Query 045317
Match_columns 460
No_of_seqs 317 out of 1582
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 12:01:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045317.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045317hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1470 Phosphatidylinositol t 100.0 4.9E-39 1.1E-43 310.2 17.1 198 125-339 46-245 (324)
2 KOG1471 Phosphatidylinositol t 100.0 1.7E-37 3.8E-42 310.1 22.7 246 52-340 6-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 8.4E-30 1.8E-34 228.6 10.9 152 175-336 7-159 (159)
4 smart00516 SEC14 Domain in hom 99.9 2.4E-26 5.3E-31 205.8 15.2 145 181-338 14-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 1.8E-24 4E-29 192.0 14.7 147 177-336 11-157 (157)
6 PF13897 GOLD_2: Golgi-dynamic 99.9 4E-22 8.7E-27 167.2 10.5 90 354-447 1-134 (136)
7 KOG3878 Protein involved in ma 99.5 2.9E-14 6.3E-19 135.5 5.4 95 351-447 323-466 (469)
8 PF13716 CRAL_TRIO_2: Divergen 99.4 7.3E-14 1.6E-18 124.1 4.6 141 177-339 4-146 (149)
9 PF03765 CRAL_TRIO_N: CRAL/TRI 98.8 1.3E-08 2.9E-13 74.4 6.4 28 125-152 28-55 (55)
10 KOG4406 CDC42 Rho GTPase-activ 97.9 6.1E-05 1.3E-09 75.2 10.0 125 182-327 89-213 (467)
11 KOG3287 Membrane trafficking p 97.0 0.0081 1.8E-07 55.2 10.4 103 328-447 17-127 (236)
12 KOG1692 Putative cargo transpo 92.5 0.55 1.2E-05 42.7 7.5 33 419-451 81-115 (201)
13 KOG1693 emp24/gp25L/p24 family 91.5 1.2 2.6E-05 40.8 8.4 71 368-449 42-117 (209)
14 PF01105 EMP24_GP25L: emp24/gp 83.9 0.33 7.1E-06 43.7 0.0 89 352-449 4-99 (183)
15 smart00110 C1Q Complement comp 76.8 6.8 0.00015 34.0 5.8 20 414-433 39-58 (135)
16 PF14555 UBA_4: UBA-like domai 60.7 13 0.00029 25.2 3.4 24 127-150 14-37 (43)
17 PF09394 Inhibitor_I42: Chagas 57.7 32 0.0007 27.1 5.8 86 352-448 1-92 (92)
18 PF00386 C1q: C1q domain; Int 56.2 9.7 0.00021 32.3 2.6 21 415-435 34-54 (127)
19 PF02845 CUE: CUE domain; Int 54.9 28 0.00061 23.3 4.2 27 125-151 14-40 (42)
20 smart00546 CUE Domain that may 47.0 33 0.00072 23.1 3.6 26 125-150 15-40 (43)
21 PF08938 HBS1_N: HBS1 N-termin 46.3 7.9 0.00017 30.2 0.4 52 62-152 18-70 (79)
22 PF14213 DUF4325: Domain of un 41.4 1E+02 0.0022 23.4 6.0 47 242-292 19-67 (74)
23 KOG1534 Putative transcription 41.0 51 0.0011 31.1 4.8 104 220-328 75-193 (273)
24 cd05860 Ig4_SCFR Fourth immuno 34.1 2.2E+02 0.0047 23.4 7.1 82 351-448 12-99 (101)
25 PF00627 UBA: UBA/TS-N domain; 33.0 75 0.0016 20.6 3.5 24 126-149 14-37 (37)
26 TIGR03769 P_ac_wall_RPT actino 32.4 37 0.00081 22.9 1.9 17 419-435 6-22 (41)
27 PF01108 Tissue_fac: Tissue fa 31.0 1.8E+02 0.0039 23.7 6.3 53 361-413 27-85 (107)
28 smart00165 UBA Ubiquitin assoc 30.9 83 0.0018 20.1 3.4 24 126-149 13-36 (37)
29 cd00194 UBA Ubiquitin Associat 29.6 90 0.002 20.0 3.5 25 126-150 13-37 (38)
30 smart00804 TAP_C C-terminal do 28.9 2.5E+02 0.0053 20.9 6.1 27 126-152 25-51 (63)
31 PF03641 Lysine_decarbox: Poss 28.6 1.2E+02 0.0027 25.9 5.1 60 261-323 66-132 (133)
32 COG2961 ComJ Protein involved 27.2 39 0.00084 32.6 1.8 27 278-304 237-263 (279)
33 PF06394 Pepsin-I3: Pepsin inh 24.6 55 0.0012 25.4 1.9 24 59-82 35-58 (76)
34 PF04838 Baculo_LEF5: Baculovi 22.7 57 0.0012 28.6 1.9 49 261-310 16-68 (159)
35 PF04378 RsmJ: Ribosomal RNA s 21.0 52 0.0011 31.7 1.4 29 278-306 206-234 (245)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=4.9e-39 Score=310.23 Aligned_cols=198 Identities=28% Similarity=0.505 Sum_probs=172.4
Q ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCCCc-cccCCCcccc-ccceeeeccCCCCCeEEEEecCCCCCCCC
Q 045317 125 EGTDIVLLKFLKAKDYKVHDAFEMLRKTLKWRRDYLADL-IQEDGLDPDV-GKLVYSNCKDREGRPLYYNVCGAFKNREL 202 (460)
Q Consensus 125 ~~~D~~LLRFLrarkfdv~kA~~~l~~~l~wR~~~~~d~-i~~~~~~~el-~~~~~~~G~Dk~GrpV~i~~~g~~d~~~l 202 (460)
+++|.+++||||||+||+++|.+||.++|.||+.+++.. +..+.+..++ .+++|+.|+|++||||+|+++......
T Consensus 46 ~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G~D~~gRPVl~~~~~~~~qn-- 123 (324)
T KOG1470|consen 46 WCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILGHDKDGRPVLYLRPRPHRQN-- 123 (324)
T ss_pred cCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEecccCCCCeEEEEecCCCCCC--
Confidence 679999999999999999999999999999999999887 4444455555 689999999999999999965532221
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHHhccCCCCcceeEEEEeCCCCCCCCchhHHHHHHHHHHHHhhhcccccceEEE
Q 045317 203 PKKLVDLEDLCDQFIRLEVKFMEKGIKELNFKPGGANSIVQIIDLKNSKPPDIKKFRVVSKKTVMMLQDNYPELMHRNII 282 (460)
Q Consensus 203 ~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~v~~~v~I~Dl~g~s~~~~~~~~~~~k~~~~~lq~~YPerL~~i~I 282 (460)
..+..++.|+++|+||.++..+ +.+++++++++|++|+|+. +.++ ...+.++.++|+||||||++++|
T Consensus 124 -------~~t~~~~~r~~Vy~mE~Ai~~l---p~~qe~~~~L~D~~~fs~s-N~d~-~~~k~~~~~lq~hYPErLg~a~l 191 (324)
T KOG1470|consen 124 -------TKTQKELERLLVYTLENAILFL---PPGQEQFVWLFDLTGFSMS-NPDI-KFLKELLHILQDHYPERLGKALL 191 (324)
T ss_pred -------CCCHHHHHHHHHHHHHHHHHhC---CCCcceEEEEEecccCccc-CCCc-HHHHHHHHHHHHhChHHhhhhhh
Confidence 1356899999999999998765 5678999999999999876 3444 58899999999999999999999
Q ss_pred EeCChhHHHHHHHHhhcCChhhcccEEEeCCccchHhHhccCCCCCCcccCCCccCC
Q 045317 283 INVPFWYYAFHTVASKFLSPRCKRKFVFARPAKVTKTLLKFISPENLPVEYGGLYRE 339 (460)
Q Consensus 283 IN~P~~f~~~w~lvkpfL~~~t~~KI~~~~~~~~~~~L~e~Id~d~LP~~yGG~~~~ 339 (460)
+|+||+|..+|+++||||+++|++||.|+.+ ...|.+|||+++||..+||+...
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 9999999999999999999999999999986 45599999999999999995543
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=1.7e-37 Score=310.13 Aligned_cols=246 Identities=30% Similarity=0.455 Sum_probs=202.5
Q ss_pred cccccccccCCCCCHHHHHHHHHHHHHHHHHHhccccCCCCCCCCChhHHHHHhhhhhhhhhccCCCCCCCCCCCCHHHH
Q 045317 52 EDGNREAAAIIDMKFKKKKALLEFRCMVEDAVLGNYLLGKPPRSHSPKEAALARSQLKKITLWGVPLLPSKAHEGTDIVL 131 (460)
Q Consensus 52 ~~~~~~~~~~~~ls~~q~~aL~elr~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~lp~~~~~~~D~~L 131 (460)
...+.......++++.+.++++++| .+.. .++++. ...+|.+|
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~i~~lr-~~~~----------------------------------~~~l~~--~~~~d~~L 48 (317)
T KOG1471|consen 6 MLAKVAKEELNEITESEEAVIAQLR-WLLQ----------------------------------KPHLPN--KYDDDFNL 48 (317)
T ss_pred ccccccccccCCCcHHHHHHHHHHH-HHhh----------------------------------ccCCCC--CCCCHHHH
Confidence 3345567778899999999999999 2222 244552 37899999
Q ss_pred HHHHHhcCCCHHHHHHHHHHHHHHHHHcCCCccccC-CCcccccc--ceeeeccCCCCCeEEEEecCCCCCCCCcccccc
Q 045317 132 LKFLKAKDYKVHDAFEMLRKTLKWRRDYLADLIQED-GLDPDVGK--LVYSNCKDREGRPLYYNVCGAFKNRELPKKLVD 208 (460)
Q Consensus 132 LRFLrarkfdv~kA~~~l~~~l~wR~~~~~d~i~~~-~~~~el~~--~~~~~G~Dk~GrpV~i~~~g~~d~~~l~~~~~~ 208 (460)
|||||||+||+++|.+||.+++.||++++++.+... ....++.+ ....+|.|+.|+||++.+.|..|..+++..+.
T Consensus 49 lRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~~- 127 (317)
T KOG1471|consen 49 LRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKYYPQGLHGVDKEGRPVYIERLGKIDPKGLLKRTG- 127 (317)
T ss_pred HHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhhccccccccCCCCCEEEEeccCCCCcccceeecc-
Confidence 999999999999999999999999999999998865 12233332 35688999999999999999999999987643
Q ss_pred chhhHHHHHHHHHHHHHHHHHHh-----ccCCCCcceeEEEEeCCCCCCCCchhH-HHHHHHHHHHHhhhcccccceEEE
Q 045317 209 LEDLCDQFIRLEVKFMEKGIKEL-----NFKPGGANSIVQIIDLKNSKPPDIKKF-RVVSKKTVMMLQDNYPELMHRNII 282 (460)
Q Consensus 209 ~~~~~~~~~r~~~~~~E~~~~~~-----~~~~~~v~~~v~I~Dl~g~s~~~~~~~-~~~~k~~~~~lq~~YPerL~~i~I 282 (460)
..+++++.+..+|..+..+ ......++|+++|+||+|+++.++... ...++.++.++|++||++++++||
T Consensus 128 ----~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~i 203 (317)
T KOG1471|consen 128 ----SLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPERLKRIHI 203 (317)
T ss_pred ----HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHHhhceEEE
Confidence 4667777776666665322 111346899999999999988776443 478999999999999999999999
Q ss_pred EeCChhHHHHHHHHhhcCChhhcccEEEeCCccchHhHhccCCCCCCcccCCCccCCC
Q 045317 283 INVPFWYYAFHTVASKFLSPRCKRKFVFARPAKVTKTLLKFISPENLPVEYGGLYREN 340 (460)
Q Consensus 283 IN~P~~f~~~w~lvkpfL~~~t~~KI~~~~~~~~~~~L~e~Id~d~LP~~yGG~~~~~ 340 (460)
||+|++|+++|++|||||+++|++||++++ .++.++|+++|+++.||.+|||++.+.
T Consensus 204 IN~P~~f~~~~~~ikpfL~~kt~~ki~~~~-~~~~~~L~k~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 204 INAPTIFSALWKVVKPFLDEKTRKKIHVLH-SKDKESLLKYIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred EcCchhHHHHHHHHhccCCHHHHhhheecC-CCchhhhhhhCCHhhCccccCCCcccc
Confidence 999999999999999999999999999554 357999999999999999999999985
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=99.96 E-value=8.4e-30 Score=228.56 Aligned_cols=152 Identities=33% Similarity=0.592 Sum_probs=123.0
Q ss_pred cceeeeccCCCCCeEEEEecCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHhccCCCCcceeEEEEeCCCCCCCC
Q 045317 175 KLVYSNCKDREGRPLYYNVCGAFKNRELPKKLVDLEDLCDQFIRLEVKFMEKGIKELNFKPGGANSIVQIIDLKNSKPPD 254 (460)
Q Consensus 175 ~~~~~~G~Dk~GrpV~i~~~g~~d~~~l~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~v~~~v~I~Dl~g~s~~~ 254 (460)
+..+++|+|++||||+++++|++|+... +.++++++.++++|.+++.+.. .+.++++++|+|++|+++.+
T Consensus 7 ~~~~~~g~D~~gr~v~~~~~~~~~~~~~---------~~~~~~~~~~~~~E~~~~~~~~-~~~~~~~~~iiD~~g~~~~~ 76 (159)
T PF00650_consen 7 GPFYLHGRDKDGRPVIYIRLGRFDPKKF---------SPEDVIRFFVYLLERMLKRMPE-GGQVEGIVVIIDLSGFSLSN 76 (159)
T ss_dssp SCEEEEEE-TTS-EEEEEEGTT--HHTS----------HHHHHHHHHHHHHHHHHTHHH-TSHHH-EEEEEE-TT--HHH
T ss_pred eeEEECCCCCCcCEEEEEEcccCCCCcC---------CHHHHHHHHHHHHHHHHhhhcc-cccceeEEEEEeCCCceEec
Confidence 4678999999999999999999987632 3579999999999999976543 34689999999999996544
Q ss_pred chhH-HHHHHHHHHHHhhhcccccceEEEEeCChhHHHHHHHHhhcCChhhcccEEEeCCccchHhHhccCCCCCCcccC
Q 045317 255 IKKF-RVVSKKTVMMLQDNYPELMHRNIIINVPFWYYAFHTVASKFLSPRCKRKFVFARPAKVTKTLLKFISPENLPVEY 333 (460)
Q Consensus 255 ~~~~-~~~~k~~~~~lq~~YPerL~~i~IIN~P~~f~~~w~lvkpfL~~~t~~KI~~~~~~~~~~~L~e~Id~d~LP~~y 333 (460)
+... .+.++.+++++|++||+|++++||||+|++|+++|++++|||+++|++||+++++.++.+.|.++||+++||++|
T Consensus 77 ~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~ 156 (159)
T PF00650_consen 77 FDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEY 156 (159)
T ss_dssp HHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGG
T ss_pred cccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhc
Confidence 3311 468899999999999999999999999999999999999999999999999998667778999999999999999
Q ss_pred CCc
Q 045317 334 GGL 336 (460)
Q Consensus 334 GG~ 336 (460)
||+
T Consensus 157 GG~ 159 (159)
T PF00650_consen 157 GGT 159 (159)
T ss_dssp TSS
T ss_pred CCC
Confidence 997
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=99.94 E-value=2.4e-26 Score=205.81 Aligned_cols=145 Identities=30% Similarity=0.522 Sum_probs=128.6
Q ss_pred ccCCCCCeEEEEecCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHhccCCCCcceeEEEEeCCCCCCCCchhHHH
Q 045317 181 CKDREGRPLYYNVCGAFKNRELPKKLVDLEDLCDQFIRLEVKFMEKGIKELNFKPGGANSIVQIIDLKNSKPPDIKKFRV 260 (460)
Q Consensus 181 G~Dk~GrpV~i~~~g~~d~~~l~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~v~~~v~I~Dl~g~s~~~~~~~~~ 260 (460)
|+|++||||++++++++++.. .+.+++++++++.+|.+++.. ..+..++++++|+|++|+++.+. . .+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~---------~~~~~~~~~~~~~~e~~~~~~-~~~~~~~~~~~i~D~~~~~~~~~-~-~~ 81 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKS---------VTLEELLRYLVYVLEKILQRE-KKTGGIEGFTVIFDLKGLSMSNP-D-LS 81 (158)
T ss_pred CCCCCcCEEEEEeccccccCc---------CCHHHHHHHHHHHHHHHHHHH-hcCCCeeeEEEEEECCCCCcccc-c-HH
Confidence 699999999999999987543 246899999999999998752 23557899999999999987653 2 36
Q ss_pred HHHHHHHHHhhhcccccceEEEEeCChhHHHHHHHHhhcCChhhcccEEEeCCccchHhHhccCCCCCCcccCCCccC
Q 045317 261 VSKKTVMMLQDNYPELMHRNIIINVPFWYYAFHTVASKFLSPRCKRKFVFARPAKVTKTLLKFISPENLPVEYGGLYR 338 (460)
Q Consensus 261 ~~k~~~~~lq~~YPerL~~i~IIN~P~~f~~~w~lvkpfL~~~t~~KI~~~~~~~~~~~L~e~Id~d~LP~~yGG~~~ 338 (460)
.++.++++++.+||++++++||+|+|+++.++|+++++||++++++||+++++ ++.+.|.++||+++||++|||++.
T Consensus 82 ~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~-~~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 82 VLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGN-DSKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred HHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCC-CCHHHHHhhCCHhhCcHhhCCCCC
Confidence 89999999999999999999999999999999999999999999999999995 568999999999999999999974
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=99.92 E-value=1.8e-24 Score=192.04 Aligned_cols=147 Identities=33% Similarity=0.502 Sum_probs=126.5
Q ss_pred eeeeccCCCCCeEEEEecCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHhccCCCCcceeEEEEeCCCCCCCCch
Q 045317 177 VYSNCKDREGRPLYYNVCGAFKNRELPKKLVDLEDLCDQFIRLEVKFMEKGIKELNFKPGGANSIVQIIDLKNSKPPDIK 256 (460)
Q Consensus 177 ~~~~G~Dk~GrpV~i~~~g~~d~~~l~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~v~~~v~I~Dl~g~s~~~~~ 256 (460)
.+..|+|++||||+++++++.+..... ..++++++.++.+|.+++.+..+ .+++++|+|++|+++.++.
T Consensus 11 ~~~~~~D~~gr~V~~~~~~~~~~~~~~--------~~~~~~~~~~~~~e~~~~~~~~~---~~~~~~i~D~~~~~~~~~~ 79 (157)
T cd00170 11 GYLGGRDKEGRPVLIIRAGNKDLSKSL--------DSEELLRYLVYTLEKLLQEDDEQ---VEGFVVIIDLKGLSLSHLL 79 (157)
T ss_pred cccCCCCCCcCEEEEEecCCcchhhcC--------CHHHHHHHHHHHHHHHHhhhhhc---ccceEEEEECCCCChhccc
Confidence 445567999999999999976654432 13789999999999998865432 3689999999999876654
Q ss_pred hHHHHHHHHHHHHhhhcccccceEEEEeCChhHHHHHHHHhhcCChhhcccEEEeCCccchHhHhccCCCCCCcccCCCc
Q 045317 257 KFRVVSKKTVMMLQDNYPELMHRNIIINVPFWYYAFHTVASKFLSPRCKRKFVFARPAKVTKTLLKFISPENLPVEYGGL 336 (460)
Q Consensus 257 ~~~~~~k~~~~~lq~~YPerL~~i~IIN~P~~f~~~w~lvkpfL~~~t~~KI~~~~~~~~~~~L~e~Id~d~LP~~yGG~ 336 (460)
...+.++.++.+++++||++++++||+|+|++|.++|+++++|+++++++||++++++ .+.|.++||+++||.+|||+
T Consensus 80 ~~~~~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~--~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 80 PDPSLLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD--KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred hhHHHHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC--HHHHHhhCChhhCcHhhCCC
Confidence 2236889999999999999999999999999999999999999999999999999853 78999999999999999996
No 6
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=99.87 E-value=4e-22 Score=167.23 Aligned_cols=90 Identities=21% Similarity=0.424 Sum_probs=76.8
Q ss_pred hccCCcceeeeeecCCCceEEEEEEeecceeEEEEEEEeC-----------------------C----------------
Q 045317 354 VRKNTAGSVRIPVAETGVTMMWDLTVLGWDVSYKEEFIPD-----------------------D---------------- 394 (460)
Q Consensus 354 V~~g~~~~v~~~v~~~g~~l~W~f~t~~~DI~Fgi~~~~~-----------------------~---------------- 394 (460)
|++|...+|+++....|+.|.|+|.|+++|||||++|.=. .
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 6789999999999999999999999999999999999510 0
Q ss_pred -CCCeEEEEeccc--cccCCCCcccccEEEeCcCcEEEEEEECCC--ccceEEEEEEE
Q 045317 395 -EGSYRVLLQSEK--EKKGGEGESMRNSFYISEPGKIVITIDNVT--LKNKRVYYRFK 447 (460)
Q Consensus 395 -~~~~~~v~~~~~--~~~~~~~~~~~g~~~~~~~G~y~l~fdNs~--~~~K~v~Y~i~ 447 (460)
.+.+.+|+|..| ||+ .++.|++.|+.||+|+|.||||| +|+|+|+|+|-
T Consensus 81 ~~~~~~eviPv~R~dsH~----~~~~Gs~~c~~~GvYvLkFDNSYS~~rsK~l~Y~V~ 134 (136)
T PF13897_consen 81 SRPEMDEVIPVYRRDSHL----EVEAGSHTCPGPGVYVLKFDNSYSWFRSKKLYYRVY 134 (136)
T ss_pred CCCCeeEEeEeeeeecCc----ceeceEEECCCCeEEEEEeeCcceeEEeeEEEEEEE
Confidence 012678888777 565 66779999999999999999999 79999999984
No 7
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.48 E-value=2.9e-14 Score=135.50 Aligned_cols=95 Identities=20% Similarity=0.410 Sum_probs=77.3
Q ss_pred hhhhccCCcceeeeeecCCCceEEEEEEeecceeEEEEEEEe-------------CC-C---------------C-----
Q 045317 351 ELIVRKNTAGSVRIPVAETGVTMMWDLTVLGWDVSYKEEFIP-------------DD-E---------------G----- 396 (460)
Q Consensus 351 ~~~V~~g~~~~v~~~v~~~g~~l~W~f~t~~~DI~Fgi~~~~-------------~~-~---------------~----- 396 (460)
-++|+.|.+.+|+++....|+.|.|+|.|+++||||||+|.= .+ + |
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 588999999999999999999999999999999999999851 00 0 0
Q ss_pred -------------CeEEEEeccccccCCCCcccccEEEeCcCcEEEEEEECCC--ccceEEEEEEE
Q 045317 397 -------------SYRVLLQSEKEKKGGEGESMRNSFYISEPGKIVITIDNVT--LKNKRVYYRFK 447 (460)
Q Consensus 397 -------------~~~~v~~~~~~~~~~~~~~~~g~~~~~~~G~y~l~fdNs~--~~~K~v~Y~i~ 447 (460)
...+|+|..| ..++++.-.||+.-+..|.|.|.||||| +|||.|.|+|-
T Consensus 403 ~gA~~n~~~anKp~~deIvPvYR--RdCheEVYaGSH~YPGrGvYLLKFDNSYSlWRsKtlYYRVY 466 (469)
T KOG3878|consen 403 RGAVNNPTAANKPPIDEIVPVYR--RDCHEEVYAGSHSYPGRGVYLLKFDNSYSLWRSKTLYYRVY 466 (469)
T ss_pred hhhhcCCCCCCCCCcccccchhh--hhhhHHhhcccccCCCCceEEEEecchhhhhcccceEEEEE
Confidence 0345667666 2333344579999999999999999999 69999999984
No 8
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.44 E-value=7.3e-14 Score=124.13 Aligned_cols=141 Identities=20% Similarity=0.326 Sum_probs=92.2
Q ss_pred eeeeccCCCCCeEEEEecCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHhccCCCCcceeEEEEeCCCCCCCCch
Q 045317 177 VYSNCKDREGRPLYYNVCGAFKNRELPKKLVDLEDLCDQFIRLEVKFMEKGIKELNFKPGGANSIVQIIDLKNSKPPDIK 256 (460)
Q Consensus 177 ~~~~G~Dk~GrpV~i~~~g~~d~~~l~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~v~~~v~I~Dl~g~s~~~~~ 256 (460)
++..|+|++||||+++...++ +.. ...+.++.|++..+ .... ...+.++|+|+++.+..+.+
T Consensus 4 ~~~gG~d~~g~pV~~~~~~~~-~~~---------~~~~~ll~yl~~~l---~~~~-----~~~~f~vVid~~~~~~~~~~ 65 (149)
T PF13716_consen 4 FYPGGRDREGRPVVVFIASRL-PSS---------DDLERLLLYLLSTL---SEEV-----VDKPFSVVIDHTGFSRSSEP 65 (149)
T ss_dssp -EEEEEBTTS-EEEEEEGGG--C-T---------THHHHHHHHHHHHH----TTT-----TTS-EEEEEE-TT--GGG--
T ss_pred EEecccCCCcCEEEEEECCcC-cch---------hhHHHHHHHHHHhh---hHHh-----cCCCEEEEEEcCCCccccCC
Confidence 467799999999999997765 211 12344555444433 1111 23569999999998553322
Q ss_pred hHHHHHHHHHHHHhhhcccccceEEEEeCChhHHHHH-HHHhhcCChhh-cccEEEeCCccchHhHhccCCCCCCcccCC
Q 045317 257 KFRVVSKKTVMMLQDNYPELMHRNIIINVPFWYYAFH-TVASKFLSPRC-KRKFVFARPAKVTKTLLKFISPENLPVEYG 334 (460)
Q Consensus 257 ~~~~~~k~~~~~lq~~YPerL~~i~IIN~P~~f~~~w-~lvkpfL~~~t-~~KI~~~~~~~~~~~L~e~Id~d~LP~~yG 334 (460)
. ++.++++..++...|+..|+++||+|++++++.++ .+.+++.+.+. ..||.++.+ .++|.++||+++||..+|
T Consensus 66 ~-~~~l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s---l~~L~~~i~~~qL~~~lp 141 (149)
T PF13716_consen 66 S-LSWLKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS---LSELSKHIDPSQLPESLP 141 (149)
T ss_dssp --HHHHHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS---TCGGGGTSGGGG------
T ss_pred c-hHHHHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC---HHHHHhhCCHHHhcccCC
Confidence 2 46789999999999999999999999999999999 66677778888 999999985 899999999999999999
Q ss_pred CccCC
Q 045317 335 GLYRE 339 (460)
Q Consensus 335 G~~~~ 339 (460)
|+.+.
T Consensus 142 ~~~~~ 146 (149)
T PF13716_consen 142 GVLQY 146 (149)
T ss_dssp HHH--
T ss_pred CEEec
Confidence 98764
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=98.80 E-value=1.3e-08 Score=74.42 Aligned_cols=28 Identities=46% Similarity=0.839 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHHHH
Q 045317 125 EGTDIVLLKFLKAKDYKVHDAFEMLRKT 152 (460)
Q Consensus 125 ~~~D~~LLRFLrarkfdv~kA~~~l~~~ 152 (460)
..+|.+||||||||+||+++|.+||.++
T Consensus 28 ~~~d~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 28 DHDDNFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp S-SHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHccCCHHHHHHHHHhC
Confidence 6799999999999999999999999875
No 10
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=97.91 E-value=6.1e-05 Score=75.25 Aligned_cols=125 Identities=12% Similarity=0.159 Sum_probs=90.4
Q ss_pred cCCCCCeEEEEecCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHhccCCCCcceeEEEEeCCCCCCCCchhHHHH
Q 045317 182 KDREGRPLYYNVCGAFKNRELPKKLVDLEDLCDQFIRLEVKFMEKGIKELNFKPGGANSIVQIIDLKNSKPPDIKKFRVV 261 (460)
Q Consensus 182 ~Dk~GrpV~i~~~g~~d~~~l~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~v~~~v~I~Dl~g~s~~~~~~~~~~ 261 (460)
.|+.||+|+++.+.++-...-+ .-..++++.++.++..++. + .+.+.=-.|+.. .++...+.
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-YTLVYFHHGLPS-DNKPYLQL 150 (467)
T ss_pred ccccCCeeEEEEEecCCchhhh--------hhHHHHHHHHHHHHHHHhc--------c-ceeeehhcCCcc-cccchHHH
Confidence 6999999999887775432211 1123888999999988752 1 344444445533 33333344
Q ss_pred HHHHHHHHhhhcccccceEEEEeCChhHHHHHHHHhhcCChhhcccEEEeCCccchHhHhccCCCC
Q 045317 262 SKKTVMMLQDNYPELMHRNIIINVPFWYYAFHTVASKFLSPRCKRKFVFARPAKVTKTLLKFISPE 327 (460)
Q Consensus 262 ~k~~~~~lq~~YPerL~~i~IIN~P~~f~~~w~lvkpfL~~~t~~KI~~~~~~~~~~~L~e~Id~d 327 (460)
+.....-+-.+|---++.+|+|.+-|+..++|+++|||++.+..+||+-+.. .++|.++|.-+
T Consensus 151 l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~---lseL~~~l~l~ 213 (467)
T KOG4406|consen 151 LFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNS---LSELFEALKLN 213 (467)
T ss_pred HHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeeh---HHHHHHhhhhh
Confidence 4455555556788899999999999999999999999999999999999874 88888877533
No 11
>KOG3287 consensus Membrane trafficking protein, emp24/gp25L/p24 family [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.96 E-value=0.0081 Score=55.19 Aligned_cols=103 Identities=20% Similarity=0.383 Sum_probs=62.6
Q ss_pred CCcccCCCccCCCCCCCCCccchhhhhccCCcceeeeeecCCCceEEEEEEee-c---ceeEEEEEEEeCCCCCeEEEEe
Q 045317 328 NLPVEYGGLYRENDDFFPEDRTSELIVRKNTAGSVRIPVAETGVTMMWDLTVL-G---WDVSYKEEFIPDDEGSYRVLLQ 403 (460)
Q Consensus 328 ~LP~~yGG~~~~~d~~~~~d~~~~~~V~~g~~~~v~~~v~~~g~~l~W~f~t~-~---~DI~Fgi~~~~~~~~~~~~v~~ 403 (460)
.+|.+.+|...+. +..+..-++.|+||++.-.-=.|..+ .++.-++.+- | .||+|.+. .+.| ..+++
T Consensus 17 ~~~~~l~ga~g~~---pa~d~dftv~ipAGk~eCf~Q~v~~~-~tle~eyQVi~G~GDl~i~Ftl~---~P~G--~~lv~ 87 (236)
T KOG3287|consen 17 SPPVELLGAAGDQ---PADDYDFTVMIPAGKTECFYQPVPQG-ATLEVEYQVIDGAGDLDIDFTLL---NPAG--EVLVS 87 (236)
T ss_pred ccceecccccCCC---cccccceEEEecCCCceeeeeeccCC-eEEEEEEEEEecCCccceeeEEe---CCCc--cEEee
Confidence 3455665543332 11222335667777776665555544 4577666664 2 48999985 2333 23444
Q ss_pred ccccccCCCCccccc--EEEeCcCcEEEEEEECCC--ccceEEEEEEE
Q 045317 404 SEKEKKGGEGESMRN--SFYISEPGKIVITIDNVT--LKNKRVYYRFK 447 (460)
Q Consensus 404 ~~~~~~~~~~~~~~g--~~~~~~~G~y~l~fdNs~--~~~K~v~Y~i~ 447 (460)
-.+ . +.| .+...++|.|.+-||||| +.+|.|.+.+-
T Consensus 88 ~q~--k------~dg~ht~e~~e~GdY~~CfDNsFS~fs~K~Vffeli 127 (236)
T KOG3287|consen 88 DQR--K------VDGVHTVEVTETGDYQVCFDNSFSTFSRKLVFFELI 127 (236)
T ss_pred ccc--c------cCceeEeeccCCcceEEEEcCccccccceEEEEEEE
Confidence 433 1 113 345568999999999999 68899988883
No 12
>KOG1692 consensus Putative cargo transport protein EMP24 (p24 protein family) [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.53 E-value=0.55 Score=42.70 Aligned_cols=33 Identities=18% Similarity=0.317 Sum_probs=30.0
Q ss_pred EEEeCcCcEEEEEEECCC--ccceEEEEEEEEecC
Q 045317 419 SFYISEPGKIVITIDNVT--LKNKRVYYRFKTKPA 451 (460)
Q Consensus 419 ~~~~~~~G~y~l~fdNs~--~~~K~v~Y~i~v~~~ 451 (460)
+|+++.+|+|.+-|+|.. ..+|.|.+.|++-.+
T Consensus 81 tF~a~~~G~Y~fCF~N~~s~mtpk~V~F~ihvg~~ 115 (201)
T KOG1692|consen 81 TFTAPKKGTYTFCFSNKMSTMTPKTVMFTIHVGHA 115 (201)
T ss_pred EEEecCCceEEEEecCCCCCCCceEEEEEEEEeec
Confidence 789999999999999999 499999999998644
No 13
>KOG1693 consensus emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.46 E-value=1.2 Score=40.81 Aligned_cols=71 Identities=24% Similarity=0.364 Sum_probs=42.4
Q ss_pred CCCceEEEEEEee---cceeEEEEEEEeCCCCCeEEEEeccccccCCCCcccccEEEeCcCcEEEEEEECCC--ccceEE
Q 045317 368 ETGVTMMWDLTVL---GWDVSYKEEFIPDDEGSYRVLLQSEKEKKGGEGESMRNSFYISEPGKIVITIDNVT--LKNKRV 442 (460)
Q Consensus 368 ~~g~~l~W~f~t~---~~DI~Fgi~~~~~~~~~~~~v~~~~~~~~~~~~~~~~g~~~~~~~G~y~l~fdNs~--~~~K~v 442 (460)
..++++..+|.+. +.||.|-|. +++|+ +|+.... +..... .|++...|+|.+-|+|.| +..|.+
T Consensus 42 ~~~~~~~~~fqV~tGG~fDVD~~I~---aPdgk--vI~~~~k-k~~~~~-----~f~ae~~G~Y~fCFsN~fstf~~Kiv 110 (209)
T KOG1693|consen 42 KDDDTTSFEFQVQTGGHFDVDYDIE---APDGK--VIYSEKK-KRYDSF-----LFKAEGKGEYTFCFSNEFSTFSHKIV 110 (209)
T ss_pred cCCceEEEEEEEEeCCceeeEEEEE---CCCCC--EEeeccc-cccccE-----EEEEecceEEEEEecCccccccceEe
Confidence 3344455555554 348888884 34453 3332222 111111 789999999999999999 455555
Q ss_pred EEEEEEe
Q 045317 443 YYRFKTK 449 (460)
Q Consensus 443 ~Y~i~v~ 449 (460)
.-..++.
T Consensus 111 ~~~~q~~ 117 (209)
T KOG1693|consen 111 YMDFQVG 117 (209)
T ss_pred eehhhhc
Confidence 5555555
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=83.88 E-value=0.33 Score=43.68 Aligned_cols=89 Identities=22% Similarity=0.264 Sum_probs=0.0
Q ss_pred hhhccCCcceeeeeecCCCceEEEEEEeecc----eeEEEEEEEeCCCCCeEEEEeccccccCCCCcccccEEEeCcCcE
Q 045317 352 LIVRKNTAGSVRIPVAETGVTMMWDLTVLGW----DVSYKEEFIPDDEGSYRVLLQSEKEKKGGEGESMRNSFYISEPGK 427 (460)
Q Consensus 352 ~~V~~g~~~~v~~~v~~~g~~l~W~f~t~~~----DI~Fgi~~~~~~~~~~~~v~~~~~~~~~~~~~~~~g~~~~~~~G~ 427 (460)
+.|.+|...-+...+.+ |..+...|.+.++ +|.|.|+ .| +++...++.... ..++ + .=++.+.++|.
T Consensus 4 f~l~~g~~~Cf~e~v~~-~~~i~~~y~v~~~~~~~~v~~~i~-~~--~~~~~~i~~~~~--~~~~-~--~f~f~~~~~G~ 74 (183)
T PF01105_consen 4 FELEPGETECFYEEVPK-GTTIRGSYRVTDGGGAYDVDFTIR-DP--DPNGEVIYSKSD--KESE-G--SFSFTAKESGE 74 (183)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEECCCCcEEEEEEcCC-CcEEEEEEEEeeccccceEEEEEE-ec--ccCCceeeeecc--cccC-C--cEEEEeccCCC
Confidence 45667777777777766 5677777777533 4666664 12 222233332211 1011 1 11678899999
Q ss_pred EEEEEECCCc--cc-eEEEEEEEEe
Q 045317 428 IVITIDNVTL--KN-KRVYYRFKTK 449 (460)
Q Consensus 428 y~l~fdNs~~--~~-K~v~Y~i~v~ 449 (460)
|.+.|+|+.. +. +.|.+.+.+.
T Consensus 75 y~iCf~n~~~~~~~~~~v~~~~~~~ 99 (183)
T PF01105_consen 75 YQICFDNSSSSFSPSKRVSFDIDVG 99 (183)
T ss_dssp -------------------------
T ss_pred EEEEEEcCCCCccccEEEEEEEEEe
Confidence 9999999983 34 8888888775
No 15
>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=76.76 E-value=6.8 Score=34.01 Aligned_cols=20 Identities=15% Similarity=0.287 Sum_probs=17.6
Q ss_pred cccccEEEeCcCcEEEEEEE
Q 045317 414 ESMRNSFYISEPGKIVITID 433 (460)
Q Consensus 414 ~~~~g~~~~~~~G~y~l~fd 433 (460)
-+..|.|+|+.||.|.+.|.
T Consensus 39 d~~TG~Ftcpv~GvY~F~f~ 58 (135)
T smart00110 39 DPRTGKFTCPVPGVYYFSYH 58 (135)
T ss_pred cCCCCEEECeeceEEEEEEE
Confidence 34579999999999999997
No 16
>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=60.65 E-value=13 Score=25.19 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=20.6
Q ss_pred CHHHHHHHHHhcCCCHHHHHHHHH
Q 045317 127 TDIVLLKFLKAKDYKVHDAFEMLR 150 (460)
Q Consensus 127 ~D~~LLRFLrarkfdv~kA~~~l~ 150 (460)
++.....||.+.+||++.|+..+-
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 668899999999999999998864
No 17
>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=57.72 E-value=32 Score=27.10 Aligned_cols=86 Identities=19% Similarity=0.262 Sum_probs=49.6
Q ss_pred hhhccCCcceeeeeecCCCceEEEEEEeecceeEE-EEEEEeCCCCCeEEEEeccccccCCCCcccccEEEeCcCcEEEE
Q 045317 352 LIVRKNTAGSVRIPVAETGVTMMWDLTVLGWDVSY-KEEFIPDDEGSYRVLLQSEKEKKGGEGESMRNSFYISEPGKIVI 430 (460)
Q Consensus 352 ~~V~~g~~~~v~~~v~~~g~~l~W~f~t~~~DI~F-gi~~~~~~~~~~~~v~~~~~~~~~~~~~~~~g~~~~~~~G~y~l 430 (460)
++++.|+...|.++-... +=..|.+..+..-+.+ +-.|.+...+.. ++-..+...=.|.+.+||+..|
T Consensus 1 I~v~~g~~~~I~L~~nps-tGY~W~~~~~~~~l~l~~~~~~~~~~~~~----------~vG~~g~~~f~f~a~~~G~~~i 69 (92)
T PF09394_consen 1 ITVKVGDTFEIELPENPS-TGYSWSLSSDSDGLQLVSEEYIPDNSPSG----------LVGAPGTRTFTFKALKPGTTTI 69 (92)
T ss_dssp -EEETTSEEEEEEEEBCC-GTBEEEECTSTTTEEEEEEEEEESSTSST----------SSTSSEEEEEEEEESSSEEEEE
T ss_pred CeecCCCEEEEEECCCCC-CCeEEEEecCCCeEEEcCCcEEeCCCCcC----------CCCCCcEEEEEEEEecCeeEEE
Confidence 457888888888886533 4489999773333333 222332211100 1100011112688999999999
Q ss_pred EEECCC-c----cceEEEEEEEE
Q 045317 431 TIDNVT-L----KNKRVYYRFKT 448 (460)
Q Consensus 431 ~fdNs~-~----~~K~v~Y~i~v 448 (460)
.|.... + ..+++.|.|.|
T Consensus 70 ~~~y~r~we~~~~~~~~~~~V~V 92 (92)
T PF09394_consen 70 KFEYRRPWEKGSPIKTFTITVTV 92 (92)
T ss_dssp EEEEEBTTTBSTTSEEEEEEEEE
T ss_pred EEEEECcCCCCCccEEEEEEEEC
Confidence 998766 1 24677777765
No 18
>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=56.19 E-value=9.7 Score=32.26 Aligned_cols=21 Identities=14% Similarity=0.230 Sum_probs=15.4
Q ss_pred ccccEEEeCcCcEEEEEEECC
Q 045317 415 SMRNSFYISEPGKIVITIDNV 435 (460)
Q Consensus 415 ~~~g~~~~~~~G~y~l~fdNs 435 (460)
+..|.|+|+.+|+|.+.|.=.
T Consensus 34 ~~tG~Ftap~~G~Y~F~~~~~ 54 (127)
T PF00386_consen 34 PSTGIFTAPVPGVYFFSFTIM 54 (127)
T ss_dssp TTTTEEE-SS-EEEEEEEEEE
T ss_pred eecCEEecCCCCEEEEEEEEe
Confidence 446899999999999988633
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=54.86 E-value=28 Score=23.35 Aligned_cols=27 Identities=22% Similarity=0.220 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 045317 125 EGTDIVLLKFLKAKDYKVHDAFEMLRK 151 (460)
Q Consensus 125 ~~~D~~LLRFLrarkfdv~kA~~~l~~ 151 (460)
..+...+.+-|+++++|++.|..+|..
T Consensus 14 ~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 14 DLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp SS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 578889999999999999999998864
No 20
>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=47.01 E-value=33 Score=23.07 Aligned_cols=26 Identities=19% Similarity=0.173 Sum_probs=23.4
Q ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHH
Q 045317 125 EGTDIVLLKFLKAKDYKVHDAFEMLR 150 (460)
Q Consensus 125 ~~~D~~LLRFLrarkfdv~kA~~~l~ 150 (460)
..++..+.+.|++++.|++.|...|.
T Consensus 15 ~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 15 NLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 47888999999999999999998875
No 21
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=46.27 E-value=7.9 Score=30.24 Aligned_cols=52 Identities=12% Similarity=0.072 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhccccCCCCCCCCChhHHHHHhhhhhhhhhccCCCCCCCCCCC-CHHHHHHHHHhcCC
Q 045317 62 IDMKFKKKKALLEFRCMVEDAVLGNYLLGKPPRSHSPKEAALARSQLKKITLWGVPLLPSKAHEG-TDIVLLKFLKAKDY 140 (460)
Q Consensus 62 ~~ls~~q~~aL~elr~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~lp~~~~~~-~D~~LLRFLrarkf 140 (460)
..||+.+++.|.+.-..+++++ .. .. ++..|-.=|..+.|
T Consensus 18 ~~Ls~ed~~~L~~~l~~vr~~L------------------------------------g~---~~~~e~~i~eal~~~~f 58 (79)
T PF08938_consen 18 DELSPEDQAQLYSCLPQVREVL------------------------------------GD---YVPPEEQIKEALWHYYF 58 (79)
T ss_dssp HH-TCHHHHHHCHHCCCHHHHC------------------------------------CC---CC--CCHHHHHHHHTTT
T ss_pred ccCCHHHHHHHHHHHHHHHHHH------------------------------------cc---cCCCHHHHHHHHHHHcC
Confidence 4678888877777777777663 11 22 66788899999999
Q ss_pred CHHHHHHHHHHH
Q 045317 141 KVHDAFEMLRKT 152 (460)
Q Consensus 141 dv~kA~~~l~~~ 152 (460)
||++|+..|++.
T Consensus 59 DvekAl~~Ll~~ 70 (79)
T PF08938_consen 59 DVEKALDYLLSK 70 (79)
T ss_dssp -CCHHHHHHHHC
T ss_pred CHHHHHHHHHHh
Confidence 999999988753
No 22
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=41.39 E-value=1e+02 Score=23.40 Aligned_cols=47 Identities=11% Similarity=0.068 Sum_probs=31.1
Q ss_pred EEEEeCCCCCCCCchhHHHHHHHHHHHHhhhcc--cccceEEEEeCChhHHHH
Q 045317 242 VQIIDLKNSKPPDIKKFRVVSKKTVMMLQDNYP--ELMHRNIIINVPFWYYAF 292 (460)
Q Consensus 242 v~I~Dl~g~s~~~~~~~~~~~k~~~~~lq~~YP--erL~~i~IIN~P~~f~~~ 292 (460)
.+++|+.|+.... .+++-.++..+...|| +.-.++.++|+......+
T Consensus 19 ~V~lDF~gv~~~~----ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~ 67 (74)
T PF14213_consen 19 KVVLDFEGVESIT----SSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEM 67 (74)
T ss_pred eEEEECCCccccc----HHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHH
Confidence 3889999995432 2456666666666666 455788888886655444
No 23
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=41.01 E-value=51 Score=31.11 Aligned_cols=104 Identities=18% Similarity=0.237 Sum_probs=61.6
Q ss_pred HHHHHHHHHHHhcc---CCCCcceeEEEEeCCCC-CCCCchhHHHHHHHHHHHHhhhcccccceEEEEeCCh------hH
Q 045317 220 EVKFMEKGIKELNF---KPGGANSIVQIIDLKNS-KPPDIKKFRVVSKKTVMMLQDNYPELMHRNIIINVPF------WY 289 (460)
Q Consensus 220 ~~~~~E~~~~~~~~---~~~~v~~~v~I~Dl~g~-s~~~~~~~~~~~k~~~~~lq~~YPerL~~i~IIN~P~------~f 289 (460)
++|+||..+..++. ..|..+.--+|+||-|- .+ ..|+ .++++++.-++. .--++..+|++..++ +|
T Consensus 75 Lv~cmEyl~~NldwL~~~~Gd~eddylifDcPGQIEL--ytH~-pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~Kfi 150 (273)
T KOG1534|consen 75 LVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQIEL--YTHL-PVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFI 150 (273)
T ss_pred chhHHHHHHHHHHHHHhhccCccCCEEEEeCCCeeEE--eecC-hhHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHH
Confidence 46677777664432 34567788999999873 11 1232 467777777776 344666777776665 45
Q ss_pred HHHHHHHhhcCCh-----hhcccEEEeCCccchHhHhccCCCCC
Q 045317 290 YAFHTVASKFLSP-----RCKRKFVFARPAKVTKTLLKFISPEN 328 (460)
Q Consensus 290 ~~~w~lvkpfL~~-----~t~~KI~~~~~~~~~~~L~e~Id~d~ 328 (460)
+.++..+..++.= ...+|.-++++ ..++.|.++.+|+.
T Consensus 151 SG~lsAlsAMi~lE~P~INvlsKMDLlk~-~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 151 SGCLSALSAMISLEVPHINVLSKMDLLKD-KNKKELERFLNPDE 193 (273)
T ss_pred HHHHHHHHHHHHhcCcchhhhhHHHHhhh-hhHHHHHHhcCCch
Confidence 5555444433322 23555555653 34677777777653
No 24
>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=34.08 E-value=2.2e+02 Score=23.41 Aligned_cols=82 Identities=11% Similarity=0.091 Sum_probs=48.7
Q ss_pred hhhhccCCcceeeeeecC-CCce-EEEEEEee----cceeEEEEEEEeCCCCCeEEEEeccccccCCCCcccccEEEeCc
Q 045317 351 ELIVRKNTAGSVRIPVAE-TGVT-MMWDLTVL----GWDVSYKEEFIPDDEGSYRVLLQSEKEKKGGEGESMRNSFYISE 424 (460)
Q Consensus 351 ~~~V~~g~~~~v~~~v~~-~g~~-l~W~f~t~----~~DI~Fgi~~~~~~~~~~~~v~~~~~~~~~~~~~~~~g~~~~~~ 424 (460)
.+.|..|...++.+.|++ |.-. ..|.+... ..|-.+ ......+..+..++...| ++..+
T Consensus 12 ~~~v~~gE~~~L~V~ieAYP~p~~~~W~~~~~~l~~~~~~~~--~~~~~~~~rY~S~L~L~R-------------lk~~E 76 (101)
T cd05860 12 TIFVNAGENLDLIVEYEAYPKPEHQQWIYMNRTLTNTSDHYV--KSRNESNNRYVSELHLTR-------------LKGTE 76 (101)
T ss_pred eEEEECCCCEEEEEEEEeCCCCeeeEEEcCCcccCcccccee--EEeccCceEEEEEEEEee-------------cChhh
Confidence 466888999999999864 4333 89997732 223112 111112233555554444 24567
Q ss_pred CcEEEEEEECCCccceEEEEEEEE
Q 045317 425 PGKIVITIDNVTLKNKRVYYRFKT 448 (460)
Q Consensus 425 ~G~y~l~fdNs~~~~K~v~Y~i~v 448 (460)
-|.|++...|+-- ++.+.+.++|
T Consensus 77 ~G~YTf~a~N~~~-~~s~tF~l~v 99 (101)
T cd05860 77 GGTYTFLVSNSDA-SASVTFNVYV 99 (101)
T ss_pred CcEEEEEEECCCC-eEEEEEEEEE
Confidence 8999999999972 2345555554
No 25
>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=32.96 E-value=75 Score=20.56 Aligned_cols=24 Identities=21% Similarity=0.062 Sum_probs=19.2
Q ss_pred CCHHHHHHHHHhcCCCHHHHHHHH
Q 045317 126 GTDIVLLKFLKAKDYKVHDAFEML 149 (460)
Q Consensus 126 ~~D~~LLRFLrarkfdv~kA~~~l 149 (460)
.+.....+-|+++++|+++|...|
T Consensus 14 f~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 14 FSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp S-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCHHHHHHhC
Confidence 344578999999999999998764
No 26
>TIGR03769 P_ac_wall_RPT actinobacterial surface-anchored protein domain. This model describes a repeat domain that one to three times in Actinobacterial proteins, some of which have LPXTG-type sortase recognition motifs for covalent attachment to the Gram-positive cell wall. Where it occurs with duplication in an LPXTG-anchored protein, it tends to be adjacent to the substrate-binding protein of the gene trio of an ABC transporter system, where that substrate-binding protein has a single copy of this same domain. This arrangement suggests a substrate-binding relay system, with the LPXTG protein acting as a substrate receptor.
Probab=32.35 E-value=37 Score=22.94 Aligned_cols=17 Identities=18% Similarity=0.583 Sum_probs=13.8
Q ss_pred EEEeCcCcEEEEEEECC
Q 045317 419 SFYISEPGKIVITIDNV 435 (460)
Q Consensus 419 ~~~~~~~G~y~l~fdNs 435 (460)
...-.+||+|.|.|.=+
T Consensus 6 nW~FT~PG~Y~l~~~a~ 22 (41)
T TIGR03769 6 NWVFTKPGTYTLTVQAT 22 (41)
T ss_pred ceeeCCCeEEEEEEEEE
Confidence 56778999999999644
No 27
>PF01108 Tissue_fac: Tissue factor; PDB: 3OG4_B 3OG6_B 1FYH_E 1FG9_D 1JRH_I 3DGC_R 3DLQ_R 1LQS_R 1Y6M_R 1J7V_R ....
Probab=30.95 E-value=1.8e+02 Score=23.66 Aligned_cols=53 Identities=13% Similarity=0.186 Sum_probs=34.8
Q ss_pred eeeeeecCCCceEEEEE-EeecceeEEEEEEEeCCCCCeEEE-----EeccccccCCCC
Q 045317 361 SVRIPVAETGVTMMWDL-TVLGWDVSYKEEFIPDDEGSYRVL-----LQSEKEKKGGEG 413 (460)
Q Consensus 361 ~v~~~v~~~g~~l~W~f-~t~~~DI~Fgi~~~~~~~~~~~~v-----~~~~~~~~~~~~ 413 (460)
.|.+....-..+|+|+- .....++.|.|.|+...++++..+ +....|.+..+.
T Consensus 27 nv~~~s~nf~~iL~W~~~~~~~~~~~ytVq~~~~~~~~W~~v~~C~~i~~~~Cdlt~~~ 85 (107)
T PF01108_consen 27 NVTVDSVNFKHILRWDPGPGSPPNVTYTVQYKKYGSSSWKDVPGCQNITETSCDLTDET 85 (107)
T ss_dssp EEEEEEETTEEEEEEEESTTSSSTEEEEEEEEESSTSCEEEECCEEEESSSEEECTTCC
T ss_pred eeEEEEECCceEEEeCCCCCCCCCeEEEEEEEecCCcceeeccceecccccceeCcchh
Confidence 34444444457899999 334679999999986666777766 334446664433
No 28
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=30.86 E-value=83 Score=20.10 Aligned_cols=24 Identities=33% Similarity=0.193 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHhcCCCHHHHHHHH
Q 045317 126 GTDIVLLKFLKAKDYKVHDAFEML 149 (460)
Q Consensus 126 ~~D~~LLRFLrarkfdv~kA~~~l 149 (460)
.+.....+-|++.++|+++|...|
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 455689999999999999998764
No 29
>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=29.61 E-value=90 Score=20.03 Aligned_cols=25 Identities=28% Similarity=0.137 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHhcCCCHHHHHHHHH
Q 045317 126 GTDIVLLKFLKAKDYKVHDAFEMLR 150 (460)
Q Consensus 126 ~~D~~LLRFLrarkfdv~kA~~~l~ 150 (460)
.+.....+-|++.++|+++|...|.
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 3567889999999999999987763
No 30
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=28.90 E-value=2.5e+02 Score=20.93 Aligned_cols=27 Identities=7% Similarity=0.047 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHhcCCCHHHHHHHHHHH
Q 045317 126 GTDIVLLKFLKAKDYKVHDAFEMLRKT 152 (460)
Q Consensus 126 ~~D~~LLRFLrarkfdv~kA~~~l~~~ 152 (460)
..-.+..++|...+||.++|.+.+...
T Consensus 25 mn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 25 MNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 456799999999999999999998753
No 31
>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=28.56 E-value=1.2e+02 Score=25.92 Aligned_cols=60 Identities=13% Similarity=0.130 Sum_probs=42.1
Q ss_pred HHHHHHHHHhhhcccc-cc-eEEEEeCChhHHHHHHHH-----hhcCChhhcccEEEeCCccchHhHhcc
Q 045317 261 VSKKTVMMLQDNYPEL-MH-RNIIINVPFWYYAFHTVA-----SKFLSPRCKRKFVFARPAKVTKTLLKF 323 (460)
Q Consensus 261 ~~k~~~~~lq~~YPer-L~-~i~IIN~P~~f~~~w~lv-----kpfL~~~t~~KI~~~~~~~~~~~L~e~ 323 (460)
.+.+++.++.-.+=.. -+ .++++|..-++.-++.++ ..|+++.....+.++.+ .+++.++
T Consensus 66 Tl~El~~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~---~~e~~~~ 132 (133)
T PF03641_consen 66 TLDELFEALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD---PEEALEY 132 (133)
T ss_dssp HHHHHHHHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS---HHHHHHH
T ss_pred hHHHHHHHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC---HHHHHhh
Confidence 4455555555333332 33 699999887778787877 57899999999999975 6666654
No 32
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=27.17 E-value=39 Score=32.55 Aligned_cols=27 Identities=22% Similarity=0.188 Sum_probs=22.8
Q ss_pred ceEEEEeCChhHHHHHHHHhhcCChhh
Q 045317 278 HRNIIINVPFWYYAFHTVASKFLSPRC 304 (460)
Q Consensus 278 ~~i~IIN~P~~f~~~w~lvkpfL~~~t 304 (460)
..++|||+||-+.--...+-|+|....
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L 263 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLL 263 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHh
Confidence 469999999999998888888876654
No 33
>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=24.56 E-value=55 Score=25.42 Aligned_cols=24 Identities=13% Similarity=0.110 Sum_probs=19.1
Q ss_pred ccCCCCCHHHHHHHHHHHHHHHHH
Q 045317 59 AAIIDMKFKKKKALLEFRCMVEDA 82 (460)
Q Consensus 59 ~~~~~ls~~q~~aL~elr~~l~~~ 82 (460)
.++.+||++|++.|++|.+.+..-
T Consensus 35 ~~~R~Lt~~E~~eL~~y~~~v~~y 58 (76)
T PF06394_consen 35 KYARDLTPDEQQELKTYQKKVAAY 58 (76)
T ss_dssp CEEEE--HHHHHHHHHHHHHHHHH
T ss_pred EeeccCCHHHHHHHHHHHHHHHHH
Confidence 467899999999999999988874
No 34
>PF04838 Baculo_LEF5: Baculoviridae late expression factor 5 ; InterPro: IPR006923 This is a family of Baculoviridae late expression factor 5, required for late and very late gene expression.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=22.71 E-value=57 Score=28.64 Aligned_cols=49 Identities=14% Similarity=0.192 Sum_probs=42.1
Q ss_pred HHHHHHHHHhhhcccccc--eEEEEeCChhHHHHHHHHhhcCCh--hhcccEEE
Q 045317 261 VSKKTVMMLQDNYPELMH--RNIIINVPFWYYAFHTVASKFLSP--RCKRKFVF 310 (460)
Q Consensus 261 ~~k~~~~~lq~~YPerL~--~i~IIN~P~~f~~~w~lvkpfL~~--~t~~KI~~ 310 (460)
-.+.++..+-.+||.-++ ..-+.|..-.|.++|+-| |-++. +-|+.|.+
T Consensus 16 ~y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRL 68 (159)
T PF04838_consen 16 DYKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRL 68 (159)
T ss_pred CHHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhh
Confidence 346788999999999998 899999999999999987 77787 66777766
No 35
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=20.98 E-value=52 Score=31.66 Aligned_cols=29 Identities=17% Similarity=0.124 Sum_probs=20.6
Q ss_pred ceEEEEeCChhHHHHHHHHhhcCChhhcc
Q 045317 278 HRNIIINVPFWYYAFHTVASKFLSPRCKR 306 (460)
Q Consensus 278 ~~i~IIN~P~~f~~~w~lvkpfL~~~t~~ 306 (460)
..++|||+||-+....+-+-|+|.+...+
T Consensus 206 SGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 206 SGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp EEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred ceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 45999999999988888777776665443
Done!