Query 015533
Match_columns 405
No_of_seqs 146 out of 282
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 07:12:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015533.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015533hhsearch_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 3E-131 6E-136 985.3 27.5 336 53-394 40-375 (457)
2 PF01603 B56: Protein phosphat 100.0 1E-107 2E-112 836.6 26.1 329 57-394 1-331 (409)
3 PLN00122 serine/threonine prot 98.8 2.4E-09 5.2E-14 98.6 1.4 52 310-394 35-86 (170)
4 PLN00122 serine/threonine prot 97.3 0.002 4.4E-08 59.6 10.3 28 50-77 40-67 (170)
5 PF01602 Adaptin_N: Adaptin N 89.5 5.6 0.00012 41.6 12.8 176 197-385 340-520 (526)
6 PF14500 MMS19_N: Dos2-interac 85.2 22 0.00047 35.1 13.4 80 297-383 120-212 (262)
7 PF05918 API5: Apoptosis inhib 85.0 49 0.0011 36.4 17.0 105 296-400 240-359 (556)
8 smart00582 RPR domain present 58.1 18 0.00039 30.6 4.6 86 306-391 20-112 (121)
9 PF01602 Adaptin_N: Adaptin N 57.7 2.4E+02 0.0053 29.4 14.1 162 167-348 244-407 (526)
10 KOG0213 Splicing factor 3b, su 48.5 3.3E+02 0.0071 31.6 13.1 173 190-386 794-981 (1172)
11 PF08767 CRM1_C: CRM1 C termin 48.0 3.1E+02 0.0067 27.7 12.9 76 291-385 108-190 (319)
12 PF03378 CAS_CSE1: CAS/CSE pro 46.2 1.2E+02 0.0026 32.3 9.3 72 299-370 177-252 (435)
13 cd03567 VHS_GGA VHS domain fam 42.6 2.2E+02 0.0048 25.4 9.2 79 306-384 26-111 (139)
14 cd08324 CARD_NOD1_CARD4 Caspas 42.2 21 0.00045 29.8 2.3 40 195-234 45-84 (85)
15 cd03562 CID CID (CTD-Interacti 41.9 1.1E+02 0.0024 25.6 6.9 87 301-387 20-109 (114)
16 KOG0301 Phospholipase A2-activ 41.4 3.7E+02 0.0079 30.5 12.1 48 165-213 558-605 (745)
17 PF12348 CLASP_N: CLASP N term 38.1 3.3E+02 0.0071 25.2 14.8 175 206-383 17-200 (228)
18 COG5656 SXM1 Importin, protein 36.9 4E+02 0.0086 30.8 11.6 153 162-325 333-506 (970)
19 PF12460 MMS19_C: RNAPII trans 36.1 5.2E+02 0.011 26.8 17.5 206 172-384 168-389 (415)
20 PF06757 Ins_allergen_rp: Inse 31.8 1.6E+02 0.0034 27.2 6.7 54 339-394 104-163 (179)
21 cd03568 VHS_STAM VHS domain fa 28.3 4.4E+02 0.0094 23.6 9.3 80 306-385 25-106 (144)
22 COG5098 Chromosome condensatio 28.1 8.9E+02 0.019 28.1 12.4 51 326-384 272-323 (1128)
23 cd00020 ARM Armadillo/beta-cat 28.0 1.7E+02 0.0038 23.2 5.7 43 186-228 39-81 (120)
24 PF04118 Dopey_N: Dopey, N-ter 27.2 6.7E+02 0.015 25.5 11.1 77 296-384 173-249 (307)
25 PF12783 Sec7_N: Guanine nucle 26.0 2.8E+02 0.0061 24.8 7.2 39 256-294 91-129 (168)
26 cd03569 VHS_Hrs_Vps27p VHS dom 25.9 4.8E+02 0.01 23.3 9.5 80 306-385 29-110 (142)
27 smart00802 UME Domain in UVSB 24.6 2.4E+02 0.0051 24.2 6.0 27 285-312 42-68 (107)
28 KOG4189 Uncharacterized conser 24.2 1.4E+02 0.0031 28.7 5.0 49 168-245 111-161 (209)
29 cd03561 VHS VHS domain family; 23.5 4.9E+02 0.011 22.6 9.4 80 305-384 24-107 (133)
30 KOG2067 Mitochondrial processi 21.5 6.3E+02 0.014 27.2 9.4 120 217-362 304-432 (472)
31 PF02985 HEAT: HEAT repeat; I 21.5 1.7E+02 0.0037 18.9 3.6 28 198-225 2-29 (31)
32 PF12726 SEN1_N: SEN1 N termin 21.4 5.3E+02 0.011 29.0 9.6 90 183-274 510-611 (727)
33 PF06901 FrpC: RTX iron-regula 21.0 87 0.0019 30.3 2.8 50 250-313 217-269 (271)
34 PF03378 CAS_CSE1: CAS/CSE pro 20.1 3E+02 0.0064 29.3 6.9 167 102-289 117-303 (435)
No 1
>KOG2085 consensus Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]
Probab=100.00 E-value=2.5e-131 Score=985.32 Aligned_cols=336 Identities=61% Similarity=1.028 Sum_probs=331.5
Q ss_pred ccccCCCCCCCCCchHhHHHHHHHHhhccccccccCCCCCchHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 015533 53 YEIQNLPKFNDVPSSEKLNLFIKKTQLCCVLCDFNDPSKMTREKEIKHRNLQELVKFIQSDSSKINEQMQENLMRMISIN 132 (405)
Q Consensus 53 ~~~~~lp~l~dv~~~e~~~Lf~~Kl~~C~~ifDFsdp~~d~~~Ke~Kr~tL~EL~~~v~~~~~~l~e~~~~~i~~Mi~~N 132 (405)
.++++||+|+|||++++++||++|+++||++|||+||.+|.++||+||+||+||+||+.++++++++.+|+++++|+++|
T Consensus 40 ~~l~~LP~~~dv~~se~~~Lf~~Kl~~Cc~~FDF~Dp~~~~~~keikR~tL~eLvd~v~~~~~kite~~~~~vv~m~s~n 119 (457)
T KOG2085|consen 40 VELEPLPSLKDVPSSEQKELFIKKLEQCCVLFDFNDPLKDLKGKEIKRQTLLELVDDVISRRGKISEEVYSEVVKMFSVN 119 (457)
T ss_pred CCceeCCccCcCChhHhHHHHHHHHHhhheeeeccChhhhhccchhHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHH
Confidence 34999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCCCCCCCCCCCCCCCCCCCCCCccccCCCCchhHHHHHHHHHHHhhcCCChHHHhhcCCHHHHHHHhhccCCCChhH
Q 015533 133 IFRALPPAFHENTGSLPDVGEPDEEDAWLEPAWPHLQLVYEILLRYIVSNGADKKIAKRYIDHTFVLKLLDLFDTEDHRE 212 (405)
Q Consensus 133 IFR~lPp~~~~~~~~~~~~~d~eedep~~e~sWpHLqlVYeillrfv~s~~~d~k~ak~~id~~Fi~~Ll~lfdS~DpRE 212 (405)
|||++||..+++ .+|+|||||++|++|||||+||++|+||++||++|+++||+|||++||++|+++||||||||
T Consensus 120 ifR~lpp~~n~~------~~d~eedEp~le~awphLqlvye~~Lrf~~sp~~d~~vaK~yid~~FvlkLLdLFdSEDpRE 193 (457)
T KOG2085|consen 120 IFRTLPPSVNPT------GFDYEEDEPVLEPAWPHLQLVYEFLLRFLESPDFDPSVAKKYIDQKFVLKLLDLFDSEDPRE 193 (457)
T ss_pred hhccCCcccCCC------cCCccccCcccCCCchHHHHHHHHHHHHHhCcccCHHHHHHHhhHHHHHHHHHHhcCCChHH
Confidence 999999998764 38899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhccccchHHHHHHHHHHHHHhhhcccCccCHHHHHHHHHHHHhccCCCcHHHHHHHHHHHhhcCCCCC
Q 015533 213 REYLKMVLHRIYGRFMSHRPFIRAGINNVFYRFIFETERHNGIGELLEILGSIINGFALPMKEEHKLLLVRAMLPLHKPK 292 (405)
Q Consensus 213 Rd~LktiLhrIY~Kf~~~R~fIRk~i~nif~~fi~e~~~~nGIaELLeilgSIInGFa~PLKeEhk~fl~~vLiPLHk~~ 292 (405)
||+|||+|||||||||++|+|||++|||+||+|||||++||||||||||+||||||||+||||||+.|+.||||||||++
T Consensus 194 Re~LKT~LhrIygKfl~~r~firk~iNNif~~FIyEte~hnGIaELLEIlgSiIngfAlPlKEEhkiFL~rvLipLhk~k 273 (457)
T KOG2085|consen 194 REFLKTILHRIYGKFLVHRPFIRKSINNIFLRFIYETERHNGIAELLEILGSIINGFALPLKEEHKLFLVRVLIPLHKPK 273 (457)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHhhcchhhhhcccccccCCHHHHHHHHHHhcCcccCcchhHHHHHHHHhhhccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhchhHHHHHHHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhCCC
Q 015533 293 CVALYHQQLTYCVVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCLTSP 372 (405)
Q Consensus 293 ~l~~y~~qL~yci~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~~la~ci~S~ 372 (405)
+++.||+||+|||+||++|||+|++.||+||+||||+|||+|||||||||||||++++|.+|++||+|||++||+|++|+
T Consensus 274 ~l~~yh~QLaYcivQfveKd~kl~~~VIrglLK~WP~tnS~KEVmFL~ElEEILe~iep~eFqk~~~PLf~qia~c~sS~ 353 (457)
T KOG2085|consen 274 SLSLYHKQLAYCIVQFVEKDPKLTETVIRGLLKYWPKTNSSKEVMFLNELEEILEVIEPSEFQKIMVPLFRQIARCVSSP 353 (457)
T ss_pred CccccccccceeeeeeeccCccccHHHHHHHHHhcCCCCCcceeeeHhhHHHHHHhcCHHHHHHHhHHHHHHHHHHcCCh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHhhhcccccccccc
Q 015533 373 HFQVHIIVTSLIYMSCYCSAVS 394 (405)
Q Consensus 373 hfqVAErAl~i~~n~~f~~~~~ 394 (405)
|||||||||.+|+|+++.++|+
T Consensus 354 HFQVAEraL~~wnNe~i~~Li~ 375 (457)
T KOG2085|consen 354 HFQVAERALYLWNNEYIRSLIS 375 (457)
T ss_pred hHHHHHHHHHHHhhHHHHHHHH
Confidence 9999999999999999999987
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=9.7e-108 Score=836.60 Aligned_cols=329 Identities=57% Similarity=0.986 Sum_probs=287.7
Q ss_pred CCCCCCCCCchHhHHHHHHHHhhccccccccCCCCCchHHHHHHHHHHHHHHHhhcCC--CCCCHHHHHHHHHHHHHHhc
Q 015533 57 NLPKFNDVPSSEKLNLFIKKTQLCCVLCDFNDPSKMTREKEIKHRNLQELVKFIQSDS--SKINEQMQENLMRMISINIF 134 (405)
Q Consensus 57 ~lp~l~dv~~~e~~~Lf~~Kl~~C~~ifDFsdp~~d~~~Ke~Kr~tL~EL~~~v~~~~--~~l~e~~~~~i~~Mi~~NIF 134 (405)
|||+|+||+++++++||++||++||++|||+||.+|.++||+||+||+||++|+++++ +.++|++++++++||++|||
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 89999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCccccCCCCchhHHHHHHHHHHHhhcCCChHHHhhcCCHHHHHHHhhccCCCChhHHH
Q 015533 135 RALPPAFHENTGSLPDVGEPDEEDAWLEPAWPHLQLVYEILLRYIVSNGADKKIAKRYIDHTFVLKLLDLFDTEDHRERE 214 (405)
Q Consensus 135 R~lPp~~~~~~~~~~~~~d~eedep~~e~sWpHLqlVYeillrfv~s~~~d~k~ak~~id~~Fi~~Ll~lfdS~DpRERd 214 (405)
||+||.+.. .+|+|||+++.|++|||||+||++|++|++++++|+ +|+|||++|+.+|+++|+|+||||||
T Consensus 81 R~lP~~~~~-------~~~~~~d~~~~e~~WpHL~~vY~il~~~i~~~~~~~--~~~~i~~~fi~~Ll~l~~S~D~rER~ 151 (409)
T PF01603_consen 81 RPLPPIPNP-------SFDPDDDEPFLEPSWPHLQLVYEILLRFIESPPFDP--AKKYIDQKFIKKLLELFDSPDPRERD 151 (409)
T ss_dssp S-----SS---------S-GGG------TTHHHHHHHHHHHHHHHTSTT--C--CTTTS-HHHHHHHHHTTTSSTHHHHH
T ss_pred CCCCCcccc-------cCCccccccccccccHhHHHHHHHHHHHHHCccccH--HHHHcCHHHHHHHHHHcCCCCHHHHH
Confidence 999999865 367899999999999999999999999999999998 99999999999999999999999999
Q ss_pred HHHHHHHHHhhccccchHHHHHHHHHHHHHhhhcccCccCHHHHHHHHHHHHhccCCCcHHHHHHHHHHHhhcCCCCCch
Q 015533 215 YLKMVLHRIYGRFMSHRPFIRAGINNVFYRFIFETERHNGIGELLEILGSIINGFALPMKEEHKLLLVRAMLPLHKPKCV 294 (405)
Q Consensus 215 ~LktiLhrIY~Kf~~~R~fIRk~i~nif~~fi~e~~~~nGIaELLeilgSIInGFa~PLKeEhk~fl~~vLiPLHk~~~l 294 (405)
+||++|||||+||+++|++||++|+++|++|+||+++|+||+|||||+|||||||++|||+||+.|+.++|+|||+++++
T Consensus 152 ~lk~~l~~iy~k~~~~r~~Ir~~i~~~~~~fi~e~~~~~gI~elLeil~sii~gf~~plk~eh~~fl~~vllPLh~~~~~ 231 (409)
T PF01603_consen 152 YLKTILHRIYGKFPNLRSFIRKSINNIFYRFIYETERHNGIAELLEILGSIINGFAVPLKEEHKQFLRKVLLPLHKSPHL 231 (409)
T ss_dssp HHHHHHHHHHHH-TTTHHHHHHHHHHHHHHHHHTTS--STHHHHHHHHHHHHTT--SS--HHHHHHHHHTTGGGGGSTGG
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHhcCCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhCCCch
Q 015533 295 ALYHQQLTYCVVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCLTSPHF 374 (405)
Q Consensus 295 ~~y~~qL~yci~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~~la~ci~S~hf 374 (405)
+.||+||+||+++|++|||+|+..+++||+||||+||++||++||+|+++|++.+++++|++++.|+|++||+|++|+||
T Consensus 232 ~~y~~~L~~~~~~f~~kdp~l~~~~i~~llk~WP~t~s~Kev~FL~el~~il~~~~~~~f~~i~~~lf~~la~ci~S~h~ 311 (409)
T PF01603_consen 232 SSYHQQLSYCVVQFLEKDPSLAEPVIKGLLKHWPKTNSQKEVLFLNELEEILEVLPPEEFQKIMVPLFKRLAKCISSPHF 311 (409)
T ss_dssp GGTHHHHHHHHHHHHHH-GGGHHHHHHHHHHHS-SS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHTSSSH
T ss_pred HHHHHHHHHHHHHHHHhCchhHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCCH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcccccccccc
Q 015533 375 QVHIIVTSLIYMSCYCSAVS 394 (405)
Q Consensus 375 qVAErAl~i~~n~~f~~~~~ 394 (405)
|||||||.+|+|+.|+++++
T Consensus 312 qVAErAl~~w~n~~~~~li~ 331 (409)
T PF01603_consen 312 QVAERALYFWNNEYFLSLIS 331 (409)
T ss_dssp HHHHHHHGGGGSHHHHHHHH
T ss_pred HHHHHHHHHHCCHHHHHHHH
Confidence 99999999999999999884
No 3
>PLN00122 serine/threonine protein phosphatase 2A; Provisional
Probab=98.75 E-value=2.4e-09 Score=98.58 Aligned_cols=52 Identities=17% Similarity=0.102 Sum_probs=49.0
Q ss_pred HhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhCCCchHHHHHHHhhhccccc
Q 015533 310 EKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCLTSPHFQVHIIVTSLIYMSCY 389 (405)
Q Consensus 310 eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~~la~ci~S~hfqVAErAl~i~~n~~f 389 (405)
...+.++...+++|.+|||++++.||.+||++| ||||||.+|+|++|
T Consensus 35 ~~~~~~~~~~~e~l~~~~~v~~s~k~~lfl~kl---------------------------------VAERAL~lWnNe~i 81 (170)
T PLN00122 35 AVNPASVVAGYEPLPSFRDVPNSEKQNLFVRKL---------------------------------VAERALFLWNNDHI 81 (170)
T ss_pred ccCCCccccccccccCCCCCCchHHHHHHHHHH---------------------------------HHHHHHHHHccHHH
Confidence 456888999999999999999999999999999 99999999999999
Q ss_pred ccccc
Q 015533 390 CSAVS 394 (405)
Q Consensus 390 ~~~~~ 394 (405)
++|+.
T Consensus 82 ~~LI~ 86 (170)
T PLN00122 82 VNLIA 86 (170)
T ss_pred HHHHH
Confidence 99885
No 4
>PLN00122 serine/threonine protein phosphatase 2A; Provisional
Probab=97.30 E-value=0.002 Score=59.65 Aligned_cols=28 Identities=46% Similarity=0.682 Sum_probs=25.6
Q ss_pred CCcccccCCCCCCCCCchHhHHHHHHHH
Q 015533 50 IPKYEIQNLPKFNDVPSSEKLNLFIKKT 77 (405)
Q Consensus 50 ~~~~~~~~lp~l~dv~~~e~~~Lf~~Kl 77 (405)
.....+++||+|+|+|.+++++||++||
T Consensus 40 ~~~~~~e~l~~~~~v~~s~k~~lfl~kl 67 (170)
T PLN00122 40 SVVAGYEPLPSFRDVPNSEKQNLFVRKL 67 (170)
T ss_pred ccccccccccCCCCCCchHHHHHHHHHH
Confidence 4456689999999999999999999999
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=89.48 E-value=5.6 Score=41.60 Aligned_cols=176 Identities=12% Similarity=0.126 Sum_probs=117.7
Q ss_pred HHHHHhhcc-CCCChhHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhhhcccCccCHHHHHHHHHHHHhccCCCcHH
Q 015533 197 FVLKLLDLF-DTEDHREREYLKMVLHRIYGRFMSHRPFIRAGINNVFYRFIFETERHNGIGELLEILGSIINGFALPMKE 275 (405)
Q Consensus 197 Fi~~Ll~lf-dS~DpRERd~LktiLhrIY~Kf~~~R~fIRk~i~nif~~fi~e~~~~nGIaELLeilgSIInGFa~PLKe 275 (405)
.+..|+..+ +..|+.-|..+-..+..+-.++...-.|....+.+++.. .. ..-..|....+..++... ..+++
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 455566666 666887777777778888888887777766665554432 11 112446666677776652 23333
Q ss_pred HHHHHHHHHhhcCCCCCchhhchhHHHHHHHHHHHhCcc--cHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhH
Q 015533 276 EHKLLLVRAMLPLHKPKCVALYHQQLTYCVVQFVEKDYE--LADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAE 353 (405)
Q Consensus 276 Ehk~fl~~vLiPLHk~~~l~~y~~qL~yci~qF~eKDp~--L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~ 353 (405)
.-...+ +-+...-.....-.-..+|+-+|.+..+. .+..+++.+.+.|...+..=+...|..+..+....+.++
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 332223 32222233334577788999999888777 888999999999998887777888888888887776655
Q ss_pred HHHHHHHHHHHHHHhhC--CCchHHHHHHHhhhc
Q 015533 354 FQQCMGPLFRQIGRCLT--SPHFQVHIIVTSLIY 385 (405)
Q Consensus 354 f~~i~~plF~~la~ci~--S~hfqVAErAl~i~~ 385 (405)
-.+ .+...+.++.+ |.++.|-+||..+|.
T Consensus 490 ~~~---~i~~~~~~~~~~~s~~~evr~Ra~~y~~ 520 (526)
T PF01602_consen 490 VQN---EILQFLLSLATEDSSDPEVRDRAREYLR 520 (526)
T ss_dssp HHH---HHHHHHHCHHHHS-SSHHHHHHHHHHHH
T ss_pred hHH---HHHHHHHHHhccCCCCHHHHHHHHHHHH
Confidence 443 45666666667 999999999988774
No 6
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=85.19 E-value=22 Score=35.12 Aligned_cols=80 Identities=21% Similarity=0.377 Sum_probs=48.7
Q ss_pred chhHHHHHHHHHH--HhCcc---cHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhh------cCChh-H-HHHHHHHHHH
Q 015533 297 YHQQLTYCVVQFV--EKDYE---LADTVIRGLLRYWPVTNCQKEVLFLGELEEVLD------VTHPA-E-FQQCMGPLFR 363 (405)
Q Consensus 297 y~~qL~yci~qF~--eKDp~---L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe------~~~~~-~-f~~i~~plF~ 363 (405)
....+.+.+++.+ ||||. ++..+++.+++.||. .. |.+|+-+++. ..+|. + ..-...-|=.
T Consensus 120 ~~~~fv~~~i~~~~gEkDPRnLl~~F~l~~~i~~~~~~-~~-----~~e~lFd~~~cYFPI~F~pp~~dp~~IT~edLk~ 193 (262)
T PF14500_consen 120 MGDDFVYGFIQLIDGEKDPRNLLLSFKLLKVILQEFDI-SE-----FAEDLFDVFSCYFPITFRPPPNDPYGITREDLKR 193 (262)
T ss_pred chhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhccc-ch-----hHHHHHHHhhheeeeeeeCCCCCCCCCCHHHHHH
Confidence 4456677777775 89998 566888999999995 22 3344445553 12221 1 1112345777
Q ss_pred HHHHhhCCCchHHHHHHHhh
Q 015533 364 QIGRCLTSPHFQVHIIVTSL 383 (405)
Q Consensus 364 ~la~ci~S~hfqVAErAl~i 383 (405)
.|-+|+.|.+ +.|+-|+-+
T Consensus 194 ~L~~cl~s~~-~fa~~~~p~ 212 (262)
T PF14500_consen 194 ALRNCLSSTP-LFAPFAFPL 212 (262)
T ss_pred HHHHHhcCcH-hhHHHHHHH
Confidence 7888888644 456655443
No 7
>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=84.99 E-value=49 Score=36.35 Aligned_cols=105 Identities=14% Similarity=0.130 Sum_probs=59.7
Q ss_pred hchhHHHHHHHH---HHHhCcccHHHH---HHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhh
Q 015533 296 LYHQQLTYCVVQ---FVEKDYELADTV---IRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCL 369 (405)
Q Consensus 296 ~y~~qL~yci~q---F~eKDp~L~~~v---i~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~~la~ci 369 (405)
..-.++.+|+.+ |..+....+.-+ .+.++-.|=......++-+|.-+.|+...+...+...++.++|..|-..+
T Consensus 240 e~Idrli~C~~~Alp~fs~~v~Sskfv~y~~~kvlP~l~~l~e~~kl~lLk~lAE~s~~~~~~d~~~~L~~i~~~L~~ym 319 (556)
T PF05918_consen 240 ESIDRLISCLRQALPFFSRGVSSSKFVNYMCEKVLPKLSDLPEDRKLDLLKLLAELSPFCGAQDARQLLPSIFQLLKKYM 319 (556)
T ss_dssp HHHHHHHHHHHHHGGG-BTTB--HHHHHHHHHHTCCCTT-----HHHHHHHHHHHHHTT----THHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHhhHHhcCCCChHHHHHHHHHHhcCChhhCChHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHhC
Confidence 455678899888 666666654433 34444444445558899999999999999998889999999999997555
Q ss_pred C------CCchHHHHHHHhhhccccccccc---cccCccc
Q 015533 370 T------SPHFQVHIIVTSLIYMSCYCSAV---SLAGLSC 400 (405)
Q Consensus 370 ~------S~hfqVAErAl~i~~n~~f~~~~---~~~~~~~ 400 (405)
= +.+|-..|..|..+.+=..-+.- +|.|..|
T Consensus 320 P~~~~~~~l~fs~vEcLL~afh~La~k~p~~~~~lCgyk~ 359 (556)
T PF05918_consen 320 PSKKTEPKLQFSYVECLLYAFHQLARKSPNSLNFLCGYKI 359 (556)
T ss_dssp ----------HHHHHHHHHHHHHHHTT-THHHH-------
T ss_pred CCCCCCCcccchHhhHHHHHHHHHhhhCcchhhhHhhhcc
Confidence 3 45677788888777655444333 5555554
No 8
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=58.12 E-value=18 Score=30.63 Aligned_cols=86 Identities=7% Similarity=0.042 Sum_probs=58.5
Q ss_pred HHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCCh-------hHHHHHHHHHHHHHHHhhCCCchHHHH
Q 015533 306 VQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHP-------AEFQQCMGPLFRQIGRCLTSPHFQVHI 378 (405)
Q Consensus 306 ~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~-------~~f~~i~~plF~~la~ci~S~hfqVAE 378 (405)
++|+-.+..-+..+++.+.++=..+.+.+-+..|.-+.+|+-.+.. ..|.+.....|..+.......+-+=..
T Consensus 20 t~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~ki~ 99 (121)
T smart00582 20 TKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQDALRDVLGAANDETKKKIR 99 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 4444444455666777777777777777888999999999965522 245556666777777665556777788
Q ss_pred HHHhhhccccccc
Q 015533 379 IVTSLIYMSCYCS 391 (405)
Q Consensus 379 rAl~i~~n~~f~~ 391 (405)
+-+.+|..-..-.
T Consensus 100 kll~iW~~~~iF~ 112 (121)
T smart00582 100 RLLNIWEERGIFP 112 (121)
T ss_pred HHHHHHhcCCCCC
Confidence 8899998755433
No 9
>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=57.67 E-value=2.4e+02 Score=29.36 Aligned_cols=162 Identities=15% Similarity=0.174 Sum_probs=81.5
Q ss_pred hhHHHHHHHHHHHhhcCCChHHHhhcCCHHHHHHHhhccCCCChhHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhh
Q 015533 167 HLQLVYEILLRYIVSNGADKKIAKRYIDHTFVLKLLDLFDTEDHREREYLKMVLHRIYGRFMSHRPFIRAGINNVFYRFI 246 (405)
Q Consensus 167 HLqlVYeillrfv~s~~~d~k~ak~~id~~Fi~~Ll~lfdS~DpRERd~LktiLhrIY~Kf~~~R~fIRk~i~nif~~fi 246 (405)
--.++|+....++.-++.+ . .-...+..|+.++.+.|++=|-..-..|+.|-.+. .+.+...-..+| ++
T Consensus 244 ~~~V~~e~~~~i~~l~~~~-~-----~~~~~~~~L~~lL~s~~~nvr~~~L~~L~~l~~~~---~~~v~~~~~~~~--~l 312 (526)
T PF01602_consen 244 SPSVVYEAIRLIIKLSPSP-E-----LLQKAINPLIKLLSSSDPNVRYIALDSLSQLAQSN---PPAVFNQSLILF--FL 312 (526)
T ss_dssp HHHHHHHHHHHHHHHSSSH-H-----HHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHCCHC---HHHHGTHHHHHH--HH
T ss_pred ccHHHHHHHHHHHHhhcch-H-----HHHhhHHHHHHHhhcccchhehhHHHHHHHhhccc---chhhhhhhhhhh--ee
Confidence 3466777777776543321 1 33457788888999999988877777777766554 222321111111 11
Q ss_pred h-cccCccCH-HHHHHHHHHHHhccCCCcHHHHHHHHHHHhhcCCCCCchhhchhHHHHHHHHHHHhCcccHHHHHHHHh
Q 015533 247 F-ETERHNGI-GELLEILGSIINGFALPMKEEHKLLLVRAMLPLHKPKCVALYHQQLTYCVVQFVEKDYELADTVIRGLL 324 (405)
Q Consensus 247 ~-e~~~~nGI-aELLeilgSIInGFa~PLKeEhk~fl~~vLiPLHk~~~l~~y~~qL~yci~qF~eKDp~L~~~vi~~LL 324 (405)
. ++ ...| ...|+++..+.+ ++...-....|+.-.+...-..|...+...+....++.+.-..++++.++
T Consensus 313 ~~~~--d~~Ir~~~l~lL~~l~~-------~~n~~~Il~eL~~~l~~~~d~~~~~~~i~~I~~la~~~~~~~~~~v~~l~ 383 (526)
T PF01602_consen 313 LYDD--DPSIRKKALDLLYKLAN-------ESNVKEILDELLKYLSELSDPDFRRELIKAIGDLAEKFPPDAEWYVDTLL 383 (526)
T ss_dssp HCSS--SHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHGSSHHHHHHHHH
T ss_pred cCCC--ChhHHHHHHHHHhhccc-------ccchhhHHHHHHHHHHhccchhhhhhHHHHHHHHHhccCchHHHHHHHHH
Confidence 1 11 1112 244555555543 11111122222222211112236666777777777777777777777766
Q ss_pred hhCCCCCchhHHHHHHHHHHHhhc
Q 015533 325 RYWPVTNCQKEVLFLGELEEVLDV 348 (405)
Q Consensus 325 k~WP~tns~KEvlFL~EleeiLe~ 348 (405)
+.=-.++..-.-..+..+.+++..
T Consensus 384 ~ll~~~~~~~~~~~~~~i~~ll~~ 407 (526)
T PF01602_consen 384 KLLEISGDYVSNEIINVIRDLLSN 407 (526)
T ss_dssp HHHHCTGGGCHCHHHHHHHHHHHH
T ss_pred HhhhhccccccchHHHHHHHHhhc
Confidence 665544333333334445555543
No 10
>KOG0213 consensus Splicing factor 3b, subunit 1 [RNA processing and modification]
Probab=48.48 E-value=3.3e+02 Score=31.62 Aligned_cols=173 Identities=17% Similarity=0.254 Sum_probs=93.6
Q ss_pred hhcCCHHHHHHHhhccCCCChhHHHHHHHHHHHHhhccccchHH-HHHHHHHHHHHhhhcccCccCHHHHHHHHHHHHhc
Q 015533 190 KRYIDHTFVLKLLDLFDTEDHREREYLKMVLHRIYGRFMSHRPF-IRAGINNVFYRFIFETERHNGIGELLEILGSIING 268 (405)
Q Consensus 190 k~~id~~Fi~~Ll~lfdS~DpRERd~LktiLhrIY~Kf~~~R~f-IRk~i~nif~~fi~e~~~~nGIaELLeilgSIInG 268 (405)
|+|+. +.+..++-+++++-+.-|++-.+++.+|-.-.-....+ .-...++++|.|+-| ++..-.+-+|-.+.+|.|-
T Consensus 794 kpylp-qi~stiL~rLnnksa~vRqqaadlis~la~Vlktc~ee~~m~~lGvvLyEylge-eypEvLgsILgAikaI~nv 871 (1172)
T KOG0213|consen 794 KPYLP-QICSTILWRLNNKSAKVRQQAADLISSLAKVLKTCGEEKLMGHLGVVLYEYLGE-EYPEVLGSILGAIKAIVNV 871 (1172)
T ss_pred ccchH-HHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHHhccHHHHHHHhhHHHHHhcCc-ccHHHHHHHHHHHHHHHHh
Confidence 55554 57888999999999999998888877765422222111 334567899999866 3333333444444444442
Q ss_pred -----cCCCcHHHHHHHHHHHhhcCCCCCchhhchhHHHHHHHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHH-HHH
Q 015533 269 -----FALPMKEEHKLLLVRAMLPLHKPKCVALYHQQLTYCVVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFL-GEL 342 (405)
Q Consensus 269 -----Fa~PLKeEhk~fl~~vLiPLHk~~~l~~y~~qL~yci~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL-~El 342 (405)
-..|.| +.+-+ |.|..|.++=.. -..||. .+..|-.-=|.--+.+|-|=+ -||
T Consensus 872 igm~km~pPi~----dllPr-ltPILknrheKV----qen~Id------------Lvg~IadrgpE~v~aREWMRIcfeL 930 (1172)
T KOG0213|consen 872 IGMTKMTPPIK----DLLPR-LTPILKNRHEKV----QENCID------------LVGTIADRGPEYVSAREWMRICFEL 930 (1172)
T ss_pred ccccccCCChh----hhccc-chHhhhhhHHHH----HHHHHH------------HHHHHHhcCcccCCHHHHHHHHHHH
Confidence 255655 44433 667777664221 123433 222333333444455554422 234
Q ss_pred HHHhhcCChhHHHHHHHHHHHHHHHhhCC--------CchHHHHHHHhhhcc
Q 015533 343 EEVLDVTHPAEFQQCMGPLFRQIGRCLTS--------PHFQVHIIVTSLIYM 386 (405)
Q Consensus 343 eeiLe~~~~~~f~~i~~plF~~la~ci~S--------~hfqVAErAl~i~~n 386 (405)
-++|-.. ..+..+-.+--|--||+.+.- .|.+|-||-+.+++-
T Consensus 931 lelLkah-kK~iRRaa~nTfG~IakaIGPqdVLatLlnnLkvqeRq~RvcTt 981 (1172)
T KOG0213|consen 931 LELLKAH-KKEIRRAAVNTFGYIAKAIGPQDVLATLLNNLKVQERQNRVCTT 981 (1172)
T ss_pred HHHHHHH-HHHHHHHHHhhhhHHHHhcCHHHHHHHHHhcchHHHHHhchhhh
Confidence 4444322 233444445555555555432 356788887766653
No 11
>PF08767 CRM1_C: CRM1 C terminal; InterPro: IPR014877 CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat []. ; PDB: 3M1I_C 3GB8_A 1W9C_A 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D.
Probab=48.03 E-value=3.1e+02 Score=27.70 Aligned_cols=76 Identities=13% Similarity=0.186 Sum_probs=47.0
Q ss_pred CCchhhchhHHHHHHHHHHHhCcccHH-------HHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHH
Q 015533 291 PKCVALYHQQLTYCVVQFVEKDYELAD-------TVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFR 363 (405)
Q Consensus 291 ~~~l~~y~~qL~yci~qF~eKDp~L~~-------~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~ 363 (405)
.+.+......+..|....+.+|-.=.. ..++.+.++=| +.+-.++++.|..++ .
T Consensus 108 ~~~v~~I~~~vf~~Tl~MI~~d~~~yPe~r~~ff~LL~~i~~~~f---------------~~l~~lp~~~f~~~i----d 168 (319)
T PF08767_consen 108 QPQVPQILEAVFECTLPMINKDFEEYPEHRVNFFKLLRAINEHCF---------------PALLQLPPEQFKLVI----D 168 (319)
T ss_dssp CCCHHHHHHHHHHHHHHHHSSTSSSSHHHHHHHHHHHHHHHHHHT---------------HHHHHS-HHHHHHHH----H
T ss_pred hhhHHHHHHHHHHHHHHHHHhhhhhChHHHHHHHHHHHHHHHHhH---------------HHHHcCCHHHHHHHH----H
Confidence 355566667788888888877654322 12222222211 123346788787754 5
Q ss_pred HHHHhhCCCchHHHHHHHhhhc
Q 015533 364 QIGRCLTSPHFQVHIIVTSLIY 385 (405)
Q Consensus 364 ~la~ci~S~hfqVAErAl~i~~ 385 (405)
-+--++.+++..|++.+|.+..
T Consensus 169 si~wg~kh~~~~I~~~~L~~l~ 190 (319)
T PF08767_consen 169 SIVWGFKHTNREISETGLNILL 190 (319)
T ss_dssp HHHHHHTSSSHHHHHHHHHHHH
T ss_pred HHHHHhCCCcHHHHHHHHHHHH
Confidence 5667788999999999998764
No 12
>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=46.24 E-value=1.2e+02 Score=32.29 Aligned_cols=72 Identities=13% Similarity=0.211 Sum_probs=42.9
Q ss_pred hHHHHHHHHHHHhCcccHH--HHHHHHhhhCCC--CCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhC
Q 015533 299 QQLTYCVVQFVEKDYELAD--TVIRGLLRYWPV--TNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCLT 370 (405)
Q Consensus 299 ~qL~yci~qF~eKDp~L~~--~vi~~LLk~WP~--tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~~la~ci~ 370 (405)
+.|...+..|++|+|.... .-+.+++...-+ ++..-+.-=.+-|+.|++.++.+..++.+..+|..+-.=++
T Consensus 177 PalvrLL~a~i~k~~~~i~~~~~l~~iLgvFQkLi~sk~~D~~gF~LL~~iv~~~p~~~l~~yl~~I~~lll~RLq 252 (435)
T PF03378_consen 177 PALVRLLQAYIKKDPSFIVANNQLEPILGVFQKLIASKANDHYGFDLLESIVENLPPEALEPYLKQIFTLLLTRLQ 252 (435)
T ss_dssp HHHHHHHHHHHHHHGGG----S-CHHHHHHHHHHHT-TTCHHHHHHHHHHHHHHS-HHHHGGGHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHhCchhhcchhhHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHh
Confidence 6688899999999998652 222233322221 22223455557899999999998877777666655443333
No 13
>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=42.65 E-value=2.2e+02 Score=25.45 Aligned_cols=79 Identities=11% Similarity=0.074 Sum_probs=61.9
Q ss_pred HHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHH-HHHHHHHHHhhC------CCchHHHH
Q 015533 306 VQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCM-GPLFRQIGRCLT------SPHFQVHI 378 (405)
Q Consensus 306 ~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~-~plF~~la~ci~------S~hfqVAE 378 (405)
...+..++.-+...++.|.|-=-..|+.-++.-|.-|+.++..|...--..+. ......+.+.++ ..|..|-+
T Consensus 26 cD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~el~kl~~~k~~~~~~~~~Vk~ 105 (139)
T cd03567 26 CEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKT 105 (139)
T ss_pred HHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHHHHHHHhccccCCCCCCHHHHH
Confidence 44567889988999999999888888888899999999999999886545554 444456666664 26899999
Q ss_pred HHHhhh
Q 015533 379 IVTSLI 384 (405)
Q Consensus 379 rAl~i~ 384 (405)
+++.++
T Consensus 106 kil~li 111 (139)
T cd03567 106 KIIELL 111 (139)
T ss_pred HHHHHH
Confidence 998764
No 14
>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=42.25 E-value=21 Score=29.76 Aligned_cols=40 Identities=25% Similarity=0.515 Sum_probs=35.7
Q ss_pred HHHHHHHhhccCCCChhHHHHHHHHHHHHhhccccchHHH
Q 015533 195 HTFVLKLLDLFDTEDHREREYLKMVLHRIYGRFMSHRPFI 234 (405)
Q Consensus 195 ~~Fi~~Ll~lfdS~DpRERd~LktiLhrIY~Kf~~~R~fI 234 (405)
+.=+.+|+++..|--....++...+|+..|+-|..+|||.
T Consensus 45 qdkmRkLld~v~akG~~~k~~F~~iL~e~~~~y~~~~~~~ 84 (85)
T cd08324 45 PDKVRKILDLVQSKGEEVSEYFLYLLQQLADAYVDLRPWL 84 (85)
T ss_pred HHHHHHHHHHHHhcCchHHHHHHHHHHHHHHhhhhhhccc
Confidence 3446778999999999999999999999999999999985
No 15
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=41.88 E-value=1.1e+02 Score=25.61 Aligned_cols=87 Identities=8% Similarity=0.036 Sum_probs=64.0
Q ss_pred HHHHHHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCC---hhHHHHHHHHHHHHHHHhhCCCchHHH
Q 015533 301 LTYCVVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTH---PAEFQQCMGPLFRQIGRCLTSPHFQVH 377 (405)
Q Consensus 301 L~yci~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~---~~~f~~i~~plF~~la~ci~S~hfqVA 377 (405)
-..-+++++..+..-+..++..+.++=-.+.+.+-+.+|.-+.+|+-.+. ...|.....++|....+-.+..+-+=-
T Consensus 20 ~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~~~~~~~~~~f~~~~~~~~~~~r~kl 99 (114)
T cd03562 20 SIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFSEFLVPLFLDAYEKVDEKTRKKL 99 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence 33445667777777788888888888888888999999999999997663 456777778888776664444555556
Q ss_pred HHHHhhhccc
Q 015533 378 IIVTSLIYMS 387 (405)
Q Consensus 378 ErAl~i~~n~ 387 (405)
.|-+.+|..-
T Consensus 100 ~rl~~iW~~~ 109 (114)
T cd03562 100 ERLLNIWEER 109 (114)
T ss_pred HHHHHHccCC
Confidence 6777777653
No 16
>KOG0301 consensus Phospholipase A2-activating protein (contains WD40 repeats) [Lipid transport and metabolism]
Probab=41.45 E-value=3.7e+02 Score=30.55 Aligned_cols=48 Identities=13% Similarity=0.172 Sum_probs=32.7
Q ss_pred CchhHHHHHHHHHHHhhcCCChHHHhhcCCHHHHHHHhhccCCCChhHH
Q 015533 165 WPHLQLVYEILLRYIVSNGADKKIAKRYIDHTFVLKLLDLFDTEDHRER 213 (405)
Q Consensus 165 WpHLqlVYeillrfv~s~~~d~k~ak~~id~~Fi~~Ll~lfdS~DpRER 213 (405)
|.|+.-+++|+.-++.....+.-...+--.++|+..++..++ .|+-+.
T Consensus 558 ~~~~fPalDilRl~v~h~~~~s~~~~~~~~~~~~~~li~~~~-~~~an~ 605 (745)
T KOG0301|consen 558 VEMMFPALDILRLAVKHHSSNSLFCDREEGQNLVGTLIPILN-ADPANQ 605 (745)
T ss_pred HHHhhhHHHHHHHHHhccchhhhhhhhhhhhHHHHhhhcccc-cchhHH
Confidence 348999999998888765444333333334678889998888 666553
No 17
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=38.14 E-value=3.3e+02 Score=25.16 Aligned_cols=175 Identities=11% Similarity=0.042 Sum_probs=93.4
Q ss_pred CCCChhHHHHHHHHHHHHhhcc--ccchHHHHHHHH---HHHHHhhhcccCccCHHHHHHHHHHHHhccCCCcHHHHHHH
Q 015533 206 DTEDHREREYLKMVLHRIYGRF--MSHRPFIRAGIN---NVFYRFIFETERHNGIGELLEILGSIINGFALPMKEEHKLL 280 (405)
Q Consensus 206 dS~DpRERd~LktiLhrIY~Kf--~~~R~fIRk~i~---nif~~fi~e~~~~nGIaELLeilgSIInGFa~PLKeEhk~f 280 (405)
.+.|=.+|..--+-|.++-..- ...++-+-..+. ..+..-+. +.+..-+.+.+.+++.+..+....+... -..
T Consensus 17 ~~~~W~~r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i~~~l~-d~Rs~v~~~A~~~l~~l~~~l~~~~~~~-~~~ 94 (228)
T PF12348_consen 17 SESDWEERVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAIIKQLS-DLRSKVSKTACQLLSDLARQLGSHFEPY-ADI 94 (228)
T ss_dssp T-SSHHHHHHHHHHHHHHHHH-B-----HHHHHHHH---HHHHH-S--HH---HHHHHHHHHHHHHHHHGGGGHHH-HHH
T ss_pred CccCHHHHHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHHHHHHh-hhHHHHHHHHHHHHHHHHHHHhHhHHHH-HHH
Confidence 5566666666555566655544 222222222222 22222221 2333345677888888888777665544 444
Q ss_pred HHHHhhcCCCCCchhhchhHHHHHHHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCC--hhHHHHH-
Q 015533 281 LVRAMLPLHKPKCVALYHQQLTYCVVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTH--PAEFQQC- 357 (405)
Q Consensus 281 l~~vLiPLHk~~~l~~y~~qL~yci~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~--~~~f~~i- 357 (405)
+...|+-+..... ....+.-..|+..+++.-+-....++..+...+---|+.=-..-+.-+..+++..+ ...+..-
T Consensus 95 ~l~~Ll~~~~~~~-~~i~~~a~~~L~~i~~~~~~~~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~ 173 (228)
T PF12348_consen 95 LLPPLLKKLGDSK-KFIREAANNALDAIIESCSYSPKILLEILSQGLKSKNPQVREECAEWLAIILEKWGSDSSVLQKSA 173 (228)
T ss_dssp HHHHHHHGGG----HHHHHHHHHHHHHHHTTS-H--HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHTT-----GGG--HH
T ss_pred HHHHHHHHHcccc-HHHHHHHHHHHHHHHHHCCcHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHccchHhhhcccc
Confidence 4556666666543 35666677888887776551233336666666665555544566677777887777 4445443
Q ss_pred -HHHHHHHHHHhhCCCchHHHHHHHhh
Q 015533 358 -MGPLFRQIGRCLTSPHFQVHIIVTSL 383 (405)
Q Consensus 358 -~~plF~~la~ci~S~hfqVAErAl~i 383 (405)
+..+-+.|.+|++..+..|=+.|-..
T Consensus 174 ~~~~l~~~l~~~l~D~~~~VR~~Ar~~ 200 (228)
T PF12348_consen 174 FLKQLVKALVKLLSDADPEVREAAREC 200 (228)
T ss_dssp HHHHHHHHHHHHHTSS-HHHHHHHHHH
T ss_pred hHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 36788889999999999887777443
No 18
>COG5656 SXM1 Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, chaperones]
Probab=36.94 E-value=4e+02 Score=30.85 Aligned_cols=153 Identities=16% Similarity=0.166 Sum_probs=91.8
Q ss_pred CCCC----chhHHHHHHHHH--H------HhhcCCCh-HHHhhcCCHHHHHHHhhccCCCChhHHHHHHHHHHHHhhc-c
Q 015533 162 EPAW----PHLQLVYEILLR--Y------IVSNGADK-KIAKRYIDHTFVLKLLDLFDTEDHREREYLKMVLHRIYGR-F 227 (405)
Q Consensus 162 e~sW----pHLqlVYeillr--f------v~s~~~d~-k~ak~~id~~Fi~~Ll~lfdS~DpRERd~LktiLhrIY~K-f 227 (405)
+..| ||||++.+=+.- + .+..+.|| +..++|+| +.+.+.|+|-.--+++-+.-..==.+ |
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 3456 688887653321 0 22334455 34455555 56677888887766665442111111 3
Q ss_pred ccchHHHHHHHHHHHHHhhhcccC-cc--CHHHHHHHHHHHHh--ccCCCcHHHHHHHHHHHhhcCCCCCchhhchhHHH
Q 015533 228 MSHRPFIRAGINNVFYRFIFETER-HN--GIGELLEILGSIIN--GFALPMKEEHKLLLVRAMLPLHKPKCVALYHQQLT 302 (405)
Q Consensus 228 ~~~R~fIRk~i~nif~~fi~e~~~-~n--GIaELLeilgSIIn--GFa~PLKeEhk~fl~~vLiPLHk~~~l~~y~~qL~ 302 (405)
++ |..-++++|-++--...+ -| ...-.|.++.||++ .-.-|+..+...|+...++|-.+.++...=.+..
T Consensus 407 qg----iLsf~~sil~qsaa~psn~dnarq~egalr~lasi~s~itk~sp~an~me~fiv~hv~P~f~s~ygfL~Srac- 481 (970)
T COG5656 407 QG----ILSFLLSILGQSAATPSNIDNARQAEGALRLLASIKSFITKMSPAANVMEYFIVNHVIPAFRSNYGFLKSRAC- 481 (970)
T ss_pred hh----HHHHHHHHHhcccCCCCccccHHHHhhHHHHHHHHHHHhccCchHHHHHHHHHHHHhhHhhcCcccchHHHHH-
Confidence 33 556677888777544333 12 23458999999999 3355777799999999999999998654444433
Q ss_pred HHHHHHH--HhCcccHHHHHHHHhh
Q 015533 303 YCVVQFV--EKDYELADTVIRGLLR 325 (405)
Q Consensus 303 yci~qF~--eKDp~L~~~vi~~LLk 325 (405)
+-+..|- =||+.++-...++..+
T Consensus 482 e~is~~eeDfkd~~ill~aye~t~n 506 (970)
T COG5656 482 EFISTIEEDFKDNGILLEAYENTHN 506 (970)
T ss_pred HHHHHHHHhcccchHHHHHHHHHHH
Confidence 3344441 2677777666666553
No 19
>PF12460 MMS19_C: RNAPII transcription regulator C-terminal; InterPro: IPR024687 This domain, approximately 60 amino acids in length, is found in the N-terminal region of MMS19 proteins. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription [].
Probab=36.09 E-value=5.2e+02 Score=26.85 Aligned_cols=206 Identities=15% Similarity=0.136 Sum_probs=121.3
Q ss_pred HHHHHHHHhhcCCChHHHhhcCCHHHHHHHhhc-cCCCChhHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhhhccc
Q 015533 172 YEILLRYIVSNGADKKIAKRYIDHTFVLKLLDL-FDTEDHREREYLKMVLHRIYGRFMSHRPFIRAGINNVFYRFIFETE 250 (405)
Q Consensus 172 Yeillrfv~s~~~d~k~ak~~id~~Fi~~Ll~l-fdS~DpRERd~LktiLhrIY~Kf~~~R~fIRk~i~nif~~fi~e~~ 250 (405)
--++..++.+- ++++.-. -...++.+++.+ ..++|+..|-..-..+--+-.||..-- .+...+....... ....
T Consensus 168 ~~l~~~il~~l--~~~~~~~-~~~~ll~~l~~~~~~~~~~~~~~~~~~~la~LvNK~~~~~-~l~~~l~~~~~~~-~~~~ 242 (415)
T PF12460_consen 168 VILFSAILCSL--RKDVSLP-DLEELLQSLLNLALSSEDEFSRLAALQLLASLVNKWPDDD-DLDEFLDSLLQSI-SSSE 242 (415)
T ss_pred HHHHHHHHHcC--CcccCcc-CHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHcCCCChh-hHHHHHHHHHhhh-cccC
Confidence 34455555543 3322222 123478888887 577888888888888888888965532 3443443333333 1122
Q ss_pred CccCHHHHHHHHHHHHhccCCCcHHHHHHHHHHHhhcCCCCCchhhchhHH---------------HHHHHHHHHhCccc
Q 015533 251 RHNGIGELLEILGSIINGFALPMKEEHKLLLVRAMLPLHKPKCVALYHQQL---------------TYCVVQFVEKDYEL 315 (405)
Q Consensus 251 ~~nGIaELLeilgSIInGFa~PLKeEhk~fl~~vLiPLHk~~~l~~y~~qL---------------~yci~qF~eKDp~L 315 (405)
....-...++++.-|.+|...-..+....++.+ |+=|...+.++..-..- .+|.+..+=| -++
T Consensus 243 ~~~~~~~~~~~~~Wi~KaLv~R~~~~~~~~~~~-L~~lL~~~~~g~~aA~~f~il~~d~~~~l~~~~~a~vklLyk-QR~ 320 (415)
T PF12460_consen 243 DSELRPQALEILIWITKALVMRGHPLATELLDK-LLELLSSPELGQQAAKAFGILLSDSDDVLNKENHANVKLLYK-QRF 320 (415)
T ss_pred CcchhHHHHHHHHHHHHHHHHcCCchHHHHHHH-HHHHhCChhhHHHHHHHHhhHhcCcHHhcCccccchhhhHHh-HHH
Confidence 222234566777666666554444444444433 44455554333211111 1122222222 234
Q ss_pred HHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhCCCchHHHHHHHhhh
Q 015533 316 ADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCLTSPHFQVHIIVTSLI 384 (405)
Q Consensus 316 ~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~~la~ci~S~hfqVAErAl~i~ 384 (405)
...++..|+..+-.++.....-+|-=+..|+..++.+-...-+..|+..+-+|++.++-.|-..||...
T Consensus 321 F~~~~p~L~~~~~~~~~~~k~~yL~ALs~ll~~vP~~vl~~~l~~LlPLLlqsL~~~~~~v~~s~L~tL 389 (415)
T PF12460_consen 321 FTQVLPKLLEGFKEADDEIKSNYLTALSHLLKNVPKSVLLPELPTLLPLLLQSLSLPDADVLLSSLETL 389 (415)
T ss_pred HHHHHHHHHHHHhhcChhhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 555666666555555544445567788889999999999888899999999999999988877777654
No 20
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=31.79 E-value=1.6e+02 Score=27.16 Aligned_cols=54 Identities=19% Similarity=0.270 Sum_probs=39.7
Q ss_pred HHHHHHHhhcCChhHHHHHH------HHHHHHHHHhhCCCchHHHHHHHhhhcccccccccc
Q 015533 339 LGELEEVLDVTHPAEFQQCM------GPLFRQIGRCLTSPHFQVHIIVTSLIYMSCYCSAVS 394 (405)
Q Consensus 339 L~EleeiLe~~~~~~f~~i~------~plF~~la~ci~S~hfqVAErAl~i~~n~~f~~~~~ 394 (405)
=+-+.+++..+|-+++..+. .+.|+.+-+.+.|+.||..-.+ +|.++.|..++.
T Consensus 104 ~g~~~di~~~lP~~~l~aL~~~K~~~s~~F~~f~~~l~S~ef~~~~~~--~~~~~~~~~~~~ 163 (179)
T PF06757_consen 104 NGFVDDILALLPRDKLRALYEEKLATSPEFAEFVEALRSPEFQQLYNA--LWASPEFQRLLN 163 (179)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHCCHHHHHHHHHHcCHHHHHHHHH--HHcCHHHHHHHH
Confidence 34455555666666665554 6899999999999999988776 578888876654
No 21
>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=28.35 E-value=4.4e+02 Score=23.62 Aligned_cols=80 Identities=10% Similarity=0.105 Sum_probs=59.6
Q ss_pred HHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHH-HHHHHHHHHhhCC-CchHHHHHHHhh
Q 015533 306 VQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCM-GPLFRQIGRCLTS-PHFQVHIIVTSL 383 (405)
Q Consensus 306 ~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~-~plF~~la~ci~S-~hfqVAErAl~i 383 (405)
...+..++.-+..+++.|.|===..|+.-++.-|.-++.++..|+..--..+. ..+...|.+.++. .|.+|-++++.+
T Consensus 25 cD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~l 104 (144)
T cd03568 25 CDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREV 104 (144)
T ss_pred HHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHH
Confidence 34566667777777777776555689999999999999999999875433333 4455666777777 899999999987
Q ss_pred hc
Q 015533 384 IY 385 (405)
Q Consensus 384 ~~ 385 (405)
+.
T Consensus 105 i~ 106 (144)
T cd03568 105 VK 106 (144)
T ss_pred HH
Confidence 54
No 22
>COG5098 Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics / Cell division and chromosome partitioning]
Probab=28.09 E-value=8.9e+02 Score=28.14 Aligned_cols=51 Identities=22% Similarity=0.314 Sum_probs=33.8
Q ss_pred hCCCCCchhHH-HHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhCCCchHHHHHHHhhh
Q 015533 326 YWPVTNCQKEV-LFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCLTSPHFQVHIIVTSLI 384 (405)
Q Consensus 326 ~WP~tns~KEv-lFL~EleeiLe~~~~~~f~~i~~plF~~la~ci~S~hfqVAErAl~i~ 384 (405)
--|-+..+|++ +||+-+.++.+ .+|..-+.++-+.++|+||-.--.-+-++
T Consensus 272 n~~d~~Gpk~islFl~kls~l~p--------~i~lrq~~~~~~LLdses~tlRc~~~Eic 323 (1128)
T COG5098 272 NLPDLSGPKDISLFLNKLSELSP--------GIMLRQYEHFDELLDSESFTLRCCFLEIC 323 (1128)
T ss_pred ecccccChHHHHHHHHHHhhcCc--------hHHHHHHHHHHHHhcccchhHHHHHHHHH
Confidence 34666677776 68887777754 46667777788888888886544444333
No 23
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=27.95 E-value=1.7e+02 Score=23.17 Aligned_cols=43 Identities=12% Similarity=0.074 Sum_probs=34.0
Q ss_pred hHHHhhcCCHHHHHHHhhccCCCChhHHHHHHHHHHHHhhccc
Q 015533 186 KKIAKRYIDHTFVLKLLDLFDTEDHREREYLKMVLHRIYGRFM 228 (405)
Q Consensus 186 ~k~ak~~id~~Fi~~Ll~lfdS~DpRERd~LktiLhrIY~Kf~ 228 (405)
+...+.+++...+..|+.++++.|++=|...-.+|.++-....
T Consensus 39 ~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~ 81 (120)
T cd00020 39 NDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPE 81 (120)
T ss_pred HHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHccCcH
Confidence 5556666777889999999999999999888888888765443
No 24
>PF04118 Dopey_N: Dopey, N-terminal; InterPro: IPR007249 DopA is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans). DopA homologues are found in mammals. Saccharomyces cerevisiae DOP1 is essential for viability and, affects cellular morphogenesis [].
Probab=27.23 E-value=6.7e+02 Score=25.46 Aligned_cols=77 Identities=23% Similarity=0.266 Sum_probs=48.2
Q ss_pred hchhHHHHHHHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhCCCchH
Q 015533 296 LYHQQLTYCVVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLFRQIGRCLTSPHFQ 375 (405)
Q Consensus 296 ~y~~qL~yci~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF~~la~ci~S~hfq 375 (405)
.|++-|-.|+. ..|+.=...+.++.++.|+-.....-....+...+ +.++. .-+.+-++.|+.+++.-
T Consensus 173 ~F~~~lwl~ii----~sp~~Rl~al~~l~~~l~~~~~~~~~~~~~~~~~~---~~~~~-----~Llv~al~~~L~D~~iL 240 (307)
T PF04118_consen 173 YFWQCLWLCII----TSPSRRLGALNYLLRRLPKFQNDELSLSSEEQEYC---LGPDP-----GLLVRALCACLEDENIL 240 (307)
T ss_pred HHHHHHHHHHh----cCcchhHHHHHHHHHhCCcccccccccchHHHHHh---cCCCc-----cHHHHHHHHHhCCchHH
Confidence 46665666655 77888899999999999998752222222222222 21110 12556678888888777
Q ss_pred HHHHHHhhh
Q 015533 376 VHIIVTSLI 384 (405)
Q Consensus 376 VAErAl~i~ 384 (405)
|---+|.+.
T Consensus 241 VqR~~LDlL 249 (307)
T PF04118_consen 241 VQRGFLDLL 249 (307)
T ss_pred HHHHHHHHH
Confidence 777776654
No 25
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=25.99 E-value=2.8e+02 Score=24.77 Aligned_cols=39 Identities=18% Similarity=0.287 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhccCCCcHHHHHHHHHHHhhcCCCCCch
Q 015533 256 GELLEILGSIINGFALPMKEEHKLLLVRAMLPLHKPKCV 294 (405)
Q Consensus 256 aELLeilgSIInGFa~PLKeEhk~fl~~vLiPLHk~~~l 294 (405)
.-.+.++..+++.|..-||.|-..|+..++.|+..++..
T Consensus 91 ~~slri~~~l~~~~~~~Lk~ele~~l~~i~~~il~~~~~ 129 (168)
T PF12783_consen 91 SRSLRIFLTLLSRFRSHLKLELEVFLSHIILRILESDNS 129 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
Confidence 467889999999999999999999999999988877665
No 26
>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=25.90 E-value=4.8e+02 Score=23.25 Aligned_cols=80 Identities=11% Similarity=0.091 Sum_probs=57.5
Q ss_pred HHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHH-HHHHHHHHHhhC-CCchHHHHHHHhh
Q 015533 306 VQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCM-GPLFRQIGRCLT-SPHFQVHIIVTSL 383 (405)
Q Consensus 306 ~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~-~plF~~la~ci~-S~hfqVAErAl~i 383 (405)
...+..++.-+..+++.|.|-==..|+.-+..-|.-++.++..|+..--..+. ..+...+.+.++ ..|.+|-++++.+
T Consensus 29 cD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~l 108 (142)
T cd03569 29 CDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILEL 108 (142)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHH
Confidence 34566677777778887776666688888899999999999988764333333 344455555554 6899999999887
Q ss_pred hc
Q 015533 384 IY 385 (405)
Q Consensus 384 ~~ 385 (405)
+.
T Consensus 109 i~ 110 (142)
T cd03569 109 IQ 110 (142)
T ss_pred HH
Confidence 53
No 27
>smart00802 UME Domain in UVSB PI-3 kinase, MEI-41 and ESR-1. Characteristic domain in UVSP PI-3 kinase, MEI-41 and ESR-1. Found in nucleolar proteins. Associated with FAT, FATC, PI3_PI4_kinase modules.
Probab=24.60 E-value=2.4e+02 Score=24.22 Aligned_cols=27 Identities=19% Similarity=0.264 Sum_probs=16.8
Q ss_pred hhcCCCCCchhhchhHHHHHHHHHHHhC
Q 015533 285 MLPLHKPKCVALYHQQLTYCVVQFVEKD 312 (405)
Q Consensus 285 LiPLHk~~~l~~y~~qL~yci~qF~eKD 312 (405)
++-+.+ ++++.+-+|+.-|...=++++
T Consensus 42 lI~~~g-~~i~~a~pQI~acL~saL~~~ 68 (107)
T smart00802 42 LIKLMG-KHISSALPQIMACLQSALEIP 68 (107)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHhCch
Confidence 444444 566777777777776666643
No 28
>KOG4189 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.25 E-value=1.4e+02 Score=28.65 Aligned_cols=49 Identities=29% Similarity=0.533 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHhhcCCChHHHhhcCCHHHHHHHhhccCCCChhHHHHHHHHHHHHhhcccc-chHH-HHHHHHHHHHHh
Q 015533 168 LQLVYEILLRYIVSNGADKKIAKRYIDHTFVLKLLDLFDTEDHREREYLKMVLHRIYGRFMS-HRPF-IRAGINNVFYRF 245 (405)
Q Consensus 168 LqlVYeillrfv~s~~~d~k~ak~~id~~Fi~~Ll~lfdS~DpRERd~LktiLhrIY~Kf~~-~R~f-IRk~i~nif~~f 245 (405)
|..||++|.+.+.++. | +-++++-..-|.+-.. |.+| ||+++.--.|..
T Consensus 111 LefV~efl~~i~as~n-D----------------------------~s~~diakesYd~~lakhHsW~IRtAV~~amYtL 161 (209)
T KOG4189|consen 111 LEFVIEFLDQIFASTN-D----------------------------ESLKDIAKESYDKTLAKHHSWAIRTAVAAAMYTL 161 (209)
T ss_pred HHHHHHHHHHHHcCCC-c----------------------------chhhHHHHHHHHHhhhccccHHHHHHHHHHHHhC
Confidence 5578888888777652 2 1266666777886554 8899 999987655443
No 29
>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=23.46 E-value=4.9e+02 Score=22.57 Aligned_cols=80 Identities=13% Similarity=0.057 Sum_probs=59.4
Q ss_pred HHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHH-HHHHHHHHhhC---CCchHHHHHH
Q 015533 305 VVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMG-PLFRQIGRCLT---SPHFQVHIIV 380 (405)
Q Consensus 305 i~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~-plF~~la~ci~---S~hfqVAErA 380 (405)
+..-+..++.-+..+++.|.|.==..|+.-+..=|.-++.++..|+..-...+.. .....+-+.+. ..+.+|-+++
T Consensus 24 icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~ki 103 (133)
T cd03561 24 LCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKA 103 (133)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence 3445667777888888888777777898999999999999999998854444443 44445556665 4689999999
Q ss_pred Hhhh
Q 015533 381 TSLI 384 (405)
Q Consensus 381 l~i~ 384 (405)
+.+.
T Consensus 104 l~ll 107 (133)
T cd03561 104 LELI 107 (133)
T ss_pred HHHH
Confidence 8775
No 30
>KOG2067 consensus Mitochondrial processing peptidase, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=21.55 E-value=6.3e+02 Score=27.17 Aligned_cols=120 Identities=15% Similarity=0.200 Sum_probs=84.0
Q ss_pred HHHHHHHhhccccchHHHHHHHHHHHHHhhhcccCccCH---------HHHHHHHHHHHhccCCCcHHHHHHHHHHHhhc
Q 015533 217 KMVLHRIYGRFMSHRPFIRAGINNVFYRFIFETERHNGI---------GELLEILGSIINGFALPMKEEHKLLLVRAMLP 287 (405)
Q Consensus 217 ktiLhrIY~Kf~~~R~fIRk~i~nif~~fi~e~~~~nGI---------aELLeilgSIInGFa~PLKeEhk~fl~~vLiP 287 (405)
|....|+|.+.+....|+-.++. ++..|++.--.|| .+..|++..=+.+.+.-..++|.. |
T Consensus 304 KGMySrLY~~vLNry~wv~sctA---fnhsy~DtGlfgi~~s~~P~~a~~aveli~~e~~~~~~~v~~~el~---R---- 373 (472)
T KOG2067|consen 304 KGMYSRLYLNVLNRYHWVYSCTA---FNHSYSDTGLFGIYASAPPQAANDAVELIAKEMINMAGGVTQEELE---R---- 373 (472)
T ss_pred cchHHHHHHHHHhhhHHHHHhhh---hhccccCCceeEEeccCCHHHHHHHHHHHHHHHHHHhCCCCHHHHH---H----
Confidence 55678999999999999998875 6777776554443 567777666555444445555543 2
Q ss_pred CCCCCchhhchhHHHHHHHHHHHhCcccHHHHHHHHhhhCCCCCchhHHHHHHHHHHHhhcCChhHHHHHHHHHH
Q 015533 288 LHKPKCVALYHQQLTYCVVQFVEKDYELADTVIRGLLRYWPVTNCQKEVLFLGELEEVLDVTHPAEFQQCMGPLF 362 (405)
Q Consensus 288 LHk~~~l~~y~~qL~yci~qF~eKDp~L~~~vi~~LLk~WP~tns~KEvlFL~EleeiLe~~~~~~f~~i~~plF 362 (405)
=..||-.-+..=+|.-|-..+.+-|.+|.|= ..|.+ +|+-+-++.+.+++.+++...++
T Consensus 374 ---------AK~qlkS~LlMNLESR~V~~EDvGRQVL~~g----~rk~p---~e~~~~Ie~lt~~DI~rva~kvl 432 (472)
T KOG2067|consen 374 ---------AKTQLKSMLLMNLESRPVAFEDVGRQVLTTG----ERKPP---DEFIKKIEQLTPSDISRVASKVL 432 (472)
T ss_pred ---------HHHHHHHHHHhcccccchhHHHHhHHHHhcc----CcCCH---HHHHHHHHhcCHHHHHHHHHHHh
Confidence 2346766667678999999999999999982 23332 46667777888888887765443
No 31
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=21.46 E-value=1.7e+02 Score=18.85 Aligned_cols=28 Identities=21% Similarity=0.186 Sum_probs=21.7
Q ss_pred HHHHhhccCCCChhHHHHHHHHHHHHhh
Q 015533 198 VLKLLDLFDTEDHREREYLKMVLHRIYG 225 (405)
Q Consensus 198 i~~Ll~lfdS~DpRERd~LktiLhrIY~ 225 (405)
+-.++.++..++++-|+..-..|..|..
T Consensus 2 lp~l~~~l~D~~~~VR~~a~~~l~~i~~ 29 (31)
T PF02985_consen 2 LPILLQLLNDPSPEVRQAAAECLGAIAE 29 (31)
T ss_dssp HHHHHHHHT-SSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence 3457788889999999999888877764
No 32
>PF12726 SEN1_N: SEN1 N terminal; InterPro: IPR024481 The yeast helicase Sen1 is an RNA polymerase II termination factor for noncoding RNA genes []. The C-terminal domain of Sen1 is essential for cell growth, while the N-terminal domain appears to be dispensible []. This entry represents the N-terminal domain.
Probab=21.40 E-value=5.3e+02 Score=29.04 Aligned_cols=90 Identities=14% Similarity=0.115 Sum_probs=65.1
Q ss_pred CCChHHHhhcCC-HHHHHHHhhccCCCChhHHHHHHHHHHHHhhccccchHHHHHH-----------HHHHHHHhhhccc
Q 015533 183 GADKKIAKRYID-HTFVLKLLDLFDTEDHREREYLKMVLHRIYGRFMSHRPFIRAG-----------INNVFYRFIFETE 250 (405)
Q Consensus 183 ~~d~k~ak~~id-~~Fi~~Ll~lfdS~DpRERd~LktiLhrIY~Kf~~~R~fIRk~-----------i~nif~~fi~e~~ 250 (405)
+++|...+..+. +.-..-++.++=|+|..=++...+++..+|| -.+.+.-|+.. |+..+.+++ +..
T Consensus 510 ~~~~~~L~~l~~d~~~~~~i~s~lfsp~~~l~qaA~~llk~~~d-~~~R~e~i~~ll~~~~~~tL~ai~~~l~~~~-~~~ 587 (727)
T PF12726_consen 510 DFDPSHLKELLSDPDAAQAIWSLLFSPDDDLYQAAQDLLKQAFD-VDGRLEAIQALLQSNFSPTLSAINWSLRQLT-KLK 587 (727)
T ss_pred cCCHHHHHHHHcCcchhhHHHhheeCCChHHHHHHHHHHHHHhc-CCcHHHHHHHHHHHhHHHHHHHHHHHHHHHH-hhh
Confidence 578877777665 5667788889999999999999999999998 44444334433 333444443 334
Q ss_pred CccCHHHHHHHHHHHHhccCCCcH
Q 015533 251 RHNGIGELLEILGSIINGFALPMK 274 (405)
Q Consensus 251 ~~nGIaELLeilgSIInGFa~PLK 274 (405)
.+....-++.++..||++++-|..
T Consensus 588 ~~~p~pr~vr~~~DIi~~Lcdp~~ 611 (727)
T PF12726_consen 588 FFEPCPRMVRCLMDIIEVLCDPVS 611 (727)
T ss_pred hhcchHHHHHHHHHHHHHHcCCCC
Confidence 577778899999999999888744
No 33
>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=20.98 E-value=87 Score=30.26 Aligned_cols=50 Identities=36% Similarity=0.535 Sum_probs=36.6
Q ss_pred cCccCHHHHHHHHHHHHhccCC---CcHHHHHHHHHHHhhcCCCCCchhhchhHHHHHHHHHHHhCc
Q 015533 250 ERHNGIGELLEILGSIINGFAL---PMKEEHKLLLVRAMLPLHKPKCVALYHQQLTYCVVQFVEKDY 313 (405)
Q Consensus 250 ~~~nGIaELLeilgSIInGFa~---PLKeEhk~fl~~vLiPLHk~~~l~~y~~qL~yci~qF~eKDp 313 (405)
|.|..++ .||-||||++ |.-.||++.-.. -+--||+|.-..|..|+...+
T Consensus 217 E~~yS~~-----v~SCING~tV~YYP~I~~~qQ~tQQ---------ELv~YH~qvEqLvqSFvnnss 269 (271)
T PF06901_consen 217 EPHYSTA-----VGSCINGFTVQYYPFIREKQQLTQQ---------ELVGYHQQVEQLVQSFVNNSS 269 (271)
T ss_pred CCcccch-----hhhhccCceeeeehhhhhhccccHH---------HHHHHHHHHHHHHHHHhcCcC
Confidence 4555555 8999999987 556677664433 344799999999999987644
No 34
>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=20.12 E-value=3e+02 Score=29.31 Aligned_cols=167 Identities=19% Similarity=0.238 Sum_probs=87.6
Q ss_pred HHHHHHHHh-hcCCCCCCHHHHHHHHHHHHHHhccCCCCCCCCC--CCCCCCCCCCCCCcc--------------ccCCC
Q 015533 102 NLQELVKFI-QSDSSKINEQMQENLMRMISINIFRALPPAFHEN--TGSLPDVGEPDEEDA--------------WLEPA 164 (405)
Q Consensus 102 tL~EL~~~v-~~~~~~l~e~~~~~i~~Mi~~NIFR~lPp~~~~~--~~~~~~~~d~eedep--------------~~e~s 164 (405)
+|......| +++-.-+.|-+++-+-.|++.+-=-++|+....- .-..+..++.....| -.-.+
T Consensus 117 ~L~P~f~~ILq~dV~EF~PYvfQIla~Lle~~~~~~~p~~y~~L~~~Ll~p~lWe~~gniPalvrLL~a~i~k~~~~i~~ 196 (435)
T PF03378_consen 117 ALFPPFQEILQQDVQEFIPYVFQILAQLLELRPSSPLPDAYKQLFPPLLSPALWERRGNIPALVRLLQAYIKKDPSFIVA 196 (435)
T ss_dssp HHHHHHHHHHHTT-TTTHHHHHHHHHHHHHHSS--S--TTTGGGHHHHTSGGGGGSTTTHHHHHHHHHHHHHHHGGG---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHcCcchhccCCCcCcHHHHHHHHHHhCchhhcc
Confidence 344444433 3344567777888888888876522344332110 000011121111222 12245
Q ss_pred CchhHHHHHHHHHHHhhcCCChHHHhhcCCHHHHHHHhhccCCCChh-HHHHHHHHHHHHhhccccch--HHHHHHHHHH
Q 015533 165 WPHLQLVYEILLRYIVSNGADKKIAKRYIDHTFVLKLLDLFDTEDHR-EREYLKMVLHRIYGRFMSHR--PFIRAGINNV 241 (405)
Q Consensus 165 WpHLqlVYeillrfv~s~~~d~k~ak~~id~~Fi~~Ll~lfdS~DpR-ERd~LktiLhrIY~Kf~~~R--~fIRk~i~ni 241 (405)
..||+-|+.+|.+.+.|...|..-. ..+..++..+ +++ =..|+++|+.-++.+....| .|+++-+ +
T Consensus 197 ~~~l~~iLgvFQkLi~sk~~D~~gF------~LL~~iv~~~---p~~~l~~yl~~I~~lll~RLq~skT~kf~~~fv--~ 265 (435)
T PF03378_consen 197 NNQLEPILGVFQKLIASKANDHYGF------DLLESIVENL---PPEALEPYLKQIFTLLLTRLQSSKTEKFVKRFV--V 265 (435)
T ss_dssp -S-CHHHHHHHHHHHT-TTCHHHHH------HHHHHHHHHS----HHHHGGGHHHHHHHHHHHHHHC--HHHHHHHH--H
T ss_pred hhhHHHHHHHHHHHHCCCCcchHHH------HHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHhhCCcHHHHHHHH--H
Confidence 6899999999999999876654322 2455555544 232 24588888888888776655 5666555 3
Q ss_pred HHHhhhcccCccCHHHHHHHHHHHHhccCCCcHHHHHHHHHHHhhcCC
Q 015533 242 FYRFIFETERHNGIGELLEILGSIINGFALPMKEEHKLLLVRAMLPLH 289 (405)
Q Consensus 242 f~~fi~e~~~~nGIaELLeilgSIInGFa~PLKeEhk~fl~~vLiPLH 289 (405)
|+.++.- ..|...+.+++.+|-.|. ...++.++++|-.
T Consensus 266 F~~~~~~---~~g~~~li~~id~IQ~gl-------F~~il~~v~lp~~ 303 (435)
T PF03378_consen 266 FLSLFAI---KYGPDFLIQTIDSIQPGL-------FGMILEKVWLPDL 303 (435)
T ss_dssp HHHHHHH---HH-HHHHHHHHHTTSTTH-------HHHHHHHTHHHHG
T ss_pred HHHHHHH---HcCHHHHHHHHHHhcCCc-------HHHHHHHHhcCch
Confidence 3333211 228899999998887773 2355667777743
Done!