Query psy17827
Match_columns 299
No_of_seqs 146 out of 175
Neff 5.2
Searched_HMMs 46136
Date Sat Aug 17 00:00:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17827.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17827hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3661|consensus 100.0 2.4E-83 5.2E-88 641.9 16.9 258 2-298 266-526 (1019)
2 PF05224 NDT80_PhoG: NDT80 / P 100.0 3.3E-49 7.2E-54 351.0 8.3 167 23-210 1-186 (186)
3 KOG3661|consensus 99.1 4.3E-11 9.4E-16 122.6 5.0 110 61-189 229-343 (1019)
4 PF13884 Peptidase_S74: Chaper 98.0 2.1E-06 4.5E-11 62.5 1.9 35 257-293 1-35 (58)
5 PF10283 zf-CCHH: Zinc-finger 37.7 10 0.00022 23.9 -0.1 6 25-30 8-13 (26)
6 smart00675 DM11 Domains in hyp 29.4 47 0.001 29.5 2.6 22 237-259 40-61 (164)
7 PF12971 NAGLU_N: Alpha-N-acet 25.3 75 0.0016 24.8 2.9 33 173-205 20-52 (86)
8 COG4466 Veg Uncharacterized pr 25.1 26 0.00056 27.7 0.2 11 153-163 24-34 (80)
9 COG4242 CphB Cyanophycinase an 17.4 1.2E+02 0.0026 29.2 3.0 77 190-267 150-252 (293)
10 PF02883 Alpha_adaptinC2: Adap 16.7 3.3E+02 0.0072 21.5 5.0 43 22-64 1-48 (115)
No 1
>KOG3661|consensus
Probab=100.00 E-value=2.4e-83 Score=641.93 Aligned_cols=258 Identities=49% Similarity=0.804 Sum_probs=249.1
Q ss_pred CCCCeEEEEcCCCceeecCCCceEEeeeceeEEEEEEEecC--CCceEecCCCeeeeeEEEEEEEEEEEcCCceeEEeee
Q psy17827 2 MPVPIYTVDADKGFNFSNADDAFVCQKKNHFQITCHTQLQG--DPQFVKTPEGMRKITSFHLHFYGVKVESLTQTIKVEQ 79 (299)
Q Consensus 2 ~~~p~~~~~~dKGF~~s~~d~~~tCyRrN~Fqvt~~~~l~~--~p~~v~t~~g~~~I~~f~l~i~av~~~~~~qtIelvQ 79 (299)
||..++||++||||+|+..||+|+||||||||||+.|++.+ .|+||++++|++||++|+|+++|||+|+.++.|.+.|
T Consensus 266 L~~LqvhV~ADKGFNys~nDncFVnQKKNHFQvtV~iea~d~~pPkyvk~n~~lkPi~~F~Lsf~GvK~E~~nseI~IrQ 345 (1019)
T KOG3661|consen 266 LPMLQVHVDADKGFNYSVNDNCFVNQKKNHFQVTVYIEALDTMPPKYVKTNEGLKPIDCFYLSFHGVKLEALNSEINIRQ 345 (1019)
T ss_pred ccceEEEEecccCcccccCCceeeecccceeEEEEEEeecCCCCCceEeeCCccceeeheeEEeeeeecccccCcccccc
Confidence 67789999999999999999999999999999999999997 7999999999999999999999999999999999999
Q ss_pred ccccCCCCccCCCCcCCcceecCCCCCccCCCCchhhccccCCcccceeeccccccccceeeecccccceeccccccccc
Q psy17827 80 SQSDRSKKAFHPVLPVPIYTVDADKGFNFSNADDAFVCQKKNHFQDRIFMESVGAVKELCKVTQNLENRIEDETTSNNMR 159 (299)
Q Consensus 80 htpkRdK~p~~p~~~~P~~~~~~~~G~~~S~~d~a~~~Q~~nhfq~~~~~~~~G~~~~~t~~t~~~eRLqF~~aTaNNgr 159 (299)
++.+|.+.++.|++. .+.. .++||+|++ ||||+|||+||+|
T Consensus 346 S~sdRkp~~htPVlf------~i~e-------------------------------rrmTkVtVp--RLHFSETTlNNqR 386 (1019)
T KOG3661|consen 346 SQSDRKPRPHTPVLF------NIPE-------------------------------RRMTKVTVP--RLHFSETTLNNQR 386 (1019)
T ss_pred cccccCCCCCCceeE------ecch-------------------------------hheeeEeec--ceeechhhhhhhh
Confidence 999999988888876 2221 489999999 9999999999999
Q ss_pred cCCCCCCCCceeEEEEEeeeeeCCCCeEEEEEeeccceEeecCCCCCCCC-CcccCcccCCCCCeeeEecceeecCCCCC
Q psy17827 160 KKGKPNPDQRYFYLVVGLHAHCSDSNHYPIVSHASERIIVRASNPGQFES-DVELCWQRGSSPESVFHSGRVGINTERPD 238 (299)
Q Consensus 160 r~~~p~p~Qqyf~LvV~L~A~~~~~~~~~Ia~~~S~~~IVRgrsPg~f~s-~~~~~W~~g~~~~~i~~~G~vgint~~P~ 238 (299)
||++|||+|+||+|||.|+|..++++.|+|++.+||+||||+.|||.|++ +.|+.|||++++.+.+++++|||++|+||
T Consensus 387 K~~rPNPdQkyF~LVVrL~A~a~~~~~vllqa~aSErvIVRAtNPGsFEp~d~Dv~Wqrngg~l~t~g~v~vG~~~~~p~ 466 (1019)
T KOG3661|consen 387 KKGRPNPDQKYFMLVVRLQAHAQNQENVLLQAQASERVIVRATNPGSFEPQDSDVLWQRNGGPLTTFGHVRVGINTDRPD 466 (1019)
T ss_pred hcCCCCcchhhhhhhhhhhheeccCcceeeeecccceeEEeccCCCCCCCCccchhhhhcCCcceeccceeeeccCCCCc
Confidence 99999999999999999999999988999999999999999999999999 89999999999999999999999999999
Q ss_pred cceEEeeeEEEeeeeecCCchhhhccCccCChHHHHhhcceeEEEEEeechhHHhhcCCC
Q psy17827 239 EALVVHGNVKLTGHIIQPSDIRAKQHITKCNTKEQLRNVQQLNVVQFHYTPEFALHFGLA 298 (299)
Q Consensus 239 ~aL~V~Gni~~~g~~~~pSD~R~K~~i~~~dt~~~l~~i~~~r~v~y~~~~e~a~~~G~~ 298 (299)
++|+|+||||++|++|||||+|+|++|+|+||+|||+||.+||+|+|+||||+|+.|||+
T Consensus 467 a~LtV~Gdiy~sGr~m~PSDiRlKe~itE~~t~ealenl~klR~VdYrYKPEvA~~wGl~ 526 (1019)
T KOG3661|consen 467 AALTVHGDIYVSGRLMHPSDIRLKEHITEVDTTEALENLSKLRLVDYRYKPEVAASWGLE 526 (1019)
T ss_pred cceEEecceEeeceecchhhhhhhhhhchhhHHHHHHHhhhheeeeeeeChhhhhhcCcc
Confidence 999999999999999999999999999999999999999999999999999999999997
No 2
>PF05224 NDT80_PhoG: NDT80 / PhoG like DNA-binding family; InterPro: IPR024061 The NDT80 DNA-binding domain is found in the following proteins, which might all be involved in sensing nutritional status []: Yeast meiosis-specific transcription factor NDT80, the key transcription factor that ultimately allows the continuation of meiosis after the successful completion of recombination. Emericella nidulans phoG (xprG), a transcriptional activator involved in the response to nutrient limitation. Emericella nidulans putative uncharacterised protein AN6015.2. Neurospora crassa transcription factor vib-1, involved in the control of heterokaryon incompatibility. Neurospora crassa related to acid phosphatase NCU04729. Neurospora crassa related to meiosis-specific protein NDT80 NCU09915. The proteolytically resistant core NDT80 DNA-binding domain reveals a central beta-sandwich characteristic of an s-type Ig fold. The beta-sandwich contains a three-stranded sheet composed of strands a, b and e, packed against a four-stranded sheet composed of strands c', c, f and g. Each sheet of the beta-sandwich contains an additional beta-strand, as well as a variety of peripheral secondary structure elements. The NDT80 DNA-binding domain contains an N-terminal extension, which consists of a beta-hairpin and a loop []. ; GO: 0003677 DNA binding; PDB: 2EVJ_A 2EUW_A 1M6U_A 2EVF_A 1M7U_B 1MN4_A 2EVG_A 2EUV_A 2EVI_A 2EVH_A ....
Probab=100.00 E-value=3.3e-49 Score=351.05 Aligned_cols=167 Identities=29% Similarity=0.368 Sum_probs=112.6
Q ss_pred ceEEeeeceeEEEEEEEecCC--CceEe---------cCCC-eeeeeEEEEEEEEEEEcCCceeEEeeeccccCCCCccC
Q psy17827 23 AFVCQKKNHFQITCHTQLQGD--PQFVK---------TPEG-MRKITSFHLHFYGVKVESLTQTIKVEQSQSDRSKKAFH 90 (299)
Q Consensus 23 ~~tCyRrN~Fqvt~~~~l~~~--p~~v~---------t~~g-~~~I~~f~l~i~av~~~~~~qtIelvQhtpkRdK~p~~ 90 (299)
+|||||||||||+|+|+|.+. |.++. .++| +.+|.+|+|+|+|+|++++++.|+|+|||+||||+|..
T Consensus 1 ewtcYRRNyFqv~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~f~i~i~a~~~~~~~~~v~LvQht~krdk~p~~ 80 (186)
T PF05224_consen 1 EWTCYRRNYFQVSCSFSLEGWSPPRFLLQVQTILQSQYGSGETRPIKYFAISISAVKSESDGKPVELVQHTPKRDKGPQF 80 (186)
T ss_dssp EEEEETTS-EEEEEEEEETTS-HHHHHHS-EEEEEETTSCEEEEEEEEEEEEEEE-EETTTTEEEEEEEE-TTGGGS-EE
T ss_pred CcccCCcCcEEEEEEEEECCCCCCchhceeeeeeeeccCCCCEeeeeEEEEEEEEEecCCCCCceEEEEeCCccCCCCCC
Confidence 699999999999999999865 54433 1444 78999999999999999999999999999999999864
Q ss_pred -CCCcC--CcceecCCCCCccCCCCchhhccccCCcccceeeccccccccceeeecccccceeccccccccccCCCCCCC
Q psy17827 91 -PVLPV--PIYTVDADKGFNFSNADDAFVCQKKNHFQDRIFMESVGAVKELCKVTQNLENRIEDETTSNNMRKKGKPNPD 167 (299)
Q Consensus 91 -p~~~~--P~~~~~~~~G~~~S~~d~a~~~Q~~nhfq~~~~~~~~G~~~~~t~~t~~~eRLqF~~aTaNNgrr~~~p~p~ 167 (299)
|+..+ |...++...+..-+... +.- ++..-+...+.+|| |||||++||||||||++
T Consensus 81 ~P~~~~~~p~~~p~~~~~~~~~~~~--------~~~------~~~~~~~~~~~~~~--eRLQF~~ATaNNgrr~~----- 139 (186)
T PF05224_consen 81 EPPIVPLIPGPLPSHQVIKEASNIR--------NGS------KIEKFPQISTVATF--ERLQFKSATANNGRRRA----- 139 (186)
T ss_dssp --SSEEB-------HHHHHHTTTSS--------SHH------HHHHHSEEESSEEE--EEEEEETTTTSBSTTST-----
T ss_pred CCcccccCCCCCCCceecccccccc--------ccc------ccccccccceEEEE--EEeEEeehhccCCCccC-----
Confidence 43221 11000000000000000 000 00000124565666 69999999999999964
Q ss_pred CceeEEEEEeeeeeC----CCCeEEEEEeeccceEeecCCCCCCCCC
Q psy17827 168 QRYFYLVVGLHAHCS----DSNHYPIVSHASERIIVRASNPGQFESD 210 (299)
Q Consensus 168 Qqyf~LvV~L~A~~~----~~~~~~Ia~~~S~~~IVRgrsPg~f~s~ 210 (299)
||||+|+|+|+|.++ ++++++||+..|+||||||||||||+++
T Consensus 140 Qqyf~L~V~L~A~v~~~~~~~~~v~ia~~~S~piIVRGRSP~~Y~~r 186 (186)
T PF05224_consen 140 QQYFHLVVELLAVVANTLSDGQWVKIAERQSPPIIVRGRSPGHYQSR 186 (186)
T ss_dssp BEEEEEEEEEEEEE-SSSSEEEEEEEEEEE-S-EEEE-S-GGGSGG-
T ss_pred CceEEEEEEEEEEeCccCCCCcEEEEEEccCCCEEEECCCcccccCC
Confidence 999999999999754 3578999999999999999999999975
No 3
>KOG3661|consensus
Probab=99.12 E-value=4.3e-11 Score=122.58 Aligned_cols=110 Identities=29% Similarity=0.430 Sum_probs=81.0
Q ss_pred EEEEEEEEcC--CceeEEeeeccccCCCCcc---CCCCcCCcceecCCCCCccCCCCchhhccccCCcccceeecccccc
Q psy17827 61 LHFYGVKVES--LTQTIKVEQSQSDRSKKAF---HPVLPVPIYTVDADKGFNFSNADDAFVCQKKNHFQDRIFMESVGAV 135 (299)
Q Consensus 61 l~i~av~~~~--~~qtIelvQhtpkRdK~p~---~p~~~~P~~~~~~~~G~~~S~~d~a~~~Q~~nhfq~~~~~~~~G~~ 135 (299)
-.|+|...++ ..++|.|..||.+.|.... .++++++++|+++|+|||||.+|+|||||||||||+++++|+.+.
T Consensus 229 ~g~~G~~~~~~~~qq~Irf~k~QeeqW~plYDaN~~eL~~LqvhV~ADKGFNys~nDncFVnQKKNHFQvtV~iea~d~- 307 (1019)
T KOG3661|consen 229 DGLSGSYLDPYSNQQSIRFQKHQEEQWAPLYDANYKELPMLQVHVDADKGFNYSVNDNCFVNQKKNHFQVTVYIEALDT- 307 (1019)
T ss_pred ccccCCccCcccCccceeccccchhccccccccCcCcccceEEEEecccCcccccCCceeeecccceeEEEEEEeecCC-
Confidence 3455555554 5679999999999998543 489999999999999999999999999999999999999997652
Q ss_pred ccceeeecccccceeccccccccccCCCCCCCCceeEEEEEeeeeeCCCCeEEE
Q psy17827 136 KELCKVTQNLENRIEDETTSNNMRKKGKPNPDQRYFYLVVGLHAHCSDSNHYPI 189 (299)
Q Consensus 136 ~~~t~~t~~~eRLqF~~aTaNNgrr~~~p~p~Qqyf~LvV~L~A~~~~~~~~~I 189 (299)
..+-.+.+ |||-| |-.-||.--+..-++..+ +++.|
T Consensus 308 ~pPkyvk~------------n~~lk-----Pi~~F~Lsf~GvK~E~~n-seI~I 343 (1019)
T KOG3661|consen 308 MPPKYVKT------------NEGLK-----PIDCFYLSFHGVKLEALN-SEINI 343 (1019)
T ss_pred CCCceEee------------CCccc-----eeeheeEEeeeeeccccc-Ccccc
Confidence 22333344 45543 445565555566566555 55544
No 4
>PF13884 Peptidase_S74: Chaperone of endosialidase; PDB: 3GUD_A.
Probab=98.04 E-value=2.1e-06 Score=62.52 Aligned_cols=35 Identities=31% Similarity=0.447 Sum_probs=19.4
Q ss_pred CchhhhccCccCChHHHHhhcceeEEEEEeechhHHh
Q psy17827 257 SDIRAKQHITKCNTKEQLRNVQQLNVVQFHYTPEFAL 293 (299)
Q Consensus 257 SD~R~K~~i~~~dt~~~l~~i~~~r~v~y~~~~e~a~ 293 (299)
||+|+|+||+++ ..+|++|.+|+++.|+|+.++..
T Consensus 1 SD~R~K~nI~~i--~~~l~~i~~l~~~~y~~k~~~~~ 35 (58)
T PF13884_consen 1 SDRRLKTNIKDI--DNALDKIMQLKPVTYNYKDEVKE 35 (58)
T ss_dssp --STT--S--S---HHHHHHHCT---EEE--CCHHHH
T ss_pred CchhhhCCCeec--hhHHHHHhCCCcEEEEECccccc
Confidence 899999999988 45799999999999999976543
No 5
>PF10283 zf-CCHH: Zinc-finger (CX5CX6HX5H) motif; InterPro: IPR019406 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type Znf motif that in humans is part of the APLF (aprataxin- and PNK-like) forkead association domain-containing protein []. The Znf is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues, and is configured CX5CX6HX5H. Many of the proteins containing this Znf are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism. This Znf motif appears to be specialised for the non-covalent binding of poly ADP-ribose; Aprataxin also appears to covalently bind poly ADP-ribose, but not through its Znf motif [].; PDB: 2KQC_A 2KUO_A 2KQE_A 2KQD_A 2KQB_A.
Probab=37.66 E-value=10 Score=23.92 Aligned_cols=6 Identities=50% Similarity=0.988 Sum_probs=2.1
Q ss_pred EEeeec
Q psy17827 25 VCQKKN 30 (299)
Q Consensus 25 tCyRrN 30 (299)
.|||||
T Consensus 8 ~CYRkN 13 (26)
T PF10283_consen 8 KCYRKN 13 (26)
T ss_dssp G-S--S
T ss_pred hhhcCC
Confidence 488888
No 6
>smart00675 DM11 Domains in hypothetical proteins in Drosophila including 2 in CG15241 and CG9329.
Probab=29.39 E-value=47 Score=29.50 Aligned_cols=22 Identities=27% Similarity=0.533 Sum_probs=18.1
Q ss_pred CCcceEEeeeEEEeeeeecCCch
Q psy17827 237 PDEALVVHGNVKLTGHIIQPSDI 259 (299)
Q Consensus 237 P~~aL~V~Gni~~~g~~~~pSD~ 259 (299)
-++.+.|+||+.+.+.+ +|+|+
T Consensus 40 d~~~i~vsGn~t~~wdi-~P~Dr 61 (164)
T smart00675 40 DPDGLHISGNITVIWDV-QPTDR 61 (164)
T ss_pred cCCeEEEeeeEEEEEec-CCCCe
Confidence 46789999999999866 78774
No 7
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=25.29 E-value=75 Score=24.85 Aligned_cols=33 Identities=12% Similarity=0.276 Sum_probs=19.8
Q ss_pred EEEEeeeeeCCCCeEEEEEeeccceEeecCCCC
Q psy17827 173 LVVGLHAHCSDSNHYPIVSHASERIIVRASNPG 205 (299)
Q Consensus 173 LvV~L~A~~~~~~~~~Ia~~~S~~~IVRgrsPg 205 (299)
+.+++.....+.+.|-|.+-..++|.|||.|+-
T Consensus 20 f~~~~~~~~~~~d~F~l~~~~~gki~I~G~s~v 52 (86)
T PF12971_consen 20 FTFELIPSSNGKDVFELSSADNGKIVIRGNSGV 52 (86)
T ss_dssp EEEEE---BTTBEEEEEEE-SSS-EEEEESSHH
T ss_pred EEEEEecCCCCCCEEEEEeCCCCeEEEEeCCHH
Confidence 344444444344777786668889999999984
No 8
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.06 E-value=26 Score=27.74 Aligned_cols=11 Identities=36% Similarity=0.259 Sum_probs=8.8
Q ss_pred ccccccccCCC
Q psy17827 153 TTSNNMRKKGK 163 (299)
Q Consensus 153 aTaNNgrr~~~ 163 (299)
-||||||||-.
T Consensus 24 lk~ngGRKk~~ 34 (80)
T COG4466 24 LKANGGRKKTI 34 (80)
T ss_pred EEecCCceeee
Confidence 47999999854
No 9
>COG4242 CphB Cyanophycinase and related exopeptidases [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=17.41 E-value=1.2e+02 Score=29.22 Aligned_cols=77 Identities=18% Similarity=0.374 Sum_probs=51.8
Q ss_pred EEeeccceEeecCCCCCCCCCc--ccCcccCCCCCee-------------------eEecceeecCCCCC-cceEEeeeE
Q psy17827 190 VSHASERIIVRASNPGQFESDV--ELCWQRGSSPESV-------------------FHSGRVGINTERPD-EALVVHGNV 247 (299)
Q Consensus 190 a~~~S~~~IVRgrsPg~f~s~~--~~~W~~g~~~~~i-------------------~~~G~vgint~~P~-~aL~V~Gni 247 (299)
|+..|++|||-|.| +-|++.. +..-+-|..|..| .|.-+.||+.|.-. .-..+.|.+
T Consensus 150 AavM~~~mi~~g~s-~~~pn~~~v~m~~glg~lp~~ivDqHF~~R~RmGRL~sai~~~p~~LG~gIdE~T~avvd~dg~~ 228 (293)
T COG4242 150 AAVMSDHMIVAGDS-GEYPNRELVDMGFGLGFLPGVIVDQHFDNRKRMGRLISAIAQHPSRLGIGIDENTCAVVDRDGKA 228 (293)
T ss_pred hhhcCCceEeccCC-CCCCCcchhhhccccccccceeeehhhhhhhHHHHHHHHHHhChHhhcccccCCceEEEEecCce
Confidence 56789999999998 7777753 2233334445444 35678899996644 444567888
Q ss_pred EEeee----eecCCchhhhccCcc
Q psy17827 248 KLTGH----IIQPSDIRAKQHITK 267 (299)
Q Consensus 248 ~~~g~----~~~pSD~R~K~~i~~ 267 (299)
+|.|+ ++.+++.+......-
T Consensus 229 kVlG~gavt~Vd~~~~~~~n~p~~ 252 (293)
T COG4242 229 KVLGQGAVTFVDAREITYTNEPLV 252 (293)
T ss_pred EEecCCcEEEEccccccccCCccc
Confidence 88874 667888777665543
No 10
>PF02883 Alpha_adaptinC2: Adaptin C-terminal domain; InterPro: IPR008152 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. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) 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 [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. GGAs (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) are a family of monomeric clathrin adaptor proteins that are conserved from yeasts to humans. GGAs regulate clathrin-mediated the transport of proteins (such as mannose 6-phosphate receptors) from the TGN to endosomes and lysosomes through interactions with TGN-sorting receptors, sometimes in conjunction with AP-1 [, ]. GGAs bind cargo, membranes, clathrin and accessory factors. GGA1, GGA2 and GGA3 all contain a domain homologous to the ear domain of gamma-adaptin. GGAs are composed of a single polypeptide with four domains: 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 VHS domain is responsible for endocytosis and signal transduction, recognising transmembrane cargo through the ACLL sequence in the cytoplasmic domains of sorting receptors []. The GAT domain (also found in Tom1 proteins) interacts with ARF (ADP-ribosylation factor) to regulate membrane trafficking [], and with ubiquitin for receptor sorting []. The hinge region contains a clathrin box for recognition and binding to clathrin, similar to that found in AP adaptins. The GAE domain is similar to the AP gamma-adaptin ear domain, and is responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. This entry represents a beta-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, and the GAE (gamma-adaptin ear) domain of GGA adaptor proteins. These domains have an immunoglobulin-like beta-sandwich fold containing 7 or 8 strands in 2 beta-sheets in a Greek key topology [, ]. Although these domains share a similar fold, there is little sequence identity between the alpha/beta-adaptins and gamma-adaptin/GAE. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 3MNM_B 3ZY7_B 1GYU_A 1GYW_B 2A7B_A 1GYV_A 2E9G_A 1E42_B 2G30_A 2IV9_B ....
Probab=16.72 E-value=3.3e+02 Score=21.49 Aligned_cols=43 Identities=16% Similarity=0.123 Sum_probs=29.3
Q ss_pred CceEEeeeceeEEEEEEEe--cCCCceE---ecCCCeeeeeEEEEEEE
Q psy17827 22 DAFVCQKKNHFQITCHTQL--QGDPQFV---KTPEGMRKITSFHLHFY 64 (299)
Q Consensus 22 ~~~tCyRrN~Fqvt~~~~l--~~~p~~v---~t~~g~~~I~~f~l~i~ 64 (299)
++.++|..|.++|...++- .+....+ -++....+|.+|.+.+.
T Consensus 1 ~~~~~ye~~~l~I~~~~~~~~~~~~~~i~~~f~N~s~~~it~f~~q~a 48 (115)
T PF02883_consen 1 PEGVLYEDNGLQIGFKSEKSPNPNQGRIKLTFGNKSSQPITNFSFQAA 48 (115)
T ss_dssp SEEEEEEETTEEEEEEEEECCETTEEEEEEEEEE-SSS-BEEEEEEEE
T ss_pred CCEEEEeCCCEEEEEEEEecCCCCEEEEEEEEEECCCCCcceEEEEEE
Confidence 3578999999999999987 3332222 24445689999988763
Done!