Query psy17468
Match_columns 538
No_of_seqs 92 out of 94
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 23:18:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17468.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17468hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09735 Nckap1: Membrane-asso 100.0 1E-173 2E-178 1483.3 37.1 534 1-535 174-1116(1116)
2 KOG1917|consensus 100.0 1E-171 3E-176 1396.7 37.2 537 1-537 182-1122(1125)
3 KOG1917|consensus 99.2 1.4E-12 3.1E-17 146.3 1.1 206 2-229 208-414 (1125)
4 PF10266 Strumpellin: Heredita 85.7 81 0.0017 38.9 20.6 194 220-422 792-1032(1081)
5 TIGR02509 type_III_yopR type I 72.8 26 0.00056 32.9 8.7 75 194-281 11-91 (131)
6 PF05994 FragX_IP: Cytoplasmic 65.7 20 0.00043 42.8 8.0 108 249-356 518-636 (820)
7 PF14744 WASH-7_mid: WASH comp 56.5 50 0.0011 35.8 8.3 76 274-353 256-341 (350)
8 PRK15354 type III secretion sy 55.0 33 0.00071 34.8 6.3 54 139-208 45-98 (224)
9 PLN03099 PIR Protein PIR; Prov 53.4 84 0.0018 39.0 10.4 103 250-352 869-985 (1232)
10 PF14117 DUF4287: Domain of un 53.1 21 0.00045 29.4 3.8 40 124-166 2-43 (61)
11 KOG1921|consensus 41.5 45 0.00098 34.8 5.0 73 113-196 91-182 (286)
12 COG5181 HSH155 U2 snRNP splice 39.4 56 0.0012 38.2 5.8 60 249-308 378-458 (975)
13 PF10275 Peptidase_C65: Peptid 36.8 2E+02 0.0044 28.8 8.9 96 283-384 98-202 (244)
14 KOG1463|consensus 36.6 46 0.00099 36.3 4.4 30 132-168 102-131 (411)
15 PF04858 TH1: TH1 protein; In 34.0 5E+02 0.011 30.2 12.3 172 335-529 284-473 (584)
16 PF02671 PAH: Paired amphipath 32.8 18 0.0004 27.2 0.6 39 122-182 2-40 (47)
17 PF10475 DUF2450: Protein of u 32.0 5.9E+02 0.013 26.3 17.2 75 271-350 164-241 (291)
18 PRK10667 Hha toxicity attenuat 31.8 69 0.0015 29.8 4.1 54 245-298 2-77 (122)
19 PF10757 YbaJ: Biofilm formati 30.1 68 0.0015 29.9 3.8 41 245-285 2-64 (122)
20 PF10079 DUF2317: Uncharacteri 29.3 2.6E+02 0.0056 32.0 9.1 42 256-297 220-271 (542)
21 COG3516 Predicted component of 27.3 1.5E+02 0.0032 29.2 5.7 48 274-322 108-155 (169)
22 smart00126 IL6 Interleukin-6 h 27.2 2.2E+02 0.0048 27.6 6.9 37 308-344 117-153 (154)
23 PHA00022 VII minor coat protei 26.0 66 0.0014 22.7 2.3 19 316-334 1-19 (28)
24 PLN03094 Substrate binding sub 23.6 6.4E+02 0.014 27.7 10.4 36 289-324 304-339 (370)
25 PF08700 Vps51: Vps51/Vps67; 22.5 4.5E+02 0.0097 21.7 8.6 40 259-298 18-57 (87)
26 COG2257 Uncharacterized homolo 21.8 2.2E+02 0.0048 25.4 5.3 37 371-407 37-75 (92)
No 1
>PF09735 Nckap1: Membrane-associated apoptosis protein; InterPro: IPR019137 Nck-associated protein 1 is part of lamellipodial complex that controls Rac-dependent actin remodeling. It associates preferentially with the first SH3 domain of Nck and is a component of the WAVE2 complex composed of ABI1, CYFIP1/SRA1, NCKAP1/NAP1 and WASF2/WAVE2. It is also a component of the WAVE1 complex composed of ABI2, CYFIP2, C3orf10/HSPC300, NCKAP1 and WASF1/WAVE1. CYFIP2 binds to activated RAC1 which causes the complex to dissociate, releasing activated WASF1. The complex can also be activated by NCK1. Expression of this protein was found to be markedly reduced in patients with Alzheimer's disease [].; PDB: 3P8C_B.
Probab=100.00 E-value=1.1e-173 Score=1483.26 Aligned_cols=534 Identities=58% Similarity=0.975 Sum_probs=462.9
Q ss_pred CCCccchhhhhhhhchhhHHHHHHHHHHHHHHhccCcchHhhhhcCccccCCCCCcccCccccccccccccchhhhhhhh
Q psy17468 1 MDYEVPMKKLSEEFIPHAKLLFQALMSLRAIYSYRNVSADQMRNDQKLSLVGNPGQLLKPARTERMSCEYLSQESLDRWI 80 (538)
Q Consensus 1 ~dyd~PlKkL~eef~p~~~~i~~aL~Sl~~~y~rr~~~a~~wR~~~~Lsl~~~P~~~l~pa~sd~~~cE~ls~e~m~~Wi 80 (538)
+|||+|+|||+|||+||+++|++||+||+++|+|||.+|++||++|+||++++|++|++|+++|+|+|||+|+++|+|||
T Consensus 174 ~~y~~P~kkL~eef~p~~~~i~~aL~Sl~~~~~rr~~~a~~wR~~~~lsl~~~p~~il~p~~~~~~~~e~lsl~~~~~Wi 253 (1116)
T PF09735_consen 174 LDYDNPLKKLQEEFQPHSRRIGSALMSLRPIYPRRNLTADQWRSAQLLSLISPPADILTPAQTDTMACEYLSLEVMERWI 253 (1116)
T ss_dssp HHTSSHHHHHHHHTTTTHHHHHHHHHGGGGTHHHHS--HHHHHHTTTT-SSSSGGGTTS----TTHHHHHS-HHHHHHHH
T ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHhcCcccCCCChhhccCCccCcchhhhhhhhhhHHHHH
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred heeeeccCCCCCC-chhHHHHHHHhcCCceEEeechhhHhhHHHHHHHHhhhhhcccchhHHhhHHHHHHHHhhHHHHHH
Q psy17468 81 IFGFMLCHQPLSQ-EPVSKLWTAALENNWVIALFRDEVIYIHQYIQGFFDTIKGYGKRVSEVKDCYSHAVSKAALEHREK 159 (538)
Q Consensus 81 i~g~L~cp~~L~~-~~~~~lw~~aL~~~~vl~LfRdev~~iH~~~e~~~~s~K~y~Kr~~~vkE~~~~A~~~~~~~HreR 159 (538)
+||||+||++|.+ +++++||+.||++|||||||||||++||+++|++|+|+|+||||+++||||+++|+++||.+||||
T Consensus 254 i~g~L~cp~~L~~~~~~~~l~~~aL~~~~~i~LfRde~l~iH~~~~~~~~~~k~~~Kr~~~vkE~~~~A~~~~~~~HreR 333 (1116)
T PF09735_consen 254 IFGFLVCPQELLQQPSILDLWKLALQDGLVITLFRDEVLNIHKEIETFFESKKGYSKRLSEVKECAEQALQNAGDLHRER 333 (1116)
T ss_dssp HHHHHHTTHHHHH-HHHHHHHHHHHTT-SEEEEETTEEEEHHHHHHHHHTT-GGGTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hheeeechhhhcCChHHHHHHHHHhccCcEEEEeccchhhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhcchhhHHH
Confidence 9999999999988 777799999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCcchHHHHHHhhhhhhhhhHHHhhcCCCCCCCCCCCCCccccccCcchHHHH-------
Q psy17468 160 RKFLRTALKELGLLFSDQPGLLGPKALLIFIGLSYARDEVYWLLRHNDNPPVQKGKSKSAEDLVDRQLPELEM------- 232 (538)
Q Consensus 160 R~~LR~aLkel~~ll~DqPgLLgPK~l~vf~aLs~aRdEV~Wl~rH~~~~p~~~k~k~~~ed~~D~~l~eLLf------- 232 (538)
|+|||++||||+++|+|||||||||+++||||||||||||+|||||++++|++||||.+++|++|++||||||
T Consensus 334 R~~Lr~~Lkel~~l~~dqPgLLgPK~~~v~~aLs~ArdEV~W~~rH~~~~p~~~~k~~~~~d~~D~~i~eLL~~m~eLr~ 413 (1116)
T PF09735_consen 334 RRYLRQALKELVLLLTDQPGLLGPKALMVFAALSFARDEVLWLFRHNDNPPPKKKKKKTDEDYIDRQIPELLFYMEELRS 413 (1116)
T ss_dssp HHHHHHHHHHHHHHHHH-GGGGTTTHHHHHHHHHHHHHHHHHHHHHHHHS-------SSTTTT--TTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhhCccccchhHHHHHHHHHHHHHHHHHHHHccCCCCccccccCCccccccccHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999998877777899999999999999
Q ss_pred ---H----------------------------------------------------------------------------
Q psy17468 233 ---K---------------------------------------------------------------------------- 233 (538)
Q Consensus 233 ---k---------------------------------------------------------------------------- 233 (538)
|
T Consensus 414 Lv~k~~~viqrYy~~yl~~~Da~~L~~~i~~~~~~~eee~~ilss~~~~l~~l~~~~~e~~~~~Df~~lRlDW~RLqa~~ 493 (1116)
T PF09735_consen 414 LVRKYSQVIQRYYVQYLSGYDALVLNELIQNLSVCPEEESVILSSFVQTLSSLSVKQVENGEKFDFSGLRLDWFRLQAYT 493 (1116)
T ss_dssp HHHHSHHHHHHHHHHHHHHTHHHHHHHHHTT-S---HHHHHHHHHHHHHHHT--HHHHHTT-----HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhhcccHHHHHHHHHhcCCCCchHhHHHHHHHHHHHhCCccccccCCcCchHHHHHHHHHHHHHH
Confidence 0
Q ss_pred --------------------------------------------------------------------------------
Q psy17468 234 -------------------------------------------------------------------------------- 233 (538)
Q Consensus 234 -------------------------------------------------------------------------------- 233 (538)
T Consensus 494 S~~~s~l~L~~~~~L~~~mN~i~fHsk~VD~lde~L~etSdLs~lcfY~~~fe~~F~~~l~~psq~ry~iaf~~icshF~ 573 (1116)
T PF09735_consen 494 SSSRSPLQLRENEKLASLMNTIVFHSKMVDSLDELLRETSDLSILCFYPRFFEKMFRQCLEGPSQPRYSIAFPLICSHFP 573 (1116)
T ss_dssp HSTT-SS-GGG-HHHHHHHHHHHHHHHHHH-HHHHHHHHH--GGGGG-HHHHHHHHHHHHHSHHHHGGGGHHHHHGGGGG
T ss_pred hhcccccCccchHHHHHHHHHHHHHHhhhchHHHHHHHhcchhheeehhHHHHHHHHHHHhccccchHHHHHHHHHHHHH
Confidence
Q ss_pred --------------------------------------------------------------------------------
Q psy17468 234 -------------------------------------------------------------------------------- 233 (538)
Q Consensus 234 -------------------------------------------------------------------------------- 233 (538)
T Consensus 574 ~~~h~lcPEE~~~i~~~sl~~a~~fLeeiak~~~~~i~~l~~e~~~L~~qLlP~~aA~~~~~~~~~k~~k~~~k~~~~~~ 653 (1116)
T PF09735_consen 574 NCLHELCPEEREHIGERSLSLANSFLEEIAKQTSNVINQLCSEQCSLEDQLLPKHAARLISQARNKKKKKQKNKKGEPER 653 (1116)
T ss_dssp GG--TT-GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSGGGGHHHHHHHTT---------------
T ss_pred hhCCccCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHhhhcccccCcCCCCCC
Confidence
Q ss_pred --------------------------------------------------------------------------------
Q psy17468 234 -------------------------------------------------------------------------------- 233 (538)
Q Consensus 234 -------------------------------------------------------------------------------- 233 (538)
T Consensus 654 ~~PG~ES~r~~r~~~t~ld~l~~~L~eLc~aln~~~~I~V~dh~f~PrEyL~~~Le~~f~~~l~~~~~~~~~~~~i~RPS 733 (1116)
T PF09735_consen 654 VKPGAESYRKNRENLTMLDKLHQALTELCSALNHFPSIVVFDHVFVPREYLREHLENRFRRALVSMVMYNPDDQEIARPS 733 (1116)
T ss_dssp --TTGGG--S-TTS--HHHHHHHHHHHHHHHHTS-S-EEETTEEE-HHHHHHHHHHHHHHHHHHHHT--BTTTTB---HH
T ss_pred CCCchhccCCCchhhhhHHHHHHHHHHHHHHHhcCCCeEEEeeEeeHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCHH
Confidence
Q ss_pred ----------------------------------------------------------------------------Hhhc
Q psy17468 234 ----------------------------------------------------------------------------FIAE 237 (538)
Q Consensus 234 ----------------------------------------------------------------------------Fv~~ 237 (538)
||+.
T Consensus 734 ~ll~~l~a~m~vlq~le~~v~iDvt~~~~~vLLqqtq~~d~~g~~ti~~~yt~WYle~llr~~s~~~ivfSp~~~~FvS~ 813 (1116)
T PF09735_consen 734 ELLSSLRAYMSVLQSLENYVSIDVTRLFRNVLLQQTQPVDSHGEKTITTLYTNWYLENLLRDASNGGIVFSPSRKCFVSS 813 (1116)
T ss_dssp HHHHHHHHHHHHHHHGGGTSS--HHHHHHHHHHHTTSSB-TTS-B-HHHHHHHHHHHTHHHHHHTTSEEEETTTTEEEE-
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCcccCCcccHHHHHHHHHHHHHHHhccCCcEEeecHHHhhhCC
Confidence 4533
Q ss_pred -C-CcccccccCCCHHHHHHHHHhhCchhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcCCCHHHHHHHHhhhh
Q psy17468 238 -G-AIPFNAEEFSDVNELRALADLIGPYGMKLLNETLMWHIASQVQELKKLVAANKEVLLLLRTHFDKPEIMKEQSKRLH 315 (538)
Q Consensus 238 -~-~~~f~AE~ysD~~ELrAL~eLiGPYG~k~L~e~L~~hia~qv~elkklv~~N~d~L~~lr~~f~~p~~m~~~lk~L~ 315 (538)
+ +++|+||+|||++|||||||||||||||+|+++|||||++||+||||+|++|+|+|+++|+|||||++|++++|||+
T Consensus 814 ~~~~~~f~ae~ytD~~ELrAL~~LiGpyGvk~l~~~L~~~va~~v~elkk~v~~N~d~L~~l~~~~~~~~~~~~~~~~l~ 893 (1116)
T PF09735_consen 814 RPEQGPFNAEEYTDLNELRALVELIGPYGVKFLDENLMWHVASQVNELKKLVRQNRDVLEQLRSNFDKPEKMEELLKQLT 893 (1116)
T ss_dssp SSS---S-THHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHH-TT-HHHHHHHHTT--
T ss_pred CCccCCcChHHcCCHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHhhc
Confidence 3 38999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhccCchhhhhHHHHhhcCCCCCC----chHHHHHHHhCCCCCCCHHHHHH
Q psy17468 316 NVENVLQRMTIIGVILNFQRIAQLALQEVLESRVPFLLNSVQDFYQHSPVGDP----KIVNEMASAAGLLCTVDPALATA 391 (538)
Q Consensus 316 ~~e~~l~r~~iiG~iL~FR~l~~eAl~~VL~~~~Pfl~s~I~~~~~~~~~~~~----l~v~~lA~aaGl~~~vD~~Lv~a 391 (538)
++|+|++||||||+||+||+|+|||+++|+++|+|||+|+|+++++|+|+..+ ++|++||++||++|++||+|+++
T Consensus 894 ~~d~vl~r~i~iG~iL~FR~ll~eAl~~Vl~~~~Pfl~s~i~~~~~~~~~~~~~~~~l~v~~lA~~aG~~~~vD~~lv~a 973 (1116)
T PF09735_consen 894 DLDNVLQRMIIIGVILSFRQLLQEALRDVLERRIPFLMSSIEDLKEHIPNGPDIKEFLSVDELASAAGLPCDVDPALVRA 973 (1116)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH--------SSHHHHHHHHHHTT---SS-HHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHhCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999996555 45999999999999999999999
Q ss_pred HhccCCCCCchhhHHHHHHHHHHHHHhcccccCCccccccccccccchhhhHHHHHHHHHHHHhcccCCCCHHHHHHHHH
Q psy17468 392 LASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFYLASLEGHSNNIHCMASAINHIFSALFTLCGQGDLEDRMKEFL 471 (538)
Q Consensus 392 l~~~~~~~~d~~y~~w~LL~vf~avslp~l~~~~~s~y~~~~~g~~NN~HCla~aIn~l~~a~f~l~g~~~Ie~~mkeFL 471 (538)
|++++++ |||+|+.||+||||+|||+|++++|++|+|++++|||+||+||+|+|||+|++|+|+++|++||+++|||||
T Consensus 974 l~~~~~~-~~e~~~~~~lLlvf~avsl~~~~~~~~s~Y~~~~~g~~NN~Hcla~ai~~l~~al~~~~~~~di~~~mkeFl 1052 (1116)
T PF09735_consen 974 LRAQKGD-PDEEYKISWLLLVFLAVSLPTLAMWDSSVYKPELEGFSNNIHCLARAINALAAALFSLSGEADIESRMKEFL 1052 (1116)
T ss_dssp HT------HHHHHHHHHHHHHHHHHHGGGGGG-GGG-EETTTTEETT-GGGHHHHHHHHHHHHHHH-TT--HHHHHHHHH
T ss_pred HHHhCCC-chHhhhhhHHHHHHHHHHhHhccCCCccccccccccccchHHHHHHHHHHHHHHHhcccccccHHHHHHHHH
Confidence 9999997 899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhccCCCCCCcccCCcchhHhhHHHHHhcCCCCchhhhhhhchHHHHHHHHHHhhhhc
Q psy17468 472 ALTSSSLLRLGQDPDEESTRHRDSVYLLLHQIVQESPFLTMDLLESCFPYALIRNAYHAVSKQE 535 (538)
Q Consensus 472 ~lASs~lL~l~~e~~k~~~k~r~sv~ilLdqiV~~SpfLt~d~LEscfPY~LlRnaY~~~y~~~ 535 (538)
++||++|||+|+|++|+..|+|+|+|||||||||+|||||+|+||+||||+|||||||++|+++
T Consensus 1053 ~laS~~lL~l~~e~~~~~~k~~~sv~i~LD~~v~~Sp~L~~d~LE~~fPY~LiR~aY~~~y~~~ 1116 (1116)
T PF09735_consen 1053 ALASSSLLRLGQETDKSALKSRESVYIFLDQIVEESPFLTRDLLESCFPYALIRNAYHQVYENS 1116 (1116)
T ss_dssp HHHHHHHHHTTS---TTTTTTHHHHHHHHHHHHHH-TT--HHHHHHHS-HHHHHHHHHHHH---
T ss_pred HHHHHHHHHHhhhccccccccccchhhhHHHHHhcCCCCChHHHHHhCCHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999999999999999975
No 2
>KOG1917|consensus
Probab=100.00 E-value=1.2e-171 Score=1396.65 Aligned_cols=537 Identities=58% Similarity=0.940 Sum_probs=525.3
Q ss_pred CCCccchhhhhhhhchhhHHHHHHHHHHHHHHhccCcchHhhhhcCccccCCCCCcccCccccccccccccchhhhhhhh
Q psy17468 1 MDYEVPMKKLSEEFIPHAKLLFQALMSLRAIYSYRNVSADQMRNDQKLSLVGNPGQLLKPARTERMSCEYLSQESLDRWI 80 (538)
Q Consensus 1 ~dyd~PlKkL~eef~p~~~~i~~aL~Sl~~~y~rr~~~a~~wR~~~~Lsl~~~P~~~l~pa~sd~~~cE~ls~e~m~~Wi 80 (538)
+||++|+||+.|+|+||.+++++||.|+...|.+||+.|++||..++||++.+|+.+++++++|||+|||++++.|++||
T Consensus 182 ~dyenplkk~~e~f~P~~~~l~~aL~s~~h~y~~rnl~adswR~~~~lsl~~~p~~llr~~~~dt~~ceylsl~~~~~wi 261 (1125)
T KOG1917|consen 182 LDYENPLKKLNEEFLPHHRLLPDALTSLTHPYRRRNLAADSWREWQLLSLLVAPAELLRAAQTDTMLCEYLSLDAMDRWI 261 (1125)
T ss_pred HhccchHHHHhhhhCCcchhHHHHHHhcccchhhhcCCcchHHHHHHHHHhhCHHHHHhhcchhhHHHHHHhcchHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred heeeeccCCCCCC-chhHHHHHHHhcCCceEEeechhhHhhHHHHHHHHhhhhhcccchhHHhhHHHHHHHHhhHHHHHH
Q psy17468 81 IFGFMLCHQPLSQ-EPVSKLWTAALENNWVIALFRDEVIYIHQYIQGFFDTIKGYGKRVSEVKDCYSHAVSKAALEHREK 159 (538)
Q Consensus 81 i~g~L~cp~~L~~-~~~~~lw~~aL~~~~vl~LfRdev~~iH~~~e~~~~s~K~y~Kr~~~vkE~~~~A~~~~~~~HreR 159 (538)
+||.++||.++.+ ++...+|+.+|++++|+.+||||++.+|+++|+.|.++|||+||+++||||+++|++.|+.+||||
T Consensus 262 ~f~~~vch~~l~~~~~~~~~w~ial~m~~~l~~frde~~~lh~~~e~~~~~i~g~sKr~~~i~e~~~~a~q~a~~~hrer 341 (1125)
T KOG1917|consen 262 IFGQMVCHKELGIDISFASAWSLALQMSYCLLLFRDEVFVIHQVIEAKFMAIKGYSKRIKDIKEAHEQAVQLADTMHRER 341 (1125)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCcchHHHHHHhhhhhhhhhHHHhhcCCCCCCCCCCCCCccccccCcchHHHH-------
Q psy17468 160 RKFLRTALKELGLLFSDQPGLLGPKALLIFIGLSYARDEVYWLLRHNDNPPVQKGKSKSAEDLVDRQLPELEM------- 232 (538)
Q Consensus 160 R~~LR~aLkel~~ll~DqPgLLgPK~l~vf~aLs~aRdEV~Wl~rH~~~~p~~~k~k~~~ed~~D~~l~eLLf------- 232 (538)
|+|||+++|||.++++|||||||||+++|||||++|||||+||+||++++|.+||+....+|++|+++|||+|
T Consensus 342 r~flr~~l~el~l~~tdQpglLgpk~~~vf~alalardevlwllrh~~~~~~r~k~~r~~~~~iD~~~pel~f~m~eLr~ 421 (1125)
T KOG1917|consen 342 RKFLRSALKELALFLTDQPGLLGPKILFVFMALALARDEVLWLLRHADNAPSRKKAARSIEDLIDRQLPELLFYMEELRA 421 (1125)
T ss_pred HHHHHHHHHHHHHHHhcCccccCcchhHHHHHHHHHHHHHHHHHHhcccchhhhcccccCCccccccchHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999877666789999999999999
Q ss_pred ---H----------------------------------------------------------------------------
Q psy17468 233 ---K---------------------------------------------------------------------------- 233 (538)
Q Consensus 233 ---k---------------------------------------------------------------------------- 233 (538)
|
T Consensus 422 LVrKy~~v~qrYylqYLS~fda~vl~~~~q~l~vcpe~Esii~ssF~n~~~~L~~kqvfr~~RldwfrlQay~Sv~ka~l 501 (1125)
T KOG1917|consen 422 LVRKYISVMQRYYLQYLSSFDARVLNEMGQPLIVCPEDESILKSSFQNTVQHLESKQVFRIPRLDWFRLQAYTSVTKALL 501 (1125)
T ss_pred HHHHHHHHHHHHHHHHHhhhhHHHHHHHhcccccCCchhHHHHHHHHHHHHhhhhhhhccchhhhHHHhHHHHHHHhhHh
Confidence 0
Q ss_pred --------------------------------------------------------------------------------
Q psy17468 234 -------------------------------------------------------------------------------- 233 (538)
Q Consensus 234 -------------------------------------------------------------------------------- 233 (538)
T Consensus 502 ~l~~h~~la~~mnt~vfhs~mid~lee~lveTsdlslfcfy~~~fek~f~~cle~paq~ry~iAfpllcshF~~cthemc 581 (1125)
T KOG1917|consen 502 DLAKHWELALMMNTSVFHSKMIDSLEEMLVETSDLSLFCFYNKAFEKMFNMCLELPAQPRYCIAFPLLCSHFPSCTHEMC 581 (1125)
T ss_pred hhhhCHHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHhhCCccccchHHHHHHHHHHhhhhhhhhC
Confidence
Q ss_pred --------------------------------------------------------------------------------
Q psy17468 234 -------------------------------------------------------------------------------- 233 (538)
Q Consensus 234 -------------------------------------------------------------------------------- 233 (538)
T Consensus 582 PEE~~hi~~~al~~cnsflEe~akq~~nli~~ic~eq~~La~QLlPkhcA~~ls~a~~~k~~s~k~~k~~~~r~kpG~ES 661 (1125)
T KOG1917|consen 582 PEERHHIGERALSYCNSFLEEMAKQLSNLITIICSEQCTLADQLLPKHCAKTLSNASNKKKKSQKSPKGEPERDKPGHES 661 (1125)
T ss_pred chhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcchHhhhCHHHHHHHHHHHHHhhccCCCCCCCCCcCCCCcccc
Confidence
Q ss_pred --------------------------------------------------------------------------------
Q psy17468 234 -------------------------------------------------------------------------------- 233 (538)
Q Consensus 234 -------------------------------------------------------------------------------- 233 (538)
T Consensus 662 yrknr~~lt~lDklh~~LteLc~~ln~~~~i~V~eHtf~prEYL~~~Le~rf~r~~vgm~~~nqtt~ei~kPSeLla~vr 741 (1125)
T KOG1917|consen 662 YRKNRKSLTMLDKLHTALTELCFALNYVPPICVWEHTFAPREYLRQHLEGRFKRRLVGMLMYNQTTQEIAKPSELLASVR 741 (1125)
T ss_pred ccchhhhhccHHHHHHHHHHHHHHhccCCceeEEeecccHHHHHHHHHHHHHHHHHHHHHHcCCccccccChHHHHHHHH
Confidence
Q ss_pred ---------------------------------------------------------------------Hh---hcCCcc
Q psy17468 234 ---------------------------------------------------------------------FI---AEGAIP 241 (538)
Q Consensus 234 ---------------------------------------------------------------------Fv---~~~~~~ 241 (538)
|| ++|+++
T Consensus 742 ayM~vlq~leq~v~~Ditrvir~~LLqQtq~lDs~gEqTi~~lytnWYlE~LLR~vSsg~Iv~sp~~kafvs~~~e~~~~ 821 (1125)
T KOG1917|consen 742 AYMGVLQSLEQYVSIDITRVIRNILLQQTQSLDSHGEQTIAALYTNWYLEVLLRRVSSGHIVFSPAMKAFVSLPPEGELG 821 (1125)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHhhhcccCCCchhHHHHHHHHHHHHHHHHhcCCcEEechHHHhhccCCccccCC
Confidence 45 557799
Q ss_pred cccccCCCHHHHHHHHHhhCchhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcCCCHHHHHHHHhhhhcHHHHH
Q psy17468 242 FNAEEFSDVNELRALADLIGPYGMKLLNETLMWHIASQVQELKKLVAANKEVLLLLRTHFDKPEIMKEQSKRLHNVENVL 321 (538)
Q Consensus 242 f~AE~ysD~~ELrAL~eLiGPYG~k~L~e~L~~hia~qv~elkklv~~N~d~L~~lr~~f~~p~~m~~~lk~L~~~e~~l 321 (538)
|+||+|||++|||||+||+||||||+|+|+||||||+||+||||+|++|+|+|+++|+||||||+|++++++|+.+|+|+
T Consensus 822 f~aee~SDl~ElrAlvel~GpYGvk~Lse~LmwHvasqV~elkklv~tn~d~L~~~rssfdkpd~m~~~~~~l~~~D~VL 901 (1125)
T KOG1917|consen 822 FNAEEYSDLSELRALVELLGPYGVKFLSEMLMWHVASQVNELKKLVVTNKDVLEQARSSFDKPDRMKRLLKRLQIADTVL 901 (1125)
T ss_pred CChhhcCCHHHHHHHHHHhCchhhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhCCCHHHHHHHHHHHhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHhccCchhhhhHHHHhhcCCCCCCch----HHHHHHHhCCCCCCCHHHHHHHhccCC
Q psy17468 322 QRMTIIGVILNFQRIAQLALQEVLESRVPFLLNSVQDFYQHSPVGDPKI----VNEMASAAGLLCTVDPALATALASDKT 397 (538)
Q Consensus 322 ~r~~iiG~iL~FR~l~~eAl~~VL~~~~Pfl~s~I~~~~~~~~~~~~l~----v~~lA~aaGl~~~vD~~Lv~al~~~~~ 397 (538)
+||||||+||+||+|+|||+++||++|+|||+|+|+|+++|+|+++|+| +.|||++||+.|||||+||++|+++++
T Consensus 902 ~rmtiiGvil~Frdll~Ealr~Vle~~~pfL~ssi~~l~ehip~~~~iKv~~~~~emasaaGv~cdvDp~lV~ai~~~k~ 981 (1125)
T KOG1917|consen 902 QRMTIIGVILSFRDLLHEALRDVLESHIPFLHSSIEDLKEHIPEEDDIKVAIRRIEMASAAGVACDVDPALVRAILSQKP 981 (1125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccCcHHhhhHHHHHhhCCCccchhHHHHHHHHHhhcCCCCCCCHHHHHHHHHhCC
Confidence 9999999999999999999999999999999999999999999999966 667999999999999999999999999
Q ss_pred C-CCchhhHHHHHHHHHHHHHhcccccCCccccccccccccchhhhHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHhh
Q psy17468 398 D-LDEDEHVLACLLMVFVAVCIPKLARNEACFYLASLEGHSNNIHCMASAINHIFSALFTLCGQGDLEDRMKEFLALTSS 476 (538)
Q Consensus 398 ~-~~d~~y~~w~LL~vf~avslp~l~~~~~s~y~~~~~g~~NN~HCla~aIn~l~~a~f~l~g~~~Ie~~mkeFL~lASs 476 (538)
+ +||++|++|||||||+|||+|++|.+++|+|++++|||+|||||+|+|||+|+||+|++|++.||++|||||+++|||
T Consensus 982 ~~~peeey~~acLLmvfvAvsip~la~n~~S~y~~ei~g~~NNiHCla~aIn~i~aALftlh~~sdie~rmkeflalaSs 1061 (1125)
T KOG1917|consen 982 EIHPEEEYKSACLLMVFVAVSIPSLAWNDTSFYSIEIDGHSNNIHCLAKAINQIIAALFTLHHQSDIEDRMKEFLALASS 1061 (1125)
T ss_pred CCCchHhhhhhHHHHHHHHHhcchhccCCccccCccccccccchHHHHHHHHHHHHHHHhhhccccccHHHHHHHHHHHH
Confidence 9 899999999999999999999999999999999999999999999999999999999999788899999999999999
Q ss_pred hhhccCCCCCCcccCCcchhHhhHHHHHhcCCCCchhhhhhhchHHHHHHHHHHhhhhccC
Q psy17468 477 SLLRLGQDPDEESTRHRDSVYLLLHQIVQESPFLTMDLLESCFPYALIRNAYHAVSKQEHA 537 (538)
Q Consensus 477 ~lL~l~~e~~k~~~k~r~sv~ilLdqiV~~SpfLt~d~LEscfPY~LlRnaY~~~y~~~~~ 537 (538)
+|||+|||+||..+|||+++||||||+||+|||||||+|||||||+|+|||||+||+++++
T Consensus 1062 sLL~~gqetdk~~tRnresiyllLdqive~SpfLtmd~LEScfPYvLlRnaY~qvy~~~~~ 1122 (1125)
T KOG1917|consen 1062 SLLRLGQETDKVATRNRESIYLLLDQIVEESPFLTMDLLESCFPYVLLRNAYHQVYKATPS 1122 (1125)
T ss_pred HHHHHHHhhhhhhhcchhhHHHHHHHHHhhCCCccHHHHHhhchHHHHHHHHHHHHhccCC
Confidence 9999999999999999999999999999999999999999999999999999999999976
No 3
>KOG1917|consensus
Probab=99.24 E-value=1.4e-12 Score=146.28 Aligned_cols=206 Identities=10% Similarity=-0.117 Sum_probs=185.1
Q ss_pred CCccchhhhhhhhchhhHHHHHHHHHHHHHHhccCcchHhhhhcCccccCCCCCcccCccccccccccccchhhhhhhhh
Q psy17468 2 DYEVPMKKLSEEFIPHAKLLFQALMSLRAIYSYRNVSADQMRNDQKLSLVGNPGQLLKPARTERMSCEYLSQESLDRWII 81 (538)
Q Consensus 2 dyd~PlKkL~eef~p~~~~i~~aL~Sl~~~y~rr~~~a~~wR~~~~Lsl~~~P~~~l~pa~sd~~~cE~ls~e~m~~Wii 81 (538)
+|+||.++..++ +++.|...-...++.|...+|+..+|+|+.+.+. .+|..+-.+...+++.|||++.+++++|..
T Consensus 208 s~~h~y~~rnl~-adswR~~~~lsl~~~p~~llr~~~~dt~~ceyls---l~~~~~wi~f~~~vch~~l~~~~~~~~~w~ 283 (1125)
T KOG1917|consen 208 SLTHPYRRRNLA-ADSWREWQLLSLLVAPAELLRAAQTDTMLCEYLS---LDAMDRWIIFGQMVCHKELGIDISFASAWS 283 (1125)
T ss_pred hcccchhhhcCC-cchHHHHHHHHHhhCHHHHHhhcchhhHHHHHHh---cchHHHHHHHHHHHHHHHhcccHHHHHHHH
Confidence 589999999999 9999999999999999999999999999998876 566667788888999999999999999999
Q ss_pred eeeeccCCCCCC-chhHHHHHHHhcCCceEEeechhhHhhHHHHHHHHhhhhhcccchhHHhhHHHHHHHHhhHHHHHHH
Q psy17468 82 FGFMLCHQPLSQ-EPVSKLWTAALENNWVIALFRDEVIYIHQYIQGFFDTIKGYGKRVSEVKDCYSHAVSKAALEHREKR 160 (538)
Q Consensus 82 ~g~L~cp~~L~~-~~~~~lw~~aL~~~~vl~LfRdev~~iH~~~e~~~~s~K~y~Kr~~~vkE~~~~A~~~~~~~HreRR 160 (538)
+|+..|+..+.- .+...+|+.+.+....++.++.. ..++++++.+.+++|..+-....+..|.++|
T Consensus 284 ial~m~~~l~~frde~~~lh~~~e~~~~~i~g~sKr-------------~~~i~e~~~~a~q~a~~~hrerr~flr~~l~ 350 (1125)
T KOG1917|consen 284 LALQMSYCLLLFRDEVFVIHQVIEAKFMAIKGYSKR-------------IKDIKEAHEQAVQLADTMHRERRKFLRSALK 350 (1125)
T ss_pred HHHHHHHHHHhcchHHHHHHHHHHHHHHhhhhhhHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999877 99999999998888777766655 3456778889999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcCCCCCcchHHHHHHhhhhhhhhhHHHhhcCCCCCCCCCCCCCccccccCcchH
Q psy17468 161 KFLRTALKELGLLFSDQPGLLGPKALLIFIGLSYARDEVYWLLRHNDNPPVQKGKSKSAEDLVDRQLPE 229 (538)
Q Consensus 161 ~~LR~aLkel~~ll~DqPgLLgPK~l~vf~aLs~aRdEV~Wl~rH~~~~p~~~k~k~~~ed~~D~~l~e 229 (538)
++++-..+|..++.-+-|++.+|+++.-++.|.+-|+++.|..| ..+..+ .+ +++|..||.|.+
T Consensus 351 el~l~~tdQpglLgpk~~~vf~alalardevlwllrh~~~~~~r-~k~~r~-~~---~~iD~~~pel~f 414 (1125)
T KOG1917|consen 351 ELALFLTDQPGLLGPKILFVFMALALARDEVLWLLRHADNAPSR-KKAARS-IE---DLIDRQLPELLF 414 (1125)
T ss_pred HHHHHHhcCccccCcchhHHHHHHHHHHHHHHHHHHhcccchhh-hccccc-CC---ccccccchHHHH
Confidence 99999999999999999999999999999999999999999999 333333 23 899999999874
No 4
>PF10266 Strumpellin: Hereditary spastic paraplegia protein strumpellin; InterPro: IPR019393 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. Strumpellin contains one known domain called a spectrin repeat that consists of three alpha-helices of a characteristic length wrapped in a left-handed coiled coil. The spectrin proteins have multiple copies of this repeat, which can then form multimers in the cell. Spectrin associates with the cell membrane via spectrin repeats in the ankyrin protein. The spectrin repeat is a structural platform for cytoskeletal protein assemblies. Two closely situated point mutations in human strumpellin lead to the condition of hereditary spastic paraplegia.
Probab=85.71 E-value=81 Score=38.94 Aligned_cols=194 Identities=19% Similarity=0.311 Sum_probs=126.4
Q ss_pred cccccCcchHHHHHHh--hcCCcc---------ccc---ccCCCHHHHHHHHHhhCchhHHHHHHHHHHHHHHHHHHHHH
Q psy17468 220 EDLVDRQLPELEMKFI--AEGAIP---------FNA---EEFSDVNELRALADLIGPYGMKLLNETLMWHIASQVQELKK 285 (538)
Q Consensus 220 ed~~D~~l~eLLfkFv--~~~~~~---------f~A---E~ysD~~ELrAL~eLiGPYG~k~L~e~L~~hia~qv~elkk 285 (538)
++-.-..|+.|.-..+ |++..+ |.+ .|.-...-...+.+-+||+|+-=||+-+-.+|+..++.+-+
T Consensus 792 ~~~s~nFiGRLa~eiLriTDPk~T~Y~~~~~~WyD~kt~~EVlg~~~Fs~l~~aig~~GL~GLDrLlsfmi~keLq~~~~ 871 (1081)
T PF10266_consen 792 DDNSVNFIGRLAREILRITDPKTTIYLEQMNGWYDKKTHKEVLGTKTFSRLQEAIGTFGLTGLDRLLSFMIVKELQNFLS 871 (1081)
T ss_pred CCccccHHHHHHHHHHhhcCCCeeEeecccCceecCCCcchhhCHHHHHHHHHHhCccccccHHHHHHHHHHHHHHHHHH
Confidence 3455577888855322 222222 221 44446667778889999999999999999999888777666
Q ss_pred HHHHh-------HHHHHHHHhcCCC----H----HHHHHHHhhhh-cHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhccC
Q psy17468 286 LVAAN-------KEVLLLLRTHFDK----P----EIMKEQSKRLH-NVENVLQRMTIIGVILNFQRIAQLALQEVLESRV 349 (538)
Q Consensus 286 lv~~N-------~d~L~~lr~~f~~----p----~~m~~~lk~L~-~~e~~l~r~~iiG~iL~FR~l~~eAl~~VL~~~~ 349 (538)
.+..+ .++|..+.+.+.. | +.-++..+++. ..-.++..+..||++==.|+++.-.|+.--+-+.
T Consensus 872 ~~~~~l~~d~~~~~~L~~L~~~l~p~~~~p~n~~K~Y~~~~~~~~k~~~~ll~~i~~IGQ~QLLR~qIa~eL~~scK~dS 951 (1081)
T PF10266_consen 872 TIQKNLQKDKMWRDVLASLQKALTPESSIPENPSKVYEQAVKKISKSWPPLLDWILKIGQLQLLRRQIANELNSSCKFDS 951 (1081)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHhCCCccCcccchHHHHHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHHHHHHHhccCc
Confidence 55443 3778888766652 2 22345555554 5678899999999999999999999999999999
Q ss_pred chhhhhHHHH--------hhcCCCC--CCch----HHHHH---HHhCCCCCCCHHHHHHHhccCCCCCchhhHHHHHHHH
Q psy17468 350 PFLLNSVQDF--------YQHSPVG--DPKI----VNEMA---SAAGLLCTVDPALATALASDKTDLDEDEHVLACLLMV 412 (538)
Q Consensus 350 Pfl~s~I~~~--------~~~~~~~--~~l~----v~~lA---~aaGl~~~vD~~Lv~al~~~~~~~~d~~y~~w~LL~v 412 (538)
..|.++++.+ ..|+... .|.. +.|++ .++|+.. |-=+--+... ..+. +..++..
T Consensus 952 ~~L~~aL~tlN~ALL~Di~~hy~~p~s~p~P~e~LL~eLs~yL~~~Gi~d---Pl~KIYittk---plp~---~~llLfL 1022 (1081)
T PF10266_consen 952 KSLFAALETLNKALLNDIEAHYRDPDSKPYPSEDLLPELSKYLEAAGISD---PLRKIYITTK---PLPN---FPLLLFL 1022 (1081)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHhcCCC---HHHhhcccCC---CCcc---cHHHHHH
Confidence 9998887765 4565332 3322 55555 4667764 4333333322 2233 4556656
Q ss_pred HHHHHhcccc
Q psy17468 413 FVAVCIPKLA 422 (538)
Q Consensus 413 f~avslp~l~ 422 (538)
|+..-+|.+-
T Consensus 1023 ftIsqLpkl~ 1032 (1081)
T PF10266_consen 1023 FTISQLPKLQ 1032 (1081)
T ss_pred HHHHhcchhc
Confidence 6666677664
No 5
>TIGR02509 type_III_yopR type III secretion effector, YopR family. Members of this family are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yops protein is unusual in that it is released to extracellularly rather than injected directly into the target cell as are most Yops.
Probab=72.78 E-value=26 Score=32.93 Aligned_cols=75 Identities=17% Similarity=0.315 Sum_probs=52.0
Q ss_pred hhhhhhHHHhhcCCCCCCCCCCCCCccccccCcchHHHH-----HHhhc-CCcccccccCCCHHHHHHHHHhhCchhHHH
Q psy17468 194 YARDEVYWLLRHNDNPPVQKGKSKSAEDLVDRQLPELEM-----KFIAE-GAIPFNAEEFSDVNELRALADLIGPYGMKL 267 (538)
Q Consensus 194 ~aRdEV~Wl~rH~~~~p~~~k~k~~~ed~~D~~l~eLLf-----kFv~~-~~~~f~AE~ysD~~ELrAL~eLiGPYG~k~ 267 (538)
-++.|++|+--|+++.++- +.+++..|| +.+.+ ++..-.++-=.|..||||+.+=+-|.|-+.
T Consensus 11 ~~~re~lWq~~~q~~~~~~-----------~~~~~~~L~~pv~e~Ll~~F~g~~l~v~p~~D~~ELrA~lref~Plg~q~ 79 (131)
T TIGR02509 11 ATQRELLWQQYQQGKPAAG-----------TADLVPELLSPVKERLLGRFGGQQLPVVPPIDRLELRAMLRQFDPLGRQQ 79 (131)
T ss_pred HHHHHHHHHHHHccCCCcc-----------hhHHHHHHHHHHHHHHHHHhcccccCCCCccchHHHHHHHHHhCccchHH
Confidence 4678999999887776532 234455665 22211 333344555689999999999999999875
Q ss_pred HHHHHHHHHHHHHH
Q psy17468 268 LNETLMWHIASQVQ 281 (538)
Q Consensus 268 L~e~L~~hia~qv~ 281 (538)
|..+||+-+-+.
T Consensus 80 --E~~Ll~~l~~lK 91 (131)
T TIGR02509 80 --EAALLQLLGKLK 91 (131)
T ss_pred --HHHHHHHHHHcc
Confidence 888898865554
No 6
>PF05994 FragX_IP: Cytoplasmic Fragile-X interacting family; InterPro: IPR008081 Cytoplasmic fragile X mental retardation protein (FMRP) interacting protein belongs to a highly conserved but, as yet, functionally uncharacterised family. Absence of FMRP is responsible for pathologic manifestations in Fragile X Syndrome, the most frequent cause of inherited mental retardation []. FMRP is an RNA-binding protein that may have a role in local protein translation at neuronal dendrites and in dendritic spine maturation []. CYFIP1 and CYFIP2, which share a high level of sequence identity, have recently been identified as cytoplasmic FMRP interacting proteins []. CYFIP2 interacts with FMRP-related proteins FXR1P/2P, while CYFIP1 interacts exclusively with FMRP. The FMRP-CYFIP interaction involves the domain of FMRP that also mediates homo- and heteromerisation, suggesting competition between the various interaction partners. CYFIP1 also interacts with the small GTPase Rac1 implicated in development and maintenance of neuronal structures. CYFIP1/2 are both present in synaptosomal extracts []. PIR121 (121F-specific p53 inducible RNA) is another functionally uncharacterised member of this family. The PIR121 gene maps to human chromosome 5q34, a region frequently translocated in acute myeloid leukaemia but not known to be amplified or deleted in solid tumours. Interaction between PIR121 and FMRP has been demonstrated, and hence PIR121 has also been termed CYFIP2 (Cytoplasmic FMRP Interacting Protein 2) [, ]. Shyc (Selective HYbridizing Clone) is a cytoplasmic protein of unknown function, expressed in the developing and embryonic nervous system. The protein has also been designated CYFIP1 due to the high sequence identity (98.7%) to its human orthologue. The CYFIP orthologues in Caenorhabditis elegans and Drosophila melanogaster (Fruit fly) share about 51% and 67% sequence identity with the human proteins, respectively []. The high level of conservation manifest throughout the entire CYFIP sequence between various orthologues suggests a number of functionally/structurally important domains. ; PDB: 3P8C_A.
Probab=65.69 E-value=20 Score=42.80 Aligned_cols=108 Identities=20% Similarity=0.254 Sum_probs=67.0
Q ss_pred CHHHHHHHHHhhCchhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH-HHhcCCCHHHH---HHHHhhhh---cHHHHH
Q psy17468 249 DVNELRALADLIGPYGMKLLNETLMWHIASQVQELKKLVAANKEVLLL-LRTHFDKPEIM---KEQSKRLH---NVENVL 321 (538)
Q Consensus 249 D~~ELrAL~eLiGPYG~k~L~e~L~~hia~qv~elkklv~~N~d~L~~-lr~~f~~p~~m---~~~lk~L~---~~e~~l 321 (538)
-..-++|+++|+|.-|+-.+-+.|+.+|...+....+.+.+=+-.... -+-.+..+-.+ .+.++-+. ++.+|+
T Consensus 518 G~pH~~ai~rLLg~~~la~li~ell~~i~~~~~~~V~~l~~~mPk~~~lP~~dygs~g~~~~y~~~l~~~~~y~dLkevf 597 (820)
T PF05994_consen 518 GVPHFKAIVRLLGYRGLAVLIEELLKLIQNKIEPYVKALMEAMPKSCKLPPFDYGSAGVYDYYEAQLKDIIQYPDLKEVF 597 (820)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHS-SB-----GGG-HHHHHHHHHHHTHHHHS-TTTTTHH
T ss_pred ChHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccCCCccCCCHHHHHHHHHHHHHHHhchhHHHHH
Confidence 457899999999999999999999998876654333322211111111 11222223333 44555433 788999
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHH----HhccCchhhhhH
Q psy17468 322 QRMTIIGVILNFQRIAQLALQEV----LESRVPFLLNSV 356 (538)
Q Consensus 322 ~r~~iiG~iL~FR~l~~eAl~~V----L~~~~Pfl~s~I 356 (538)
+-+-.||+++-|=.|+-+||... +-.-.||.-...
T Consensus 598 q~frEiGN~i~f~~lLd~al~q~e~~~~~~aapf~~~~p 636 (820)
T PF05994_consen 598 QAFREIGNAIVFCLLLDQALSQEEVCDLLQAAPFQGIIP 636 (820)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT---
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCC
Confidence 99999999999999999999321 233455554433
No 7
>PF14744 WASH-7_mid: WASH complex subunit 7
Probab=56.50 E-value=50 Score=35.81 Aligned_cols=76 Identities=18% Similarity=0.183 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHhcCCCHHHHHHHHhhhh----------cHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q psy17468 274 WHIASQVQELKKLVAANKEVLLLLRTHFDKPEIMKEQSKRLH----------NVENVLQRMTIIGVILNFQRIAQLALQE 343 (538)
Q Consensus 274 ~hia~qv~elkklv~~N~d~L~~lr~~f~~p~~m~~~lk~L~----------~~e~~l~r~~iiG~iL~FR~l~~eAl~~ 343 (538)
+||-+++..=-+...+|++.. .+-+.=|+.+...|.++ -+|-+=+..|+||++++|=+|++.|-..
T Consensus 256 e~IksrL~kd~r~~~e~k~~~----~~~Yp~erAekf~k~irkLG~~~dG~sylD~FR~LItqIGNA~gyVRmirsggl~ 331 (350)
T PF14744_consen 256 EHIKSRLLKDIRFFRENKESK----DQKYPYERAEKFNKGIRKLGLSDDGQSYLDQFRQLITQIGNAMGYVRMIRSGGLH 331 (350)
T ss_pred HHHHHHHHHHHHHHHHhhhcc----CCCCCHHHHHHHHHHHHHcCCCCCcchHHHHHHHHHHHHhHHHHHHHHHHHHhHH
Confidence 344444443334456666542 23334344455544444 3677777789999999999999999998
Q ss_pred HHhccCchhh
Q psy17468 344 VLESRVPFLL 353 (538)
Q Consensus 344 VL~~~~Pfl~ 353 (538)
.....+.|+-
T Consensus 332 ~~~~a~~fvp 341 (350)
T PF14744_consen 332 YCSNAIRFVP 341 (350)
T ss_pred HhcCCcccCC
Confidence 8888887764
No 8
>PRK15354 type III secretion system protein SsaK; Provisional
Probab=54.97 E-value=33 Score=34.80 Aligned_cols=54 Identities=24% Similarity=0.228 Sum_probs=44.9
Q ss_pred hHHhhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhhcCCCCCcchHHHHHHhhhhhhhhhHHHhhcCCC
Q psy17468 139 SEVKDCYSHAVSKAALEHREKRKFLRTALKELGLLFSDQPGLLGPKALLIFIGLSYARDEVYWLLRHNDN 208 (538)
Q Consensus 139 ~~vkE~~~~A~~~~~~~HreRR~~LR~aLkel~~ll~DqPgLLgPK~l~vf~aLs~aRdEV~Wl~rH~~~ 208 (538)
..+++|+..|..---.-|+++|..++++-++...+.. =...+-|..|+-||..-
T Consensus 45 ~il~~A~rkA~~I~q~A~~~~~~ll~qaqqqad~L~~----------------~~~~~~E~~~L~qHV~w 98 (224)
T PRK15354 45 AIVSSAYRKAEKIIRDAYRYQREQKVEQQQELACLRK----------------NTLEKMEVEWLEQHVKH 98 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHH
Confidence 4677777777766667799999999999999999887 45678999999999754
No 9
>PLN03099 PIR Protein PIR; Provisional
Probab=53.43 E-value=84 Score=39.01 Aligned_cols=103 Identities=19% Similarity=0.322 Sum_probs=70.9
Q ss_pred HHHHHHHHHhhCchhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH----HHhcCCCHHHHHHHHhhhhc------HHH
Q psy17468 250 VNELRALADLIGPYGMKLLNETLMWHIASQVQELKKLVAANKEVLLL----LRTHFDKPEIMKEQSKRLHN------VEN 319 (538)
Q Consensus 250 ~~ELrAL~eLiGPYG~k~L~e~L~~hia~qv~elkklv~~N~d~L~~----lr~~f~~p~~m~~~lk~L~~------~e~ 319 (538)
..-+.|+++|+|.-|+-.+-+.|+.||.+.++.|...|..=++++-. -+--+-.|-.|.-..-||++ --+
T Consensus 869 ~pH~~ai~rLlG~~~la~vi~~lL~~i~~~i~~l~~~v~~L~~~mPk~~~Lp~~dyG~~g~~~~~~~qL~~~~~yelk~e 948 (1232)
T PLN03099 869 LPHMFAIVKLLGSRSLPWLIRALLDHLSQKITTLEPMIEDLREAMPKAIGLPSFDGGVAGCMKIFREQLQWGTKYEGKSE 948 (1232)
T ss_pred cHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCccccCchHHHHHHHHHHhHHhhhhhhHH
Confidence 46689999999999999999999999999999887777665554111 11122233344322223331 235
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHH----HhccCchh
Q psy17468 320 VLQRMTIIGVILNFQRIAQLALQEV----LESRVPFL 352 (538)
Q Consensus 320 ~l~r~~iiG~iL~FR~l~~eAl~~V----L~~~~Pfl 352 (538)
|++-.-.||.++-|=.++-.||+.+ +-.-+||+
T Consensus 949 v~q~fREiGn~i~f~~Lld~aL~qee~~~~~~aAPfl 985 (1232)
T PLN03099 949 VLRGLKEIGSLIFWMSLLDIAMREVETVQFMQVAPWL 985 (1232)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcccc
Confidence 6777788999999999999888765 44455665
No 10
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=53.08 E-value=21 Score=29.38 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=30.2
Q ss_pred HHHHHhhh-hhcccchhHHhhHHHHHHHH-hhHHHHHHHHHHHHH
Q psy17468 124 IQGFFDTI-KGYGKRVSEVKDCYSHAVSK-AALEHREKRKFLRTA 166 (538)
Q Consensus 124 ~e~~~~s~-K~y~Kr~~~vkE~~~~A~~~-~~~~HreRR~~LR~a 166 (538)
++++|++| |.|||-+.+-.+ .+-.. .+..|.||..+||.+
T Consensus 2 ~~sy~~~Ie~kTGk~~~~W~~---~~~~~~~~~k~~e~v~WLK~e 43 (61)
T PF14117_consen 2 FQSYLPNIEKKTGKTLDEWLA---LAREGGPLTKHGEIVAWLKDE 43 (61)
T ss_pred HHHHHhHhHHHHCcCHHHHHH---HHHHhCCCCcHHHHHHHHHHH
Confidence 57889999 568988655544 34444 788999999999985
No 11
>KOG1921|consensus
Probab=41.51 E-value=45 Score=34.75 Aligned_cols=73 Identities=22% Similarity=0.391 Sum_probs=50.1
Q ss_pred echhhHhhHHHHHHHHhhhhhcc----cchhHHhhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhhcC-----------
Q psy17468 113 FRDEVIYIHQYIQGFFDTIKGYG----KRVSEVKDCYSHAVSKAALEHREKRKFLRTALKELGLLFSDQ----------- 177 (538)
Q Consensus 113 fRdev~~iH~~~e~~~~s~K~y~----Kr~~~vkE~~~~A~~~~~~~HreRR~~LR~aLkel~~ll~Dq----------- 177 (538)
.||||-. +. ..++|.|| -.+..+.|..=.-+..+.++|...=+||++ .+.|++|+
T Consensus 91 TKDevt~-----~A-m~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkk----ta~IL~d~f~gDIP~~v~d 160 (286)
T KOG1921|consen 91 TKDEVTA-----AA-MLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKK----TAKILQDKFDGDIPDTVED 160 (286)
T ss_pred hHHHHHH-----HH-HHHHHHhcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHH----HHHHHHHHhCCCCchhHHH
Confidence 5888754 22 24556666 234444555444456788899999999764 67777777
Q ss_pred ----CCCCcchHHHHHHhhhhhh
Q psy17468 178 ----PGLLGPKALLIFIGLSYAR 196 (538)
Q Consensus 178 ----PgLLgPK~l~vf~aLs~aR 196 (538)
|| +|||+-.+-|+.+..+
T Consensus 161 LlsLPG-VGPKMa~L~m~~AWn~ 182 (286)
T KOG1921|consen 161 LLSLPG-VGPKMAHLTMQVAWNK 182 (286)
T ss_pred HhcCCC-CchHHHHHHHHHHhcc
Confidence 77 7999999988877665
No 12
>COG5181 HSH155 U2 snRNP spliceosome subunit [RNA processing and modification]
Probab=39.36 E-value=56 Score=38.20 Aligned_cols=60 Identities=33% Similarity=0.591 Sum_probs=41.1
Q ss_pred CHHHHHHHHHhhCchhHHHHHHH--HHHHHHHHH-----HHHHHHH-------------HHhHHHHHHHHhcCCCHH-HH
Q psy17468 249 DVNELRALADLIGPYGMKLLNET--LMWHIASQV-----QELKKLV-------------AANKEVLLLLRTHFDKPE-IM 307 (538)
Q Consensus 249 D~~ELrAL~eLiGPYG~k~L~e~--L~~hia~qv-----~elkklv-------------~~N~d~L~~lr~~f~~p~-~m 307 (538)
..+.|-+|+++.||||+..+|+- .+|.=++|- ..+-|.+ --.++..+.++.-|+.|| +|
T Consensus 378 tA~alS~lae~~~Pygie~fd~vl~pLw~g~~~hrgk~l~sfLkA~g~iiplm~peYa~h~tre~m~iv~ref~spdeem 457 (975)
T COG5181 378 TANALSYLAELVGPYGIEQFDEVLCPLWEGASQHRGKELVSFLKAMGFIIPLMSPEYACHDTREHMEIVFREFKSPDEEM 457 (975)
T ss_pred hHhHHHHHHHhcCCcchHHHHHHHHHHHHHHHhcCCchHHHHHHHhccccccCChHhhhhhHHHHHHHHHHHhCCchhhc
Confidence 34788999999999999999974 467655542 2222222 124667778888899887 56
Q ss_pred H
Q psy17468 308 K 308 (538)
Q Consensus 308 ~ 308 (538)
+
T Consensus 458 k 458 (975)
T COG5181 458 K 458 (975)
T ss_pred c
Confidence 3
No 13
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=36.83 E-value=2e+02 Score=28.76 Aligned_cols=96 Identities=15% Similarity=0.147 Sum_probs=52.8
Q ss_pred HHHHHHHhHHHHHHHHhcCCCHHHHHHHHhhhhcHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhccCchhh----hhHHH
Q psy17468 283 LKKLVAANKEVLLLLRTHFDKPEIMKEQSKRLHNVENVLQRMTIIGVILNFQRIAQLALQEVLESRVPFLL----NSVQD 358 (538)
Q Consensus 283 lkklv~~N~d~L~~lr~~f~~p~~m~~~lk~L~~~e~~l~r~~iiG~iL~FR~l~~eAl~~VL~~~~Pfl~----s~I~~ 358 (538)
.+.+..+-.+.|+.+++.-...++.+++++.+.+-+.-- ..+.-||=++..=++.-=+.-.|||- ..+++
T Consensus 98 ~~~f~~~f~~~l~~i~~~~~~~~~~~~l~~~f~~~~~s~------~iV~flRLlts~~l~~~~d~y~~fi~~~~~~tve~ 171 (244)
T PF10275_consen 98 FEDFYDEFLELLEKIANGESNSQRQEELLEAFNDEEISD------YIVIFLRLLTSAYLKSNSDEYEPFIDGLEYLTVEE 171 (244)
T ss_dssp HHHHHHHHHHHHHHHHCTSSHHH---HHHHHHTSHHHHH------HHHHHHHHHHHHHHHHTHHHHGGGSSTT--S-HHH
T ss_pred HHHHHHHHHHHHHHHHccCCccchHHHHHHHHhCcCccc------HHHHHHHHHHHHHHHhhHHHHhhhhcccccCCHHH
Confidence 344445555556666655555544446666665433211 14555664444445555566699998 55888
Q ss_pred Hh-hcCCC---CCC-chHHHHHHHhCCCCCC
Q psy17468 359 FY-QHSPV---GDP-KIVNEMASAAGLLCTV 384 (538)
Q Consensus 359 ~~-~~~~~---~~~-l~v~~lA~aaGl~~~v 384 (538)
++ .++.+ +.+ +.+..||.+.|++..|
T Consensus 172 ~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v 202 (244)
T PF10275_consen 172 FCSQEVEPMGKEADHVQIIALAQALGVPIRV 202 (244)
T ss_dssp HHHHHTSSTT--B-HHHHHHHHHHHT--EEE
T ss_pred HHHhhcccccccchhHHHHHHHHHhCCeEEE
Confidence 87 33322 333 7799999999999866
No 14
>KOG1463|consensus
Probab=36.62 E-value=46 Score=36.30 Aligned_cols=30 Identities=40% Similarity=0.737 Sum_probs=25.4
Q ss_pred hhcccchhHHhhHHHHHHHHhhHHHHHHHHHHHHHHH
Q psy17468 132 KGYGKRVSEVKDCYSHAVSKAALEHREKRKFLRTALK 168 (538)
Q Consensus 132 K~y~Kr~~~vkE~~~~A~~~~~~~HreRR~~LR~aLk 168 (538)
.+.|-++.-.+||.+-|. ||.|.|||++|.
T Consensus 102 ~~~~~~i~l~~~cIeWA~-------~ekRtFLRq~Le 131 (411)
T KOG1463|consen 102 DGTGDQIELCTECIEWAK-------REKRTFLRQSLE 131 (411)
T ss_pred CCcchHHHHHHHHHHHHH-------HHhHHHHHHHHH
Confidence 457777888999999886 799999999885
No 15
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=34.02 E-value=5e+02 Score=30.22 Aligned_cols=172 Identities=18% Similarity=0.216 Sum_probs=92.7
Q ss_pred HHHHHHHHHHHhccCchhhhhHHHHhhcCCCCCCchHHHHHHHhCCCCCCCHHHHHHHhcc--CCC-CCchhhHHHHHHH
Q psy17468 335 RIAQLALQEVLESRVPFLLNSVQDFYQHSPVGDPKIVNEMASAAGLLCTVDPALATALASD--KTD-LDEDEHVLACLLM 411 (538)
Q Consensus 335 ~l~~eAl~~VL~~~~Pfl~s~I~~~~~~~~~~~~l~v~~lA~aaGl~~~vD~~Lv~al~~~--~~~-~~d~~y~~w~LL~ 411 (538)
..+.+|+..+|+++.. =.+.|.-+++.|...+|=.|.-| -+|.+...|-.. +.+ .-..+++.-|..+
T Consensus 284 p~a~~ai~smLs~~~l-~paDI~~Ly~~Y~~~~pPPV~lL---------R~P~~l~lLld~LF~pg~~i~~e~r~kyi~L 353 (584)
T PF04858_consen 284 PEACQAIASMLSSNAL-NPADITKLYRMYSSPDPPPVELL---------RHPQFLDLLLDALFKPGSKINPEHRSKYIYL 353 (584)
T ss_pred chHHHHHHHHHhcCCC-CHHHHHHHHHHhccCCCCCchhh---------cCHHHHHHHHHHHcCCCccCCHHHHHHHHHH
Confidence 3567888899988776 45557777777765544111100 033333333210 111 2234555555555
Q ss_pred HHHHHHhcccccCCccccccccccccchhhhHHHHHHHHHHHH----hcccCCCCHHHHHHHHHH-----HHhhhhhccC
Q psy17468 412 VFVAVCIPKLARNEACFYLASLEGHSNNIHCMASAINHIFSAL----FTLCGQGDLEDRMKEFLA-----LTSSSLLRLG 482 (538)
Q Consensus 412 vf~avslp~l~~~~~s~y~~~~~g~~NN~HCla~aIn~l~~a~----f~l~g~~~Ie~~mkeFL~-----lASs~lL~l~ 482 (538)
.-+|+|.+.....+. + ++ .=|...+..+..++-.|. ....|..+....+..++. ++|+++|++-
T Consensus 354 LAYAasV~e~~~~~~----~--~~-~~~~del~~t~~ale~a~~ic~~~~~g~~~~~~el~~L~~~i~~PvVa~GVL~wi 426 (584)
T PF04858_consen 354 LAYAASVVETPAKNQ----P--DR-SLNCDELKSTKQALEKAHAICCNAARGSSELQAELPKLYSCIRYPVVAMGVLRWI 426 (584)
T ss_pred HHHHHHcccccccCc----c--cc-cccHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhCCChhhHHHHHHH
Confidence 566666543321111 1 11 113345555333332222 112244567778888877 8999999985
Q ss_pred CC--CCC----cccCCcchhHhhHHHHHhcCCCCchhhhhhhchHHHHHHHHH
Q psy17468 483 QD--PDE----ESTRHRDSVYLLLHQIVQESPFLTMDLLESCFPYALIRNAYH 529 (538)
Q Consensus 483 ~e--~~k----~~~k~r~sv~ilLdqiV~~SpfLt~d~LEscfPY~LlRnaY~ 529 (538)
+. ++. .....-...+.+||.|+...|.+-..+|+ +|+..+.
T Consensus 427 ~~~l~~~~~~~~~~~~~p~~L~LLdeIa~~Hp~lr~~vl~------lL~~~le 473 (584)
T PF04858_consen 427 ESFLTDPSYFSSITELTPVHLALLDEIATRHPLLRPSVLD------LLVRLLE 473 (584)
T ss_pred HHHhcCcchhhhccccCchHHHHhhHHHhcCHhhHHHHHH------HHHHHHH
Confidence 43 122 11212245778999999999999888873 5555554
No 16
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=32.80 E-value=18 Score=27.22 Aligned_cols=39 Identities=21% Similarity=0.407 Sum_probs=26.0
Q ss_pred HHHHHHHhhhhhcccchhHHhhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhhcCCCCCc
Q psy17468 122 QYIQGFFDTIKGYGKRVSEVKDCYSHAVSKAALEHREKRKFLRTALKELGLLFSDQPGLLG 182 (538)
Q Consensus 122 ~~~e~~~~s~K~y~Kr~~~vkE~~~~A~~~~~~~HreRR~~LR~aLkel~~ll~DqPgLLg 182 (538)
+.|++|++-++.|.++..+.+|. .+++..+|++.|.|+.
T Consensus 2 ~~Y~~FL~il~~y~~~~~~~~~v----------------------~~~v~~Ll~~hpdLl~ 40 (47)
T PF02671_consen 2 EVYNEFLKILNDYKKGRISRSEV----------------------IEEVSELLRGHPDLLE 40 (47)
T ss_dssp HHHHHHHHHHHHHHCTCSCHHHH----------------------HHHHHHHTTT-HHHHH
T ss_pred hHHHHHHHHHHHHHhcCCCHHHH----------------------HHHHHHHHccCHHHHH
Confidence 35788888888888775555542 3356677888777653
No 17
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=32.02 E-value=5.9e+02 Score=26.32 Aligned_cols=75 Identities=20% Similarity=0.314 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHH-HHHHHhcCCCHH--HHHHHHhhhhcHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhc
Q psy17468 271 TLMWHIASQVQELKKLVAANKEV-LLLLRTHFDKPE--IMKEQSKRLHNVENVLQRMTIIGVILNFQRIAQLALQEVLES 347 (538)
Q Consensus 271 ~L~~hia~qv~elkklv~~N~d~-L~~lr~~f~~p~--~m~~~lk~L~~~e~~l~r~~iiG~iL~FR~l~~eAl~~VL~~ 347 (538)
+=+.|+.++++++.+.+.+..|. |..+..+||.+. ..-+...-|-+.+.++..+.. .|-+.+......|+.+
T Consensus 164 ~c~~~L~~~L~e~~~~i~~~ld~~l~~~~~~Fd~~~Y~~v~~AY~lLgk~~~~~dkl~~-----~f~~~i~~~~~~vv~~ 238 (291)
T PF10475_consen 164 SCVRHLSSQLQETLELIEEQLDSDLSKVCQDFDPDKYSKVQEAYQLLGKTQSAMDKLQM-----HFTSAIHSTTFSVVRS 238 (291)
T ss_pred hHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhhHHHHHHHHH-----HHHHHHHHHHHHHHHH
Confidence 34557778888888888887775 778888887643 223333444445555554433 3777777777777766
Q ss_pred cCc
Q psy17468 348 RVP 350 (538)
Q Consensus 348 ~~P 350 (538)
.+-
T Consensus 239 ~~~ 241 (291)
T PF10475_consen 239 YVE 241 (291)
T ss_pred HHH
Confidence 543
No 18
>PRK10667 Hha toxicity attenuator; Provisional
Probab=31.75 E-value=69 Score=29.77 Aligned_cols=54 Identities=20% Similarity=0.310 Sum_probs=37.3
Q ss_pred ccCC----CHHHHHHHHHhhCchhHHHHH------------------HHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q psy17468 245 EEFS----DVNELRALADLIGPYGMKLLN------------------ETLMWHIASQVQELKKLVAANKEVLLLLR 298 (538)
Q Consensus 245 E~ys----D~~ELrAL~eLiGPYG~k~L~------------------e~L~~hia~qv~elkklv~~N~d~L~~lr 298 (538)
+||| |+.||+=|||=+=--||.-|. +.|++|||+-+-..|-=--++.++-+++-
T Consensus 2 DEYSPkrhDIAqLkyLCe~L~~e~i~~L~~s~hgWvNDptS~~nlqLNeLIEHIa~f~~~fKIKYp~~~~l~~~id 77 (122)
T PRK10667 2 DEYSPKRHDIAQLKFLCETLYHECLANLGESNHGWVNDPTSAVNLQLNELIEHIATFALNFKIKYPEDSKLIEQID 77 (122)
T ss_pred CCCCcccccHHHHHHHHHHHHHHHHHHhccCCCCCcCCCchHhhhhHHHHHHHHHHHHHHhhccCCcHhhHHHHHH
Confidence 4666 999999999877777777755 57999999988766643334444433333
No 19
>PF10757 YbaJ: Biofilm formation regulator YbaJ; InterPro: IPR019693 YbaJ regulates biofilm formation. It also has an important role in the regulation of motility in the biofilm. YbaJ functions in increasing conjugation, aggregation and decreasing the motility, resulting in an increase of biofilm [].
Probab=30.07 E-value=68 Score=29.86 Aligned_cols=41 Identities=27% Similarity=0.422 Sum_probs=32.1
Q ss_pred ccCC----CHHHHHHHHHhhCchhHHHHH------------------HHHHHHHHHHHHHHHH
Q psy17468 245 EEFS----DVNELRALADLIGPYGMKLLN------------------ETLMWHIASQVQELKK 285 (538)
Q Consensus 245 E~ys----D~~ELrAL~eLiGPYG~k~L~------------------e~L~~hia~qv~elkk 285 (538)
+||| |+.||+=|||-+=--||.-|+ +.|++|||+-+-..|-
T Consensus 2 DEYspk~~DIaqLk~LCe~L~~e~~~~L~~s~~gWvNDptS~~nlqLNeLIEHIA~F~~~fKI 64 (122)
T PF10757_consen 2 DEYSPKRHDIAQLKYLCESLYDEAIATLGDSHHGWVNDPTSAVNLQLNELIEHIAAFIWNFKI 64 (122)
T ss_pred CCCCcccccHHHHHHHHHHHHHHHHHHhccCCCCCcCCCchhhhhhHHHHHHHHHHHHHhhee
Confidence 4666 999999999888777887765 5699999988866553
No 20
>PF10079 DUF2317: Uncharacterized protein conserved in bacteria (DUF2317); InterPro: IPR011199 Members of this protein family include BshC, which is an enzyme required for bacillithiol biosynthesis and described as a cysteine-adding enzyme. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes.
Probab=29.31 E-value=2.6e+02 Score=32.02 Aligned_cols=42 Identities=21% Similarity=0.360 Sum_probs=30.3
Q ss_pred HHHhhCchhHH----------HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q psy17468 256 LADLIGPYGMK----------LLNETLMWHIASQVQELKKLVAANKEVLLLL 297 (538)
Q Consensus 256 L~eLiGPYG~k----------~L~e~L~~hia~qv~elkklv~~N~d~L~~l 297 (538)
+.+|||+||+= .+...++...-.+-.++.+.|.+..+.|+++
T Consensus 220 ~~~LF~~~GLv~lD~~~~~lr~l~~p~f~~~l~~~~~~~~~v~~~~~~l~~~ 271 (542)
T PF10079_consen 220 MHELFGDYGLVLLDPDDPELRKLEAPVFKRELEHNEAIQQAVSEQAEKLEEL 271 (542)
T ss_pred HHHHHhhCCeEEECCCCHHHHHHhHHHHHHHHHhcHHHHHHHHHHHHHHHHC
Confidence 34999999964 4556667777777778877777777777764
No 21
>COG3516 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.25 E-value=1.5e+02 Score=29.22 Aligned_cols=48 Identities=33% Similarity=0.360 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHhcCCCHHHHHHHHhhhhcHHHHHH
Q psy17468 274 WHIASQVQELKKLVAANKEVLLLLRTHFDKPEIMKEQSKRLHNVENVLQ 322 (538)
Q Consensus 274 ~hia~qv~elkklv~~N~d~L~~lr~~f~~p~~m~~~lk~L~~~e~~l~ 322 (538)
..|+.||-+|++++ +-++.|..|.+.++.-...++.+.++-.=+..++
T Consensus 108 ~~Va~qVp~L~kLL-eaR~~L~~L~~~ldg~~~~e~~l~~lL~n~~~l~ 155 (169)
T COG3516 108 DAVARQVPELKKLL-EARTALADLKGPLDGNPAFEELLQDLLKNEELLQ 155 (169)
T ss_pred HHHHHhhHHHHHHH-HHHHHHHHHhccccCcHHHHHHHHHHHcCHHHHH
Confidence 56899999999976 5688899999999986656666555554444443
No 22
>smart00126 IL6 Interleukin-6 homologues. Family includes granulocyte colony-stimulating factor (G-CSF) and myelomonocytic growth factor (MGF). IL-6 is also known as B-cell stimulatory factor 2.
Probab=27.18 E-value=2.2e+02 Score=27.56 Aligned_cols=37 Identities=16% Similarity=0.260 Sum_probs=34.7
Q ss_pred HHHHhhhhcHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q psy17468 308 KEQSKRLHNVENVLQRMTIIGVILNFQRIAQLALQEV 344 (538)
Q Consensus 308 ~~~lk~L~~~e~~l~r~~iiG~iL~FR~l~~eAl~~V 344 (538)
..++.+|+.-+...+++++.++.=+|.+-++.|+|.+
T Consensus 117 ~~ll~~l~s~~~W~r~~t~~lILr~Le~FL~~a~Ral 153 (154)
T smart00126 117 RGLLPKLQSQNQWVRNATGFLILSSLERFLQFALRAL 153 (154)
T ss_pred hhhhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 7889999999999999999999999999999999875
No 23
>PHA00022 VII minor coat protein
Probab=25.96 E-value=66 Score=22.70 Aligned_cols=19 Identities=16% Similarity=0.541 Sum_probs=16.6
Q ss_pred cHHHHHHHHHHHHHHHhHH
Q psy17468 316 NVENVLQRMTIIGVILNFQ 334 (538)
Q Consensus 316 ~~e~~l~r~~iiG~iL~FR 334 (538)
+.|++.+-++.+|..++|-
T Consensus 1 ~~D~i~q~v~~lglVi~Fg 19 (28)
T PHA00022 1 DFDTIYQVVIALGLVICFG 19 (28)
T ss_pred ChHhHHHHHHHHhHHHhhc
Confidence 3689999999999999983
No 24
>PLN03094 Substrate binding subunit of ER-derived-lipid transporter; Provisional
Probab=23.59 E-value=6.4e+02 Score=27.68 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=23.0
Q ss_pred HhHHHHHHHHhcCCCHHHHHHHHhhhhcHHHHHHHH
Q psy17468 289 ANKEVLLLLRTHFDKPEIMKEQSKRLHNVENVLQRM 324 (538)
Q Consensus 289 ~N~d~L~~lr~~f~~p~~m~~~lk~L~~~e~~l~r~ 324 (538)
++.+-+.++.+++.+|+.+..+-+.+..++..++.+
T Consensus 304 ~as~~l~~l~~~l~~p~~~~~L~qtl~sl~~t~~ni 339 (370)
T PLN03094 304 EASEDLRRLNSSILTPENTELLRQSIYTLTKTLKHI 339 (370)
T ss_pred HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 334456666677777777766666666666666555
No 25
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=22.49 E-value=4.5e+02 Score=21.72 Aligned_cols=40 Identities=23% Similarity=0.190 Sum_probs=31.6
Q ss_pred hhCchhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q psy17468 259 LIGPYGMKLLNETLMWHIASQVQELKKLVAANKEVLLLLR 298 (538)
Q Consensus 259 LiGPYG~k~L~e~L~~hia~qv~elkklv~~N~d~L~~lr 298 (538)
=-..-+++.+.+.|...+...-++|+++|..|-.-+....
T Consensus 18 ~~s~~~i~~~~~~L~~~i~~~~~eLr~~V~~nY~~fI~as 57 (87)
T PF08700_consen 18 NSSIKEIRQLENKLRQEIEEKDEELRKLVYENYRDFIEAS 57 (87)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 3345678888999999999999999999999976544443
No 26
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=21.76 E-value=2.2e+02 Score=25.43 Aligned_cols=37 Identities=22% Similarity=0.214 Sum_probs=31.8
Q ss_pred HHHHHHHhCCCCCCCHHHHHHHhccCCC--CCchhhHHH
Q psy17468 371 VNEMASAAGLLCTVDPALATALASDKTD--LDEDEHVLA 407 (538)
Q Consensus 371 v~~lA~aaGl~~~vD~~Lv~al~~~~~~--~~d~~y~~w 407 (538)
+-++|...|++..=||.|+..|+..--| -|++=|.+-
T Consensus 37 II~~Ake~~Vpi~edp~Lv~~L~~lelg~~IPeelY~vV 75 (92)
T COG2257 37 IIEKAKEHGVPIQEDPLLVELLLKLELGDEIPEELYEVV 75 (92)
T ss_pred HHHHHHHcCCCcccCHHHHHHHHhccccccCCHHHHHHH
Confidence 8899999999999999999999887555 588878754
Done!