Query 034384
Match_columns 96
No_of_seqs 116 out of 1050
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 12:52:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034384.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034384hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00265 MADS_MEF2_like MEF2 (m 100.0 1.5E-33 3.3E-38 174.7 4.5 74 2-75 1-74 (77)
2 KOG0014 MADS box transcription 100.0 3.3E-33 7.1E-38 195.7 5.7 86 1-86 1-88 (195)
3 cd00266 MADS_SRF_like SRF-like 100.0 8.7E-32 1.9E-36 168.9 5.7 81 2-82 1-82 (83)
4 smart00432 MADS MADS domain. 100.0 1E-29 2.2E-34 150.6 4.8 59 2-60 1-59 (59)
5 cd00120 MADS MADS: MCM1, Agamo 100.0 4.6E-29 9.9E-34 147.8 3.6 59 2-60 1-59 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 1.7E-27 3.7E-32 137.3 0.8 51 9-59 1-51 (51)
7 KOG0015 Regulator of arginine 99.9 8.9E-23 1.9E-27 152.2 2.1 84 2-85 63-146 (338)
8 COG5068 ARG80 Regulator of arg 99.6 1.2E-15 2.5E-20 117.9 3.4 69 1-69 81-149 (412)
9 PF10491 Nrf1_DNA-bind: NLS-bi 78.8 3.2 6.9E-05 30.3 3.5 47 26-72 35-88 (214)
10 PF09151 DUF1936: Domain of un 75.3 3.8 8.3E-05 21.3 2.3 25 34-58 2-26 (36)
11 COG4888 Uncharacterized Zn rib 57.3 8.8 0.00019 25.0 1.9 54 1-57 1-58 (104)
12 PF11232 Med25: Mediator compl 50.6 27 0.00058 24.2 3.5 36 37-72 109-145 (152)
13 PF14263 DUF4354: Domain of un 49.7 5.7 0.00012 26.7 0.1 44 11-59 41-84 (124)
14 cd01365 KISc_KIF1A_KIF1B Kines 47.9 24 0.00051 26.9 3.2 33 36-68 83-118 (356)
15 COG0139 HisI Phosphoribosyl-AM 46.3 6.2 0.00013 26.0 -0.1 28 27-54 69-96 (111)
16 PF10584 Proteasome_A_N: Prote 44.9 2.6 5.7E-05 20.2 -1.5 11 45-55 5-15 (23)
17 cd00106 KISc Kinesin motor dom 42.4 33 0.00072 25.5 3.2 26 36-61 73-101 (328)
18 TIGR01916 F420_cofE F420-0:gam 40.6 28 0.0006 25.9 2.5 27 33-59 133-159 (243)
19 cd01368 KISc_KIF23_like Kinesi 36.7 45 0.00097 25.4 3.2 31 36-66 83-116 (345)
20 cd01371 KISc_KIF3 Kinesin moto 36.2 43 0.00094 25.3 3.1 25 36-60 76-103 (333)
21 PF09941 DUF2173: Uncharacteri 35.9 65 0.0014 21.0 3.4 27 32-59 3-29 (108)
22 PF13082 DUF3931: Protein of u 35.8 9.8 0.00021 22.1 -0.4 34 4-37 6-39 (66)
23 cd01376 KISc_KID_like Kinesin 35.4 51 0.0011 24.7 3.3 24 36-59 75-101 (319)
24 smart00129 KISc Kinesin motor, 34.8 50 0.0011 24.7 3.2 23 37-59 75-100 (335)
25 PF01502 PRA-CH: Phosphoribosy 34.4 10 0.00022 23.3 -0.5 33 21-53 22-63 (75)
26 PF14009 DUF4228: Domain of un 34.1 69 0.0015 21.1 3.5 34 39-72 12-46 (181)
27 PRK13293 F420-0--gamma-glutamy 33.9 40 0.00087 25.1 2.5 27 33-59 134-160 (245)
28 cd01370 KISc_KIP3_like Kinesin 33.8 49 0.0011 25.1 3.0 33 36-68 82-117 (338)
29 PF00225 Kinesin: Kinesin moto 33.5 24 0.00052 26.3 1.3 24 36-59 69-95 (335)
30 cd01366 KISc_C_terminal Kinesi 33.4 48 0.001 24.8 2.9 24 36-59 72-98 (329)
31 cd01363 Motor_domain Myosin an 32.8 38 0.00083 23.2 2.1 24 36-59 18-44 (186)
32 PF15119 APOC4: Apolipoprotein 32.8 21 0.00046 22.7 0.8 19 22-40 76-96 (99)
33 cd01369 KISc_KHC_KIF5 Kinesin 32.3 50 0.0011 24.7 2.8 24 37-60 72-98 (325)
34 PRK09555 feoA ferrous iron tra 32.2 78 0.0017 18.9 3.2 33 26-58 20-52 (74)
35 cd01367 KISc_KIF2_like Kinesin 31.3 50 0.0011 24.8 2.7 25 36-60 79-106 (322)
36 cd01374 KISc_CENP_E Kinesin mo 30.7 57 0.0012 24.4 2.9 24 37-60 69-95 (321)
37 cd03063 TRX_Fd_FDH_beta TRX-li 30.7 85 0.0018 19.7 3.3 36 38-73 44-81 (92)
38 PF00383 dCMP_cyt_deam_1: Cyti 30.3 86 0.0019 18.9 3.3 29 27-55 6-38 (102)
39 PF13540 RCC1_2: Regulator of 29.7 49 0.0011 16.1 1.7 23 36-59 3-25 (30)
40 PF15208 Rab15_effector: Rab15 29.1 51 0.0011 24.3 2.3 34 21-54 137-172 (236)
41 PF02824 TGS: TGS domain; Int 28.3 1.1E+02 0.0023 17.3 3.2 24 45-68 1-25 (60)
42 smart00782 PhnA_Zn_Ribbon PhnA 26.1 30 0.00066 19.2 0.6 22 28-49 2-23 (47)
43 PF03850 Tfb4: Transcription f 25.2 1.3E+02 0.0028 22.5 4.0 27 35-61 39-65 (276)
44 COG5068 ARG80 Regulator of arg 24.1 45 0.00097 26.7 1.3 46 8-59 18-63 (412)
45 cd01668 TGS_RelA_SpoT TGS_RelA 24.0 1.3E+02 0.0028 16.0 2.9 24 46-69 2-26 (60)
46 PF07676 PD40: WD40-like Beta 23.4 93 0.002 15.4 2.1 18 42-59 10-27 (39)
47 PRK09732 hypothetical protein; 23.2 1.4E+02 0.0031 19.9 3.5 31 28-58 15-45 (134)
48 cd01284 Riboflavin_deaminase-r 21.9 1.3E+02 0.0029 19.3 3.1 28 29-56 1-34 (115)
49 PTZ00366 Surface antigen (SAG 21.1 51 0.0011 26.2 1.1 28 17-44 3-30 (392)
50 PF01996 F420_ligase: F420-0:G 20.8 25 0.00055 25.5 -0.6 27 33-59 141-167 (228)
51 PRK13294 F420-0--gamma-glutamy 20.7 89 0.0019 25.1 2.4 27 33-59 134-160 (448)
52 COG3411 Ferredoxin [Energy pro 20.4 1.4E+02 0.0029 17.8 2.6 28 45-72 19-47 (64)
53 cd06397 PB1_UP1 Uncharacterize 20.2 2.3E+02 0.0051 17.6 3.9 43 26-68 23-66 (82)
54 PF06020 Roughex: Drosophila r 20.0 52 0.0011 25.4 0.9 15 36-50 183-197 (334)
No 1
>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.98 E-value=1.5e-33 Score=174.74 Aligned_cols=74 Identities=64% Similarity=0.967 Sum_probs=71.7
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccCCchHHHHHHhhhcccc
Q 034384 2 AREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSSSSMKEILEKHRVHSKN 75 (96)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s~~~~~vl~ry~~~s~~ 75 (96)
||+||+|++|+|+..|++||+||+.||||||.|||+||||+||||||+|+|++++|+++++++||+||+..+..
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~~~ 74 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTSGS 74 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhcccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999988654
No 2
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.98 E-value=3.3e-33 Score=195.69 Aligned_cols=86 Identities=48% Similarity=0.813 Sum_probs=78.1
Q ss_pred CCcccceeEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccCCc--hHHHHHHhhhccccccc
Q 034384 1 MAREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSSSS--MKEILEKHRVHSKNLER 78 (96)
Q Consensus 1 MgR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s~~--~~~vl~ry~~~s~~~~~ 78 (96)
|||+||+|++|+|++.|++||+|||.||||||+||||||||+||+|||+|+|++|.|++++ +++++++|.........
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~ 80 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEPSRK 80 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhhhhc
Confidence 9999999999999999999999999999999999999999999999999999999998866 99999999998877655
Q ss_pred CCCCChhh
Q 034384 79 VDQPSVEL 86 (96)
Q Consensus 79 ~~~~~~e~ 86 (96)
....+.+.
T Consensus 81 ~~~~~~~~ 88 (195)
T KOG0014|consen 81 KKRVNLES 88 (195)
T ss_pred ccccchhh
Confidence 44444443
No 3
>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.97 E-value=8.7e-32 Score=168.92 Aligned_cols=81 Identities=46% Similarity=0.742 Sum_probs=75.1
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccCCc-hHHHHHHhhhcccccccCC
Q 034384 2 AREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSSSS-MKEILEKHRVHSKNLERVD 80 (96)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s~~-~~~vl~ry~~~s~~~~~~~ 80 (96)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|+.++|++++ ++++|++|..++..+++..
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 80 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSALERKKK 80 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHhhhhcc
Confidence 899999999999999999999999999999999999999999999999999999887755 9999999999998877655
Q ss_pred CC
Q 034384 81 QP 82 (96)
Q Consensus 81 ~~ 82 (96)
.+
T Consensus 81 ~~ 82 (83)
T cd00266 81 AV 82 (83)
T ss_pred CC
Confidence 43
No 4
>smart00432 MADS MADS domain.
Probab=99.96 E-value=1e-29 Score=150.63 Aligned_cols=59 Identities=71% Similarity=1.108 Sum_probs=57.3
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccCC
Q 034384 2 AREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSSS 60 (96)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s~ 60 (96)
||+||+|++|+|++.|++||+||+.||+|||+|||+||||+||+|||+|+|++++|++|
T Consensus 1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~p 59 (59)
T smart00432 1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP 59 (59)
T ss_pred CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccCC
Confidence 89999999999999999999999999999999999999999999999999999998764
No 5
>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.95 E-value=4.6e-29 Score=147.81 Aligned_cols=59 Identities=69% Similarity=1.076 Sum_probs=57.1
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccCC
Q 034384 2 AREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSSS 60 (96)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s~ 60 (96)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|++++|+++
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~~ 59 (59)
T cd00120 1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS 59 (59)
T ss_pred CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccCC
Confidence 79999999999999999999999999999999999999999999999999999998763
No 6
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=99.93 E-value=1.7e-27 Score=137.30 Aligned_cols=51 Identities=61% Similarity=1.045 Sum_probs=46.9
Q ss_pred EEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccC
Q 034384 9 KKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 9 ~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
++|+|+..|++||+||+.||+|||.|||+|||++||||||+|+|++++|+|
T Consensus 1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~g~~~~f~s 51 (51)
T PF00319_consen 1 KRIENKSRRKVTFSKRKKGLFKKASELSTLCGVDVALIVFSPDGKLYTFPS 51 (51)
T ss_dssp S--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETTSEEEEEES
T ss_pred CCccchhHhHhHHHHHHhhhhhccceeeeecCCeEEEEEECCCCCEEEecC
Confidence 589999999999999999999999999999999999999999999999986
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.86 E-value=8.9e-23 Score=152.19 Aligned_cols=84 Identities=32% Similarity=0.520 Sum_probs=70.9
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccCCchHHHHHHhhhcccccccCCC
Q 034384 2 AREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSSSSMKEILEKHRVHSKNLERVDQ 81 (96)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s~~~~~vl~ry~~~s~~~~~~~~ 81 (96)
||+||+|++|+|+.+|.+||+|||.||||||+|||+|+|.+|.|+|.+++|.+|+|..+.++.||..-....-...+.+.
T Consensus 63 gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~s~~Gk~lIq~cLn~ 142 (338)
T KOG0015|consen 63 GRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMITSDEGKALIQACLNA 142 (338)
T ss_pred ceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccccchhhHHHHHHHhcC
Confidence 79999999999999999999999999999999999999999999999999999999999888887654322222334444
Q ss_pred CChh
Q 034384 82 PSVE 85 (96)
Q Consensus 82 ~~~e 85 (96)
|+.+
T Consensus 143 pd~~ 146 (338)
T KOG0015|consen 143 PDTP 146 (338)
T ss_pred CCCC
Confidence 4433
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.57 E-value=1.2e-15 Score=117.92 Aligned_cols=69 Identities=39% Similarity=0.590 Sum_probs=64.8
Q ss_pred CCcccceeEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccCCchHHHHHHh
Q 034384 1 MAREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSSSSMKEILEKH 69 (96)
Q Consensus 1 MgR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s~~~~~vl~ry 69 (96)
|||+||.|.+|+|+.+|.+||+||+.||+|||.||++|.|.+|.|+|.+.+|.+++|..++.+.|+..-
T Consensus 81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~~~ 149 (412)
T COG5068 81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVKSL 149 (412)
T ss_pred cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCccccccccc
Confidence 789999999999999999999999999999999999999999999999999999999998777776443
No 9
>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
Probab=78.75 E-value=3.2 Score=30.29 Aligned_cols=47 Identities=4% Similarity=0.222 Sum_probs=37.2
Q ss_pred chhhhhh----HhhhhccccceEEEEecCCC---ceeeccCCchHHHHHHhhhc
Q 034384 26 RGIFKKA----EELSVLCDADVALIIFSATG---KLFEYSSSSMKEILEKHRVH 72 (96)
Q Consensus 26 ~gL~kKa----~Els~LC~~~v~liv~~~~g---~~~~~~s~~~~~vl~ry~~~ 72 (96)
.-|+.|- .|+++-+|-++.|+|++|+. ..-+|+...++.||..|...
T Consensus 35 ~rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~~ 88 (214)
T PF10491_consen 35 TRLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKPV 88 (214)
T ss_pred HHHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHHH
Confidence 3455554 79999999999999999853 35579998999998888765
No 10
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=75.34 E-value=3.8 Score=21.27 Aligned_cols=25 Identities=16% Similarity=0.381 Sum_probs=17.7
Q ss_pred hhhhccccceEEEEecCCCceeecc
Q 034384 34 ELSVLCDADVALIIFSATGKLFEYS 58 (96)
Q Consensus 34 Els~LC~~~v~liv~~~~g~~~~~~ 58 (96)
.|+--||+-|.+.||+..|..-+|-
T Consensus 2 hlcpkcgvgvl~pvy~~kgeikvfr 26 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQKGEIKVFR 26 (36)
T ss_dssp -B-TTTSSSBEEEEE-TTS-EEEEE
T ss_pred ccCCccCceEEEEeecCCCcEEEEE
Confidence 4677799999999999999876653
No 11
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=57.31 E-value=8.8 Score=25.00 Aligned_cols=54 Identities=20% Similarity=0.236 Sum_probs=31.1
Q ss_pred CCcccceeEEecCCCCcccccccccchhhhhhHhhhhcccc----ceEEEEecCCCceeec
Q 034384 1 MAREKIQIKKIDNATARQVTFSKRRRGIFKKAEELSVLCDA----DVALIIFSATGKLFEY 57 (96)
Q Consensus 1 MgR~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~----~v~liv~~~~g~~~~~ 57 (96)
|||++...+.|-. .|+..+.|+-..++ =-+|.++.|-+ .+++++.+-.|.-+..
T Consensus 1 MG~rr~krr~~ik--~~~~~L~k~FtCp~-Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 1 MGRRRRKRRKIIK--RRPQVLPKTFTCPR-CGHEKVSSCTVKKTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred CCcccccccccCc--ccCccCCceEecCc-cCCeeeeEEEEEecCceeEEEcccCcceEEE
Confidence 9999988887653 22332344333332 12455555544 4677777777876654
No 12
>PF11232 Med25: Mediator complex subunit 25 PTOV activation and synapsin 2; InterPro: IPR021394 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear []. ; PDB: 2KY6_A 2L23_A 2XNF_A 2L6U_A.
Probab=50.56 E-value=27 Score=24.22 Aligned_cols=36 Identities=17% Similarity=0.403 Sum_probs=24.5
Q ss_pred hccccceEEEEecCCCceee-ccCCchHHHHHHhhhc
Q 034384 37 VLCDADVALIIFSATGKLFE-YSSSSMKEILEKHRVH 72 (96)
Q Consensus 37 ~LC~~~v~liv~~~~g~~~~-~~s~~~~~vl~ry~~~ 72 (96)
.-|++.|.+++|+++.+.|. |-.-+-...+.+++..
T Consensus 109 p~c~iKvL~LlYs~kk~~flG~IP~DQ~~Fv~~lr~V 145 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKAFLGFIPNDQEGFVNRLRQV 145 (152)
T ss_dssp SSSS-SEEEEEEETTTTEEEEEEESTHHHHHHHHHHH
T ss_pred CCCceEEEEEEEcCCCceEEEEcCCCHHHHHHHHHHH
Confidence 46889999999999988664 6555555555555443
No 13
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=49.74 E-value=5.7 Score=26.65 Aligned_cols=44 Identities=23% Similarity=0.387 Sum_probs=31.7
Q ss_pred ecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccC
Q 034384 11 IDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 11 I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
+.++.....||.=.-..+..+.-+|+.+| ++.|+|+|+-+...+
T Consensus 41 v~~k~~ytktF~V~vaN~s~~~idLsk~C-----f~a~~~~gk~f~ldT 84 (124)
T PF14263_consen 41 VGGKSFYTKTFDVTVANLSDKDIDLSKMC-----FKAYSPDGKEFKLDT 84 (124)
T ss_dssp ETTEEEEEEEEEEEEEE-SSS-EE-TT-E-----EEEEETTS-EEEEEE
T ss_pred ecCccceEEEEEEEEecCCCCccccccch-----hhhccccCCEEEecc
Confidence 45677778888888899999999999986 999999998775543
No 14
>cd01365 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.
Probab=47.92 E-value=24 Score=26.94 Aligned_cols=33 Identities=18% Similarity=0.351 Sum_probs=23.5
Q ss_pred hhccccceEEEEecC--CCceee-ccCCchHHHHHH
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSSSSMKEILEK 68 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s~~~~~vl~r 68 (96)
+++-|..++|++|++ +||.|+ |+...-..|+.|
T Consensus 83 ~~l~G~n~~i~ayGqtGSGKT~Tm~G~~~~~Gli~r 118 (356)
T cd01365 83 HAFEGYNVCLFAYGQTGSGKSYTMMGYKEEKGIIPR 118 (356)
T ss_pred HHhCCCceEEEEecCCCCCCeEEecCCCCCCchHHH
Confidence 468899999999998 578886 666443344433
No 15
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=46.27 E-value=6.2 Score=26.03 Aligned_cols=28 Identities=29% Similarity=0.497 Sum_probs=22.2
Q ss_pred hhhhhhHhhhhccccceEEEEecCCCce
Q 034384 27 GIFKKAEELSVLCDADVALIIFSATGKL 54 (96)
Q Consensus 27 gL~kKa~Els~LC~~~v~liv~~~~g~~ 54 (96)
|=+-|..|+.+-||.|..++++.+.|.+
T Consensus 69 G~~q~v~~i~~DCD~Dall~~V~q~gg~ 96 (111)
T COG0139 69 GHTQKVVEIRLDCDGDALLLLVEQIGGP 96 (111)
T ss_pred CceEEEEEEEcCCCCCEEEEEEEeCCCC
Confidence 3445567899999999999999986643
No 16
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=44.86 E-value=2.6 Score=20.22 Aligned_cols=11 Identities=45% Similarity=0.951 Sum_probs=8.4
Q ss_pred EEEecCCCcee
Q 034384 45 LIIFSATGKLF 55 (96)
Q Consensus 45 liv~~~~g~~~ 55 (96)
+.+|||+|+++
T Consensus 5 ~t~FSp~Grl~ 15 (23)
T PF10584_consen 5 ITTFSPDGRLF 15 (23)
T ss_dssp TTSBBTTSSBH
T ss_pred ceeECCCCeEE
Confidence 44789999875
No 17
>cd00106 KISc Kinesin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coil
Probab=42.36 E-value=33 Score=25.51 Aligned_cols=26 Identities=23% Similarity=0.456 Sum_probs=19.7
Q ss_pred hhccccceEEEEecC--CCceee-ccCCc
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSSSS 61 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s~~ 61 (96)
+++.|.++++++|++ +||.|+ +++..
T Consensus 73 ~~~~G~~~~i~~yG~tgSGKT~tl~G~~~ 101 (328)
T cd00106 73 SVLEGYNGTIFAYGQTGSGKTYTMFGSPK 101 (328)
T ss_pred HHhCCCceeEEEecCCCCCCeEEecCCCC
Confidence 346799999999998 578886 66543
No 18
>TIGR01916 F420_cofE F420-0:gamma-glutamyl ligase. This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates.
Probab=40.60 E-value=28 Score=25.92 Aligned_cols=27 Identities=30% Similarity=0.437 Sum_probs=22.3
Q ss_pred HhhhhccccceEEEEecCCCceeeccC
Q 034384 33 EELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 33 ~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
.+|.-.+|++|++||.+..|.++.-+.
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 159 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQ 159 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCC
Confidence 457778999999999999998876555
No 19
>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, a
Probab=36.73 E-value=45 Score=25.41 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=22.1
Q ss_pred hhccccceEEEEecC--CCceee-ccCCchHHHH
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSSSSMKEIL 66 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s~~~~~vl 66 (96)
+++-|..+++++|+. +||.|+ ++.+.-..|+
T Consensus 83 ~~l~G~n~ti~aYGqtGSGKTyTm~G~~~~~Gli 116 (345)
T cd01368 83 DLLKGKNSLLFTYGVTNSGKTYTMQGSPGDGGIL 116 (345)
T ss_pred HHhCCCceEEEEeCCCCCCCeEEecCCCCCCchH
Confidence 467899999999998 578887 5554333333
No 20
>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins. Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this group the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain
Probab=36.24 E-value=43 Score=25.26 Aligned_cols=25 Identities=28% Similarity=0.357 Sum_probs=19.9
Q ss_pred hhccccceEEEEecC--CCceee-ccCC
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSSS 60 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s~ 60 (96)
+++-|.++++++|+. +||.|+ ++..
T Consensus 76 ~~~~G~n~~i~ayG~tgSGKTyTm~G~~ 103 (333)
T cd01371 76 SVLEGYNGTIFAYGQTGTGKTFTMEGVR 103 (333)
T ss_pred HHhCCCceeEEecCCCCCCCcEeecCCC
Confidence 677899999999998 578887 5543
No 21
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=35.88 E-value=65 Score=21.04 Aligned_cols=27 Identities=33% Similarity=0.349 Sum_probs=20.5
Q ss_pred hHhhhhccccceEEEEecCCCceeeccC
Q 034384 32 AEELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 32 a~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
-.||..|-||-+ ...|+++|++.+|-.
T Consensus 3 l~~Lm~lpGv~A-Ag~Fs~~G~l~e~~G 29 (108)
T PF09941_consen 3 LDKLMKLPGVVA-AGEFSDDGKLVEYKG 29 (108)
T ss_pred HHHhhcCCCeEE-EEEECCCCeEEeeec
Confidence 356777777754 467899999998876
No 22
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=35.76 E-value=9.8 Score=22.10 Aligned_cols=34 Identities=24% Similarity=0.251 Sum_probs=27.2
Q ss_pred ccceeEEecCCCCcccccccccchhhhhhHhhhh
Q 034384 4 EKIQIKKIDNATARQVTFSKRRRGIFKKAEELSV 37 (96)
Q Consensus 4 ~ki~i~~I~~~~~R~~tf~kRk~gL~kKa~Els~ 37 (96)
+|-++--|+.+++..-||+--+--.-.|.+|+|.
T Consensus 6 kkcnvisidgkkkksdtysypklvvenktyefss 39 (66)
T PF13082_consen 6 KKCNVISIDGKKKKSDTYSYPKLVVENKTYEFSS 39 (66)
T ss_pred ccccEEEeccccccCCcccCceEEEeCceEEEEE
Confidence 4556667788888888998888888889999874
No 23
>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup. Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through
Probab=35.37 E-value=51 Score=24.73 Aligned_cols=24 Identities=13% Similarity=0.375 Sum_probs=18.9
Q ss_pred hhccccceEEEEecC--CCceee-ccC
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSS 59 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s 59 (96)
+++-|.++++++|++ +||.|+ ++.
T Consensus 75 ~~~~G~n~~i~ayG~tgSGKTyTm~G~ 101 (319)
T cd01376 75 HLLSGQNATVFAYGSTGAGKTHTMLGD 101 (319)
T ss_pred HHhCCCceEEEEECCCCCCCcEEEeCC
Confidence 466799999999998 578887 544
No 24
>smart00129 KISc Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
Probab=34.77 E-value=50 Score=24.72 Aligned_cols=23 Identities=17% Similarity=0.414 Sum_probs=18.3
Q ss_pred hccccceEEEEecC--CCceee-ccC
Q 034384 37 VLCDADVALIIFSA--TGKLFE-YSS 59 (96)
Q Consensus 37 ~LC~~~v~liv~~~--~g~~~~-~~s 59 (96)
++-|.++++++|++ +||.|+ +++
T Consensus 75 ~~~G~~~~i~~yG~tgSGKT~tl~G~ 100 (335)
T smart00129 75 VLEGYNATIFAYGQTGSGKTYTMSGT 100 (335)
T ss_pred HhcCCceeEEEeCCCCCCCceEecCC
Confidence 57799999999998 577776 555
No 25
>PF01502 PRA-CH: Phosphoribosyl-AMP cyclohydrolase; InterPro: IPR002496 Phosphoribosyl-AMP cyclohydrolase 3.5.4.19 from EC catalyses the third step in the histidine biosynthetic pathway: 5-phosphoribosyl-AMP + H2O = 5-(5-phospho-D-ribosylaminoformimino)-1-(5-phospho-ribosyl) imidazole-4-carboxamide It requires Zn2+ ions for activity [].; GO: 0004635 phosphoribosyl-AMP cyclohydrolase activity, 0000105 histidine biosynthetic process; PDB: 1ZPS_B.
Probab=34.45 E-value=10 Score=23.27 Aligned_cols=33 Identities=27% Similarity=0.570 Sum_probs=23.8
Q ss_pred cccccchhh---------hhhHhhhhccccceEEEEecCCCc
Q 034384 21 FSKRRRGIF---------KKAEELSVLCDADVALIIFSATGK 53 (96)
Q Consensus 21 f~kRk~gL~---------kKa~Els~LC~~~v~liv~~~~g~ 53 (96)
|++-|++|- -++.|+.+-||.|..|+.+.|.|.
T Consensus 22 ~SRSR~~lW~KGetSG~~q~v~~i~~DCD~D~ll~~V~~~G~ 63 (75)
T PF01502_consen 22 YSRSRNRLWRKGETSGNTQKVVEIRLDCDGDALLFKVEQVGP 63 (75)
T ss_dssp EETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-
T ss_pred EEccCCcEeeEECCCCCEEEEEEEEecCCCCeEEEEEEeCCC
Confidence 455555554 445789999999999999988776
No 26
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=34.10 E-value=69 Score=21.11 Aligned_cols=34 Identities=15% Similarity=0.312 Sum_probs=25.1
Q ss_pred cccceEEEEecCCCceeeccC-CchHHHHHHhhhc
Q 034384 39 CDADVALIIFSATGKLFEYSS-SSMKEILEKHRVH 72 (96)
Q Consensus 39 C~~~v~liv~~~~g~~~~~~s-~~~~~vl~ry~~~ 72 (96)
++...++-|..++|.+..|.. -.+.+|+..|=.+
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h 46 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGH 46 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCC
Confidence 344455555568999999887 5899999887666
No 27
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=33.94 E-value=40 Score=25.09 Aligned_cols=27 Identities=30% Similarity=0.431 Sum_probs=22.1
Q ss_pred HhhhhccccceEEEEecCCCceeeccC
Q 034384 33 EELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 33 ~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
.+|.-.+|++|++||.+..|.++-.+.
T Consensus 134 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 160 (245)
T PRK13293 134 EGLEELTGKKVGVIITDTNGRPFRKGQ 160 (245)
T ss_pred HHHHHHHCCCEEEEEEcCCCcccccCC
Confidence 456778999999999999898876655
No 28
>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a sec
Probab=33.82 E-value=49 Score=25.11 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=22.9
Q ss_pred hhccccceEEEEecC--CCceee-ccCCchHHHHHH
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSSSSMKEILEK 68 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s~~~~~vl~r 68 (96)
+++-|..+++++|++ +||.|+ ++.+.-..|+.+
T Consensus 82 ~~~~G~n~~i~ayGqtGSGKTyTm~G~~~~~Giipr 117 (338)
T cd01370 82 GVLNGYNATVFAYGATGAGKTHTMLGTDSDPGLMVL 117 (338)
T ss_pred HHHCCCCceEEeeCCCCCCCeEEEcCCCCCCchHHH
Confidence 457899999999998 578887 555433344433
No 29
>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport. The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....
Probab=33.54 E-value=24 Score=26.33 Aligned_cols=24 Identities=25% Similarity=0.531 Sum_probs=18.0
Q ss_pred hhccccceEEEEecC--CCceee-ccC
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSS 59 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s 59 (96)
+++-|.+++|++|++ +||.|+ +++
T Consensus 69 ~~l~G~n~~i~ayG~tgSGKT~Tm~G~ 95 (335)
T PF00225_consen 69 SVLDGYNATIFAYGQTGSGKTYTMFGS 95 (335)
T ss_dssp HHHTT-EEEEEEEESTTSSHHHHHTBS
T ss_pred HhhcCCceEEEeecccccccccccccc
Confidence 567899999999997 567775 554
No 30
>cd01366 KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for mi
Probab=33.36 E-value=48 Score=24.82 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=18.9
Q ss_pred hhccccceEEEEecC--CCceee-ccC
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSS 59 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s 59 (96)
+++-|.+++++.|++ +||.|+ ++.
T Consensus 72 ~~~~G~~~~i~ayG~tgSGKT~tl~G~ 98 (329)
T cd01366 72 SALDGYNVCIFAYGQTGSGKTYTMEGP 98 (329)
T ss_pred HHhCCCceEEEEeCCCCCCCcEEecCC
Confidence 456799999999998 578886 454
No 31
>cd01363 Motor_domain Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Probab=32.82 E-value=38 Score=23.23 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=18.2
Q ss_pred hhccccceEEEEecCC--Cceee-ccC
Q 034384 36 SVLCDADVALIIFSAT--GKLFE-YSS 59 (96)
Q Consensus 36 s~LC~~~v~liv~~~~--g~~~~-~~s 59 (96)
.++.|-++++++|+++ ||.|+ ++.
T Consensus 18 ~~~~G~n~~i~~yG~tGsGKT~Tm~G~ 44 (186)
T cd01363 18 SALDGYNVCIFAYGQTGSGKTYTMEGK 44 (186)
T ss_pred HHhCCcceeEEEECCCCCcceEecCCC
Confidence 3467899999999985 77776 443
No 32
>PF15119 APOC4: Apolipoprotein C4
Probab=32.81 E-value=21 Score=22.75 Aligned_cols=19 Identities=21% Similarity=0.597 Sum_probs=14.6
Q ss_pred ccccchhhhhhHhhh--hccc
Q 034384 22 SKRRRGIFKKAEELS--VLCD 40 (96)
Q Consensus 22 ~kRk~gL~kKa~Els--~LC~ 40 (96)
..-|.+|++||+.|| +||+
T Consensus 76 ~sSkd~llnk~~sLCPrllC~ 96 (99)
T PF15119_consen 76 RSSKDSLLNKTHSLCPRLLCG 96 (99)
T ss_pred HHhHHHHHHHHHhhCchhhcc
Confidence 345789999999987 5664
No 33
>cd01369 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-c
Probab=32.32 E-value=50 Score=24.70 Aligned_cols=24 Identities=17% Similarity=0.346 Sum_probs=19.0
Q ss_pred hccccceEEEEecC--CCceee-ccCC
Q 034384 37 VLCDADVALIIFSA--TGKLFE-YSSS 60 (96)
Q Consensus 37 ~LC~~~v~liv~~~--~g~~~~-~~s~ 60 (96)
++-|.++++++|++ +||.|+ ++.+
T Consensus 72 ~~~G~n~~i~ayG~tgSGKT~Tm~G~~ 98 (325)
T cd01369 72 VLNGYNGTIFAYGQTGSGKTYTMEGPP 98 (325)
T ss_pred HHcCccceEEEeCCCCCCceEEecCCC
Confidence 57899999999997 578887 4543
No 34
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=32.16 E-value=78 Score=18.92 Aligned_cols=33 Identities=12% Similarity=0.137 Sum_probs=28.3
Q ss_pred chhhhhhHhhhhccccceEEEEecCCCceeecc
Q 034384 26 RGIFKKAEELSVLCDADVALIIFSATGKLFEYS 58 (96)
Q Consensus 26 ~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~ 58 (96)
..+..+-.++-++.|++|-++-..|-|.|..+.
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i~ 52 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHIE 52 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEEE
Confidence 557888999999999999999999988876653
No 35
>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group. KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and lo
Probab=31.27 E-value=50 Score=24.82 Aligned_cols=25 Identities=12% Similarity=0.278 Sum_probs=19.5
Q ss_pred hhccccceEEEEecC--CCceee-ccCC
Q 034384 36 SVLCDADVALIIFSA--TGKLFE-YSSS 60 (96)
Q Consensus 36 s~LC~~~v~liv~~~--~g~~~~-~~s~ 60 (96)
+++-|..++++.|++ +||.|+ ++..
T Consensus 79 ~~~~G~n~~i~ayGqtGSGKTyTm~G~~ 106 (322)
T cd01367 79 HVFEGGVATCFAYGQTGSGKTYTMLGDE 106 (322)
T ss_pred HHhCCCceEEEeccCCCCCCceEecCcC
Confidence 467799999999997 578887 5443
No 36
>cd01374 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to
Probab=30.74 E-value=57 Score=24.38 Aligned_cols=24 Identities=17% Similarity=0.320 Sum_probs=18.8
Q ss_pred hccccceEEEEecC--CCceee-ccCC
Q 034384 37 VLCDADVALIIFSA--TGKLFE-YSSS 60 (96)
Q Consensus 37 ~LC~~~v~liv~~~--~g~~~~-~~s~ 60 (96)
++-|.++++++|++ +||.|+ ++..
T Consensus 69 ~l~G~n~~i~ayG~tgSGKT~T~~G~~ 95 (321)
T cd01374 69 ALEGYNGTIFAYGQTSSGKTFTMSGDE 95 (321)
T ss_pred HHCCCceeEEeecCCCCCCceeccCCC
Confidence 57799999999997 678887 5443
No 37
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=30.69 E-value=85 Score=19.71 Aligned_cols=36 Identities=6% Similarity=0.160 Sum_probs=24.8
Q ss_pred ccccceEEEEecCCCc-eeeccC-CchHHHHHHhhhcc
Q 034384 38 LCDADVALIIFSATGK-LFEYSS-SSMKEILEKHRVHS 73 (96)
Q Consensus 38 LC~~~v~liv~~~~g~-~~~~~s-~~~~~vl~ry~~~s 73 (96)
+|..+-.+.|..|+|. .|..-. .++.+|++.+...+
T Consensus 44 ~C~~ePlV~V~~p~g~v~Y~~V~~edv~~Iv~~~~~~~ 81 (92)
T cd03063 44 MYWLEPLVEVETPGGRVAYGPVTPADVASLLDAGALEG 81 (92)
T ss_pred ecCCCCEEEEEeCCCcEEEEeCCHHHHHHHHHHHhhcC
Confidence 4777777778778774 344334 68888998877643
No 38
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=30.28 E-value=86 Score=18.91 Aligned_cols=29 Identities=24% Similarity=0.352 Sum_probs=21.1
Q ss_pred hhhhhhHhhhhcc----ccceEEEEecCCCcee
Q 034384 27 GIFKKAEELSVLC----DADVALIIFSATGKLF 55 (96)
Q Consensus 27 gL~kKa~Els~LC----~~~v~liv~~~~g~~~ 55 (96)
-+++.|.+++... +..|+-++++++|+..
T Consensus 6 ~~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i 38 (102)
T PF00383_consen 6 EFMRIAIELAKRSRPCGNFPVGAVIVDPDGKII 38 (102)
T ss_dssp HHHHHHHHHHHTHBTTTSSSEEEEEEETTTEEE
T ss_pred HHHHHHHHHHHhccccCCCCEEEEEEeccCccE
Confidence 3567777776666 7789999999776644
No 39
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=29.68 E-value=49 Score=16.07 Aligned_cols=23 Identities=13% Similarity=0.395 Sum_probs=16.2
Q ss_pred hhccccceEEEEecCCCceeeccC
Q 034384 36 SVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 36 s~LC~~~v~liv~~~~g~~~~~~s 59 (96)
+|-||....+++.+ +|.++.|..
T Consensus 3 ~ia~G~~ht~al~~-~g~v~~wG~ 25 (30)
T PF13540_consen 3 QIACGGYHTCALTS-DGEVYCWGD 25 (30)
T ss_dssp EEEEESSEEEEEE--TTEEEEEE-
T ss_pred EEEecCCEEEEEEc-CCCEEEEcC
Confidence 45678777777755 699999986
No 40
>PF15208 Rab15_effector: Rab15 effector
Probab=29.05 E-value=51 Score=24.29 Aligned_cols=34 Identities=38% Similarity=0.555 Sum_probs=26.0
Q ss_pred cccccchhhhhhHhhhhccccc-eE-EEEecCCCce
Q 034384 21 FSKRRRGIFKKAEELSVLCDAD-VA-LIIFSATGKL 54 (96)
Q Consensus 21 f~kRk~gL~kKa~Els~LC~~~-v~-liv~~~~g~~ 54 (96)
=.-|+++.+.|-.|+|.|-|-| .+ .|+|+--|++
T Consensus 137 ~~s~~k~rfeKLeEFC~lIG~DClgLFiiFGvpgkp 172 (236)
T PF15208_consen 137 ESSRNKNRFEKLEEFCNLIGEDCLGLFIIFGVPGKP 172 (236)
T ss_pred hhhccccHHHHHHHHHHhhchhhheeeeEecCCCCc
Confidence 3458899999999999999887 44 4557755554
No 41
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=28.31 E-value=1.1e+02 Score=17.27 Aligned_cols=24 Identities=13% Similarity=0.313 Sum_probs=17.8
Q ss_pred EEEecCCCceeeccC-CchHHHHHH
Q 034384 45 LIIFSATGKLFEYSS-SSMKEILEK 68 (96)
Q Consensus 45 liv~~~~g~~~~~~s-~~~~~vl~r 68 (96)
+.||-|+|+...++. .++.++...
T Consensus 1 I~v~lpdG~~~~~~~g~T~~d~A~~ 25 (60)
T PF02824_consen 1 IRVYLPDGSIKELPEGSTVLDVAYS 25 (60)
T ss_dssp EEEEETTSCEEEEETTBBHHHHHHH
T ss_pred CEEECCCCCeeeCCCCCCHHHHHHH
Confidence 346669999999888 667777644
No 42
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=26.14 E-value=30 Score=19.20 Aligned_cols=22 Identities=23% Similarity=0.676 Sum_probs=17.0
Q ss_pred hhhhhHhhhhccccceEEEEec
Q 034384 28 IFKKAEELSVLCDADVALIIFS 49 (96)
Q Consensus 28 L~kKa~Els~LC~~~v~liv~~ 49 (96)
|.+.+..-+-||+++..|.+|.
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~ 23 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYA 23 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEe
Confidence 4556666788999999888865
No 43
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=25.22 E-value=1.3e+02 Score=22.54 Aligned_cols=27 Identities=30% Similarity=0.356 Sum_probs=21.8
Q ss_pred hhhccccceEEEEecCCCceeeccCCc
Q 034384 35 LSVLCDADVALIIFSATGKLFEYSSSS 61 (96)
Q Consensus 35 ls~LC~~~v~liv~~~~g~~~~~~s~~ 61 (96)
|+.-...+||||..++++.-+.||++.
T Consensus 39 L~l~~~N~vaVIAs~~~~s~~LYP~~~ 65 (276)
T PF03850_consen 39 LALNHSNQVAVIASHSNSSKFLYPSPS 65 (276)
T ss_pred HhhCccCCEEEEEEcCCccEEEeCCCc
Confidence 555567789999999999888898855
No 44
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=24.07 E-value=45 Score=26.72 Aligned_cols=46 Identities=26% Similarity=0.339 Sum_probs=37.3
Q ss_pred eEEecCCCCcccccccccchhhhhhHhhhhccccceEEEEecCCCceeeccC
Q 034384 8 IKKIDNATARQVTFSKRRRGIFKKAEELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 8 i~~I~~~~~R~~tf~kRk~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
|+.+-|...-..+|++|..| |++.+|+.++-..++...--..+|+.
T Consensus 18 i~~~~d~~~ps~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~ 63 (412)
T COG5068 18 IQGDSDANIPSNTINRLSPG------ELSQQNDGKFDVMIFDSKHSVRVYSN 63 (412)
T ss_pred cccccccCCccccccccCcc------cchhhccCCcccccccccccccccCC
Confidence 77788888889999999999 99999999888777665545555555
No 45
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=24.04 E-value=1.3e+02 Score=16.04 Aligned_cols=24 Identities=13% Similarity=0.380 Sum_probs=18.3
Q ss_pred EEecCCCceeeccC-CchHHHHHHh
Q 034384 46 IIFSATGKLFEYSS-SSMKEILEKH 69 (96)
Q Consensus 46 iv~~~~g~~~~~~s-~~~~~vl~ry 69 (96)
.||-|+|..+.++. .++.+++...
T Consensus 2 ~~~~~~g~~~~~~~~~t~~~~~~~~ 26 (60)
T cd01668 2 YVFTPKGEIIELPAGATVLDFAYAI 26 (60)
T ss_pred EEECCCCCEEEcCCCCCHHHHHHHH
Confidence 57888899999887 6777777643
No 46
>PF07676 PD40: WD40-like Beta Propeller Repeat; InterPro: IPR011659 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This region appears to be related to the IPR001680 from INTERPRO repeat. This model is likely to miss copies within a sequence.; PDB: 2HQS_D 1C5K_A 2IVZ_A 2W8B_D 3IAX_A 1CRZ_A 1N6F_D 1N6D_C 1N6E_C 1K32_A ....
Probab=23.40 E-value=93 Score=15.35 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=12.8
Q ss_pred ceEEEEecCCCceeeccC
Q 034384 42 DVALIIFSATGKLFEYSS 59 (96)
Q Consensus 42 ~v~liv~~~~g~~~~~~s 59 (96)
.-.-..++|+|+-..|.+
T Consensus 10 ~~~~p~~SpDGk~i~f~s 27 (39)
T PF07676_consen 10 DDGSPAWSPDGKYIYFTS 27 (39)
T ss_dssp SEEEEEE-TTSSEEEEEE
T ss_pred cccCEEEecCCCEEEEEe
Confidence 445567899999888876
No 47
>PRK09732 hypothetical protein; Provisional
Probab=23.22 E-value=1.4e+02 Score=19.92 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=23.4
Q ss_pred hhhhhHhhhhccccceEEEEecCCCceeecc
Q 034384 28 IFKKAEELSVLCDADVALIIFSATGKLFEYS 58 (96)
Q Consensus 28 L~kKa~Els~LC~~~v~liv~~~~g~~~~~~ 58 (96)
+..-|.+.+.-=|..|++.|++.+|.+..|.
T Consensus 15 ~~~aA~~~A~~~g~~v~iaVvD~~G~l~a~~ 45 (134)
T PRK09732 15 IIAAGQEEAQKNNWSVSIAVADDGGHLLALS 45 (134)
T ss_pred HHHHHHHHHHHhCCCEEEEEEcCCCCEEEEE
Confidence 3445555666668899999999999987764
No 48
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=21.86 E-value=1.3e+02 Score=19.34 Aligned_cols=28 Identities=21% Similarity=0.368 Sum_probs=20.3
Q ss_pred hhhhHhhhhcc------ccceEEEEecCCCceee
Q 034384 29 FKKAEELSVLC------DADVALIIFSATGKLFE 56 (96)
Q Consensus 29 ~kKa~Els~LC------~~~v~liv~~~~g~~~~ 56 (96)
|+.|.|++-.+ +..|+-++++++|.+..
T Consensus 1 m~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~ 34 (115)
T cd01284 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVG 34 (115)
T ss_pred CHHHHHHHHhcccccCCCCCEEEEEEeCCCeEEE
Confidence 45677777766 66888888887787654
No 49
>PTZ00366 Surface antigen (SAG) superfamily; Provisional
Probab=21.10 E-value=51 Score=26.18 Aligned_cols=28 Identities=32% Similarity=0.482 Sum_probs=22.0
Q ss_pred cccccccccchhhhhhHhhhhccccceE
Q 034384 17 RQVTFSKRRRGIFKKAEELSVLCDADVA 44 (96)
Q Consensus 17 R~~tf~kRk~gL~kKa~Els~LC~~~v~ 44 (96)
|...-.+|+.|+--||++|.-.|=.-|.
T Consensus 3 r~~~~~~r~~g~~s~a~kl~avc~~gvl 30 (392)
T PTZ00366 3 RTGRMQQRRGGFRSKARKLMAVCMGGVL 30 (392)
T ss_pred cccchhhcccccccchhhhheeeeeeEE
Confidence 4555678999999999999999944333
No 50
>PF01996 F420_ligase: F420-0:Gamma-glutamyl ligase; InterPro: IPR002847 This entry contains F420-0:gamma-glutamyl ligase and related proteins. F420-0:gamma-glutamyl ligase catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives [, , , ].; PDB: 2G9I_A 2PHN_A.
Probab=20.78 E-value=25 Score=25.52 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=18.4
Q ss_pred HhhhhccccceEEEEecCCCceeeccC
Q 034384 33 EELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 33 ~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
.+|.-.+|.+|++||.+++|.++..++
T Consensus 141 ~~l~~~~g~~v~ViI~Dt~gr~~r~G~ 167 (228)
T PF01996_consen 141 EELKERTGKDVGVIITDTNGRPWRLGQ 167 (228)
T ss_dssp HHHHHHHS---EEEEEEEEEETTEECE
T ss_pred HHHHHHHCCceEEEEECCCCcEEecCC
Confidence 567778999999999998886655443
No 51
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=20.67 E-value=89 Score=25.07 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=22.0
Q ss_pred HhhhhccccceEEEEecCCCceeeccC
Q 034384 33 EELSVLCDADVALIIFSATGKLFEYSS 59 (96)
Q Consensus 33 ~Els~LC~~~v~liv~~~~g~~~~~~s 59 (96)
.+|.-.+|++|+|||.+..|.++--+.
T Consensus 134 ~~l~~~~g~~v~vii~Dt~gr~~r~g~ 160 (448)
T PRK13294 134 AGLRERLGVDVAVVVTDTMGRAWRNGQ 160 (448)
T ss_pred HHHHHHHCCCEEEEEecCCCCccccCc
Confidence 457778999999999998888776554
No 52
>COG3411 Ferredoxin [Energy production and conversion]
Probab=20.36 E-value=1.4e+02 Score=17.83 Aligned_cols=28 Identities=11% Similarity=0.334 Sum_probs=19.9
Q ss_pred EEEecCCCceeeccC-CchHHHHHHhhhc
Q 034384 45 LIIFSATGKLFEYSS-SSMKEILEKHRVH 72 (96)
Q Consensus 45 liv~~~~g~~~~~~s-~~~~~vl~ry~~~ 72 (96)
++++-|+|-.|..-+ ++++.|++....-
T Consensus 19 vl~vYpegvWY~~V~p~~a~rIv~~hl~~ 47 (64)
T COG3411 19 VLVVYPEGVWYTRVDPEDARRIVQSHLLG 47 (64)
T ss_pred EEEEecCCeeEeccCHHHHHHHHHHHHhC
Confidence 445567787777666 6899999877663
No 53
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=20.23 E-value=2.3e+02 Score=17.64 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=31.5
Q ss_pred chhhhhhHhhhhccccceEEEEecCCCceeeccC-CchHHHHHH
Q 034384 26 RGIFKKAEELSVLCDADVALIIFSATGKLFEYSS-SSMKEILEK 68 (96)
Q Consensus 26 ~gL~kKa~Els~LC~~~v~liv~~~~g~~~~~~s-~~~~~vl~r 68 (96)
.+|..|-.+|--|....++|--.+.+|...+-+| .+++++...
T Consensus 23 ~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d~~~~ 66 (82)
T cd06397 23 EALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQDFYRL 66 (82)
T ss_pred HHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHHHHHh
Confidence 5788888888888766566555777888888887 567766553
No 54
>PF06020 Roughex: Drosophila roughex protein; InterPro: IPR009259 This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialised cell cycle inhibitor for cyclin A-dependent kinase activity []. Rux is though to regulate the metaphase to anaphase transition during development [].
Probab=20.03 E-value=52 Score=25.42 Aligned_cols=15 Identities=7% Similarity=0.359 Sum_probs=12.6
Q ss_pred hhccccceEEEEecC
Q 034384 36 SVLCDADVALIIFSA 50 (96)
Q Consensus 36 s~LC~~~v~liv~~~ 50 (96)
.-+||.+|||+||..
T Consensus 183 ~~~~~~EICLavYek 197 (334)
T PF06020_consen 183 GQVSGFEICLAVYEK 197 (334)
T ss_pred CccccceEEeeehhh
Confidence 357899999999985
Done!