Query psy10998
Match_columns 514
No_of_seqs 215 out of 692
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 15:33:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0401|consensus 100.0 1.7E-46 3.6E-51 431.5 19.6 426 35-506 187-647 (970)
2 PF02854 MIF4G: MIF4G domain; 100.0 5.4E-33 1.2E-37 262.8 18.5 200 185-423 1-209 (209)
3 smart00543 MIF4G Middle domain 100.0 7.4E-29 1.6E-33 234.8 20.7 192 186-423 2-200 (200)
4 KOG2141|consensus 99.7 3.1E-16 6.6E-21 170.8 18.1 217 168-428 294-525 (822)
5 KOG2140|consensus 99.7 1.3E-15 2.8E-20 161.3 15.7 208 165-427 128-352 (739)
6 KOG3942|consensus 99.0 2.8E-09 6.1E-14 107.5 12.5 182 200-429 150-338 (348)
7 KOG2051|consensus 98.5 1.1E-06 2.4E-11 100.5 14.5 189 183-420 422-614 (1128)
8 KOG0401|consensus 98.5 5.9E-08 1.3E-12 113.6 2.5 275 160-445 588-891 (970)
9 KOG2051|consensus 97.8 0.00054 1.2E-08 79.2 17.1 99 321-421 723-835 (1128)
10 PF05456 eIF_4EBP: Eukaryotic 96.0 0.0026 5.5E-08 56.9 0.9 56 25-82 18-79 (116)
11 PF12152 eIF_4G1: Eukaryotic t 95.9 0.0022 4.7E-08 53.1 0.0 22 49-72 52-73 (75)
12 KOG1104|consensus 91.8 5.7 0.00012 45.7 16.0 197 182-428 25-248 (759)
13 PF02847 MA3: MA3 domain; Int 85.5 12 0.00027 32.2 10.7 63 185-249 2-66 (113)
14 PF05918 API5: Apoptosis inhib 84.9 5.6 0.00012 44.8 10.1 67 182-248 177-251 (556)
15 smart00544 MA3 Domain in DAP-5 79.6 16 0.00034 31.6 9.1 63 185-249 2-66 (113)
16 KOG2140|consensus 53.1 1.1E+02 0.0023 34.7 10.3 52 197-249 465-516 (739)
17 PF05841 Apc15p: Apc15p protei 50.2 29 0.00062 31.5 4.8 47 404-450 76-123 (125)
18 cd03568 VHS_STAM VHS domain fa 46.8 2.4E+02 0.0052 26.1 10.5 110 326-446 18-131 (144)
19 PF07817 GLE1: GLE1-like prote 46.6 3.3E+02 0.0071 27.6 13.9 176 182-379 27-241 (256)
20 PF04147 Nop14: Nop14-like fam 45.6 2.6E+02 0.0056 33.4 12.9 90 185-283 428-527 (840)
21 cd03569 VHS_Hrs_Vps27p VHS dom 38.8 2.7E+02 0.0058 25.6 9.4 109 326-445 22-134 (142)
22 PF01602 Adaptin_N: Adaptin N 36.6 4.9E+02 0.011 28.2 12.7 85 327-413 434-519 (526)
23 KOG2141|consensus 35.9 4.2E+02 0.0092 31.1 11.9 55 194-249 628-682 (822)
24 cd03567 VHS_GGA VHS domain fam 34.9 3.7E+02 0.008 24.8 11.2 108 326-443 19-131 (139)
25 smart00288 VHS Domain present 32.1 3.8E+02 0.0083 24.2 10.8 110 326-445 18-131 (133)
26 cd03561 VHS VHS domain family; 31.8 3.8E+02 0.0083 24.1 9.2 90 326-421 18-111 (133)
27 smart00139 MyTH4 Domain in Myo 30.0 59 0.0013 30.1 3.5 34 216-249 42-76 (144)
28 KOG2213|consensus 26.6 8.9E+02 0.019 26.7 14.4 66 182-248 150-223 (460)
29 PF00790 VHS: VHS domain; Int 26.3 4.9E+02 0.011 23.5 9.1 108 327-444 24-137 (140)
30 PF09733 VEFS-Box: VEFS-Box of 25.6 78 0.0017 29.4 3.5 29 325-353 112-140 (140)
31 KOG4728|consensus 21.6 1.5E+02 0.0033 28.7 4.7 69 182-250 60-131 (176)
32 PF10666 Phage_Gp14: Phage pro 20.8 1.5E+02 0.0032 27.2 4.1 31 215-249 75-105 (140)
No 1
>KOG0401|consensus
Probab=100.00 E-value=1.7e-46 Score=431.46 Aligned_cols=426 Identities=32% Similarity=0.466 Sum_probs=300.6
Q ss_pred ccccccCCCCCCCCccccccHHHHhhccCccCCCCCCCCCCchHH-HhhcCCCCCCCCCCCCCcCCCCCCCCCCCCCCCC
Q psy10998 35 YHEFKYQWSPINQEGVKKYSRDFLLELQFEAMSKPKPANLPDLEI-VLKDLSKPSYPNKNSNISHNIMPHGSRNNDILFP 113 (514)
Q Consensus 35 ~~~~~~qw~p~n~~gKk~Ydr~fLl~lq~~~~~~~kP~~lP~~~~-vl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p 113 (514)
+.+..+.|.|..+++++.|++.+.+.++|...|+.++++.+.+.+ ++........+.+....+. + .+...+|
T Consensus 187 ~~~~~~~~~~~~~e~~~~~~~~~~l~~~~~~~~~~~~e~~~~~~d~~~~~~e~~~~~~~~e~~~~-~------~~~~~~~ 259 (970)
T KOG0401|consen 187 SEDGIPFEKPPDPEEQKASDRMDALTLAFSEELLLEAENTPRSSDEYVRRIEAEQEPLRPEEPSG-L------RAIQKIP 259 (970)
T ss_pred ccccCCCCCCCCcccccccccchhhhhhhhhhhhhhhhhcCCcchHHHHHHHHHhhccCCccchh-h------hcccccc
Confidence 577889999999999999999999999999999999998888643 3322221101111111111 0 1222233
Q ss_pred CCCCCCCCCccccc-------ccCccc-----ccccCCCCCCCCCCCCCCC-cccccccccCccccccCCcccCCCC---
Q psy10998 114 HYANKPGNMRQNIR-------QQQPVL-----KARSIQGGKVPKPAPKSPN-IVLSISLKDDIKLRESENAWRPNNN--- 177 (514)
Q Consensus 114 ~f~~~~~~~~~~~r-------g~~p~~-----~~r~~~~g~~~~~~~~~p~-i~~~~~~~~dvkL~~senaW~P~~~--- 177 (514)
.++... .....++ +..|.. ..|.++++... +|. +. ..-..+|.+.....+|.|...
T Consensus 260 ~~~~~~-~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~-----e~~~~~--~~~~~~~~~~~~~~~~~ps~k~a~ 331 (970)
T KOG0401|consen 260 EKATER-RAEESGRDKPEHEDQTKPAGNRLLDEPRESQPAENG-----EPAKKG--VEEVEEVVLNFAQKAPSPSPKRAK 331 (970)
T ss_pred cccccc-cccccccccccccccccccccccccchhhhcccccc-----cccccc--chhhhHHHHHhccCCCCCcchhhc
Confidence 333211 1000011 111210 01112211111 111 11 122344556666666666552
Q ss_pred -----C------ChhHHHHHHHHHHhhcCCccchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcCCcchHHHHHHHHHH
Q psy10998 178 -----C------DEDEKFYKQVRGVLNKLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEM 246 (514)
Q Consensus 178 -----~------de~e~l~rkVr~iLNKLTp~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L 246 (514)
. ...+++.+.|++|||+|||.+|+.++.+++.+.|++.+.|++||.+||||||.||+||.|||+||..|
T Consensus 332 ~~~~~~~~~~~~~~~~el~~~vrsilnkltp~~~~~l~~q~~~~~i~t~~~l~~vi~~vfdkAi~EP~f~~~yA~lc~~l 411 (970)
T KOG0401|consen 332 SKSDQGAERKDVELKEELAKRVRSLLNKLTPERKELLIEQLIELNVDTDDALKEVIELVFDKAINEPTFCAMYARLCFDL 411 (970)
T ss_pred cccccccccchhHHHHHHHHHHhhhcCCCchHHHHHHHHHHHhhccCcHHHHhHHHHHHHHhhhcccccchhcchhcccc
Confidence 1 12389999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhccccCCCCCCCCCCCCccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHHhHHHHHHHHhhhhh
Q psy10998 247 MKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKKKELRLMFEEEERLIRKRSV 326 (514)
Q Consensus 247 ~~~ev~~e~~~v~~d~~~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~~~eE~~~~~rrR~l 326 (514)
.. . ... ...+......+||++||++||++|+.... ...+++.....++. +..++++++...++|.+
T Consensus 412 ~~-~-~~~---~~~~~~~~~~~fr~~lL~rcq~~fe~~~~------~~~~~~~~~~~~~~---~e~~le~~k~~~~~rtl 477 (970)
T KOG0401|consen 412 EG-P-PSE---PELDMGGDEINFRRLLLNRCQKEFEGEDD------KIADEYSEAEEPDE---LEEELEEEKYILRRRTL 477 (970)
T ss_pred cC-C-ccC---CCcCCCCCcccHHHHHHHHhHHHhhcccH------HHHHHhhhhcCchh---HHHHHHhccceecCCcc
Confidence 87 2 111 01344456789999999999999997541 11233333333332 34566777778899999
Q ss_pred hHHHHHHHHhhcccCcHHHHHHHHHHhhcC--CCChhHHHHHHHHHHHhhhhhcCCCCchh-HHHHHHHHHHHHhhhcCC
Q psy10998 327 GNCRFIGELYKLNMLTTKIMHHCISELLKK--TEEEPLERACKLLSTIGKDLESHDKDPTQ-MKGYFTTMEELASKKNSH 403 (514)
Q Consensus 327 GnirFIGELfk~~mLt~~Im~~cI~~LL~~--~dEeslEcLc~LL~tiGk~Ld~~~k~~~~-md~~F~~L~~i~~~k~~~ 403 (514)
|||+|||+||+..|++++|||.||..||.. ++|+++||+|+|++|||+.||... .... |+.||.+++.+... .
T Consensus 478 gn~~~ig~l~~~~ml~e~i~~~~v~~Ll~~~~~~ee~ie~lc~f~~tig~~lD~~~-~s~r~md~~~~~~k~~~~~---~ 553 (970)
T KOG0401|consen 478 GNFRFIGELFKLKMLTEKIVHACVQKLLSDDQPSEESIECLCRFLTTIGKKLDFSK-ESPRNMDEYFNSMKNLKRK---P 553 (970)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhhHHhhhhcccccccccC-cccchhHHHHHHHHHhhhh---h
Confidence 999999999999999999999999999998 899999999999999999999884 4455 99999999998875 5
Q ss_pred CCChHHHHHHHHHHHHHhCCCCCCCCCCCCC-CHHHHHHHHHHhHhccccCCCCCCCCCCCCCcCCCCccccccc-CCCC
Q psy10998 404 AISSRVRFMLQDVIDLRKNKWIPRRNENKPK-TIQQIQYEAESEKFGNVNKKPLLDKPYSLEKPMLDNDRKSAFQ-QQQK 481 (514)
Q Consensus 404 ~lssRIRFMIqdliDLR~nnW~~r~~~~~Pk-TI~qI~keae~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 481 (514)
.+++|+|||+++++|||.++|++|+.+.++. +|++||.++..+.. ..+....++ ..++.+. ....
T Consensus 554 ~~s~r~RfM~~~~idlR~~~w~~rr~~~~~~~~ieei~~~~~~~~~----~~p~~~~~~---------~~~~~~~~~~~~ 620 (970)
T KOG0401|consen 554 QRSNRIRFMLQSVIDLRKSGWGPRRAEETNDKPIEEIAPEAPSANR----WSPKSLSKK---------TEGRLAEESDSG 620 (970)
T ss_pred hhccchhhhhccccccccccccchhcccCCCCchhhcchhhhhhcc----cCccccccc---------cccccccccccc
Confidence 8999999999999999999999999988766 99999999987533 111111111 1111112 2344
Q ss_pred CCccCC--CCCCCCCcccCcccceeEE
Q psy10998 482 DWNKPN--NPIYKASYQFDKTKFVSIR 506 (514)
Q Consensus 482 ~w~~~~--~~~~~~~~~~~~~~~~~~~ 506 (514)
+|...+ +.+..+.+.+++++|.+|+
T Consensus 621 ~~~~~~~~~~~~~~~~~~~~e~~~~i~ 647 (970)
T KOG0401|consen 621 LLGKEVVERKGKSGLRKLTPEMFDKIS 647 (970)
T ss_pred ccCccccccccccccccCChhhccccc
Confidence 588643 4556788899999998884
No 2
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=100.00 E-value=5.4e-33 Score=262.84 Aligned_cols=200 Identities=39% Similarity=0.716 Sum_probs=172.0
Q ss_pred HHHHHHHhhcCCccchHHHHHHhhccccCc-HHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhccccCCCCCCCCCCC
Q psy10998 185 YKQVRGVLNKLTPENFESMKMQFKEFPINT-TKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKREVVDETKPVNKDGK 263 (514)
Q Consensus 185 ~rkVr~iLNKLTp~nFd~l~~qll~l~I~t-~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ev~~e~~~v~~d~~ 263 (514)
.|+|+++|||||++||+.++++|..+.+.+ ++.++.+++.||++|+.+|+|+.+||+||..|+... +
T Consensus 1 ~r~v~~~lnklt~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~-~----------- 68 (209)
T PF02854_consen 1 LRKVRGILNKLTPSNFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRF-P----------- 68 (209)
T ss_dssp HHHHHHHHHHCSSTTHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHC-H-----------
T ss_pred CchHHHHHHHCCHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccc-h-----------
Confidence 489999999999999999999999888765 899999999999999999999999999999998742 1
Q ss_pred CccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHHhHHHHHHHHhhhhhhHHHHHHHHhhcccCcH
Q psy10998 264 RPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKKKELRLMFEEEERLIRKRSVGNCRFIGELYKLNMLTT 343 (514)
Q Consensus 264 ~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~~~eE~~~~~rrR~lGnirFIGELfk~~mLt~ 343 (514)
..|+..||++||++|+.... ....++.....++|..|+++||||||+.+++++
T Consensus 69 ---~~f~~~ll~~~~~~f~~~~~------------------------~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~ 121 (209)
T PF02854_consen 69 ---SEFRSLLLNRCQEEFEERYS------------------------NEELEENRQSSKQRRRGNIRFLAELFNFGVVSE 121 (209)
T ss_dssp ---HHHHHHHHHHHHHHHHHHT-------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCH
T ss_pred ---hhHHHHHHHHHHHHHHHhhh------------------------hhhHHHHHHHHHHHHhhhhhHHHhhHhhccccc
Confidence 36999999999999997420 001122233456778999999999999999999
Q ss_pred HHHHHHHHHhhcCCCC--------hhHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhcCCCCChHHHHHHHH
Q psy10998 344 KIMHHCISELLKKTEE--------EPLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAISSRVRFMLQD 415 (514)
Q Consensus 344 ~Im~~cI~~LL~~~dE--------eslEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~~~~lssRIRFMIqd 415 (514)
++|++|+..|+....+ ++|||+|.+|.+||+.|+..+..+..|+.||..++.+...+....+++|+||||++
T Consensus 122 ~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~r~~~~l~~ 201 (209)
T PF02854_consen 122 KIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKKLENSEESPKALDEIFERLQKYANSKKDPNLSSRIRFMLED 201 (209)
T ss_dssp HHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCHSSSSSHHHHHHHHH
T ss_pred hhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhhcccCCCHHHHHHHHH
Confidence 9999999999987555 89999999999999999933236789999999999998862225899999999999
Q ss_pred HHHHHhCC
Q psy10998 416 VIDLRKNK 423 (514)
Q Consensus 416 liDLR~nn 423 (514)
|+|+|+||
T Consensus 202 l~~lr~~~ 209 (209)
T PF02854_consen 202 LIELRNNK 209 (209)
T ss_dssp HHHHHHTC
T ss_pred HHHHhcCC
Confidence 99999986
No 3
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=99.96 E-value=7.4e-29 Score=234.80 Aligned_cols=192 Identities=39% Similarity=0.649 Sum_probs=167.7
Q ss_pred HHHHHHhhcCCccchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhccccCCCCCCCCCCCCc
Q psy10998 186 KQVRGVLNKLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKREVVDETKPVNKDGKRP 265 (514)
Q Consensus 186 rkVr~iLNKLTp~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ev~~e~~~v~~d~~~~ 265 (514)
++|+++|||||++||+.++++|..+.+.+.+..+.+++.||++|+.+|+|+.+||+||..|....
T Consensus 2 ~~v~~~lnkLs~~n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~--------------- 66 (200)
T smart00543 2 KKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKN--------------- 66 (200)
T ss_pred hHHHHHHhhCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHH---------------
Confidence 68999999999999999999999998888889999999999999999999999999999998742
Q ss_pred cccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHHhHHHHHHHHhhhhhhHHHHHHHHhhcccCcHHH
Q psy10998 266 SVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKKKELRLMFEEEERLIRKRSVGNCRFIGELYKLNMLTTKI 345 (514)
Q Consensus 266 ~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~~~eE~~~~~rrR~lGnirFIGELfk~~mLt~~I 345 (514)
..|+..||+.|+++|+... ++.....+++..|+++||||||+.++++..+
T Consensus 67 -~~f~~~ll~~~~~~f~~~~-----------------------------e~~~~~~~~~~~~~i~fl~eL~~~~~i~~~~ 116 (200)
T smart00543 67 -PDFGSLLLERLQEEFEKGL-----------------------------ESEEESDKQRRLGLVRFLGELYNFQVLTSKI 116 (200)
T ss_pred -HHHHHHHHHHHHHHHHHHH-----------------------------HHHHHHhhhhHHhHHHHHHHHHHcccCcHHH
Confidence 2599999999999999631 0011123466789999999999999999999
Q ss_pred HHHHHHHhhcCCCC-------hhHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhcCCCCChHHHHHHHHHHH
Q psy10998 346 MHHCISELLKKTEE-------EPLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAISSRVRFMLQDVID 418 (514)
Q Consensus 346 m~~cI~~LL~~~dE-------eslEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~~~~lssRIRFMIqdliD 418 (514)
+++|+..|+....+ .++||+|.+|.+||..|+.. ..+..|+.+|..++.....++...+++|+|||++++++
T Consensus 117 i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~~l~~~-~~~~~~~~~l~~l~~~~~~~~~~~~~~r~~~~l~~l~~ 195 (200)
T smart00543 117 ILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGKDLERE-KSPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIE 195 (200)
T ss_pred HHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhHHHcCc-ccHHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHH
Confidence 99999999998654 89999999999999999952 36789999999999998764333799999999999999
Q ss_pred HHhCC
Q psy10998 419 LRKNK 423 (514)
Q Consensus 419 LR~nn 423 (514)
||++.
T Consensus 196 l~~~~ 200 (200)
T smart00543 196 LRKNK 200 (200)
T ss_pred HhhCc
Confidence 99864
No 4
>KOG2141|consensus
Probab=99.70 E-value=3.1e-16 Score=170.78 Aligned_cols=217 Identities=24% Similarity=0.352 Sum_probs=166.2
Q ss_pred cCCcccCCCC-----CC---hh-HHHHHHHHHHhhcCCccchHHHHHHhhccccCcH-HHHHHHHHHHHHhhhcCC----
Q psy10998 168 SENAWRPNNN-----CD---ED-EKFYKQVRGVLNKLTPENFESMKMQFKEFPINTT-KRLDKVIDLVFQKAIAEP---- 233 (514)
Q Consensus 168 senaW~P~~~-----~d---e~-e~l~rkVr~iLNKLTp~nFd~l~~qll~l~I~t~-e~L~~VI~lIFeKAi~Ep---- 233 (514)
+...|+|+++ ++ |+ .++.|+|+++||||+..|+..|+..|..|+..+. -.++..+.-..-+|+..|
T Consensus 294 s~sKYvPPslRkkl~~~~~sE~l~rl~rkv~g~LNKLSdaNi~~I~~~i~~Ly~~~sr~~v~~sLtk~l~~~~~~~~~~l 373 (822)
T KOG2141|consen 294 SSSKYVPPSLRKKLETSSESEQLQRLRRKVNGSLNKLSDANIIKIIAGIAELYMNNSRYDVTSSLTKLLLKALLGPFRLL 373 (822)
T ss_pred cccccCCHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhhhHHHH
Confidence 4458999983 22 22 7899999999999999999999999999987543 233344444444555544
Q ss_pred -cchHHHHHHHHHHHhccccCCCCCCCCCCCCccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHH
Q psy10998 234 -SFSEFYAKMCYEMMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKKKELRL 312 (514)
Q Consensus 234 -~fs~~YA~LC~~L~~~ev~~e~~~v~~d~~~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~ 312 (514)
.++..||.|...|+.. +. ..|..++|+..-+.|-.....+ +. .
T Consensus 374 d~~~~~y~AL~~~l~~~-vg--------------~eigahf~q~~ve~f~~~~~~~----------~~-----------~ 417 (822)
T KOG2141|consen 374 DSLLTTYAALAAMLHTM-VG--------------NEIGAHFLQTFVEDFLKSYKEE----------EE-----------M 417 (822)
T ss_pred HHHHHHHHHHHHHHHHH-Hh--------------hHHHHHHHHHHHHHHHHHHHHH----------Hh-----------c
Confidence 4788999999998874 22 2355555655555666543210 00 0
Q ss_pred hHHHHHHHHhhhhhhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCChhHHHHHHHHHHHhhhhhcCCCCchhHHHHHHH
Q psy10998 313 MFEEEERLIRKRSVGNCRFIGELYKLNMLTTKIMHHCISELLKKTEEEPLERACKLLSTIGKDLESHDKDPTQMKGYFTT 392 (514)
Q Consensus 313 ~~eE~~~~~rrR~lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEeslEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~ 392 (514)
.+. -+.+-|.+.|+++||+++++++.+|+++|..|+.+.+|-++|||..++..||..|..+ .+..|.+++..
T Consensus 418 ~~~------~K~~~Nl~~~l~ylynF~ivs~~LiydiI~kl~~~l~e~~ve~ll~ii~~~G~~LRkD--Dp~alk~~i~e 489 (822)
T KOG2141|consen 418 DLK------DKSLNNIVLFLSYLYNFGIVSCSLIYDIIRKLAENLNETNVEALLTIIANCGFSLRKD--DPLALKDIITE 489 (822)
T ss_pred ccc------cchhhhHHHHHHHHHHhhcccHHHHHHHHHHHHhchhhhhHHHHHHHHHHccchhcCC--ChHHHHHHHHH
Confidence 011 2447799999999999999999999999999999999999999999999999999988 47899999999
Q ss_pred HHHHHhhhcCCCCChHHHHHHHHHHHHHhCCCCCCC
Q psy10998 393 MEELASKKNSHAISSRVRFMLQDVIDLRKNKWIPRR 428 (514)
Q Consensus 393 L~~i~~~k~~~~lssRIRFMIqdliDLR~nnW~~r~ 428 (514)
|+..++.......++|+|||+..+++|++|+-.+-.
T Consensus 490 iq~~a~~a~~s~~~pR~rFmleti~aLKnN~~kki~ 525 (822)
T KOG2141|consen 490 IQSKAASAKISAISPRLRFMLETISALKNNKLKKIP 525 (822)
T ss_pred HHHHhhcCCccccchHHHHHHHHHHHHhcCCCcCCC
Confidence 998887654334689999999999999998877643
No 5
>KOG2140|consensus
Probab=99.66 E-value=1.3e-15 Score=161.26 Aligned_cols=208 Identities=20% Similarity=0.365 Sum_probs=169.4
Q ss_pred ccccCCcccCCC--------CCChh---------HHHHHHHHHHhhcCCccchHHHHHHhhccccCcHHHHHHHHHHHHH
Q psy10998 165 LRESENAWRPNN--------NCDED---------EKFYKQVRGVLNKLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQ 227 (514)
Q Consensus 165 L~~senaW~P~~--------~~de~---------e~l~rkVr~iLNKLTp~nFd~l~~qll~l~I~t~e~L~~VI~lIFe 227 (514)
.-++..+|.|+. .+|++ +.+.+.|.+|+|||+.+|+..++.+|+..+|--...| +..-|++
T Consensus 128 ~trtGG~YIPPaKL~~mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl--~crsv~~ 205 (739)
T KOG2140|consen 128 RTRTGGAYIPPAKLRMMQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGL--LCRSVMQ 205 (739)
T ss_pred hccCCCeecCHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccch--hHHHHHH
Confidence 358999999987 24432 7899999999999999999999999998665433322 4455666
Q ss_pred hhhcCCcchHHHHHHHHHHHhccccCCCCCCCCCCCCccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHH
Q psy10998 228 KAIAEPSFSEFYAKMCYEMMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKK 307 (514)
Q Consensus 228 KAi~Ep~fs~~YA~LC~~L~~~ev~~e~~~v~~d~~~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~k 307 (514)
-....|.|+.+||.|..-|.. .+|. ...+||.+.--.|.+... |
T Consensus 206 aq~asp~ft~vyaALvAviNs-kfP~---------------IgElLlkrLilqf~r~f~----R---------------- 249 (739)
T KOG2140|consen 206 AQAASPGFTPVYAALVAVINS-KFPQ---------------IGELLLKRLILQFKRSFR----R---------------- 249 (739)
T ss_pred HHhcCCCCcHHHHHHHHHHcc-CCch---------------HHHHHHHHHHHHHHHHhc----c----------------
Confidence 666789999999999887765 3442 455677666666665431 0
Q ss_pred HHHHHhHHHHHHHHhhhhhhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCChhHHHHHHHHHHHhhhhhcCCCCchhHH
Q psy10998 308 KELRLMFEEEERLIRKRSVGNCRFIGELYKLNMLTTKIMHHCISELLKKTEEEPLERACKLLSTIGKDLESHDKDPTQMK 387 (514)
Q Consensus 308 kel~~~~eE~~~~~rrR~lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEeslEcLc~LL~tiGk~Ld~~~k~~~~md 387 (514)
.-+--+++.++||++|+++++.++-+...++.-||..|++++||.++.+|+.||..|-.. ++..++
T Consensus 250 ------------nDk~~c~~~~kfiahLinq~VahEIv~Leil~lLLe~PTddSvevaI~flkecGakL~~V--Spr~~n 315 (739)
T KOG2140|consen 250 ------------NDKVSCLNASKFIAHLINQQVAHEIVALEILTLLLERPTDDSVEVAIAFLKECGAKLAEV--SPRALN 315 (739)
T ss_pred ------------cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHHh--ChHHHh
Confidence 012347889999999999999999999999999999999999999999999999999876 678899
Q ss_pred HHHHHHHHHHhhhcCCCCChHHHHHHHHHHHHHhCCCCCC
Q psy10998 388 GYFTTMEELASKKNSHAISSRVRFMLQDVIDLRKNKWIPR 427 (514)
Q Consensus 388 ~~F~~L~~i~~~k~~~~lssRIRFMIqdliDLR~nnW~~r 427 (514)
.+|+++..|+.. ..++.|++|||+.+...|+.+++.-
T Consensus 316 ~IfErlR~ILhe---~Eld~rvqy~iEtlf~iRkdkfk~~ 352 (739)
T KOG2140|consen 316 GIFERLRYILHE---GELDRRVQYMIETLFQIRKDKFKSH 352 (739)
T ss_pred HHHHHHHHHHhH---hhHHHHHHHHHHHHHHHHHHhhccC
Confidence 999999999975 4799999999999999999998753
No 6
>KOG3942|consensus
Probab=99.01 E-value=2.8e-09 Score=107.51 Aligned_cols=182 Identities=18% Similarity=0.179 Sum_probs=140.9
Q ss_pred hHHHHHHhhccccCcHHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhccccCCCCCCCCCCCCccccHHHHHHHHHHH
Q psy10998 200 FESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQK 279 (514)
Q Consensus 200 Fd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ev~~e~~~v~~d~~~~~~~FR~~LL~rCQ~ 279 (514)
|..-+.+++.-.. +.|.|-.++-.|+.+||+.-.|.-.-++||..|...+.. +..|+..||+.|++
T Consensus 150 ~t~~mealin~a~-~de~l~rc~~~~~r~avegg~ggl~v~klC~n~~~~~~~-------------gt~f~~~Lln~lrq 215 (348)
T KOG3942|consen 150 LTMPMEALINPAY-DDEMLFRCGPTIARQAVEGGGGGLFVCKLCTNLGSSWRN-------------GTQFMDELLNLLRQ 215 (348)
T ss_pred cchHHHHHhCcch-hHHHHHHHHHHHHHHHHhcCCCchhHHHHhhhhhhhhhc-------------cchHHHHHHHHHHH
Confidence 3334444444322 347788899999999999999999999999999876432 34699999999999
Q ss_pred HHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHHhHHHHHHHHhhhhhhHHHHHHHHhhcc-----cCcHHHHHHHHHHhh
Q psy10998 280 EFEKNEFEERKNDIKLDEIEAEQDPEKKKELRLMFEEEERLIRKRSVGNCRFIGELYKLN-----MLTTKIMHHCISELL 354 (514)
Q Consensus 280 eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~~~eE~~~~~rrR~lGnirFIGELfk~~-----mLt~~Im~~cI~~LL 354 (514)
-|+-.. ++. .....|+++.|.|++|||-.- ++=..+++.|+..|+
T Consensus 216 ~f~~r~-----------gl~-------------------s~~~~rw~~fisfltelf~nlgs~p~~vL~~~l~~cl~~ll 265 (348)
T KOG3942|consen 216 GFLLRT-----------GLS-------------------SLASCRWWRFISFLTELFDNLGSCPQVVLQRSLRLCLQILL 265 (348)
T ss_pred hhccch-----------hcc-------------------chhHHHHHHHHHHHHHHHhhcCCCChhhHHHHHHHHHHHHc
Confidence 999531 110 123578999999999999874 566678999999999
Q ss_pred cCCC--ChhHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhcCCCCChHHHHHHHHHHHHHhCCCCCCCC
Q psy10998 355 KKTE--EEPLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAISSRVRFMLQDVIDLRKNKWIPRRN 429 (514)
Q Consensus 355 ~~~d--EeslEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~~~~lssRIRFMIqdliDLR~nnW~~r~~ 429 (514)
..|+ +..+|||.-.|..+|..|++. -+..|-.+|......+-..+ .-=.-+|.||.-||+|.++.|.++..
T Consensus 266 rspd~~~~e~ecl~~~L~~~g~dle~q--lP~ql~lL~~s~rDafL~~s--ep~a~~r~~lllliel~As~wqlpt~ 338 (348)
T KOG3942|consen 266 RSPDWPEFEYECLSMKLAVEGLDLEKQ--LPFQLLLLFPSRRDAFLVRS--EPLAPWRCPLLLLIELPASAWQLPTT 338 (348)
T ss_pred cCCCcchHHHHHHHHHHHHcCccchhh--hhHHHHHHHHHHHHhhhccc--cccccccchhhhccccCccccCCCCC
Confidence 9876 689999999999999999976 57788888887776554431 22234699999999999999998754
No 7
>KOG2051|consensus
Probab=98.52 E-value=1.1e-06 Score=100.46 Aligned_cols=189 Identities=19% Similarity=0.324 Sum_probs=135.0
Q ss_pred HHHHHHHHHhhcCCc----cchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhccccCCCCCC
Q psy10998 183 KFYKQVRGVLNKLTP----ENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKREVVDETKPV 258 (514)
Q Consensus 183 ~l~rkVr~iLNKLTp----~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ev~~e~~~v 258 (514)
.+..+|-..|-+|-- +=.|.++-.+... ++|...=+.+|..+|.---+.-..-..|++|...|... .+
T Consensus 422 ~~~~~~d~Fl~~L~~~vsrdliD~~a~ef~~n-lNtKa~RkrLvKal~~vprt~ldllPyYsRlVAtl~~~-M~------ 493 (1128)
T KOG2051|consen 422 QVVSNVDCFLLDLPNCVSRDLIDQAAIEFCSN-LNTKANRKRLVKALFVVPRTRLDLLPYYSRLVATLSKC-MP------ 493 (1128)
T ss_pred hHHHHHHHHHccCcchHHHHHHHHHHHHHHHH-hccHHHHHHHHHhhhcccchhhhhhhHHHHHHHHHHhh-hh------
Confidence 344455555555542 3334444444332 56666667788888876555556678899999888763 22
Q ss_pred CCCCCCccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHHhHHHHHHHHhhhhhhHHHHHHHHhhc
Q psy10998 259 NKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKKKELRLMFEEEERLIRKRSVGNCRFIGELYKL 338 (514)
Q Consensus 259 ~~d~~~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~~~eE~~~~~rrR~lGnirFIGELfk~ 338 (514)
.|-.-|++...++|..... +| . +...+ ..+-+|+|||||.|.
T Consensus 494 ---------dvat~lv~~L~~eFr~~~h------kK-------------~--q~~ie--------tk~~~VrfIsEL~KF 535 (1128)
T KOG2051|consen 494 ---------DVATELVTMLRKEFRSHLH------KK-------------A--QINIE--------TKLKIVRFISELCKF 535 (1128)
T ss_pred ---------HHHHHHHHHHHHHHHHHHh------hh-------------h--hhhhh--------hhhhhhhhHHhhhhh
Confidence 3667788888888886431 01 0 00110 124579999999999
Q ss_pred ccCcHHHHHHHHHHhhcCCCChhHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhcCCCCChHHHHHHHHHHH
Q psy10998 339 NMLTTKIMHHCISELLKKTEEEPLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAISSRVRFMLQDVID 418 (514)
Q Consensus 339 ~mLt~~Im~~cI~~LL~~~dEeslEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~~~~lssRIRFMIqdliD 418 (514)
++++..-++.|++.||....-.+||.+|.||++||.-|-..+.++..|..+++.|...-. ...+.+|-.-+|+|.+-
T Consensus 536 ~lv~~~~if~cLk~ll~dF~~hnIEm~c~lLE~~GrfLlr~pEt~lrM~~~Le~i~rkK~---a~~lDsr~~~~iENay~ 612 (1128)
T KOG2051|consen 536 QLVPKFEIFSCLKMLLNDFTHHNIEMACVLLESCGRFLLRSPETKLRMRVFLEQIKRKKR---ASALDSRQATLIENAYY 612 (1128)
T ss_pred CccChHHHHHHHHHHHHhcccccHHHHHHHHHhcchhhhcChhHHHHHHHHHHHHHHHHH---HhhhchHHHHHHHHhHH
Confidence 999999999999999999888899999999999999998776677889999988885433 24788888888888887
Q ss_pred HH
Q psy10998 419 LR 420 (514)
Q Consensus 419 LR 420 (514)
+=
T Consensus 613 ~~ 614 (1128)
T KOG2051|consen 613 LC 614 (1128)
T ss_pred hc
Confidence 74
No 8
>KOG0401|consensus
Probab=98.47 E-value=5.9e-08 Score=113.56 Aligned_cols=275 Identities=21% Similarity=0.244 Sum_probs=179.7
Q ss_pred ccCccccccCCcccCCCCCC--------h--h-----HHHHHHHHHHhhcCCccchHHHHHHhhccc-----cCcHHHHH
Q psy10998 160 KDDIKLRESENAWRPNNNCD--------E--D-----EKFYKQVRGVLNKLTPENFESMKMQFKEFP-----INTTKRLD 219 (514)
Q Consensus 160 ~~dvkL~~senaW~P~~~~d--------e--~-----e~l~rkVr~iLNKLTp~nFd~l~~qll~l~-----I~t~e~L~ 219 (514)
.+-.++-.+++.|.|...++ + . +...+.+.+.++++++++|+.+...++... -.+.+..+
T Consensus 588 eei~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~i~~~~~~~~~~~~~e~~~~~~k 667 (970)
T KOG0401|consen 588 EEIAPEAPSANRWSPKSLSKKTEGRLAEESDSGLLGKEVVERKGKSGLRKLTPEMFDKISDPILDIADQSMDEEDGEASK 667 (970)
T ss_pred hhcchhhhhhcccCcccccccccccccccccccccCccccccccccccccCChhhcccccccccccchhhccccccchhh
Confidence 33346777888899988421 1 1 455789999999999999999999987553 23567899
Q ss_pred HHHHHHHHhhhcCCcchHHHHHHHHHHHhccccCCCCCCCCCCCCccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhh
Q psy10998 220 KVIDLVFQKAIAEPSFSEFYAKMCYEMMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIE 299 (514)
Q Consensus 220 ~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ev~~e~~~v~~d~~~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie 299 (514)
.++..++.||..+++|+.+|+..|.......-.+ .......+......+...+..+|+.+|...|..+..........
T Consensus 668 ~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~s~~-~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~- 745 (970)
T KOG0401|consen 668 QKGEQGGRKASDEQHFSSMRAPALEKVVPSLSSD-IDDKRNRGSNGELLSDSYLSARCHEEFENGWSRELPSGKDGERE- 745 (970)
T ss_pred hcccccccccCccccccccCCccccccccccccc-cccccccCCccccccccccchhhhhhccccccccCCCCcccccc-
Confidence 9999999999999999999999998876532110 00111223344567888999999999998886533221111100
Q ss_pred hhcChHHHHHHHHhHHHHHHHHhhhhhhHHHHHHHHhhcccCcHHHHHHHHHHhhcC---CCChhHHHHHHHHHHHhhhh
Q psy10998 300 AEQDPEKKKELRLMFEEEERLIRKRSVGNCRFIGELYKLNMLTTKIMHHCISELLKK---TEEEPLERACKLLSTIGKDL 376 (514)
Q Consensus 300 ~~~d~e~kkel~~~~eE~~~~~rrR~lGnirFIGELfk~~mLt~~Im~~cI~~LL~~---~dEeslEcLc~LL~tiGk~L 376 (514)
++ .+.-++. .....+++.+|++ +......+.+++..|++.|+...+.+ ...+.++..|.++.+||..+
T Consensus 746 ----~e---~~~~~~~-~~~~~~~~~~~~v-~~~~~~~l~~~sk~l~ee~~~~~~~~~~~~~ie~l~S~~~~~~~v~~~v 816 (970)
T KOG0401|consen 746 ----PE---MMSPEYY-AAKAAKRAGLGLV-IALSSELLELLSKSLLEEFLSLRLEKEALKCIEELESPSLLLKTVGENI 816 (970)
T ss_pred ----hh---hcCcccc-hhhhhhccCCcch-hhhhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccchhhhHHHHHHhc
Confidence 00 0111111 1234567899999 77788888899999999998877765 56789999999999999999
Q ss_pred hcCCCCchhHHHHHHHHHHHHhhhc-----CCCCChHHHHHHHHHHHHH-hCCCCCCCCCCCCCCHHHHHHHHHH
Q psy10998 377 ESHDKDPTQMKGYFTTMEELASKKN-----SHAISSRVRFMLQDVIDLR-KNKWIPRRNENKPKTIQQIQYEAES 445 (514)
Q Consensus 377 d~~~k~~~~md~~F~~L~~i~~~k~-----~~~lssRIRFMIqdliDLR-~nnW~~r~~~~~PkTI~qI~keae~ 445 (514)
+..-.....+..+..+|-.+...++ ....+.++.|-+.+-+.++ -..|.--....+|.+++.|+.+.|.
T Consensus 817 ~~~l~~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~d~pk~w~~~~e~~gp~~~~~~~~~~e~ 891 (970)
T KOG0401|consen 817 EPTLEKSPQAVEELLQLLDILVSKNPLSIETLEIGYREKFKLADDKELDLPKGWNYIKEFLGPLIHQKILDESEL 891 (970)
T ss_pred CcccccChhHHHHHHHHHHHHHhcCcccHHHHhhhHHHHHhhhHHHhcccccchhHHHHhhhhHhhhccccHHHH
Confidence 8653223344444444433322110 1134455555555544443 3456655555667777777665544
No 9
>KOG2051|consensus
Probab=97.83 E-value=0.00054 Score=79.20 Aligned_cols=99 Identities=17% Similarity=0.382 Sum_probs=80.3
Q ss_pred HhhhhhhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCC--------------hhHHHHHHHHHHHhhhhhcCCCCchhH
Q psy10998 321 IRKRSVGNCRFIGELYKLNMLTTKIMHHCISELLKKTEE--------------EPLERACKLLSTIGKDLESHDKDPTQM 386 (514)
Q Consensus 321 ~rrR~lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dE--------------eslEcLc~LL~tiGk~Ld~~~k~~~~m 386 (514)
.+.|++.+++|+||||...|+...+|...|-.++...-. .-|-.+|.||.|||..++.. +.+..|
T Consensus 723 ~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV~~lL~tc~~yf~rg-s~kkkl 801 (1128)
T KOG2051|consen 723 SNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLVCMLLQTCGPYFTRG-STKKKL 801 (1128)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHHHHHHHHcccccccc-hhHHHH
Confidence 456778999999999999999999999999888764211 35789999999999999976 578889
Q ss_pred HHHHHHHHHHHhhhcCCCCChHHHHHHHHHHHHHh
Q psy10998 387 KGYFTTMEELASKKNSHAISSRVRFMLQDVIDLRK 421 (514)
Q Consensus 387 d~~F~~L~~i~~~k~~~~lssRIRFMIqdliDLR~ 421 (514)
+.|+-..+..+--+.+ ..|--+.++++|++.+-.
T Consensus 802 ~~fL~~fq~Y~~iKk~-~~Pld~~~~f~d~~~~~r 835 (1128)
T KOG2051|consen 802 DQFLVAFQRYILIKKS-QQPLDMEYEFEDFLELVR 835 (1128)
T ss_pred HHHHHHHHHHhhcccc-cCCCchhhhHHhhhhhcc
Confidence 9998888876554322 378999999999998853
No 10
>PF05456 eIF_4EBP: Eukaryotic translation initiation factor 4E binding protein (EIF4EBP); InterPro: IPR008606 This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1, -2 and -3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F [].; GO: 0008190 eukaryotic initiation factor 4E binding, 0045947 negative regulation of translational initiation; PDB: 2JGB_B 2V8Y_F 1WKW_B 3HXG_C 3U7X_D 3M94_C 3M93_C 2V8X_B 3HXI_C 2V8W_B ....
Probab=95.97 E-value=0.0026 Score=56.90 Aligned_cols=56 Identities=27% Similarity=0.252 Sum_probs=9.0
Q ss_pred EEeecCCcccccccc--cC----CCCCCCCccccccHHHHhhccCccCCCCCCCCCCchHHHhh
Q psy10998 25 YTISLANYSAYHEFK--YQ----WSPINQEGVKKYSRDFLLELQFEAMSKPKPANLPDLEIVLK 82 (514)
Q Consensus 25 ~~~~~~~~~~~~~~~--~q----w~p~n~~gKk~Ydr~fLl~lq~~~~~~~kP~~lP~~~~vl~ 82 (514)
|++.+++.+--.|.. +. ..|. .=|..|||+|||.+++.|.++-.|.+||+|-.|..
T Consensus 18 v~i~d~~qlP~~ystTPGGTlfsTTPG--GTRIIYdR~FLL~~RnSPlSrTPP~~Lp~IPgvt~ 79 (116)
T PF05456_consen 18 VTINDPSQLPHDYSTTPGGTLFSTTPG--GTRIIYDRKFLLECRNSPLSRTPPRNLPNIPGVTS 79 (116)
T ss_dssp ------------------------------------HHHHHCTCG-------------------
T ss_pred EecCCcccCchhhccCCCCceEEeccC--CcEEEEeHHHHHHhcCCCcccCCCCccCCCCcccc
Confidence 566677776544443 22 2343 23889999999999999999999999999865543
No 11
>PF12152 eIF_4G1: Eukaryotic translation initiation factor 4G1; InterPro: IPR022745 The eukaryotic initiation factor 4G (eIF4G) is the core of a multicomponent switch controlling gene expression at the level of translation initiation. It interacts with the small ribosomal subunit interacting protein, eIF3, and the eIF4E/cap-mRNA complex in order to load the ribosome onto mRNA during cap-dependent translation. This entry represents the eIF4E-binding domain of eIF4G []. Binding of this domain to its substrate triggers a coupled folding transition where it forms a right-handed helical ring that wraps around the N terminus of eIF4E.; PDB: 1RF8_B.
Probab=95.88 E-value=0.0022 Score=53.12 Aligned_cols=22 Identities=45% Similarity=0.709 Sum_probs=12.5
Q ss_pred ccccccHHHHhhccCccCCCCCCC
Q psy10998 49 GVKKYSRDFLLELQFEAMSKPKPA 72 (514)
Q Consensus 49 gKk~Ydr~fLl~lq~~~~~~~kP~ 72 (514)
||.+||++||| ||+..|+.||+
T Consensus 52 ~kf~Yd~~FLL--QF~~v~~~kpd 73 (75)
T PF12152_consen 52 KKFRYDPDFLL--QFQDVFKEKPD 73 (75)
T ss_dssp -SS---HHHHH--HHHHHH----S
T ss_pred CccccCHHHHH--HHHHHhccCCC
Confidence 99999999996 78899999996
No 12
>KOG1104|consensus
Probab=91.81 E-value=5.7 Score=45.68 Aligned_cols=197 Identities=16% Similarity=0.237 Sum_probs=133.3
Q ss_pred HHHHHHHHHHhhcCCccchHHHHHHhhccc---cCc-HHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhccccCCCCC
Q psy10998 182 EKFYKQVRGVLNKLTPENFESMKMQFKEFP---INT-TKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKREVVDETKP 257 (514)
Q Consensus 182 e~l~rkVr~iLNKLTp~nFd~l~~qll~l~---I~t-~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ev~~e~~~ 257 (514)
+.+.+++.+..-++....-..+-..+..|. ... +..-..+++.+-.=|+.-|.=...||-|...+...
T Consensus 25 e~l~krl~~~i~~vg~~s~ss~e~~l~~l~~~l~~~~~~~~~~iL~~L~~ca~~lP~K~~~yaTLvgllN~k-------- 96 (759)
T KOG1104|consen 25 ETLEKRLESLIREVGEPSGSSVEDNLENLVAVLEADLENFKSKILDILNTCAVYLPEKITAYATLVGLLNLK-------- 96 (759)
T ss_pred HHHHHHHHHHHHhhcCCCCCcHHHhHHHHHHHHHhhHHHHHHHHHHHHHHHHHHcccchhHHHHHHHHHhcc--------
Confidence 677888888888887332222222222211 111 12344678888888999999999999998777642
Q ss_pred CCCCCCCccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHHhHHHHHHHHhhhhhhHHHHHHHHhh
Q psy10998 258 VNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKKKELRLMFEEEERLIRKRSVGNCRFIGELYK 337 (514)
Q Consensus 258 v~~d~~~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~~~eE~~~~~rrR~lGnirFIGELfk 337 (514)
...|...++...-.+|..... .. . + .++-+.+||+..|+.
T Consensus 97 --------n~~fg~~~v~~~~~~~q~sl~-------------~~-----------~----~----n~ar~llrfL~dL~~ 136 (759)
T KOG1104|consen 97 --------NFNFGGEFVEYMIEELQESLK-------------SG-----------N----W----NEARYLLRFLSDLSN 136 (759)
T ss_pred --------chhhHHHHHHHHHHHHHHHhh-------------cC-----------C----h----HHHHHHHHHHHHHhc
Confidence 124666666554444442110 00 0 0 123389999999999
Q ss_pred cccCcHHHHHHHHHHhhcCCC---------ChhHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhcCCCCC--
Q psy10998 338 LNMLTTKIMHHCISELLKKTE---------EEPLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAIS-- 406 (514)
Q Consensus 338 ~~mLt~~Im~~cI~~LL~~~d---------EeslEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~~~~ls-- 406 (514)
-+||...-|......|+.... +--+=|+..-|--+|+.|... .+..|+.++..++..+..+...+++
T Consensus 137 ~~vl~~~sli~l~esl~~~~~e~~~Pqvr~D~~v~~vLs~lPw~g~el~e~--~~~~~e~ll~~ie~Yl~~R~~shi~lL 214 (759)
T KOG1104|consen 137 CHVLQADSLINLFESLLDAAIEENVPQVRRDYYVYCVLSSLPWFGRELNEK--KPTEMEELLVYIEIYLKKRKKSHINLL 214 (759)
T ss_pred CCccChHHHHHHHHHHHHHHHhhcCcchhhhHHHHHHHhccchhhhhhccc--chHHHHHHHHHHHHHHHHhcccccchh
Confidence 999999888888888887533 345678888888999999854 5689999999999888765411111
Q ss_pred ------------hHHHHHHHHHHHHHhCCCCCCC
Q psy10998 407 ------------SRVRFMLQDVIDLRKNKWIPRR 428 (514)
Q Consensus 407 ------------sRIRFMIqdliDLR~nnW~~r~ 428 (514)
-=++.+...|.-+|.|+|....
T Consensus 215 ~vw~~~~~~~qeeyle~L~~qI~~lr~n~w~e~h 248 (759)
T KOG1104|consen 215 NVWSGEPDHPQEEYLELLWAQIQKLRQNDWAENH 248 (759)
T ss_pred hcCCCCCCchHHHHHHHHHHHHHHHHhcCccccc
Confidence 1367888999999999999843
No 13
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=85.46 E-value=12 Score=32.18 Aligned_cols=63 Identities=21% Similarity=0.408 Sum_probs=45.3
Q ss_pred HHHHHHHhhcCC-ccchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcC-CcchHHHHHHHHHHHhc
Q psy10998 185 YKQVRGVLNKLT-PENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAE-PSFSEFYAKMCYEMMKR 249 (514)
Q Consensus 185 ~rkVr~iLNKLT-p~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~E-p~fs~~YA~LC~~L~~~ 249 (514)
.|+++.+|.--- -...+..+..|.++.+. .....||..+++.+.++ ..+..+|+.|...|...
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~ 66 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECLKELKLP--SQHHEVVKVILECALEEKKSYREYYSKLLSHLCKR 66 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHT
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhc
Confidence 455555554322 24677777888777665 66677888888888888 89999999999999864
No 14
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=84.92 E-value=5.6 Score=44.75 Aligned_cols=67 Identities=21% Similarity=0.342 Sum_probs=51.0
Q ss_pred HHHHHHHHHHhhcCCccchHHHHHHhhcccc----CcHHHHHHHHHHHHHhhhcCCcc----hHHHHHHHHHHHh
Q psy10998 182 EKFYKQVRGVLNKLTPENFESMKMQFKEFPI----NTTKRLDKVIDLVFQKAIAEPSF----SEFYAKMCYEMMK 248 (514)
Q Consensus 182 e~l~rkVr~iLNKLTp~nFd~l~~qll~l~I----~t~e~L~~VI~lIFeKAi~Ep~f----s~~YA~LC~~L~~ 248 (514)
+-+...|+.+|..+|.+.|+.++.=|-.+.+ .+.+....+|++|.++|--+..| .....++..++..
T Consensus 177 ~~i~~~ikkvL~DVTaeEF~l~m~lL~~lk~~~~~~t~~g~qeLv~ii~eQa~Ld~~f~~sD~e~Idrli~C~~~ 251 (556)
T PF05918_consen 177 EFIVDEIKKVLQDVTAEEFELFMSLLKSLKIYGGKQTIEGRQELVDIIEEQADLDQPFDPSDPESIDRLISCLRQ 251 (556)
T ss_dssp HHHHHHHHHHCTT--HHHHHHHHHHHHTSGG---GSSHHHHHHHHHHHHHHHTTTS---SSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHHhCccccccCChHHHHHHHHHHHHHhccCCCCCCcCHHHHHHHHHHHHH
Confidence 6778899999999999999999977767776 57888999999999999543334 4667777776655
No 15
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=79.57 E-value=16 Score=31.61 Aligned_cols=63 Identities=11% Similarity=0.278 Sum_probs=47.7
Q ss_pred HHHHHHHhhcC-CccchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcC-CcchHHHHHHHHHHHhc
Q psy10998 185 YKQVRGVLNKL-TPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAE-PSFSEFYAKMCYEMMKR 249 (514)
Q Consensus 185 ~rkVr~iLNKL-Tp~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~E-p~fs~~YA~LC~~L~~~ 249 (514)
.++|..+|+.- +...++..+.-|.++.+. .....+|..++.-|+++ ..+..+|+.|...|+..
T Consensus 2 ~k~i~~~l~ey~~~~D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~ 66 (113)
T smart00544 2 KKKIFLIIEEYLSSGDTDEAVHCLLELKLP--EQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQA 66 (113)
T ss_pred hhHHHHHHHHHHHcCCHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHc
Confidence 34555555443 356888888889888776 45677888888888888 58999999999999864
No 16
>KOG2140|consensus
Probab=53.10 E-value=1.1e+02 Score=34.72 Aligned_cols=52 Identities=12% Similarity=0.281 Sum_probs=41.3
Q ss_pred ccchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhc
Q psy10998 197 PENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKR 249 (514)
Q Consensus 197 p~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ 249 (514)
-=.|+..+..|+.+.|.+.- -++++++|++=+..|-.|...|.-|..+++.+
T Consensus 465 SldfeEaaHKLLKmkip~~q-~~elc~mii~cc~QerTy~kFYglL~eRfc~l 516 (739)
T KOG2140|consen 465 SLDFEEAAHKLLKMKIPESQ-EKELCNMIIDCCAQERTYEKFYGLLGERFCML 516 (739)
T ss_pred cCcHHHHHHHHHhccCCchh-hHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 44699999999888876532 35688899998889999999999888877763
No 17
>PF05841 Apc15p: Apc15p protein; InterPro: IPR008402 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. Members of this family are components of the anaphase-promoting complex homologous to subunit Apc15/MND2 [].; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0031145 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process, 0005680 anaphase-promoting complex
Probab=50.25 E-value=29 Score=31.48 Aligned_cols=47 Identities=23% Similarity=0.232 Sum_probs=34.5
Q ss_pred CCChHHHHHHHHHHHHHhCCCCCCCCCCCCCCHHHHHH-HHHHhHhcc
Q psy10998 404 AISSRVRFMLQDVIDLRKNKWIPRRNENKPKTIQQIQY-EAESEKFGN 450 (514)
Q Consensus 404 ~lssRIRFMIqdliDLR~nnW~~r~~~~~PkTI~qI~k-eae~e~~~~ 450 (514)
.+....+.|..-+...|+=+|.-=+..--+||+.||+. ++|+|++++
T Consensus 76 ~L~~~e~~~~~r~~~Ir~~G~~wikPiGv~KTm~~~~eE~~E~eE~~~ 123 (125)
T PF05841_consen 76 RLSMEEQQLERRKQNIRNFGYNWIKPIGVPKTMQQMREEEAEREEHQE 123 (125)
T ss_pred hhhHHHHHHHHHHHHHHHhCccceeCCCccHHHHHHHHHHHHHHHHHh
Confidence 35566666777777778778877777777999999996 556666554
No 18
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=46.82 E-value=2.4e+02 Score=26.09 Aligned_cols=110 Identities=13% Similarity=0.154 Sum_probs=69.8
Q ss_pred hhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCCh----hHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhc
Q psy10998 326 VGNCRFIGELYKLNMLTTKIMHHCISELLKKTEEE----PLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKN 401 (514)
Q Consensus 326 lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEe----slEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~ 401 (514)
++.+.=|+++.+.+-...+-...+|++-|.+.+.. .|..|=.+++.||..+..+ -.-..+.+.|..++..
T Consensus 18 w~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~e----vask~Fl~eL~kl~~~-- 91 (144)
T cd03568 18 WGLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQE----VASRDFTQELKKLIND-- 91 (144)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHH----HhhHHHHHHHHHHhcc--
Confidence 46677788888887666666566666666666653 4555556667778777755 1224556667777764
Q ss_pred CCCCChHHHHHHHHHHHHHhCCCCCCCCCCCCCCHHHHHHHHHHh
Q psy10998 402 SHAISSRVRFMLQDVIDLRKNKWIPRRNENKPKTIQQIQYEAESE 446 (514)
Q Consensus 402 ~~~lssRIRFMIqdliDLR~nnW~~r~~~~~PkTI~qI~keae~e 446 (514)
+.+..|+-+|..+|..-..... .+....-|.+++++...+
T Consensus 92 --~~~~~Vk~kil~li~~W~~~f~---~~~~l~~i~~~y~~L~~~ 131 (144)
T cd03568 92 --RVHPTVKEKLREVVKQWADEFK---NDPSLSLMSDLYKKLKNE 131 (144)
T ss_pred --cCCHHHHHHHHHHHHHHHHHhC---CCcccHHHHHHHHHHHHc
Confidence 3778888888888876443332 123345577777777643
No 19
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=46.56 E-value=3.3e+02 Score=27.55 Aligned_cols=176 Identities=14% Similarity=0.123 Sum_probs=89.1
Q ss_pred HHHHHHHHHHhhcCCcc--chHHHHHHhhcc-------------ccC-cH----HHHHHHHHHHHHhhhc----CCcchH
Q psy10998 182 EKFYKQVRGVLNKLTPE--NFESMKMQFKEF-------------PIN-TT----KRLDKVIDLVFQKAIA----EPSFSE 237 (514)
Q Consensus 182 e~l~rkVr~iLNKLTp~--nFd~l~~qll~l-------------~I~-t~----e~L~~VI~lIFeKAi~----Ep~fs~ 237 (514)
..+.|.|..-+|+||.. .+..++.+|.++ ... .+ -.|..+++.|...|-. .|..+.
T Consensus 27 ~~~kr~I~~~vgQls~~~~qi~~i~~~i~~ll~~~~~~~~~~~~~~~~~~~~~~~~l~~lAk~iv~Q~e~ev~~~~~~A~ 106 (256)
T PF07817_consen 27 FDLKRKINPKVGQLSNSSSQINRIINQISNLLSGQPVKSNDLQQSKNDHPLAYKYLLNFLAKKIVSQAETEVSANPESAF 106 (256)
T ss_dssp HHHHHHHCCHHHC--SBHHHHHHHHHHHHHH----------HHTTTT-SHHHHHHHHHHHHHHHHHHHHHHHHH-GGGHH
T ss_pred HHhhhhCcCcHhhccCcHHHHHHHHHHHHHHhhhhhhchhhhhhhccCCchHHHHHHHHHHHHHHHHHHHHhccCCchhh
Confidence 56777788888888865 355555555554 111 12 2455555556655554 577788
Q ss_pred HHHHHHHHHHhccccCCCCCCCCCCCCccccHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcChHHHHHHHHhHH--
Q psy10998 238 FYAKMCYEMMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPEKKKELRLMFE-- 315 (514)
Q Consensus 238 ~YA~LC~~L~~~ev~~e~~~v~~d~~~~~~~FR~~LL~rCQ~eFe~~~~~~~~~~~k~keie~~~d~e~kkel~~~~e-- 315 (514)
-+|.++..|... .+ .|..+|+.+....-==.. .-.... .....+++-++.|--..+
T Consensus 107 PlA~v~~~l~~~-~p---------------~~~dillA~l~k~Cp~~v-P~~~~~-----~~~~~~e~~~k~lGyk~~~~ 164 (256)
T PF07817_consen 107 PLARVAVQLWSQ-HP---------------EFGDILLARLHKKCPYLV-PKYPGF-----TCDQSTEEYRKRLGYKRDDG 164 (256)
T ss_dssp HHHHHHHHHHHH-ST---------------CHHHHHHHHHHHH-GGGG-----T----------SSHHHHHHTT--B-TT
T ss_pred hHHHHHHHHHHc-CC---------------cHHHHHHHHHHHcCceeE-eecCcc-----cCCCCHHHHHHHcCCccCCC
Confidence 889998887763 22 377777776543211000 000000 000011122221110000
Q ss_pred --HHHHHHhhhhhhHHHHHHHHhhccc---------CcHHHHHHHHHHhhcCC--CChhHHHHHHHHHHHhhhhhcC
Q psy10998 316 --EEERLIRKRSVGNCRFIGELYKLNM---------LTTKIMHHCISELLKKT--EEEPLERACKLLSTIGKDLESH 379 (514)
Q Consensus 316 --E~~~~~rrR~lGnirFIGELfk~~m---------Lt~~Im~~cI~~LL~~~--dEeslEcLc~LL~tiGk~Ld~~ 379 (514)
|.+...-.|+-|.+++-+-+-.... ....--=..+..+|..+ .+-...+|...|+.+|..|-..
T Consensus 165 ~~E~~~~y~~Rm~Gi~~lyaAi~~~~~~~~~~~~~p~~~~~~W~wlAr~lN~~p~~~~~~~lL~~~Le~ag~~l~~~ 241 (256)
T PF07817_consen 165 GWESEDQYLKRMTGIIRLYAAIIQTPPPKGQKTSNPHGLEHGWRWLARILNLPPAPNITATLLHSFLEVAGFRLLQI 241 (256)
T ss_dssp SB--HHHHHHHHHHHHHHHHHHHHS---CCCCTT-SS-THHHHHHHHHHHCS-CC-HHHHHHHHHHHHHHHHHHHHH
T ss_pred CccchHHHHHHHHHHHHHHHHHHhccCCcCCCCCCCCCcHHHHHHHHHHhCCCCCcccHHHHHHHHHHHHHHHHHHH
Confidence 1122334678899999998886532 12222233455555543 2456788999999999998754
No 20
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=45.63 E-value=2.6e+02 Score=33.41 Aligned_cols=90 Identities=16% Similarity=0.273 Sum_probs=57.1
Q ss_pred HHHHHHHhhcCCccchHHHHHHhhccc-----cCcHHHHHHHHHHHHHh----hhcC-CcchHHHHHHHHHHHhccccCC
Q psy10998 185 YKQVRGVLNKLTPENFESMKMQFKEFP-----INTTKRLDKVIDLVFQK----AIAE-PSFSEFYAKMCYEMMKREVVDE 254 (514)
Q Consensus 185 ~rkVr~iLNKLTp~nFd~l~~qll~l~-----I~t~e~L~~VI~lIFeK----Ai~E-p~fs~~YA~LC~~L~~~ev~~e 254 (514)
+..+..+|...+++....|+..|..++ -.|.+.|..+..++++- |... +....+.-.||..|.... ..
T Consensus 428 ~eel~~lL~~~~~~~~~~iI~RIrk~~hpsLa~~NK~Kl~~f~~vLlq~i~~la~~~~~~~~~~ld~L~~~L~~La-q~- 505 (840)
T PF04147_consen 428 HEELLELLDGYSPEDQPTIIQRIRKCYHPSLAEGNKEKLQVFFGVLLQHILYLASQDSPPPFEVLDSLIPHLYDLA-QK- 505 (840)
T ss_pred HHHHHHHHhcCCHHHHhHHHHHHHHhCCCCCCcchHHHHHHHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHHHH-HH-
Confidence 556788899999999999999998765 24666666555555444 3333 444455677888887642 10
Q ss_pred CCCCCCCCCCccccHHHHHHHHHHHHHHh
Q psy10998 255 TKPVNKDGKRPSVNFKNLLLNKCQKEFEK 283 (514)
Q Consensus 255 ~~~v~~d~~~~~~~FR~~LL~rCQ~eFe~ 283 (514)
.+.....+||. +|..||..|..
T Consensus 506 ------~p~~~a~~~r~-~L~~~~~~~~~ 527 (840)
T PF04147_consen 506 ------YPEEAAECFRE-VLKEMQKRFRK 527 (840)
T ss_pred ------HHHHHHHHHHH-HHHHHHHHHhh
Confidence 11123445664 56677777775
No 21
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=38.84 E-value=2.7e+02 Score=25.64 Aligned_cols=109 Identities=9% Similarity=0.120 Sum_probs=68.2
Q ss_pred hhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCCh----hHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhc
Q psy10998 326 VGNCRFIGELYKLNMLTTKIMHHCISELLKKTEEE----PLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKN 401 (514)
Q Consensus 326 lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEe----slEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~ 401 (514)
++.+.-|+++.+..-...+-...+|++-|...+.. .|+.|=.+++.||..+... -.-..+.+.|..++..
T Consensus 22 w~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~e----vas~~fl~~l~~l~~~-- 95 (142)
T cd03569 22 LASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDE----VASREFMDELKDLIKT-- 95 (142)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHH----HhhHHHHHHHHHHHcc--
Confidence 46777888888877666666666666667766653 4555555666777777755 2234556667777653
Q ss_pred CCCCChHHHHHHHHHHHHHhCCCCCCCCCCCCCCHHHHHHHHHH
Q psy10998 402 SHAISSRVRFMLQDVIDLRKNKWIPRRNENKPKTIQQIQYEAES 445 (514)
Q Consensus 402 ~~~lssRIRFMIqdliDLR~nnW~~r~~~~~PkTI~qI~keae~ 445 (514)
..+.+|+-.+..+|.--...... +..=.-|.+++++..+
T Consensus 96 --~~~~~Vk~kil~li~~W~~~f~~---~~~l~~i~~~y~~L~~ 134 (142)
T cd03569 96 --TKNEEVRQKILELIQAWALAFRN---KPQLKYVVDTYQILKA 134 (142)
T ss_pred --cCCHHHHHHHHHHHHHHHHHhCC---CcccHHHHHHHHHHHH
Confidence 57888888888888765433321 1112245566665543
No 22
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=36.57 E-value=4.9e+02 Score=28.16 Aligned_cols=85 Identities=18% Similarity=0.207 Sum_probs=50.9
Q ss_pred hHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCChhHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhc-CCCC
Q psy10998 327 GNCRFIGELYKLNMLTTKIMHHCISELLKKTEEEPLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKN-SHAI 405 (514)
Q Consensus 327 GnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEeslEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~-~~~l 405 (514)
..+-.|||--..---+. ++.+++..|+....+++.+.-+.+|++..|.+-..+ ....-+.++..+..+....+ +..+
T Consensus 434 ~~~wilGEy~~~~~~~~-~~~~~~~~l~~~~~~~~~~vk~~ilt~~~Kl~~~~~-~~~~~~~i~~~~~~~~~~~s~~~ev 511 (526)
T PF01602_consen 434 AAIWILGEYGELIENTE-SAPDILRSLIENFIEESPEVKLQILTALAKLFKRNP-ENEVQNEILQFLLSLATEDSSDPEV 511 (526)
T ss_dssp HHHHHHHHHCHHHTTTT-HHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHSC-STTHHHHHHHHHHCHHHHS-SSHHH
T ss_pred HHHhhhcccCCcccccc-cHHHHHHHHHHhhccccHHHHHHHHHHHHHHHhhCC-chhhHHHHHHHHHHHhccCCCCHHH
Confidence 55666777443322223 556666666666666778888899999999887762 22233466666666555211 2356
Q ss_pred ChHHHHHH
Q psy10998 406 SSRVRFML 413 (514)
Q Consensus 406 ssRIRFMI 413 (514)
..|.+|.+
T Consensus 512 r~Ra~~y~ 519 (526)
T PF01602_consen 512 RDRAREYL 519 (526)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 66666654
No 23
>KOG2141|consensus
Probab=35.90 E-value=4.2e+02 Score=31.14 Aligned_cols=55 Identities=11% Similarity=0.321 Sum_probs=43.1
Q ss_pred cCCccchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhc
Q psy10998 194 KLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKR 249 (514)
Q Consensus 194 KLTp~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ 249 (514)
-+|.+.|....+.|+.|.+.. ....+++..|+.=+..|-.|-..||-|+.++|.+
T Consensus 628 ImsaeDyiDAFEklLkL~LK~-~Q~rEI~~VllhC~l~EK~yNpfYa~lA~KfCe~ 682 (822)
T KOG2141|consen 628 IMSAEDYIDAFEKLLKLSLKG-KQEREIARVLLHCCLNEKTYNPFYALLALKFCEF 682 (822)
T ss_pred eecchHHHHHHHHHHhccCCC-cchHHHHHHHHHHHhhhcccchHHHHHHHHHHHH
Confidence 355666666777777777665 3346788888888899999999999999999975
No 24
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=34.94 E-value=3.7e+02 Score=24.80 Aligned_cols=108 Identities=12% Similarity=0.119 Sum_probs=65.8
Q ss_pred hhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCCh----hHHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhc
Q psy10998 326 VGNCRFIGELYKLNMLTTKIMHHCISELLKKTEEE----PLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKN 401 (514)
Q Consensus 326 lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEe----slEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~ 401 (514)
++.+.-|+++.+.+--..+.-...|.+-|.+++.. .|..|=.+++.||..+... -.-..+++.|.+++..+.
T Consensus 19 w~~ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~e----vas~~Fl~el~kl~~~k~ 94 (139)
T cd03567 19 WEAIQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSE----VGKFRFLNELIKLVSPKY 94 (139)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHH----HHhHHHHHHHHHHhcccc
Confidence 46677788888877666555555566666666653 4455555666778877654 122344445555554221
Q ss_pred -CCCCChHHHHHHHHHHHHHhCCCCCCCCCCCCCCHHHHHHHH
Q psy10998 402 -SHAISSRVRFMLQDVIDLRKNKWIPRRNENKPKTIQQIQYEA 443 (514)
Q Consensus 402 -~~~lssRIRFMIqdliDLR~nnW~~r~~~~~PkTI~qI~kea 443 (514)
....+..|+-.|..||..-..... ..|+ +.+.-.+.
T Consensus 95 ~~~~~~~~Vk~kil~li~~W~~~f~-----~~p~-~~~~Y~~L 131 (139)
T cd03567 95 LGSRTSEKVKTKIIELLYSWTLELP-----HEPK-IKEAYDML 131 (139)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHhc-----ccch-HHHHHHHH
Confidence 135789999999999987654443 2355 44444443
No 25
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=32.07 E-value=3.8e+02 Score=24.16 Aligned_cols=110 Identities=12% Similarity=0.045 Sum_probs=65.8
Q ss_pred hhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCChh----HHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhc
Q psy10998 326 VGNCRFIGELYKLNMLTTKIMHHCISELLKKTEEEP----LERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKN 401 (514)
Q Consensus 326 lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEes----lEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~ 401 (514)
.+.+.-|+++.+.+-...+....+|++=|.++++.. |..|=.+++.||..+... -.-..+.+.|..++..+
T Consensus 18 w~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~e----v~s~~fl~~L~~l~~~~- 92 (133)
T smart00288 18 WELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLE----VASKEFLNELVKLIKPK- 92 (133)
T ss_pred HHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHH----HHhHHHHHHHHHHHcCC-
Confidence 466777888888887777777777777777777654 444445556667777654 12234455666666542
Q ss_pred CCCCChHHHHHHHHHHHHHhCCCCCCCCCCCCCCHHHHHHHHHH
Q psy10998 402 SHAISSRVRFMLQDVIDLRKNKWIPRRNENKPKTIQQIQYEAES 445 (514)
Q Consensus 402 ~~~lssRIRFMIqdliDLR~nnW~~r~~~~~PkTI~qI~keae~ 445 (514)
.....|+-.+..++.--..... .+.....|.+.+++..+
T Consensus 93 --~~~~~Vk~kil~li~~W~~~f~---~~~~~~~i~~~y~~L~~ 131 (133)
T smart00288 93 --YPLPLVKKRILELIQEWADAFK---NDPDLSQIVDVYDLLKK 131 (133)
T ss_pred --CCcHHHHHHHHHHHHHHHHHHc---CCCCchHHHHHHHHHHH
Confidence 2222366666666654333222 14456677777776543
No 26
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=31.79 E-value=3.8e+02 Score=24.05 Aligned_cols=90 Identities=14% Similarity=0.066 Sum_probs=58.2
Q ss_pred hhHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCChhHH----HHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhc
Q psy10998 326 VGNCRFIGELYKLNMLTTKIMHHCISELLKKTEEEPLE----RACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKN 401 (514)
Q Consensus 326 lGnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEeslE----cLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~ 401 (514)
...+..|+++...+-...+-...+|++-|...+....- .|=.+++.||..+... -.-..++..|..++..+
T Consensus 18 ~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~----i~s~~fl~~l~~l~~~~- 92 (133)
T cd03561 18 WALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQ----VADKEFLLELVKIAKNS- 92 (133)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHH----HhhHHHHHHHHHHhCCC-
Confidence 46677788888888777777777788878877765444 4444455556655543 11134455566666532
Q ss_pred CCCCChHHHHHHHHHHHHHh
Q psy10998 402 SHAISSRVRFMLQDVIDLRK 421 (514)
Q Consensus 402 ~~~lssRIRFMIqdliDLR~ 421 (514)
...+..++-.+..++.--.
T Consensus 93 -~~~~~~Vk~kil~ll~~W~ 111 (133)
T cd03561 93 -PKYDPKVREKALELILAWS 111 (133)
T ss_pred -CCCCHHHHHHHHHHHHHHH
Confidence 3678899998888887544
No 27
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=29.96 E-value=59 Score=30.08 Aligned_cols=34 Identities=18% Similarity=0.479 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHhhhcCCcc-hHHHHHHHHHHHhc
Q psy10998 216 KRLDKVIDLVFQKAIAEPSF-SEFYAKMCYEMMKR 249 (514)
Q Consensus 216 e~L~~VI~lIFeKAi~Ep~f-s~~YA~LC~~L~~~ 249 (514)
.....++..|+..+++.|.. -++|.+||+.+..+
T Consensus 42 ~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~N 76 (144)
T smart00139 42 DSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTDN 76 (144)
T ss_pred chHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhCC
Confidence 44567889999999998876 68999999998753
No 28
>KOG2213|consensus
Probab=26.58 E-value=8.9e+02 Score=26.66 Aligned_cols=66 Identities=12% Similarity=0.183 Sum_probs=49.4
Q ss_pred HHHHHHHHHHhhcCCccchHHHHHHhhcccc----CcHHHHHHHHHHHHHhhhcCCcchH----HHHHHHHHHHh
Q psy10998 182 EKFYKQVRGVLNKLTPENFESMKMQFKEFPI----NTTKRLDKVIDLVFQKAIAEPSFSE----FYAKMCYEMMK 248 (514)
Q Consensus 182 e~l~rkVr~iLNKLTp~nFd~l~~qll~l~I----~t~e~L~~VI~lIFeKAi~Ep~fs~----~YA~LC~~L~~ 248 (514)
..+...|+..|-.+|-+.|...++-|-++.+ ...+.|.+++..+=++|-.+. |-. .--++..++..
T Consensus 150 ~~iv~eikkal~dVtgeef~lfm~~L~~lk~~~~k~~~a~lqeLa~~~e~~a~lda-f~~sD~d~VdRfisCl~~ 223 (460)
T KOG2213|consen 150 RHIVDEIKKALEDVTGEEFTLFMDILASLKSLQTKAGEARLQELAEEQEGLADLDA-FNVSDADYVDRFISCLLM 223 (460)
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHhhhhccCc-ccCCChHHHHHHHHHHHH
Confidence 6778889999999999999888888776654 347899999999988886654 433 33456565554
No 29
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=26.32 E-value=4.9e+02 Score=23.53 Aligned_cols=108 Identities=13% Similarity=0.129 Sum_probs=63.0
Q ss_pred hHHHHHHHHhhcccCcHHHHHHHHHHhhcCCCChh----HHHHHHHHHHHhhhhhcCCCCchhHHHHHHHHHHHHhhhcC
Q psy10998 327 GNCRFIGELYKLNMLTTKIMHHCISELLKKTEEEP----LERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNS 402 (514)
Q Consensus 327 GnirFIGELfk~~mLt~~Im~~cI~~LL~~~dEes----lEcLc~LL~tiGk~Ld~~~k~~~~md~~F~~L~~i~~~k~~ 402 (514)
+.+.-|+++.+.+-...+....+|++=|.+.+... |..|-.+++.||..+...-.+ ..+++.|..++..+
T Consensus 24 ~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~----~~fl~~l~~l~~~~-- 97 (140)
T PF00790_consen 24 SLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVAS----KEFLDELVKLIKSK-- 97 (140)
T ss_dssp HHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTS----HHHHHHHHHHHHHT--
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhH----HHHHHHHHHHHccC--
Confidence 45556788888876666666667777777766543 444555566677777654112 34566677766643
Q ss_pred CCCChH--HHHHHHHHHHHHhCCCCCCCCCCCCCCHHHHHHHHH
Q psy10998 403 HAISSR--VRFMLQDVIDLRKNKWIPRRNENKPKTIQQIQYEAE 444 (514)
Q Consensus 403 ~~lssR--IRFMIqdliDLR~nnW~~r~~~~~PkTI~qI~keae 444 (514)
..... ||-++..+|.--.... +.+..-..|.+..+...
T Consensus 98 -~~~~~~~Vk~k~l~ll~~W~~~f---~~~~~~~~i~~~y~~Lk 137 (140)
T PF00790_consen 98 -KTDPETPVKEKILELLQEWAEAF---KSDPELSLIQDTYKRLK 137 (140)
T ss_dssp -TTHHHSHHHHHHHHHHHHHHHHT---TTSTTGHHHHHHHHHHH
T ss_pred -CCCchhHHHHHHHHHHHHHHHHH---CCCCCchHHHHHHHHHH
Confidence 33333 8888888876544333 12223344555555444
No 30
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=25.64 E-value=78 Score=29.40 Aligned_cols=29 Identities=14% Similarity=0.329 Sum_probs=25.5
Q ss_pred hhhHHHHHHHHhhcccCcHHHHHHHHHHh
Q psy10998 325 SVGNCRFIGELYKLNMLTTKIMHHCISEL 353 (514)
Q Consensus 325 ~lGnirFIGELfk~~mLt~~Im~~cI~~L 353 (514)
..+.+.|+..|+..|+|+...|..|+..|
T Consensus 112 ~~~f~lHl~~L~d~glLd~~~i~~c~~~l 140 (140)
T PF09733_consen 112 RREFLLHLINLWDFGLLDARTIDECMKIL 140 (140)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHhhC
Confidence 34677999999999999999999999765
No 31
>KOG4728|consensus
Probab=21.56 E-value=1.5e+02 Score=28.68 Aligned_cols=69 Identities=13% Similarity=0.196 Sum_probs=51.7
Q ss_pred HHHHHHHHHHhhcCCccchHHHHHHhhccccCcHHHHHHHHHHHHHhhhcCC---cchHHHHHHHHHHHhcc
Q psy10998 182 EKFYKQVRGVLNKLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEP---SFSEFYAKMCYEMMKRE 250 (514)
Q Consensus 182 e~l~rkVr~iLNKLTp~nFd~l~~qll~l~I~t~e~L~~VI~lIFeKAi~Ep---~fs~~YA~LC~~L~~~e 250 (514)
-+.++.+=..+++.-+.+|..+++||.-..-+-.+....|+.-+|+-.|.-- .|....+.||......+
T Consensus 60 ~~~Lr~~Gd~~e~r~~s~F~t~~~qL~it~~~a~~~f~~V~~~lF~~Gi~wg~~va~~~~~g~la~~~~~~~ 131 (176)
T KOG4728|consen 60 HRVLRRAGDEFERRYRSVFKTMLDQLHITPEDAYDSFSQVANELFEDGINWGRRVALLIFGGGLAVHSVQIE 131 (176)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHhccccccceeeeehhhHHHHHHHHHhc
Confidence 4667777778999999999999999864433345788899999999987743 34444566788777653
No 32
>PF10666 Phage_Gp14: Phage protein Gp14; InterPro: IPR018923 This Listeria phage Gp14 protein family is of unknown function but is expressed from within a cluster of tail- and base plate genes [].
Probab=20.85 E-value=1.5e+02 Score=27.23 Aligned_cols=31 Identities=26% Similarity=0.579 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHhhhcCCcchHHHHHHHHHHHhc
Q psy10998 215 TKRLDKVIDLVFQKAIAEPSFSEFYAKMCYEMMKR 249 (514)
Q Consensus 215 ~e~L~~VI~lIFeKAi~Ep~fs~~YA~LC~~L~~~ 249 (514)
.+.|+..|.++| .+|-.|..+|+. |+.|...
T Consensus 75 re~L~ea~~~~l---~de~tfee~Ye~-~k~~~~M 105 (140)
T PF10666_consen 75 REALKEAIEIFL---GDENTFEECYEK-CKDLVNM 105 (140)
T ss_pred HHHHHHHHHHHh---CcHhHHHHHHHH-HHHHHHH
Confidence 456777777777 468899999998 9998864
Done!