Query 016325
Match_columns 391
No_of_seqs 191 out of 473
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 05:50:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016325.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016325hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5602 SIN3 Histone deacetyla 100.0 2.9E-79 6.3E-84 642.9 25.6 199 174-374 489-699 (1163)
2 smart00761 HDAC_interact Histo 100.0 2.6E-46 5.6E-51 311.9 7.1 96 178-273 1-97 (102)
3 PF08295 Sin3_corepress: Sin3 100.0 8.2E-45 1.8E-49 304.0 7.6 96 178-273 1-96 (101)
4 KOG4204 Histone deacetylase co 99.8 1.6E-20 3.5E-25 178.8 3.3 193 43-271 18-210 (231)
5 PF02671 PAH: Paired amphipath 99.5 7.6E-15 1.6E-19 106.6 5.8 47 63-109 1-47 (47)
6 COG5602 SIN3 Histone deacetyla 99.0 9.7E-10 2.1E-14 118.7 8.7 69 44-113 269-337 (1163)
7 KOG4204 Histone deacetylase co 98.9 3.2E-09 7E-14 101.6 7.9 70 43-113 126-195 (231)
8 cd07354 HN_L-delphilin-R1_like 83.4 5.2 0.00011 32.6 6.7 67 45-113 3-71 (80)
9 PF08349 DUF1722: Protein of u 55.3 37 0.00081 29.0 6.1 50 44-99 55-104 (117)
10 PF15011 CK2S: Casein Kinase 2 49.7 49 0.0011 30.4 6.2 89 241-348 11-99 (168)
11 cd07347 harmonin_N_like N-term 40.8 1.4E+02 0.0031 24.2 6.9 64 45-112 3-68 (78)
12 TIGR03036 trp_2_3_diox tryptop 39.5 73 0.0016 31.6 6.0 71 254-331 73-147 (264)
13 PRK10167 hypothetical protein; 38.7 35 0.00076 31.5 3.5 50 44-99 96-145 (169)
14 PF08221 HTH_9: RNA polymerase 37.9 65 0.0014 24.5 4.3 43 292-334 4-46 (62)
15 PF00611 FCH: Fes/CIP4, and EF 35.4 2.1E+02 0.0046 22.2 7.5 39 315-355 8-46 (91)
16 PF12083 DUF3560: Domain of un 33.7 85 0.0018 27.7 4.9 64 278-341 42-118 (126)
17 PF14775 NYD-SP28_assoc: Sperm 28.2 74 0.0016 24.4 3.2 59 50-108 2-60 (60)
18 KOG4424 Predicted Rho/Rac guan 27.4 3.5E+02 0.0077 29.9 9.1 74 289-377 101-183 (623)
19 TIGR00373 conserved hypothetic 26.0 99 0.0021 28.0 4.2 47 289-335 2-48 (158)
20 PF12174 RST: RCD1-SRO-TAF4 (R 25.6 1.9E+02 0.0041 22.9 5.2 43 50-95 14-56 (70)
21 PRK15326 type III secretion sy 24.9 1.3E+02 0.0029 24.5 4.3 42 303-346 27-71 (80)
22 PF11537 DUF3227: Protein of u 23.9 1.3E+02 0.0028 25.6 4.1 27 289-315 47-73 (102)
23 PF14244 UBN2_3: gag-polypepti 21.3 3.1E+02 0.0067 24.0 6.4 51 44-94 81-132 (152)
24 PF14483 Cut8_M: Cut8 dimerisa 21.2 1.2E+02 0.0026 21.2 2.9 31 79-109 8-38 (38)
No 1
>COG5602 SIN3 Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=100.00 E-value=2.9e-79 Score=642.92 Aligned_cols=199 Identities=30% Similarity=0.465 Sum_probs=194.1
Q ss_pred cccccCcccCcccccCCcCCCCCCCCCCcccccccccCccccc-cCCCCccchhhhhhchhHHHHhhcccchhhHHHHHH
Q 016325 174 LDLSKCKQVSPSYWRLPEYYWMPLASNRSEIGDQVLNDNLVCA-STGTERSSFKQRRRTKQEEVLFKCEDDRFELDLLLG 252 (391)
Q Consensus 174 ~d~s~c~~~gpSYr~LP~~~~~~~cSgR~~l~~~VLND~wVs~-~~~SEd~~f~~~rKnqyEE~Lfr~EDER~E~D~~ie 252 (391)
.|++.|+.||||||+||+.+...+|||||+|||+||||+|||| ||+|||++|++||||||||+||++||||||||.+||
T Consensus 489 ~~le~~~~~GpSYR~LP~~e~~i~CSGRDDl~w~VLND~wVs~Pt~aSEdSgfI~hrkNqyEEaL~kiEeERyEyDr~Ie 568 (1163)
T COG5602 489 KDLEKFEKCGPSYRLLPKSEEEIKCSGRDDLAWEVLNDDWVSHPTWASEDSGFIAHRKNQYEEALFKIEEERYEYDRHIE 568 (1163)
T ss_pred cCHhHhhhhCcchhcCCchhhhCCccCcchhhHhhhccccccCCCcccccccceeecccHHHHHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999999999999999999999999999 599999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCcchhhcccccccCCcc----hhhHHHHHHHHh-cchHHHHHHHhhCCCcchhHhhhhHHH
Q 016325 253 WMHSAAENVEKLMIKIDDQNQDDEKSSKIEIEGHLG----ISDLRCIERLYA-EHGLDVIDNLHKNPETALPVILKSLKQ 327 (391)
Q Consensus 253 ~~~~tI~~Le~l~~~i~~~~~~~~~~~~~~l~~~l~----~i~~r~I~riYG-~~g~evl~~l~~nP~~alPvVL~RLkq 327 (391)
++.+||+.|+.++.++..|++ .+++.+.|.++|| +|++.+|++||| +||.+||++|.++|++|+||||+|||+
T Consensus 569 a~~~~Ik~Le~i~d~~~~~~e--~Eka~~~Lp~glg~~S~sIyKkvik~VY~KEhA~eile~L~k~P~vt~PiVlkRLk~ 646 (1163)
T COG5602 569 ATQRTIKALEQIIDKIKDMEE--SEKANKTLPGGLGLPSKSIYKKVIKKVYDKEHAPEILEALLKKPHVTIPIVLKRLKM 646 (1163)
T ss_pred HHHHHHHHHHHHHHHhhcchh--hHHHHhcCCCcCCCccHHHHHHHHHHHhchhhHHHHHHHHHhCCCcchHHHHHHHHH
Confidence 999999999999999999998 7788888887776 899999999999 899999999999999999999999999
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHhhhhhh------hhhhhhcccchhhhHHHHH
Q 016325 328 KVEELVERRSDCNKIWAHVCAKNHDKLQ------EMQRELKNSKREDLVAKEE 374 (391)
Q Consensus 328 K~eEw~~~r~~~nk~Wrev~~kny~kSL------fK~~DkK~~~~K~l~~eie 374 (391)
|++|||+++++|||+||++.+|||+||| ||+.|||.+++|.||.||+
T Consensus 647 Kd~EWR~~kRew~kiWReIEeKN~~ksLD~~g~sfK~rDKk~lstk~il~eid 699 (1163)
T COG5602 647 KDEEWRSCKREWNKIWREIEEKNYHKSLDHQGVSFKSRDKKILSTKNILEEID 699 (1163)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhHHhhhhhcccceeccccccchHHHHHHHhh
Confidence 9999999999999999999999999999 9999999999999999999
No 2
>smart00761 HDAC_interact Histone deacetylase (HDAC) interacting. This domain is found on transcriptional regulators. It forms interactions with histone deacetylases.
Probab=100.00 E-value=2.6e-46 Score=311.85 Aligned_cols=96 Identities=39% Similarity=0.642 Sum_probs=94.0
Q ss_pred cCcccCcccccCCcCCCCCCCCCCcccccccccCccccccCC-CCccchhhhhhchhHHHHhhcccchhhHHHHHHHHHH
Q 016325 178 KCKQVSPSYWRLPEYYWMPLASNRSEIGDQVLNDNLVCASTG-TERSSFKQRRRTKQEEVLFKCEDDRFELDLLLGWMHS 256 (391)
Q Consensus 178 ~c~~~gpSYr~LP~~~~~~~cSgR~~l~~~VLND~wVs~~~~-SEd~~f~~~rKnqyEE~Lfr~EDER~E~D~~ie~~~~ 256 (391)
+|++||||||+||++|+.++||||++||++||||+|||||+| |||++|++||||||||+||||||||||+||+|+++.+
T Consensus 1 ~c~~~gpSYr~Lpk~~~~~~cSgR~~l~~~VLND~wvsvps~~SED~~F~~~rKNqyEE~Lfr~EDeR~E~D~~ie~~~~ 80 (102)
T smart00761 1 NCERCGPSYRLLPKSEKQPKCSGRDELCKEVLNDTWVSHPTWASEDSGFVAHRKNQYEEALFRCEDERFELDMVIESNSS 80 (102)
T ss_pred CCcccCcchhhCCcccCCCCCCCccHHHHHHhCCceEeecCCcccccchhhhhccHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence 599999999999999999999999999999999999999865 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhccCc
Q 016325 257 AAENVEKLMIKIDDQNQ 273 (391)
Q Consensus 257 tI~~Le~l~~~i~~~~~ 273 (391)
||+.|++|+++|+.|++
T Consensus 81 ti~~le~l~~~~~~~~~ 97 (102)
T smart00761 81 TIKLLEEILNKIEDMSD 97 (102)
T ss_pred HHHHHHHHHHHHhcCCh
Confidence 99999999999999998
No 3
>PF08295 Sin3_corepress: Sin3 family co-repressor; InterPro: IPR013194 This domain is found on transcriptional regulators. It forms interactions with histone deacetylases [].
Probab=100.00 E-value=8.2e-45 Score=303.96 Aligned_cols=96 Identities=42% Similarity=0.651 Sum_probs=94.6
Q ss_pred cCcccCcccccCCcCCCCCCCCCCcccccccccCccccccCCCCccchhhhhhchhHHHHhhcccchhhHHHHHHHHHHH
Q 016325 178 KCKQVSPSYWRLPEYYWMPLASNRSEIGDQVLNDNLVCASTGTERSSFKQRRRTKQEEVLFKCEDDRFELDLLLGWMHSA 257 (391)
Q Consensus 178 ~c~~~gpSYr~LP~~~~~~~cSgR~~l~~~VLND~wVs~~~~SEd~~f~~~rKnqyEE~Lfr~EDER~E~D~~ie~~~~t 257 (391)
+|++||||||+||++|+.++||||++||++||||+|||||+||||++|++||||||||+||||||||||+||+|+++++|
T Consensus 1 ~c~~~gpSYr~LP~~~~~~~cSgR~~l~~~VLND~wvs~p~~sEd~~f~~~kKnqyEE~lf~~EDeR~E~D~~ie~~~~t 80 (101)
T PF08295_consen 1 NCERCGPSYRLLPKSYQNPPCSGRDELCWSVLNDTWVSVPSWSEDSSFKAMKKNQYEEALFRCEDERFELDMLIESNRST 80 (101)
T ss_pred CCCcCccchhhCCcccCCCCCCCCchhhhhhcCCEEEEeCCccccccccchhhhHHHHHHHHhhhhhHHHHHHHHHHHHH
Confidence 59999999999999999999999999999999999999998889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhccCc
Q 016325 258 AENVEKLMIKIDDQNQ 273 (391)
Q Consensus 258 I~~Le~l~~~i~~~~~ 273 (391)
|+.|++|+.+|+.|++
T Consensus 81 I~~Le~l~~~i~~~~~ 96 (101)
T PF08295_consen 81 IKLLEELQEKIQDMSP 96 (101)
T ss_pred HHHHHHHHHHHhcCCH
Confidence 9999999999999998
No 4
>KOG4204 consensus Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=99.80 E-value=1.6e-20 Score=178.77 Aligned_cols=193 Identities=19% Similarity=0.146 Sum_probs=141.5
Q ss_pred hHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccChHHHHHHchhccCcCCCccCCCCCC
Q 016325 43 LRGAAVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNVFVRNEADDEEDGAGGD 122 (391)
Q Consensus 43 l~~dAl~F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hpdLi~~F~~FLp~~~~~~~~~~G~~ 122 (391)
.++||++|+++||.+|++ +|++|.+||+||++|+.++||..+|+++|++||+||||||.|||.|||+++.+.-...+.-
T Consensus 18 t~~DAlsYl~~VK~~f~d-~p~kY~~FL~im~d~ka~~iD~~~vi~rv~eLfK~h~~Ll~gfN~fLP~~~~i~~~~~~~~ 96 (231)
T KOG4204|consen 18 TLDDALAYLKAVKEAFQD-EPEKYDEFLEIMKDFKAQRIDTPGVIARVKELLKGHPDLLLGFNTFLPPGYKITLSSEAKD 96 (231)
T ss_pred ChHHHHHHHHHHHHHHhc-ChHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHccCHHHHHHHHhhCcccceeccCccccc
Confidence 489999999999999988 6999999999999999999999999999999999999999999999999998763221100
Q ss_pred CCCCCCCCCchhhHHHHHHhhccccCChHHHHHHHHhhhhhcccccccccccccccCcccCcccccCCcCCCCCCCCCCc
Q 016325 123 SDHDDDDNHEPELKTEVAKLFGDEHGDLYEEFERYVAKCREQKHVIKSIQDLDLSKCKQVSPSYWRLPEYYWMPLASNRS 202 (391)
Q Consensus 123 ~~~~~dk~~~~e~~~ev~~lf~d~~~d~~~efer~~~~~~~~~~~~~p~~e~d~s~c~~~gpSYr~LP~~~~~~~cSgR~ 202 (391)
. . ....... +.+..-.-+. ......+. . ..|.+..-.|+.++..|+...
T Consensus 97 ~-~---~~~~~~~----------~~~~~~~~~~----~~~~~~~~-----~---~~~~~a~~fv~klk~rf~~~~----- 145 (231)
T KOG4204|consen 97 E-F---TIYGATS----------YLPSPKVAFH----EEILKLLE-----D---VEFDRAISFVNKLKTRFQGDD----- 145 (231)
T ss_pred c-c---ccccccc----------cCCCcccccc----chhhhhcc-----c---chHHHHHHHHHHHHHHhcCCH-----
Confidence 0 0 0000000 0000000000 00000000 0 344555667888888887664
Q ss_pred ccccccccCccccccCCCCccchhhhhhchhHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHHhcc
Q 016325 203 EIGDQVLNDNLVCASTGTERSSFKQRRRTKQEEVLFKCEDDRFELDLLLGWMHSAAENVEKLMIKIDDQ 271 (391)
Q Consensus 203 ~l~~~VLND~wVs~~~~SEd~~f~~~rKnqyEE~Lfr~EDER~E~D~~ie~~~~tI~~Le~l~~~i~~~ 271 (391)
+|.+.-|......+|+..++.--+...+.-++++||.+.|++..+-....+......+...+..+
T Consensus 146 ----~v~~s~l~il~~y~~~~ks~~e~~~eV~~L~~~~~DL~~ef~~~lp~~~~~~~~~~~~~~~~~~~ 210 (231)
T KOG4204|consen 146 ----HVYKSFLEILRMYQEGNKSVSEVYQEVEALLQGHEDLLEEFSHFLPTDPATGSLNQKLRSVLTVR 210 (231)
T ss_pred ----HHHHHHHHHHHHHhhccchHHHHHHHHHHHHccCHHHHHHHHhhccCCcccccchhhhhhhhHhh
Confidence 89999999998889998888888999999999999999999998888877777776666655443
No 5
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=99.55 E-value=7.6e-15 Score=106.59 Aligned_cols=47 Identities=34% Similarity=0.705 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccChHHHHHHchhcc
Q 016325 63 DGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNVFVR 109 (391)
Q Consensus 63 p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hpdLi~~F~~FLp 109 (391)
|++|++||++|++|++++++..+|+++|+.||++||||+.+|+.|||
T Consensus 1 p~~Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~hpdLl~~F~~FlP 47 (47)
T PF02671_consen 1 PEVYNEFLKILNDYKKGRISRSEVIEEVSELLRGHPDLLEEFNRFLP 47 (47)
T ss_dssp HHHHHHHHHHHHHHHCTCSCHHHHHHHHHHHTTT-HHHHHHHHHHSS
T ss_pred ChHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHccCHHHHHHHHhhCc
Confidence 78999999999999999999999999999999999999999999998
No 6
>COG5602 SIN3 Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=98.99 E-value=9.7e-10 Score=118.69 Aligned_cols=69 Identities=17% Similarity=0.389 Sum_probs=65.7
Q ss_pred HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccChHHHHHHchhccCcCC
Q 016325 44 RGAAVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNVFVRNEAD 113 (391)
Q Consensus 44 ~~dAl~F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hpdLi~~F~~FLp~~~~ 113 (391)
.+.|+.|+++||.||.++ |+.|..||++|+.|+....++.+|+.+|+.||..+|||+++|+.|||...-
T Consensus 269 ~nqAI~~vnkVK~r~~~~-pe~y~~fl~~Lrtyq~~qr~i~ev~~~Vt~lfa~~PdLleeFk~FLPd~~~ 337 (1163)
T COG5602 269 FNQAIIFVNKVKVRFQNN-PEMYYDFLDSLRTYQMKQRSIQEVYARVTKLFAEAPDLLEEFKEFLPDSSV 337 (1163)
T ss_pred hhHHHHHHHHHHHhcCCC-chhHHHHHHHHHHHHhhhccHHHHHHHHHHHHhhChHHHHHHHHhCccccc
Confidence 689999999999999775 999999999999999999999999999999999999999999999999643
No 7
>KOG4204 consensus Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics]
Probab=98.90 E-value=3.2e-09 Score=101.58 Aligned_cols=70 Identities=21% Similarity=0.524 Sum_probs=65.4
Q ss_pred hHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccChHHHHHHchhccCcCC
Q 016325 43 LRGAAVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNVFVRNEAD 113 (391)
Q Consensus 43 l~~dAl~F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hpdLi~~F~~FLp~~~~ 113 (391)
..+.|.+|+++||+||+++ +++|..||.+|++|+.+..+..+|+..|..||++|+||+.+|..|||....
T Consensus 126 ~~~~a~~fv~klk~rf~~~-~~v~~s~l~il~~y~~~~ks~~e~~~eV~~L~~~~~DL~~ef~~~lp~~~~ 195 (231)
T KOG4204|consen 126 EFDRAISFVNKLKTRFQGD-DHVYKSFLEILRMYQEGNKSVSEVYQEVEALLQGHEDLLEEFSHFLPTDPA 195 (231)
T ss_pred hHHHHHHHHHHHHHHhcCC-HHHHHHHHHHHHHHhhccchHHHHHHHHHHHHccCHHHHHHHHhhccCCcc
Confidence 3678999999999999764 799999999999999999999999999999999999999999999998754
No 8
>cd07354 HN_L-delphilin-R1_like First harmonin_N_like domain (repeat 1) of L-delphilin, and related domains. This subgroup contains the first of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin, isoform 1), and related domains. Delphilin is a scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. The N-terminus of L-delphilin contains this harmonin_N_like domain preceded by a postsynaptic density-95/discs-large/ZO-1 (PDZ) protein-binding domain, PDZ1. L-delphilin, in common with the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta) has a second harmonin_N_like domain (not belonging to this subgroup) and a second PDZ domain, PDZ2. This first harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=83.45 E-value=5.2 Score=32.58 Aligned_cols=67 Identities=15% Similarity=0.251 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhc--cChHHHHHHchhccCcCC
Q 016325 45 GAAVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFK--GHDDLIHKYNVFVRNEAD 113 (391)
Q Consensus 45 ~dAl~F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~--~hpdLi~~F~~FLp~~~~ 113 (391)
..|..|..+|...+.+ +|..=..-...|+.|.++. +...++..+..+|. .|.-|++.-..|+|....
T Consensus 3 ~kA~eF~~Kvd~iL~~-dp~~Ke~l~~aLk~Ya~~k-~vd~l~~aL~~~L~~e~~~~Lld~IR~fIP~KHr 71 (80)
T cd07354 3 RKAQEFSRKVDAILGD-DPVKKEQVFAALKQYAADK-NVDCLVWALCGLLQTEAHKKLLDEIRIFIPKKHR 71 (80)
T ss_pred hHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHc-CHHHHHHHHHHHhCcHHHHHHHHHhHhcCCchhH
Confidence 4688999999999965 6999999999999999876 67888888888884 455788888888887654
No 9
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=55.33 E-value=37 Score=28.98 Aligned_cols=50 Identities=18% Similarity=0.232 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccChH
Q 016325 44 RGAAVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDD 99 (391)
Q Consensus 44 ~~dAl~F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hpd 99 (391)
..+...|| |+.+ + ++.=..|+++|..|+++.|+...++..++.+...+++
T Consensus 55 l~Hi~Gyf---k~~l-s--~~EK~~~~~~i~~yr~g~i~l~~~l~~L~~~~~ry~~ 104 (117)
T PF08349_consen 55 LQHIFGYF---KKKL-S--SEEKQHFLDLIEDYREGKIPLSVPLTLLKHLARRYPD 104 (117)
T ss_pred HHHHHHHH---HHhC-C--HHHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHCCC
Confidence 35555554 4555 2 3456779999999999999999999999999988874
No 10
>PF15011 CK2S: Casein Kinase 2 substrate
Probab=49.69 E-value=49 Score=30.38 Aligned_cols=89 Identities=16% Similarity=0.159 Sum_probs=52.0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcchhhcccccccCCcchhhHHHHHHHHhcchHHHHHHHhhCCCcchhH
Q 016325 241 EDDRFELDLLLGWMHSAAENVEKLMIKIDDQNQDDEKSSKIEIEGHLGISDLRCIERLYAEHGLDVIDNLHKNPETALPV 320 (391)
Q Consensus 241 EDER~E~D~~ie~~~~tI~~Le~l~~~i~~~~~~~~~~~~~~l~~~l~~i~~r~I~riYG~~g~evl~~l~~nP~~alPv 320 (391)
|+++=-.|=.......-+..|..|.+++.....-.....+ | +.+..|..|...+++ .++=.
T Consensus 11 ~~~~~~W~~~~~~~~~~l~sl~nL~eqL~al~~~~~~~~p--L-~~fpdl~~rL~~Kq~----------------~ale~ 71 (168)
T PF15011_consen 11 EEQMEKWDSALSRCLPLLSSLANLAEQLQALQNVKNYGTP--L-RSFPDLQERLRRKQL----------------EALET 71 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCc--c-cccccHHHHHHHHHH----------------HHHHH
Confidence 3333334444444455555555665555443321111111 1 123344445555444 45678
Q ss_pred hhhhHHHHHHHHHHHHHHhhHHHHHHHH
Q 016325 321 ILKSLKQKVEELVERRSDCNKIWAHVCA 348 (391)
Q Consensus 321 VL~RLkqK~eEw~~~r~~~nk~Wrev~~ 348 (391)
|+.+|+.+.++....+..+.+.++++..
T Consensus 72 vl~~L~e~l~~l~~v~~~l~~~~~~~~~ 99 (168)
T PF15011_consen 72 VLAKLRETLEELQKVRDSLSRQVRDVFQ 99 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999988754
No 11
>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=40.83 E-value=1.4e+02 Score=24.17 Aligned_cols=64 Identities=9% Similarity=0.127 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccCh--HHHHHHchhccCcC
Q 016325 45 GAAVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHD--DLIHKYNVFVRNEA 112 (391)
Q Consensus 45 ~dAl~F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hp--dLi~~F~~FLp~~~ 112 (391)
..|-.|-.+|..-+ + ++ .-..|...|+.|.++. ++.+++.-+..+|..+. .|+.+-..++|+..
T Consensus 3 ~~~r~f~~q~~~LL-~-~~-Er~~~~~~L~~Y~~~~-~Vd~LV~~L~~vLdtPaK~~Ll~~iR~lIp~~d 68 (78)
T cd07347 3 VQAREFSQQVDHLL-T-DA-EREQVTRALERYHQER-NVDDLVRDLYLVLDTPAKLPLLQFLRQVIPPKD 68 (78)
T ss_pred hHHHHHHHHHHHHC-C-HH-HHHHHHHHHHHHHhcC-CHHHHHHHHHHHcCcHhHHHHHHHHHHHcCHHH
Confidence 45678999999999 4 23 4668999999999999 99999999999886544 56666666666543
No 12
>TIGR03036 trp_2_3_diox tryptophan 2,3-dioxygenase. Members of this family are tryptophan 2,3-dioxygenase, as confirmed by several experimental characterizations, and by conserved operon structure for many of the other members. This enzyme represents the first of a two-step degradation to L-kynurenine, and a three-step pathway (via kynurenine) to anthranilate plus alanine.
Probab=39.47 E-value=73 Score=31.58 Aligned_cols=71 Identities=14% Similarity=0.193 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHhccCcchhhccccc--ccCCcc--hhhHHHHHHHHhcchHHHHHHHhhCCCcchhHhhhhHHHHH
Q 016325 254 MHSAAENVEKLMIKIDDQNQDDEKSSKIE--IEGHLG--ISDLRCIERLYAEHGLDVIDNLHKNPETALPVILKSLKQKV 329 (391)
Q Consensus 254 ~~~tI~~Le~l~~~i~~~~~~~~~~~~~~--l~~~l~--~i~~r~I~riYG~~g~evl~~l~~nP~~alPvVL~RLkqK~ 329 (391)
.....+.|..-..-+..|+| .+...|+ |++.+| |...|-|+-+=|.+-..++. |....|-+..+|.+-.
T Consensus 73 v~~i~~~L~~~~~vL~tMtp--~df~~FR~~Lg~aSGfQS~qyR~iE~~lG~k~~~~l~-----~~~~~p~~~~~L~~~l 145 (264)
T TIGR03036 73 VSRIQEQLNQAWDVLATMTP--AEYSEFRDALGQSSGFQSYQYREIEFLLGNKNAAMLR-----PHEHDPELHAELEAAL 145 (264)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHHhCCcchhhhHHHHHHHHHhCCCcHHHhc-----cccCChHHHHHHHHHh
Confidence 33334444444555568888 6666665 344444 89999999999977766665 4555666666666554
Q ss_pred HH
Q 016325 330 EE 331 (391)
Q Consensus 330 eE 331 (391)
.+
T Consensus 146 ~~ 147 (264)
T TIGR03036 146 HA 147 (264)
T ss_pred cC
Confidence 43
No 13
>PRK10167 hypothetical protein; Provisional
Probab=38.68 E-value=35 Score=31.52 Aligned_cols=50 Identities=6% Similarity=0.074 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccChH
Q 016325 44 RGAAVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDD 99 (391)
Q Consensus 44 ~~dAl~F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hpd 99 (391)
..+...||. +.+ + ++.=.+|++++..|+++.++....+..+..++..||+
T Consensus 96 L~Hi~GYFK---k~L-s--~~EKq~l~~lI~~Yr~g~vpl~vpltlL~h~~~~y~~ 145 (169)
T PRK10167 96 LMHVQGYFR---PHI-D--STERQQLAALIDSYRRGEQPLLAPLMRIKHYMALYPD 145 (169)
T ss_pred HHHHHHHHH---hhC-C--HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHCCc
Confidence 355555553 344 2 3344589999999999999999999999999999984
No 14
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=37.85 E-value=65 Score=24.55 Aligned_cols=43 Identities=16% Similarity=0.099 Sum_probs=33.7
Q ss_pred HHHHHHHHhcchHHHHHHHhhCCCcchhHhhhhHHHHHHHHHH
Q 016325 292 LRCIERLYAEHGLDVIDNLHKNPETALPVILKSLKQKVEELVE 334 (391)
Q Consensus 292 ~r~I~riYG~~g~evl~~l~~nP~~alPvVL~RLkqK~eEw~~ 334 (391)
..+|+..||+-...|.+.|..+...++|.|.++.+=...+-+.
T Consensus 4 ~~ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~ 46 (62)
T PF08221_consen 4 TLIIEEHFGEIVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKK 46 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHH
T ss_pred HHHHHHHcChHHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHH
Confidence 4578999999999999999999999999999987754444443
No 15
>PF00611 FCH: Fes/CIP4, and EFC/F-BAR homology domain; InterPro: IPR001060 The FCH domain is a short conserved region of around 60 amino acids first described as a region of homology between FER and CIP4 proteins []. Many proteins containing an FCH domain are involved in the regulation of cytoskeletal rearrangements, vesicular transport and endocytosis. In the CIP4 protein the FCH domain binds to microtubules []. The FCH domain is always found N-terminally and is followed by a coiled-coil region. Proteins containing an FCH domain can be divided in 3 classes []: A subfamily of protein kinases usually associated with an SH2 domain: Fps/fes (Fujimani poultry sarcoma/feline sarcoma) proto-oncogenes. They are non-receptor protein-tyrosine kinases preferentially expressed in myeloid lineage. The viral oncogene has an unregulated kinase activity which abrogates the need for cytokines and influences differentiation of haematopoietic progenitor cells. Fes related protein (fer). It is an ubiquitously expressed homologue of Fes. Adaptor proteins usually associated with a C-terminal SH3 domain: Schizosaccharomyces pombe CDC15 protein. It mediates cytoskeletal rearrangements required for cytokinesis. It is essential for viability. CD2 cytoplasmic domain binding protein. Mammalian Cdc42-interacting protein 4 (CIP4). It may act as a link between Cdc42 signaling and regulation of the actin cytoskeleton. Mammalian PACSIN proteins. A family of cytoplasmic phosphoproteins playing a role in vesicle formation and transport. A subfamily of Rho-GAP proteins: Mammalian RhoGAP4 proteins. They may down-regulate Rho-like GTPases in hematopoietic cells. Yeast hypothetical protein YBR260C. Caenorhabditis elegans hypothetical protein ZK669.1. ; PDB: 2EFK_A 2EFL_A 2X3W_A 2X3X_C 2X3V_C 3I2W_A 3ABH_B 3Q0K_B 3HAJ_A 3ACO_B ....
Probab=35.39 E-value=2.1e+02 Score=22.18 Aligned_cols=39 Identities=23% Similarity=0.141 Sum_probs=32.2
Q ss_pred CcchhHhhhhHHHHHHHHHHHHHHhhHHHHHHHHHhhhhhh
Q 016325 315 ETALPVILKSLKQKVEELVERRSDCNKIWAHVCAKNHDKLQ 355 (391)
Q Consensus 315 ~~alPvVL~RLkqK~eEw~~~r~~~nk~Wrev~~kny~kSL 355 (391)
...+++|..|+++-...-.....-+.+ |..+++.|.|+|
T Consensus 8 ~~g~~~l~~~~~~~~~~~~~l~~~~ke--Ra~lE~~Yak~L 46 (91)
T PF00611_consen 8 WDGFEVLFKRLKQGIKLLEELASFFKE--RASLEEEYAKSL 46 (91)
T ss_dssp TCTTHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Confidence 467899999999988877777776665 568899999999
No 16
>PF12083 DUF3560: Domain of unknown function (DUF3560); InterPro: IPR021944 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif.
Probab=33.70 E-value=85 Score=27.71 Aligned_cols=64 Identities=19% Similarity=0.237 Sum_probs=46.1
Q ss_pred cccccccCCcchhhHHHHHHHHh--cchHHHHHHH----------h-hCCCcchhHhhhhHHHHHHHHHHHHHHhhH
Q 016325 278 SSKIEIEGHLGISDLRCIERLYA--EHGLDVIDNL----------H-KNPETALPVILKSLKQKVEELVERRSDCNK 341 (391)
Q Consensus 278 ~~~~~l~~~l~~i~~r~I~riYG--~~g~evl~~l----------~-~nP~~alPvVL~RLkqK~eEw~~~r~~~nk 341 (391)
..||.++.++..=+.|.++|+.. +.+.+..+.- - .--..-.|.+|.||+.++.+.+..|+.+..
T Consensus 42 GQPIlVGHHSE~R~Rr~~eR~~~~m~kav~~~~kA~y~~~rA~aa~~~~i~~~~Pda~~ri~~~la~~r~~q~~mk~ 118 (126)
T PF12083_consen 42 GQPILVGHHSEKRHRRYRERIHNRMGKAVEAMDKAEYYEQRAAAAGRTAISSDDPDALRRIKKKLAELRASQRRMKA 118 (126)
T ss_pred CCCeeccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhccChHHHHHHHHHHHHHHHHHHHHHH
Confidence 56788888888899999999887 4444332211 1 112344678899999999999999998753
No 17
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=28.17 E-value=74 Score=24.39 Aligned_cols=59 Identities=14% Similarity=0.262 Sum_probs=48.8
Q ss_pred HHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhccChHHHHHHchhc
Q 016325 50 FLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNVFV 108 (391)
Q Consensus 50 F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~~hpdLi~~F~~FL 108 (391)
|..++...|.+..-..|..+.+-|..|.+--.++..++..+..|=+.+.+|..=.+.+|
T Consensus 2 yW~~~~~vip~~~~~~W~~L~~~l~rY~~vL~~R~~l~~e~~~L~~qN~eLr~lLkqYl 60 (60)
T PF14775_consen 2 YWERLANVIPDEKIRLWDALENFLKRYNKVLLDRAALIQEKESLEQQNEELRSLLKQYL 60 (60)
T ss_pred HHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 66777777765556789999999999999999999999999999999988877665543
No 18
>KOG4424 consensus Predicted Rho/Rac guanine nucleotide exchange factor/faciogenital dysplasia protein 3 [Signal transduction mechanisms]
Probab=27.42 E-value=3.5e+02 Score=29.86 Aligned_cols=74 Identities=19% Similarity=0.243 Sum_probs=49.5
Q ss_pred hhhHHHHHHHHhc-------chHHHHHHHhhCCCcchhHhhhhHHHHHHHHHHHHHHhhHHHHHHHHHhhhhhh--hhhh
Q 016325 289 ISDLRCIERLYAE-------HGLDVIDNLHKNPETALPVILKSLKQKVEELVERRSDCNKIWAHVCAKNHDKLQ--EMQR 359 (391)
Q Consensus 289 ~i~~r~I~riYG~-------~g~evl~~l~~nP~~alPvVL~RLkqK~eEw~~~r~~~nk~Wrev~~kny~kSL--fK~~ 359 (391)
.|.-.+|.+|+|+ ||.-++..+.+.+ +-+--....=+-|.+. .|.|||-+|+ |...
T Consensus 101 ~~~~~~v~~lf~nIssi~~fh~qfllp~l~~r~--------------Iadv~qKlAPFLKmYs-eY~knydrA~~L~~~l 165 (623)
T KOG4424|consen 101 SIPADVITGLFGNISSIHNFHGQFLLPELEKRI--------------IADVFQKLAPFLKMYS-EYAKNYDRALKLFQTL 165 (623)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHhhhHHHhhH--------------HHHHHHHhhhHHHHHH-HHHhcchhHHHHHHHH
Confidence 4566677777774 4444544444444 3333334445666665 4899999999 9888
Q ss_pred hhcccchhhhHHHHHHhh
Q 016325 360 ELKNSKREDLVAKEEKLQ 377 (391)
Q Consensus 360 DkK~~~~K~l~~eie~~~ 377 (391)
-.|+---+..|.|||+.-
T Consensus 166 t~rsp~F~~vl~~Iek~~ 183 (623)
T KOG4424|consen 166 TSRSPQFRKVVEEIEKQP 183 (623)
T ss_pred HhhChHHHHHHHHHhhch
Confidence 888888888888888643
No 19
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=26.03 E-value=99 Score=27.98 Aligned_cols=47 Identities=19% Similarity=-0.045 Sum_probs=33.5
Q ss_pred hhhHHHHHHHHhcchHHHHHHHhhCCCcchhHhhhhHHHHHHHHHHH
Q 016325 289 ISDLRCIERLYAEHGLDVIDNLHKNPETALPVILKSLKQKVEELVER 335 (391)
Q Consensus 289 ~i~~r~I~riYG~~g~evl~~l~~nP~~alPvVL~RLkqK~eEw~~~ 335 (391)
++.+..+..+||+.+..|+++|..+-..+.=-|-.-|+-+..+.|+.
T Consensus 2 ~~~~~~~~~~~g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~ 48 (158)
T TIGR00373 2 ELLNEVVGRAAEEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKA 48 (158)
T ss_pred hHHHHHHHHHcChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHH
Confidence 34567889999999999999998776666555555555555555443
No 20
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=25.57 E-value=1.9e+02 Score=22.87 Aligned_cols=43 Identities=14% Similarity=0.304 Sum_probs=35.3
Q ss_pred HHHHHHHHhccCChHHHHHHHHHHHHhhcCCCChhhHHHHHHHHhc
Q 016325 50 FLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFK 95 (391)
Q Consensus 50 F~~kVK~rf~~~~p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf~ 95 (391)
-|..++..+ .|+.-..-.+....|+++.|++.+++..+..+-|
T Consensus 14 L~~~l~~~l---~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVG 56 (70)
T PF12174_consen 14 LFSALSKHL---PPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVG 56 (70)
T ss_pred HHHHHHHHC---CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 466677777 2567777777888899999999999999999887
No 21
>PRK15326 type III secretion system needle complex protein PrgI; Provisional
Probab=24.89 E-value=1.3e+02 Score=24.52 Aligned_cols=42 Identities=21% Similarity=0.385 Sum_probs=30.5
Q ss_pred hHHHHHHHhhCCCcchhHhhhhHHHHHHHHHHHHHH---hhHHHHHH
Q 016325 303 GLDVIDNLHKNPETALPVILKSLKQKVEELVERRSD---CNKIWAHV 346 (391)
Q Consensus 303 g~evl~~l~~nP~~alPvVL~RLkqK~eEw~~~r~~---~nk~Wrev 346 (391)
-.+.++.|..+|. =|++|..+..|..||.-+|.. .-|.-+++
T Consensus 27 l~~Al~~l~~~pd--nP~~LA~~Qa~l~eyn~~RNaQSn~iKa~KD~ 71 (80)
T PRK15326 27 VTEALDKLAAKPS--DPALLAAYQSKLSEYNLYRNAQSNTVKVFKDI 71 (80)
T ss_pred HHHHHHHhhcCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456778878876 499999999999999876653 33444443
No 22
>PF11537 DUF3227: Protein of unknown function (DUF3227); InterPro: IPR021609 This archaeal family of proteins has no known function. ; PDB: 2P9X_C.
Probab=23.92 E-value=1.3e+02 Score=25.62 Aligned_cols=27 Identities=11% Similarity=0.158 Sum_probs=21.3
Q ss_pred hhhHHHHHHHHhcchHHHHHHHhhCCC
Q 016325 289 ISDLRCIERLYAEHGLDVIDNLHKNPE 315 (391)
Q Consensus 289 ~i~~r~I~riYG~~g~evl~~l~~nP~ 315 (391)
.-+++++.++||+.+.+++..+.-++.
T Consensus 47 ~~F~~avsklfGe~sA~l~~~~ii~~l 73 (102)
T PF11537_consen 47 KKFYEAVSKLFGEYSARLFEMMIINEL 73 (102)
T ss_dssp HHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 468999999999999999987765543
No 23
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=21.28 E-value=3.1e+02 Score=24.01 Aligned_cols=51 Identities=12% Similarity=0.188 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHhccCC-hHHHHHHHHHHHHhhcCCCChhhHHHHHHHHh
Q 016325 44 RGAAVAFLKEMRKRFRKQH-DGIFVRFCQLLSDFTKSKIDRDSLGLEVKELF 94 (391)
Q Consensus 44 ~~dAl~F~~kVK~rf~~~~-p~~Y~eFLkiL~~y~~~~I~~~ev~~~V~~Lf 94 (391)
.+.|..+.+.++.+|.+.. ....-+.-.-|...+++..++.+.+.+++.|-
T Consensus 81 ~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l~~~kq~~~sv~ey~~~lk~l~ 132 (152)
T PF14244_consen 81 CETAKEIWDALKERFSQKSNASRVFQLRNELHSLKQGDKSVTEYFNKLKSLW 132 (152)
T ss_pred hhhHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHh
Confidence 5788999999999997554 34555677788888899999999998888854
No 24
>PF14483 Cut8_M: Cut8 dimerisation domain; PDB: 3Q5W_A 3Q5X_A.
Probab=21.17 E-value=1.2e+02 Score=21.20 Aligned_cols=31 Identities=16% Similarity=0.329 Sum_probs=24.4
Q ss_pred CCCChhhHHHHHHHHhccChHHHHHHchhcc
Q 016325 79 SKIDRDSLGLEVKELFKGHDDLIHKYNVFVR 109 (391)
Q Consensus 79 ~~I~~~ev~~~V~~Lf~~hpdLi~~F~~FLp 109 (391)
+..|...+...+..+...||++-.+...-.|
T Consensus 8 E~Ld~~qL~~lL~~l~~~HPei~~~i~~~~P 38 (38)
T PF14483_consen 8 ETLDKDQLQSLLQSLCERHPEIQQEIRSIAP 38 (38)
T ss_dssp TTS-HHHHHHHHHHHHHHSTHHHHHHHTTS-
T ss_pred HHcCHHHHHHHHHHHHHhChhHHHHHHhhCc
Confidence 4568889999999999999999888765544
Done!