Query 039560
Match_columns 344
No_of_seqs 241 out of 1482
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 10:54:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039560.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039560hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0014 MADS box transcription 100.0 1.1E-31 2.4E-36 241.9 5.2 171 1-190 1-177 (195)
2 cd00265 MADS_MEF2_like MEF2 (m 99.9 6.3E-28 1.4E-32 187.8 3.1 72 2-74 1-72 (77)
3 cd00266 MADS_SRF_like SRF-like 99.9 3.9E-27 8.5E-32 185.9 5.0 80 2-81 1-80 (83)
4 smart00432 MADS MADS domain. 99.9 3E-25 6.6E-30 163.8 4.1 58 2-59 1-58 (59)
5 cd00120 MADS MADS: MCM1, Agamo 99.9 7.4E-25 1.6E-29 161.8 3.6 58 2-59 1-58 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 3E-23 6.5E-28 148.5 -1.5 51 9-59 1-51 (51)
7 KOG0015 Regulator of arginine 99.7 9.5E-19 2.1E-23 163.9 2.3 65 2-67 63-127 (338)
8 PF01486 K-box: K-box region; 99.3 3E-12 6.5E-17 104.4 6.1 76 121-196 9-84 (100)
9 COG5068 ARG80 Regulator of arg 99.3 1.7E-12 3.6E-17 127.2 2.8 66 1-67 81-146 (412)
10 PF07106 TBPIP: Tat binding pr 85.8 6.6 0.00014 34.6 9.3 56 126-182 111-166 (169)
11 PHA03155 hypothetical protein; 83.0 9.8 0.00021 31.8 8.3 59 123-181 7-65 (115)
12 PHA03162 hypothetical protein; 78.3 16 0.00034 31.4 8.1 60 124-183 13-76 (135)
13 PF05812 Herpes_BLRF2: Herpesv 72.4 22 0.00047 30.0 7.5 59 125-183 4-66 (118)
14 PRK04098 sec-independent trans 66.8 17 0.00036 32.2 6.0 48 126-180 56-103 (158)
15 PF09432 THP2: Tho complex sub 64.2 52 0.0011 28.2 8.1 74 57-146 34-107 (132)
16 KOG4603 TBP-1 interacting prot 63.8 79 0.0017 28.5 9.5 58 124-182 116-173 (201)
17 PF07106 TBPIP: Tat binding pr 58.9 39 0.00084 29.7 7.0 58 125-186 80-137 (169)
18 PF06717 DUF1202: Protein of u 50.6 71 0.0015 31.0 7.5 132 15-158 44-186 (308)
19 PF06698 DUF1192: Protein of u 46.2 50 0.0011 24.4 4.6 33 150-182 13-45 (59)
20 KOG4603 TBP-1 interacting prot 45.9 2E+02 0.0043 26.1 9.1 30 157-186 115-144 (201)
21 COG3883 Uncharacterized protei 44.2 1.5E+02 0.0031 28.6 8.6 56 125-190 53-108 (265)
22 PF14723 SSFA2_C: Sperm-specif 43.6 47 0.001 29.8 4.9 19 161-179 159-177 (179)
23 PF10584 Proteasome_A_N: Prote 39.4 5.2 0.00011 24.1 -1.2 13 44-56 4-16 (23)
24 PF06657 Cep57_MT_bd: Centroso 39.1 1.8E+02 0.004 22.5 8.0 55 126-184 19-73 (79)
25 PF07926 TPR_MLP1_2: TPR/MLP1/ 38.9 1.6E+02 0.0035 24.8 7.4 61 127-192 69-131 (132)
26 KOG0994 Extracellular matrix g 38.3 1.6E+02 0.0035 34.1 8.8 68 118-185 1219-1291(1758)
27 PF13870 DUF4201: Domain of un 38.1 1.5E+02 0.0032 26.2 7.4 59 126-185 8-66 (177)
28 PF08700 Vps51: Vps51/Vps67; 38.1 1.5E+02 0.0033 22.5 6.6 51 126-176 21-73 (87)
29 PF02183 HALZ: Homeobox associ 37.4 1.1E+02 0.0024 21.2 5.0 34 97-146 8-41 (45)
30 COG2433 Uncharacterized conser 36.8 85 0.0018 33.6 6.3 40 99-147 427-466 (652)
31 PF15188 CCDC-167: Coiled-coil 34.4 1.9E+02 0.0041 23.0 6.5 50 124-179 5-54 (85)
32 smart00787 Spc7 Spc7 kinetocho 33.4 2.7E+02 0.0057 27.3 8.9 33 153-185 196-228 (312)
33 COG0139 HisI Phosphoribosyl-AM 31.6 23 0.00051 29.5 1.0 37 18-54 51-96 (111)
34 PF09177 Syntaxin-6_N: Syntaxi 30.0 2.6E+02 0.0056 22.1 6.9 52 128-179 43-95 (97)
35 PF11559 ADIP: Afadin- and alp 29.7 3.5E+02 0.0076 23.0 10.4 17 94-110 52-68 (151)
36 PF14282 FlxA: FlxA-like prote 29.5 3.1E+02 0.0067 22.3 7.6 55 124-187 19-73 (106)
37 PF03233 Cauli_AT: Aphid trans 28.4 2.3E+02 0.0051 25.2 6.7 47 127-183 114-160 (163)
38 PF08287 DASH_Spc19: Spc19; I 27.5 4.2E+02 0.0091 23.2 8.3 63 124-186 75-148 (153)
39 COG4575 ElaB Uncharacterized c 27.4 3.1E+02 0.0068 22.6 6.8 51 126-184 10-60 (104)
40 PRK10884 SH3 domain-containing 27.2 4.9E+02 0.011 23.9 10.1 8 211-218 171-178 (206)
41 PRK11546 zraP zinc resistance 27.0 2.4E+02 0.0053 24.5 6.6 9 70-78 41-49 (143)
42 PF10491 Nrf1_DNA-bind: NLS-bi 26.9 47 0.001 30.7 2.3 47 27-73 36-88 (214)
43 PF15066 CAGE1: Cancer-associa 26.5 3.5E+02 0.0076 28.2 8.5 137 34-187 255-419 (527)
44 PF08317 Spc7: Spc7 kinetochor 26.4 4.5E+02 0.0098 25.6 9.2 31 154-184 202-232 (325)
45 PF10234 Cluap1: Clusterin-ass 25.9 3.7E+02 0.0081 25.8 8.2 65 123-196 196-262 (267)
46 PF09006 Surfac_D-trimer: Lung 25.9 1.1E+02 0.0023 21.6 3.3 19 129-147 4-22 (46)
47 PF01486 K-box: K-box region; 25.8 1.2E+02 0.0026 24.2 4.3 56 94-150 12-68 (100)
48 PRK15422 septal ring assembly 25.3 1.9E+02 0.0041 22.7 4.9 15 127-141 21-35 (79)
49 PRK12726 flagellar biosynthesi 25.1 71 0.0015 32.5 3.3 17 22-38 38-54 (407)
50 COG1579 Zn-ribbon protein, pos 24.6 3.1E+02 0.0068 25.9 7.3 47 126-172 54-100 (239)
51 PRK09039 hypothetical protein; 24.6 4.2E+02 0.0091 26.2 8.6 24 124-147 137-160 (343)
52 PF14257 DUF4349: Domain of un 24.6 4E+02 0.0086 24.9 8.2 22 159-180 160-181 (262)
53 KOG2391 Vacuolar sorting prote 24.4 1.8E+02 0.0039 29.0 5.8 39 126-164 255-295 (365)
54 PRK11637 AmiB activator; Provi 23.9 4.4E+02 0.0095 26.6 8.9 19 162-180 111-129 (428)
55 TIGR01478 STEVOR variant surfa 23.9 1.4E+02 0.003 29.1 4.9 44 7-71 25-68 (295)
56 PRK10884 SH3 domain-containing 23.7 1.5E+02 0.0032 27.3 4.9 15 127-141 96-110 (206)
57 COG5185 HEC1 Protein involved 23.5 2.6E+02 0.0057 29.2 6.9 60 124-186 337-396 (622)
58 KOG0804 Cytoplasmic Zn-finger 23.4 2.6E+02 0.0057 28.9 6.9 20 162-181 418-437 (493)
59 cd00089 HR1 Protein kinase C-r 23.4 3.2E+02 0.0069 20.3 6.1 57 124-184 9-65 (72)
60 PF01502 PRA-CH: Phosphoribosy 23.3 21 0.00047 27.7 -0.6 37 17-53 18-63 (75)
61 TIGR02231 conserved hypothetic 23.2 1.8E+02 0.0038 30.3 6.0 28 157-184 123-150 (525)
62 PF04799 Fzo_mitofusin: fzo-li 22.5 5.2E+02 0.011 23.2 7.9 17 128-144 124-140 (171)
63 PF06008 Laminin_I: Laminin Do 22.2 3.1E+02 0.0067 25.7 7.0 57 124-181 87-143 (264)
64 PF10018 Med4: Vitamin-D-recep 21.9 4.5E+02 0.0099 23.4 7.7 38 128-174 26-63 (188)
65 PF09726 Macoilin: Transmembra 21.4 2.5E+02 0.0054 30.7 6.8 27 125-151 546-572 (697)
66 PF09941 DUF2173: Uncharacteri 21.3 1E+02 0.0022 25.6 3.0 28 31-59 2-29 (108)
67 PF09151 DUF1936: Domain of un 21.3 75 0.0016 20.6 1.7 24 34-57 2-25 (36)
68 PF05120 GvpG: Gas vesicle pro 21.2 3.6E+02 0.0079 21.0 5.9 43 134-182 31-73 (79)
69 PF04111 APG6: Autophagy prote 20.8 2.8E+02 0.006 27.1 6.5 15 97-111 46-60 (314)
70 PRK10132 hypothetical protein; 20.7 4.4E+02 0.0096 21.7 6.7 52 123-182 11-62 (108)
71 PRK11637 AmiB activator; Provi 20.5 2.9E+02 0.0064 27.9 6.9 24 161-184 103-126 (428)
72 PHA02109 hypothetical protein 20.2 1.3E+02 0.0028 27.3 3.6 29 124-152 200-228 (233)
73 PF00521 DNA_topoisoIV: DNA gy 20.1 3.5E+02 0.0076 27.5 7.3 32 152-183 382-413 (426)
No 1
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.97 E-value=1.1e-31 Score=241.91 Aligned_cols=171 Identities=37% Similarity=0.525 Sum_probs=123.3
Q ss_pred CCcccceeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccccc-hhhhHHhhhcCCChhhhh
Q 039560 1 MGRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRK-RIEDVFSRYVNLPDQERE 79 (344)
Q Consensus 1 MgR~Ki~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss~~-~ve~VIeRY~~l~~~er~ 79 (344)
|||+||+|++|+|+++|+|||+|||.||||||+||||||||+||||||||+|++|.||+.. ++.+|++||.+.+...+.
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 9999999999999999999999999999999999999999999999999999999986643 499999999998877665
Q ss_pred hhccCCCCCCCCcchhhHHHHHH-HHHhhhhhhHHHhhcCcccccccHHHHHHHHHHHHHHHHHH---HhhhhccCCCCC
Q 039560 80 HAIIFPDQGRHPDIQNKEYLLRT-LQQLRSENDIALQLANPAAINNDIEELQQEVGRLQQQLQMA---EDQIRIYEPDPL 155 (344)
Q Consensus 80 ~~~~~~~~~~~~~~~~~e~L~~~-l~KLk~e~d~~~~~~~~~~~n~~iE~Lq~Ei~~Lq~qle~l---e~~lR~~~gd~L 155 (344)
+... ....++... +.++..+.+. ..........+...+....+.+ ....+.+.+.++
T Consensus 81 ~~~~----------~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l 141 (195)
T KOG0014|consen 81 KKRV----------NLESFLRNKKLTELVEEEEK---------EELKLQLKKSLESSLKVDPEDLELLELEQRKLTGEDL 141 (195)
T ss_pred cccc----------chhhHhhhhhhhcccchhhh---------hhccchhhhhhhhhhhcchhhhhhhHHHHHHHhcccc
Confidence 5422 222222211 1111110000 0000011122222333333332 244677888999
Q ss_pred CCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 039560 156 RITSI-KDIESCEKNLVDTLTQVSQRKEFLLSNHLS 190 (344)
Q Consensus 156 ~~lSl-eEL~~LE~~Le~~L~~Vr~RK~~Ll~~qi~ 190 (344)
..++. .+|..++..|+..+..++.++...+.+++.
T Consensus 142 ~~l~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~ 177 (195)
T KOG0014|consen 142 QSLSSLNELNSLESQLESSLHNSRSSKSKPLSDSNF 177 (195)
T ss_pred ccCCHHHHhcchhhHHHHhhcCCCCCCCcCCcchhh
Confidence 99999 999999999999999999998777666553
No 2
>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=99.94 E-value=6.3e-28 Score=187.77 Aligned_cols=72 Identities=64% Similarity=0.982 Sum_probs=68.9
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccccchhhhHHhhhcCCC
Q 039560 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRKRIEDVFSRYVNLP 74 (344)
Q Consensus 2 gR~Ki~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss~~~ve~VIeRY~~l~ 74 (344)
||+||+|++|+|++.|++||+|||.||||||+|||+||||+||+|||||+|+++.|++ +++++||+||.+.+
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s-~s~~~vl~ry~~~~ 72 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSS-PSMEKIIERYQKTS 72 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecC-CCHHHHHHHHHhcc
Confidence 8999999999999999999999999999999999999999999999999999999955 67899999999765
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=99.93 E-value=3.9e-27 Score=185.89 Aligned_cols=80 Identities=53% Similarity=0.804 Sum_probs=74.9
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccccchhhhHHhhhcCCChhhhhhh
Q 039560 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRKRIEDVFSRYVNLPDQEREHA 81 (344)
Q Consensus 2 gR~Ki~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss~~~ve~VIeRY~~l~~~er~~~ 81 (344)
||+||+|++|+|+.+|++||+|||.||+|||+||||||||+||+|||||+|+.+.||+..++..+|+||..++..++.+.
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 89999999999999999999999999999999999999999999999999999998776559999999999988777654
No 4
>smart00432 MADS MADS domain.
Probab=99.91 E-value=3e-25 Score=163.77 Aligned_cols=58 Identities=72% Similarity=1.120 Sum_probs=56.6
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccc
Q 039560 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSG 59 (344)
Q Consensus 2 gR~Ki~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss 59 (344)
||+||+|++|+|++.|++||+|||.||+|||+||||||||+||+|||||+|+++.|++
T Consensus 1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~ 58 (59)
T smart00432 1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFAS 58 (59)
T ss_pred CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccC
Confidence 8999999999999999999999999999999999999999999999999999999864
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=99.90 E-value=7.4e-25 Score=161.77 Aligned_cols=58 Identities=71% Similarity=1.064 Sum_probs=56.6
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccc
Q 039560 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSG 59 (344)
Q Consensus 2 gR~Ki~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss 59 (344)
||+||+|++|+|++.|++||+|||.||+|||+||||||||+||+|||||+|+++.|++
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~ 58 (59)
T cd00120 1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWS 58 (59)
T ss_pred CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccC
Confidence 8999999999999999999999999999999999999999999999999999999865
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=99.85 E-value=3e-23 Score=148.54 Aligned_cols=51 Identities=63% Similarity=1.025 Sum_probs=46.5
Q ss_pred EEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccc
Q 039560 9 KRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSG 59 (344)
Q Consensus 9 k~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss 59 (344)
|+|+|++.|++||+|||.||+|||+|||+||||+||||||+|+|++++|++
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 589999999999999999999999999999999999999999999999964
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.73 E-value=9.5e-19 Score=163.92 Aligned_cols=65 Identities=43% Similarity=0.724 Sum_probs=60.4
Q ss_pred CcccceeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccccchhhhHH
Q 039560 2 GRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRKRIEDVF 67 (344)
Q Consensus 2 gR~Ki~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss~~~ve~VI 67 (344)
||+||+|+||+|+.+|.+||||||.||||||+|||||+|.+|.|+|.|.+|.+|+|+. +.++.||
T Consensus 63 gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaT-pKLep~i 127 (338)
T KOG0015|consen 63 GRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT-PKLEPMI 127 (338)
T ss_pred ceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEecc-ccccccc
Confidence 7999999999999999999999999999999999999999999999999999999944 5566555
No 8
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=99.31 E-value=3e-12 Score=104.37 Aligned_cols=76 Identities=25% Similarity=0.401 Sum_probs=71.3
Q ss_pred cccccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCch
Q 039560 121 AINNDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFLLSNHLSSYDPSS 196 (344)
Q Consensus 121 ~~n~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll~~qi~~l~~~~ 196 (344)
......+.+..|+.+|+.+++.++..+|++.|++|+++|++||..||+.|+.+|.+||+||.+++.++|..++++.
T Consensus 9 ~~~~~~e~~~~e~~~L~~~~~~L~~~~R~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~l~~ke 84 (100)
T PF01486_consen 9 LWDSQHEELQQEIAKLRKENESLQKELRHLMGEDLESLSLKELQQLEQQLESALKRVRSRKDQLLMEQIEELKKKE 84 (100)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456778899999999999999999999999999999999999999999999999999999999999999887776
No 9
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.27 E-value=1.7e-12 Score=127.22 Aligned_cols=66 Identities=39% Similarity=0.643 Sum_probs=60.2
Q ss_pred CCcccceeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccccchhhhHH
Q 039560 1 MGRVKLEIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRKRIEDVF 67 (344)
Q Consensus 1 MgR~Ki~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss~~~ve~VI 67 (344)
|||+||.|.+|+|+.+|.|||+|||.||+|||+||+||+|.+|+|++.|..|+++.|+. +..+.|+
T Consensus 81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~t-p~~e~v~ 146 (412)
T COG5068 81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTT-PKLESVV 146 (412)
T ss_pred cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecC-Ccccccc
Confidence 79999999999999999999999999999999999999999999999999999999944 3344444
No 10
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=85.85 E-value=6.6 Score=34.59 Aligned_cols=56 Identities=21% Similarity=0.287 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKE 182 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~ 182 (344)
.++|..++..|+.++..++.++..+.+ .-...|.+|...+++......+..+.||.
T Consensus 111 ~~el~~~i~~l~~e~~~l~~kL~~l~~-~~~~vs~ee~~~~~~~~~~~~k~w~kRKr 166 (169)
T PF07106_consen 111 NEELREEIEELEEEIEELEEKLEKLRS-GSKPVSPEEKEKLEKEYKKWRKEWKKRKR 166 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456777777777777777777766654 34457899999999999999999999885
No 11
>PHA03155 hypothetical protein; Provisional
Probab=83.04 E-value=9.8 Score=31.78 Aligned_cols=59 Identities=19% Similarity=0.257 Sum_probs=49.5
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 039560 123 NNDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRK 181 (344)
Q Consensus 123 n~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK 181 (344)
+..+|+|..|+.+|+-++..|...++.-.+.+...|+..+-+.+-......|...-.+|
T Consensus 7 ~~tvEeLaaeL~kL~~ENK~LKkkl~~~~~p~d~~LT~~qKea~I~s~v~~Lt~~A~~K 65 (115)
T PHA03155 7 CADVEELEKELQKLKIENKALKKKLLQHGNPEDELLTPAQKDAIINSLVNKLTKKAEEK 65 (115)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999997765666788999999888888888887776666
No 12
>PHA03162 hypothetical protein; Provisional
Probab=78.29 E-value=16 Score=31.38 Aligned_cols=60 Identities=20% Similarity=0.172 Sum_probs=48.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDP----LRITSIKDIESCEKNLVDTLTQVSQRKEF 183 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~----L~~lSleEL~~LE~~Le~~L~~Vr~RK~~ 183 (344)
..+|+|..|+.+|+-++..|..+++.-.|.+ ...|+..+-+.+-......|...-.+|-+
T Consensus 13 ~tmEeLaaeL~kLqmENK~LKkkl~~~~~~~~~p~d~~LTp~qKea~I~s~v~~Lts~A~kKIe 76 (135)
T PHA03162 13 PTMEDLAAEIAKLQLENKALKKKIKEGTDDDPLPGDPILTPAAKEAMIGAATAALTRQAAKKIE 76 (135)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999997765555 55689888888888888887777776633
No 13
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=72.38 E-value=22 Score=29.99 Aligned_cols=59 Identities=19% Similarity=0.180 Sum_probs=44.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHhhhhccCC----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 125 DIEELQQEVGRLQQQLQMAEDQIRIYEP----DPLRITSIKDIESCEKNLVDTLTQVSQRKEF 183 (344)
Q Consensus 125 ~iE~Lq~Ei~~Lq~qle~le~~lR~~~g----d~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~ 183 (344)
.+|+|..|+.+|+-++..|...++.-.| .+-..||..+=+.+-......|...-.+|-+
T Consensus 4 t~EeLaaeL~kLqmENk~LKkkl~~~~~p~~~p~~~~LTp~qKe~~I~s~~~~Lss~A~~KIe 66 (118)
T PF05812_consen 4 TMEELAAELQKLQMENKALKKKLRQSVGPGPSPDDEVLTPAQKEAMITSAVSKLSSQASKKIE 66 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTT---S-TT--B--HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCccccChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999999999999988776 5677889999888888888888777766633
No 14
>PRK04098 sec-independent translocase; Provisional
Probab=66.82 E-value=17 Score=32.24 Aligned_cols=48 Identities=10% Similarity=0.299 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQR 180 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~R 180 (344)
+.+++++..+++..++.+...+|.. +++++|...-..+....+.+..-
T Consensus 56 ~~elk~e~~k~k~~l~~~~~~l~~~-------~~~eel~~~~~~~~~~~~~~~~~ 103 (158)
T PRK04098 56 IEEIKEEALKYKKEFESAVESLKKK-------LKFEELDDLKITAENEIKSIQDL 103 (158)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhc-------cChHHHHHHhhhhhhcchhHHHH
Confidence 4568888888888888888877642 67888888866555544444433
No 15
>PF09432 THP2: Tho complex subunit THP2; InterPro: IPR018557 The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1 [].
Probab=64.20 E-value=52 Score=28.15 Aligned_cols=74 Identities=18% Similarity=0.320 Sum_probs=47.6
Q ss_pred ccccchhhhHHhhhcCCChhhhhhhccCCCCCCCCcchhhHHHHHHHHHhhhhhhHHHhhcCcccccccHHHHHHHHHHH
Q 039560 57 FSGRKRIEDVFSRYVNLPDQEREHAIIFPDQGRHPDIQNKEYLLRTLQQLRSENDIALQLANPAAINNDIEELQQEVGRL 136 (344)
Q Consensus 57 ~ss~~~ve~VIeRY~~l~~~er~~~~~~~~~~~~~~~~~~e~L~~~l~KLk~e~d~~~~~~~~~~~n~~iE~Lq~Ei~~L 136 (344)
|+....+..|+++|..-....... ...|.+-|.++|.+- ..+.+.|.-.++..+..|.+|+..=
T Consensus 34 ~~pP~el~~iLe~y~~~~~d~~~l---------------r~~L~~YLD~IKm~R-AkY~lENky~L~~tL~~LtkEVn~W 97 (132)
T PF09432_consen 34 WNPPKELQSILEKYNTPSTDTEEL---------------RAQLDRYLDDIKMER-AKYSLENKYSLQDTLNQLTKEVNYW 97 (132)
T ss_pred CCCCHHHHHHHHHHcCCCccHHHH---------------HHHHHHHHHHHHHHH-HHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 555678999999998743322222 234556666666632 3455556666667777788888877
Q ss_pred HHHHHHHHhh
Q 039560 137 QQQLQMAEDQ 146 (344)
Q Consensus 137 q~qle~le~~ 146 (344)
+++-+.++.-
T Consensus 98 r~ewd~iE~~ 107 (132)
T PF09432_consen 98 RKEWDNIEML 107 (132)
T ss_pred HHHHHHHHHH
Confidence 7777766653
No 16
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=63.78 E-value=79 Score=28.52 Aligned_cols=58 Identities=16% Similarity=0.209 Sum_probs=45.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKE 182 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~ 182 (344)
-.+++++.++..|+.......+++..+. ......+.+|-.+.++.-.+..+.-|.||.
T Consensus 116 Lt~eemQe~i~~L~kev~~~~erl~~~k-~g~~~vtpedk~~v~~~y~~~~~~wrk~kr 173 (201)
T KOG4603|consen 116 LTTEEMQEEIQELKKEVAGYRERLKNIK-AGTNHVTPEDKEQVYREYQKYCKEWRKRKR 173 (201)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHH-HhcccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567888888888888877777776653 356667889999999999999998888886
No 17
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=58.93 E-value=39 Score=29.67 Aligned_cols=58 Identities=17% Similarity=0.331 Sum_probs=41.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 125 DIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFLLS 186 (344)
Q Consensus 125 ~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll~ 186 (344)
++..|+.++..|+.++..+..+++.+. ..+|.+||...-..|..-+..+..|-..|-.
T Consensus 80 ei~~L~~el~~l~~~~k~l~~eL~~L~----~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 80 EIKELREELAELKKEVKSLEAELASLS----SEPTNEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh----cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566666666666666666665553 3468899999999999999999888777654
No 18
>PF06717 DUF1202: Protein of unknown function (DUF1202); InterPro: IPR009592 This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.
Probab=50.58 E-value=71 Score=30.99 Aligned_cols=132 Identities=14% Similarity=0.166 Sum_probs=73.7
Q ss_pred CCcccccccccchhhhhhhhhhcccCccEEEEeec---CCCcccccccc--------chhhhHHhhhcCCChhhhhhhcc
Q 039560 15 TNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFS---PSGRLSHFSGR--------KRIEDVFSRYVNLPDQEREHAII 83 (344)
Q Consensus 15 ~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifs---p~gk~~~~ss~--------~~ve~VIeRY~~l~~~er~~~~~ 83 (344)
..-|+||+- .|.+--+.+|-|.-|.-.--+++- ..|++.-||.- ++-.-.+--| .+....++..+-
T Consensus 44 ~GNqaT~sa--eGd~s~~~dlY~~vg~~~DY~~~ektW~k~~~vKFSAml~s~Gt~dsGW~t~fySl-QmAa~~~G~~v~ 120 (308)
T PF06717_consen 44 KGNQATWSA--EGDMSSSEDLYTWVGMAADYEFVEKTWTKDKPVKFSAMLTSKGTPDSGWKTNFYSL-QMAAKNNGRPVP 120 (308)
T ss_pred ccCccceec--cCcccccchhHHHhhhhhhhhHHhhhhcCCCCcchhhHHhcCCCCCCcceeeeeeh-hhhcccCCCcCC
Confidence 455777773 688888888877665443322221 12444444210 0000001011 122222222222
Q ss_pred CCCCCCCCcchhhHHHHHHHHHhhhhhhHHHhhcCcccccccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCC
Q 039560 84 FPDQGRHPDIQNKEYLLRTLQQLRSENDIALQLANPAAINNDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRIT 158 (344)
Q Consensus 84 ~~~~~~~~~~~~~e~L~~~l~KLk~e~d~~~~~~~~~~~n~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~l 158 (344)
..+..+..-+.|-+-+...|.+++.+-. .-+..|..|+.++..|+.++..+++++..|||.+.++-
T Consensus 121 ~i~tn~KYLIvn~~~F~~rf~~Ied~~~---------~kK~~I~~L~~qisaLdkqi~ai~Kkid~yWgkda~gk 186 (308)
T PF06717_consen 121 DIKTNDKYLIVNDQDFNYRFNQIEDEYN---------RKKNKIPGLNKQISALDKQIVAINKKIDRYWGKDANGK 186 (308)
T ss_pred ccccCCcEEEecchhHHHHHHHHHHHHH---------HHhhhhHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCC
Confidence 2222222334444445567777776432 23567899999999999999999999999999887775
No 19
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=46.22 E-value=50 Score=24.43 Aligned_cols=33 Identities=12% Similarity=0.138 Sum_probs=28.1
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 150 YEPDPLRITSIKDIESCEKNLVDTLTQVSQRKE 182 (344)
Q Consensus 150 ~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~ 182 (344)
..|.+|+.+|++||..--..|+.=+.|++....
T Consensus 13 ~ig~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~ 45 (59)
T PF06698_consen 13 EIGEDLSLLSVEELEERIALLEAEIARLEAAIA 45 (59)
T ss_pred ccCCCchhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999998888877643
No 20
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=45.85 E-value=2e+02 Score=26.06 Aligned_cols=30 Identities=7% Similarity=0.122 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 157 ITSIKDIESCEKNLVDTLTQVSQRKEFLLS 186 (344)
Q Consensus 157 ~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll~ 186 (344)
-||++|++.--..|.+-...-|+|-..+-.
T Consensus 115 ~Lt~eemQe~i~~L~kev~~~~erl~~~k~ 144 (201)
T KOG4603|consen 115 ALTTEEMQEEIQELKKEVAGYRERLKNIKA 144 (201)
T ss_pred hcChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468899999988888888888888766543
No 21
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.22 E-value=1.5e+02 Score=28.60 Aligned_cols=56 Identities=20% Similarity=0.408 Sum_probs=36.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 039560 125 DIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFLLSNHLS 190 (344)
Q Consensus 125 ~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll~~qi~ 190 (344)
+|+.|..++..++.++..+++++-. +=.++..|++.+...-.+|++|++-| .+++.
T Consensus 53 ei~~L~~qi~~~~~k~~~~~~~i~~---------~~~eik~l~~eI~~~~~~I~~r~~~l-~~raR 108 (265)
T COG3883 53 EIESLDNQIEEIQSKIDELQKEIDQ---------SKAEIKKLQKEIAELKENIVERQELL-KKRAR 108 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Confidence 4455555555555555555554422 24688899999999999999998654 45554
No 22
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=43.65 E-value=47 Score=29.82 Aligned_cols=19 Identities=26% Similarity=0.417 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 039560 161 KDIESCEKNLVDTLTQVSQ 179 (344)
Q Consensus 161 eEL~~LE~~Le~~L~~Vr~ 179 (344)
.||+.||.+|++.|..|++
T Consensus 159 qElqELE~QL~DRl~~l~e 177 (179)
T PF14723_consen 159 QELQELEFQLEDRLLQLRE 177 (179)
T ss_pred HHHHHHHHHHHHHHHHHHc
Confidence 5899999999999998875
No 23
>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=39.40 E-value=5.2 Score=24.05 Aligned_cols=13 Identities=46% Similarity=0.864 Sum_probs=10.0
Q ss_pred EEEeecCCCcccc
Q 039560 44 ALIMFSPSGRLSH 56 (344)
Q Consensus 44 ~liifsp~gk~~~ 56 (344)
.+.+|||+|+++.
T Consensus 4 ~~t~FSp~Grl~Q 16 (23)
T PF10584_consen 4 SITTFSPDGRLFQ 16 (23)
T ss_dssp STTSBBTTSSBHH
T ss_pred CceeECCCCeEEe
Confidence 3568999999864
No 24
>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein). It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].
Probab=39.12 E-value=1.8e+02 Score=22.53 Aligned_cols=55 Identities=15% Similarity=0.303 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFL 184 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~L 184 (344)
+..|+.|+..++-+...+...++... ...+...-..|+..|+..++++..+-+++
T Consensus 19 l~~LqDE~~hm~~e~~~L~~~~~~~d----~s~~~~~R~~L~~~l~~lv~~mE~K~dQI 73 (79)
T PF06657_consen 19 LKALQDEFGHMKMEHQELQDEYKQMD----PSLGRRKRRDLEQELEELVKRMEAKADQI 73 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc----cccChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34466677777777777766665542 24577888999999999999888776554
No 25
>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore
Probab=38.86 E-value=1.6e+02 Score=24.78 Aligned_cols=61 Identities=25% Similarity=0.318 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH--HHHHHhhhhcC
Q 039560 127 EELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRK--EFLLSNHLSSY 192 (344)
Q Consensus 127 E~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK--~~Ll~~qi~~l 192 (344)
..++.++..|+...+.+...+.. .....-.+-..|++.+.+.-.++-+=. +.||.+||..+
T Consensus 69 ~~~~~~~~~l~~~~~~a~~~l~~-----~e~sw~~qk~~le~e~~~~~~r~~dL~~QN~lLh~QlE~l 131 (132)
T PF07926_consen 69 QELQQEINELKAEAESAKAELEE-----SEASWEEQKEQLEKELSELEQRIEDLNEQNKLLHDQLESL 131 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-----HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34445555555555444444321 111123455556666666555555443 45777777643
No 26
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=38.30 E-value=1.6e+02 Score=34.15 Aligned_cols=68 Identities=25% Similarity=0.273 Sum_probs=43.0
Q ss_pred CcccccccHHHHHHHHHHHHHHHHHHHhhhhccCCC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 118 NPAAINNDIEELQQEVGRLQQQLQMAEDQIRIYEPD-----PLRITSIKDIESCEKNLVDTLTQVSQRKEFLL 185 (344)
Q Consensus 118 ~~~~~n~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd-----~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll 185 (344)
++......|++|-..+..|+++|+.+.+.+-..+-+ +-..++-+||..|++..+..++-+++-++++.
T Consensus 1219 ~~svs~~~i~~l~~~~~~lr~~l~~~~e~L~~~E~~Lsdi~~~~~~a~~~LesLq~~~~~l~~~~keL~e~~~ 1291 (1758)
T KOG0994|consen 1219 APSVSAEDIAQLASATESLRRQLQALTEDLPQEEETLSDITNSLPLAGKDLESLQREFNGLLTTYKELREQLE 1291 (1758)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444566777777777777777666655443211 11234568999999888887777777776653
No 27
>PF13870 DUF4201: Domain of unknown function (DUF4201)
Probab=38.09 E-value=1.5e+02 Score=26.16 Aligned_cols=59 Identities=24% Similarity=0.220 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFLL 185 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll 185 (344)
+++++-....++.++..++.+++... +--+++.+-|..+|.-.-.....+|.+|-.+|.
T Consensus 8 i~~~Rl~~~~lk~~l~k~~~ql~~ke-~lge~L~~iDFeqLkien~~l~~kIeERn~eL~ 66 (177)
T PF13870_consen 8 ISKLRLKNITLKHQLAKLEEQLRQKE-ELGEGLHLIDFEQLKIENQQLNEKIEERNKELL 66 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HhcCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555566666666666665542 122456777777776666666666666655443
No 28
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=38.06 E-value=1.5e+02 Score=22.54 Aligned_cols=51 Identities=22% Similarity=0.341 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCC--CCHHHHHHHHHHHHHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEPDPLRI--TSIKDIESCEKNLVDTLTQ 176 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~--lSleEL~~LE~~Le~~L~~ 176 (344)
+.++.+-..+|..++......+|...++.-.. ...+++..|+..+......
T Consensus 21 ~~~i~~~~~~L~~~i~~~~~eLr~~V~~nY~~fI~as~~I~~m~~~~~~l~~~ 73 (87)
T PF08700_consen 21 IKEIRQLENKLRQEIEEKDEELRKLVYENYRDFIEASDEISSMENDLSELRNL 73 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555556666666666666654442111 1246666666664443333
No 29
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=37.42 E-value=1.1e+02 Score=21.23 Aligned_cols=34 Identities=24% Similarity=0.426 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhhhhhHHHhhcCcccccccHHHHHHHHHHHHHHHHHHHhh
Q 039560 97 EYLLRTLQQLRSENDIALQLANPAAINNDIEELQQEVGRLQQQLQMAEDQ 146 (344)
Q Consensus 97 e~L~~~l~KLk~e~d~~~~~~~~~~~n~~iE~Lq~Ei~~Lq~qle~le~~ 146 (344)
++|+.....|+.+++ .|.+|...|+.++..+...
T Consensus 8 ~~LK~~yd~Lk~~~~----------------~L~~E~~~L~aev~~L~~k 41 (45)
T PF02183_consen 8 DALKASYDSLKAEYD----------------SLKKENEKLRAEVQELKEK 41 (45)
T ss_pred HHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHh
Confidence 456666666666543 4666666666666655544
No 30
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=36.80 E-value=85 Score=33.59 Aligned_cols=40 Identities=28% Similarity=0.567 Sum_probs=21.2
Q ss_pred HHHHHHHhhhhhhHHHhhcCcccccccHHHHHHHHHHHHHHHHHHHhhh
Q 039560 99 LLRTLQQLRSENDIALQLANPAAINNDIEELQQEVGRLQQQLQMAEDQI 147 (344)
Q Consensus 99 L~~~l~KLk~e~d~~~~~~~~~~~n~~iE~Lq~Ei~~Lq~qle~le~~l 147 (344)
+-+++++|+.+|. .+...+++++.++.+|+.+++.+..+.
T Consensus 427 ~~~~ve~l~~e~~---------~L~~~~ee~k~eie~L~~~l~~~~r~~ 466 (652)
T COG2433 427 LEETVERLEEENS---------ELKRELEELKREIEKLESELERFRREV 466 (652)
T ss_pred HHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5556666665543 123345555566666655555554444
No 31
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=34.40 E-value=1.9e+02 Score=23.02 Aligned_cols=50 Identities=22% Similarity=0.357 Sum_probs=37.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQ 179 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~ 179 (344)
.+|+.+...+...+..++.++.++|. ..+|.++-..+|+.+....+++..
T Consensus 5 ~eId~lEekl~~cr~~le~ve~rL~~------~eLs~e~R~~lE~E~~~l~~~l~~ 54 (85)
T PF15188_consen 5 KEIDGLEEKLAQCRRRLEAVESRLRR------RELSPEARRSLEKELNELKEKLEN 54 (85)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHcc------cCCChHHHHHHHHHHHHHHHHhhc
Confidence 35667778888888999999988864 346889999999776665555544
No 32
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=33.36 E-value=2.7e+02 Score=27.35 Aligned_cols=33 Identities=15% Similarity=0.215 Sum_probs=25.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 153 DPLRITSIKDIESCEKNLVDTLTQVSQRKEFLL 185 (344)
Q Consensus 153 d~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll 185 (344)
+.++.++.++|..+...|......|..++..+.
T Consensus 196 ~e~~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~ 228 (312)
T smart00787 196 DELEDCDPTELDRAKEKLKKLLQEIMIKVKKLE 228 (312)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566777888999988888888888877776543
No 33
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=31.65 E-value=23 Score=29.46 Aligned_cols=37 Identities=27% Similarity=0.423 Sum_probs=27.1
Q ss_pred ccccccccchhh---------hhhhhhhcccCccEEEEeecCCCcc
Q 039560 18 QVTFSKRRNGLI---------KKAYELSILCDIDIALIMFSPSGRL 54 (344)
Q Consensus 18 ~~TfsKR~~GL~---------KKA~ELs~LCd~~v~liifsp~gk~ 54 (344)
..-||+-|.-|- -|..|+.+-||.|..++++.+.|.+
T Consensus 51 ~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~Dall~~V~q~gg~ 96 (111)
T COG0139 51 AHYYSRSRQELWTKGETSGHTQKVVEIRLDCDGDALLLLVEQIGGP 96 (111)
T ss_pred EEEEEcchhhheccccccCceEEEEEEEcCCCCCEEEEEEEeCCCC
Confidence 334466666454 4568999999999999999886644
No 34
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=30.01 E-value=2.6e+02 Score=22.14 Aligned_cols=52 Identities=23% Similarity=0.332 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhhccCCCCCC-CCCHHHHHHHHHHHHHHHHHHHH
Q 039560 128 ELQQEVGRLQQQLQMAEDQIRIYEPDPLR-ITSIKDIESCEKNLVDTLTQVSQ 179 (344)
Q Consensus 128 ~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~-~lSleEL~~LE~~Le~~L~~Vr~ 179 (344)
+|...+..++.+|+.+++-++....++-. +++..||..-...+...-.+|..
T Consensus 43 eL~~~l~~ie~~L~DL~~aV~ive~np~kF~l~~~Ei~~Rr~fv~~~~~~i~~ 95 (97)
T PF09177_consen 43 ELRNALQSIEWDLEDLEEAVRIVEKNPSKFNLSEEEISRRRQFVSAIRNQIKQ 95 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHT-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45555555666666666655554444333 46778888887777766666654
No 35
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=29.73 E-value=3.5e+02 Score=23.00 Aligned_cols=17 Identities=35% Similarity=0.499 Sum_probs=9.7
Q ss_pred hhhHHHHHHHHHhhhhh
Q 039560 94 QNKEYLLRTLQQLRSEN 110 (344)
Q Consensus 94 ~~~e~L~~~l~KLk~e~ 110 (344)
...+-|..++.++..+.
T Consensus 52 ~~~e~l~~~~~~l~~d~ 68 (151)
T PF11559_consen 52 EQREDLSDKLRRLRSDI 68 (151)
T ss_pred HHHHHHHHHHHHHHhHH
Confidence 34455666666666543
No 36
>PF14282 FlxA: FlxA-like protein
Probab=29.53 E-value=3.1e+02 Score=22.30 Aligned_cols=55 Identities=24% Similarity=0.259 Sum_probs=32.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFLLSN 187 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll~~ 187 (344)
+.|+.|++.+..|+.+|..+... ..++.++-...-+.|..-|..|.....++..+
T Consensus 19 ~~I~~L~~Qi~~Lq~ql~~l~~~---------~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q 73 (106)
T PF14282_consen 19 SQIEQLQKQIKQLQEQLQELSQD---------SDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQ 73 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcc---------cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666666666655544431 34567777777777777777666666555444
No 37
>PF03233 Cauli_AT: Aphid transmission protein; InterPro: IPR004917 This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus []. This protein interacts with the PIII protein []. ; GO: 0019089 transmission of virus
Probab=28.37 E-value=2.3e+02 Score=25.23 Aligned_cols=47 Identities=21% Similarity=0.372 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 127 EELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEF 183 (344)
Q Consensus 127 E~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~ 183 (344)
++.++.+.+|+.+...+... ..+..++..+-+.+++.|+.||+.-..
T Consensus 114 ~e~snki~kLe~~~k~L~d~----------Iv~~~~i~e~IKd~de~L~~I~d~iK~ 160 (163)
T PF03233_consen 114 EEISNKIRKLETEVKKLKDN----------IVTEKLIEELIKDFDERLKEIRDKIKK 160 (163)
T ss_pred HHHHHHHHHHHHHHHhHhhh----------ccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444445555444444433 345688999999999999999987543
No 38
>PF08287 DASH_Spc19: Spc19; InterPro: IPR013251 Spc19 is a component of the DASH complex. The DASH complex associates with the spindle pole body and is important for spindle and kinetochore integrity during cell division [, ].
Probab=27.53 E-value=4.2e+02 Score=23.18 Aligned_cols=63 Identities=21% Similarity=0.297 Sum_probs=36.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCC-----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITS-----------IKDIESCEKNLVDTLTQVSQRKEFLLS 186 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lS-----------leEL~~LE~~Le~~L~~Vr~RK~~Ll~ 186 (344)
..++.|+.+...|+.+.+..+.++......+..... ..-....-..=...|+.++.||+.|..
T Consensus 75 ~~l~kL~Rr~~tL~ak~EL~~~RL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Lk~L~~kKerL~y 148 (153)
T PF08287_consen 75 KHLEKLQRREETLKAKCELQQGRLSNYESTDSSSESGESEEERLSTDPVVMKSSDEEELERLKALRQKKERLKY 148 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCccCCccccccchhhhhhccchhhcccccHHHHHHHHHHHHHHHHHHH
Confidence 467788888888998888777777654433222111 000011111113347888999988754
No 39
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=27.37 E-value=3.1e+02 Score=22.64 Aligned_cols=51 Identities=18% Similarity=0.184 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFL 184 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~L 184 (344)
++.+..|+..|-..+ ++-++.+ | ..+-+|+..+-..++..|+++|.|-...
T Consensus 10 ~~~l~~el~~L~d~l---EevL~ss-g----~~a~~e~~~lR~r~~~~Lk~~r~rl~~~ 60 (104)
T COG4575 10 IDQLLAELQELLDTL---EEVLKSS-G----SLAGDEAEELRSKAESALKEARDRLGDT 60 (104)
T ss_pred HHHHHHHHHHHHHHH---HHHHHhc-c----cchhhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 456677766554444 4444332 3 3567899999999999999999986554
No 40
>PRK10884 SH3 domain-containing protein; Provisional
Probab=27.24 E-value=4.9e+02 Score=23.89 Aligned_cols=8 Identities=38% Similarity=0.982 Sum_probs=4.4
Q ss_pred hcccCCCC
Q 039560 211 VGWLPGGG 218 (344)
Q Consensus 211 ~~wl~e~~ 218 (344)
..|+..|+
T Consensus 171 ~~wf~~Gg 178 (206)
T PRK10884 171 MQWFMYGG 178 (206)
T ss_pred HHHHHHch
Confidence 45665554
No 41
>PRK11546 zraP zinc resistance protein; Provisional
Probab=26.97 E-value=2.4e+02 Score=24.55 Aligned_cols=9 Identities=11% Similarity=0.224 Sum_probs=4.4
Q ss_pred hcCCChhhh
Q 039560 70 YVNLPDQER 78 (344)
Q Consensus 70 Y~~l~~~er 78 (344)
|.+++++.+
T Consensus 41 ~~~LT~EQQ 49 (143)
T PRK11546 41 AAPLTTEQQ 49 (143)
T ss_pred cccCCHHHH
Confidence 445555443
No 42
>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=26.93 E-value=47 Score=30.69 Aligned_cols=47 Identities=17% Similarity=0.240 Sum_probs=35.7
Q ss_pred hhhhhh----hhhhcccCccEEEEeecCCCc--cccccccchhhhHHhhhcCC
Q 039560 27 GLIKKA----YELSILCDIDIALIMFSPSGR--LSHFSGRKRIEDVFSRYVNL 73 (344)
Q Consensus 27 GL~KKA----~ELs~LCd~~v~liifsp~gk--~~~~ss~~~ve~VIeRY~~l 73 (344)
-|+.|. .|++|-+|-++.||+++|+-. .|...|...++.||..|...
T Consensus 36 rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~~ 88 (214)
T PF10491_consen 36 RLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKPV 88 (214)
T ss_pred HHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHHH
Confidence 455554 799999999999999998632 22224878899999999754
No 43
>PF15066 CAGE1: Cancer-associated gene protein 1 family
Probab=26.52 E-value=3.5e+02 Score=28.20 Aligned_cols=137 Identities=19% Similarity=0.245 Sum_probs=0.0
Q ss_pred hhhcccCccEEEEeecCCCcccccc------------ccchhhhHHhhhcCCChhhhhhhccCCCCCCCCcchhhHHHHH
Q 039560 34 ELSILCDIDIALIMFSPSGRLSHFS------------GRKRIEDVFSRYVNLPDQEREHAIIFPDQGRHPDIQNKEYLLR 101 (344)
Q Consensus 34 ELs~LCd~~v~liifsp~gk~~~~s------------s~~~ve~VIeRY~~l~~~er~~~~~~~~~~~~~~~~~~e~L~~ 101 (344)
|+++-|--+|.+--...-+-...|+ ..-.+.++=.-|..+.+.+..-. |.+
T Consensus 255 e~sv~~qkev~~e~~e~p~~~s~wspagis~~~~a~~e~c~~~d~eqs~Eslqpleedma-----------------LNE 317 (527)
T PF15066_consen 255 EMSVSHQKEVTVEGVESPEIASTWSPAGISWSSGASQEDCKTPDTEQSFESLQPLEEDMA-----------------LNE 317 (527)
T ss_pred ccccchhhhcchhcccCcccccCCCCCcccccccchhhhccCCCHHhhhhccCCcHHHHH-----------------HHH
Q ss_pred HHHHhhhhhh-----HHHhhcCcccccccHHHHHHHH----------HHHHHHHHHH-HhhhhccCCCCCCCCCHHHHHH
Q 039560 102 TLQQLRSEND-----IALQLANPAAINNDIEELQQEV----------GRLQQQLQMA-EDQIRIYEPDPLRITSIKDIES 165 (344)
Q Consensus 102 ~l~KLk~e~d-----~~~~~~~~~~~n~~iE~Lq~Ei----------~~Lq~qle~l-e~~lR~~~gd~L~~lSleEL~~ 165 (344)
.|.||++.|. |..-....-.+.++|++||-.+ .+|+..++.| +..-|...-...-.-++..|+.
T Consensus 318 vL~kLk~tn~kQq~~IqdLq~sN~yLe~kvkeLQ~k~~kQqvfvDiinkLk~niEeLIedKY~viLEKnd~~k~lqnLqe 397 (527)
T PF15066_consen 318 VLQKLKHTNRKQQNRIQDLQCSNLYLEKKVKELQMKITKQQVFVDIINKLKENIEELIEDKYRVILEKNDIEKTLQNLQE 397 (527)
T ss_pred HHHHHHhhhHHHHHHHHHhhhccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhHhHhhhhhhhHHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 039560 166 CEKNLVDTLTQVSQRKEFLLSN 187 (344)
Q Consensus 166 LE~~Le~~L~~Vr~RK~~Ll~~ 187 (344)
.-....+-|..-|.-|+-|..+
T Consensus 398 ~la~tqk~LqEsr~eKetLqle 419 (527)
T PF15066_consen 398 ALANTQKHLQESRNEKETLQLE 419 (527)
T ss_pred HHHHHHHHHHHHHhhHHHHHHH
No 44
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=26.43 E-value=4.5e+02 Score=25.62 Aligned_cols=31 Identities=13% Similarity=0.306 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 154 PLRITSIKDIESCEKNLVDTLTQVSQRKEFL 184 (344)
Q Consensus 154 ~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~L 184 (344)
.++.++-++|..+...|...-..|..+|..+
T Consensus 202 e~~~~D~~eL~~lr~eL~~~~~~i~~~k~~l 232 (325)
T PF08317_consen 202 EIESCDQEELEALRQELAEQKEEIEAKKKEL 232 (325)
T ss_pred hhhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3666777888888888777777776665444
No 45
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=25.93 E-value=3.7e+02 Score=25.85 Aligned_cols=65 Identities=25% Similarity=0.283 Sum_probs=37.5
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhhhcCCCch
Q 039560 123 NNDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVS--QRKEFLLSNHLSSYDPSS 196 (344)
Q Consensus 123 n~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr--~RK~~Ll~~qi~~l~~~~ 196 (344)
+.+|+....|+.+.++.++.++.- ..-=|+|.+.||..|...-..=- -|--..+..++..+.+.+
T Consensus 196 e~KIekkk~ELER~qKRL~sLq~v---------RPAfmdEyEklE~EL~~lY~~Y~~kfRNl~yLe~qle~~~~~e 262 (267)
T PF10234_consen 196 EAKIEKKKQELERNQKRLQSLQSV---------RPAFMDEYEKLEEELQKLYEIYVEKFRNLDYLEHQLEEYNRRE 262 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc---------ChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 445555566666666666555532 22237999999999887644322 223345566666554443
No 46
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=25.87 E-value=1.1e+02 Score=21.64 Aligned_cols=19 Identities=37% Similarity=0.424 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 039560 129 LQQEVGRLQQQLQMAEDQI 147 (344)
Q Consensus 129 Lq~Ei~~Lq~qle~le~~l 147 (344)
|++++..|+.+++.|+..+
T Consensus 4 LrqQv~aL~~qv~~Lq~~f 22 (46)
T PF09006_consen 4 LRQQVEALQGQVQRLQAAF 22 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4444445555554444443
No 47
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.81 E-value=1.2e+02 Score=24.16 Aligned_cols=56 Identities=32% Similarity=0.442 Sum_probs=30.7
Q ss_pred hhhHHHHHHHHHhhhhhhHHHhhcCcccccccHHHHH-HHHHHHHHHHHHHHhhhhcc
Q 039560 94 QNKEYLLRTLQQLRSENDIALQLANPAAINNDIEELQ-QEVGRLQQQLQMAEDQIRIY 150 (344)
Q Consensus 94 ~~~e~L~~~l~KLk~e~d~~~~~~~~~~~n~~iE~Lq-~Ei~~Lq~qle~le~~lR~~ 150 (344)
.+.+++...+.+|+.+++. ++.........+++.|. .|+..|.++++..-.++|..
T Consensus 12 ~~~e~~~~e~~~L~~~~~~-L~~~~R~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~r 68 (100)
T PF01486_consen 12 SQHEELQQEIAKLRKENES-LQKELRHLMGEDLESLSLKELQQLEQQLESALKRVRSR 68 (100)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHhccccccccccchHHHHHHHHhhhhhHHHHHHH
Confidence 4456677777787776662 11111111222344444 56677777777666666543
No 48
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=25.32 E-value=1.9e+02 Score=22.73 Aligned_cols=15 Identities=27% Similarity=0.346 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHHHHH
Q 039560 127 EELQQEVGRLQQQLQ 141 (344)
Q Consensus 127 E~Lq~Ei~~Lq~qle 141 (344)
.-|+.||..|+.+..
T Consensus 21 ~LLqmEieELKekn~ 35 (79)
T PRK15422 21 TLLQMEIEELKEKNN 35 (79)
T ss_pred HHHHHHHHHHHHHHH
Confidence 334444444444433
No 49
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=25.09 E-value=71 Score=32.54 Aligned_cols=17 Identities=29% Similarity=0.587 Sum_probs=13.5
Q ss_pred ccccchhhhhhhhhhcc
Q 039560 22 SKRRNGLIKKAYELSIL 38 (344)
Q Consensus 22 sKR~~GL~KKA~ELs~L 38 (344)
.-||-|+|||-+|....
T Consensus 38 ~~~~~~~~~~~~~~~~~ 54 (407)
T PRK12726 38 RVTKLGIFKKQYEVTAV 54 (407)
T ss_pred HHHHhhhhhhhheeeee
Confidence 45789999999997543
No 50
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=24.61 E-value=3.1e+02 Score=25.92 Aligned_cols=47 Identities=15% Similarity=0.317 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVD 172 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~ 172 (344)
++++..++..++..++.+.+++....-.--...+.+++.+|...+..
T Consensus 54 ~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ 100 (239)
T COG1579 54 LEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQI 100 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence 34444444444444444433332111011223456666666554433
No 51
>PRK09039 hypothetical protein; Validated
Probab=24.57 E-value=4.2e+02 Score=26.22 Aligned_cols=24 Identities=29% Similarity=0.475 Sum_probs=13.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhh
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQI 147 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~l 147 (344)
.+|..|+++|..|+.|+..++..+
T Consensus 137 ~~V~~L~~qI~aLr~Qla~le~~L 160 (343)
T PRK09039 137 AQVELLNQQIAALRRQLAALEAAL 160 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666666655555544
No 52
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=24.56 E-value=4e+02 Score=24.91 Aligned_cols=22 Identities=18% Similarity=0.370 Sum_probs=15.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHH
Q 039560 159 SIKDIESCEKNLVDTLTQVSQR 180 (344)
Q Consensus 159 SleEL~~LE~~Le~~L~~Vr~R 180 (344)
+++|+..+|..|.+.-..|..-
T Consensus 160 ~~~d~l~ie~~L~~v~~eIe~~ 181 (262)
T PF14257_consen 160 TVEDLLEIERELSRVRSEIEQL 181 (262)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH
Confidence 7999999999866554444433
No 53
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.44 E-value=1.8e+02 Score=29.00 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCC--CCCCCCCHHHHH
Q 039560 126 IEELQQEVGRLQQQLQMAEDQIRIYEP--DPLRITSIKDIE 164 (344)
Q Consensus 126 iE~Lq~Ei~~Lq~qle~le~~lR~~~g--d~L~~lSleEL~ 164 (344)
+|.|+++...|+..++.+....+.-.+ ++++.++++|-.
T Consensus 255 ~etLEqq~~~L~~niDIL~~k~~eal~~~~n~~~~~~D~~~ 295 (365)
T KOG2391|consen 255 KETLEQQLQSLQKNIDILKSKVREALEKAENLEALDIDEAI 295 (365)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHhhhccCcCCCchhhh
Confidence 345555555555555555444433111 135555555543
No 54
>PRK11637 AmiB activator; Provisional
Probab=23.92 E-value=4.4e+02 Score=26.62 Aligned_cols=19 Identities=11% Similarity=0.120 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 039560 162 DIESCEKNLVDTLTQVSQR 180 (344)
Q Consensus 162 EL~~LE~~Le~~L~~Vr~R 180 (344)
++..++..|+..-..+..|
T Consensus 111 eI~~~q~~l~~~~~~l~~r 129 (428)
T PRK11637 111 SIAKLEQQQAAQERLLAAQ 129 (428)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444333
No 55
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=23.87 E-value=1.4e+02 Score=29.05 Aligned_cols=44 Identities=23% Similarity=0.462 Sum_probs=31.1
Q ss_pred eeEEecCCCCcccccccccchhhhhhhhhhcccCccEEEEeecCCCccccccccchhhhHHhhhc
Q 039560 7 EIKRIENNTNRQVTFSKRRNGLIKKAYELSILCDIDIALIMFSPSGRLSHFSGRKRIEDVFSRYV 71 (344)
Q Consensus 7 ~ik~I~~~~~R~~TfsKR~~GL~KKA~ELs~LCd~~v~liifsp~gk~~~~ss~~~ve~VIeRY~ 71 (344)
.|.+|.|.+.|..+=++ .||..+.+ +.| .|-..++|++|+++|.
T Consensus 25 n~~li~n~tqr~t~~sR-------------~L~Ecel~---~~p-----~Y~nDpEmK~iid~~n 68 (295)
T TIGR01478 25 NVSYIQNNTQMTSTKSR-------------LLAEIQRP---KNP-----HYHNDPELKEIIDKLN 68 (295)
T ss_pred ceecccCccccccccce-------------ehhhhccc---cCC-----CCCCcHHHHHHHHHHh
Confidence 46778888877766332 46877764 333 4667899999999986
No 56
>PRK10884 SH3 domain-containing protein; Provisional
Probab=23.72 E-value=1.5e+02 Score=27.33 Aligned_cols=15 Identities=27% Similarity=0.523 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHHH
Q 039560 127 EELQQEVGRLQQQLQ 141 (344)
Q Consensus 127 E~Lq~Ei~~Lq~qle 141 (344)
..+++|+..++.++.
T Consensus 96 p~le~el~~l~~~l~ 110 (206)
T PRK10884 96 PDLENQVKTLTDKLN 110 (206)
T ss_pred HHHHHHHHHHHHHHH
Confidence 334444444443333
No 57
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=23.55 E-value=2.6e+02 Score=29.24 Aligned_cols=60 Identities=17% Similarity=0.262 Sum_probs=39.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFLLS 186 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~Ll~ 186 (344)
.+++....|+..|+.++..+..+++.- ++..-.++...+=-..|..-|.+|...+..|+.
T Consensus 337 ~eie~kEeei~~L~~~~d~L~~q~~kq---~Is~e~fe~mn~Ere~L~reL~~i~~~~~~L~k 396 (622)
T COG5185 337 SEIELKEEEIKALQSNIDELHKQLRKQ---GISTEQFELMNQEREKLTRELDKINIQSDKLTK 396 (622)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHhc---CCCHHHHHHHHHHHHHHHHHHHHhcchHHHHHH
Confidence 456777778888888888888887653 332222333444445677778888777777655
No 58
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=23.45 E-value=2.6e+02 Score=28.95 Aligned_cols=20 Identities=10% Similarity=0.190 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 039560 162 DIESCEKNLVDTLTQVSQRK 181 (344)
Q Consensus 162 EL~~LE~~Le~~L~~Vr~RK 181 (344)
.|..+++.+.+.+..-...+
T Consensus 418 kl~~~~e~~~~~~~s~d~~I 437 (493)
T KOG0804|consen 418 KLKELEEREKEALGSKDEKI 437 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444333333
No 59
>cd00089 HR1 Protein kinase C-related kinase homology region 1 domain; also known as the ACC (antiparallel coiled-coil) finger domain or Rho-binding domain. Found in vertebrate PRK1 and yeast PKC1 protein kinases C; those found in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 repeats often occur in tandem repeat arrangments, seperated by a short linker region.
Probab=23.39 E-value=3.2e+02 Score=20.34 Aligned_cols=57 Identities=21% Similarity=0.258 Sum_probs=36.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKEFL 184 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~L 184 (344)
..+++|++++..-....+.++.-++.|...+. ...+...+..|.++-.+|..=+.+|
T Consensus 9 ~~l~~L~~~l~~E~~~r~Gaenm~~~~~~~~~----~~~~~~~~~~l~es~~ki~~Lr~~L 65 (72)
T cd00089 9 SRLERLEKELSIELKVKEGAENLLRLYSDEKK----KKLLAEAEQMLRESKQKLELLKMQL 65 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC----ccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777766655556667776666654432 2677777888888877776655554
No 60
>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=23.27 E-value=21 Score=27.66 Aligned_cols=37 Identities=32% Similarity=0.495 Sum_probs=26.5
Q ss_pred cccccccccchhhhh---------hhhhhcccCccEEEEeecCCCc
Q 039560 17 RQVTFSKRRNGLIKK---------AYELSILCDIDIALIMFSPSGR 53 (344)
Q Consensus 17 R~~TfsKR~~GL~KK---------A~ELs~LCd~~v~liifsp~gk 53 (344)
+.+-||+-|++|-.| +.|+.+-||.|.-|+.+-|.|.
T Consensus 18 ~~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~D~ll~~V~~~G~ 63 (75)
T PF01502_consen 18 RATYYSRSRNRLWRKGETSGNTQKVVEIRLDCDGDALLFKVEQVGP 63 (75)
T ss_dssp B-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-
T ss_pred cEEEEEccCCcEeeEECCCCCEEEEEEEEecCCCCeEEEEEEeCCC
Confidence 334457777777554 5789999999999999988776
No 61
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=23.23 E-value=1.8e+02 Score=30.30 Aligned_cols=28 Identities=4% Similarity=-0.124 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 157 ITSIKDIESCEKNLVDTLTQVSQRKEFL 184 (344)
Q Consensus 157 ~lSleEL~~LE~~Le~~L~~Vr~RK~~L 184 (344)
..++.++.++-..+.+.+..++.++..+
T Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (525)
T TIGR02231 123 EPDLKEWFQAFDFNGSEIERLLTEDREA 150 (525)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888888888888887777766543
No 62
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=22.48 E-value=5.2e+02 Score=23.25 Aligned_cols=17 Identities=35% Similarity=0.636 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q 039560 128 ELQQEVGRLQQQLQMAE 144 (344)
Q Consensus 128 ~Lq~Ei~~Lq~qle~le 144 (344)
+|+.||..|..+++.++
T Consensus 124 eL~~eI~~L~~~i~~le 140 (171)
T PF04799_consen 124 ELEDEIKQLEKEIQRLE 140 (171)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444444444444333
No 63
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex
Probab=22.19 E-value=3.1e+02 Score=25.73 Aligned_cols=57 Identities=16% Similarity=0.204 Sum_probs=45.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRK 181 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK 181 (344)
...+.|...+..+...+..+-.....+.+ ....++-.+|...-+..+..|..||.|-
T Consensus 87 ~~a~~L~~~i~~l~~~i~~l~~~~~~l~~-~~~~~~~~~l~~~l~ea~~mL~emr~r~ 143 (264)
T PF06008_consen 87 QRAQDLEQFIQNLQDNIQELIEQVESLNE-NGDQLPSEDLQRALAEAQRMLEEMRKRD 143 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCc-ccCCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 34566777888888888877777766644 5677888999999999999999999984
No 64
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=21.91 E-value=4.5e+02 Score=23.45 Aligned_cols=38 Identities=24% Similarity=0.372 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHH
Q 039560 128 ELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTL 174 (344)
Q Consensus 128 ~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L 174 (344)
+++.+|..|+.++..+..+++.+ ++.|..+++.|...+
T Consensus 26 ~~~~~I~~L~~e~~~ld~~i~~~---------~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 26 ENQARIQQLRAEIEELDEQIRDI---------LKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHH
Confidence 35566666777776666666554 677777777777776
No 65
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=21.44 E-value=2.5e+02 Score=30.74 Aligned_cols=27 Identities=33% Similarity=0.540 Sum_probs=17.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHhhhhccC
Q 039560 125 DIEELQQEVGRLQQQLQMAEDQIRIYE 151 (344)
Q Consensus 125 ~iE~Lq~Ei~~Lq~qle~le~~lR~~~ 151 (344)
...+|+.|+.+|+.++...+++++.+.
T Consensus 546 r~~~lE~E~~~lr~elk~kee~~~~~e 572 (697)
T PF09726_consen 546 RRRQLESELKKLRRELKQKEEQIRELE 572 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666777777777766666665553
No 66
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=21.35 E-value=1e+02 Score=25.58 Aligned_cols=28 Identities=32% Similarity=0.362 Sum_probs=22.4
Q ss_pred hhhhhhcccCccEEEEeecCCCccccccc
Q 039560 31 KAYELSILCDIDIALIMFSPSGRLSHFSG 59 (344)
Q Consensus 31 KA~ELs~LCd~~v~liifsp~gk~~~~ss 59 (344)
|-.+|..|-||- |...||++|++.+|-|
T Consensus 2 ~l~~Lm~lpGv~-AAg~Fs~~G~l~e~~G 29 (108)
T PF09941_consen 2 KLDKLMKLPGVV-AAGEFSDDGKLVEYKG 29 (108)
T ss_pred cHHHhhcCCCeE-EEEEECCCCeEEeeec
Confidence 346788888885 6689999999999866
No 67
>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=21.30 E-value=75 Score=20.55 Aligned_cols=24 Identities=17% Similarity=0.466 Sum_probs=17.5
Q ss_pred hhhcccCccEEEEeecCCCccccc
Q 039560 34 ELSILCDIDIALIMFSPSGRLSHF 57 (344)
Q Consensus 34 ELs~LCd~~v~liifsp~gk~~~~ 57 (344)
.|+--||+-|.+-+|...|..-.|
T Consensus 2 hlcpkcgvgvl~pvy~~kgeikvf 25 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQKGEIKVF 25 (36)
T ss_dssp -B-TTTSSSBEEEEE-TTS-EEEE
T ss_pred ccCCccCceEEEEeecCCCcEEEE
Confidence 467789999999999999987666
No 68
>PF05120 GvpG: Gas vesicle protein G ; InterPro: IPR007804 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
Probab=21.19 E-value=3.6e+02 Score=21.04 Aligned_cols=43 Identities=19% Similarity=0.333 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 134 GRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKE 182 (344)
Q Consensus 134 ~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~ 182 (344)
..++.++..++..+ ....+|-+|....|..|-+.|..++.++.
T Consensus 31 ~~i~~~L~~L~~~~------e~GEIseeEf~~~E~eLL~rL~~~~~~~~ 73 (79)
T PF05120_consen 31 AAIRRELAELQEAL------EAGEISEEEFERREDELLDRLEEARRREA 73 (79)
T ss_pred HHHHHHHHHHHHHH------HcCCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44555555555543 24457899999999999999999998764
No 69
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=20.79 E-value=2.8e+02 Score=27.13 Aligned_cols=15 Identities=33% Similarity=0.477 Sum_probs=8.1
Q ss_pred HHHHHHHHHhhhhhh
Q 039560 97 EYLLRTLQQLRSEND 111 (344)
Q Consensus 97 e~L~~~l~KLk~e~d 111 (344)
..+.+.+.+++.|..
T Consensus 46 ~~~~~el~~le~Ee~ 60 (314)
T PF04111_consen 46 EELEEELEKLEQEEE 60 (314)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 345556666665443
No 70
>PRK10132 hypothetical protein; Provisional
Probab=20.68 E-value=4.4e+02 Score=21.73 Aligned_cols=52 Identities=13% Similarity=0.281 Sum_probs=35.2
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 123 NNDIEELQQEVGRLQQQLQMAEDQIRIYEPDPLRITSIKDIESCEKNLVDTLTQVSQRKE 182 (344)
Q Consensus 123 n~~iE~Lq~Ei~~Lq~qle~le~~lR~~~gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~ 182 (344)
+.+++.|..++..|-..++.+-.. ....+-+++..+-..++..|...|++-.
T Consensus 11 ~~q~e~L~~Dl~~L~~~le~ll~~--------~~~~~~~~~~~lR~r~~~~L~~ar~~l~ 62 (108)
T PRK10132 11 DDGVQDIQNDVNQLADSLESVLKS--------WGSDAKGEAEAARRKAQALLKETRARMH 62 (108)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHH--------HhhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345667777777776666554332 1233567888898999999999887654
No 71
>PRK11637 AmiB activator; Provisional
Probab=20.55 E-value=2.9e+02 Score=27.87 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 161 KDIESCEKNLVDTLTQVSQRKEFL 184 (344)
Q Consensus 161 eEL~~LE~~Le~~L~~Vr~RK~~L 184 (344)
.++..++..|.+.-.+|..++..|
T Consensus 103 ~ei~~l~~eI~~~q~~l~~~~~~l 126 (428)
T PRK11637 103 KQIDELNASIAKLEQQQAAQERLL 126 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666666655544
No 72
>PHA02109 hypothetical protein
Probab=20.22 E-value=1.3e+02 Score=27.30 Aligned_cols=29 Identities=10% Similarity=0.200 Sum_probs=16.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhccCC
Q 039560 124 NDIEELQQEVGRLQQQLQMAEDQIRIYEP 152 (344)
Q Consensus 124 ~~iE~Lq~Ei~~Lq~qle~le~~lR~~~g 152 (344)
..++-|..|++.++++++.+....|.+..
T Consensus 200 ~ki~~LS~E~~Q~~~Ki~N~R~~Vk~~LS 228 (233)
T PHA02109 200 IKLEALSDEACQVKHKILNLRAEVKRRLS 228 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666666666666655555554433
No 73
>PF00521 DNA_topoisoIV: DNA gyrase/topoisomerase IV, subunit A; InterPro: IPR002205 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent C-terminal region in eukaryotic topoisomerase II composed of a single polypeptide. This subunit has DNA-binding capacity. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 1ZVU_A 1AB4_A 1X75_A 3NUH_A 1BJT_A 1BGW_A 2RGR_A 3KSB_B 3FOE_B 2NOV_C ....
Probab=20.06 E-value=3.5e+02 Score=27.51 Aligned_cols=32 Identities=19% Similarity=0.345 Sum_probs=23.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 039560 152 PDPLRITSIKDIESCEKNLVDTLTQVSQRKEF 183 (344)
Q Consensus 152 gd~L~~lSleEL~~LE~~Le~~L~~Vr~RK~~ 183 (344)
.-+|..++-++...|.+.+++..+.+..=+..
T Consensus 382 ~m~L~~LT~~e~~kL~~e~~~l~~ei~~l~~~ 413 (426)
T PF00521_consen 382 SMPLRRLTKEEIEKLQKEIKELEKEIEELEKI 413 (426)
T ss_dssp TSBGGGGSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hchHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44677888888888888888777766655443
Done!