Query 011383
Match_columns 487
No_of_seqs 315 out of 1439
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 00:44:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011383.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011383hhsearch_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 2.2E-38 4.8E-43 314.7 17.0 199 156-371 44-244 (324)
2 KOG1471 Phosphatidylinositol t 100.0 6.3E-38 1.4E-42 319.0 19.7 227 139-373 24-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 1.6E-29 3.4E-34 230.6 11.5 152 208-369 7-159 (159)
4 smart00516 SEC14 Domain in hom 99.9 7.8E-26 1.7E-30 205.9 13.7 144 214-370 14-157 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 2.1E-24 4.6E-29 194.2 13.5 147 210-369 11-157 (157)
6 PF13897 GOLD_2: Golgi-dynamic 99.9 2.2E-21 4.8E-26 168.7 11.1 92 389-481 1-134 (136)
7 KOG3878 Protein involved in ma 99.5 6.7E-15 1.5E-19 144.3 6.6 96 386-481 323-466 (469)
8 PF13716 CRAL_TRIO_2: Divergen 99.4 1.9E-13 4.1E-18 124.0 6.1 142 209-372 3-146 (149)
9 PF03765 CRAL_TRIO_N: CRAL/TRI 98.3 6.9E-07 1.5E-11 67.4 4.2 30 156-185 26-55 (55)
10 KOG4406 CDC42 Rho GTPase-activ 97.9 5.2E-05 1.1E-09 78.1 9.8 125 215-360 89-213 (467)
11 KOG3287 Membrane trafficking p 96.7 0.017 3.7E-07 54.9 10.7 82 386-480 37-126 (236)
12 KOG1693 emp24/gp25L/p24 family 95.3 0.11 2.4E-06 49.0 9.0 73 401-483 40-117 (209)
13 KOG1692 Putative cargo transpo 94.9 0.12 2.7E-06 48.4 7.9 73 391-483 39-113 (201)
14 PF01105 EMP24_GP25L: emp24/gp 83.9 0.33 7.1E-06 44.5 0.0 88 387-483 4-99 (183)
15 PF09394 Inhibitor_I42: Chagas 72.1 47 0.001 26.9 9.6 86 387-482 1-92 (92)
16 smart00110 C1Q Complement comp 55.4 11 0.00024 33.7 2.9 24 444-467 35-58 (135)
17 PF14555 UBA_4: UBA-like domai 52.2 20 0.00044 25.2 3.3 24 160-183 14-37 (43)
18 PF00386 C1q: C1q domain; Int 49.5 14 0.0003 32.2 2.5 24 446-469 31-54 (127)
19 PF02845 CUE: CUE domain; Int 43.7 42 0.00091 23.4 3.8 26 159-184 15-40 (42)
20 smart00546 CUE Domain that may 40.4 46 0.00099 23.2 3.6 25 159-183 16-40 (43)
21 PF14213 DUF4325: Domain of un 39.3 75 0.0016 25.0 5.1 46 276-325 20-67 (74)
22 KOG1534 Putative transcription 31.7 1.1E+02 0.0024 30.0 5.6 105 253-361 75-193 (273)
23 TIGR02364 dha_pts dihydroxyace 29.5 2.6E+02 0.0056 24.6 7.4 49 272-331 60-108 (125)
24 COG4499 Predicted membrane pro 29.5 77 0.0017 33.4 4.5 41 32-73 327-367 (434)
25 PF11964 SpoIIAA-like: SpoIIAA 28.7 1.6E+02 0.0035 24.2 5.8 73 247-332 14-87 (109)
26 PF06394 Pepsin-I3: Pepsin inh 24.6 78 0.0017 25.6 2.8 25 38-62 34-58 (76)
27 TIGR03769 P_ac_wall_RPT actino 23.4 79 0.0017 22.3 2.4 18 452-469 5-22 (41)
28 PRK14484 phosphotransferase ma 21.6 2.4E+02 0.0052 24.9 5.6 47 272-331 58-104 (124)
29 PF03641 Lysine_decarbox: Poss 20.7 1.9E+02 0.0041 25.5 4.9 43 312-357 86-133 (133)
30 PF04151 PPC: Bacterial pre-pe 20.4 3.9E+02 0.0085 20.3 7.3 19 449-467 51-69 (70)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=2.2e-38 Score=314.73 Aligned_cols=199 Identities=30% Similarity=0.529 Sum_probs=175.0
Q ss_pred CCCCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHhCCCCC-cccchhhhhh-hcceeecccCCCCCeEEEEeccccCch
Q 011383 156 GAEGIDVILLKFLRAREFKVNDALEMLKNTLQWRKGNKIDS-ILDEDLEVDL-SSAAYMNGVDREGHPVCYNIYGVFESD 233 (487)
Q Consensus 156 ~~~~~D~~LLRFLrAr~fdv~~A~~~L~~~l~WRk~~~id~-i~~~~~~~el-~~~~~~~G~Dk~GrPV~~~~~g~~d~~ 233 (487)
..+++|.++|||||||+|||.+|.+||.++|.||+.+++.. +..+++..++ .|++|+.|+|++||||+|+++....
T Consensus 44 ~~~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G~D~~gRPVl~~~~~~~~-- 121 (324)
T KOG1470|consen 44 SKWCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILGHDKDGRPVLYLRPRPHR-- 121 (324)
T ss_pred HhcCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEecccCCCCeEEEEecCCCC--
Confidence 45679999999999999999999999999999999999988 6656676666 6899999999999999999654321
Q ss_pred hhhhhhcCChhhHHHHHHHHHHHHHHHHHhhcCCCCCeeeeEEEEeCCCCCccchhhHHHHHHHHHHHhcccccccccee
Q 011383 234 ELYQKTFGTEEKRGQFLRWRLRLMEQGIQKLDFKPGGISSLLQINDLKNAPVLAKKELRVATKQAVDLLQNNYPEFVARN 313 (487)
Q Consensus 234 ~l~~~~~~~e~~~~~~lr~~i~~~E~~l~~l~~~~~~i~~iv~IiDl~g~s~~~~~~l~~~~k~ii~llq~~YPE~L~~i 313 (487)
+++ .+...+.|+.+|+||.++..| +.++.++++|+|++|+++. +.++ ...+.++++||+||||||+..
T Consensus 122 ---qn~----~t~~~~~r~~Vy~mE~Ai~~l---p~~qe~~~~L~D~~~fs~s-N~d~-~~~k~~~~~lq~hYPErLg~a 189 (324)
T KOG1470|consen 122 ---QNT----KTQKELERLLVYTLENAILFL---PPGQEQFVWLFDLTGFSMS-NPDI-KFLKELLHILQDHYPERLGKA 189 (324)
T ss_pred ---CCC----CCHHHHHHHHHHHHHHHHHhC---CCCcceEEEEEecccCccc-CCCc-HHHHHHHHHHHHhChHHhhhh
Confidence 121 346889999999999999776 6788999999999999954 4444 688999999999999999999
Q ss_pred EEEeCchHHHHHHHHhcccCChhhhcceEEeCCccchHHHhccCCCCCcccccCCccc
Q 011383 314 IIINAPFWYYALNALISPFLTQRTKSKFVVARPAKVTETLLKYIPAEELPVQYGGFKR 371 (487)
Q Consensus 314 ~IINaP~~f~~lw~ivkpfL~~~Tr~KI~~~~~~~~~e~L~k~Id~e~LP~~yGG~~~ 371 (487)
+|+|+||+|..+|++++|||++.|++||+|..+ .+.|.+|||+++||..|||...
T Consensus 190 ~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~---~~~l~~~~d~~~l~s~~GG~~~ 244 (324)
T KOG1470|consen 190 LLVNAPWIFQPFWKIIKPFLDPKTASKVKFVEP---KDDLSEYFDESQLPSLFGGKLL 244 (324)
T ss_pred hhcCChHHHHHHHHHhhhccChhhhceeEEecC---hhHHHhhCCccccchhhCCCcc
Confidence 999999999999999999999999999999986 4559999999999999999654
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=6.3e-38 Score=318.96 Aligned_cols=227 Identities=36% Similarity=0.557 Sum_probs=192.9
Q ss_pred cchhhhh-hhcCCCCCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHhCCCCCcccc-hhhhhhhc--ceeecc
Q 011383 139 EVDKDIA-LWGVPLLPSKGAEGIDVILLKFLRAREFKVNDALEMLKNTLQWRKGNKIDSILDE-DLEVDLSS--AAYMNG 214 (487)
Q Consensus 139 ~~~~~~~-~wg~~l~p~~~~~~~D~~LLRFLrAr~fdv~~A~~~L~~~l~WRk~~~id~i~~~-~~~~el~~--~~~~~G 214 (487)
+.+..++ +|+.+.++. ...+|.+||||||||+||+++|.+||.+++.||+.+++|.+... ....++.+ ...++|
T Consensus 24 ~~i~~lr~~~~~~~l~~--~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~~~~~~~~ 101 (317)
T KOG1471|consen 24 AVIAQLRWLLQKPHLPN--KYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKYYPQGLHG 101 (317)
T ss_pred HHHHHHHHHhhccCCCC--CCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhhccccccc
Confidence 4566776 889998853 57899999999999999999999999999999999999998865 22234433 456889
Q ss_pred cCCCCCeEEEEeccccCchhhhhhhcCChhhHHHHHHHHHHHHHHHHHhh-----cCCCCCeeeeEEEEeCCCCCccchh
Q 011383 215 VDREGHPVCYNIYGVFESDELYQKTFGTEEKRGQFLRWRLRLMEQGIQKL-----DFKPGGISSLLQINDLKNAPVLAKK 289 (487)
Q Consensus 215 ~Dk~GrPV~~~~~g~~d~~~l~~~~~~~e~~~~~~lr~~i~~~E~~l~~l-----~~~~~~i~~iv~IiDl~g~s~~~~~ 289 (487)
.|++|+||++.++|..|.++++..+. ..+++++.+..+|+....+ .....+++++++|+||+|+++.++.
T Consensus 102 ~~~~g~~v~~~~~g~~~~~~l~~~~~-----~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~ 176 (317)
T KOG1471|consen 102 VDKEGRPVYIERLGKIDPKGLLKRTG-----SLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLL 176 (317)
T ss_pred cCCCCCEEEEeccCCCCcccceeecc-----HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHH
Confidence 99999999999999999999987643 4777777777777766322 1224579999999999999987764
Q ss_pred h-HHHHHHHHHHHhccccccccceeEEEeCchHHHHHHHHhcccCChhhhcceEEeCCccchHHHhccCCCCCcccccCC
Q 011383 290 E-LRVATKQAVDLLQNNYPEFVARNIIINAPFWYYALNALISPFLTQRTKSKFVVARPAKVTETLLKYIPAEELPVQYGG 368 (487)
Q Consensus 290 ~-l~~~~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw~ivkpfL~~~Tr~KI~~~~~~~~~e~L~k~Id~e~LP~~yGG 368 (487)
. ....++.++.++|+|||++++++||||+|++|+++|++|+|||+++|++||++++ +++.++|+++|++++||.+|||
T Consensus 177 ~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~-~~~~~~L~k~i~~~~LP~~yGG 255 (317)
T KOG1471|consen 177 KPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLH-SKDKESLLKYIPPEVLPEEYGG 255 (317)
T ss_pred HHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecC-CCchhhhhhhCCHhhCccccCC
Confidence 4 3678999999999999999999999999999999999999999999999999554 3689999999999999999999
Q ss_pred cccCC
Q 011383 369 FKREN 373 (487)
Q Consensus 369 ~~~~~ 373 (487)
++.+.
T Consensus 256 ~~~~~ 260 (317)
T KOG1471|consen 256 TCGDL 260 (317)
T ss_pred Ccccc
Confidence 99984
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=1.6e-29 Score=230.55 Aligned_cols=152 Identities=30% Similarity=0.539 Sum_probs=123.8
Q ss_pred cceeecccCCCCCeEEEEeccccCchhhhhhhcCChhhHHHHHHHHHHHHHHHHHhhcCCCCCeeeeEEEEeCCCCCccc
Q 011383 208 SAAYMNGVDREGHPVCYNIYGVFESDELYQKTFGTEEKRGQFLRWRLRLMEQGIQKLDFKPGGISSLLQINDLKNAPVLA 287 (487)
Q Consensus 208 ~~~~~~G~Dk~GrPV~~~~~g~~d~~~l~~~~~~~e~~~~~~lr~~i~~~E~~l~~l~~~~~~i~~iv~IiDl~g~s~~~ 287 (487)
+..+++|+|++||||+|.++|++|+.. .+.++++++.++++|.+++.+.. .+.++++++|+|++|+++.+
T Consensus 7 ~~~~~~g~D~~gr~v~~~~~~~~~~~~---------~~~~~~~~~~~~~~E~~~~~~~~-~~~~~~~~~iiD~~g~~~~~ 76 (159)
T PF00650_consen 7 GPFYLHGRDKDGRPVIYIRLGRFDPKK---------FSPEDVIRFFVYLLERMLKRMPE-GGQVEGIVVIIDLSGFSLSN 76 (159)
T ss_dssp SCEEEEEE-TTS-EEEEEEGTT--HHT---------S-HHHHHHHHHHHHHHHHHTHHH-TSHHH-EEEEEE-TT--HHH
T ss_pred eeEEECCCCCCcCEEEEEEcccCCCCc---------CCHHHHHHHHHHHHHHHHhhhcc-cccceeEEEEEeCCCceEec
Confidence 567899999999999999999988752 23579999999999999976643 46788999999999999643
Q ss_pred hhh-HHHHHHHHHHHhccccccccceeEEEeCchHHHHHHHHhcccCChhhhcceEEeCCccchHHHhccCCCCCccccc
Q 011383 288 KKE-LRVATKQAVDLLQNNYPEFVARNIIINAPFWYYALNALISPFLTQRTKSKFVVARPAKVTETLLKYIPAEELPVQY 366 (487)
Q Consensus 288 ~~~-l~~~~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw~ivkpfL~~~Tr~KI~~~~~~~~~e~L~k~Id~e~LP~~y 366 (487)
... ....++.+++++|++||++++++||||+|++|+++|++++|||+++|++||+++++.++.+.|.++|++++||.+|
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 331 1578899999999999999999999999999999999999999999999999998767778999999999999999
Q ss_pred CCc
Q 011383 367 GGF 369 (487)
Q Consensus 367 GG~ 369 (487)
||+
T Consensus 157 GG~ 159 (159)
T PF00650_consen 157 GGT 159 (159)
T ss_dssp TSS
T ss_pred CCC
Confidence 996
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=7.8e-26 Score=205.92 Aligned_cols=144 Identities=31% Similarity=0.566 Sum_probs=128.1
Q ss_pred ccCCCCCeEEEEeccccCchhhhhhhcCChhhHHHHHHHHHHHHHHHHHhhcCCCCCeeeeEEEEeCCCCCccchhhHHH
Q 011383 214 GVDREGHPVCYNIYGVFESDELYQKTFGTEEKRGQFLRWRLRLMEQGIQKLDFKPGGISSLLQINDLKNAPVLAKKELRV 293 (487)
Q Consensus 214 G~Dk~GrPV~~~~~g~~d~~~l~~~~~~~e~~~~~~lr~~i~~~E~~l~~l~~~~~~i~~iv~IiDl~g~s~~~~~~l~~ 293 (487)
|.|++||||+|.++|+++... .+.+++++++++.+|.+++. ...+..+.++++|+|++|+++.+. . .+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~---------~~~~~~~~~~~~~~e~~~~~-~~~~~~~~~~~~i~D~~~~~~~~~-~-~~ 81 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKS---------VTLEELLRYLVYVLEKILQR-EKKTGGIEGFTVIFDLKGLSMSNP-D-LS 81 (158)
T ss_pred CCCCCcCEEEEEeccccccCc---------CCHHHHHHHHHHHHHHHHHH-HhcCCCeeeEEEEEECCCCCcccc-c-HH
Confidence 699999999999999987532 34689999999999999875 223567899999999999986542 2 47
Q ss_pred HHHHHHHHhccccccccceeEEEeCchHHHHHHHHhcccCChhhhcceEEeCCccchHHHhccCCCCCcccccCCcc
Q 011383 294 ATKQAVDLLQNNYPEFVARNIIINAPFWYYALNALISPFLTQRTKSKFVVARPAKVTETLLKYIPAEELPVQYGGFK 370 (487)
Q Consensus 294 ~~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw~ivkpfL~~~Tr~KI~~~~~~~~~e~L~k~Id~e~LP~~yGG~~ 370 (487)
.++.++.+++++||++++++||||+|+++.++|+++++||++++++||+++++ ++.+.|.++||+++||.+|||++
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 89999999999999999999999999999999999999999999999999985 56899999999999999999986
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=2.1e-24 Score=194.19 Aligned_cols=147 Identities=32% Similarity=0.523 Sum_probs=125.7
Q ss_pred eeecccCCCCCeEEEEeccccCchhhhhhhcCChhhHHHHHHHHHHHHHHHHHhhcCCCCCeeeeEEEEeCCCCCccchh
Q 011383 210 AYMNGVDREGHPVCYNIYGVFESDELYQKTFGTEEKRGQFLRWRLRLMEQGIQKLDFKPGGISSLLQINDLKNAPVLAKK 289 (487)
Q Consensus 210 ~~~~G~Dk~GrPV~~~~~g~~d~~~l~~~~~~~e~~~~~~lr~~i~~~E~~l~~l~~~~~~i~~iv~IiDl~g~s~~~~~ 289 (487)
.+..|.|++||||++.++++.+..... +.++++++.++.+|.+++.+..+ .+++++|+|++|.++.++.
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 445567999999999999976554322 13789999999999998876432 2679999999999965443
Q ss_pred hHHHHHHHHHHHhccccccccceeEEEeCchHHHHHHHHhcccCChhhhcceEEeCCccchHHHhccCCCCCcccccCCc
Q 011383 290 ELRVATKQAVDLLQNNYPEFVARNIIINAPFWYYALNALISPFLTQRTKSKFVVARPAKVTETLLKYIPAEELPVQYGGF 369 (487)
Q Consensus 290 ~l~~~~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw~ivkpfL~~~Tr~KI~~~~~~~~~e~L~k~Id~e~LP~~yGG~ 369 (487)
...+.++.++.+++++||++++++||||+|++|+++|+++++|+++++++||++++++ .+.|.++|++++||.+|||+
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 2347899999999999999999999999999999999999999999999999999853 78999999999999999996
No 6
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=99.86 E-value=2.2e-21 Score=168.70 Aligned_cols=92 Identities=23% Similarity=0.355 Sum_probs=80.6
Q ss_pred ecCCCeEEEEEeecCCCceEEEEEEEcCcceEEEEEEecC---------------C--------C----------C----
Q 011383 389 LKAGSTETIEIQAPEIGTTITWDLTVLGWEVSYKEEFVPT---------------D--------E----------G---- 431 (487)
Q Consensus 389 VkaG~~~~v~i~v~e~gs~l~Wef~t~~~DI~Fgi~~~~~---------------~--------~----------~---- 431 (487)
|++|...+|.++....|..|+|+|.|+++|||||++|.=+ + + |
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 6789999999999999999999999999999999998610 0 0 0
Q ss_pred ---ceEEEeecceecCCCcccccceEEcCcCcEEEEEEEcCCC--CceEEEEEEE
Q 011383 432 ---SYTIIVQKGKKMGSHEGPIRNTFKNNEAGKLVLTIDNASS--KKKRVLYRYK 481 (487)
Q Consensus 432 ---~~~~iv~~~~r~~~~~~p~~gs~~~~~~G~yvL~fDNs~S--~~Kkv~Y~~~ 481 (487)
.+.+| .|..|++||.+++.|++.|+.||+|+|.|||||| |+|+|+|+|-
T Consensus 81 ~~~~~~ev-iPv~R~dsH~~~~~Gs~~c~~~GvYvLkFDNSYS~~rsK~l~Y~V~ 134 (136)
T PF13897_consen 81 SRPEMDEV-IPVYRRDSHLEVEAGSHTCPGPGVYVLKFDNSYSWFRSKKLYYRVY 134 (136)
T ss_pred CCCCeeEE-eEeeeeecCcceeceEEECCCCeEEEEEeeCcceeEEeeEEEEEEE
Confidence 14445 5789999999999999999999999999999999 9999999984
No 7
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.54 E-value=6.7e-15 Score=144.34 Aligned_cols=96 Identities=25% Similarity=0.402 Sum_probs=82.8
Q ss_pred EEEecCCCeEEEEEeecCCCceEEEEEEEcCcceEEEEEEe---c-C-----------CC--------------Cc----
Q 011383 386 EITLKAGSTETIEIQAPEIGTTITWDLTVLGWEVSYKEEFV---P-T-----------DE--------------GS---- 432 (487)
Q Consensus 386 ~v~VkaG~~~~v~i~v~e~gs~l~Wef~t~~~DI~Fgi~~~---~-~-----------~~--------------~~---- 432 (487)
.|+|+.|.+.+|.++..+.|+.|.|+|.|+++||||||+|. | + ++ |+
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 69999999999999999999999999999999999999986 1 1 00 10
Q ss_pred -------------eEEEeecceecCCCcccccceEEcCcCcEEEEEEEcCCC--CceEEEEEEE
Q 011383 433 -------------YTIIVQKGKKMGSHEGPIRNTFKNNEAGKLVLTIDNASS--KKKRVLYRYK 481 (487)
Q Consensus 433 -------------~~~iv~~~~r~~~~~~p~~gs~~~~~~G~yvL~fDNs~S--~~Kkv~Y~~~ 481 (487)
....|.|..|..||.+...||+..+.-|.|.|.|||||| |+|.|.||+-
T Consensus 403 ~gA~~n~~~anKp~~deIvPvYRRdCheEVYaGSH~YPGrGvYLLKFDNSYSlWRsKtlYYRVY 466 (469)
T KOG3878|consen 403 RGAVNNPTAANKPPIDEIVPVYRRDCHEEVYAGSHSYPGRGVYLLKFDNSYSLWRSKTLYYRVY 466 (469)
T ss_pred hhhhcCCCCCCCCCcccccchhhhhhhHHhhcccccCCCCceEEEEecchhhhhcccceEEEEE
Confidence 112345788899999989999999999999999999999 9999999974
No 8
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.42 E-value=1.9e-13 Score=123.97 Aligned_cols=142 Identities=21% Similarity=0.295 Sum_probs=93.2
Q ss_pred ceeecccCCCCCeEEEEeccccCchhhhhhhcCChhhHHHHHHHHHHHHHHHHHhhcCCCCCeeeeEEEEeCCCCCccch
Q 011383 209 AAYMNGVDREGHPVCYNIYGVFESDELYQKTFGTEEKRGQFLRWRLRLMEQGIQKLDFKPGGISSLLQINDLKNAPVLAK 288 (487)
Q Consensus 209 ~~~~~G~Dk~GrPV~~~~~g~~d~~~l~~~~~~~e~~~~~~lr~~i~~~E~~l~~l~~~~~~i~~iv~IiDl~g~s~~~~ 288 (487)
.++..|+|++||||+++...++ +.. ...+.++.|.+..+... . .. .++++|+|+++.+..+.
T Consensus 3 ~~~~gG~d~~g~pV~~~~~~~~-~~~---------~~~~~ll~yl~~~l~~~---~--~~---~~f~vVid~~~~~~~~~ 64 (149)
T PF13716_consen 3 FFYPGGRDREGRPVVVFIASRL-PSS---------DDLERLLLYLLSTLSEE---V--VD---KPFSVVIDHTGFSRSSE 64 (149)
T ss_dssp E-EEEEEBTTS-EEEEEEGGG--C-T---------THHHHHHHHHHHHH-TT---T--TT---S-EEEEEE-TT--GGG-
T ss_pred EEEecccCCCcCEEEEEECCcC-cch---------hhHHHHHHHHHHhhhHH---h--cC---CCEEEEEEcCCCccccC
Confidence 3567899999999999997665 211 22455555555555211 1 11 23999999999875332
Q ss_pred hhHHHHHHHHHHHhccccccccceeEEEeCchHHHHHH-HHhcccCChhh-hcceEEeCCccchHHHhccCCCCCccccc
Q 011383 289 KELRVATKQAVDLLQNNYPEFVARNIIINAPFWYYALN-ALISPFLTQRT-KSKFVVARPAKVTETLLKYIPAEELPVQY 366 (487)
Q Consensus 289 ~~l~~~~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw-~ivkpfL~~~T-r~KI~~~~~~~~~e~L~k~Id~e~LP~~y 366 (487)
.. ...++++..++...|+..|+++||||++++++.++ .+.+++++.+. ..||+++.+ ...|.++||+++||..+
T Consensus 65 ~~-~~~l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s---l~~L~~~i~~~qL~~~l 140 (149)
T PF13716_consen 65 PS-LSWLKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS---LSELSKHIDPSQLPESL 140 (149)
T ss_dssp ---HHHHHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS---TCGGGGTSGGGG-----
T ss_pred Cc-hHHHHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC---HHHHHhhCCHHHhcccC
Confidence 22 46789999999999999999999999999999999 66678888888 999999974 89999999999999999
Q ss_pred CCcccC
Q 011383 367 GGFKRE 372 (487)
Q Consensus 367 GG~~~~ 372 (487)
||....
T Consensus 141 p~~~~~ 146 (149)
T PF13716_consen 141 PGVLQY 146 (149)
T ss_dssp -HHH--
T ss_pred CCEEec
Confidence 998754
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=98.31 E-value=6.9e-07 Score=67.36 Aligned_cols=30 Identities=50% Similarity=0.748 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhhhcCCCHHHHHHHHHHH
Q 011383 156 GAEGIDVILLKFLRAREFKVNDALEMLKNT 185 (487)
Q Consensus 156 ~~~~~D~~LLRFLrAr~fdv~~A~~~L~~~ 185 (487)
....+|.+||||||||+|||++|.+||+++
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 345699999999999999999999999875
No 10
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=97.91 E-value=5.2e-05 Score=78.07 Aligned_cols=125 Identities=10% Similarity=0.141 Sum_probs=92.0
Q ss_pred cCCCCCeEEEEeccccCchhhhhhhcCChhhHHHHHHHHHHHHHHHHHhhcCCCCCeeeeEEEEeCCCCCccchhhHHHH
Q 011383 215 VDREGHPVCYNIYGVFESDELYQKTFGTEEKRGQFLRWRLRLMEQGIQKLDFKPGGISSLLQINDLKNAPVLAKKELRVA 294 (487)
Q Consensus 215 ~Dk~GrPV~~~~~g~~d~~~l~~~~~~~e~~~~~~lr~~i~~~E~~l~~l~~~~~~i~~iv~IiDl~g~s~~~~~~l~~~ 294 (487)
.|+.||+|+++...++-...-+ .-..++++.++.++..++.- .+.|+=-.|+. ..+++.++.
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--------DDIRLISYLVYTIDKYVEND---------YTLVYFHHGLP-SDNKPYLQL 150 (467)
T ss_pred ccccCCeeEEEEEecCCchhhh--------hhHHHHHHHHHHHHHHHhcc---------ceeeehhcCCc-ccccchHHH
Confidence 6999999999888776543211 11338999999999988642 33443334443 233333455
Q ss_pred HHHHHHHhccccccccceeEEEeCchHHHHHHHHhcccCChhhhcceEEeCCccchHHHhccCCCC
Q 011383 295 TKQAVDLLQNNYPEFVARNIIINAPFWYYALNALISPFLTQRTKSKFVVARPAKVTETLLKYIPAE 360 (487)
Q Consensus 295 ~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw~ivkpfL~~~Tr~KI~~~~~~~~~e~L~k~Id~e 360 (487)
+.....-+-.+|---++.+|+|..-|+..++|++++||++.+..+||+.+. +.++|.++|.-+
T Consensus 151 l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n---~lseL~~~l~l~ 213 (467)
T KOG4406|consen 151 LFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFN---SLSELFEALKLN 213 (467)
T ss_pred HHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEee---hHHHHHHhhhhh
Confidence 555555566668888999999999999999999999999999999999985 488888887533
No 11
>KOG3287 consensus Membrane trafficking protein, emp24/gp25L/p24 family [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.69 E-value=0.017 Score=54.95 Aligned_cols=82 Identities=24% Similarity=0.479 Sum_probs=51.5
Q ss_pred EEEecCCCeEEEEEeecCCCceEEEEEEEc-C---cceEEEEEEecCCCCceEEEeecceecCCCcccccceEE--cCcC
Q 011383 386 EITLKAGSTETIEIQAPEIGTTITWDLTVL-G---WEVSYKEEFVPTDEGSYTIIVQKGKKMGSHEGPIRNTFK--NNEA 459 (487)
Q Consensus 386 ~v~VkaG~~~~v~i~v~e~gs~l~Wef~t~-~---~DI~Fgi~~~~~~~~~~~~iv~~~~r~~~~~~p~~gs~~--~~~~ 459 (487)
++.|.||++.-.=-++.. |.++.-++.+. | .||+|.+.- |. | ..+++..++. .|.++ ..++
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 TVMIPAGKTECFYQPVPQ-GATLEVEYQVIDGAGDLDIDFTLLN-PA--G--EVLVSDQRKV-------DGVHTVEVTET 103 (236)
T ss_pred EEEecCCCceeeeeeccC-CeEEEEEEEEEecCCccceeeEEeC-CC--c--cEEeeccccc-------CceeEeeccCC
Confidence 567777777665555544 35666666653 2 578888742 21 2 1333433333 44444 4689
Q ss_pred cEEEEEEEcCCC--CceEEEEEE
Q 011383 460 GKLVLTIDNASS--KKKRVLYRY 480 (487)
Q Consensus 460 G~yvL~fDNs~S--~~Kkv~Y~~ 480 (487)
|.|.|+|||++| .+|.|.+.+
T Consensus 104 GdY~~CfDNsFS~fs~K~Vffel 126 (236)
T KOG3287|consen 104 GDYQVCFDNSFSTFSRKLVFFEL 126 (236)
T ss_pred cceEEEEcCccccccceEEEEEE
Confidence 999999999999 566676666
No 12
>KOG1693 consensus emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.30 E-value=0.11 Score=49.04 Aligned_cols=73 Identities=22% Similarity=0.409 Sum_probs=44.6
Q ss_pred ecCCCceEEEEEEEc---CcceEEEEEEecCCCCceEEEeecceecCCCcccccceEEcCcCcEEEEEEEcCCC-CceEE
Q 011383 401 APEIGTTITWDLTVL---GWEVSYKEEFVPTDEGSYTIIVQKGKKMGSHEGPIRNTFKNNEAGKLVLTIDNASS-KKKRV 476 (487)
Q Consensus 401 v~e~gs~l~Wef~t~---~~DI~Fgi~~~~~~~~~~~~iv~~~~r~~~~~~p~~gs~~~~~~G~yvL~fDNs~S-~~Kkv 476 (487)
+...++++..+|.|. +.||+|-|+ .|+ |+. ..-.+.+|.+ .-.|++...|+|.++|+|.+| .++|+
T Consensus 40 ~~~~~~~~~~~fqV~tGG~fDVD~~I~-aPd--gkv-I~~~~kk~~~------~~~f~ae~~G~Y~fCFsN~fstf~~Ki 109 (209)
T KOG1693|consen 40 LKKDDDTTSFEFQVQTGGHFDVDYDIE-APD--GKV-IYSEKKKRYD------SFLFKAEGKGEYTFCFSNEFSTFSHKI 109 (209)
T ss_pred cccCCceEEEEEEEEeCCceeeEEEEE-CCC--CCE-Eeeccccccc------cEEEEEecceEEEEEecCccccccceE
Confidence 334445566666653 478888875 332 332 2212234444 346889999999999999999 55555
Q ss_pred EE-EEEee
Q 011383 477 LY-RYKTK 483 (487)
Q Consensus 477 ~Y-~~~v~ 483 (487)
-| ..++.
T Consensus 110 v~~~~q~~ 117 (209)
T KOG1693|consen 110 VYMDFQVG 117 (209)
T ss_pred eeehhhhc
Confidence 44 44443
No 13
>KOG1692 consensus Putative cargo transport protein EMP24 (p24 protein family) [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.85 E-value=0.12 Score=48.42 Aligned_cols=73 Identities=22% Similarity=0.340 Sum_probs=51.0
Q ss_pred CCCeEEEEEeecCCCceEEEEEEEcCcceEEEEEEecCCCCceEEEeecceecCCCcccccceEEcCcCcEEEEEEEcCC
Q 011383 391 AGSTETIEIQAPEIGTTITWDLTVLGWEVSYKEEFVPTDEGSYTIIVQKGKKMGSHEGPIRNTFKNNEAGKLVLTIDNAS 470 (487)
Q Consensus 391 aG~~~~v~i~v~e~gs~l~Wef~t~~~DI~Fgi~~~~~~~~~~~~iv~~~~r~~~~~~p~~gs~~~~~~G~yvL~fDNs~ 470 (487)
.|.+..+.|.+.++|. -||+|.|. .|++. ++.+..+-++ -.=+|+++.+|+|.++|+|.+
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 EGDKLSVSFEVIDGGF----------LGVDVEIT-GPDGK-----IIHKGKRESS----GKYTFTAPKKGTYTFCFSNKM 98 (201)
T ss_pred cCCEEEEEEEEecCCc----------cceeEEEE-CCCCc-----hhhhcccccC----ceEEEEecCCceEEEEecCCC
Confidence 5677777777766431 35777774 34322 3444443322 255688999999999999999
Q ss_pred C--CceEEEEEEEee
Q 011383 471 S--KKKRVLYRYKTK 483 (487)
Q Consensus 471 S--~~Kkv~Y~~~v~ 483 (487)
| ..|.|.+.|.+-
T Consensus 99 s~mtpk~V~F~ihvg 113 (201)
T KOG1692|consen 99 STMTPKTVMFTIHVG 113 (201)
T ss_pred CCCCceEEEEEEEEe
Confidence 9 999999999874
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=83.90 E-value=0.33 Score=44.51 Aligned_cols=88 Identities=28% Similarity=0.410 Sum_probs=0.0
Q ss_pred EEecCCCeEEEEEeecCCCceEEEEEEEcCc----ceEEEEEEecCCCCceEEEeecceecCCCcccc-cceEEcCcCcE
Q 011383 387 ITLKAGSTETIEIQAPEIGTTITWDLTVLGW----EVSYKEEFVPTDEGSYTIIVQKGKKMGSHEGPI-RNTFKNNEAGK 461 (487)
Q Consensus 387 v~VkaG~~~~v~i~v~e~gs~l~Wef~t~~~----DI~Fgi~~~~~~~~~~~~iv~~~~r~~~~~~p~-~gs~~~~~~G~ 461 (487)
+.|.+|...-+-..+.. |..+...|.+.++ +|.|.|. .|+..+ ..++... .. .+. .=+|.+.++|.
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-DPDPNG--EVIYSKS-DK----ESEGSFSFTAKESGE 74 (183)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEECCCCcEEEEEEcCC-CcEEEEEEEEeeccccceEEEEEE-ecccCC--ceeeeec-cc----ccCCcEEEEeccCCC
Confidence 45666766666666655 5677777777543 3555554 222111 2232211 11 111 44577889999
Q ss_pred EEEEEEcCCCC--c-eEEEEEEEee
Q 011383 462 LVLTIDNASSK--K-KRVLYRYKTK 483 (487)
Q Consensus 462 yvL~fDNs~S~--~-Kkv~Y~~~v~ 483 (487)
|.++|+|+.++ . +.|.+.+.+.
T Consensus 75 y~iCf~n~~~~~~~~~~v~~~~~~~ 99 (183)
T PF01105_consen 75 YQICFDNSSSSFSPSKRVSFDIDVG 99 (183)
T ss_dssp -------------------------
T ss_pred EEEEEEcCCCCccccEEEEEEEEEe
Confidence 99999999983 3 7888777764
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=72.14 E-value=47 Score=26.92 Aligned_cols=86 Identities=24% Similarity=0.353 Sum_probs=52.0
Q ss_pred EEecCCCeEEEEEeecCCCceEEEEEEEcCcceEE-EEEEecCCCCceEEEeecceecCCCcccccceEEcCcCcEEEEE
Q 011383 387 ITLKAGSTETIEIQAPEIGTTITWDLTVLGWEVSY-KEEFVPTDEGSYTIIVQKGKKMGSHEGPIRNTFKNNEAGKLVLT 465 (487)
Q Consensus 387 v~VkaG~~~~v~i~v~e~gs~l~Wef~t~~~DI~F-gi~~~~~~~~~~~~iv~~~~r~~~~~~p~~gs~~~~~~G~yvL~ 465 (487)
|+++.|....|.++-.- ++=..|.+.....-+.+ +-.|.|...+. .+++.- ....=.|.+..+|+..|.
T Consensus 1 I~v~~g~~~~I~L~~np-stGY~W~~~~~~~~l~l~~~~~~~~~~~~--------~~vG~~-g~~~f~f~a~~~G~~~i~ 70 (92)
T PF09394_consen 1 ITVKVGDTFEIELPENP-STGYSWSLSSDSDGLQLVSEEYIPDNSPS--------GLVGAP-GTRTFTFKALKPGTTTIK 70 (92)
T ss_dssp -EEETTSEEEEEEEEBC-CGTBEEEECTSTTTEEEEEEEEEESSTSS--------TSSTSS-EEEEEEEEESSSEEEEEE
T ss_pred CeecCCCEEEEEECCCC-CCCeEEEEecCCCeEEEcCCcEEeCCCCc--------CCCCCC-cEEEEEEEEecCeeEEEE
Confidence 57899999999988744 34578998773333444 22333321110 022221 123567889999999999
Q ss_pred EEcCCC-----CceEEEEEEEe
Q 011383 466 IDNASS-----KKKRVLYRYKT 482 (487)
Q Consensus 466 fDNs~S-----~~Kkv~Y~~~v 482 (487)
|....+ ..+++.|.+.|
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 988655 23567777664
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=55.39 E-value=11 Score=33.72 Aligned_cols=24 Identities=17% Similarity=0.253 Sum_probs=20.5
Q ss_pred CCCcccccceEEcCcCcEEEEEEE
Q 011383 444 GSHEGPIRNTFKNNEAGKLVLTID 467 (487)
Q Consensus 444 ~~~~~p~~gs~~~~~~G~yvL~fD 467 (487)
+.+-.+..|.|+|+-||.|.+.|.
T Consensus 35 g~~yd~~TG~Ftcpv~GvY~F~f~ 58 (135)
T smart00110 35 QGHYDPRTGKFTCPVPGVYYFSYH 58 (135)
T ss_pred CCCccCCCCEEECeeceEEEEEEE
Confidence 344557799999999999999998
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=52.18 E-value=20 Score=25.19 Aligned_cols=24 Identities=13% Similarity=0.320 Sum_probs=20.0
Q ss_pred CHHHHHHHhhhcCCCHHHHHHHHH
Q 011383 160 IDVILLKFLRAREFKVNDALEMLK 183 (487)
Q Consensus 160 ~D~~LLRFLrAr~fdv~~A~~~L~ 183 (487)
++.....||.+++||++.|+..+-
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 557889999999999999998764
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=49.53 E-value=14 Score=32.15 Aligned_cols=24 Identities=13% Similarity=0.177 Sum_probs=17.7
Q ss_pred CcccccceEEcCcCcEEEEEEEcC
Q 011383 446 HEGPIRNTFKNNEAGKLVLTIDNA 469 (487)
Q Consensus 446 ~~~p~~gs~~~~~~G~yvL~fDNs 469 (487)
+-.+..|.|+|+.+|+|.+.|.=.
T Consensus 31 ~yn~~tG~Ftap~~G~Y~F~~~~~ 54 (127)
T PF00386_consen 31 AYNPSTGIFTAPVPGVYFFSFTIM 54 (127)
T ss_dssp -EETTTTEEE-SS-EEEEEEEEEE
T ss_pred ccEeecCEEecCCCCEEEEEEEEe
Confidence 344679999999999999998754
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=43.69 E-value=42 Score=23.38 Aligned_cols=26 Identities=19% Similarity=0.141 Sum_probs=22.3
Q ss_pred CCHHHHHHHhhhcCCCHHHHHHHHHH
Q 011383 159 GIDVILLKFLRAREFKVNDALEMLKN 184 (487)
Q Consensus 159 ~~D~~LLRFLrAr~fdv~~A~~~L~~ 184 (487)
.+...+.+-|+++++|++.|..+|-.
T Consensus 15 ~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 15 LDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp S-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 67888999999999999999998754
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=40.38 E-value=46 Score=23.25 Aligned_cols=25 Identities=16% Similarity=0.105 Sum_probs=22.6
Q ss_pred CCHHHHHHHhhhcCCCHHHHHHHHH
Q 011383 159 GIDVILLKFLRAREFKVNDALEMLK 183 (487)
Q Consensus 159 ~~D~~LLRFLrAr~fdv~~A~~~L~ 183 (487)
.++..+.+-|+++++|++.|..+|.
T Consensus 16 l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 16 LDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 6788999999999999999998875
No 21
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=39.26 E-value=75 Score=25.00 Aligned_cols=46 Identities=15% Similarity=0.103 Sum_probs=30.5
Q ss_pred EEEeCCCCCccchhhHHHHHHHHHHHhccccc--cccceeEEEeCchHHHHH
Q 011383 276 QINDLKNAPVLAKKELRVATKQAVDLLQNNYP--EFVARNIIINAPFWYYAL 325 (487)
Q Consensus 276 ~IiDl~g~s~~~~~~l~~~~k~ii~llq~~YP--E~L~~i~IINaP~~f~~l 325 (487)
+++|+.|+.... .+++-.++..+...|+ +.-.++.++|+......+
T Consensus 20 V~lDF~gv~~~~----ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~ 67 (74)
T PF14213_consen 20 VVLDFEGVESIT----SSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEM 67 (74)
T ss_pred EEEECCCccccc----HHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHH
Confidence 789999997533 2355556655555566 556788899987655443
No 22
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=31.66 E-value=1.1e+02 Score=29.98 Aligned_cols=105 Identities=20% Similarity=0.197 Sum_probs=59.6
Q ss_pred HHHHHHHHHHhhc---CCCCCeeeeEEEEeCCCCCccchhhHHHHHHHHHHHhccccccccceeEEEeCch------HHH
Q 011383 253 RLRLMEQGIQKLD---FKPGGISSLLQINDLKNAPVLAKKELRVATKQAVDLLQNNYPEFVARNIIINAPF------WYY 323 (487)
Q Consensus 253 ~i~~~E~~l~~l~---~~~~~i~~iv~IiDl~g~s~~~~~~l~~~~k~ii~llq~~YPE~L~~i~IINaP~------~f~ 323 (487)
.+++||..+..++ ...|..+.-.+|+|+-|-= --..|+ ..+++++.-++. .--++..+|++..++ +|+
T Consensus 75 Lv~cmEyl~~NldwL~~~~Gd~eddylifDcPGQI-ELytH~-pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~KfiS 151 (273)
T KOG1534|consen 75 LVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQI-ELYTHL-PVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFIS 151 (273)
T ss_pred chhHHHHHHHHHHHHHhhccCccCCEEEEeCCCee-EEeecC-hhHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHHH
Confidence 3566777665543 2234455667899998742 112233 567778877776 333555666666654 444
Q ss_pred HHH----HHhcccCCh-hhhcceEEeCCccchHHHhccCCCCC
Q 011383 324 ALN----ALISPFLTQ-RTKSKFVVARPAKVTETLLKYIPAEE 361 (487)
Q Consensus 324 ~lw----~ivkpfL~~-~Tr~KI~~~~~~~~~e~L~k~Id~e~ 361 (487)
... +|+.-=++. +..+|.-++++ ..++.|.++++++.
T Consensus 152 G~lsAlsAMi~lE~P~INvlsKMDLlk~-~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 152 GCLSALSAMISLEVPHINVLSKMDLLKD-KNKKELERFLNPDE 193 (273)
T ss_pred HHHHHHHHHHHhcCcchhhhhHHHHhhh-hhHHHHHHhcCCch
Confidence 333 333322333 34667766664 45677777777653
No 23
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to
Probab=29.48 E-value=2.6e+02 Score=24.60 Aligned_cols=49 Identities=27% Similarity=0.368 Sum_probs=32.9
Q ss_pred eeeEEEEeCCCCCccchhhHHHHHHHHHHHhccccccccceeEEEeCchHHHHHHHHhcc
Q 011383 272 SSLLQINDLKNAPVLAKKELRVATKQAVDLLQNNYPEFVARNIIINAPFWYYALNALISP 331 (487)
Q Consensus 272 ~~iv~IiDl~g~s~~~~~~l~~~~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw~ivkp 331 (487)
++++++.|+ |.+.++ ...++.++. ++.++++..+|+|.+..++-..+.-
T Consensus 60 dgVlvl~DL-Ggs~~n-------~e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~ 108 (125)
T TIGR02364 60 DGVLIFYDL-GSAVMN-------AEMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEA 108 (125)
T ss_pred CCEEEEEcC-CCcHhH-------HHHHHHHhc---cccccEEEEechhHHHHHHHHHHHH
Confidence 559999999 655211 111333333 3556889999999999988877654
No 24
>COG4499 Predicted membrane protein [Function unknown]
Probab=29.47 E-value=77 Score=33.36 Aligned_cols=41 Identities=20% Similarity=0.204 Sum_probs=23.5
Q ss_pred CCccccccccccchHHHHHHHHHHHHHHHHHHhcCCCCCCcc
Q 011383 32 SSYKEESNFLSDLKEFERKALNEFKAKLEEAILGNSLLNKEE 73 (487)
Q Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 (487)
+-|++-=|+..-|-+.+.--++=- .++++....+.++....
T Consensus 327 Ge~~eAinIAr~L~D~d~~~~Al~-k~~eevksn~~lsg~~r 367 (434)
T COG4499 327 GEFKEAINIARNLDDNDLTLLALT-KLYEEVKSNTDLSGDKR 367 (434)
T ss_pred ccHHHHhhHHHhCCcchhHHHHHH-HHHHHHhcccCCCchHH
Confidence 446666666666666666544433 35566666555655443
No 25
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=28.73 E-value=1.6e+02 Score=24.25 Aligned_cols=73 Identities=12% Similarity=0.169 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCeeeeEEEEeCC-CCCccchhhHHHHHHHHHHHhccccccccceeEEEeCchHHHHH
Q 011383 247 GQFLRWRLRLMEQGIQKLDFKPGGISSLLQINDLK-NAPVLAKKELRVATKQAVDLLQNNYPEFVARNIIINAPFWYYAL 325 (487)
Q Consensus 247 ~~~lr~~i~~~E~~l~~l~~~~~~i~~iv~IiDl~-g~s~~~~~~l~~~~k~ii~llq~~YPE~L~~i~IINaP~~f~~l 325 (487)
+++-+ .+..++..+.. ...+-+++|++ ++..+.. ..+.....+... +...+.++=||-.+.+...+
T Consensus 14 ed~~~-~~~~~~~~~~~-------~~~~~ll~d~~~~~~~~~~----~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~ 80 (109)
T PF11964_consen 14 EDYKE-LLPALEELIAD-------HGKIRLLVDLRRDFEGWSP----EARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMI 80 (109)
T ss_dssp HHHHH-HHHHHHHHHTT-------SSSEEEEEEEC-CEEEEHH----HHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHH
T ss_pred HHHHH-HHHHHHHHHhc-------CCceEEEEEecCccCCCCH----HHHHHHHHhchh-hhcccCEEEEEECcHHHHHH
Confidence 44444 34455555431 22377888888 7653332 333434444444 78888888888888888888
Q ss_pred HHHhccc
Q 011383 326 NALISPF 332 (487)
Q Consensus 326 w~ivkpf 332 (487)
.+++.+|
T Consensus 81 ~~~~~~~ 87 (109)
T PF11964_consen 81 ANFFAAF 87 (109)
T ss_dssp HHHHHHH
T ss_pred HHHHHhc
Confidence 8888886
No 26
>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=24.65 E-value=78 Score=25.56 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=19.7
Q ss_pred ccccccchHHHHHHHHHHHHHHHHH
Q 011383 38 SNFLSDLKEFERKALNEFKAKLEEA 62 (487)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (487)
..++.+|++.|++.|+.+...+.+-
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 4678999999999999999888753
No 27
>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=23.39 E-value=79 Score=22.26 Aligned_cols=18 Identities=17% Similarity=0.344 Sum_probs=14.3
Q ss_pred ceEEcCcCcEEEEEEEcC
Q 011383 452 NTFKNNEAGKLVLTIDNA 469 (487)
Q Consensus 452 gs~~~~~~G~yvL~fDNs 469 (487)
.++.-.+||.|.|.|.=+
T Consensus 5 ~nW~FT~PG~Y~l~~~a~ 22 (41)
T TIGR03769 5 ANWVFTKPGTYTLTVQAT 22 (41)
T ss_pred cceeeCCCeEEEEEEEEE
Confidence 456778999999999643
No 28
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=21.61 E-value=2.4e+02 Score=24.87 Aligned_cols=47 Identities=26% Similarity=0.370 Sum_probs=30.0
Q ss_pred eeeEEEEeCCCCCccchhhHHHHHHHHHHHhccccccccceeEEEeCchHHHHHHHHhcc
Q 011383 272 SSLLQINDLKNAPVLAKKELRVATKQAVDLLQNNYPEFVARNIIINAPFWYYALNALISP 331 (487)
Q Consensus 272 ~~iv~IiDl~g~s~~~~~~l~~~~k~ii~llq~~YPE~L~~i~IINaP~~f~~lw~ivkp 331 (487)
++++++.|| |.+.++ ....+.++..- .+++++++|.+=.++-..+.-
T Consensus 58 dGVlVltDL-Gssp~n-------~~~a~e~~~~~-----~~v~~~daPlVEGa~~Aav~~ 104 (124)
T PRK14484 58 DGVLIFFDL-GSAEMN-------AEMAIEMLDGE-----KKIIIIDAPIVEGAFTAAVLL 104 (124)
T ss_pred CCeEEEEeC-CChHHH-------HHHHHHhcCCC-----CcEEEECCcHHHHHHHHHHHH
Confidence 669999999 654211 12234444322 899999999876666655543
No 29
>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=20.71 E-value=1.9e+02 Score=25.48 Aligned_cols=43 Identities=19% Similarity=0.298 Sum_probs=33.7
Q ss_pred eeEEEeCchHHHHHHHHh-----cccCChhhhcceEEeCCccchHHHhccC
Q 011383 312 RNIIINAPFWYYALNALI-----SPFLTQRTKSKFVVARPAKVTETLLKYI 357 (487)
Q Consensus 312 ~i~IINaP~~f~~lw~iv-----kpfL~~~Tr~KI~~~~~~~~~e~L~k~I 357 (487)
.++++|..-++.-++.++ ..|++++....+.++.+ .+++.++|
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~---~~e~~~~i 133 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD---PEEALEYI 133 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS---HHHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC---HHHHHhhC
Confidence 699999887777777766 57999999999999964 66666554
No 30
>PF04151 PPC: Bacterial pre-peptidase C-terminal domain; InterPro: IPR007280 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, IPR001570 from INTERPRO), M9A amd M9B (microbial collangenase, IPR002169 from INTERPRO), M28 (aminopeptidase Ap1, IPR007484 from INTERPRO) and S8 (subtilisin family peptidases, IPR000209 from INTERPRO).; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4DY5_B 4DXZ_A 4DY3_B 3JQW_A 3JQX_C 1NQJ_B 1NQD_A 2O8O_A 1WMF_A 1WME_A ....
Probab=20.44 E-value=3.9e+02 Score=20.28 Aligned_cols=19 Identities=21% Similarity=0.228 Sum_probs=15.1
Q ss_pred cccceEEcCcCcEEEEEEE
Q 011383 449 PIRNTFKNNEAGKLVLTID 467 (487)
Q Consensus 449 p~~gs~~~~~~G~yvL~fD 467 (487)
.+...|..+.+|+|.|...
T Consensus 51 ~~~i~~~~~~~GtYyi~V~ 69 (70)
T PF04151_consen 51 DESITFTAPAAGTYYIRVY 69 (70)
T ss_dssp EEEEEEEESSSEEEEEEEE
T ss_pred ccEEEEEcCCCEEEEEEEE
Confidence 4567788899999999753
Done!