Query 046768
Match_columns 314
No_of_seqs 152 out of 485
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 04:18:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046768.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046768hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1162 Predicted small molecu 100.0 1.9E-71 4.1E-76 565.6 10.0 229 50-312 351-614 (617)
2 PF03124 EXS: EXS family; Int 100.0 1.3E-61 2.9E-66 466.1 12.0 214 44-290 86-345 (345)
3 COG5409 EXS domain-containing 100.0 2.7E-49 6E-54 377.9 7.1 245 21-303 98-380 (384)
4 KOG1161 Protein involved in va 82.2 1.2 2.5E-05 43.7 3.1 27 2-30 121-147 (310)
5 PF08557 Lipid_DES: Sphingolip 21.0 63 0.0014 22.5 1.4 14 5-18 20-33 (39)
6 PF11753 DUF3310: Protein of u 20.7 41 0.00089 25.0 0.5 13 129-141 28-40 (60)
7 cd07347 harmonin_N_like N-term 18.8 66 0.0014 25.5 1.3 29 115-143 22-50 (78)
8 cd07353 harmonin_N N-terminal 17.7 73 0.0016 25.1 1.3 24 117-140 25-48 (79)
9 PF02268 TFIIA_gamma_N: Transc 17.2 86 0.0019 22.8 1.5 11 5-15 34-44 (49)
10 COG2426 Predicted membrane pro 16.4 1E+02 0.0023 26.9 2.1 52 5-57 35-96 (142)
No 1
>KOG1162 consensus Predicted small molecule transporter [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.9e-71 Score=565.60 Aligned_cols=229 Identities=49% Similarity=0.781 Sum_probs=205.5
Q ss_pred HHHhhcccccchhhHHHHHHHhhHhhccCceeeecchhhhhhcccccccch--------------------------hhh
Q 046768 50 AMLFLPFNILYRSSRFFFLTCLFHCIAVPLYKVTIPDFFLADQFTSQTSSV--------------------------YQT 103 (314)
Q Consensus 50 ~~l~~P~~i~~~~~R~~~l~~l~r~l~~p~~~V~F~DfflaD~ltSls~~~--------------------------~~~ 103 (314)
+++++|++++|+++|+|+++++.||+++|+++|.|.|||+|||+||++.++ +..
T Consensus 351 ~~L~~Pf~~fY~sSRf~ll~~l~rvi~spl~~V~~~DFfl~Dql~S~v~a~~~l~~~~C~y~~~~~~~~~~~~~~~~~~~ 430 (617)
T KOG1162|consen 351 FLLVCPFNTFYRSSRFWLLKRLFRVLSSPLYKVLFVDFFLADQLTSLVLALRDLEFFICYYGTGDFQARRTCYCKDDYIE 430 (617)
T ss_pred heeeccchhhhHhhHHHHHHHHHHHHhccceeeccccccHHHHHHHHHHHHHhHHHhheeecccccccccccccccchHH
Confidence 457889999999999999999999999999999999999999999995421 345
Q ss_pred HhHHHhHHHHHHHHHHHHHHHHhcCCCccchhhHHHHHHHHHHHHHHHHhhcCCC---Cchhhhhhhhhh------hhhh
Q 046768 104 FNFIVAVIPHKSRLLQCLRLLFEEKYPMQGYNGLKYFLTIVAVCMRTALSLNGVG---GLGWKIIAWIFS------DIVF 174 (314)
Q Consensus 104 ~~~ii~~lP~~iR~~QCLrry~dt~~~~hL~Na~KY~sa~~~v~~~~~~~~~~~~---~~~W~~~~~i~S------Dv~m 174 (314)
+.++++++|+++|++||+|||.|++..+||+||+||++++++++++++|+.+..+ ...|++++.++| |++|
T Consensus 431 ~~~iva~lP~~~RfLQClRR~~d~~~~~hL~NAlKY~~~i~~v~~~~~y~~~~~~~~~~~l~~~~s~vaS~y~~~WDvv~ 510 (617)
T KOG1162|consen 431 FQSIVAVLPYWFRFLQCLRRYRDEKAFPHLLNALKYSTTILAVMLTTLYRILPGSSLWFALWILSSKVASLYTTYWDVVM 510 (617)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccchHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHHHHHHHhe
Confidence 7889999999999999999999998899999999999999999999999887643 246777777777 9999
Q ss_pred hccCccCCCCCccCCcccccCCCceEEEEEEEcCCCCCCCcccccccceeEEeccchhhhhhcccceeeehhhhhhhhcc
Q 046768 175 DWGLLNWHSKNCWLRDKLLVPHKSVYFIGMVSNNKTYMKSPSRLRVSKAVVVISDNSLIVKLQDLNALLRFAWLQNVLNF 254 (314)
Q Consensus 175 DWgLl~~~s~~~~LR~~l~y~~~~~Yy~aiv~~~~~~~~~~~rl~~~~~~~~~~~~~~~~~~~~~NliLRf~W~~~l~~~ 254 (314)
||||++++++ +|||++++||++++||+||+. |++||++|++.++..
T Consensus 511 DWgLl~~~~~-~~lRd~l~~p~k~vYy~aiv~---------------------------------N~vLR~aW~~~~i~~ 556 (617)
T KOG1162|consen 511 DWGLLNRKSK-PWLRDNLLYPQKWVYYSAIVL---------------------------------NFVLRFAWFFKTILV 556 (617)
T ss_pred ecccccccCc-hhhHHHhcccchheehhHHHH---------------------------------HHHHHHHHHHHHHHH
Confidence 9999999998 999999999999999999999 999999998887754
Q ss_pred ccccccchhHHHHHHHHHHHhhhceeeeeehhhhhhccCCceecccccCCCCCCCCcc
Q 046768 255 NFTFLHRNTMITIVASLEIIRRSIWNFFRLENEHLSNVGKYRAFKSVPLPFNDDEDEE 312 (314)
Q Consensus 255 ~~~~~~~~~~~~il~~lEI~RR~iWnffRvEnEhi~N~~~~ra~~~iplp~~~~~d~~ 312 (314)
.+....++.++++++.+||+||++||||||||||+||||+|||+++||+|++.++++|
T Consensus 557 ~~~~~~~~~~~~i~a~LEIiRRfiWnfFRLEnEhlnN~g~fRa~~~v~l~~~~~~~~d 614 (617)
T KOG1162|consen 557 FHEEFLSDSMVFIMALLEIIRRFIWNFFRLENEHLNNVGKFRAFRDVPLPFSYMDESD 614 (617)
T ss_pred HHHhhhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhhccccccCCchhhhccccc
Confidence 4322227889999999999999999999999999999999999999999988777665
No 2
>PF03124 EXS: EXS family; InterPro: IPR004342 The EXS domain is named after ERD1/XPR1/SYG1 and proteins containing this motif include the C-terminal of the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be Murine leukemia virus (MLV) receptors (XPR1. The N-terminal of these proteins often have an SPX domain (IPR004331 from INTERPRO) []. While the N-terminal is thought to be involved in signal transduction, the role of the C-terminal is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention defective) S. cerevisiae proteins. ERD1 proteins are involved in the localization of endogenous endoplasmic reticulum (ER) proteins. Erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localization label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via `salvage' vesicles [].; GO: 0016021 integral to membrane
Probab=100.00 E-value=1.3e-61 Score=466.14 Aligned_cols=214 Identities=42% Similarity=0.690 Sum_probs=191.5
Q ss_pred hHHH-----HHHHHhhcccccchhhHHHHHHHhhHhhccCceeeecchhhhhhcccccccchhh----------------
Q 046768 44 AAPL-----LFAMLFLPFNILYRSSRFFFLTCLFHCIAVPLYKVTIPDFFLADQFTSQTSSVYQ---------------- 102 (314)
Q Consensus 44 ~~p~-----~~~~l~~P~~i~~~~~R~~~l~~l~r~l~~p~~~V~F~DfflaD~ltSls~~~~~---------------- 102 (314)
+.|+ +++++++|++++++++|+|+++++.|++.+|+.+|+|+|+|+||||||+++++-+
T Consensus 86 ~~Pll~~~~~~~~l~~P~~~~~~~~R~~~~~~l~ril~~~~~~v~f~d~~laD~LtS~~~~l~D~~~~~c~~~~~~~~~~ 165 (345)
T PF03124_consen 86 YIPLLLLLILLLLLFFPFNIFYRSSRRWFLRTLKRILLAPFYPVRFRDFFLADQLTSLSKVLGDLEFTICYYFSGSFTSP 165 (345)
T ss_pred HhhHHHHHHHHHHhhcccchhhhhHHHHHHHHHHHHHhcccccchHHHHHHHHHHHhHHHHHHHHHHHHHHHhcccccCC
Confidence 5675 3457899999999999999999999999999999999999999999999886410
Q ss_pred ---------hHhHHHhHHHHHHHHHHHHHHHHhcCCC-ccchhhHHHHHHHHHHHHHHHHhhcCCCC------chhhhhh
Q 046768 103 ---------TFNFIVAVIPHKSRLLQCLRLLFEEKYP-MQGYNGLKYFLTIVAVCMRTALSLNGVGG------LGWKIIA 166 (314)
Q Consensus 103 ---------~~~~ii~~lP~~iR~~QCLrry~dt~~~-~hL~Na~KY~sa~~~v~~~~~~~~~~~~~------~~W~~~~ 166 (314)
...|+++++|++||++||+|||+|||+. +||+||+||++|+++++++..++.+..+. ..|++++
T Consensus 166 ~~~c~~~~~~~~~~~~~lP~~iR~~QClrry~~~~~~~~hL~Na~KY~~~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~ 245 (345)
T PF03124_consen 166 SNQCGSSSWYIDPIVASLPYWIRFLQCLRRYRDTGDRFPHLFNALKYSSSIPVIILSALYRFYPSSDSSIWLFILWIIFA 245 (345)
T ss_pred CCcCccccHhHHhHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHH
Confidence 2349999999999999999999999998 99999999999999998887777665432 5799898
Q ss_pred hhhh------hhhhhccCccCC--CCCccCCcccccCCCceEEEEEEEcCCCCCCCcccccccceeEEeccchhhhhhcc
Q 046768 167 WIFS------DIVFDWGLLNWH--SKNCWLRDKLLVPHKSVYFIGMVSNNKTYMKSPSRLRVSKAVVVISDNSLIVKLQD 238 (314)
Q Consensus 167 ~i~S------Dv~mDWgLl~~~--s~~~~LR~~l~y~~~~~Yy~aiv~~~~~~~~~~~rl~~~~~~~~~~~~~~~~~~~~ 238 (314)
++|| |++|||||++++ +++++||++++||+|++||+||+.
T Consensus 246 ~i~s~Ys~~WDv~~DWgL~~~~~~~~~~~LR~~l~~~~~~~Yy~ai~~-------------------------------- 293 (345)
T PF03124_consen 246 LINSLYSFYWDVKMDWGLFQPKKKSKNWLLRRRLLYPRKWFYYFAIIL-------------------------------- 293 (345)
T ss_pred HHHHHHHHHHHHHhcccccCCccccCCCCCccccccCCcchhhhHHHH--------------------------------
Confidence 8888 999999999988 789999999999998999999999
Q ss_pred cceeeehhhhhhhhccccc-cccchhHHHHHHHHHHHhhhceeeeeehhhhhh
Q 046768 239 LNALLRFAWLQNVLNFNFT-FLHRNTMITIVASLEIIRRSIWNFFRLENEHLS 290 (314)
Q Consensus 239 ~NliLRf~W~~~l~~~~~~-~~~~~~~~~il~~lEI~RR~iWnffRvEnEhi~ 290 (314)
|+++||+|++++++.... ..+++.+.++++++||+||++||+|||||||+|
T Consensus 294 -n~ilRf~W~~~~~~~~~~~~~~~~~~~~~~~~lEi~RR~iWnffRlE~Ehin 345 (345)
T PF03124_consen 294 -NFILRFAWILTLSPPHFSHIDNSEIFIFILAILEIFRRFIWNFFRLENEHIN 345 (345)
T ss_pred -HHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHHHHHHHhhheeeeeHhhcC
Confidence 999999999999985533 335788999999999999999999999999996
No 3
>COG5409 EXS domain-containing protein [Signal transduction mechanisms]
Probab=100.00 E-value=2.7e-49 Score=377.90 Aligned_cols=245 Identities=31% Similarity=0.394 Sum_probs=206.8
Q ss_pred HHHHHHHHhhcCCCCcccccchhhHHHH-----HHHHhhcccccchhhHHHHHHHhhHhhccCceeeecchhhhhhcccc
Q 046768 21 VETTFIKHFSNSNRSKGFLSGRTAAPLL-----FAMLFLPFNILYRSSRFFFLTCLFHCIAVPLYKVTIPDFFLADQFTS 95 (314)
Q Consensus 21 ~~~l~i~~Fa~~~r~~a~~~~~~~~p~~-----~~~l~~P~~i~~~~~R~~~l~~l~r~l~~p~~~V~F~DfflaD~ltS 95 (314)
+.+++++.=+.+. .++.+...+..|++ ..++++|+++.++.+|+|++.++.|++..|...|+|+||++||++||
T Consensus 98 ~~slfiFl~~v~g-~~~~l~~~~~~P~l~v~~vf~~ll~Pf~ii~y~sRr~Li~sliRv~l~~~~~v~f~dF~f~di~~S 176 (384)
T COG5409 98 TTSLFIFLNAVEG-LKFILLFVYFLPLLQVGTVFWFLLKPFQIIYYWSRRYLIESLIRVFLFGYSLVRFTDFFFGDILIS 176 (384)
T ss_pred HHHHHHHHHHhhc-cccceehhhhccHHHHHHHHHHhhcccceeeecchhhHHHHHHHHHHhccceeeeeeeehhhHHHH
Confidence 3566666666666 67777777888864 34789999999999999999999999999999999999999999999
Q ss_pred cccch---------h-------------hhHhHHHhHHHHHHHHHHHHHHHHhcCC-CccchhhHHHHHHHHHHHHHHHH
Q 046768 96 QTSSV---------Y-------------QTFNFIVAVIPHKSRLLQCLRLLFEEKY-PMQGYNGLKYFLTIVAVCMRTAL 152 (314)
Q Consensus 96 ls~~~---------~-------------~~~~~ii~~lP~~iR~~QCLrry~dt~~-~~hL~Na~KY~sa~~~v~~~~~~ 152 (314)
+++++ + ..+.++++++|.++|++||||||.|++. .|||.||+||++++++.....+|
T Consensus 177 lTya~gdi~~FfCv~~~~~~~pLc~sshs~~~g~~~~lP~ivR~lQCLRry~ds~~~fphLlNALKYs~~i~v~~~~~~~ 256 (384)
T COG5409 177 LTYALGDIYIFFCVYSLLFREPLCKSSHSDLSGLAALLPVIVRFLQCLRRYRDSLHEFPHLLNALKYSLNIPVLFCLWLY 256 (384)
T ss_pred HHHhhhhhhhHHHHHhhhccccccccCCcchHhHHHhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHH
Confidence 98532 1 2356789999999999999999999976 59999999999999988888888
Q ss_pred hhcCCC---Cchhhhhhhhhh------hhhhhccCccCCCCC-ccCCcccccCCCceEEEEEEEcCCCCCCCcccccccc
Q 046768 153 SLNGVG---GLGWKIIAWIFS------DIVFDWGLLNWHSKN-CWLRDKLLVPHKSVYFIGMVSNNKTYMKSPSRLRVSK 222 (314)
Q Consensus 153 ~~~~~~---~~~W~~~~~i~S------Dv~mDWgLl~~~s~~-~~LR~~l~y~~~~~Yy~aiv~~~~~~~~~~~rl~~~~ 222 (314)
+..+.+ ...|+++|.+|| ||.|||++..++++. +-+|++++++ |++||+.
T Consensus 257 r~~~~~~~l~~l~~~~a~lnS~yT~~WDV~mDW~l~~~~~~~~~~kr~~~~l~----y~~a~~i---------------- 316 (384)
T COG5409 257 RVYEGEERLFHLQIWFALLNSIYTSFWDVFMDWSLDSLTSLRSWSKRAVTLLK----YHIAMII---------------- 316 (384)
T ss_pred HhccCcceeehHHHHHHHHHHHHHHhHHhheeeeecccccchhccccchhHHH----HHHHHHH----------------
Confidence 876533 267888898888 999999998777554 4467766554 8899988
Q ss_pred eeEEeccchhhhhhcccceeeehhhhhhhhccccccccchhHHHHHHHHHHHhhhceeeeeehhhhhhccCCceeccccc
Q 046768 223 AVVVISDNSLIVKLQDLNALLRFAWLQNVLNFNFTFLHRNTMITIVASLEIIRRSIWNFFRLENEHLSNVGKYRAFKSVP 302 (314)
Q Consensus 223 ~~~~~~~~~~~~~~~~~NliLRf~W~~~l~~~~~~~~~~~~~~~il~~lEI~RR~iWnffRvEnEhi~N~~~~ra~~~ip 302 (314)
|+++|++|++...|.++.....+...++++++||+||++|++||||+||.+|+..+|+.++.+
T Consensus 317 -----------------nFllR~~Wi~~~~~~~~~~~~~~~~~F~m~~lEi~RR~vW~~FrveaE~~~n~~~~~~~~~~~ 379 (384)
T COG5409 317 -----------------NFLLRFSWIVYYLPPNHIQHSADIFIFIMQLLEILRRFVWVFFRVEAEHSINFASFRAAGELK 379 (384)
T ss_pred -----------------HHHHHHHHHHhhcchhhhhhhhhhHHHHHHHHHHHHhheeeEEEeehHHHhhHHHhhhcccCC
Confidence 999999999999886654334555558999999999999999999999999999999999988
Q ss_pred C
Q 046768 303 L 303 (314)
Q Consensus 303 l 303 (314)
.
T Consensus 380 ~ 380 (384)
T COG5409 380 V 380 (384)
T ss_pred C
Confidence 3
No 4
>KOG1161 consensus Protein involved in vacuolar polyphosphate accumulation, contains SPX domain [Inorganic ion transport and metabolism]
Probab=82.25 E-value=1.2 Score=43.72 Aligned_cols=27 Identities=30% Similarity=0.397 Sum_probs=18.8
Q ss_pred hhHHHHHHHHHHHHhHHHHHHHHHHHHhh
Q 046768 2 LAFSKIMKKYDEVSKLMERVETTFIKHFS 30 (314)
Q Consensus 2 ~~~~~~~~~~~~~~~l~~~~~~l~i~~Fa 30 (314)
.||.||||||||-++ ...-..|+.-..
T Consensus 121 tGf~KILKK~DKrtg--~~l~~~f~~~l~ 147 (310)
T KOG1161|consen 121 TGFAKILKKHDKRTG--YRLRPYFQVRLL 147 (310)
T ss_pred HHHHHHHHHHhcccc--cccccHHHHHHH
Confidence 489999999999775 444444444433
No 5
>PF08557 Lipid_DES: Sphingolipid Delta4-desaturase (DES); InterPro: IPR013866 Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine []. Some proteins in this entry have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis []. This small protein associates with FA_desaturase IPR005804 from INTERPRO and appears to be specific to sphingolipid delta 4-desaturase. ; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0006633 fatty acid biosynthetic process, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=20.96 E-value=63 Score=22.51 Aligned_cols=14 Identities=50% Similarity=0.712 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHhHH
Q 046768 5 SKIMKKYDEVSKLM 18 (314)
Q Consensus 5 ~~~~~~~~~~~~l~ 18 (314)
..|||||-+|.+||
T Consensus 20 k~IL~k~PeIk~L~ 33 (39)
T PF08557_consen 20 KEILKKHPEIKKLM 33 (39)
T ss_pred HHHHHhChHHHHHh
Confidence 36999999998887
No 6
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.74 E-value=41 Score=25.03 Aligned_cols=13 Identities=23% Similarity=0.222 Sum_probs=10.1
Q ss_pred CCccchhhHHHHH
Q 046768 129 YPMQGYNGLKYFL 141 (314)
Q Consensus 129 ~~~hL~Na~KY~s 141 (314)
..-+++||+||++
T Consensus 28 ~~f~~gnaiKY~~ 40 (60)
T PF11753_consen 28 LGFCLGNAIKYLW 40 (60)
T ss_pred hhHHHHHHHHHHH
Confidence 3467899999984
No 7
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=18.84 E-value=66 Score=25.49 Aligned_cols=29 Identities=14% Similarity=0.109 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHhcCCCccchhhHHHHHHH
Q 046768 115 SRLLQCLRLLFEEKYPMQGYNGLKYFLTI 143 (314)
Q Consensus 115 iR~~QCLrry~dt~~~~hL~Na~KY~sa~ 143 (314)
--+.|||++|..+++...|.++++-...-
T Consensus 22 ~~~~~~L~~Y~~~~~Vd~LV~~L~~vLdt 50 (78)
T cd07347 22 EQVTRALERYHQERNVDDLVRDLYLVLDT 50 (78)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHcCc
Confidence 34689999999999878887777655443
No 8
>cd07353 harmonin_N N-terminal protein-binding module of harmonin. Harmonin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein, which organizes the Usher protein network of the inner ear and the retina. Harmonin contains a single copy of this domain, which is found at the N-terminus of all three harmonin isoform classes (a, b and c), and which preceeds the first PDZ protein-binding domain, PDZ1. This harmonin_N domain binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network.
Probab=17.75 E-value=73 Score=25.11 Aligned_cols=24 Identities=21% Similarity=0.162 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCCCccchhhHHHH
Q 046768 117 LLQCLRLLFEEKYPMQGYNGLKYF 140 (314)
Q Consensus 117 ~~QCLrry~dt~~~~hL~Na~KY~ 140 (314)
+.|.||.|.+|++-+.|.|-+|-.
T Consensus 25 lY~~Lr~YHqSm~lp~li~Dlk~V 48 (79)
T cd07353 25 LYDVLRMYHQSMNLPVLVGDLKLV 48 (79)
T ss_pred HHHHHHHHHhccCHHHHHHHHHHH
Confidence 578999999999988888888854
No 9
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=17.19 E-value=86 Score=22.82 Aligned_cols=11 Identities=18% Similarity=0.564 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 046768 5 SKIMKKYDEVS 15 (314)
Q Consensus 5 ~~~~~~~~~~~ 15 (314)
.|||.+|||+-
T Consensus 34 ~kVL~~FDksi 44 (49)
T PF02268_consen 34 MKVLEQFDKSI 44 (49)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 58999999963
No 10
>COG2426 Predicted membrane protein [Function unknown]
Probab=16.37 E-value=1e+02 Score=26.95 Aligned_cols=52 Identities=15% Similarity=0.297 Sum_probs=34.6
Q ss_pred HHHH-HHHHHHHhHHHHHHH--------HHHHHhhcCCCC-cccccchhhHHHHHHHHhhccc
Q 046768 5 SKIM-KKYDEVSKLMERVET--------TFIKHFSNSNRS-KGFLSGRTAAPLLFAMLFLPFN 57 (314)
Q Consensus 5 ~~~~-~~~~~~~~l~~~~~~--------l~i~~Fa~~~r~-~a~~~~~~~~p~~~~~l~~P~~ 57 (314)
+-+| |-+|.+.++|++.|+ +|...-...-|| ++++.-.-++= +.++...|++
T Consensus 35 ~~lL~~~l~~id~im~kl~~~rl~r~~~lY~~~~~r~~rka~~yVER~G~iG-L~iFvAIPLP 96 (142)
T COG2426 35 SLLLPLLLDPIDRIMLKLKWTRLQRPACLYDWLVNRTRRKAKGYVERYGFIG-LIIFVAIPLP 96 (142)
T ss_pred HHHHHHHHhHHHHHHHHHhhcccCchHHHHHHHHHHHHHhccCcHhhhhhhh-hhheeeccCC
Confidence 4467 788999999999999 888777665555 56665444433 3334444555
Done!