Query psy16819
Match_columns 289
No_of_seqs 295 out of 1340
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 22:52:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16819hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00059 FH Forkhead (FH), also 100.0 2.5E-34 5.4E-39 222.9 6.6 78 110-195 1-78 (78)
2 smart00339 FH FORKHEAD. FORKHE 100.0 2.7E-32 5.8E-37 216.2 6.8 85 110-202 1-85 (89)
3 PF00250 Fork_head: Fork head 100.0 4E-32 8.7E-37 217.9 0.5 87 110-204 1-87 (96)
4 KOG3563|consensus 100.0 2E-29 4.4E-34 239.9 4.9 88 107-202 170-257 (454)
5 KOG2294|consensus 99.9 1.2E-28 2.5E-33 239.3 -1.0 88 106-200 126-214 (454)
6 KOG3562|consensus 99.9 3.2E-26 7E-31 206.7 3.9 88 107-202 10-97 (277)
7 COG5025 Transcription factor o 99.9 5E-24 1.1E-28 216.4 1.8 170 106-288 82-387 (610)
8 cd00059 FH Forkhead (FH), also 99.8 3.9E-21 8.4E-26 149.2 4.7 51 233-288 1-51 (78)
9 KOG4385|consensus 99.8 8.6E-21 1.9E-25 186.2 -1.1 89 106-207 364-452 (581)
10 smart00339 FH FORKHEAD. FORKHE 99.8 1.2E-19 2.5E-24 144.0 4.7 52 233-289 1-52 (89)
11 PF00250 Fork_head: Fork head 99.7 1.8E-19 3.9E-24 144.7 -0.6 51 233-288 1-51 (96)
12 KOG3563|consensus 99.7 1.9E-18 4.1E-23 165.2 2.9 63 222-289 162-224 (454)
13 COG5025 Transcription factor o 99.7 1.1E-17 2.3E-22 170.5 5.3 95 100-202 327-421 (610)
14 KOG2294|consensus 99.6 2.9E-17 6.4E-22 159.7 -2.3 56 229-288 126-182 (454)
15 KOG3562|consensus 99.5 4.1E-15 8.9E-20 135.0 1.6 58 227-289 7-64 (277)
16 KOG4385|consensus 99.3 1.1E-12 2.4E-17 129.6 1.2 56 228-288 363-418 (581)
17 PF00538 Linker_histone: linke 92.4 0.16 3.4E-06 38.8 3.5 33 114-146 4-37 (77)
18 smart00526 H15 Domain in histo 91.7 0.37 8E-06 35.6 4.7 32 114-145 6-38 (66)
19 cd00073 H15 linker histone 1 a 89.5 0.52 1.1E-05 37.0 4.0 33 114-146 6-39 (88)
20 smart00526 H15 Domain in histo 87.7 0.79 1.7E-05 33.8 3.7 33 237-269 6-39 (66)
21 PF00538 Linker_histone: linke 87.7 0.57 1.2E-05 35.7 3.0 33 237-269 4-37 (77)
22 KOG4012|consensus 82.2 1.3 2.8E-05 41.7 3.2 40 111-150 43-83 (243)
23 cd00073 H15 linker histone 1 a 76.0 3.6 7.9E-05 32.2 3.6 33 237-269 6-39 (88)
24 PF14338 Mrr_N: Mrr N-terminal 60.9 2.9 6.2E-05 32.7 0.1 82 114-203 1-89 (92)
25 PF05066 HARE-HTH: HB1, ASXL, 59.5 7.5 0.00016 28.9 2.2 60 113-179 1-62 (72)
26 COG2958 Uncharacterized protei 52.4 18 0.00039 34.8 3.8 66 113-182 5-77 (307)
27 KOG4012|consensus 41.3 27 0.00059 32.9 3.2 37 235-271 44-81 (243)
28 PF12872 OST-HTH: OST-HTH/LOTU 38.2 40 0.00086 24.6 3.1 38 114-151 5-44 (74)
29 cd05071 PTKc_Src Catalytic dom 36.2 38 0.00082 29.8 3.2 34 112-145 229-262 (262)
30 cd06649 PKc_MEK2 Catalytic dom 32.6 24 0.00053 32.6 1.5 47 114-167 276-322 (331)
31 smart00258 SAND SAND domain. 32.5 18 0.00039 28.1 0.5 14 155-168 48-61 (73)
32 cd08229 STKc_Nek7 Catalytic do 30.5 53 0.0011 28.6 3.2 30 114-143 236-265 (267)
33 cd05051 PTKc_DDR Catalytic dom 28.9 50 0.0011 29.3 2.8 28 114-141 268-295 (296)
34 cd05040 PTKc_Ack_like Catalyti 28.7 45 0.00097 28.9 2.4 30 112-141 227-256 (257)
35 cd05072 PTKc_Lyn Catalytic dom 28.5 56 0.0012 28.4 3.0 31 112-142 230-260 (261)
36 PF13565 HTH_32: Homeodomain-l 27.7 1.4E+02 0.0031 21.7 4.7 27 117-145 37-63 (77)
37 PF01342 SAND: SAND domain; I 27.4 21 0.00047 27.9 0.1 14 154-167 56-69 (82)
38 cd05061 PTKc_InsR Catalytic do 27.3 72 0.0016 28.4 3.5 38 112-149 247-285 (288)
39 cd05041 PTKc_Fes_like Catalyti 27.2 61 0.0013 27.9 2.9 29 113-141 222-250 (251)
40 cd05034 PTKc_Src_like Catalyti 26.9 66 0.0014 27.9 3.1 31 112-142 230-260 (261)
41 PHA02988 hypothetical protein; 26.5 71 0.0015 28.9 3.3 36 112-147 248-283 (283)
42 cd05060 PTKc_Syk_like Catalyti 26.4 75 0.0016 27.6 3.4 31 114-144 226-256 (257)
43 cd05048 PTKc_Ror Catalytic Dom 25.4 60 0.0013 28.6 2.6 31 112-142 252-282 (283)
44 cd05044 PTKc_c-ros Catalytic d 25.4 65 0.0014 28.1 2.8 29 113-141 240-268 (269)
45 cd05115 PTKc_Zap-70 Catalytic 24.3 70 0.0015 28.1 2.8 32 113-144 225-256 (257)
46 cd05036 PTKc_ALK_LTK Catalytic 23.1 67 0.0015 28.4 2.5 29 113-141 248-276 (277)
47 cd05096 PTKc_DDR1 Catalytic do 23.1 69 0.0015 28.8 2.6 30 112-141 274-303 (304)
48 cd05094 PTKc_TrkC Catalytic do 22.8 79 0.0017 28.3 2.9 31 113-143 252-282 (291)
49 cd06609 STKc_MST3_like Catalyt 22.0 82 0.0018 27.6 2.8 33 114-151 226-258 (274)
50 KOG0592|consensus 22.0 73 0.0016 33.7 2.7 35 115-161 314-348 (604)
51 PF12872 OST-HTH: OST-HTH/LOTU 21.4 82 0.0018 22.9 2.3 37 238-274 6-44 (74)
52 PRK09462 fur ferric uptake reg 21.4 1.3E+02 0.0028 25.3 3.8 29 117-145 20-48 (148)
53 cd05045 PTKc_RET Catalytic dom 21.4 88 0.0019 27.8 2.9 32 113-144 256-287 (290)
54 cd07860 STKc_CDK2_3 Catalytic 20.6 61 0.0013 28.6 1.7 23 116-138 258-280 (284)
55 cd06610 STKc_OSR1_SPAK Catalyt 20.4 74 0.0016 27.4 2.2 25 114-138 239-263 (267)
56 cd05038 PTKc_Jak_rpt2 Catalyti 20.2 1.1E+02 0.0024 26.7 3.3 30 113-142 253-282 (284)
57 cd05067 PTKc_Lck_Blk Catalytic 20.0 99 0.0021 26.9 2.9 31 112-142 229-259 (260)
No 1
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=100.00 E-value=2.5e-34 Score=222.94 Aligned_cols=78 Identities=45% Similarity=0.738 Sum_probs=75.8
Q ss_pred CCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCCc
Q psy16819 110 WGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPTSAKLE 189 (289)
Q Consensus 110 kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~~~g~g 189 (289)
||++||++||++||+++|+++|||+|||+||+++||||+.++ .|||||||||| |+|+||+|+++..+.+|+|
T Consensus 1 kP~~sY~~LI~~Ai~~sp~~~lTL~eIy~~I~~~~pyyr~~~-----~gWknSIRHnL---S~n~~F~kv~r~~~~~gkg 72 (78)
T cd00059 1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAP-----AGWQNSIRHNL---SLNKCFVKVPREPDEPGKG 72 (78)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCCccccCC-----CCCccceeEec---ccccceEECCCCCCCCCCC
Confidence 799999999999999999999999999999999999999986 89999999999 9999999999999999999
Q ss_pred cccccc
Q psy16819 190 DFETLG 195 (289)
Q Consensus 190 ~~w~v~ 195 (289)
+||+|+
T Consensus 73 ~~W~i~ 78 (78)
T cd00059 73 SYWTLD 78 (78)
T ss_pred CeeeeC
Confidence 999986
No 2
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=99.97 E-value=2.7e-32 Score=216.21 Aligned_cols=85 Identities=36% Similarity=0.635 Sum_probs=80.9
Q ss_pred CCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCCc
Q psy16819 110 WGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPTSAKLE 189 (289)
Q Consensus 110 kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~~~g~g 189 (289)
||++||++||++||+++|+++|||+|||+||+++||||+.+. .|||||||||| |+|+||+|+++..+.+|+|
T Consensus 1 kP~~sY~~lI~~ai~~sp~~~ltl~~Iy~~I~~~~pyy~~~~-----~~WknSIRHnL---S~n~~F~kv~~~~~~~gkg 72 (89)
T smart00339 1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENR-----AGWQNSIRHNL---SLNDCFVKVPREGDRPGKG 72 (89)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCchhhcCc-----ccccccccccc---chhhceeecCcCCCCCCCC
Confidence 799999999999999999999999999999999999999987 69999999999 9999999999998888999
Q ss_pred ccccccchhHhhh
Q psy16819 190 DFETLGGELSALL 202 (289)
Q Consensus 190 ~~w~v~ge~sal~ 202 (289)
+||+|+++...++
T Consensus 73 ~~W~i~~~~~~~~ 85 (89)
T smart00339 73 SYWTLDPDAENMF 85 (89)
T ss_pred CEEEECccHHHHH
Confidence 9999999987643
No 3
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=99.97 E-value=4e-32 Score=217.85 Aligned_cols=87 Identities=38% Similarity=0.651 Sum_probs=79.7
Q ss_pred CCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCCc
Q psy16819 110 WGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPTSAKLE 189 (289)
Q Consensus 110 kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~~~g~g 189 (289)
||+|||++||++||+++|+++|||+|||+||+++||||+.+. .|||||||||| |+|+||+|+++..+..|+|
T Consensus 1 KPp~sY~~LI~~Ai~~sp~~~Ltl~eIy~~i~~~~pyyr~~~-----~~WknSIRHnL---S~~~~F~kv~~~~~~~gkg 72 (96)
T PF00250_consen 1 KPPYSYATLIAMAILSSPDKRLTLSEIYEWIEENFPYYRDAS-----KGWKNSIRHNL---SLNKCFVKVPRDPSEPGKG 72 (96)
T ss_dssp -SSS-HHHHHHHHHHTSTTSEBEHHHHHHHHHHHCGHHHCTH-----CHHHHHHHHHH---HHSTTEEEESCCTSSSSSS
T ss_pred CCCCcHHHHHHHHHHhCCCCCccHHHHHHHHHHhhccccccc-----hhhhhHHhhhc---cccceeeecCcCCCCCCCc
Confidence 799999999999999999999999999999999999999875 79999999999 9999999999988889999
Q ss_pred ccccccchhHhhhhh
Q psy16819 190 DFETLGGELSALLSE 204 (289)
Q Consensus 190 ~~w~v~ge~sal~Se 204 (289)
++|+|+++....+..
T Consensus 73 ~~W~i~~~~~~~~~~ 87 (96)
T PF00250_consen 73 SYWTIDPEAIEEFEK 87 (96)
T ss_dssp EEEEE-CTHHHHHHH
T ss_pred eeEEeCHHHHHHHhc
Confidence 999999999887643
No 4
>KOG3563|consensus
Probab=99.95 E-value=2e-29 Score=239.85 Aligned_cols=88 Identities=31% Similarity=0.548 Sum_probs=85.1
Q ss_pred CCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCC
Q psy16819 107 RNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPTSA 186 (289)
Q Consensus 107 ~~~kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~~~ 186 (289)
-++||||||+.||+|||+.+|.|+|||+|||+||++-|||||.+. .-|||||||.| |-|+|||||+|.++.|
T Consensus 170 ~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQ-----QRWQNSIRHSL---SFNDCFVKVaRSPDKP 241 (454)
T KOG3563|consen 170 THAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQ-----QRWQNSIRHSL---SFNDCFVKVARSPDKP 241 (454)
T ss_pred cCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhH-----HHHHhhhhhhc---cccceeeeccCCCCCC
Confidence 589999999999999999999999999999999999999999987 89999999999 9999999999999999
Q ss_pred CCcccccccchhHhhh
Q psy16819 187 KLEDFETLGGELSALL 202 (289)
Q Consensus 187 g~g~~w~v~ge~sal~ 202 (289)
|||+||++.++...+|
T Consensus 242 GKGSfWTLHpdsGNMF 257 (454)
T KOG3563|consen 242 GKGSFWTLHPDSGNMF 257 (454)
T ss_pred CCccceeecCCcCccc
Confidence 9999999999988776
No 5
>KOG2294|consensus
Probab=99.94 E-value=1.2e-28 Score=239.27 Aligned_cols=88 Identities=31% Similarity=0.484 Sum_probs=84.0
Q ss_pred CCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHh-cCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCC
Q psy16819 106 RRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQ-NVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPT 184 (289)
Q Consensus 106 ~~~~kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~-~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~ 184 (289)
+.+.||+|||+.||+|||+++|+|||||+|||+||+. +||||+++.+ .|||||||||| |+|+||+|+++..+
T Consensus 126 ~~~~kpp~SY~~LI~mAI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~----~gWqNSIRHNL---SLn~cF~Kvpr~~~ 198 (454)
T KOG2294|consen 126 GAGVKPPYSYSGLIAMAIRLSPGKRLTLGGIYFYILLEHFPYYRDANM----PGWKNSIRHNL---SLNKCFVKVPRERG 198 (454)
T ss_pred CCCcCCccccccccccccccCCCcceeecCeeEEEEeccccccccCCC----ccchhhccccc---ccccCccccCCccc
Confidence 6789999999999999999999999999999999995 9999999863 79999999999 99999999999999
Q ss_pred CCCCcccccccchhHh
Q psy16819 185 SAKLEDFETLGGELSA 200 (289)
Q Consensus 185 ~~g~g~~w~v~ge~sa 200 (289)
.+|||+||+++++...
T Consensus 199 ~~gKg~~W~ldP~~~~ 214 (454)
T KOG2294|consen 199 RPGKGNYWTLDPDDEN 214 (454)
T ss_pred CCCCCCccccCcchhc
Confidence 9999999999998887
No 6
>KOG3562|consensus
Probab=99.92 E-value=3.2e-26 Score=206.66 Aligned_cols=88 Identities=26% Similarity=0.485 Sum_probs=85.4
Q ss_pred CCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCC
Q psy16819 107 RNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPTSA 186 (289)
Q Consensus 107 ~~~kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~~~ 186 (289)
-..||+|||+.|-+|||+++|+|.|-|+|||.||+++|||||.+. .-||||+|||| |-|+||+|++|.++.+
T Consensus 10 ~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNT-----QrWQNSLRHNL---SFNDCFIKiPRr~drp 81 (277)
T KOG3562|consen 10 GDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNT-----QRWQNSLRHNL---SFNDCFIKIPRRPDRP 81 (277)
T ss_pred cccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhch-----HHHHHHhhccc---cccceeeecCCCCCCC
Confidence 578999999999999999999999999999999999999999987 89999999999 9999999999999999
Q ss_pred CCcccccccchhHhhh
Q psy16819 187 KLEDFETLGGELSALL 202 (289)
Q Consensus 187 g~g~~w~v~ge~sal~ 202 (289)
|||+||++.+....+|
T Consensus 82 GKGsyWalHP~a~dMF 97 (277)
T KOG3562|consen 82 GKGSYWALHPSAFDMF 97 (277)
T ss_pred CCccceeeccchhhhc
Confidence 9999999999998887
No 7
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.88 E-value=5e-24 Score=216.37 Aligned_cols=170 Identities=28% Similarity=0.416 Sum_probs=136.8
Q ss_pred CCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCC
Q psy16819 106 RRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPTS 185 (289)
Q Consensus 106 ~~~~kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~~ 185 (289)
--..+|+|+|+.||.++|+.+++++|||..||.||...|.||.... .+|+|+||||| ++++.|.++.++.+-
T Consensus 82 ~t~~v~~~s~a~gr~~~il~s~~~~lt~s~~~~~~~~~~~~~~k~~-----~~~~~sIr~Nl---s~~~a~~~i~g~~g~ 153 (610)
T COG5025 82 WTYYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVV-----SRWQNSIRHNL---SLNDAFIKIEGRNGA 153 (610)
T ss_pred cccccCCeeeeeccccccccCcccCCcccceeeeeeeccccccccc-----chhhhhhhccc---ccCceEEEEeccCCc
Confidence 3447899999999999999999999999999999999999999987 89999999999 999999999999999
Q ss_pred CCCcccccccchhHhhhhhccc---cC-----------------------------------------------------
Q psy16819 186 AKLEDFETLGGELSALLSESKC---NG----------------------------------------------------- 209 (289)
Q Consensus 186 ~g~g~~w~v~ge~sal~Se~~~---gg----------------------------------------------------- 209 (289)
.++|.||.+++.....|-...+ ++
T Consensus 154 ~~~g~~~~igP~~~~~~l~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~p~~~~~~~~~~nn~~~~~~~~~~~~~i~~ 233 (610)
T COG5025 154 KVKGHFWSIGPGHETQFLKSGLRLDGGGKQMMFTLPSSTEIKITYSSTHSMPLLESNDSLNSNNERELLDIIKSSALIRI 233 (610)
T ss_pred cccceeeccCCCccceeeccccccccccccccccCccccceecccccccccCccccCcCcccccchhhhcccccchhhcc
Confidence 9999999888855433200000 00
Q ss_pred ---------------------------------------------------CCCCCCCCCC-------------------
Q psy16819 210 ---------------------------------------------------GLLNCPTAGG------------------- 219 (289)
Q Consensus 210 ---------------------------------------------------G~~~sp~aGg------------------- 219 (289)
+..+++....
T Consensus 234 ~~~ss~~~~~sl~~~~~~~~~~~~~~~~~~~~e~~i~~~n~~~~~~~~~~~~~~~si~ss~~~s~l~~~~~~~~k~~~s~ 313 (610)
T COG5025 234 PADSSSNLDVSLGHHISQPSTHTPVLDNHSSGEENISRINNSSQIDSPTPNYRMSSIDSSVNPSRLANNKDEGRKGSKSS 313 (610)
T ss_pred ccccchhhhhcccccccccCCCcccccCCCchhhhccccccccccccCCCCccccccccccCchhhccCcccccccCCCC
Confidence 0000000000
Q ss_pred ----------ccccccccccCCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhcCCcccccCCCCCCCCCCCCCccC
Q psy16819 220 ----------LALKKTATSRRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKFFKKF 288 (289)
Q Consensus 220 ----------~~~k~~~~srr~~KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~~~pyfr~~~d~~~~~gWkNSIR~ 288 (289)
.........++..||..+|+.||..||+.+|.++|+|.+||.||..+|||||... .+|+|||||
T Consensus 314 p~~~~~~~~~~~s~~s~~~~~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p-----~~w~nSiRh 387 (610)
T COG5025 314 PVPKDAAPPSTLSDLSADVNRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKP-----TAWQNSIRH 387 (610)
T ss_pred CCccccccCCCcCccccccccCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCC-----cccCchhhh
Confidence 0011123345678999999999999999999999999999999999999999976 899999998
No 8
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=99.83 E-value=3.9e-21 Score=149.18 Aligned_cols=51 Identities=53% Similarity=0.893 Sum_probs=49.5
Q ss_pred CCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhcCCcccccCCCCCCCCCCCCCccC
Q psy16819 233 WGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKFFKKF 288 (289)
Q Consensus 233 KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~~~pyfr~~~d~~~~~gWkNSIR~ 288 (289)
||++||++||++||+++|+++|||+|||+||+++|||||.++ .||||||||
T Consensus 1 kP~~sY~~LI~~Ai~~sp~~~lTL~eIy~~I~~~~pyyr~~~-----~gWknSIRH 51 (78)
T cd00059 1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAP-----AGWQNSIRH 51 (78)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCCccccCC-----CCCccceeE
Confidence 799999999999999999999999999999999999999976 899999997
No 9
>KOG4385|consensus
Probab=99.79 E-value=8.6e-21 Score=186.23 Aligned_cols=89 Identities=28% Similarity=0.442 Sum_probs=79.1
Q ss_pred CCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCC
Q psy16819 106 RRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDEPSPPTS 185 (289)
Q Consensus 106 ~~~~kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~~~~~~~ 185 (289)
..+-+|||+||.||.+||+.+|++.|||+|||.||...|-|||.+. +.|||+||||| |+++||+++..
T Consensus 364 ~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNa-----ATWKnAVRHNL---SLHKCF~RVEn---- 431 (581)
T KOG4385|consen 364 NADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNA-----ATWKNAVRHNL---SLHKCFVRVEN---- 431 (581)
T ss_pred ccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccc-----hhHhHHHhhhh---HHHHHHHHHHH----
Confidence 3467899999999999999999999999999999999999999998 99999999999 99999999987
Q ss_pred CCCcccccccchhHhhhhhccc
Q psy16819 186 AKLEDFETLGGELSALLSESKC 207 (289)
Q Consensus 186 ~g~g~~w~v~ge~sal~Se~~~ 207 (289)
-+|-.|+++...-..+.+-++
T Consensus 432 -vkgavwtvDe~e~~krr~~k~ 452 (581)
T KOG4385|consen 432 -VKGAVWTVDEREFQKRRPQKI 452 (581)
T ss_pred -HhcceeeeehhhhhhhcCccc
Confidence 588999999866554444333
No 10
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=99.78 E-value=1.2e-19 Score=144.01 Aligned_cols=52 Identities=44% Similarity=0.813 Sum_probs=49.7
Q ss_pred CCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhcCCcccccCCCCCCCCCCCCCccCC
Q psy16819 233 WGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKFFKKFR 289 (289)
Q Consensus 233 KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~~~pyfr~~~d~~~~~gWkNSIR~~ 289 (289)
||++||++||++||+++|+++|||++||+||+++|||||.++ .|||||||+.
T Consensus 1 kP~~sY~~lI~~ai~~sp~~~ltl~~Iy~~I~~~~pyy~~~~-----~~WknSIRHn 52 (89)
T smart00339 1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENR-----AGWQNSIRHN 52 (89)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCchhhcCc-----cccccccccc
Confidence 799999999999999999999999999999999999999976 6999999983
No 11
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=99.74 E-value=1.8e-19 Score=144.72 Aligned_cols=51 Identities=49% Similarity=0.877 Sum_probs=47.3
Q ss_pred CCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhcCCcccccCCCCCCCCCCCCCccC
Q psy16819 233 WGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKFFKKF 288 (289)
Q Consensus 233 KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~~~pyfr~~~d~~~~~gWkNSIR~ 288 (289)
||+|||++||++||++||+++|||+|||+||+.+||||+.+. .|||||||+
T Consensus 1 KPp~sY~~LI~~Ai~~sp~~~Ltl~eIy~~i~~~~pyyr~~~-----~~WknSIRH 51 (96)
T PF00250_consen 1 KPPYSYATLIAMAILSSPDKRLTLSEIYEWIEENFPYYRDAS-----KGWKNSIRH 51 (96)
T ss_dssp -SSS-HHHHHHHHHHTSTTSEBEHHHHHHHHHHHCGHHHCTH-----CHHHHHHHH
T ss_pred CCCCcHHHHHHHHHHhCCCCCccHHHHHHHHHHhhccccccc-----hhhhhHHhh
Confidence 799999999999999999999999999999999999999865 799999996
No 12
>KOG3563|consensus
Probab=99.72 E-value=1.9e-18 Score=165.24 Aligned_cols=63 Identities=33% Similarity=0.576 Sum_probs=57.2
Q ss_pred ccccccccCCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhcCCcccccCCCCCCCCCCCCCccCC
Q psy16819 222 LKKTATSRRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKFFKKFR 289 (289)
Q Consensus 222 ~k~~~~srr~~KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~~~pyfr~~~d~~~~~gWkNSIR~~ 289 (289)
.+.-+++-.+.||||||+.||.|||+.+|.+.|||+|||+|||+-|||||.+. +.||||||++
T Consensus 162 pktyRRsY~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQ-----QRWQNSIRHS 224 (454)
T KOG3563|consen 162 PKTYRRSYTHAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQ-----QRWQNSIRHS 224 (454)
T ss_pred CceeeccccCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhH-----HHHHhhhhhh
Confidence 34445577789999999999999999999999999999999999999999976 8999999984
No 13
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.70 E-value=1.1e-17 Score=170.48 Aligned_cols=95 Identities=29% Similarity=0.470 Sum_probs=90.2
Q ss_pred cccCCCCCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCCCCCCCCCCC
Q psy16819 100 KKTATSRRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPLPRPDNYVDE 179 (289)
Q Consensus 100 ~~~~~~~~~~kP~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~s~~~~F~k~ 179 (289)
-+.....++.||+++|+.+|++||+.++.+.|+|++||.||..+||||+.+. .+|+||||||| ++|++|.|+
T Consensus 327 ~~s~~~~~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p-----~~w~nSiRhnl---SlNksf~kv 398 (610)
T COG5025 327 DLSADVNRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKP-----TAWQNSIRHNL---SLNKSFEKV 398 (610)
T ss_pred ccccccccCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCC-----cccCchhhhhh---hhccccccC
Confidence 3455678999999999999999999999999999999999999999999998 89999999999 999999999
Q ss_pred CCCCCCCCCcccccccchhHhhh
Q psy16819 180 PSPPTSAKLEDFETLGGELSALL 202 (289)
Q Consensus 180 ~~~~~~~g~g~~w~v~ge~sal~ 202 (289)
++..+.+|||.||.++.++...+
T Consensus 399 P~sa~~pGKg~fw~i~~s~~~~~ 421 (610)
T COG5025 399 PRSASQPGKGCFWKIDYSYIYEK 421 (610)
T ss_pred CCCcCCCCCcccCccChhhhhhh
Confidence 99999999999999999999876
No 14
>KOG2294|consensus
Probab=99.61 E-value=2.9e-17 Score=159.66 Aligned_cols=56 Identities=36% Similarity=0.612 Sum_probs=52.6
Q ss_pred cCCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhc-CCcccccCCCCCCCCCCCCCccC
Q psy16819 229 RRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQ-NVPYFKDKGDSNSSAGWKFFKKF 288 (289)
Q Consensus 229 rr~~KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~-~~pyfr~~~d~~~~~gWkNSIR~ 288 (289)
+...||+|||++||+|||++||++||||++||+||+. +|||||+++| .||||||||
T Consensus 126 ~~~~kpp~SY~~LI~mAI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~----~gWqNSIRH 182 (454)
T KOG2294|consen 126 GAGVKPPYSYSGLIAMAIRLSPGKRLTLGGIYFYILLEHFPYYRDANM----PGWKNSIRH 182 (454)
T ss_pred CCCcCCccccccccccccccCCCcceeecCeeEEEEeccccccccCCC----ccchhhccc
Confidence 5678999999999999999999999999999999995 9999999763 799999998
No 15
>KOG3562|consensus
Probab=99.50 E-value=4.1e-15 Score=134.99 Aligned_cols=58 Identities=31% Similarity=0.560 Sum_probs=53.6
Q ss_pred cccCCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhcCCcccccCCCCCCCCCCCCCccCC
Q psy16819 227 TSRRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKFFKKFR 289 (289)
Q Consensus 227 ~srr~~KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~~~pyfr~~~d~~~~~gWkNSIR~~ 289 (289)
.+..++||+|||+.|-+|||++||++.|.|+|||+||+++|||||.+- +.||||+|+.
T Consensus 7 ~sY~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNT-----QrWQNSLRHN 64 (277)
T KOG3562|consen 7 NSYGDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNT-----QRWQNSLRHN 64 (277)
T ss_pred ccccccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhch-----HHHHHHhhcc
Confidence 355678999999999999999999999999999999999999999864 8999999973
No 16
>KOG4385|consensus
Probab=99.26 E-value=1.1e-12 Score=129.57 Aligned_cols=56 Identities=36% Similarity=0.697 Sum_probs=52.6
Q ss_pred ccCCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHhcCCcccccCCCCCCCCCCCCCccC
Q psy16819 228 SRRNAWGSSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKFFKKF 288 (289)
Q Consensus 228 srr~~KP~~SYa~LI~~AI~sSP~~rLTL~eIY~~i~~~~pyfr~~~d~~~~~gWkNSIR~ 288 (289)
.+.+.+|||.|+.||..||+.||++.|||+|||.||...|.|||.+. +.|||+||+
T Consensus 363 k~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNa-----ATWKnAVRH 418 (581)
T KOG4385|consen 363 KNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNA-----ATWKNAVRH 418 (581)
T ss_pred hccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccc-----hhHhHHHhh
Confidence 34568999999999999999999999999999999999999999987 899999997
No 17
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=92.39 E-value=0.16 Score=38.81 Aligned_cols=33 Identities=24% Similarity=0.394 Sum_probs=29.2
Q ss_pred cHHHHHHHHHhcCCC-CCcCHHHHHHHHHhcCCc
Q psy16819 114 SYADLISQAIQSSPE-QRLTLSQIYDWMIQNVPY 146 (289)
Q Consensus 114 SYa~LI~~AI~ssp~-~~LTL~eIY~wi~~~~py 146 (289)
+|.+||.+||.+..+ +-.+++.|..||.++|+.
T Consensus 4 ~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~ 37 (77)
T PF00538_consen 4 PYSDMILEAIKALKERKGSSLQAIKKYIKAKYKV 37 (77)
T ss_dssp CHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSC
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCc
Confidence 699999999998665 569999999999999864
No 18
>smart00526 H15 Domain in histone families 1 and 5.
Probab=91.72 E-value=0.37 Score=35.58 Aligned_cols=32 Identities=25% Similarity=0.484 Sum_probs=28.5
Q ss_pred cHHHHHHHHHhcCCCCC-cCHHHHHHHHHhcCC
Q psy16819 114 SYADLISQAIQSSPEQR-LTLSQIYDWMIQNVP 145 (289)
Q Consensus 114 SYa~LI~~AI~ssp~~~-LTL~eIY~wi~~~~p 145 (289)
+|.+||..||....++. .+++.|..||.++|+
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 89999999999976644 999999999999965
No 19
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=89.52 E-value=0.52 Score=37.00 Aligned_cols=33 Identities=18% Similarity=0.395 Sum_probs=28.4
Q ss_pred cHHHHHHHHHhcCCC-CCcCHHHHHHHHHhcCCc
Q psy16819 114 SYADLISQAIQSSPE-QRLTLSQIYDWMIQNVPY 146 (289)
Q Consensus 114 SYa~LI~~AI~ssp~-~~LTL~eIY~wi~~~~py 146 (289)
+|.+||.+||....+ +-.+++.|..||.++|+.
T Consensus 6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~ 39 (88)
T cd00073 6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKV 39 (88)
T ss_pred CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCc
Confidence 799999999988544 448999999999999774
No 20
>smart00526 H15 Domain in histone families 1 and 5.
Probab=87.74 E-value=0.79 Score=33.81 Aligned_cols=33 Identities=24% Similarity=0.458 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHcCCCCc-ccHHHHHHHHhcCCcc
Q psy16819 237 SYADLISQAIQSSPEQR-LTLSQIYDWMIQNVPY 269 (289)
Q Consensus 237 SYa~LI~~AI~sSP~~r-LTL~eIY~~i~~~~py 269 (289)
+|..||..||....++. .++..|..||.++|..
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~ 39 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYKV 39 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCC
Confidence 79999999999988754 8899999999999653
No 21
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=87.69 E-value=0.57 Score=35.72 Aligned_cols=33 Identities=24% Similarity=0.394 Sum_probs=29.4
Q ss_pred CHHHHHHHHHHcCCC-CcccHHHHHHHHhcCCcc
Q psy16819 237 SYADLISQAIQSSPE-QRLTLSQIYDWMIQNVPY 269 (289)
Q Consensus 237 SYa~LI~~AI~sSP~-~rLTL~eIY~~i~~~~py 269 (289)
+|..||..||...-+ +-.++..|..||.++|+.
T Consensus 4 ~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~ 37 (77)
T PF00538_consen 4 PYSDMILEAIKALKERKGSSLQAIKKYIKAKYKV 37 (77)
T ss_dssp CHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSC
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCc
Confidence 599999999999766 778999999999999964
No 22
>KOG4012|consensus
Probab=82.21 E-value=1.3 Score=41.66 Aligned_cols=40 Identities=23% Similarity=0.404 Sum_probs=34.5
Q ss_pred CCCcHHHHHHHHHhcCCCCC-cCHHHHHHHHHhcCCccccC
Q psy16819 111 GSSSYADLISQAIQSSPEQR-LTLSQIYDWMIQNVPYFKDK 150 (289)
Q Consensus 111 P~~SYa~LI~~AI~ssp~~~-LTL~eIY~wi~~~~pyf~~~ 150 (289)
+.-+|.+||..||...-++. .++.-|+.||..+|+.|.-.
T Consensus 43 ~~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~ 83 (243)
T KOG4012|consen 43 AHPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVE 83 (243)
T ss_pred CCCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhh
Confidence 34579999999999987776 89999999999999877753
No 23
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=76.04 E-value=3.6 Score=32.21 Aligned_cols=33 Identities=18% Similarity=0.395 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHcCCC-CcccHHHHHHHHhcCCcc
Q psy16819 237 SYADLISQAIQSSPE-QRLTLSQIYDWMIQNVPY 269 (289)
Q Consensus 237 SYa~LI~~AI~sSP~-~rLTL~eIY~~i~~~~py 269 (289)
+|..||..||...-+ +..++..|..||..+|+.
T Consensus 6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~ 39 (88)
T cd00073 6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKV 39 (88)
T ss_pred CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCc
Confidence 799999999998554 456789999999999874
No 24
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=60.88 E-value=2.9 Score=32.74 Aligned_cols=82 Identities=15% Similarity=0.238 Sum_probs=48.0
Q ss_pred cHHHHHHHHHhcCC--CCCcCHHHHHHHHHhcCCccccCCC----CCCC-CCcccccccccCCCCCCCCCCCCCCCCCCC
Q psy16819 114 SYADLISQAIQSSP--EQRLTLSQIYDWMIQNVPYFKDKGD----SNSS-AGWKMRIRSNTWPLPRPDNYVDEPSPPTSA 186 (289)
Q Consensus 114 SYa~LI~~AI~ssp--~~~LTL~eIY~wi~~~~pyf~~~~d----s~s~-~gWknSIRHNL~~~s~~~~F~k~~~~~~~~ 186 (289)
+|.+|+.-.|..-. .+.++.+||++.|.++|..=...-. ++.. .-|+|.|+=.+ + ..+...-...+
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~---~----~L~~aGli~~~ 73 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWAR---S----YLKKAGLIERP 73 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHH---H----HHHHCCCccCC
Confidence 35556554444433 5789999999999999874321000 1111 26999888766 2 22333333444
Q ss_pred CCcccccccchhHhhhh
Q psy16819 187 KLEDFETLGGELSALLS 203 (289)
Q Consensus 187 g~g~~w~v~ge~sal~S 203 (289)
+.| .|.+...-...+.
T Consensus 74 ~rG-~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 74 KRG-IWRITEKGRKALA 89 (92)
T ss_pred CCC-ceEECHhHHHHHh
Confidence 444 8888877665553
No 25
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=59.48 E-value=7.5 Score=28.91 Aligned_cols=60 Identities=10% Similarity=0.204 Sum_probs=36.1
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCcccccccccCCC-C-CCCCCCCC
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNTWPL-P-RPDNYVDE 179 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL~~~-s-~~~~F~k~ 179 (289)
+||.+++.+.|.... +-||.+||++-|.+.--|=.. ++...++|+-.|.-. . ....|+++
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~~~~------~k~p~~~i~a~ly~~~~~~d~~F~~v 62 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQERGLYKKS------GKTPEATIAAQLYTDIKNEDSRFVKV 62 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS---------GGGGGHHHH-HHHHHHH-T-SS-EES
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCCCcc------cCCHHHHHHHHHHHHcccCCCCEEEe
Confidence 588899999888875 889999999999987443222 256777777444100 1 34466665
No 26
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.42 E-value=18 Score=34.75 Aligned_cols=66 Identities=14% Similarity=0.195 Sum_probs=42.3
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccc------cCCCCCC-CCCcccccccccCCCCCCCCCCCCCCC
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFK------DKGDSNS-SAGWKMRIRSNTWPLPRPDNYVDEPSP 182 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~------~~~ds~s-~~gWknSIRHNL~~~s~~~~F~k~~~~ 182 (289)
++|..+|...++. .+..+|..|||+|+.+.||-=. ..+|..- ..+=.-+.|-|| ..+.-|.|+...
T Consensus 5 l~~~e~vl~~Lq~-~~ep~t~~eI~eka~e~~~~~~~~kk~~s~g~tp~q~va~~iy~~~~l---q~~~pflKvte~ 77 (307)
T COG2958 5 LNLIEIVLSVLQT-SEEPFTAREIAEKAFETFPAECQEKKFDSGGDTPQQLVAEIIYTRPNL---QEKHPFLKVTEG 77 (307)
T ss_pred hhhHHHHHHHHHc-cCCCCcHHHHHHHHHHhccHHHHHHhhccccccHHHHHHHHHhcCccc---cccCcccccccC
Confidence 4566666555555 8999999999999999997422 2211000 011124567788 777889888654
No 27
>KOG4012|consensus
Probab=41.29 E-value=27 Score=32.91 Aligned_cols=37 Identities=24% Similarity=0.448 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHcCCCCc-ccHHHHHHHHhcCCcccc
Q psy16819 235 SSSYADLISQAIQSSPEQR-LTLSQIYDWMIQNVPYFK 271 (289)
Q Consensus 235 ~~SYa~LI~~AI~sSP~~r-LTL~eIY~~i~~~~pyfr 271 (289)
.-+|+.||..||..+-++. .++.-|+.||..||+-|.
T Consensus 44 ~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~ 81 (243)
T KOG4012|consen 44 HPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDD 81 (243)
T ss_pred CCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccch
Confidence 4579999999999987765 669999999999997764
No 28
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=38.21 E-value=40 Score=24.58 Aligned_cols=38 Identities=18% Similarity=0.275 Sum_probs=28.9
Q ss_pred cHHHHHHHHHhcCCC--CCcCHHHHHHHHHhcCCccccCC
Q psy16819 114 SYADLISQAIQSSPE--QRLTLSQIYDWMIQNVPYFKDKG 151 (289)
Q Consensus 114 SYa~LI~~AI~ssp~--~~LTL~eIY~wi~~~~pyf~~~~ 151 (289)
.-..+|..+|.+.++ +.+.|++|..++.+.+|-|....
T Consensus 5 ~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~ 44 (74)
T PF12872_consen 5 ELKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRD 44 (74)
T ss_dssp HHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCC
T ss_pred HHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccc
Confidence 346788888855543 58999999999999998888764
No 29
>cd05071 PTKc_Src Catalytic domain of the Protein Tyrosine Kinase, Src. Protein Tyrosine Kinase (PTK) family; Src kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src (or c-Src) is a cytoplasmic (or non-receptor) tyr kinase, containing an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region with a conserved tyr. It is activated by autophosphorylation at the tyr kinase domain, and is negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). c-Src is the vertebrate homolog of the oncogenic protein (v-Src) from Rous sarcoma virus. Together with other Src subfamily proteins, it is invo
Probab=36.16 E-value=38 Score=29.83 Aligned_cols=34 Identities=24% Similarity=0.384 Sum_probs=30.2
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCC
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVP 145 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~p 145 (289)
+....+||..++.-.|++|.|..+|.+++.+-|.
T Consensus 229 ~~~l~~li~~~l~~~p~~Rp~~~~~~~~l~~~~~ 262 (262)
T cd05071 229 PESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFT 262 (262)
T ss_pred CHHHHHHHHHHccCCcccCCCHHHHHHHHHHhcC
Confidence 4568899999999999999999999999987663
No 30
>cd06649 PKc_MEK2 Catalytic domain of the dual-specificity Protein Kinase, MAP/ERK Kinase 2. Protein kinases (PKs), MAP/ERK Kinase (MEK) 2 subfamily, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The MEK subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The mitogen-activated protein (MAP) kinase signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising the MAP kinase (MAPK), which is phosphorylated and activated by a MAPK kinase (MAPKK or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAPKKK or MKKK). MEK2 is a dual-specificity PK that phosphorylates and activates the downst
Probab=32.63 E-value=24 Score=32.58 Aligned_cols=47 Identities=9% Similarity=0.296 Sum_probs=37.6
Q ss_pred cHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCccccccccc
Q psy16819 114 SYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKMRIRSNT 167 (289)
Q Consensus 114 SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWknSIRHNL 167 (289)
.+.+||..++.-.|+.|.|+.||.+ .|||+... ....+|++.+.-+|
T Consensus 276 ~l~~li~~~L~~~P~~Rpt~~ell~-----h~~~~~~~--~~~~~~~~~~~~~~ 322 (331)
T cd06649 276 DFQEFVNKCLIKNPAERADLKMLMN-----HTFIKRSE--VEEVDFAGWLCKTL 322 (331)
T ss_pred HHHHHHHHHccCCcccCCCHHHHhc-----ChHHhhcc--cccccHHHHHHHhh
Confidence 3689999999999999999999974 47777543 23478888888888
No 31
>smart00258 SAND SAND domain.
Probab=32.54 E-value=18 Score=28.10 Aligned_cols=14 Identities=36% Similarity=0.532 Sum_probs=11.8
Q ss_pred CCCCcccccccccC
Q psy16819 155 SSAGWKMRIRSNTW 168 (289)
Q Consensus 155 s~~gWknSIRHNL~ 168 (289)
+++.||-|||||=+
T Consensus 48 ~~K~WK~sIR~~g~ 61 (73)
T smart00258 48 KSKDWKRSIRCGGS 61 (73)
T ss_pred ccCCcchheeECCc
Confidence 46899999999863
No 32
>cd08229 STKc_Nek7 Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A-related kinase 7. Serine/Threonine Kinases (STKs), Never In Mitosis gene A (NIMA)-related kinase 7 (Nek7) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek7 subfamily is one of a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Nek7 is required for mitotic spindle formation and cytokinesis. It is enriched in the centrosome and is critical for microtubule nucleation. Nek7 is activated by Nek9 during mitosis, and may regulate the p70 ribosomal S6 kinase.
Probab=30.53 E-value=53 Score=28.59 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=26.2
Q ss_pred cHHHHHHHHHhcCCCCCcCHHHHHHHHHhc
Q psy16819 114 SYADLISQAIQSSPEQRLTLSQIYDWMIQN 143 (289)
Q Consensus 114 SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~ 143 (289)
....||.+++...|++|.|+.+||+-+.+-
T Consensus 236 ~~~~li~~~l~~~p~~Rpt~~~i~~~~~~~ 265 (267)
T cd08229 236 ELRQLVNMCINPDPEKRPDITYVYDVAKRM 265 (267)
T ss_pred HHHHHHHHhcCCCcccCCCHHHHHHHHhhh
Confidence 477899999999999999999999987654
No 33
>cd05051 PTKc_DDR Catalytic domain of the Protein Tyrosine Kinases, Discoidin Domain Receptors. Protein Tyrosine Kinase (PTK) family; Discoidin Domain Receptor (DDR) subfamily; catalytic (c) domain. The DDR subfamily consists of homologs of mammalian DDR1, DDR2, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR subfamily members are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDRs regulate cell adhesion, proliferation, and extracellular matrix remodeling. They have been linke
Probab=28.93 E-value=50 Score=29.35 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=25.9
Q ss_pred cHHHHHHHHHhcCCCCCcCHHHHHHHHH
Q psy16819 114 SYADLISQAIQSSPEQRLTLSQIYDWMI 141 (289)
Q Consensus 114 SYa~LI~~AI~ssp~~~LTL~eIY~wi~ 141 (289)
....||..++...|.+|.|..||++++.
T Consensus 268 ~l~~li~~cl~~~p~~Rpt~~el~~~L~ 295 (296)
T cd05051 268 DIYELMLECWRRDEEDRPTFREIHLFLQ 295 (296)
T ss_pred HHHHHHHHHhccChhcCCCHHHHHHHhc
Confidence 5789999999999999999999999875
No 34
>cd05040 PTKc_Ack_like Catalytic domain of the Protein Tyrosine Kinase, Activated Cdc42-associated kinase. Protein Tyrosine Kinase (PTK) family; Activated Cdc42-associated kinase (Ack) subfamily; catalytic (c) domain. Ack subfamily members include Ack1, thirty-eight-negative kinase 1 (Tnk1), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ack subfamily members are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal catalytic domain, an SH3 domain, a Cdc42-binding CRIB domain, and a proline-rich region. They are mainly expressed in brain and skeletal tissues and are involved in the regulation of cell adhesion and growth, receptor degradation, and axonal guidance. Ack1 is also associated with and
Probab=28.66 E-value=45 Score=28.88 Aligned_cols=30 Identities=13% Similarity=0.316 Sum_probs=26.9
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHH
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMI 141 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~ 141 (289)
+-...+||..++...|.+|.|+.||++.+.
T Consensus 227 ~~~~~~li~~~l~~~p~~Rps~~~~~~~l~ 256 (257)
T cd05040 227 PQDIYNVMLQCWAHNPADRPTFAALREFLP 256 (257)
T ss_pred CHHHHHHHHHHCCCCcccCCCHHHHHHHhc
Confidence 457889999999999999999999999875
No 35
>cd05072 PTKc_Lyn Catalytic domain of the Protein Tyrosine Kinase, Lyn. Protein Tyrosine Kinase (PTK) family; Lyn kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Lyn is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Src proteins are involved in signaling pathways that regulate cytokine and growth fa
Probab=28.49 E-value=56 Score=28.41 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=27.3
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHHh
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMIQ 142 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~ 142 (289)
+....+||..++.-.|++|.|..+|.+++.+
T Consensus 230 ~~~~~~li~~~l~~~p~~Rp~~~~i~~~l~~ 260 (261)
T cd05072 230 PDELYDIMKTCWKEKAEERPTFDYLQSVLDD 260 (261)
T ss_pred CHHHHHHHHHHccCCcccCcCHHHHHHHHhc
Confidence 3467889999999999999999999999864
No 36
>PF13565 HTH_32: Homeodomain-like domain
Probab=27.71 E-value=1.4e+02 Score=21.67 Aligned_cols=27 Identities=22% Similarity=0.373 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCCCCcCHHHHHHHHHhcCC
Q psy16819 117 DLISQAIQSSPEQRLTLSQIYDWMIQNVP 145 (289)
Q Consensus 117 ~LI~~AI~ssp~~~LTL~eIY~wi~~~~p 145 (289)
+.|...|...| ++|+.+|.++|.+.|.
T Consensus 37 ~~i~~~~~~~p--~wt~~~i~~~L~~~~g 63 (77)
T PF13565_consen 37 ERIIALIEEHP--RWTPREIAEYLEEEFG 63 (77)
T ss_pred HHHHHHHHhCC--CCCHHHHHHHHHHHhC
Confidence 66777777766 9999999999999865
No 37
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=27.40 E-value=21 Score=27.92 Aligned_cols=14 Identities=43% Similarity=0.669 Sum_probs=10.3
Q ss_pred CCCCCccccccccc
Q psy16819 154 NSSAGWKMRIRSNT 167 (289)
Q Consensus 154 ~s~~gWknSIRHNL 167 (289)
.+++.||.|||++-
T Consensus 56 ~~sK~WK~SIr~~g 69 (82)
T PF01342_consen 56 GSSKDWKRSIRCGG 69 (82)
T ss_dssp CTCS-HHHHSEETT
T ss_pred ccCCCCCccEEECC
Confidence 35688999999864
No 38
>cd05061 PTKc_InsR Catalytic domain of the Protein Tyrosine Kinase, Insulin Receptor. Protein Tyrosine Kinase (PTK) family; Insulin Receptor (InsR); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. InsR is a receptor tyr kinase (RTK) that is composed of two alphabeta heterodimers. Binding of the insulin ligand to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, stimulating downstream kinase activities, which initiate signaling cascades and biological function. InsR signaling plays an important role in many cellular processes including glucose homeostasis, glycogen synthesis, lipid and protein meta
Probab=27.29 E-value=72 Score=28.45 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=32.6
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHHh-cCCcccc
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMIQ-NVPYFKD 149 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~-~~pyf~~ 149 (289)
+-....||..++...|++|.|+.||.+.+.+ ..|.|+.
T Consensus 247 ~~~~~~li~~~l~~~p~~Rps~~~ll~~l~~~~~~~~~~ 285 (288)
T cd05061 247 PERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPE 285 (288)
T ss_pred CHHHHHHHHHHcCCChhHCcCHHHHHHHHHhhcCCCCCC
Confidence 3568899999999999999999999998886 5677776
No 39
>cd05041 PTKc_Fes_like Catalytic domain of Fes-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Fes subfamily; catalytic (c) domain. Fes subfamily members include Fes (or Fps), Fer, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fes subfamily proteins are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal region with FCH (Fes/Fer/CIP4 homology) and coiled-coil domains, followed by a SH2 domain, and a C-terminal catalytic domain. The genes for Fes (feline sarcoma) and Fps (Fujinami poultry sarcoma) were first isolated from tumor-causing retroviruses. The viral oncogenes encode chimeric Fes proteins consisting of Gag sequences at the N-termini, resulting in unregulated tyr k
Probab=27.25 E-value=61 Score=27.92 Aligned_cols=29 Identities=28% Similarity=0.389 Sum_probs=26.0
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHH
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMI 141 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~ 141 (289)
-....||.+++...|++|.|..||.+.+.
T Consensus 222 ~~~~~li~~~l~~~p~~Rp~~~ell~~l~ 250 (251)
T cd05041 222 EEIYRLMLQCWAYDPENRPSFSEIYNELQ 250 (251)
T ss_pred HHHHHHHHHHhccChhhCcCHHHHHHHhh
Confidence 36788999999999999999999998874
No 40
>cd05034 PTKc_Src_like Catalytic domain of Src kinase-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Src kinase subfamily; catalytic (c) domain. Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, and Yes. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src (or c-Src) proteins are cytoplasmic (or non-receptor) tyr kinases which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-t
Probab=26.87 E-value=66 Score=27.89 Aligned_cols=31 Identities=23% Similarity=0.379 Sum_probs=27.3
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHHh
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMIQ 142 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~ 142 (289)
+-....||..+|...|++|.|..+|++++..
T Consensus 230 ~~~~~~~i~~~l~~~p~~Rp~~~~l~~~l~~ 260 (261)
T cd05034 230 PEELYDLMLQCWDKDPEERPTFEYLQSFLED 260 (261)
T ss_pred CHHHHHHHHHHcccCcccCCCHHHHHHHHhc
Confidence 3468899999999999999999999998764
No 41
>PHA02988 hypothetical protein; Provisional
Probab=26.46 E-value=71 Score=28.85 Aligned_cols=36 Identities=8% Similarity=0.059 Sum_probs=31.3
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCcc
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYF 147 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf 147 (289)
+-....||.+++...|++|.|.+||.+-+...+-||
T Consensus 248 ~~~l~~li~~cl~~dp~~Rps~~ell~~l~~~~~~~ 283 (283)
T PHA02988 248 PLEIKCIVEACTSHDSIKRPNIKEILYNLSLYKFYI 283 (283)
T ss_pred cHHHHHHHHHHhcCCcccCcCHHHHHHHHHHHHhcC
Confidence 345889999999999999999999999998876654
No 42
>cd05060 PTKc_Syk_like Catalytic domain of Spleen Tyrosine Kinase-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Spleen Tyrosine Kinase (Syk) subfamily; catalytic (c) domain. The Syk subfamily is composed of Syk, ZAP-70, Shark, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk subfamily kinases are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. They are involved in the signaling downstream of activated receptors (including B-cell, T-cell, and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferation, differentiation, survival, adhesion, mi
Probab=26.38 E-value=75 Score=27.59 Aligned_cols=31 Identities=16% Similarity=0.221 Sum_probs=27.4
Q ss_pred cHHHHHHHHHhcCCCCCcCHHHHHHHHHhcC
Q psy16819 114 SYADLISQAIQSSPEQRLTLSQIYDWMIQNV 144 (289)
Q Consensus 114 SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~ 144 (289)
...+||.+++.-.|++|.|+.+|.+.|.+.+
T Consensus 226 ~l~~li~~cl~~~p~~Rp~~~~l~~~l~~~~ 256 (257)
T cd05060 226 EIYSIMLSCWKYRPEDRPTFSELESTFRRDP 256 (257)
T ss_pred HHHHHHHHHhcCChhhCcCHHHHHHHHHhcc
Confidence 5678999999999999999999999988653
No 43
>cd05048 PTKc_Ror Catalytic Domain of the Protein Tyrosine Kinases, Receptor tyrosine kinase-like Orphan Receptors. Protein Tyrosine Kinase (PTK) family; Receptor tyrosine kinase-like Orphan Receptor (Ror) subfamily; catalytic (c) domain. The Ror subfamily consists of Ror1, Ror2, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ror proteins are orphan receptor tyr kinases (RTKs) containing an extracellular region with immunoglobulin-like, cysteine-rich, and kringle domains, a transmembrane segment, and an intracellular catalytic domain. Ror RTKs are unrelated to the nuclear receptor subfamily called retinoid-related orphan receptors (RORs). RTKs are usually activated through ligand binding, which causes dimer
Probab=25.42 E-value=60 Score=28.60 Aligned_cols=31 Identities=13% Similarity=0.185 Sum_probs=27.2
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHHh
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMIQ 142 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~ 142 (289)
+.....||..++...|.+|.|.+||++.+..
T Consensus 252 ~~~~~~l~~~c~~~~p~~Rp~~~~i~~~l~~ 282 (283)
T cd05048 252 PARVYALMIECWNEIPARRPRFKDIHTRLRS 282 (283)
T ss_pred CHHHHHHHHHHccCChhhCcCHHHHHHHHhc
Confidence 3467899999999999999999999998753
No 44
>cd05044 PTKc_c-ros Catalytic domain of the Protein Tyrosine Kinase, C-ros. Protein Tyrosine Kinases (PTK) family; C-ros and Drosophila Sevenless proteins; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The proto-oncogene c-ros encodes an orphan receptor tyr kinase (RTK) with an unknown ligand. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. C-ros is expressed in embryonic cells of the kidney, intestine and lung, but disappears soon after birth. It persists only in the adult epididymis. Male
Probab=25.39 E-value=65 Score=28.06 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=25.1
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHH
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMI 141 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~ 141 (289)
-.-..||.+++...|.+|.|+.+|++-+.
T Consensus 240 ~~~~~li~~~l~~~p~~Rp~~~~i~~~l~ 268 (269)
T cd05044 240 DKIYQLMTNCWAQDPSERPTFDRIQEILQ 268 (269)
T ss_pred HHHHHHHHHHcCCCcccCCCHHHHHHHHh
Confidence 34578999999999999999999998764
No 45
>cd05115 PTKc_Zap-70 Catalytic domain of the Protein Tyrosine Kinase, Zeta-chain-associated protein of 70kDa. Protein Tyrosine Kinase (PTK) family; Zeta-chain-associated protein of 70kDa (Zap-70); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Zap-70 is a member of the Syk subfamily of kinases, which are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Zap-70 is primarily expressed in T-cells and NK cells, and is a crucial component in T-cell receptor (TCR) signaling. Zap-70 binds the phosphorylated ITAM (immunoreceptor tyr activation motif) sequences of the activated TCR zeta-chain through its SH2 domains, leading to its pho
Probab=24.26 E-value=70 Score=28.09 Aligned_cols=32 Identities=13% Similarity=0.089 Sum_probs=28.2
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcC
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMIQNV 144 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~ 144 (289)
-....||.+++...|+.|+|+.+|++.|...|
T Consensus 225 ~~l~~li~~c~~~~~~~Rp~~~~i~~~l~~~~ 256 (257)
T cd05115 225 PEMYALMKDCWIYKWEDRPNFAKVEERMRTYY 256 (257)
T ss_pred HHHHHHHHHHcCCChhhCcCHHHHHHHHhhhc
Confidence 45678999999999999999999999998754
No 46
>cd05036 PTKc_ALK_LTK Catalytic domain of the Protein Tyrosine Kinases, Anaplastic Lymphoma Kinase and Leukocyte Tyrosine Kinase. Protein Tyrosine Kinase (PTK) family; Anaplastic Lymphoma Kinase (ALK) and Leukocyte Tyrosine (tyr) Kinase (LTK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyr residues in protein substrates. ALK and LTK are orphan receptor tyr kinases (RTKs) whose ligands are not yet well-defined. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. They are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. ALK appears to play an important role in mammalian neural development as well
Probab=23.13 E-value=67 Score=28.40 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=26.0
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHH
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMI 141 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~ 141 (289)
-....||..++...|+.|+|+.+|.+.+.
T Consensus 248 ~~~~~~i~~cl~~~p~~Rps~~~vl~~l~ 276 (277)
T cd05036 248 GPVYRIMTDCWQHTPEDRPNFATILERIQ 276 (277)
T ss_pred HHHHHHHHHHcCCCcccCcCHHHHHHHhh
Confidence 36789999999999999999999998875
No 47
>cd05096 PTKc_DDR1 Catalytic domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 1. Protein Tyrosine Kinase (PTK) family; mammalian Discoidin Domain Receptor 1 (DDR1) and homologs; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR1 is a member of the DDR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDR1 binds to all collagens tested to date (types I-IV). It is widely expressed in many tissues. It is abundant in the brain and is also found in k
Probab=23.12 E-value=69 Score=28.84 Aligned_cols=30 Identities=17% Similarity=0.258 Sum_probs=26.9
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHH
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMI 141 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~ 141 (289)
+....+||.+++...|.+|.|..||..+|.
T Consensus 274 ~~~~~~li~~cl~~~p~~RPs~~~i~~~l~ 303 (304)
T cd05096 274 PQGLYELMLQCWSRDCRERPSFSDIHAFLT 303 (304)
T ss_pred CHHHHHHHHHHccCCchhCcCHHHHHHHHh
Confidence 456889999999999999999999998875
No 48
>cd05094 PTKc_TrkC Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase C (TrkC); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some n
Probab=22.83 E-value=79 Score=28.26 Aligned_cols=31 Identities=26% Similarity=0.421 Sum_probs=27.6
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHHhc
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMIQN 143 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~ 143 (289)
-...+||.+++...|++|.|+.+|++.+.+-
T Consensus 252 ~~~~~li~~~l~~~P~~Rpt~~~v~~~l~~~ 282 (291)
T cd05094 252 KEVYDIMLGCWQREPQQRLNIKEIYKILHAL 282 (291)
T ss_pred HHHHHHHHHHcccChhhCcCHHHHHHHHHHH
Confidence 3578899999999999999999999998764
No 49
>cd06609 STKc_MST3_like Catalytic domain of Mammalian Ste20-like protein kinase 3-like Protein Serine/Threonine Kinases. Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 3 (MST3)-like subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST3-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily is composed of MST3, MST4, STK25, Schizosaccharomyces pombe Nak1 and Sid1, Saccharomyces cerevisiae sporulation-specific protein 1 (SPS1), and related proteins. Nak1 is required by fission yeast for polarizing the tips of actin cytoskeleton and is involved in cell growth, cell separation, cell morphology and cell-cycle progression. Sid1 is a component in the septation initiation network (SIN)
Probab=21.97 E-value=82 Score=27.64 Aligned_cols=33 Identities=15% Similarity=0.446 Sum_probs=28.6
Q ss_pred cHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCC
Q psy16819 114 SYADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKG 151 (289)
Q Consensus 114 SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ 151 (289)
...+||..++...|++|+|..+|+. .|||+.+.
T Consensus 226 ~~~~~l~~~l~~~p~~Rpt~~~il~-----~~~~~~~~ 258 (274)
T cd06609 226 PFKDFVSLCLNKDPKERPSAKELLK-----HKFIKKAK 258 (274)
T ss_pred HHHHHHHHHhhCChhhCcCHHHHhh-----ChhhcCCC
Confidence 4789999999999999999999976 58888765
No 50
>KOG0592|consensus
Probab=21.96 E-value=73 Score=33.68 Aligned_cols=35 Identities=34% Similarity=0.669 Sum_probs=30.1
Q ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCCCCCCCCCccc
Q psy16819 115 YADLISQAIQSSPEQRLTLSQIYDWMIQNVPYFKDKGDSNSSAGWKM 161 (289)
Q Consensus 115 Ya~LI~~AI~ssp~~~LTL~eIY~wi~~~~pyf~~~~ds~s~~gWkn 161 (289)
=.+||..-|.--|..|||++|| +..|||.. ..|+|
T Consensus 314 a~dLv~KLLv~dp~~Rlt~~qI-----k~HpFF~~-------Vdw~n 348 (604)
T KOG0592|consen 314 ARDLIKKLLVRDPSDRLTSQQI-----KAHPFFEG-------VDWEN 348 (604)
T ss_pred HHHHHHHHHccCccccccHHHH-----hhCccccc-------CChhh
Confidence 3578888888899999999997 56799988 68999
No 51
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=21.40 E-value=82 Score=22.87 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=27.2
Q ss_pred HHHHHHHHHHcCCC--CcccHHHHHHHHhcCCcccccCC
Q psy16819 238 YADLISQAIQSSPE--QRLTLSQIYDWMIQNVPYFKDKG 274 (289)
Q Consensus 238 Ya~LI~~AI~sSP~--~rLTL~eIY~~i~~~~pyfr~~~ 274 (289)
...+|..+|.+.+. +.++|+++..++...+|-|....
T Consensus 6 ~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~ 44 (74)
T PF12872_consen 6 LKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRD 44 (74)
T ss_dssp HHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCC
T ss_pred HHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccc
Confidence 34667788856554 48999999999999998887643
No 52
>PRK09462 fur ferric uptake regulator; Provisional
Probab=21.39 E-value=1.3e+02 Score=25.26 Aligned_cols=29 Identities=14% Similarity=0.233 Sum_probs=23.5
Q ss_pred HHHHHHHhcCCCCCcCHHHHHHHHHhcCC
Q psy16819 117 DLISQAIQSSPEQRLTLSQIYDWMIQNVP 145 (289)
Q Consensus 117 ~LI~~AI~ssp~~~LTL~eIY~wi~~~~p 145 (289)
..|..+|.+..++-||..|||+.+.+..|
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~~ 48 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMGE 48 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhCC
Confidence 45667777766678999999999998876
No 53
>cd05045 PTKc_RET Catalytic domain of the Protein Tyrosine Kinase, REarranged during Transfection protein. Protein Tyrosine Kinase (PTK) family; RET (REarranged during Transfection) protein; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. RET is a receptor tyr kinase (RTK) containing an extracellular region with four cadherin-like repeats, a calcium-binding site, and a cysteine-rich domain, a transmembrane segment, and an intracellular catalytic domain. It is part of a multisubunit complex that binds glial-derived neurotropic factor (GDNF) family ligands (GFLs) including GDNF, neurturin, artemin, and persephin. GFLs bind RET along with four GPI-anchored coreceptors, bringing two RET molecules together, leadi
Probab=21.37 E-value=88 Score=27.84 Aligned_cols=32 Identities=16% Similarity=0.264 Sum_probs=29.0
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcC
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMIQNV 144 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~~~ 144 (289)
.....||..++.-.|++|.|..||++.+.+-+
T Consensus 256 ~~~~~~i~~cl~~~P~~Rp~~~~i~~~l~~~~ 287 (290)
T cd05045 256 EEMYNLMLTCWKQEPDKRPTFADISKELEKMM 287 (290)
T ss_pred HHHHHHHHHHccCCcccCCCHHHHHHHHHHHH
Confidence 47889999999999999999999999988754
No 54
>cd07860 STKc_CDK2_3 Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase 2 and 3. Serine/Threonine Kinases (STKs), Cyclin-dependent protein kinase 2 (CDK2) and CDK3 subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The CDK2/3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. CDK2 is regulated by cyclin E or cyclin A. Upon activation by cyclin E, it phosphorylates the retinoblastoma (pRb) protein which activates E2F mediated transcription and allows cells to move into S phase. The CDK2/cyclin A complex
Probab=20.65 E-value=61 Score=28.59 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=20.8
Q ss_pred HHHHHHHHhcCCCCCcCHHHHHH
Q psy16819 116 ADLISQAIQSSPEQRLTLSQIYD 138 (289)
Q Consensus 116 a~LI~~AI~ssp~~~LTL~eIY~ 138 (289)
.+||.+++.-.|.+|+|..||..
T Consensus 258 ~~li~~~l~~~P~~Rpt~~~~l~ 280 (284)
T cd07860 258 RDLLSQMLHYDPNKRISAKAALA 280 (284)
T ss_pred HHHHHHhcCCCcccCCCHHHHhc
Confidence 47999999999999999999874
No 55
>cd06610 STKc_OSR1_SPAK Catalytic domain of the Protein Serine/Threonine Kinases, Oxidative stress response kinase and Ste20-related proline alanine-rich kinase. Serine/threonine kinases (STKs), oxidative stress response kinase (OSR1) and Ste20-related proline alanine-rich kinase (SPAK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The OSR1 and SPAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. SPAK is also referred to as STK39 or PASK (proline-alanine-rich STE20-related kinase). OSR1 and SPAK regulate the activity of cation-chloride cotransporters through direct interaction and phosphorylation. They are also implicated in cytoskeletal rearrangement, cell differentiation, transformation and proliferation. OSR1
Probab=20.37 E-value=74 Score=27.43 Aligned_cols=25 Identities=28% Similarity=0.526 Sum_probs=22.5
Q ss_pred cHHHHHHHHHhcCCCCCcCHHHHHH
Q psy16819 114 SYADLISQAIQSSPEQRLTLSQIYD 138 (289)
Q Consensus 114 SYa~LI~~AI~ssp~~~LTL~eIY~ 138 (289)
.+.+||..++...|++|.|+.||..
T Consensus 239 ~~~~li~~~l~~~p~~Rp~~~~ll~ 263 (267)
T cd06610 239 SFRKMISLCLQKDPSKRPTAEELLK 263 (267)
T ss_pred HHHHHHHHHcCCChhhCcCHHHHhh
Confidence 4689999999999999999999875
No 56
>cd05038 PTKc_Jak_rpt2 Catalytic (repeat 2) domain of the Protein Tyrosine Kinases, Janus kinases. Protein Tyrosine Kinase (PTK) family; Janus kinase (Jak) subfamily; catalytic (c) domain (repeat 2). The Jak subfamily is composed of Jak1, Jak2, Jak3, TYK2, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jak subfamily proteins are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase catalytic domain. Most Jaks are expressed in a wide variety of tissues, except for Jak3, which is expressed only in hematopoietic cells. Jaks are crucial for cytokine receptor signaling. They are activated by aut
Probab=20.20 E-value=1.1e+02 Score=26.66 Aligned_cols=30 Identities=13% Similarity=0.252 Sum_probs=26.8
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHHh
Q psy16819 113 SSYADLISQAIQSSPEQRLTLSQIYDWMIQ 142 (289)
Q Consensus 113 ~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~ 142 (289)
-....||.+++.-.|+.|.|..||.+.+..
T Consensus 253 ~~~~~li~~cl~~~p~~Rpt~~ei~~~l~~ 282 (284)
T cd05038 253 DEVYDLMKLCWEAEPQDRPSFADLILIVDR 282 (284)
T ss_pred HHHHHHHHHHhccChhhCCCHHHHHHHHhh
Confidence 467899999999999999999999998865
No 57
>cd05067 PTKc_Lck_Blk Catalytic domain of the Protein Tyrosine Kinases, Lymphocyte-specific kinase and Blk. Protein Tyrosine Kinase (PTK) family; Lck and Blk kinases; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Lck (lymphocyte-specific kinase) and Blk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Sr
Probab=20.02 E-value=99 Score=26.90 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=27.6
Q ss_pred CCcHHHHHHHHHhcCCCCCcCHHHHHHHHHh
Q psy16819 112 SSSYADLISQAIQSSPEQRLTLSQIYDWMIQ 142 (289)
Q Consensus 112 ~~SYa~LI~~AI~ssp~~~LTL~eIY~wi~~ 142 (289)
+-....||.+++...|++|.|..+|..++.+
T Consensus 229 ~~~~~~li~~~l~~~p~~Rp~~~~l~~~l~~ 259 (260)
T cd05067 229 PEELYELMRLCWKEKPEERPTFEYLRSVLED 259 (260)
T ss_pred CHHHHHHHHHHccCChhhCCCHHHHHHHhhc
Confidence 3469999999999999999999999998764
Done!