Query 015127
Match_columns 413
No_of_seqs 146 out of 268
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:22:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015127hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2085 Serine/threonine prote 100.0 2E-136 5E-141 1027.7 27.5 325 84-412 39-363 (457)
2 PF01603 B56: Protein phosphat 100.0 2E-109 5E-114 846.8 24.4 317 89-412 1-319 (409)
3 PLN00122 serine/threonine prot 97.6 2.5E-05 5.3E-10 72.7 2.0 33 340-372 35-67 (170)
4 PLN00122 serine/threonine prot 97.2 0.0022 4.7E-08 59.9 9.1 27 83-109 41-67 (170)
5 PF01602 Adaptin_N: Adaptin N 79.5 20 0.00043 37.4 11.3 172 227-411 340-516 (526)
6 PF05918 API5: Apoptosis inhib 78.1 20 0.00043 39.6 11.0 111 290-400 196-320 (556)
7 PF14500 MMS19_N: Dos2-interac 73.1 60 0.0013 32.2 12.1 78 326-410 119-209 (262)
8 PF04802 SMK-1: Component of I 43.2 1E+02 0.0022 29.5 7.5 49 334-382 135-184 (193)
9 cd08324 CARD_NOD1_CARD4 Caspas 34.9 29 0.00062 29.4 2.0 37 228-264 48-84 (85)
10 cd07920 Pumilio Pumilio-family 31.0 5.1E+02 0.011 25.3 11.6 36 376-411 209-245 (322)
11 PF04388 Hamartin: Hamartin pr 28.0 9.1E+02 0.02 27.4 12.9 58 228-295 6-63 (668)
12 KOG1991 Nuclear transport rece 27.7 8.8E+02 0.019 29.1 12.7 149 196-355 343-509 (1010)
13 COG5656 SXM1 Importin, protein 27.3 5.8E+02 0.013 29.9 11.0 152 192-354 333-505 (970)
14 PF01602 Adaptin_N: Adaptin N 27.0 4.8E+02 0.01 27.2 10.0 53 199-257 246-298 (526)
15 PF11131 PhrC_PhrF: Rap-phr ex 25.0 29 0.00062 25.0 0.4 10 402-411 27-36 (37)
16 KOG1825 Fry-like conserved pro 24.9 1.1E+02 0.0024 38.8 5.4 82 225-323 217-299 (2206)
17 cd00160 RhoGEF Guanine nucleot 24.1 4.9E+02 0.011 22.8 9.5 23 389-411 146-170 (181)
18 TIGR00777 ahpD alkylhydroperox 23.9 90 0.0019 29.7 3.5 16 264-279 75-90 (177)
19 cd03567 VHS_GGA VHS domain fam 23.8 5.3E+02 0.011 23.3 8.4 79 334-412 24-109 (139)
20 PF12783 Sec7_N: Guanine nucle 23.6 2.9E+02 0.0062 24.8 6.7 60 264-324 70-129 (168)
21 KOG3887 Predicted small GTPase 23.2 53 0.0011 33.4 2.0 51 200-260 189-240 (347)
22 PF04499 SAPS: SIT4 phosphatas 22.2 3.9E+02 0.0085 29.0 8.4 52 200-251 34-88 (475)
23 PF03378 CAS_CSE1: CAS/CSE pro 21.4 1.5E+02 0.0032 31.7 5.0 105 193-318 195-302 (435)
24 KOG3769 Ribonuclease III domai 20.8 90 0.0019 32.3 3.1 32 329-360 125-157 (333)
25 PF06901 FrpC: RTX iron-regula 20.2 75 0.0016 31.1 2.3 44 291-343 223-269 (271)
No 1
>KOG2085 consensus Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]
Probab=100.00 E-value=2.3e-136 Score=1027.66 Aligned_cols=325 Identities=70% Similarity=1.167 Sum_probs=320.2
Q ss_pred CcccccCCCCCCCChHHhHHHHHHHHhccCccccccCCCCCchhHHHHHHHHHHHHHHhhhCCCCCCHHHHHHHHHHHHh
Q 015127 84 LAYYEALPSFKDVPNAEKQNLFVRKLNLCCVVFDFTDPTKNLKEKDIKRQTLVELVDYVSSANGKFPEVVMQEMVKMVSA 163 (413)
Q Consensus 84 ~~~l~~LP~~~dv~~~e~~~Lf~~Kl~~C~~ifDFsDp~~d~k~Ke~Kr~tL~ELvd~v~~~~~~lte~~~~~i~~Mis~ 163 (413)
..++++||+|+|||++++++||++|+++||++|||+||.+|.++|++||+||+||+||+.+.++++||.+|+++++|+++
T Consensus 39 ~~~l~~LP~~~dv~~se~~~Lf~~Kl~~Cc~~FDF~Dp~~~~~~keikR~tL~eLvd~v~~~~~kite~~~~~vv~m~s~ 118 (457)
T KOG2085|consen 39 NVELEPLPSLKDVPSSEQKELFIKKLEQCCVLFDFNDPLKDLKGKEIKRQTLLELVDDVISRRGKISEEVYSEVVKMFSV 118 (457)
T ss_pred CCCceeCCccCcCChhHhHHHHHHHHHhhheeeeccChhhhhccchhHHHHHHHHHHHHhhccccccHHHHHHHHHHHHH
Confidence 45599999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCCCCCCCCcccccCCCCCCCCCCCCCCchHHHHHHHHHHHhcCCccCHHHHhccCCHHHHHHHhhccCCCChhHH
Q 015127 164 NLFRTLTSPPRENKVLEAFDLEEEEPSMDPAWPHLQVVYEFLLRFVASPETDAKLAKRYIDHSFVLRLLDLFDSEDPRER 243 (413)
Q Consensus 164 NiFR~lPp~~~~~~~~~~~d~eedep~~EpsWPHLqlVYelllrfv~s~~~d~~~ak~~id~~Fi~~Ll~lfdSeDpRER 243 (413)
||||+|||..+++ .+|+|||||++|++|||||+|||+|+||++||++|+++||+|||++||++||+||||||||||
T Consensus 119 nifR~lpp~~n~~----~~d~eedEp~le~awphLqlvye~~Lrf~~sp~~d~~vaK~yid~~FvlkLLdLFdSEDpRER 194 (457)
T KOG2085|consen 119 NIFRTLPPSVNPT----GFDYEEDEPVLEPAWPHLQLVYEFLLRFLESPDFDPSVAKKYIDQKFVLKLLDLFDSEDPRER 194 (457)
T ss_pred HhhccCCcccCCC----cCCccccCcccCCCchHHHHHHHHHHHHHhCcccCHHHHHHHhhHHHHHHHHHHhcCCChHHH
Confidence 9999999998755 389999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcccCChHHHHHHHHHHHhhhhhccccccCHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHhccCCCCc
Q 015127 244 EYLKTVLHRIYGKFMVHRPFIRKAINNIFYRFIFETEKHNGIAELLEILGSIINGFALPLKEEHKLFLVRALIPLHKPKC 323 (413)
Q Consensus 244 d~LKtiLHrIY~Kf~~~R~fIRk~Innif~~fiyEte~~nGIaELLEIlgSIInGFa~PLKeEHk~fl~rvLiPLHk~~~ 323 (413)
|+|||+|||||||||+||+|||++||||||+||||||+|||||||||||||||||||+|||||||+||.||||||||+++
T Consensus 195 e~LKT~LhrIygKfl~~r~firk~iNNif~~FIyEte~hnGIaELLEIlgSiIngfAlPlKEEhkiFL~rvLipLhk~k~ 274 (457)
T KOG2085|consen 195 EFLKTILHRIYGKFLVHRPFIRKSINNIFLRFIYETERHNGIAELLEILGSIINGFALPLKEEHKLFLVRVLIPLHKPKS 274 (457)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHhhcchhhhhcccccccCCHHHHHHHHHHhcCcccCcchhHHHHHHHHhhhccccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhHHHHHHHHHHHhCCCcHHHHHHHhhhcCCCCCchhHHHhHHHHHHHHhcCChhhHHhhHHHHHHHHHHhhCCCc
Q 015127 324 VAMYHQQLSYCITQFVEKDCKLADTVIRGLLKYWPVTNSTKEVMFLGELEEVLESTQPGEFQRCMVPLFHQIGRCLSSSH 403 (413)
Q Consensus 324 ~~~Yh~qL~yCi~qFveKDp~L~~~vi~glLk~WP~tns~KEvlFL~EleeiLe~~~~~ef~~i~~pLF~~la~Cl~S~h 403 (413)
++.||+||+|||+||+||||+|+++||+|||||||+|||+||||||+|||||||+++|.+|++||+|||+|||+|++|+|
T Consensus 275 l~~yh~QLaYcivQfveKd~kl~~~VIrglLK~WP~tnS~KEVmFL~ElEEILe~iep~eFqk~~~PLf~qia~c~sS~H 354 (457)
T KOG2085|consen 275 LSLYHKQLAYCIVQFVEKDPKLTETVIRGLLKYWPKTNSSKEVMFLNELEEILEVIEPSEFQKIMVPLFRQIARCVSSPH 354 (457)
T ss_pred ccccccccceeeeeeeccCccccHHHHHHHHHhcCCCCCcceeeeHhhHHHHHHhcCHHHHHHHhHHHHHHHHHHcCChh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhhhhc
Q 015127 404 FQVGSSLLS 412 (413)
Q Consensus 404 fqVAErAL~ 412 (413)
||||||||.
T Consensus 355 FQVAEraL~ 363 (457)
T KOG2085|consen 355 FQVAERALY 363 (457)
T ss_pred HHHHHHHHH
Confidence 999999985
No 2
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=100.00 E-value=2.3e-109 Score=846.84 Aligned_cols=317 Identities=64% Similarity=1.101 Sum_probs=276.4
Q ss_pred cCCCCCCCChHHhHHHHHHHHhccCccccccCCCCCchhHHHHHHHHHHHHHHhhhCC--CCCCHHHHHHHHHHHHhhcc
Q 015127 89 ALPSFKDVPNAEKQNLFVRKLNLCCVVFDFTDPTKNLKEKDIKRQTLVELVDYVSSAN--GKFPEVVMQEMVKMVSANLF 166 (413)
Q Consensus 89 ~LP~~~dv~~~e~~~Lf~~Kl~~C~~ifDFsDp~~d~k~Ke~Kr~tL~ELvd~v~~~~--~~lte~~~~~i~~Mis~NiF 166 (413)
|||+|+||+++++++||++||++||++|||+|+.+|.++|++||+||+||++||+++. +.++|++++++++||++|||
T Consensus 1 ~lP~l~dv~~~e~~~lf~~Kl~~C~~ifDF~d~~~d~~~Ke~K~~~L~el~~~v~~~~~~~~l~e~~~~~i~~Mi~~Nif 80 (409)
T PF01603_consen 1 PLPSLPDVPPPERQELFLKKLQQCCVIFDFSDPSSDLKEKEIKRQTLNELVDYVSNSRIQGILTEPVYPEIFNMISANIF 80 (409)
T ss_dssp ------SS-SSSCSCHTTHHHHHHHHHSTTSSSSSSHHHHHSHHHHHHHHHHHHCSSS--SSS-TTSHHHHHHHHHHHH-
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHhCCEeeCCCCccchHHHHHHHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHhcc
Confidence 6999999999999999999999999999999999999999999999999999999987 99999999999999999999
Q ss_pred ccCCCCCCCCcccccCCCCCCCCCCCCCCchHHHHHHHHHHHhcCCccCHHHHhccCCHHHHHHHhhccCCCChhHHHHH
Q 015127 167 RTLTSPPRENKVLEAFDLEEEEPSMDPAWPHLQVVYEFLLRFVASPETDAKLAKRYIDHSFVLRLLDLFDSEDPREREYL 246 (413)
Q Consensus 167 R~lPp~~~~~~~~~~~d~eedep~~EpsWPHLqlVYelllrfv~s~~~d~~~ak~~id~~Fi~~Ll~lfdSeDpRERd~L 246 (413)
|++||.+. ..+|+|||+++.||+|||||+||++|++|++++++++ +|+|||++||.+|+++|+|+||||||+|
T Consensus 81 R~lP~~~~-----~~~~~~~d~~~~e~~WpHL~~vY~il~~~i~~~~~~~--~~~~i~~~fi~~Ll~l~~S~D~rER~~l 153 (409)
T PF01603_consen 81 RPLPPIPN-----PSFDPDDDEPFLEPSWPHLQLVYEILLRFIESPPFDP--AKKYIDQKFIKKLLELFDSPDPRERDYL 153 (409)
T ss_dssp S-----SS-------S-GGG------TTHHHHHHHHHHHHHHHTSTT--C--CTTTS-HHHHHHHHHTTTSSTHHHHHHH
T ss_pred CCCCCccc-----ccCCccccccccccccHhHHHHHHHHHHHHHCccccH--HHHHcCHHHHHHHHHHcCCCCHHHHHHH
Confidence 99999875 3478899999999999999999999999999999999 9999999999999999999999999999
Q ss_pred HHHHHHHhhcccCChHHHHHHHHHHHhhhhhccccccCHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHhccCCCCcccc
Q 015127 247 KTVLHRIYGKFMVHRPFIRKAINNIFYRFIFETEKHNGIAELLEILGSIINGFALPLKEEHKLFLVRALIPLHKPKCVAM 326 (413)
Q Consensus 247 KtiLHrIY~Kf~~~R~fIRk~Innif~~fiyEte~~nGIaELLEIlgSIInGFa~PLKeEHk~fl~rvLiPLHk~~~~~~ 326 (413)
|++||||||||+++|++||++|+++|++|+||++.|+||+|||||+|||||||++|||+||+.||.++|+|||++++++.
T Consensus 154 k~~l~~iy~k~~~~r~~Ir~~i~~~~~~fi~e~~~~~gI~elLeil~sii~gf~~plk~eh~~fl~~vllPLh~~~~~~~ 233 (409)
T PF01603_consen 154 KTILHRIYGKFPNLRSFIRKSINNIFYRFIYETERHNGIAELLEILGSIINGFAVPLKEEHKQFLRKVLLPLHKSPHLSS 233 (409)
T ss_dssp HHHHHHHHHH-TTTHHHHHHHHHHHHHHHHHTTS--STHHHHHHHHHHHHTT--SS--HHHHHHHHHTTGGGGGSTGGGG
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHhcCCcHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHhCCCcHHHHHHHhhhcCCCCCchhHHHhHHHHHHHHhcCChhhHHhhHHHHHHHHHHhhCCCchHH
Q 015127 327 YHQQLSYCITQFVEKDCKLADTVIRGLLKYWPVTNSTKEVMFLGELEEVLESTQPGEFQRCMVPLFHQIGRCLSSSHFQV 406 (413)
Q Consensus 327 Yh~qL~yCi~qFveKDp~L~~~vi~glLk~WP~tns~KEvlFL~EleeiLe~~~~~ef~~i~~pLF~~la~Cl~S~hfqV 406 (413)
||+||+||+++|++|||+|+..+++||+||||+||++||++||+||++||+.+++++|++++.|||++||+|++|+||||
T Consensus 234 y~~~L~~~~~~f~~kdp~l~~~~i~~llk~WP~t~s~Kev~FL~el~~il~~~~~~~f~~i~~~lf~~la~ci~S~h~qV 313 (409)
T PF01603_consen 234 YHQQLSYCVVQFLEKDPSLAEPVIKGLLKHWPKTNSQKEVLFLNELEEILEVLPPEEFQKIMVPLFKRLAKCISSPHFQV 313 (409)
T ss_dssp THHHHHHHHHHHHHH-GGGHHHHHHHHHHHS-SS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHTSSSHHH
T ss_pred HHHHHHHHHHHHHHhCchhHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhhc
Q 015127 407 GSSLLS 412 (413)
Q Consensus 407 AErAL~ 412 (413)
|||||.
T Consensus 314 AErAl~ 319 (409)
T PF01603_consen 314 AERALY 319 (409)
T ss_dssp HHHHHG
T ss_pred HHHHHH
Confidence 999985
No 3
>PLN00122 serine/threonine protein phosphatase 2A; Provisional
Probab=97.62 E-value=2.5e-05 Score=72.72 Aligned_cols=33 Identities=21% Similarity=0.204 Sum_probs=31.0
Q ss_pred HhCCCcHHHHHHHhhhcCCCCCchhHHHhHHHH
Q 015127 340 EKDCKLADTVIRGLLKYWPVTNSTKEVMFLGEL 372 (413)
Q Consensus 340 eKDp~L~~~vi~glLk~WP~tns~KEvlFL~El 372 (413)
...+.++...+++|++|||++++.||.+||++|
T Consensus 35 ~~~~~~~~~~~e~l~~~~~v~~s~k~~lfl~kl 67 (170)
T PLN00122 35 AVNPASVVAGYEPLPSFRDVPNSEKQNLFVRKL 67 (170)
T ss_pred ccCCCccccccccccCCCCCCchHHHHHHHHHH
Confidence 457889999999999999999999999999999
No 4
>PLN00122 serine/threonine protein phosphatase 2A; Provisional
Probab=97.18 E-value=0.0022 Score=59.91 Aligned_cols=27 Identities=78% Similarity=1.157 Sum_probs=25.5
Q ss_pred CCcccccCCCCCCCChHHhHHHHHHHH
Q 015127 83 PLAYYEALPSFKDVPNAEKQNLFVRKL 109 (413)
Q Consensus 83 ~~~~l~~LP~~~dv~~~e~~~Lf~~Kl 109 (413)
....+++||+|+|||.++|+.||++||
T Consensus 41 ~~~~~e~l~~~~~v~~s~k~~lfl~kl 67 (170)
T PLN00122 41 VVAGYEPLPSFRDVPNSEKQNLFVRKL 67 (170)
T ss_pred cccccccccCCCCCCchHHHHHHHHHH
Confidence 377799999999999999999999999
No 5
>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=79.50 E-value=20 Score=37.40 Aligned_cols=172 Identities=15% Similarity=0.169 Sum_probs=112.3
Q ss_pred HHHHHhhcc-CCCChhHHHHHHHHHHHHhhcccCChHHHHHHHHHHHhhhhhccccccCHHHHHHHHHHHhcccCCCCHH
Q 015127 227 FVLRLLDLF-DSEDPREREYLKTVLHRIYGKFMVHRPFIRKAINNIFYRFIFETEKHNGIAELLEILGSIINGFALPLKE 305 (413)
Q Consensus 227 Fi~~Ll~lf-dSeDpRERd~LKtiLHrIY~Kf~~~R~fIRk~Innif~~fiyEte~~nGIaELLEIlgSIInGFa~PLKe 305 (413)
.+..|+..+ +..|+.=|..+-..+..+-.++...-.|.-..+-+++.. .. ..-..|....+..++... ..+++
T Consensus 340 Il~eL~~~l~~~~d~~~~~~~i~~I~~la~~~~~~~~~~v~~l~~ll~~----~~-~~~~~~~~~~i~~ll~~~-~~~~~ 413 (526)
T PF01602_consen 340 ILDELLKYLSELSDPDFRRELIKAIGDLAEKFPPDAEWYVDTLLKLLEI----SG-DYVSNEIINVIRDLLSNN-PELRE 413 (526)
T ss_dssp HHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHGSSHHHHHHHHHHHHHC----TG-GGCHCHHHHHHHHHHHHS-TTTHH
T ss_pred HHHHHHHHHHhccchhhhhhHHHHHHHHHhccCchHHHHHHHHHHhhhh----cc-ccccchHHHHHHHHhhcC-hhhhH
Confidence 445555566 666777777777777778788877766766555444432 11 122556677777776542 22333
Q ss_pred HHHHHHHHHHhccCCCCccccchhHHHHHHHHHHHhCCC--cHHHHHHHhhhcCCCCCchhHHHhHHHHHHHHhcCChhh
Q 015127 306 EHKLFLVRALIPLHKPKCVAMYHQQLSYCITQFVEKDCK--LADTVIRGLLKYWPVTNSTKEVMFLGELEEVLESTQPGE 383 (413)
Q Consensus 306 EHk~fl~rvLiPLHk~~~~~~Yh~qL~yCi~qFveKDp~--L~~~vi~glLk~WP~tns~KEvlFL~EleeiLe~~~~~e 383 (413)
.-...+ +-+-..-.....-.-.++|+-+|.+..+. .+..+++.+...|...+..=....|..+-.+....+.++
T Consensus 414 ~~l~~L----~~~l~~~~~~~~~~~~~wilGEy~~~~~~~~~~~~~~~~l~~~~~~~~~~vk~~ilt~~~Kl~~~~~~~~ 489 (526)
T PF01602_consen 414 KILKKL----IELLEDISSPEALAAAIWILGEYGELIENTESAPDILRSLIENFIEESPEVKLQILTALAKLFKRNPENE 489 (526)
T ss_dssp HHHHHH----HHHHTSSSSHHHHHHHHHHHHHHCHHHTTTTHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHSCSTT
T ss_pred HHHHHH----HHHHHHhhHHHHHHHHHhhhcccCCcccccccHHHHHHHHHHhhccccHHHHHHHHHHHHHHHhhCCchh
Confidence 322222 32222233345678889999999888877 899999999999988877667778888888887766655
Q ss_pred HHhhHHHHHHHHHHhhC--CCchHHHhhhh
Q 015127 384 FQRCMVPLFHQIGRCLS--SSHFQVGSSLL 411 (413)
Q Consensus 384 f~~i~~pLF~~la~Cl~--S~hfqVAErAL 411 (413)
-.+ .+...+.++.. |.++.|-+||.
T Consensus 490 ~~~---~i~~~~~~~~~~~s~~~evr~Ra~ 516 (526)
T PF01602_consen 490 VQN---EILQFLLSLATEDSSDPEVRDRAR 516 (526)
T ss_dssp HHH---HHHHHHHCHHHHS-SSHHHHHHHH
T ss_pred hHH---HHHHHHHHHhccCCCCHHHHHHHH
Confidence 544 45566666667 99999999996
No 6
>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=78.05 E-value=20 Score=39.59 Aligned_cols=111 Identities=14% Similarity=0.230 Sum_probs=61.2
Q ss_pred HHHHHHhcccCC---CCHHHHHHHHHHHHh---ccCCC--CccccchhHHHHHHHH---HHHhCCCcH---HHHHHHhhh
Q 015127 290 EILGSIINGFAL---PLKEEHKLFLVRALI---PLHKP--KCVAMYHQQLSYCITQ---FVEKDCKLA---DTVIRGLLK 355 (413)
Q Consensus 290 EIlgSIInGFa~---PLKeEHk~fl~rvLi---PLHk~--~~~~~Yh~qL~yCi~q---FveKDp~L~---~~vi~glLk 355 (413)
+++-+|.+.+.+ .=..+..+.|..++. -|..+ .+-...-.++.+|+.+ |+.+...-+ ..+.+.++-
T Consensus 196 ~l~m~lL~~lk~~~~~~t~~g~qeLv~ii~eQa~Ld~~f~~sD~e~Idrli~C~~~Alp~fs~~v~Sskfv~y~~~kvlP 275 (556)
T PF05918_consen 196 ELFMSLLKSLKIYGGKQTIEGRQELVDIIEEQADLDQPFDPSDPESIDRLISCLRQALPFFSRGVSSSKFVNYMCEKVLP 275 (556)
T ss_dssp HHHHHHHHTSGG---GSSHHHHHHHHHHHHHHHTTTS---SSSHHHHHHHHHHHHHHGGG-BTTB--HHHHHHHHHHTCC
T ss_pred HHHHHHHHhCccccccCChHHHHHHHHHHHHHhccCCCCCCcCHHHHHHHHHHHHHhhHHhcCCCChHHHHHHHHHHhcC
Confidence 344445554433 112445555555444 12222 1223455688899988 766666544 444444555
Q ss_pred cCCCCCchhHHHhHHHHHHHHhcCChhhHHhhHHHHHHHHHHhhC
Q 015127 356 YWPVTNSTKEVMFLGELEEVLESTQPGEFQRCMVPLFHQIGRCLS 400 (413)
Q Consensus 356 ~WP~tns~KEvlFL~EleeiLe~~~~~ef~~i~~pLF~~la~Cl~ 400 (413)
.|=.......+-+|.-+.|+...+...+-..++.++|..|-.++=
T Consensus 276 ~l~~l~e~~kl~lLk~lAE~s~~~~~~d~~~~L~~i~~~L~~ymP 320 (556)
T PF05918_consen 276 KLSDLPEDRKLDLLKLLAELSPFCGAQDARQLLPSIFQLLKKYMP 320 (556)
T ss_dssp CTT-----HHHHHHHHHHHHHTT----THHHHHHHHHHHHHTTS-
T ss_pred ChhhCChHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHhCC
Confidence 555555688889999999999999888888999999999876553
No 7
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=73.09 E-value=60 Score=32.20 Aligned_cols=78 Identities=22% Similarity=0.322 Sum_probs=49.0
Q ss_pred cchhHHHHHHHHHH--HhCCC---cHHHHHHHhhhcCCCCCchhHHHhHHHHHHHHhcCChhhHH--------hhHHHHH
Q 015127 326 MYHQQLSYCITQFV--EKDCK---LADTVIRGLLKYWPVTNSTKEVMFLGELEEVLESTQPGEFQ--------RCMVPLF 392 (413)
Q Consensus 326 ~Yh~qL~yCi~qFv--eKDp~---L~~~vi~glLk~WP~tns~KEvlFL~EleeiLe~~~~~ef~--------~i~~pLF 392 (413)
.....+.+.+++.+ ||||+ ++-.+++.+++.||. . -|..|+-+++..-=|-+|. --...|=
T Consensus 119 ~~~~~fv~~~i~~~~gEkDPRnLl~~F~l~~~i~~~~~~-~-----~~~e~lFd~~~cYFPI~F~pp~~dp~~IT~edLk 192 (262)
T PF14500_consen 119 SMGDDFVYGFIQLIDGEKDPRNLLLSFKLLKVILQEFDI-S-----EFAEDLFDVFSCYFPITFRPPPNDPYGITREDLK 192 (262)
T ss_pred hchhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhccc-c-----hhHHHHHHHhhheeeeeeeCCCCCCCCCCHHHHH
Confidence 34556778888886 89995 566778899999995 2 2344555555411122222 1235678
Q ss_pred HHHHHhhCCCchHHHhhh
Q 015127 393 HQIGRCLSSSHFQVGSSL 410 (413)
Q Consensus 393 ~~la~Cl~S~hfqVAErA 410 (413)
..|-.|+.|.+ +.|+-|
T Consensus 193 ~~L~~cl~s~~-~fa~~~ 209 (262)
T PF14500_consen 193 RALRNCLSSTP-LFAPFA 209 (262)
T ss_pred HHHHHHhcCcH-hhHHHH
Confidence 88999999855 445544
No 8
>PF04802 SMK-1: Component of IIS longevity pathway SMK-1; InterPro: IPR006887 This is a conserved region which characterises a number of eukaryotic proteins of unknown function.
Probab=43.18 E-value=1e+02 Score=29.45 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=23.9
Q ss_pred HHHHHHHhCCCcHHHHHHHhhhcCCCCC-chhHHHhHHHHHHHHhcCChh
Q 015127 334 CITQFVEKDCKLADTVIRGLLKYWPVTN-STKEVMFLGELEEVLESTQPG 382 (413)
Q Consensus 334 Ci~qFveKDp~L~~~vi~glLk~WP~tn-s~KEvlFL~EleeiLe~~~~~ 382 (413)
+|++++.+|+..-..+...+-.-=+... -..-+.||.|+-.+.-.+++.
T Consensus 135 ~Iv~~l~~d~~fL~~Lf~~l~~~~~~~~~r~d~v~fL~e~c~~ak~lq~~ 184 (193)
T PF04802_consen 135 EIVNMLQDDENFLEELFAILKDPSTSDERRRDGVKFLHEFCSLAKNLQPQ 184 (193)
T ss_pred HHHHHHHhCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 6777777777555555544411000000 011355777666665555443
No 9
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=34.92 E-value=29 Score=29.38 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=34.3
Q ss_pred HHHHhhccCCCChhHHHHHHHHHHHHhhcccCChHHH
Q 015127 228 VLRLLDLFDSEDPREREYLKTVLHRIYGKFMVHRPFI 264 (413)
Q Consensus 228 i~~Ll~lfdSeDpRERd~LKtiLHrIY~Kf~~~R~fI 264 (413)
+.+|+++..|.-....++...+|+.+|.-+..+|||+
T Consensus 48 mRkLld~v~akG~~~k~~F~~iL~e~~~~y~~~~~~~ 84 (85)
T cd08324 48 VRKILDLVQSKGEEVSEYFLYLLQQLADAYVDLRPWL 84 (85)
T ss_pred HHHHHHHHHhcCchHHHHHHHHHHHHHHhhhhhhccc
Confidence 5679999999999999999999999999999999985
No 10
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=31.05 E-value=5.1e+02 Score=25.27 Aligned_cols=36 Identities=22% Similarity=0.177 Sum_probs=16.9
Q ss_pred HhcCChhhHHhhHHHHHHHHHHh-hCCCchHHHhhhh
Q 015127 376 LESTQPGEFQRCMVPLFHQIGRC-LSSSHFQVGSSLL 411 (413)
Q Consensus 376 Le~~~~~ef~~i~~pLF~~la~C-l~S~hfqVAErAL 411 (413)
|+..+++....++..+-..+... .+..-..|+|+++
T Consensus 209 l~~~~~~~~~~i~~~l~~~~~~l~~~k~Gs~Vve~~l 245 (322)
T cd07920 209 LELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCL 245 (322)
T ss_pred HhcCCHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHH
Confidence 34444444444444444444442 2233345666655
No 11
>PF04388 Hamartin: Hamartin protein; InterPro: IPR007483 This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein IPR003913 from INTERPRO. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterised by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation in either TSC1 or TSC2 tumour suppressor genes. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin IPR003913 from INTERPRO. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking [].
Probab=27.96 E-value=9.1e+02 Score=27.38 Aligned_cols=58 Identities=26% Similarity=0.411 Sum_probs=42.3
Q ss_pred HHHHhhccCCCChhHHHHHHHHHHHHhhcccCChHHHHHHHHHHHhhhhhccccccCHHHHHHHHHHH
Q 015127 228 VLRLLDLFDSEDPREREYLKTVLHRIYGKFMVHRPFIRKAINNIFYRFIFETEKHNGIAELLEILGSI 295 (413)
Q Consensus 228 i~~Ll~lfdSeDpRERd~LKtiLHrIY~Kf~~~R~fIRk~Innif~~fiyEte~~nGIaELLEIlgSI 295 (413)
|.+|+.+++|.|..+.+.+|..+++..+. ..-+|+- |.+..|..+| |-.-.++||.++
T Consensus 6 ~~~l~~~l~s~~~~~~~~~~~~~~~~~~~--~~~~~l~----~~l~~y~~~t----~s~~~~~il~~~ 63 (668)
T PF04388_consen 6 ITELLSLLESNDLSVLEEIKALLQELLNS--DREPWLV----NGLVDYYLST----NSQRALEILVGV 63 (668)
T ss_pred HHHHHHHhcCCchhhHHHHHHHHHHHhhc--cchHHHH----HHHHHHHhhc----CcHHHHHHHHhc
Confidence 67899999999999999999999998876 3334553 4444554555 445577777654
No 12
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.71 E-value=8.8e+02 Score=29.06 Aligned_cols=149 Identities=19% Similarity=0.283 Sum_probs=0.0
Q ss_pred chHH-HHHHHHHHHhcCCccCH--------HHHhccCCHHHHHHHhhccCCCChhHHHHHHHHHHHH-hhcccCChHHHH
Q 015127 196 PHLQ-VVYEFLLRFVASPETDA--------KLAKRYIDHSFVLRLLDLFDSEDPREREYLKTVLHRI-YGKFMVHRPFIR 265 (413)
Q Consensus 196 PHLq-lVYelllrfv~s~~~d~--------~~ak~~id~~Fi~~Ll~lfdSeDpRERd~LKtiLHrI-Y~Kf~~~R~fIR 265 (413)
|||| ++-++..-.+--++-|. +..++++| +.+-+.|+|..=-++|-+.-..= =.+|++ |-
T Consensus 343 PHl~~ii~~vIFPlmc~~d~deelwe~DP~EYiR~~~D------i~ed~~sp~~Aa~~~l~~~~~KR~ke~l~k----~l 412 (1010)
T KOG1991|consen 343 PHLQVIIQDVIFPLMCFNDEDEELWEEDPYEYIRKKFD------IFEDGYSPDTAALDFLTTLVSKRGKETLPK----IL 412 (1010)
T ss_pred hHHHHHHHHhhhhhcCCCcccHHHHhcCHHHHHHhcCc------hhcccCCCcHHHHHHHHHHHHhcchhhhhh----HH
Q ss_pred HHHHHHHhhhhhc-cccccC--HHHHHHHHHHHhc--ccCCCCHHHHHHHHHHHHhccCCCCccccchhHHHHHHHHHH-
Q 015127 266 KAINNIFYRFIFE-TEKHNG--IAELLEILGSIIN--GFALPLKEEHKLFLVRALIPLHKPKCVAMYHQQLSYCITQFV- 339 (413)
Q Consensus 266 k~Innif~~fiyE-te~~nG--IaELLEIlgSIIn--GFa~PLKeEHk~fl~rvLiPLHk~~~~~~Yh~qL~yCi~qFv- 339 (413)
.-+.+||-+|.-. .+..|. .---|-++||+.. -=.-|.|.+...|+...++|.-++ .++.-..+-.+-+.+|.
T Consensus 413 ~F~~~Il~~~~~~~~~~~~~rqkdGAL~~vgsl~~~L~K~s~~~~~mE~flv~hVfP~f~s-~~g~Lrarac~vl~~~~~ 491 (1010)
T KOG1991|consen 413 SFIVDILTRYKEASPPNKNPRQKDGALRMVGSLASILLKKSPYKSQMEYFLVNHVFPEFQS-PYGYLRARACWVLSQFSS 491 (1010)
T ss_pred HHHHHHHHhhcccCCCccChhhhhhHHHHHHHHHHHHccCCchHHHHHHHHHHHhhHhhcC-chhHHHHHHHHHHHHHHh
Q ss_pred --HhCCCcHHHHHHHhhh
Q 015127 340 --EKDCKLADTVIRGLLK 355 (413)
Q Consensus 340 --eKDp~L~~~vi~glLk 355 (413)
=||+.+....++...+
T Consensus 492 ~df~d~~~l~~ale~t~~ 509 (1010)
T KOG1991|consen 492 IDFKDPNNLSEALELTHN 509 (1010)
T ss_pred ccCCChHHHHHHHHHHHH
No 13
>COG5656 SXM1 Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, chaperones]
Probab=27.35 E-value=5.8e+02 Score=29.91 Aligned_cols=152 Identities=20% Similarity=0.201 Sum_probs=87.8
Q ss_pred CCCC----chHHHHHHHHHHH--------hcCCccCH-HHHhccCCHHHHHHHhhccCCCChhHHHHHHHHHHHHhhc-c
Q 015127 192 DPAW----PHLQVVYEFLLRF--------VASPETDA-KLAKRYIDHSFVLRLLDLFDSEDPREREYLKTVLHRIYGK-F 257 (413)
Q Consensus 192 EpsW----PHLqlVYelllrf--------v~s~~~d~-~~ak~~id~~Fi~~Ll~lfdSeDpRERd~LKtiLHrIY~K-f 257 (413)
+.-| ||||++.+=+.-= .+..+.|| +..++|+| +-+.+.|+|-.--+++-+.--.==.+ |
T Consensus 333 d~tw~l~ePhlq~ii~~vIfPllc~see~eElfEnDp~eyirry~d------f~d~g~spdlaal~fl~~~~sKrke~Tf 406 (970)
T COG5656 333 DQTWRLMEPHLQYIISGVIFPLLCLSEEEEELFENDPDEYIRRYYD------FFDNGLSPDLAALFFLIISKSKRKEETF 406 (970)
T ss_pred HhhHhhhccHHHHHHHhhhhhhcCCChhhHHHHhcCHHHHHHHhcc------hhcCCCChhHHHHHHHHHHhcccchhhh
Confidence 4556 6888765532210 11223344 45556665 56677888887777765541111111 3
Q ss_pred cCChHHHHHHHHHHHhhhhhcccc-cc--CHHHHHHHHHHHhc--ccCCCCHHHHHHHHHHHHhccCCCCccccchhHHH
Q 015127 258 MVHRPFIRKAINNIFYRFIFETEK-HN--GIAELLEILGSIIN--GFALPLKEEHKLFLVRALIPLHKPKCVAMYHQQLS 332 (413)
Q Consensus 258 ~~~R~fIRk~Innif~~fiyEte~-~n--GIaELLEIlgSIIn--GFa~PLKeEHk~fl~rvLiPLHk~~~~~~Yh~qL~ 332 (413)
++ |-.-+++||-++--...+ -| -+.-.|.++.||++ --.-|+.-+...|+...++|-.+.+.. .-..+-.
T Consensus 407 qg----iLsf~~sil~qsaa~psn~dnarq~egalr~lasi~s~itk~sp~an~me~fiv~hv~P~f~s~yg-fL~Srac 481 (970)
T COG5656 407 QG----ILSFLLSILGQSAATPSNIDNARQAEGALRLLASIKSFITKMSPAANVMEYFIVNHVIPAFRSNYG-FLKSRAC 481 (970)
T ss_pred hh----HHHHHHHHHhcccCCCCccccHHHHhhHHHHHHHHHHHhccCchHHHHHHHHHHHHhhHhhcCccc-chHHHHH
Confidence 44 445556777666433322 11 13347889999998 234466678899999999999988654 3344444
Q ss_pred HHHHHHH--HhCCCcHHHHHHHhh
Q 015127 333 YCITQFV--EKDCKLADTVIRGLL 354 (413)
Q Consensus 333 yCi~qFv--eKDp~L~~~vi~glL 354 (413)
+-+..|- =||+.++-...++..
T Consensus 482 e~is~~eeDfkd~~ill~aye~t~ 505 (970)
T COG5656 482 EFISTIEEDFKDNGILLEAYENTH 505 (970)
T ss_pred HHHHHHHHhcccchHHHHHHHHHH
Confidence 5555552 167777766666554
No 14
>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=26.99 E-value=4.8e+02 Score=27.17 Aligned_cols=53 Identities=21% Similarity=0.251 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhcCCccCHHHHhccCCHHHHHHHhhccCCCChhHHHHHHHHHHHHhhcc
Q 015127 199 QVVYEFLLRFVASPETDAKLAKRYIDHSFVLRLLDLFDSEDPREREYLKTVLHRIYGKF 257 (413)
Q Consensus 199 qlVYelllrfv~s~~~d~~~ak~~id~~Fi~~Ll~lfdSeDpRERd~LKtiLHrIY~Kf 257 (413)
.++|+...-++.-+...+ .-...+..|+.++.+.|+.=|-..-..|+.|-.+.
T Consensus 246 ~V~~e~~~~i~~l~~~~~------~~~~~~~~L~~lL~s~~~nvr~~~L~~L~~l~~~~ 298 (526)
T PF01602_consen 246 SVVYEAIRLIIKLSPSPE------LLQKAINPLIKLLSSSDPNVRYIALDSLSQLAQSN 298 (526)
T ss_dssp HHHHHHHHHHHHHSSSHH------HHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHCCHC
T ss_pred HHHHHHHHHHHHhhcchH------HHHhhHHHHHHHhhcccchhehhHHHHHHHhhccc
Confidence 455665555553222111 22345666778888888877766555556554443
No 15
>PF11131 PhrC_PhrF: Rap-phr extracellular signalling
Probab=24.98 E-value=29 Score=25.01 Aligned_cols=10 Identities=20% Similarity=0.384 Sum_probs=8.9
Q ss_pred CchHHHhhhh
Q 015127 402 SHFQVGSSLL 411 (413)
Q Consensus 402 ~hfqVAErAL 411 (413)
.+|+||||+|
T Consensus 27 ~~f~VaqRgM 36 (37)
T PF11131_consen 27 HQFHVAQRGM 36 (37)
T ss_pred hhhhHHhhcc
Confidence 7899999986
No 16
>KOG1825 consensus Fry-like conserved proteins [General function prediction only]
Probab=24.94 E-value=1.1e+02 Score=38.77 Aligned_cols=82 Identities=17% Similarity=0.220 Sum_probs=58.3
Q ss_pred HHHHHHHhhccCCCChhHHHHHHHHHHHHhh-cccCChHHHHHHHHHHHhhhhhccccccCHHHHHHHHHHHhcccCCCC
Q 015127 225 HSFVLRLLDLFDSEDPREREYLKTVLHRIYG-KFMVHRPFIRKAINNIFYRFIFETEKHNGIAELLEILGSIINGFALPL 303 (413)
Q Consensus 225 ~~Fi~~Ll~lfdSeDpRERd~LKtiLHrIY~-Kf~~~R~fIRk~Innif~~fiyEte~~nGIaELLEIlgSIInGFa~PL 303 (413)
..|+.++=.+-.+ ++++-+ -.+.|+||| +|+.. +.|-.|.++.-+.++..+++.+.--+--+
T Consensus 217 ~~f~ae~~~l~~~-~s~~~~--~s~vsLI~gMRyLrl--------------~~y~~~~~e~S~~F~~~l~~l~~~v~~~~ 279 (2206)
T KOG1825|consen 217 DRFIAETERIDGK-ISPVAE--SSTVSLINGMRYLKL--------------GVYPLEDFEASASFMQSLSSLFLKVKDKV 279 (2206)
T ss_pred HHHHHHHHhcccc-CChHHH--HHHHHHHHhhhhhee--------------ccccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 3466666555545 665544 356788887 66654 45777888888889999999875443337
Q ss_pred HHHHHHHHHHHHhccCCCCc
Q 015127 304 KEEHKLFLVRALIPLHKPKC 323 (413)
Q Consensus 304 KeEHk~fl~rvLiPLHk~~~ 323 (413)
|.|..-.+...|+||-.+=.
T Consensus 280 k~~~a~~~~elL~pl~a~~~ 299 (2206)
T KOG1825|consen 280 KHALAGLLVELLLPLAAAVT 299 (2206)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 88888889999999987633
No 17
>cd00160 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Probab=24.06 E-value=4.9e+02 Score=22.81 Aligned_cols=23 Identities=13% Similarity=0.063 Sum_probs=14.0
Q ss_pred HHHHHHHHHhhCCCc--hHHHhhhh
Q 015127 389 VPLFHQIGRCLSSSH--FQVGSSLL 411 (413)
Q Consensus 389 ~pLF~~la~Cl~S~h--fqVAErAL 411 (413)
.-|++.|.+|....| +.-...|+
T Consensus 146 ~lLL~~l~k~t~~~~~d~~~l~~a~ 170 (181)
T cd00160 146 PLLLKELLKHTPDGHEDREDLKKAL 170 (181)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHH
Confidence 457788888877644 44444443
No 18
>TIGR00777 ahpD alkylhydroperoxidase, AhpD family. Members of this family are alkylhydroperoxidases, which catalyze the reduction of peroxides to their corresponding alcohols via oxidation of cysteine residues. In these alkylhydroperoxidases, the cysteines are located in a conserved -CXXC- motif located towards the COOH terminus. In Mycobacterium tuberculosis, two non-homologous alkylhydroperoxidases, AhpD and AhpC, are found in the same operon.
Probab=23.87 E-value=90 Score=29.72 Aligned_cols=16 Identities=38% Similarity=0.391 Sum_probs=12.6
Q ss_pred HHHHHHHHHhhhhhcc
Q 015127 264 IRKAINNIFYRFIFET 279 (413)
Q Consensus 264 IRk~Innif~~fiyEt 279 (413)
-.-+|||+||||+.=.
T Consensus 75 s~MamnNv~Yr~~hl~ 90 (177)
T TIGR00777 75 AIMAMNNVFYRGRHLL 90 (177)
T ss_pred HHHhhhhHHHHhHhhc
Confidence 4567999999998654
No 19
>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=23.82 E-value=5.3e+02 Score=23.27 Aligned_cols=79 Identities=10% Similarity=0.119 Sum_probs=59.3
Q ss_pred HHHHHHHhCCCcHHHHHHHhhhcCCCCCchhHHHhHHHHHHHHhcCChhhHHhhH-HHHHHHHHHhhC------CCchHH
Q 015127 334 CITQFVEKDCKLADTVIRGLLKYWPVTNSTKEVMFLGELEEVLESTQPGEFQRCM-VPLFHQIGRCLS------SSHFQV 406 (413)
Q Consensus 334 Ci~qFveKDp~L~~~vi~glLk~WP~tns~KEvlFL~EleeiLe~~~~~ef~~i~-~pLF~~la~Cl~------S~hfqV 406 (413)
=|...|..++.-+...++.|.|-=-..|+.-++.-|.-||.+...|...--+.|. ......+.+.+. ..|..|
T Consensus 24 eicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~el~kl~~~k~~~~~~~~~V 103 (139)
T cd03567 24 AFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKV 103 (139)
T ss_pred HHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHHHHHHHhccccCCCCCCHHH
Confidence 3456788899999999999998888888887888899999999888765444444 344445666663 268899
Q ss_pred Hhhhhc
Q 015127 407 GSSLLS 412 (413)
Q Consensus 407 AErAL~ 412 (413)
-+|.|.
T Consensus 104 k~kil~ 109 (139)
T cd03567 104 KTKIIE 109 (139)
T ss_pred HHHHHH
Confidence 988774
No 20
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=23.65 E-value=2.9e+02 Score=24.85 Aligned_cols=60 Identities=13% Similarity=0.257 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhhhhccccccCHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHhccCCCCcc
Q 015127 264 IRKAINNIFYRFIFETEKHNGIAELLEILGSIINGFALPLKEEHKLFLVRALIPLHKPKCV 324 (413)
Q Consensus 264 IRk~Innif~~fiyEte~~nGIaELLEIlgSIInGFa~PLKeEHk~fl~rvLiPLHk~~~~ 324 (413)
+|..+-..+.+.+...+ ..=..-.|.|+..+++.|.--||.|-..|+..++.|+-.++.-
T Consensus 70 lk~~l~~~Ll~~~~~~~-~~i~~~slri~~~l~~~~~~~Lk~ele~~l~~i~~~il~~~~~ 129 (168)
T PF12783_consen 70 LKDDLCPALLKNLSSSD-FPIFSRSLRIFLTLLSRFRSHLKLELEVFLSHIILRILESDNS 129 (168)
T ss_pred HHHHHHHHHHHHHhhhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
Confidence 44444344444443322 2223557889999999999999999999999999988776654
No 21
>KOG3887 consensus Predicted small GTPase involved in nuclear protein import [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.23 E-value=53 Score=33.38 Aligned_cols=51 Identities=25% Similarity=0.383 Sum_probs=41.3
Q ss_pred HHHHHHHHHhcCCccCHHHHhccCCH-HHHHHHhhccCCCChhHHHHHHHHHHHHhhcccCC
Q 015127 200 VVYEFLLRFVASPETDAKLAKRYIDH-SFVLRLLDLFDSEDPREREYLKTVLHRIYGKFMVH 260 (413)
Q Consensus 200 lVYelllrfv~s~~~d~~~ak~~id~-~Fi~~Ll~lfdSeDpRERd~LKtiLHrIY~Kf~~~ 260 (413)
-+||.|.|.|+ +.|.+ .++.+||+.|-|.-.-|..+|-+++..||-.--..
T Consensus 189 SIfEAFSkvVQ----------kLipqLptLEnlLnif~s~S~ieKafLFDv~SKIYiaTDS~ 240 (347)
T KOG3887|consen 189 SIFEAFSKVVQ----------KLIPQLPTLENLLNIFISNSKIEKAFLFDVLSKIYIATDSS 240 (347)
T ss_pred HHHHHHHHHHH----------HHhhhchhHHHHHHHHhhccchhhhhhhhhhheeEEecCCC
Confidence 47888888775 44443 57899999999999999999999999999765443
No 22
>PF04499 SAPS: SIT4 phosphatase-associated protein; InterPro: IPR007587 The SAPS family consists of proteins that associate with the SIT4 phosphatase protein []. This association is required for SIT4's role in G1 cyclin transcription and for bud formation in yeast.
Probab=22.23 E-value=3.9e+02 Score=28.96 Aligned_cols=52 Identities=13% Similarity=0.374 Sum_probs=33.8
Q ss_pred HHHHHHHHHhcCCc--cCHHHHhccCCHHHHHHHhhccCCCChhHH-HHHHHHHH
Q 015127 200 VVYEFLLRFVASPE--TDAKLAKRYIDHSFVLRLLDLFDSEDPRER-EYLKTVLH 251 (413)
Q Consensus 200 lVYelllrfv~s~~--~d~~~ak~~id~~Fi~~Ll~lfdSeDpRER-d~LKtiLH 251 (413)
.+-|+|+|+|.... ....+..-.-++.+|.+|+++|+.+...++ ...-.+|.
T Consensus 34 ~ImDlLLklIs~d~~~~~~~ilewL~~q~LI~~Li~~L~p~~~~~~q~naa~~L~ 88 (475)
T PF04499_consen 34 AIMDLLLKLISTDKPESPTGILEWLAEQNLIPRLIDLLSPSYSSDVQSNAADFLK 88 (475)
T ss_pred HHHHHHHHHHccCcccchHHHHHHHHHhCHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 57789999998543 223444444578999999999975554444 33333433
No 23
>PF03378 CAS_CSE1: CAS/CSE protein, C-terminus; InterPro: IPR005043 Mammalian cellular apoptosis susceptibility (CAS) proteins and the yeast chromosome-segregation protein, CSE1 are homologous []. CAS is involved in both cellular apoptosis and proliferation [, ]. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle [], as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway []. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins []. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins []. This entry represents the C-terminal portion of these proteins. Structural studies of the yeast CSE1 protein indicate that this domain binds to both the transport-orchestrating protein RanGTP and the cargo molecule that is being exported [].; GO: 0005515 protein binding; PDB: 1Z3H_B 1WA5_C.
Probab=21.44 E-value=1.5e+02 Score=31.68 Aligned_cols=105 Identities=17% Similarity=0.331 Sum_probs=63.5
Q ss_pred CCCchHHHHHHHHHHHhcCCccCHHHHhccCCHHHHHHHhhccCCCChhH-HHHHHHHHHHHhhcccCCh--HHHHHHHH
Q 015127 193 PAWPHLQVVYEFLLRFVASPETDAKLAKRYIDHSFVLRLLDLFDSEDPRE-REYLKTVLHRIYGKFMVHR--PFIRKAIN 269 (413)
Q Consensus 193 psWPHLqlVYelllrfv~s~~~d~~~ak~~id~~Fi~~Ll~lfdSeDpRE-Rd~LKtiLHrIY~Kf~~~R--~fIRk~In 269 (413)
.+..||+-|+.+|-+.+.|...|..-. ..+.-++..+ +++- ..|+++|+.-++.+....| .|+|+-+.
T Consensus 195 ~~~~~l~~iLgvFQkLi~sk~~D~~gF------~LL~~iv~~~---p~~~l~~yl~~I~~lll~RLq~skT~kf~~~fv~ 265 (435)
T PF03378_consen 195 VANNQLEPILGVFQKLIASKANDHYGF------DLLESIVENL---PPEALEPYLKQIFTLLLTRLQSSKTEKFVKRFVV 265 (435)
T ss_dssp ---S-CHHHHHHHHHHHT-TTCHHHHH------HHHHHHHHHS----HHHHGGGHHHHHHHHHHHHHHC--HHHHHHHHH
T ss_pred cchhhHHHHHHHHHHHHCCCCcchHHH------HHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHhhCCcHHHHHHHHH
Confidence 467999999999999999876554211 1333344433 3322 4588888888888877666 56776662
Q ss_pred HHHhhhhhccccccCHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHhcc
Q 015127 270 NIFYRFIFETEKHNGIAELLEILGSIINGFALPLKEEHKLFLVRALIPL 318 (413)
Q Consensus 270 nif~~fiyEte~~nGIaELLEIlgSIInGFa~PLKeEHk~fl~rvLiPL 318 (413)
.+.-++.. .|...+.+++.+|-.|.- ...+.++++|-
T Consensus 266 -F~~~~~~~----~g~~~li~~id~IQ~glF-------~~il~~v~lp~ 302 (435)
T PF03378_consen 266 -FLSLFAIK----YGPDFLIQTIDSIQPGLF-------GMILEKVWLPD 302 (435)
T ss_dssp -HHHHHHHH----H-HHHHHHHHHTTSTTHH-------HHHHHHTHHHH
T ss_pred -HHHHHHHH----cCHHHHHHHHHHhcCCcH-------HHHHHHHhcCc
Confidence 22333322 299999999999887731 35566777773
No 24
>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]
Probab=20.82 E-value=90 Score=32.27 Aligned_cols=32 Identities=19% Similarity=0.258 Sum_probs=26.8
Q ss_pred hHHHHHHHHHH-HhCCCcHHHHHHHhhhcCCCC
Q 015127 329 QQLSYCITQFV-EKDCKLADTVIRGLLKYWPVT 360 (413)
Q Consensus 329 ~qL~yCi~qFv-eKDp~L~~~vi~glLk~WP~t 360 (413)
+-+++|+++|+ .|=|++-+..|+++..||=-+
T Consensus 125 ~~~~~~v~~~l~~kyPrlP~E~l~ai~n~ll~e 157 (333)
T KOG3769|consen 125 QFLSFYVTEYLKCKYPRLPEEGLHAIVNGLLGE 157 (333)
T ss_pred HHHHHHHHHHHHHhccCCcHHHHHHHHHHhhhH
Confidence 45789999996 788999999999999888543
No 25
>PF06901 FrpC: RTX iron-regulated protein FrpC; InterPro: IPR010692 This family consists of several RTX iron-regulated FrpC proteins which appear to be found exclusively in Neisseria meningitidis. FrpC has been shown to be related to the RTX family of bacterial cytotoxins. FrpC is found in the meningococcal outer membrane. The function of this family is unknown although it is thought to be a virulence factor [].
Probab=20.23 E-value=75 Score=31.12 Aligned_cols=44 Identities=32% Similarity=0.588 Sum_probs=33.6
Q ss_pred HHHHHhcccCC---CCHHHHHHHHHHHHhccCCCCccccchhHHHHHHHHHHHhCC
Q 015127 291 ILGSIINGFAL---PLKEEHKLFLVRALIPLHKPKCVAMYHQQLSYCITQFVEKDC 343 (413)
Q Consensus 291 IlgSIInGFa~---PLKeEHk~fl~rvLiPLHk~~~~~~Yh~qL~yCi~qFveKDp 343 (413)
-.||-||||++ |.-.||++.-..- +--||+|.-..|..|+...+
T Consensus 223 ~v~SCING~tV~YYP~I~~~qQ~tQQE---------Lv~YH~qvEqLvqSFvnnss 269 (271)
T PF06901_consen 223 AVGSCINGFTVQYYPFIREKQQLTQQE---------LVGYHQQVEQLVQSFVNNSS 269 (271)
T ss_pred hhhhhccCceeeeehhhhhhccccHHH---------HHHHHHHHHHHHHHHhcCcC
Confidence 47999999987 6667887654443 44799999999999987643
Done!