Query psy14921
Match_columns 148
No_of_seqs 159 out of 791
Neff 5.6
Searched_HMMs 46136
Date Sat Aug 17 00:21:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14921.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14921hhsearch_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 1.8E-42 3.8E-47 241.0 7.0 78 11-88 1-78 (78)
2 PF00250 Fork_head: Fork head 100.0 5.9E-42 1.3E-46 246.3 1.2 89 11-99 1-89 (96)
3 smart00339 FH FORKHEAD. FORKHE 100.0 2.9E-40 6.2E-45 234.8 6.4 83 11-93 1-83 (89)
4 KOG3563|consensus 100.0 3.4E-38 7.4E-43 269.2 8.3 87 8-94 170-256 (454)
5 KOG3562|consensus 100.0 1E-36 2.3E-41 246.8 2.8 97 8-104 10-108 (277)
6 KOG2294|consensus 100.0 6.3E-36 1.4E-40 258.2 1.3 86 8-93 127-214 (454)
7 KOG4385|consensus 99.9 3.8E-28 8.2E-33 213.4 2.1 85 4-93 361-445 (581)
8 COG5025 Transcription factor o 99.9 8.4E-24 1.8E-28 191.7 3.7 94 8-101 334-427 (610)
9 COG5025 Transcription factor o 99.6 5E-17 1.1E-21 147.8 -0.8 89 9-97 84-172 (610)
10 PF00538 Linker_histone: linke 95.9 0.012 2.6E-07 40.1 4.0 33 15-47 4-37 (77)
11 smart00526 H15 Domain in histo 95.6 0.024 5.2E-07 37.4 4.3 33 15-47 6-39 (66)
12 cd00073 H15 linker histone 1 a 94.8 0.051 1.1E-06 38.0 4.2 35 15-49 6-41 (88)
13 PF05066 HARE-HTH: HB1, ASXL, 90.5 0.26 5.5E-06 32.8 2.5 58 14-73 1-63 (72)
14 KOG4012|consensus 89.3 0.39 8.5E-06 40.0 3.3 66 13-88 44-115 (243)
15 COG2958 Uncharacterized protei 70.4 6.4 0.00014 33.6 3.9 58 15-73 6-75 (307)
16 PF12872 OST-HTH: OST-HTH/LOTU 70.1 8.9 0.00019 24.9 3.9 58 12-70 2-62 (74)
17 PF08078 PsaX: PsaX family; I 59.0 7.7 0.00017 23.3 1.7 19 7-25 5-26 (37)
18 PF14338 Mrr_N: Mrr N-terminal 52.5 16 0.00034 25.3 2.7 71 15-90 1-83 (92)
19 PF10264 Stork_head: Winged he 49.8 32 0.0007 24.1 3.9 46 16-64 12-59 (80)
20 PRK09462 fur ferric uptake reg 47.7 32 0.0007 25.6 4.0 31 18-48 20-50 (148)
21 COG0735 Fur Fe2+/Zn2+ uptake r 38.9 47 0.001 25.0 3.7 28 20-48 26-53 (145)
22 PF10826 DUF2551: Protein of u 38.6 37 0.0008 24.0 2.8 20 28-47 22-41 (83)
23 PF12317 IFT46_B_C: Intraflage 38.0 24 0.00053 29.0 2.1 27 67-93 53-79 (214)
24 KOG1528|consensus 37.7 13 0.00028 32.4 0.5 33 61-93 109-142 (351)
25 cd06649 PKc_MEK2 Catalytic dom 37.1 25 0.00054 28.7 2.1 48 16-68 277-327 (331)
26 COG3343 RpoE DNA-directed RNA 36.5 52 0.0011 26.3 3.6 34 14-47 11-46 (175)
27 PF13565 HTH_32: Homeodomain-l 36.4 1.1E+02 0.0025 19.6 4.9 37 9-47 26-64 (77)
28 PF08671 SinI: Anti-repressor 34.6 90 0.0019 17.8 3.5 24 16-43 5-28 (30)
29 cd07153 Fur_like Ferric uptake 33.5 74 0.0016 22.2 3.8 28 19-47 5-32 (116)
30 KOG0036|consensus 33.4 58 0.0012 29.6 3.8 38 7-44 43-80 (463)
31 PF01475 FUR: Ferric uptake re 32.4 51 0.0011 23.4 2.8 29 19-48 12-40 (120)
32 PF08100 Dimerisation: Dimeris 31.3 32 0.0007 21.8 1.4 23 20-42 11-33 (51)
33 PF04504 DUF573: Protein of un 30.3 52 0.0011 23.4 2.5 41 3-43 20-60 (98)
34 smart00258 SAND SAND domain. 29.3 20 0.00044 24.6 0.2 15 51-65 48-62 (73)
35 PF12367 PFO_beta_C: Pyruvate 28.7 24 0.00051 23.8 0.5 12 1-14 44-55 (67)
36 PF06894 Phage_lambd_GpG: Bact 24.8 81 0.0017 23.8 2.8 32 17-48 58-96 (127)
37 PF12157 DUF3591: Protein of u 24.7 1.2E+02 0.0025 27.7 4.3 59 18-92 245-303 (457)
38 COG5112 UFD2 U1-like Zn-finger 24.1 49 0.0011 24.7 1.5 55 59-113 31-95 (126)
39 cd07977 TFIIE_beta_winged_heli 24.0 1.7E+02 0.0036 19.8 4.1 34 10-43 4-37 (75)
40 PF13592 HTH_33: Winged helix- 23.9 68 0.0015 20.4 2.0 19 29-47 2-20 (60)
41 PF09661 DUF2398: Protein of u 22.7 88 0.0019 27.4 3.1 45 11-56 69-113 (368)
42 PF05402 PqqD: Coenzyme PQQ sy 22.6 1E+02 0.0022 19.4 2.7 18 29-46 27-44 (68)
43 PF12990 DUF3874: Domain of un 22.5 1.2E+02 0.0026 20.7 3.1 18 30-47 24-41 (73)
44 PF10978 DUF2785: Protein of u 22.5 90 0.0019 24.2 2.8 67 4-70 6-88 (175)
45 KOG4385|consensus 21.4 32 0.00069 31.8 0.1 31 55-90 472-502 (581)
46 PF09821 AAA_assoc_C: C-termin 21.4 1.9E+02 0.0041 21.3 4.2 34 14-47 63-96 (120)
47 cd01770 p47_UBX p47-like ubiqu 21.2 76 0.0016 21.5 1.9 15 32-46 25-39 (79)
48 cd05094 PTKc_TrkC Catalytic do 20.8 1.1E+02 0.0023 24.2 3.0 31 14-44 252-282 (291)
49 PF01342 SAND: SAND domain; I 20.6 28 0.00061 24.1 -0.4 13 50-62 56-68 (82)
50 PF04703 FaeA: FaeA-like prote 20.5 29 0.00062 22.9 -0.3 32 57-88 30-61 (62)
51 PF11927 DUF3445: Protein of u 20.3 79 0.0017 26.1 2.2 33 28-60 41-81 (249)
52 PF06531 DUF1108: Protein of u 20.1 71 0.0015 22.7 1.6 12 34-45 62-73 (86)
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=1.8e-42 Score=240.96 Aligned_cols=78 Identities=62% Similarity=1.173 Sum_probs=76.7
Q ss_pred CCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeec
Q psy14921 11 KCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAID 88 (148)
Q Consensus 11 KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id 88 (148)
||||||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+||+||
T Consensus 1 kP~~sY~~LI~~Ai~~sp~~~lTL~eIy~~I~~~~pyyr~~~~gWknSIRHnLS~n~~F~kv~r~~~~~gkg~~W~i~ 78 (78)
T cd00059 1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFVKVPREPDEPGKGSYWTLD 78 (78)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCCccccCCCCCccceeEecccccceEECCCCCCCCCCCCeeeeC
Confidence 899999999999999999999999999999999999999999999999999999999999999998889999999997
No 2
>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=100.00 E-value=5.9e-42 Score=246.34 Aligned_cols=89 Identities=56% Similarity=1.005 Sum_probs=81.0
Q ss_pred CCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecCC
Q psy14921 11 KCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYN 90 (148)
Q Consensus 11 KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~~ 90 (148)
||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+++.+++|||+||+|+++
T Consensus 1 KPp~sY~~LI~~Ai~~sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS~~~~F~kv~~~~~~~gkg~~W~i~~~ 80 (96)
T PF00250_consen 1 KPPYSYATLIAMAILSSPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLSLNKCFVKVPRDPSEPGKGSYWTIDPE 80 (96)
T ss_dssp -SSS-HHHHHHHHHHTSTTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHHHSTTEEEESCCTSSSSSSEEEEE-CT
T ss_pred CCCCcHHHHHHHHHHhCCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhccccceeeecCcCCCCCCCceeEEeCHH
Confidence 89999999999999999999999999999999999999999999999999999999999999998888999999999999
Q ss_pred CCCCCCCCc
Q psy14921 91 HTADDGPSK 99 (148)
Q Consensus 91 ~~~~~~~~r 99 (148)
+.......+
T Consensus 81 ~~~~~~~~~ 89 (96)
T PF00250_consen 81 AIEEFEKGR 89 (96)
T ss_dssp HHHHHHHSC
T ss_pred HHHHHhcch
Confidence 987554433
No 3
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=100.00 E-value=2.9e-40 Score=234.78 Aligned_cols=83 Identities=58% Similarity=1.051 Sum_probs=80.7
Q ss_pred CCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecCC
Q psy14921 11 KCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYN 90 (148)
Q Consensus 11 KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~~ 90 (148)
|||+||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+.+|||+||+|+++
T Consensus 1 kP~~sY~~lI~~ai~~sp~~~ltl~~Iy~~I~~~~pyy~~~~~~WknSIRHnLS~n~~F~kv~~~~~~~gkg~~W~i~~~ 80 (89)
T smart00339 1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFVKVPREGDRPGKGSYWTLDPD 80 (89)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCchhhcCccccccccccccchhhceeecCcCCCCCCCCCEEEECcc
Confidence 89999999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred CCC
Q psy14921 91 HTA 93 (148)
Q Consensus 91 ~~~ 93 (148)
+..
T Consensus 81 ~~~ 83 (89)
T smart00339 81 AEN 83 (89)
T ss_pred HHH
Confidence 875
No 4
>KOG3563|consensus
Probab=100.00 E-value=3.4e-38 Score=269.25 Aligned_cols=87 Identities=51% Similarity=0.901 Sum_probs=84.7
Q ss_pred CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeee
Q psy14921 8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAI 87 (148)
Q Consensus 8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~i 87 (148)
.+.||||||+.||.|||+.+|.++|||+|||+||++.|||||.+...|||||||.||+|+|||||+|.+|+||||+||+|
T Consensus 170 ~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfWTL 249 (454)
T KOG3563|consen 170 THAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFWTL 249 (454)
T ss_pred cCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccceee
Confidence 48899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCC
Q psy14921 88 DYNHTAD 94 (148)
Q Consensus 88 d~~~~~~ 94 (148)
.|++..-
T Consensus 250 HpdsGNM 256 (454)
T KOG3563|consen 250 HPDSGNM 256 (454)
T ss_pred cCCcCcc
Confidence 9999863
No 5
>KOG3562|consensus
Probab=100.00 E-value=1e-36 Score=246.80 Aligned_cols=97 Identities=44% Similarity=0.855 Sum_probs=88.9
Q ss_pred CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeee
Q psy14921 8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAI 87 (148)
Q Consensus 8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~i 87 (148)
+++||||||+.|.+|||++||+++|.|+|||+||+++|||||.++..||||+|||||.|+||+||+|..+.+|||+||++
T Consensus 10 ~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWal 89 (277)
T KOG3562|consen 10 GDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWAL 89 (277)
T ss_pred cccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCccceee
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCC--CCCCCccccCC
Q psy14921 88 DYNHTA--DDGPSKKKVKL 104 (148)
Q Consensus 88 d~~~~~--~~~~~rkk~r~ 104 (148)
.|.+.. |+++-.+|+||
T Consensus 90 HP~a~dMFENGS~LRRrKR 108 (277)
T KOG3562|consen 90 HPSAFDMFENGSLLRRRKR 108 (277)
T ss_pred ccchhhhcccchHHHHhhh
Confidence 999986 45543333333
No 6
>KOG2294|consensus
Probab=100.00 E-value=6.3e-36 Score=258.15 Aligned_cols=86 Identities=55% Similarity=1.000 Sum_probs=82.9
Q ss_pred CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHh-hCCCccccc-ccccccchhhcccccccccccCCCCCCCCccee
Q psy14921 8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITH-TFPYYREAN-AGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYW 85 (148)
Q Consensus 8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~-~fPyyr~~~-~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W 85 (148)
...||||||++||+|||+.+++++|||+|||+||.. +||||++.. .|||||||||||||+||+||+|..+++|||+||
T Consensus 127 ~~~kpp~SY~~LI~mAI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~~gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~W 206 (454)
T KOG2294|consen 127 AGVKPPYSYSGLIAMAIRLSPGKRLTLGGIYFYILLEHFPYYRDANMPGWKNSIRHNLSLNKCFVKVPRERGRPGKGNYW 206 (454)
T ss_pred CCcCCccccccccccccccCCCcceeecCeeEEEEeccccccccCCCccchhhcccccccccCccccCCcccCCCCCCcc
Confidence 468999999999999999999999999999999995 999999999 999999999999999999999988889999999
Q ss_pred eecCCCCC
Q psy14921 86 AIDYNHTA 93 (148)
Q Consensus 86 ~id~~~~~ 93 (148)
+||++...
T Consensus 207 ~ldP~~~~ 214 (454)
T KOG2294|consen 207 TLDPDDEN 214 (454)
T ss_pred ccCcchhc
Confidence 99998886
No 7
>KOG4385|consensus
Probab=99.94 E-value=3.8e-28 Score=213.37 Aligned_cols=85 Identities=47% Similarity=0.869 Sum_probs=80.7
Q ss_pred ecCCCCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcc
Q psy14921 4 TYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGS 83 (148)
Q Consensus 4 ~y~~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~ 83 (148)
|||+.+.+|||+||.||.+||.++|++.|||+|||.|+.+.|.|||.+.+.|||+||||||+++||++|+- -||.
T Consensus 361 fyk~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEn-----vkga 435 (581)
T KOG4385|consen 361 FYKNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VKGA 435 (581)
T ss_pred hhhccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHH-----Hhcc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999983 6899
Q ss_pred eeeecCCCCC
Q psy14921 84 YWAIDYNHTA 93 (148)
Q Consensus 84 ~W~id~~~~~ 93 (148)
-|++|+...-
T Consensus 436 vwtvDe~e~~ 445 (581)
T KOG4385|consen 436 VWTVDEREFQ 445 (581)
T ss_pred eeeeehhhhh
Confidence 9999976543
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.88 E-value=8.4e-24 Score=191.71 Aligned_cols=94 Identities=47% Similarity=0.843 Sum_probs=88.8
Q ss_pred CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeee
Q psy14921 8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAI 87 (148)
Q Consensus 8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~i 87 (148)
...||+.+|+.||++||..+++++|+|.+||.||..+||||+.+..+|+||||||||+|++|.||+|...++|||+||.|
T Consensus 334 ~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pGKg~fw~i 413 (610)
T COG5025 334 RTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPGKGCFWKI 413 (610)
T ss_pred cCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCCCcccCcc
Confidence 37899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCccc
Q psy14921 88 DYNHTADDGPSKKK 101 (148)
Q Consensus 88 d~~~~~~~~~~rkk 101 (148)
+.++..+..+.+.+
T Consensus 414 ~~s~~~~~~sk~~~ 427 (610)
T COG5025 414 DYSYIYEKESKRNP 427 (610)
T ss_pred Chhhhhhhcccccc
Confidence 99999877654443
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.61 E-value=5e-17 Score=147.81 Aligned_cols=89 Identities=39% Similarity=0.602 Sum_probs=83.9
Q ss_pred CCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeec
Q psy14921 9 NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAID 88 (148)
Q Consensus 9 ~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id 88 (148)
-.||+|+|+.+|.++|..++.+.|||..||.||-..|.||.....+|+|||||||++++.|.|+.++.+..++|.||.|.
T Consensus 84 ~~v~~~s~a~gr~~~il~s~~~~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~ig 163 (610)
T COG5025 84 YYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWSIG 163 (610)
T ss_pred cccCCeeeeeccccccccCcccCCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceeeccC
Confidence 36999999999999999999999999999999999999999999999999999999999999999998989999999999
Q ss_pred CCCCCCCCC
Q psy14921 89 YNHTADDGP 97 (148)
Q Consensus 89 ~~~~~~~~~ 97 (148)
|+.......
T Consensus 164 P~~~~~~l~ 172 (610)
T COG5025 164 PGHETQFLK 172 (610)
T ss_pred CCccceeec
Confidence 988865443
No 10
>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=95.94 E-value=0.012 Score=40.07 Aligned_cols=33 Identities=21% Similarity=0.362 Sum_probs=29.3
Q ss_pred hHHHHHHHHHhhCCC-CCcCHHHHHHHHHhhCCC
Q psy14921 15 SYASLIRLAISNAPQ-GRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 15 SYa~LI~~AI~~sp~-~~LtL~eIY~~i~~~fPy 47 (148)
+|.+||.+||.+..+ +..++..|..||+++|+.
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 589999999999666 559999999999999975
No 11
>smart00526 H15 Domain in histone families 1 and 5.
Probab=95.61 E-value=0.024 Score=37.37 Aligned_cols=33 Identities=24% Similarity=0.440 Sum_probs=29.0
Q ss_pred hHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhCCC
Q psy14921 15 SYASLIRLAISNAPQGR-MTLNEIYQFITHTFPY 47 (148)
Q Consensus 15 SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~fPy 47 (148)
+|..||.+||.+..++. .++..|..||+.+|+.
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~ 39 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYKV 39 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCC
Confidence 79999999999976644 9999999999999663
No 12
>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=94.82 E-value=0.051 Score=38.00 Aligned_cols=35 Identities=17% Similarity=0.319 Sum_probs=29.6
Q ss_pred hHHHHHHHHHhhCCCC-CcCHHHHHHHHHhhCCCcc
Q psy14921 15 SYASLIRLAISNAPQG-RMTLNEIYQFITHTFPYYR 49 (148)
Q Consensus 15 SYa~LI~~AI~~sp~~-~LtL~eIY~~i~~~fPyyr 49 (148)
+|..||.+||.+..++ ..++..|..||+.+|+.-.
T Consensus 6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~ 41 (88)
T cd00073 6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDD 41 (88)
T ss_pred CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcch
Confidence 7899999999995544 4999999999999988643
No 13
>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=90.46 E-value=0.26 Score=32.80 Aligned_cols=58 Identities=21% Similarity=0.249 Sum_probs=38.0
Q ss_pred chHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcc-----ccccccccc
Q psy14921 14 SSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLS-----LNKCFTKVA 73 (148)
Q Consensus 14 ~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS-----~n~~F~Kv~ 73 (148)
+||..++...|+... +.|+.+||++.|.+.--+ ....+...++|+-.|. .+..|++|.
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~-~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg 63 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQERGLY-KKSGKTPEATIAAQLYTDIKNEDSRFVKVG 63 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS----GGGGGHHHH-HHHHHHH-T-SS-EESS
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCC-CcccCCHHHHHHHHHHHHcccCCCCEEEeC
Confidence 478888998898886 779999999999987655 2225566777773333 445898874
No 14
>KOG4012|consensus
Probab=89.34 E-value=0.39 Score=40.05 Aligned_cols=66 Identities=24% Similarity=0.396 Sum_probs=46.2
Q ss_pred CchHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhCCCcccccccccccchhhccccc-----ccccccCCCCCCCCcceee
Q psy14921 13 TSSYASLIRLAISNAPQGR-MTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNK-----CFTKVARPKDDPGKGSYWA 86 (148)
Q Consensus 13 p~SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~-----~F~Kv~r~~~~~gkg~~W~ 86 (148)
.-+|.+||..||....++. .++.-|+.||..+|+.|.-.. +--|.+++|+. .|+++- |.|.-|.
T Consensus 44 ~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k----~n~~lk~alK~~v~~g~l~Qtk------G~GAsGs 113 (243)
T KOG4012|consen 44 HPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEK----NNSRLKLALKKGVSKGVLVQTK------GTGASGS 113 (243)
T ss_pred CCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhh----hhHHHHHHHHhhhccCceeeec------cCCcccc
Confidence 4479999999999987776 999999999999998876432 12355555543 454433 5555555
Q ss_pred ec
Q psy14921 87 ID 88 (148)
Q Consensus 87 id 88 (148)
+.
T Consensus 114 Fk 115 (243)
T KOG4012|consen 114 FK 115 (243)
T ss_pred cc
Confidence 44
No 15
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.45 E-value=6.4 Score=33.61 Aligned_cols=58 Identities=21% Similarity=0.171 Sum_probs=41.9
Q ss_pred hHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCc------ccccccc------cccchhhccccccccccc
Q psy14921 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYY------REANAGW------KNSIRHNLSLNKCFTKVA 73 (148)
Q Consensus 15 SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyy------r~~~~gW------knSIRHnLS~n~~F~Kv~ 73 (148)
+|..+|-..++. .++.+|..|||+|+.+.||-= ...++.= --+.|-||-.+.-|.||.
T Consensus 6 ~~~e~vl~~Lq~-~~ep~t~~eI~eka~e~~~~~~~~kk~~s~g~tp~q~va~~iy~~~~lq~~~pflKvt 75 (307)
T COG2958 6 NLIEIVLSVLQT-SEEPFTAREIAEKAFETFPAECQEKKFDSGGDTPQQLVAEIIYTRPNLQEKHPFLKVT 75 (307)
T ss_pred hhHHHHHHHHHc-cCCCCcHHHHHHHHHHhccHHHHHHhhccccccHHHHHHHHHhcCccccccCcccccc
Confidence 466666666666 788899999999999999853 2222222 245677888888999987
No 16
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=70.13 E-value=8.9 Score=24.87 Aligned_cols=58 Identities=19% Similarity=0.328 Sum_probs=37.5
Q ss_pred CCchHHHHHHHHHhhCCC--CCcCHHHHHHHHHhhCCCcccccccccccchhhc-ccccccc
Q psy14921 12 CTSSYASLIRLAISNAPQ--GRMTLNEIYQFITHTFPYYREANAGWKNSIRHNL-SLNKCFT 70 (148)
Q Consensus 12 Pp~SYa~LI~~AI~~sp~--~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnL-S~n~~F~ 70 (148)
++-.-..+|..+|.+.++ |.+.|+++-.++.+++|-|....=|.. ++++-| ++-..|+
T Consensus 2 ~~~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~-~l~~ll~~~~~~~~ 62 (74)
T PF12872_consen 2 SLEELKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFS-SLSELLESLPDVVE 62 (74)
T ss_dssp --HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSS-SHHHHHHT-TTTEE
T ss_pred hHHHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCC-cHHHHHHhCCCeEE
Confidence 444556789999955543 579999999999999998876655554 355555 4344443
No 17
>PF08078 PsaX: PsaX family; InterPro: IPR012986 This family consists of the PsaX family of photosystem I (PSI) protein subunits. PSI is a large multi-subunit pigment protein complex embedded in the thylakoid membranes of green plants and cyanobacteria. PsaX is one of the 12 protein subunits found in PSI and these subunits are arranged as monomers or trimers within the membrane as shown by the structure of the trimeric complex from Synechococcus elongatus [].; PDB: 3PCQ_X 1JB0_X.
Probab=58.98 E-value=7.7 Score=23.26 Aligned_cols=19 Identities=26% Similarity=0.307 Sum_probs=8.0
Q ss_pred CCCCCCCchH---HHHHHHHHh
Q psy14921 7 TGNIKCTSSY---ASLIRLAIS 25 (148)
Q Consensus 7 ~~~~KPp~SY---a~LI~~AI~ 25 (148)
++..||||.| .+|+-+||.
T Consensus 5 ~k~akp~Y~frt~Wa~llLaIN 26 (37)
T PF08078_consen 5 NKTAKPPYTFRTGWALLLLAIN 26 (37)
T ss_dssp ---------HHHHHHHHHHHHH
T ss_pred cCCCCCCeehhHHHHHHHHHHH
Confidence 5678999999 788888875
No 18
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=52.51 E-value=16 Score=25.26 Aligned_cols=71 Identities=27% Similarity=0.430 Sum_probs=46.3
Q ss_pred hHHHHHHHHHhh--CCCCCcCHHHHHHHHHhhCCCccc-------cc---ccccccchhhcccccccccccCCCCCCCCc
Q psy14921 15 SYASLIRLAISN--APQGRMTLNEIYQFITHTFPYYRE-------AN---AGWKNSIRHNLSLNKCFTKVARPKDDPGKG 82 (148)
Q Consensus 15 SYa~LI~~AI~~--sp~~~LtL~eIY~~i~~~fPyyr~-------~~---~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg 82 (148)
+|..|+...|+. .-++.++.+||++.|.++|..=.. ++ .-|+|.|+=.++-=++.--|++ +++|
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~----~~rG 76 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIER----PKRG 76 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccC----CCCC
Confidence 456666655544 225789999999999999985411 12 2599999876665444444444 3344
Q ss_pred ceeeecCC
Q psy14921 83 SYWAIDYN 90 (148)
Q Consensus 83 ~~W~id~~ 90 (148)
.|.|.+.
T Consensus 77 -~~~iT~~ 83 (92)
T PF14338_consen 77 -IWRITEK 83 (92)
T ss_pred -ceEECHh
Confidence 8998754
No 19
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=49.82 E-value=32 Score=24.06 Aligned_cols=46 Identities=13% Similarity=0.229 Sum_probs=33.9
Q ss_pred HHHHHHHHHhh--CCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcc
Q psy14921 16 YASLIRLAISN--APQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLS 64 (148)
Q Consensus 16 Ya~LI~~AI~~--sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS 64 (148)
-+..|+.||.+ +.+...|+..|.+++.++||--..-. +..|++.|.
T Consensus 12 L~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps---~e~l~~~L~ 59 (80)
T PF10264_consen 12 LPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPS---QEVLYNTLG 59 (80)
T ss_pred HHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCC---HHHHHHHHH
Confidence 46778888866 77777999999999999999865322 234555554
No 20
>PRK09462 fur ferric uptake regulator; Provisional
Probab=47.66 E-value=32 Score=25.61 Aligned_cols=31 Identities=6% Similarity=0.062 Sum_probs=24.5
Q ss_pred HHHHHHHhhCCCCCcCHHHHHHHHHhhCCCc
Q psy14921 18 SLIRLAISNAPQGRMTLNEIYQFITHTFPYY 48 (148)
Q Consensus 18 ~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyy 48 (148)
..|..+|.++.++-+|..|||+.+.+..|-.
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i 50 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMGEEI 50 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhCCCC
Confidence 3566677776667899999999999988753
No 21
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=38.85 E-value=47 Score=25.02 Aligned_cols=28 Identities=14% Similarity=0.173 Sum_probs=22.0
Q ss_pred HHHHHhhCCCCCcCHHHHHHHHHhhCCCc
Q psy14921 20 IRLAISNAPQGRMTLNEIYQFITHTFPYY 48 (148)
Q Consensus 20 I~~AI~~sp~~~LtL~eIY~~i~~~fPyy 48 (148)
|...|..+.+. +|..|||+.+.+.+|--
T Consensus 26 vl~~L~~~~~~-~sAeei~~~l~~~~p~i 53 (145)
T COG0735 26 VLELLLEADGH-LSAEELYEELREEGPGI 53 (145)
T ss_pred HHHHHHhcCCC-CCHHHHHHHHHHhCCCC
Confidence 44556666666 99999999999998864
No 22
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=38.58 E-value=37 Score=24.01 Aligned_cols=20 Identities=20% Similarity=0.444 Sum_probs=17.5
Q ss_pred CCCCcCHHHHHHHHHhhCCC
Q psy14921 28 PQGRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 28 p~~~LtL~eIY~~i~~~fPy 47 (148)
..+.+|..|||+.+.++|.-
T Consensus 22 ~~~~~T~~di~e~L~~~f~v 41 (83)
T PF10826_consen 22 KGKKFTTDDIYERLKEKFDV 41 (83)
T ss_pred hCCCeeHHHHHHHHHHHcCc
Confidence 46889999999999999764
No 23
>PF12317 IFT46_B_C: Intraflagellar transport complex B protein 46 C terminal; InterPro: IPR022088 This entry represents proteins is found in eukaryotes. Proteins are typically between 298 and 416 amino acids in length. It is thought to be a flagellar protein of complex B and like all IFT proteins, it is required for transport of IFT particles into the flagella [].
Probab=38.04 E-value=24 Score=29.00 Aligned_cols=27 Identities=26% Similarity=0.406 Sum_probs=23.5
Q ss_pred cccccccCCCCCCCCcceeeecCCCCC
Q psy14921 67 KCFTKVARPKDDPGKGSYWAIDYNHTA 93 (148)
Q Consensus 67 ~~F~Kv~r~~~~~gkg~~W~id~~~~~ 93 (148)
+.|.||+|+.+.+-+-+++.+|+-+..
T Consensus 53 DaFiKVpRPD~~~d~LGL~vLDEP~~~ 79 (214)
T PF12317_consen 53 DAFIKVPRPDGKPDNLGLTVLDEPSAN 79 (214)
T ss_pred ccceeccCCCCCccccCCEEecCCCcc
Confidence 689999999888878889999998864
No 24
>KOG1528|consensus
Probab=37.73 E-value=13 Score=32.41 Aligned_cols=33 Identities=21% Similarity=0.378 Sum_probs=24.3
Q ss_pred hhcccccccccccCCCCCC-CCcceeeecCCCCC
Q psy14921 61 HNLSLNKCFTKVARPKDDP-GKGSYWAIDYNHTA 93 (148)
Q Consensus 61 HnLS~n~~F~Kv~r~~~~~-gkg~~W~id~~~~~ 93 (148)
.-||..+...-+.|...+. .||.+|.+||-...
T Consensus 109 ~~ls~~dvl~aID~G~s~GG~kGrhWvLDPIDGT 142 (351)
T KOG1528|consen 109 SPLSSDDVLKAIDRGNSEGGPKGRHWVLDPIDGT 142 (351)
T ss_pred CCCCHHHHHHHHhcccccCCCCCceEEeccCCCc
Confidence 3477777777787765444 48999999997663
No 25
>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=37.10 E-value=25 Score=28.74 Aligned_cols=48 Identities=13% Similarity=0.333 Sum_probs=38.9
Q ss_pred HHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCccc---ccccccccchhhcccccc
Q psy14921 16 YASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE---ANAGWKNSIRHNLSLNKC 68 (148)
Q Consensus 16 Ya~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~---~~~gWknSIRHnLS~n~~ 68 (148)
+..||...+.-.|+.|.|..||.+ .|||+. ....|++.+..+|+++.-
T Consensus 277 l~~li~~~L~~~P~~Rpt~~ell~-----h~~~~~~~~~~~~~~~~~~~~~~~~~~ 327 (331)
T cd06649 277 FQEFVNKCLIKNPAERADLKMLMN-----HTFIKRSEVEEVDFAGWLCKTLRLNQP 327 (331)
T ss_pred HHHHHHHHccCCcccCCCHHHHhc-----ChHHhhcccccccHHHHHHHhhccccc
Confidence 678999999999999999999964 466654 356788888888887743
No 26
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=36.49 E-value=52 Score=26.31 Aligned_cols=34 Identities=24% Similarity=0.228 Sum_probs=28.0
Q ss_pred chHHHHHHHH--HhhCCCCCcCHHHHHHHHHhhCCC
Q psy14921 14 SSYASLIRLA--ISNAPQGRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 14 ~SYa~LI~~A--I~~sp~~~LtL~eIY~~i~~~fPy 47 (148)
.++.+||.+| |..-..+.|++++|.+-|.+.+-+
T Consensus 11 ~~els~IevA~~ile~~~~~~~F~dii~EI~~~~~~ 46 (175)
T COG3343 11 LSELSLIEVAHAILEEKKKPFNFSDIINEIQKLLGV 46 (175)
T ss_pred HHHHHHHHHHHHHHHHcCCCccHHHHHHHHHHHhCc
Confidence 4788888777 777767789999999999988766
No 27
>PF13565 HTH_32: Homeodomain-like domain
Probab=36.42 E-value=1.1e+02 Score=19.55 Aligned_cols=37 Identities=22% Similarity=0.225 Sum_probs=26.1
Q ss_pred CCCCCc-hHH-HHHHHHHhhCCCCCcCHHHHHHHHHhhCCC
Q psy14921 9 NIKCTS-SYA-SLIRLAISNAPQGRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 9 ~~KPp~-SYa-~LI~~AI~~sp~~~LtL~eIY~~i~~~fPy 47 (148)
..+|.- .-. +.|...+...| .+|+.+|.++|+..|..
T Consensus 26 ~Grp~~~~e~~~~i~~~~~~~p--~wt~~~i~~~L~~~~g~ 64 (77)
T PF13565_consen 26 PGRPRKDPEQRERIIALIEEHP--RWTPREIAEYLEEEFGI 64 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHhCC
Confidence 444433 333 56666666666 89999999999998763
No 28
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=34.62 E-value=90 Score=17.84 Aligned_cols=24 Identities=25% Similarity=0.458 Sum_probs=17.5
Q ss_pred HHHHHHHHHhhCCCCCcCHHHHHHHHHh
Q psy14921 16 YASLIRLAISNAPQGRMTLNEIYQFITH 43 (148)
Q Consensus 16 Ya~LI~~AI~~sp~~~LtL~eIY~~i~~ 43 (148)
+..||.+|+.. .||..||=+|+..
T Consensus 5 W~~Li~eA~~~----Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKES----GLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHT----T--HHHHHHHHHH
T ss_pred HHHHHHHHHHc----CCCHHHHHHHHHh
Confidence 57899999875 4999999888764
No 29
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=33.49 E-value=74 Score=22.17 Aligned_cols=28 Identities=25% Similarity=0.375 Sum_probs=21.9
Q ss_pred HHHHHHhhCCCCCcCHHHHHHHHHhhCCC
Q psy14921 19 LIRLAISNAPQGRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 19 LI~~AI~~sp~~~LtL~eIY~~i~~~fPy 47 (148)
.|..+|..+ ++-+|..|||+.+.+..|-
T Consensus 5 ~Il~~l~~~-~~~~sa~ei~~~l~~~~~~ 32 (116)
T cd07153 5 AILEVLLES-DGHLTAEEIYERLRKKGPS 32 (116)
T ss_pred HHHHHHHhC-CCCCCHHHHHHHHHhcCCC
Confidence 466677766 5669999999999987663
No 30
>KOG0036|consensus
Probab=33.35 E-value=58 Score=29.64 Aligned_cols=38 Identities=16% Similarity=0.253 Sum_probs=33.5
Q ss_pred CCCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhh
Q psy14921 7 TGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHT 44 (148)
Q Consensus 7 ~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~ 44 (148)
..+++|++.|+.+|..++....++++.++|.-.|+.++
T Consensus 43 l~~~~~~~~~~~~l~~~~d~~~dg~vDy~eF~~Y~~~~ 80 (463)
T KOG0036|consen 43 LDHPKPNYEAAKMLFSAMDANRDGRVDYSEFKRYLDNK 80 (463)
T ss_pred cCCCCCchHHHHHHHHhcccCcCCcccHHHHHHHHHHh
Confidence 45669999999999999999999999999988887654
No 31
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=32.37 E-value=51 Score=23.38 Aligned_cols=29 Identities=24% Similarity=0.376 Sum_probs=23.0
Q ss_pred HHHHHHhhCCCCCcCHHHHHHHHHhhCCCc
Q psy14921 19 LIRLAISNAPQGRMTLNEIYQFITHTFPYY 48 (148)
Q Consensus 19 LI~~AI~~sp~~~LtL~eIY~~i~~~fPyy 48 (148)
.|..+|.+.+. -+|..|||+.+....|-.
T Consensus 12 ~Il~~l~~~~~-~~ta~ei~~~l~~~~~~i 40 (120)
T PF01475_consen 12 AILELLKESPE-HLTAEEIYDKLRKKGPRI 40 (120)
T ss_dssp HHHHHHHHHSS-SEEHHHHHHHHHHTTTT-
T ss_pred HHHHHHHcCCC-CCCHHHHHHHhhhccCCc
Confidence 46677777777 799999999999877653
No 32
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=31.26 E-value=32 Score=21.78 Aligned_cols=23 Identities=35% Similarity=0.371 Sum_probs=16.7
Q ss_pred HHHHHhhCCCCCcCHHHHHHHHH
Q psy14921 20 IRLAISNAPQGRMTLNEIYQFIT 42 (148)
Q Consensus 20 I~~AI~~sp~~~LtL~eIY~~i~ 42 (148)
|..+|.++.++.+|+.||-.-+.
T Consensus 11 I~dii~~~g~~~ls~~eia~~l~ 33 (51)
T PF08100_consen 11 IPDIIHNAGGGPLSLSEIAARLP 33 (51)
T ss_dssp HHHHHHHHTTS-BEHHHHHHTST
T ss_pred cHHHHHHcCCCCCCHHHHHHHcC
Confidence 56678777778899999976544
No 33
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=30.26 E-value=52 Score=23.40 Aligned_cols=41 Identities=12% Similarity=0.137 Sum_probs=31.1
Q ss_pred eecCCCCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHh
Q psy14921 3 ITYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITH 43 (148)
Q Consensus 3 ~~y~~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~ 43 (148)
|+|..++.+.|+....-...+|..+-....+..|+|+-|..
T Consensus 20 ~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kirr 60 (98)
T PF04504_consen 20 IDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRR 60 (98)
T ss_pred HHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence 56777777777777767777888877777888888887764
No 34
>smart00258 SAND SAND domain.
Probab=29.30 E-value=20 Score=24.65 Aligned_cols=15 Identities=40% Similarity=0.525 Sum_probs=11.9
Q ss_pred ccccccccchhhccc
Q psy14921 51 ANAGWKNSIRHNLSL 65 (148)
Q Consensus 51 ~~~gWknSIRHnLS~ 65 (148)
..+.||-|||+|=+.
T Consensus 48 ~~K~WK~sIR~~g~~ 62 (73)
T smart00258 48 KSKDWKRSIRCGGSS 62 (73)
T ss_pred ccCCcchheeECCcc
Confidence 467899999988544
No 35
>PF12367 PFO_beta_C: Pyruvate ferredoxin oxidoreductase beta subunit C terminal
Probab=28.73 E-value=24 Score=23.76 Aligned_cols=12 Identities=33% Similarity=0.371 Sum_probs=9.7
Q ss_pred CceecCCCCCCCCc
Q psy14921 1 LCITYKTGNIKCTS 14 (148)
Q Consensus 1 ~~~~y~~~~~KPp~ 14 (148)
|||+|++. +|.|
T Consensus 44 lGIfY~~~--~ptf 55 (67)
T PF12367_consen 44 LGIFYRNE--RPTF 55 (67)
T ss_pred EEEEEeCC--CCCH
Confidence 69999998 7763
No 36
>PF06894 Phage_lambd_GpG: Bacteriophage lambda minor tail protein (GpG); InterPro: IPR010027 This entry is represented by Bacteriophage lambda, GpG, a minor tail protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry identifies a family of bacteriophage proteins including G of phage lambda. This protein has been described as undergoing a translational frameshift at a Gly-Lys dipeptide near the C terminus of protein G from phage lambda, with about 4% efficiency, to produce tail assembly protein G-T.
Probab=24.83 E-value=81 Score=23.78 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=27.1
Q ss_pred HHHHHHHHhhC-------CCCCcCHHHHHHHHHhhCCCc
Q psy14921 17 ASLIRLAISNA-------PQGRMTLNEIYQFITHTFPYY 48 (148)
Q Consensus 17 a~LI~~AI~~s-------p~~~LtL~eIY~~i~~~fPyy 48 (148)
+=||++.|-.+ ++..=.+.+|++-|+..||+=
T Consensus 58 A~LVA~SLwh~h~~k~~~~~~~~~v~~lq~eVm~tWp~e 96 (127)
T PF06894_consen 58 AWLVAMSLWHSHPQKGEYPDPEEDVEELQQEVMSTWPPE 96 (127)
T ss_pred HHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHhCCHH
Confidence 45888998877 667788999999999999983
No 37
>PF12157 DUF3591: Protein of unknown function (DUF3591); InterPro: IPR022591 This functionally uncharacterised domain is found centrally in the eukaryotic transcription initiation factor TFIID subunit 1.
Probab=24.69 E-value=1.2e+02 Score=27.72 Aligned_cols=59 Identities=20% Similarity=0.411 Sum_probs=40.3
Q ss_pred HHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecCCCC
Q psy14921 18 SLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYNHT 92 (148)
Q Consensus 18 ~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~~~~ 92 (148)
.+|...+..+..+++.+.+| .++||... ..+||..|-.--.| .|.+. ...+|.+.++..
T Consensus 245 ~~iyRlf~~~~~~ri~~~di----~~~Fp~~s------e~~iRkrLKe~~~~---~R~g~---~~~~W~lk~~~~ 303 (457)
T PF12157_consen 245 MIIYRLFNKSQPRRIKVDDI----KKHFPDQS------ESQIRKRLKEFADF---QRTGD---DSGWWVLKPGFR 303 (457)
T ss_pred HHHHHHHhhccCCccCHHHH----HHhCCCCc------HHHHHHHHHHHHhc---cCCCC---CCCeEEECCCCC
Confidence 35666677788889999988 55677754 34588888644444 44322 267999999765
No 38
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=24.09 E-value=49 Score=24.75 Aligned_cols=55 Identities=24% Similarity=0.365 Sum_probs=37.5
Q ss_pred chhhcccccccccccCCCCCCCCcceeeecCCCCC----------CCCCCccccCCCCCCCCCcc
Q psy14921 59 IRHNLSLNKCFTKVARPKDDPGKGSYWAIDYNHTA----------DDGPSKKKVKLPRVSPYSPV 113 (148)
Q Consensus 59 IRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~~~~~----------~~~~~rkk~r~~~~~p~~~~ 113 (148)
|..-||-.+.|.|++-+++.||-|.++.|.-+--. ...-.++|.+..|..||..-
T Consensus 31 i~nDls~~Es~~Klp~Dp~lPGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRevpytQe 95 (126)
T COG5112 31 IKNDLSTKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREVPYTQE 95 (126)
T ss_pred HHHhcchhhhhccCCCCCCCCCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcCcchhH
Confidence 44567888899999999999999999998654321 11122444444677777654
No 39
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=24.04 E-value=1.7e+02 Score=19.82 Aligned_cols=34 Identities=18% Similarity=0.144 Sum_probs=27.6
Q ss_pred CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHh
Q psy14921 10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITH 43 (148)
Q Consensus 10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~ 43 (148)
.+--+|+.+.|-.-|+.....-+|+.||.+++..
T Consensus 4 g~~~~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~ 37 (75)
T cd07977 4 GTHVFTQLAKIVDYMKKRHQHPLTLDEILDYLSL 37 (75)
T ss_pred CcchhhhHHHHHHHHHhcCCCCccHHHHHHHHhc
Confidence 4456788888888899887677999999999874
No 40
>PF13592 HTH_33: Winged helix-turn helix
Probab=23.91 E-value=68 Score=20.37 Aligned_cols=19 Identities=42% Similarity=0.621 Sum_probs=14.0
Q ss_pred CCCcCHHHHHHHHHhhCCC
Q psy14921 29 QGRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 29 ~~~LtL~eIY~~i~~~fPy 47 (148)
++..|+.+|.++|++.|--
T Consensus 2 ~~~wt~~~i~~~I~~~fgv 20 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGV 20 (60)
T ss_pred CCcccHHHHHHHHHHHHCC
Confidence 3457888888888887764
No 41
>PF09661 DUF2398: Protein of unknown function (DUF2398); InterPro: IPR013494 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=22.69 E-value=88 Score=27.38 Aligned_cols=45 Identities=11% Similarity=0.135 Sum_probs=33.8
Q ss_pred CCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCccccccccc
Q psy14921 11 KCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWK 56 (148)
Q Consensus 11 KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWk 56 (148)
+--|-|.+|+.+++.. .+.+.||+++.+.|...++--.-..-.|.
T Consensus 69 ~r~Y~~lcl~La~Le~-~~~Qf~Ls~L~e~v~~~a~~~~~~~~d~~ 113 (368)
T PF09661_consen 69 PRRYALLCLVLAFLED-AGEQFTLSELAERVRAAAAEEGLEEFDWT 113 (368)
T ss_pred hHHHHHHHHHHHHHCC-CCCeEEHHHHHHHHHHhcccccccccCcc
Confidence 3467888888888888 78889999999999977774332224465
No 42
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=22.57 E-value=1e+02 Score=19.39 Aligned_cols=18 Identities=22% Similarity=0.433 Sum_probs=14.6
Q ss_pred CCCcCHHHHHHHHHhhCC
Q psy14921 29 QGRMTLNEIYQFITHTFP 46 (148)
Q Consensus 29 ~~~LtL~eIY~~i~~~fP 46 (148)
++..|+.||.+.+.++|.
T Consensus 27 ~g~~t~~ei~~~l~~~y~ 44 (68)
T PF05402_consen 27 DGPRTVEEIVDALAEEYD 44 (68)
T ss_dssp -SSS-HHHHHHHHHHHTT
T ss_pred cCCCCHHHHHHHHHHHcC
Confidence 578999999999999984
No 43
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=22.54 E-value=1.2e+02 Score=20.66 Aligned_cols=18 Identities=17% Similarity=0.329 Sum_probs=16.0
Q ss_pred CCcCHHHHHHHHHhhCCC
Q psy14921 30 GRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 30 ~~LtL~eIY~~i~~~fPy 47 (148)
..||..||++.|.+++|-
T Consensus 24 e~lsa~~If~~L~k~~~~ 41 (73)
T PF12990_consen 24 EWLSAAEIFERLQKKSPA 41 (73)
T ss_pred eeecHHHHHHHHHHhCcc
Confidence 349999999999999986
No 44
>PF10978 DUF2785: Protein of unknown function (DUF2785); InterPro: IPR021247 Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family has no known function.
Probab=22.47 E-value=90 Score=24.24 Aligned_cols=67 Identities=18% Similarity=0.274 Sum_probs=48.0
Q ss_pred ecCCCCCCCCchHHHHHHHHHhhCCCCC--cCHHHHHHHHHhhCCCccc--------ccccccccchhh------ccccc
Q psy14921 4 TYKTGNIKCTSSYASLIRLAISNAPQGR--MTLNEIYQFITHTFPYYRE--------ANAGWKNSIRHN------LSLNK 67 (148)
Q Consensus 4 ~y~~~~~KPp~SYa~LI~~AI~~sp~~~--LtL~eIY~~i~~~fPyyr~--------~~~gWknSIRHn------LS~n~ 67 (148)
+-++.+.=-.-||++||--.|....... ||-++|..++..-.-|... ...||-=+|-|- |..+.
T Consensus 6 ~e~~~d~vf~RSFsaL~la~il~~d~~~~fL~~~~~~~~~~~~~~Yl~~E~D~RGfv~~~GWaHa~AH~aD~l~el~~~p 85 (175)
T PF10978_consen 6 GEPGNDAVFTRSFSALLLALILYADRNYPFLSQEERQELIDQLIRYLLLEKDTRGFVEEKGWAHAFAHGADLLDELVQHP 85 (175)
T ss_pred CCCCCcceeeehHHHHHHHHHHhcCCcccCCCHHHHHHHHHHHHHHHHHccccccCCccCcHHHHHHHHHHHHHHHHcCC
Confidence 3334444556799999988888755433 9999999999888888742 467999999884 45555
Q ss_pred ccc
Q psy14921 68 CFT 70 (148)
Q Consensus 68 ~F~ 70 (148)
.|.
T Consensus 86 ~~~ 88 (175)
T PF10978_consen 86 ELD 88 (175)
T ss_pred CCC
Confidence 554
No 45
>KOG4385|consensus
Probab=21.43 E-value=32 Score=31.83 Aligned_cols=31 Identities=16% Similarity=0.224 Sum_probs=26.5
Q ss_pred ccccchhhcccccccccccCCCCCCCCcceeeecCC
Q psy14921 55 WKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYN 90 (148)
Q Consensus 55 WknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~~ 90 (148)
-.++++|+|+.|.||.++. +|+|+-|+++.-
T Consensus 472 ~~a~l~~al~~~~~~lls~-----a~~~~~~s~~~L 502 (581)
T KOG4385|consen 472 PNAALQAALAENSLPLLSE-----AGMGNNWSVGEL 502 (581)
T ss_pred hhHHHHHHhhcCccccccc-----hhccCCcchhhH
Confidence 4688999999999999877 689999988653
No 46
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=21.40 E-value=1.9e+02 Score=21.28 Aligned_cols=34 Identities=18% Similarity=0.282 Sum_probs=30.2
Q ss_pred chHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCC
Q psy14921 14 SSYASLIRLAISNAPQGRMTLNEIYQFITHTFPY 47 (148)
Q Consensus 14 ~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPy 47 (148)
..+++.|..++.+.+++++.-..+.+.++..||.
T Consensus 63 ~Pl~~~I~~~L~~~~~~~~~~~~~~~~L~~~~~~ 96 (120)
T PF09821_consen 63 VPLAAHIRRVLRERPNHRLPEERFLDELEDHFSP 96 (120)
T ss_pred CCHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCCh
Confidence 3578899999999999999999999999998864
No 47
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=21.17 E-value=76 Score=21.52 Aligned_cols=15 Identities=20% Similarity=0.518 Sum_probs=12.7
Q ss_pred cCHHHHHHHHHhhCC
Q psy14921 32 MTLNEIYQFITHTFP 46 (148)
Q Consensus 32 LtL~eIY~~i~~~fP 46 (148)
-|+.+||+||..+.|
T Consensus 25 ~tv~~l~~~v~~~~~ 39 (79)
T cd01770 25 HRVSDVRDFIVNARP 39 (79)
T ss_pred CcHHHHHHHHHHhCC
Confidence 489999999998754
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=20.80 E-value=1.1e+02 Score=24.21 Aligned_cols=31 Identities=19% Similarity=0.373 Sum_probs=26.9
Q ss_pred chHHHHHHHHHhhCCCCCcCHHHHHHHHHhh
Q psy14921 14 SSYASLIRLAISNAPQGRMTLNEIYQFITHT 44 (148)
Q Consensus 14 ~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~ 44 (148)
-....||...+...|.+|.|+.||.+.+.+-
T Consensus 252 ~~~~~li~~~l~~~P~~Rpt~~~v~~~l~~~ 282 (291)
T cd05094 252 KEVYDIMLGCWQREPQQRLNIKEIYKILHAL 282 (291)
T ss_pred HHHHHHHHHHcccChhhCcCHHHHHHHHHHH
Confidence 3477899999999999999999999988754
No 49
>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=20.59 E-value=28 Score=24.10 Aligned_cols=13 Identities=38% Similarity=0.734 Sum_probs=9.2
Q ss_pred cccccccccchhh
Q psy14921 50 EANAGWKNSIRHN 62 (148)
Q Consensus 50 ~~~~gWknSIRHn 62 (148)
...+.||.|||.+
T Consensus 56 ~~sK~WK~SIr~~ 68 (82)
T PF01342_consen 56 GSSKDWKRSIRCG 68 (82)
T ss_dssp CTCS-HHHHSEET
T ss_pred ccCCCCCccEEEC
Confidence 3456799999973
No 50
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=20.53 E-value=29 Score=22.94 Aligned_cols=32 Identities=28% Similarity=0.384 Sum_probs=20.3
Q ss_pred ccchhhcccccccccccCCCCCCCCcceeeec
Q psy14921 57 NSIRHNLSLNKCFTKVARPKDDPGKGSYWAID 88 (148)
Q Consensus 57 nSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id 88 (148)
..+||=|..=.---+|.+.+...|+.-||.++
T Consensus 30 ~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~l~ 61 (62)
T PF04703_consen 30 YQARYYLEKLEKEGKVERSPVRRGKSTYWRLN 61 (62)
T ss_dssp HHHHHHHHHHHHCTSEEEES-SSSSS-EEEES
T ss_pred HHHHHHHHHHHHCCCEEEecCCCCcceeeeec
Confidence 45777777655455666655556777799986
No 51
>PF11927 DUF3445: Protein of unknown function (DUF3445); InterPro: IPR021848 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 264 to 418 amino acids in length. This protein has a conserved RLP sequence motif. This protein has two completely conserved R residues that may be functionally important.
Probab=20.30 E-value=79 Score=26.08 Aligned_cols=33 Identities=21% Similarity=0.671 Sum_probs=20.2
Q ss_pred CCCCcCHHHHHHHHH----hhCC-Cccccccc---ccccch
Q psy14921 28 PQGRMTLNEIYQFIT----HTFP-YYREANAG---WKNSIR 60 (148)
Q Consensus 28 p~~~LtL~eIY~~i~----~~fP-yyr~~~~g---WknSIR 60 (148)
|+...-..|+|+++. .+|| +|.....+ |.|.+-
T Consensus 41 p~~~~A~~Ell~~v~~~L~~ryP~~F~~~~~~~~~~~n~~~ 81 (249)
T PF11927_consen 41 PGSEAAVWELLELVLDYLPARYPQYFSLDGDGDRWWHNRLT 81 (249)
T ss_pred ccHHHHHHHHHHHHHHHHHHhCchheEEcCCCceeEEeccC
Confidence 444444567776655 5899 77765555 666543
No 52
>PF06531 DUF1108: Protein of unknown function (DUF1108); InterPro: IPR009494 This entry is represented by Bacteriophage 92, Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown.
Probab=20.09 E-value=71 Score=22.70 Aligned_cols=12 Identities=25% Similarity=0.484 Sum_probs=9.5
Q ss_pred HHHHHHHHHhhC
Q psy14921 34 LNEIYQFITHTF 45 (148)
Q Consensus 34 L~eIY~~i~~~f 45 (148)
.+.||+||+++-
T Consensus 62 ~~aiyewIE~nT 73 (86)
T PF06531_consen 62 NQAIYEWIEENT 73 (86)
T ss_pred HHHHHHHHHhCc
Confidence 467999999863
Done!