhcCCCHHHHHHHHHH
Q 009270 208 DDRTDVILLKFLRARDFKVRDAFVMIKN 235 (538)
Q Consensus 208 ~~~~D~~LLRFLRArkfdVekA~~mL~~ 235 (538)
|..+...+.+-|+++++|++.|..+|-.
T Consensus 13 P~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 13 PDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp SSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 4578899999999999999999998854
No 20
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=44.43 E-value=17 Score=32.20 Aligned_cols=20 Identities=10% Similarity=0.036 Sum_probs=15.7
Q ss_pred ecCeEEcCcCcEEEEEEECC
Q 009270 503 VCQRFKVDELGKILLTVDNP 522 (538)
Q Consensus 503 e~Gs~~~~epG~yvL~fDNs 522 (538)
..|.|+|+.+|+|.+.|.=.
T Consensus 35 ~tG~Ftap~~G~Y~F~~~~~ 54 (127)
T PF00386_consen 35 STGIFTAPVPGVYFFSFTIM 54 (127)
T ss_dssp TTTEEE-SS-EEEEEEEEEE
T ss_pred ecCEEecCCCCEEEEEEEEe
Confidence 58999999999999999644
No 21
>cd05860 Ig4_SCFR Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). Ig4_SCFR: The fourth Immunoglobulin (Ig)-like domain in stem cell factor receptor (SCFR). SCFR is organized as an extracellular component having five IG-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR. This fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth domain abolishes the ligand-induced dimerization of SCFR and completely inhibits signal transduction.
Probab=37.47 E-value=2.8e+02 Score=24.27 Aligned_cols=81 Identities=17% Similarity=0.143 Sum_probs=49.9
Q ss_pred ccccccCCCceeEEEEEec--C-eeEEEEEEEe----cceeeEEEEEeecCCC--ceEEEEecCcccCCCCcceecCeEE
Q 009270 438 TEITVKPATKQNVEIIIYE--K-CTVVWEIRVV----GWEVSYGAEFVPEAKD--KYTIIIQKPTKLSPTDEPVVCQRFK 508 (538)
Q Consensus 438 ~~v~V~~gs~~~v~i~V~~--g-~~L~WeF~t~----~~DI~Fgi~f~~~~~g--~~~~~V~~~~r~~~~~~pve~Gs~~ 508 (538)
..+.|..|....+.+.|.+ + ....|.+... ..|-.+ .....+ .|+. +....|+ +
T Consensus 11 ~~~~v~~gE~~~L~V~ieAYP~p~~~~W~~~~~~l~~~~~~~~----~~~~~~~~rY~S-~L~L~Rl------------k 73 (101)
T cd05860 11 TTIFVNAGENLDLIVEYEAYPKPEHQQWIYMNRTLTNTSDHYV----KSRNESNNRYVS-ELHLTRL------------K 73 (101)
T ss_pred ceEEEECCCCEEEEEEEEeCCCCeeeEEEcCCcccCcccccee----EEeccCceEEEE-EEEEeec------------C
Confidence 3567888999999888886 3 3489986632 223111 221222 2332 2333333 3
Q ss_pred cCcCcEEEEEEECCCCCceeEEEEEEee
Q 009270 509 VDELGKILLTVDNPTSKKKKLLYRFKVE 536 (538)
Q Consensus 509 ~~epG~yvL~fDNs~S~sKkv~Y~i~v~ 536 (538)
..+.|.|.+...|+. .++.+.+.++|+
T Consensus 74 ~~E~G~YTf~a~N~~-~~~s~tF~l~v~ 100 (101)
T cd05860 74 GTEGGTYTFLVSNSD-ASASVTFNVYVN 100 (101)
T ss_pred hhhCcEEEEEEECCC-CeEEEEEEEEEe
Confidence 467899999999987 666677777764
No 22
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=36.68 E-value=56 Score=23.47 Aligned_cols=27 Identities=11% Similarity=0.124 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhhhcCCCHHHHHHHHH
Q 009270 208 DDRTDVILLKFLRARDFKVRDAFVMIK 234 (538)
Q Consensus 208 ~~~~D~~LLRFLRArkfdVekA~~mL~ 234 (538)
|..++..+.+-|+++++|++.|...|.
T Consensus 14 P~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 14 PNLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 457889999999999999999998875
No 23
>PF07462 MSP1_C: Merozoite surface protein 1 (MSP1) C-terminus; InterPro: IPR010901 This entry represents the C-terminal region of merozoite surface protein 1 (MSP1), which is found in a number of Plasmodium species. MSP-1 is a 200 kDa protein expressed on the surface of the Plasmodium vivax merozoite. MSP-1 of Plasmodium species is synthesised as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19 kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate [].; GO: 0009405 pathogenesis, 0016020 membrane
Probab=27.24 E-value=96 Score=34.83 Aligned_cols=27 Identities=19% Similarity=0.204 Sum_probs=13.6
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHHHHHHc
Q 009270 214 ILLKFLRARDFKVRDAFVMIKNTIQWRKDF 243 (538)
Q Consensus 214 ~LLRFLRArkfdVekA~~mL~~~l~WRk~~ 243 (538)
.|.+..-|-+= ....||...++=|.-|
T Consensus 391 qlenhv~afnt---NitdmLdSRlkKRnyF 417 (574)
T PF07462_consen 391 QLENHVNAFNT---NITDMLDSRLKKRNYF 417 (574)
T ss_pred HHHHHHHHHHh---hHHHHHHHHHHHHHHH
Confidence 34444444332 2345666666666554
No 24
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=27.20 E-value=24 Score=29.22 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=20.6
Q ss_pred CHHHHHHHhhhcCCCHHHHHHHHHHH
Q 009270 211 TDVILLKFLRARDFKVRDAFVMIKNT 236 (538)
Q Consensus 211 ~D~~LLRFLRArkfdVekA~~mL~~~ 236 (538)
++..|-.=|..++|||++|+..|++.
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 66778888999999999999998764
No 25
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=26.34 E-value=42 Score=27.87 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=19.4
Q ss_pred cCcCCCCCHHHHHHHHHHHHHHHHH
Q 009270 109 SNVIADLSDSERKALQELKQLVQEA 133 (538)
Q Consensus 109 s~~~~~L~~~e~~aL~e~r~~~~~~ 133 (538)
..++.||+++|++.|+.|+..+.+-
T Consensus 34 g~~~R~Lt~~E~~eL~~y~~~v~~y 58 (76)
T PF06394_consen 34 GKYARDLTPDEQQELKTYQKKVAAY 58 (76)
T ss_dssp TCEEEE--HHHHHHHHHHHHHHHHH
T ss_pred CEeeccCCHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999988753
No 26
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=26.17 E-value=1.8e+02 Score=23.43 Aligned_cols=45 Identities=16% Similarity=0.055 Sum_probs=29.2
Q ss_pred EEEeCCCCCCCCchhHHHHHHHHHHhhccccc--cccceEEEEeCChHHHH
Q 009270 327 QVNDLKNSPGPGKRELRIATKQALQLLQDNYP--EFVAKQVFINVPWWYLA 375 (538)
Q Consensus 327 ~IiDl~g~sgl~~~~l~~~~k~il~llq~~YP--E~L~rI~IINaP~~f~~ 375 (538)
+++|+.|+.+++ .+++-.++..+...|+ +.-.++.++|+......
T Consensus 20 V~lDF~gv~~~~----ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~ 66 (74)
T PF14213_consen 20 VVLDFEGVESIT----SSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKE 66 (74)
T ss_pred EEEECCCccccc----HHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHH
Confidence 789999886543 2444555555555566 56678888898655443
No 27
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=23.84 E-value=1.1e+02 Score=20.83 Aligned_cols=24 Identities=29% Similarity=0.137 Sum_probs=19.9
Q ss_pred CCHHHHHHHhhhcCCCHHHHHHHH
Q 009270 210 RTDVILLKFLRARDFKVRDAFVMI 233 (538)
Q Consensus 210 ~~D~~LLRFLRArkfdVekA~~mL 233 (538)
.+....++-|+.+++|+++|...|
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 456688999999999999998765
No 28
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=22.43 E-value=1.3e+02 Score=20.68 Aligned_cols=25 Identities=24% Similarity=0.076 Sum_probs=20.8
Q ss_pred CCHHHHHHHhhhcCCCHHHHHHHHH
Q 009270 210 RTDVILLKFLRARDFKVRDAFVMIK 234 (538)
Q Consensus 210 ~~D~~LLRFLRArkfdVekA~~mL~ 234 (538)
++....++-|+++++|+++|...|.
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4467788999999999999987763
No 29
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=21.87 E-value=1.3e+02 Score=20.75 Aligned_cols=23 Identities=22% Similarity=0.067 Sum_probs=17.2
Q ss_pred CHHHHHHHhhhcCCCHHHHHHHH
Q 009270 211 TDVILLKFLRARDFKVRDAFVMI 233 (538)
Q Consensus 211 ~D~~LLRFLRArkfdVekA~~mL 233 (538)
+.....+-|+++++|++.|...|
T Consensus 15 ~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 15 SREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp -HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHhC
Confidence 44577788888888888887754
No 30
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=20.67 E-value=1.3e+02 Score=27.10 Aligned_cols=43 Identities=14% Similarity=0.362 Sum_probs=34.7
Q ss_pred eEEEEeCChHHHHHHHhh-----cccCChhhhcceEEcCCCCchHHHhccc
Q 009270 363 KQVFINVPWWYLAFHTMI-----SPFMTQRTKSKFVFAGPSKSTETLFKYI 408 (538)
Q Consensus 363 rI~IINaP~~f~~lw~lV-----KpfL~~~Tr~KI~~lg~~~~~e~L~k~I 408 (538)
-++++|..-++.-++.++ ..|+++.....+.++. ..+++.++|
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d---~~~e~~~~i 133 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVD---DPEEALEYI 133 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEES---SHHHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeC---CHHHHHhhC
Confidence 699999887777777877 6799999999999984 567777654
Done!