Query 039654
Match_columns 225
No_of_seqs 187 out of 1456
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 11:49:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039654hhsearch_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 6.3E-35 1.4E-39 238.7 7.6 76 10-85 1-78 (195)
2 cd00265 MADS_MEF2_like MEF2 (m 100.0 4.7E-34 1E-38 199.6 3.6 72 11-82 1-72 (77)
3 cd00266 MADS_SRF_like SRF-like 100.0 6E-31 1.3E-35 186.6 5.2 72 11-82 1-73 (83)
4 smart00432 MADS MADS domain. 100.0 6.5E-31 1.4E-35 173.6 4.9 59 11-69 1-59 (59)
5 cd00120 MADS MADS: MCM1, Agamo 100.0 6.4E-30 1.4E-34 169.0 4.1 59 11-69 1-59 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 1.6E-27 3.4E-32 152.6 1.2 51 18-68 1-51 (51)
7 KOG0015 Regulator of arginine 99.8 4E-22 8.8E-27 167.2 3.2 70 6-75 58-127 (338)
8 COG5068 ARG80 Regulator of arg 99.5 1.1E-14 2.3E-19 128.0 3.7 69 9-77 80-148 (412)
9 PF01486 K-box: K-box region; 98.1 2.3E-05 5E-10 57.3 8.2 41 136-176 37-77 (100)
10 PF15079 DUF4546: Domain of un 80.4 14 0.00029 29.5 7.8 63 99-175 47-109 (205)
11 KOG4252 GTP-binding protein [S 73.4 9.3 0.0002 31.2 5.3 27 48-80 91-117 (246)
12 cd00187 TOP4c DNA Topoisomeras 73.0 30 0.00065 32.0 9.3 59 16-80 257-326 (445)
13 PF09151 DUF1936: Domain of un 66.9 4.4 9.5E-05 22.9 1.5 28 43-70 2-31 (36)
14 PF10584 Proteasome_A_N: Prote 66.2 2.3 5E-05 22.5 0.3 12 54-65 5-16 (23)
15 KOG4302 Microtubule-associated 66.1 86 0.0019 30.6 10.9 34 138-171 150-183 (660)
16 PF06698 DUF1192: Protein of u 64.3 19 0.00041 23.6 4.4 31 137-167 13-43 (59)
17 PF10491 Nrf1_DNA-bind: NLS-bi 63.8 20 0.00044 29.5 5.4 41 40-80 44-87 (214)
18 PHA02592 52 DNA topisomerase I 58.1 58 0.0012 30.2 8.0 41 35-80 285-325 (439)
19 PF04120 Iron_permease: Low af 50.9 1.1E+02 0.0024 23.4 7.7 28 140-167 90-117 (132)
20 KOG3366 Mitochondrial F1F0-ATP 49.8 61 0.0013 25.9 5.9 15 140-154 128-142 (172)
21 PF04521 Viral_P18: ssRNA posi 49.0 58 0.0013 24.5 5.3 23 27-49 4-26 (120)
22 smart00787 Spc7 Spc7 kinetocho 47.0 1.7E+02 0.0038 25.7 9.0 29 140-168 196-224 (312)
23 PF08181 DegQ: DegQ (SacQ) fam 46.7 53 0.0011 19.8 3.9 12 147-158 6-17 (46)
24 PF09403 FadA: Adhesion protei 44.7 1.4E+02 0.003 22.7 9.7 22 148-169 89-110 (126)
25 PF12325 TMF_TATA_bd: TATA ele 43.6 1.4E+02 0.003 22.4 8.4 26 146-171 94-119 (120)
26 TIGR01916 F420_cofE F420-0:gam 42.8 26 0.00057 29.7 3.0 29 42-70 133-161 (243)
27 PF05700 BCAS2: Breast carcino 41.5 1.5E+02 0.0032 24.5 7.4 65 100-171 98-162 (221)
28 PF14009 DUF4228: Domain of un 41.5 23 0.00049 27.6 2.4 33 48-80 12-45 (181)
29 PF09941 DUF2173: Uncharacteri 40.3 22 0.00049 26.3 2.0 26 40-66 2-27 (108)
30 PF08317 Spc7: Spc7 kinetochor 40.0 2.6E+02 0.0056 24.5 9.8 29 140-168 201-229 (325)
31 PRK04098 sec-independent trans 40.0 50 0.0011 26.1 4.0 27 145-171 81-107 (158)
32 PF09432 THP2: Tho complex sub 39.8 1.7E+02 0.0037 22.3 7.8 12 69-80 38-49 (132)
33 PF10654 DUF2481: Protein of u 37.3 1.2E+02 0.0025 22.7 5.3 53 99-156 27-79 (126)
34 COG3883 Uncharacterized protei 36.9 2.8E+02 0.006 23.9 8.7 28 147-174 79-106 (265)
35 KOG4304 Transcriptional repres 35.4 30 0.00065 29.5 2.3 24 91-114 37-60 (250)
36 KOG1029 Endocytic adaptor prot 34.6 4.3E+02 0.0094 26.6 10.0 32 23-54 435-467 (1118)
37 COG5000 NtrY Signal transducti 34.4 30 0.00066 33.4 2.3 28 45-73 374-401 (712)
38 PF11944 DUF3461: Protein of u 34.3 2.1E+02 0.0045 21.7 6.3 24 147-170 101-124 (125)
39 smart00782 PhnA_Zn_Ribbon PhnA 34.2 15 0.00032 22.9 0.2 22 37-58 2-23 (47)
40 PRK05561 DNA topoisomerase IV 34.0 3.1E+02 0.0068 27.3 9.3 25 53-80 337-361 (742)
41 PRK01919 tatB sec-independent 33.7 2.2E+02 0.0048 22.8 6.8 10 52-61 15-24 (169)
42 KOG4673 Transcription factor T 33.6 4E+02 0.0087 26.4 9.5 30 146-175 930-959 (961)
43 KOG3048 Molecular chaperone Pr 33.0 96 0.0021 24.2 4.5 26 140-165 8-33 (153)
44 KOG0432 Valyl-tRNA synthetase 31.9 1E+02 0.0022 31.1 5.5 18 39-56 880-897 (995)
45 PF05700 BCAS2: Breast carcino 31.2 2.8E+02 0.0062 22.9 7.5 25 110-134 147-171 (221)
46 PF00843 Arena_nucleocap: Aren 31.1 93 0.002 28.8 4.8 26 141-166 87-112 (533)
47 PF07106 TBPIP: Tat binding pr 30.9 2.6E+02 0.0056 21.8 8.9 30 144-173 108-137 (169)
48 KOG1318 Helix loop helix trans 30.6 3.7E+02 0.0079 24.8 8.5 35 14-48 221-259 (411)
49 PF11460 DUF3007: Protein of u 30.6 52 0.0011 24.1 2.5 18 141-158 86-103 (104)
50 PRK02224 chromosome segregatio 30.2 3.9E+02 0.0084 26.7 9.6 12 68-79 463-474 (880)
51 PF14257 DUF4349: Domain of un 30.2 3.3E+02 0.0072 22.8 8.0 110 35-166 62-180 (262)
52 PF09158 MotCF: Bacteriophage 29.8 14 0.0003 27.1 -0.5 53 14-81 19-72 (103)
53 TIGR03752 conj_TIGR03752 integ 28.9 4E+02 0.0086 25.0 8.5 29 98-126 65-93 (472)
54 PF14263 DUF4354: Domain of un 28.7 11 0.00024 28.6 -1.2 41 20-65 41-81 (124)
55 COG4575 ElaB Uncharacterized c 28.5 2.4E+02 0.0052 20.7 7.4 28 144-171 33-60 (104)
56 PF08317 Spc7: Spc7 kinetochor 28.3 4.1E+02 0.0088 23.3 8.4 19 144-162 272-290 (325)
57 PHA02109 hypothetical protein 28.0 1.4E+02 0.0031 24.1 4.8 28 139-166 182-211 (233)
58 PRK13293 F420-0--gamma-glutamy 27.9 64 0.0014 27.4 3.0 29 42-70 134-162 (245)
59 TIGR02231 conserved hypothetic 27.7 5.1E+02 0.011 24.2 10.1 18 100-117 72-89 (525)
60 KOG4171 Adenylate/guanylate ki 27.6 2.1E+02 0.0046 28.0 6.7 92 55-147 333-440 (671)
61 PF06020 Roughex: Drosophila r 26.8 30 0.00066 30.0 0.9 16 45-60 183-198 (334)
62 KOG4637 Adaptor for phosphoino 26.8 42 0.0009 30.3 1.8 40 42-81 367-411 (464)
63 COG4917 EutP Ethanolamine util 26.2 54 0.0012 25.3 2.1 23 44-66 59-81 (148)
64 COG4831 Roadblock/LC7 domain [ 26.1 72 0.0016 23.1 2.6 28 39-67 3-30 (109)
65 PF14723 SSFA2_C: Sperm-specif 26.1 1.9E+02 0.0041 23.3 5.1 27 144-171 138-164 (179)
66 PF07960 CBP4: CBP4; InterPro 26.0 3E+02 0.0065 21.0 8.3 28 50-79 14-41 (128)
67 PRK04863 mukB cell division pr 25.9 6.8E+02 0.015 27.2 10.6 24 140-163 430-453 (1486)
68 PTZ00108 DNA topoisomerase 2-l 25.8 3.4E+02 0.0073 29.2 8.3 26 53-80 962-987 (1388)
69 PRK06851 hypothetical protein; 25.6 5E+02 0.011 23.4 9.2 28 34-61 43-70 (367)
70 TIGR02420 dksA RNA polymerase- 25.6 1.7E+02 0.0037 21.3 4.7 29 145-173 1-29 (110)
71 PF05852 DUF848: Gammaherpesvi 25.6 3.3E+02 0.0071 21.3 9.2 33 142-174 83-115 (146)
72 PRK09631 DNA topoisomerase IV 25.4 4.9E+02 0.011 25.5 8.8 62 12-80 247-318 (635)
73 PRK00736 hypothetical protein; 25.3 2.1E+02 0.0046 19.0 4.8 12 153-164 38-49 (68)
74 PF04678 DUF607: Protein of un 25.2 3.5E+02 0.0077 21.5 7.6 43 66-117 32-75 (180)
75 PF15233 SYCE1: Synaptonemal c 24.8 2.6E+02 0.0056 21.4 5.4 12 69-80 6-17 (134)
76 COG0212 5-formyltetrahydrofola 24.7 33 0.00071 27.8 0.8 15 211-225 128-142 (191)
77 PRK00295 hypothetical protein; 24.1 2.3E+02 0.0049 18.9 4.8 7 156-162 41-47 (68)
78 PF00383 dCMP_cyt_deam_1: Cyti 24.0 74 0.0016 22.3 2.4 32 36-67 6-41 (102)
79 KOG0184 20S proteasome, regula 23.9 39 0.00085 28.3 1.0 21 45-65 3-23 (254)
80 PLN03128 DNA topoisomerase 2; 23.8 4.7E+02 0.01 27.5 8.8 26 53-80 961-986 (1135)
81 PF05873 Mt_ATP-synt_D: ATP sy 23.6 1.8E+02 0.0038 23.0 4.7 14 140-153 126-139 (161)
82 PRK01770 sec-independent trans 23.1 1.3E+02 0.0027 24.2 3.7 16 43-60 8-23 (171)
83 cd01365 KISc_KIF1A_KIF1B Kines 22.9 75 0.0016 28.2 2.7 36 35-70 70-111 (356)
84 PF06717 DUF1202: Protein of u 22.8 4.5E+02 0.0097 23.0 7.1 11 135-145 176-186 (308)
85 PF06632 XRCC4: DNA double-str 22.7 5.6E+02 0.012 22.9 9.5 21 151-171 183-203 (342)
86 PF06694 Plant_NMP1: Plant nuc 22.1 4.5E+02 0.0097 23.2 7.1 23 143-165 203-225 (325)
87 TIGR03545 conserved hypothetic 22.0 5.7E+02 0.012 24.5 8.5 31 34-65 88-120 (555)
88 PF15290 Syntaphilin: Golgi-lo 21.9 5.4E+02 0.012 22.5 7.9 16 98-113 88-103 (305)
89 PRK04325 hypothetical protein; 21.9 2.7E+02 0.0057 18.9 4.8 7 101-107 11-17 (74)
90 PF06034 DUF919: Nucleopolyhed 21.9 2.5E+02 0.0054 18.6 6.7 19 146-164 36-54 (62)
91 PRK10333 5-formyltetrahydrofol 21.9 38 0.00083 27.1 0.6 13 213-225 122-134 (182)
92 PRK10884 SH3 domain-containing 21.8 4.6E+02 0.0099 21.6 8.6 19 99-117 93-111 (206)
93 KOG2856 Adaptor protein PACSIN 21.7 6.2E+02 0.013 23.1 9.4 27 142-168 171-197 (472)
94 cd04751 Commd3 COMM_Domain con 21.6 1.3E+02 0.0029 21.4 3.3 23 144-166 70-92 (95)
95 PF06937 EURL: EURL protein; 21.1 1.6E+02 0.0035 25.4 4.2 28 139-166 213-240 (285)
96 PHA00727 hypothetical protein 21.1 3.9E+02 0.0085 22.0 6.2 55 100-164 19-73 (278)
97 PRK13729 conjugal transfer pil 21.0 7E+02 0.015 23.4 13.0 12 68-79 51-62 (475)
98 PF15119 APOC4: Apolipoprotein 20.8 52 0.0011 23.4 1.0 20 30-49 75-96 (99)
99 cd01284 Riboflavin_deaminase-r 20.8 1E+02 0.0022 22.8 2.7 33 38-70 1-39 (115)
100 KOG0183 20S proteasome, regula 20.7 55 0.0012 27.3 1.3 16 50-65 4-19 (249)
101 KOG2662 Magnesium transporters 20.6 6.7E+02 0.015 23.1 10.0 36 140-175 212-250 (414)
102 TIGR02727 MTHFS_bact 5,10-meth 20.6 43 0.00093 26.7 0.6 13 213-225 128-140 (181)
103 COG3096 MukB Uncharacterized p 20.4 9.1E+02 0.02 24.5 10.4 34 36-79 473-506 (1480)
104 PRK03918 chromosome segregatio 20.4 5.4E+02 0.012 25.6 8.5 21 29-49 416-436 (880)
105 PF11598 COMP: Cartilage oligo 20.3 2.3E+02 0.0049 17.5 4.3 23 148-170 8-30 (45)
106 PF01996 F420_ligase: F420-0:G 20.3 40 0.00087 28.2 0.4 29 42-70 141-169 (228)
107 PHA00451 protein kinase 20.1 5.5E+02 0.012 22.5 7.2 21 48-68 193-218 (362)
108 PRK00064 recF recombination pr 20.1 2.5E+02 0.0055 24.9 5.6 38 39-80 103-141 (361)
109 COG0099 RpsM Ribosomal protein 20.1 2.5E+02 0.0054 21.2 4.6 36 140-175 43-85 (121)
No 1
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=100.00 E-value=6.3e-35 Score=238.72 Aligned_cols=76 Identities=57% Similarity=0.930 Sum_probs=72.6
Q ss_pred CCccceeeEeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCcc--hhhhhhhhhcCCCCC
Q 039654 10 KGRQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPC--VETIVDRYLTRNPPQ 85 (225)
Q Consensus 10 mgR~Ki~i~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~ps--v~~Vi~Ry~~~~~~~ 85 (225)
|||+||+|++|+|+++|||||+|||.||||||+||||||||+||||||||+|++|+||+|+ |+.|++||.....+.
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 78 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEPS 78 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhhh
Confidence 8999999999999999999999999999999999999999999999999999999999998 999999999865544
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=100.00 E-value=4.7e-34 Score=199.64 Aligned_cols=72 Identities=49% Similarity=0.877 Sum_probs=70.2
Q ss_pred CccceeeEeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhhhhhhcCC
Q 039654 11 GRQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIVDRYLTRN 82 (225)
Q Consensus 11 gR~Ki~i~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~~~~ 82 (225)
||+||+|++|+|+++|++||+|||.||||||+|||+||||+||+|||||+|++|+|++|++++||+||++.+
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 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTS 72 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhcc
Confidence 899999999999999999999999999999999999999999999999999999999999999999999754
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=99.96 E-value=6e-31 Score=186.62 Aligned_cols=72 Identities=49% Similarity=0.847 Sum_probs=69.3
Q ss_pred CccceeeEeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCcc-hhhhhhhhhcCC
Q 039654 11 GRQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPC-VETIVDRYLTRN 82 (225)
Q Consensus 11 gR~Ki~i~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~ps-v~~Vi~Ry~~~~ 82 (225)
||+||+|++|+|+.+|++||+|||.||||||+||||||||+||+|||||+|+.+.|++++ ++.+|++|...+
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~ 73 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLS 73 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcC
Confidence 799999999999999999999999999999999999999999999999999999998877 999999998754
No 4
>smart00432 MADS MADS domain.
Probab=99.96 E-value=6.5e-31 Score=173.62 Aligned_cols=59 Identities=58% Similarity=1.001 Sum_probs=58.1
Q ss_pred CccceeeEeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCc
Q 039654 11 GRQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHP 69 (225)
Q Consensus 11 gR~Ki~i~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~p 69 (225)
||+||+|++|+|+++|++||+|||.||||||+||||||||+||+|||||+|++++|++|
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 89999999999999999999999999999999999999999999999999999999987
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=99.96 E-value=6.4e-30 Score=169.02 Aligned_cols=59 Identities=56% Similarity=0.928 Sum_probs=57.6
Q ss_pred CccceeeEeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCc
Q 039654 11 GRQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHP 69 (225)
Q Consensus 11 gR~Ki~i~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~p 69 (225)
||+||+|++|+|+..|++||+|||.||||||+||||||||+||+|||||+|+++.|++|
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 79999999999999999999999999999999999999999999999999999999875
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=1.6e-27 Score=152.56 Aligned_cols=51 Identities=59% Similarity=0.977 Sum_probs=46.4
Q ss_pred EeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCC
Q 039654 18 VKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGH 68 (225)
Q Consensus 18 ~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~ 68 (225)
|+|+|++.|++||+|||.||||||+||||||||+||+|||||+|++|+|++
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=99.84 E-value=4e-22 Score=167.25 Aligned_cols=70 Identities=41% Similarity=0.653 Sum_probs=66.4
Q ss_pred CCCCCCccceeeEeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhh
Q 039654 6 SKKSKGRQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIV 75 (225)
Q Consensus 6 ~~~~mgR~Ki~i~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi 75 (225)
+|++.||+||+|++|+|+..|.+||||||.||||||+|||||+|.+|-|+|.|.+|.+|+|+.|..+.||
T Consensus 58 ~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i 127 (338)
T KOG0015|consen 58 GKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMI 127 (338)
T ss_pred CccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccc
Confidence 6899999999999999999999999999999999999999999999999999999999999999765444
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.50 E-value=1.1e-14 Score=127.95 Aligned_cols=69 Identities=35% Similarity=0.538 Sum_probs=65.5
Q ss_pred CCCccceeeEeeCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhhhh
Q 039654 9 SKGRQKVEMVKMPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIVDR 77 (225)
Q Consensus 9 ~mgR~Ki~i~~I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi~R 77 (225)
+|||+||.|..|+|+.+|.|||+||+.||+|||.||++|.|.+|.++|.|..|.++.|+.|+.+.|+.-
T Consensus 80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~~ 148 (412)
T COG5068 80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVKS 148 (412)
T ss_pred ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCcccccccc
Confidence 689999999999999999999999999999999999999999999999999999999999987766644
No 9
>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=98.09 E-value=2.3e-05 Score=57.35 Aligned_cols=41 Identities=27% Similarity=0.409 Sum_probs=37.8
Q ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 039654 136 CWWEAPIEELNLPQLEQLKMSLEELKKNVGKQAEKMLIQSS 176 (225)
Q Consensus 136 ~~w~~~l~~Ls~eEL~~L~~~Le~l~~~V~~r~~~L~~q~~ 176 (225)
+..|++|++|+++||..|+..|+..+..|+.|+.+++.+..
T Consensus 37 ~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i 77 (100)
T PF01486_consen 37 HLMGEDLESLSLKELQQLEQQLESALKRVRSRKDQLLMEQI 77 (100)
T ss_pred ccccccccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHH
Confidence 56799999999999999999999999999999999987753
No 10
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=80.40 E-value=14 Score=29.53 Aligned_cols=63 Identities=21% Similarity=0.423 Sum_probs=44.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 039654 99 ASVRELNMQLTQVLNQLEIEKKRGEELNQMRKASQAQCWWEAPIEELNLPQLEQLKMSLEELKKNVGKQAEKMLIQS 175 (225)
Q Consensus 99 ~~i~~l~~ql~~l~~~le~ekk~~e~L~~l~k~~~~~~~w~~~l~~Ls~eEL~~L~~~Le~l~~~V~~r~~~L~~q~ 175 (225)
.-.++|..++..+.++| +.+.|++.++.. |-|-+.+-|.+|...+.+..+...++++-|+.-+
T Consensus 47 G~T~eLkNeLREVREEL---kEKmeEIKQIKd-----------iMDKDFDKL~EFVEIMKeMQkDMDEKMDvLiNiQ 109 (205)
T PF15079_consen 47 GGTQELKNELREVREEL---KEKMEEIKQIKD-----------IMDKDFDKLHEFVEIMKEMQKDMDEKMDVLINIQ 109 (205)
T ss_pred cccHHHHHHHHHHHHHH---HHHHHHHHHHHH-----------HHhhhHHHHHHHHHHHHHHHHhHHHhhhHHhhcc
Confidence 34467777777776665 455566666543 3345678899999999999999999998886433
No 11
>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=73.37 E-value=9.3 Score=31.15 Aligned_cols=27 Identities=26% Similarity=0.561 Sum_probs=19.8
Q ss_pred ccCcEEEEEecCCCcccccCCcchhhhhhhhhc
Q 039654 48 CGADIAIIVFSPGKKVFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 48 C~aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~~ 80 (225)
-||.+||+|||.++. + |.+.+++=|..
T Consensus 91 rgaqa~vLVFSTTDr-~-----SFea~~~w~~k 117 (246)
T KOG4252|consen 91 RGAQASVLVFSTTDR-Y-----SFEATLEWYNK 117 (246)
T ss_pred ccccceEEEEecccH-H-----HHHHHHHHHHH
Confidence 489999999999864 3 34666666654
No 12
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=72.98 E-value=30 Score=32.04 Aligned_cols=59 Identities=25% Similarity=0.523 Sum_probs=35.1
Q ss_pred eeEeeCCCCccc-hhhh---ccc-------chHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhhhhhhc
Q 039654 16 EMVKMPNESNLQ-VTFS---KRR-------TGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 16 ~i~~I~n~~~R~-vTFs---KRr-------~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~~ 80 (225)
.|.-|.+++++. +.|- ||. .+|+|+ ..|.+--.+ -+++|.++|++..| ++.+||+.|..
T Consensus 257 ~I~~~~D~s~~~~vrivI~lk~~~~~~~~~~~L~k~-t~L~~s~~~--Nm~~~~~~g~p~~~---~l~~iL~~f~~ 326 (445)
T cd00187 257 GISDVRDESDREGIRFVIELKRGAMAEVVLNGLYKV-TKLQTTFGI--NMVAFDPNGRPKKL---NLKEILQEFLD 326 (445)
T ss_pred ccceeeeccCCCceEEEEEECCCccHHHHHHHHHHh-cCCceeeee--eEEEEecCCeeEEe---CHHHHHHHHHH
Confidence 355666666662 3331 222 245533 233333333 67788888988777 88999999875
No 13
>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=66.91 E-value=4.4 Score=22.92 Aligned_cols=28 Identities=25% Similarity=0.665 Sum_probs=18.3
Q ss_pred HHhhhccCcEEEEEecCCCcc--cccCCcc
Q 039654 43 ELCTLCGADIAIIVFSPGKKV--FSFGHPC 70 (225)
Q Consensus 43 ELs~LC~aeva~Ivfsp~gk~--~~f~~ps 70 (225)
.||--||+-|-+-||...|.. |-.+.|.
T Consensus 2 hlcpkcgvgvl~pvy~~kgeikvfrcsnpa 31 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQKGEIKVFRCSNPA 31 (36)
T ss_dssp -B-TTTSSSBEEEEE-TTS-EEEEEES-TT
T ss_pred ccCCccCceEEEEeecCCCcEEEEEcCCCc
Confidence 478889999999999999864 4445553
No 14
>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=66.20 E-value=2.3 Score=22.45 Aligned_cols=12 Identities=42% Similarity=0.858 Sum_probs=9.6
Q ss_pred EEEecCCCcccc
Q 039654 54 IIVFSPGKKVFS 65 (225)
Q Consensus 54 ~Ivfsp~gk~~~ 65 (225)
+.+|||+|++|.
T Consensus 5 ~t~FSp~Grl~Q 16 (23)
T PF10584_consen 5 ITTFSPDGRLFQ 16 (23)
T ss_dssp TTSBBTTSSBHH
T ss_pred ceeECCCCeEEe
Confidence 458999999874
No 15
>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=66.08 E-value=86 Score=30.58 Aligned_cols=34 Identities=35% Similarity=0.474 Sum_probs=27.4
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 138 WEAPIEELNLPQLEQLKMSLEELKKNVGKQAEKM 171 (225)
Q Consensus 138 w~~~l~~Ls~eEL~~L~~~Le~l~~~V~~r~~~L 171 (225)
...+..+|+++.|.+|...|..+.+.-..|.+++
T Consensus 150 ~~~D~~dlsl~kLeelr~~L~~L~~ek~~Rlekv 183 (660)
T KOG4302|consen 150 LIADESDLSLEKLEELREHLNELQKEKSDRLEKV 183 (660)
T ss_pred cccCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456789999999999999998887777766655
No 16
>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=64.33 E-value=19 Score=23.63 Aligned_cols=31 Identities=16% Similarity=0.064 Sum_probs=23.7
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 039654 137 WWEAPIEELNLPQLEQLKMSLEELKKNVGKQ 167 (225)
Q Consensus 137 ~w~~~l~~Ls~eEL~~L~~~Le~l~~~V~~r 167 (225)
..+.+|+.||++||..-...|+.=..+++..
T Consensus 13 ~ig~dLs~lSv~EL~~RIa~L~aEI~R~~~~ 43 (59)
T PF06698_consen 13 EIGEDLSLLSVEELEERIALLEAEIARLEAA 43 (59)
T ss_pred ccCCCchhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999888888555555443
No 17
>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=63.83 E-value=20 Score=29.54 Aligned_cols=41 Identities=22% Similarity=0.352 Sum_probs=33.2
Q ss_pred HHHHHhhhccCcEEEEEecCCCc---ccccCCcchhhhhhhhhc
Q 039654 40 KASELCTLCGADIAIIVFSPGKK---VFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 40 KA~ELs~LC~aeva~Ivfsp~gk---~~~f~~psv~~Vi~Ry~~ 80 (225)
=..|++|-+|-+++|++.+|+.. .-.||.-..+.||..|+.
T Consensus 44 ~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~ 87 (214)
T PF10491_consen 44 TIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKP 87 (214)
T ss_pred HHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHH
Confidence 34899999999999999999742 235788888888888874
No 18
>PHA02592 52 DNA topisomerase II medium subunit; Provisional
Probab=58.15 E-value=58 Score=30.16 Aligned_cols=41 Identities=15% Similarity=0.242 Sum_probs=27.4
Q ss_pred chHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhhhhhhc
Q 039654 35 TGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 35 ~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~~ 80 (225)
.+|+|+- .|.+- .-+-+++|+++|++..| .++.+||+.|..
T Consensus 285 ~~L~k~~-~L~~~--~~~Nm~~~d~~g~~~~~--~~~~~Il~~f~~ 325 (439)
T PHA02592 285 EKIMKDF-GLIER--VSQNITVINENGKLKVY--ENAEDLIRDFVE 325 (439)
T ss_pred HHHHHhc-Cchhe--eeeeEEEEecCCeeeec--CCHHHHHHHHHH
Confidence 4666543 33332 24678889899987655 568899998864
No 19
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=50.87 E-value=1.1e+02 Score=23.42 Aligned_cols=28 Identities=25% Similarity=0.432 Sum_probs=23.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 039654 140 APIEELNLPQLEQLKMSLEELKKNVGKQ 167 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~~~Le~l~~~V~~r 167 (225)
-++++|+.+||..+...++..-+.-+.+
T Consensus 90 i~iE~l~~~el~~~~~~~~~~~~~~~~~ 117 (132)
T PF04120_consen 90 IDIEDLTEEELEEIRKRYERLAEQARER 117 (132)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHHhhhh
Confidence 5899999999999999999776666554
No 20
>KOG3366 consensus Mitochondrial F1F0-ATP synthase, subunit d/ATP7 [Energy production and conversion]
Probab=49.77 E-value=61 Score=25.94 Aligned_cols=15 Identities=20% Similarity=0.510 Sum_probs=10.2
Q ss_pred CCCCCCCHHHHHHHH
Q 039654 140 APIEELNLPQLEQLK 154 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~ 154 (225)
.|++.|+.+++.+-.
T Consensus 128 ~P~demT~ed~~ea~ 142 (172)
T KOG3366|consen 128 RPFDEMTMEDLNEAF 142 (172)
T ss_pred CCcccccHHHHHHhC
Confidence 467788877776543
No 21
>PF04521 Viral_P18: ssRNA positive strand viral 18kD cysteine rich protein; InterPro: IPR007609 This family represents the 18kDa cysteine-rich protein from ssRNA positive strand viruses.
Probab=49.04 E-value=58 Score=24.47 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=18.4
Q ss_pred chhhhcccchHHHHHHHHhhhcc
Q 039654 27 QVTFSKRRTGLFKKASELCTLCG 49 (225)
Q Consensus 27 ~vTFsKRr~GL~KKA~ELs~LC~ 49 (225)
-++|+|+|..++||-.+-.+-|.
T Consensus 4 ~~~~rk~R~~~y~~lgl~~vkC~ 26 (120)
T PF04521_consen 4 FRCVRKYRASVYKKLGLSAVKCR 26 (120)
T ss_pred hHHHHHHHHHHHHHcCCeeeeec
Confidence 46899999999999888666453
No 22
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=47.04 E-value=1.7e+02 Score=25.71 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=21.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 039654 140 APIEELNLPQLEQLKMSLEELKKNVGKQA 168 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~~~Le~l~~~V~~r~ 168 (225)
+++++++.++|..+...|......+....
T Consensus 196 ~e~~~~d~~eL~~lk~~l~~~~~ei~~~~ 224 (312)
T smart00787 196 DELEDCDPTELDRAKEKLKKLLQEIMIKV 224 (312)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 57888899999999888876655554433
No 23
>PF08181 DegQ: DegQ (SacQ) family; InterPro: IPR012554 This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [].
Probab=46.71 E-value=53 Score=19.76 Aligned_cols=12 Identities=42% Similarity=0.562 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHH
Q 039654 147 LPQLEQLKMSLE 158 (225)
Q Consensus 147 ~eEL~~L~~~Le 158 (225)
++||.+|...||
T Consensus 6 ieelkqll~rle 17 (46)
T PF08181_consen 6 IEELKQLLWRLE 17 (46)
T ss_pred HHHHHHHHHHHH
Confidence 455555555555
No 24
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=44.69 E-value=1.4e+02 Score=22.71 Aligned_cols=22 Identities=14% Similarity=0.273 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 039654 148 PQLEQLKMSLEELKKNVGKQAE 169 (225)
Q Consensus 148 eEL~~L~~~Le~l~~~V~~r~~ 169 (225)
++-.+|....++.++.+...+.
T Consensus 89 ~eYk~llk~y~~~~~~L~k~I~ 110 (126)
T PF09403_consen 89 DEYKELLKKYKDLLNKLDKEIA 110 (126)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666666666666655443
No 25
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=43.59 E-value=1.4e+02 Score=22.44 Aligned_cols=26 Identities=19% Similarity=0.436 Sum_probs=20.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 146 NLPQLEQLKMSLEELKKNVGKQAEKM 171 (225)
Q Consensus 146 s~eEL~~L~~~Le~l~~~V~~r~~~L 171 (225)
-.++..+|..-+.+++.-.+.+++++
T Consensus 94 K~E~veEL~~Dv~DlK~myr~Qi~~l 119 (120)
T PF12325_consen 94 KSEEVEELRADVQDLKEMYREQIDQL 119 (120)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45777788888888888888888776
No 26
>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=42.76 E-value=26 Score=29.71 Aligned_cols=29 Identities=24% Similarity=0.402 Sum_probs=24.4
Q ss_pred HHHhhhccCcEEEEEecCCCcccccCCcc
Q 039654 42 SELCTLCGADIAIIVFSPGKKVFSFGHPC 70 (225)
Q Consensus 42 ~ELs~LC~aeva~Ivfsp~gk~~~f~~ps 70 (225)
.+|.-.+|++|+|||..+.|.+|--|.+.
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~~g 161 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQVG 161 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCCCC
Confidence 45667899999999999999988877664
No 27
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=41.53 E-value=1.5e+02 Score=24.54 Aligned_cols=65 Identities=26% Similarity=0.354 Sum_probs=36.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 100 SVRELNMQLTQVLNQLEIEKKRGEELNQMRKASQAQCWWEAPIEELNLPQLEQLKMSLEELKKNVGKQAEKM 171 (225)
Q Consensus 100 ~i~~l~~ql~~l~~~le~ekk~~e~L~~l~k~~~~~~~w~~~l~~Ls~eEL~~L~~~Le~l~~~V~~r~~~L 171 (225)
.+..|..-+......++-..-+...|..|.+... ..| - ...++|..+...|+..+..++..++.+
T Consensus 98 d~~~w~~al~na~a~lehq~~R~~NLeLl~~~g~-naW-~-----~~n~~Le~~~~~le~~l~~~k~~ie~v 162 (221)
T PF05700_consen 98 DVEAWKEALDNAYAQLEHQRLRLENLELLSKYGE-NAW-L-----IHNEQLEAMLKRLEKELAKLKKEIEEV 162 (221)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-HHH-H-----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555555555555555555554322 224 2 345777777777777777766666665
No 28
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=41.49 E-value=23 Score=27.57 Aligned_cols=33 Identities=18% Similarity=0.252 Sum_probs=22.9
Q ss_pred ccCcEEEEEecCCCcccccCCc-chhhhhhhhhc
Q 039654 48 CGADIAIIVFSPGKKVFSFGHP-CVETIVDRYLT 80 (225)
Q Consensus 48 C~aeva~Ivfsp~gk~~~f~~p-sv~~Vi~Ry~~ 80 (225)
|+...++-|..++|++..|..| .+.+|+..|=.
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~ 45 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPG 45 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCC
Confidence 3444455444489999999877 57888877744
No 29
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=40.32 E-value=22 Score=26.25 Aligned_cols=26 Identities=31% Similarity=0.395 Sum_probs=20.4
Q ss_pred HHHHHhhhccCcEEEEEecCCCccccc
Q 039654 40 KASELCTLCGADIAIIVFSPGKKVFSF 66 (225)
Q Consensus 40 KA~ELs~LC~aeva~Ivfsp~gk~~~f 66 (225)
|-.+|-.|-|| +|+..||++|++.+|
T Consensus 2 ~l~~Lm~lpGv-~AAg~Fs~~G~l~e~ 27 (108)
T PF09941_consen 2 KLDKLMKLPGV-VAAGEFSDDGKLVEY 27 (108)
T ss_pred cHHHhhcCCCe-EEEEEECCCCeEEee
Confidence 34678888888 456889999998876
No 30
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=40.00 E-value=2.6e+02 Score=24.54 Aligned_cols=29 Identities=28% Similarity=0.406 Sum_probs=21.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 039654 140 APIEELNLPQLEQLKMSLEELKKNVGKQA 168 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~~~Le~l~~~V~~r~ 168 (225)
..++.++.++|..+...|......|..+.
T Consensus 201 ~e~~~~D~~eL~~lr~eL~~~~~~i~~~k 229 (325)
T PF08317_consen 201 EEIESCDQEELEALRQELAEQKEEIEAKK 229 (325)
T ss_pred hhhhhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45888999999999998886666665433
No 31
>PRK04098 sec-independent translocase; Provisional
Probab=39.95 E-value=50 Score=26.13 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=19.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 145 LNLPQLEQLKMSLEELKKNVGKQAEKM 171 (225)
Q Consensus 145 Ls~eEL~~L~~~Le~l~~~V~~r~~~L 171 (225)
+++++|.++...++...+.+..-...+
T Consensus 81 ~~~eel~~~~~~~~~~~~~~~~~~~~~ 107 (158)
T PRK04098 81 LKFEELDDLKITAENEIKSIQDLLQDY 107 (158)
T ss_pred cChHHHHHHhhhhhhcchhHHHHHhhh
Confidence 788899888877777666666555544
No 32
>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=39.76 E-value=1.7e+02 Score=22.33 Aligned_cols=12 Identities=25% Similarity=0.553 Sum_probs=9.9
Q ss_pred cchhhhhhhhhc
Q 039654 69 PCVETIVDRYLT 80 (225)
Q Consensus 69 psv~~Vi~Ry~~ 80 (225)
+.+.+|++.|..
T Consensus 38 ~el~~iLe~y~~ 49 (132)
T PF09432_consen 38 KELQSILEKYNT 49 (132)
T ss_pred HHHHHHHHHHcC
Confidence 358899999985
No 33
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.31 E-value=1.2e+02 Score=22.75 Aligned_cols=53 Identities=19% Similarity=0.259 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCHHHHHHHHHH
Q 039654 99 ASVRELNMQLTQVLNQLEIEKKRGEELNQMRKASQAQCWWEAPIEELNLPQLEQLKMS 156 (225)
Q Consensus 99 ~~i~~l~~ql~~l~~~le~ekk~~e~L~~l~k~~~~~~~w~~~l~~Ls~eEL~~L~~~ 156 (225)
+...+|+.+|.+|+++--.||.+.-.-...++.... ...+++++.|+-.|..+
T Consensus 27 ~~~k~LqkeLn~Lm~~nTEeK~kt~~~kt~~r~v~~-----K~we~iti~Efi~LR~A 79 (126)
T PF10654_consen 27 SKRKELQKELNQLMNENTEEKMKTYWTKTFDRIVGN-----KNWEEITIREFIELRHA 79 (126)
T ss_pred HHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhc-----ccHhHhhHHHHHHHHhc
Confidence 345677888888877665555544333333332222 33467888888777653
No 34
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.93 E-value=2.8e+02 Score=23.95 Aligned_cols=28 Identities=21% Similarity=0.385 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 039654 147 LPQLEQLKMSLEELKKNVGKQAEKMLIQ 174 (225)
Q Consensus 147 ~eEL~~L~~~Le~l~~~V~~r~~~L~~q 174 (225)
-.++..|+..|+.+...|+.|.+-|-.+
T Consensus 79 ~~eik~l~~eI~~~~~~I~~r~~~l~~r 106 (265)
T COG3883 79 KAEIKKLQKEIAELKENIVERQELLKKR 106 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777777777777766655433
No 35
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=35.42 E-value=30 Score=29.48 Aligned_cols=24 Identities=21% Similarity=0.362 Sum_probs=19.3
Q ss_pred hhHHhhhhhhHHHHHHHHHHHHHH
Q 039654 91 QLIEAHRNASVRELNMQLTQVLNQ 114 (225)
Q Consensus 91 ~~~E~~~~~~i~~l~~ql~~l~~~ 114 (225)
.++|..|+++|.+.-.+|..|+-+
T Consensus 37 pl~EKkRRaRIN~~L~eLK~Li~e 60 (250)
T KOG4304|consen 37 PLLEKKRRARINRCLDELKDLIPE 60 (250)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999888888777653
No 36
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.57 E-value=4.3e+02 Score=26.63 Aligned_cols=32 Identities=16% Similarity=0.108 Sum_probs=23.9
Q ss_pred CCccchhhhcccchHHHHHHHHh-hhccCcEEE
Q 039654 23 ESNLQVTFSKRRTGLFKKASELC-TLCGADIAI 54 (225)
Q Consensus 23 ~~~R~vTFsKRr~GL~KKA~ELs-~LC~aeva~ 54 (225)
..++..+..-+-..|=-|-.+|+ -|||+.+.+
T Consensus 435 ~nak~~ql~~eletLn~k~qqls~kl~Dvr~~~ 467 (1118)
T KOG1029|consen 435 LNAKKKQLQQELETLNFKLQQLSGKLQDVRVDI 467 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhheecc
Confidence 45666677777788888888887 588888764
No 37
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=34.41 E-value=30 Score=33.38 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=22.6
Q ss_pred hhhccCcEEEEEecCCCcccccCCcchhh
Q 039654 45 CTLCGADIAIIVFSPGKKVFSFGHPCVET 73 (225)
Q Consensus 45 s~LC~aeva~Ivfsp~gk~~~f~~psv~~ 73 (225)
|+|.|+-++||+|.++|.++.+ +|+.+.
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~-N~~ae~ 401 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTV-NPSAEQ 401 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEee-cchHHH
Confidence 6999999999999999998875 344333
No 38
>PF11944 DUF3461: Protein of unknown function (DUF3461); InterPro: IPR020911 This entry describes proteins of unknown function.
Probab=34.29 E-value=2.1e+02 Score=21.70 Aligned_cols=24 Identities=21% Similarity=0.325 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 147 LPQLEQLKMSLEELKKNVGKQAEK 170 (225)
Q Consensus 147 ~eEL~~L~~~Le~l~~~V~~r~~~ 170 (225)
++||.-|+..+......|++.+++
T Consensus 101 L~dL~HLE~Vv~~KIaEIe~dlek 124 (125)
T PF11944_consen 101 LDDLRHLEKVVNSKIAEIERDLEK 124 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 567777887777777777776654
No 39
>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=34.18 E-value=15 Score=22.94 Aligned_cols=22 Identities=32% Similarity=0.915 Sum_probs=17.4
Q ss_pred HHHHHHHHhhhccCcEEEEEec
Q 039654 37 LFKKASELCTLCGADIAIIVFS 58 (225)
Q Consensus 37 L~KKA~ELs~LC~aeva~Ivfs 58 (225)
|.+.+..-|-|||++..+.||-
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~ 23 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYA 23 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEe
Confidence 4555666799999999998885
No 40
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=33.99 E-value=3.1e+02 Score=27.25 Aligned_cols=25 Identities=8% Similarity=0.127 Sum_probs=17.3
Q ss_pred EEEEecCCCcccccCCcchhhhhhhhhc
Q 039654 53 AIIVFSPGKKVFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 53 a~Ivfsp~gk~~~f~~psv~~Vi~Ry~~ 80 (225)
-+++|+++|++.. -++.+||+.|..
T Consensus 337 n~~~~d~~~~p~~---~~l~~il~~f~~ 361 (742)
T PRK05561 337 NMNAIGLDGRPRV---KGLKEILSEWLD 361 (742)
T ss_pred eEEEEccCCEEEE---CCHHHHHHHHHH
Confidence 5677777776532 477888888864
No 41
>PRK01919 tatB sec-independent translocase; Provisional
Probab=33.66 E-value=2.2e+02 Score=22.77 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=8.3
Q ss_pred EEEEEecCCC
Q 039654 52 IAIIVFSPGK 61 (225)
Q Consensus 52 va~Ivfsp~g 61 (225)
||||||+|..
T Consensus 15 VALiV~GPek 24 (169)
T PRK01919 15 VALVVIGPER 24 (169)
T ss_pred HHHheeCchH
Confidence 7899999953
No 42
>KOG4673 consensus Transcription factor TMF, TATA element modulatory factor [Transcription]
Probab=33.64 E-value=4e+02 Score=26.42 Aligned_cols=30 Identities=27% Similarity=0.410 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 039654 146 NLPQLEQLKMSLEELKKNVGKQAEKMLIQS 175 (225)
Q Consensus 146 s~eEL~~L~~~Le~l~~~V~~r~~~L~~q~ 175 (225)
-.+++++|.--|++++..-+.++++|+.+-
T Consensus 930 k~Ee~EELrlDl~dlK~mYk~QIdeLl~~~ 959 (961)
T KOG4673|consen 930 KDEELEELRLDLVDLKEMYKEQIDELLNKI 959 (961)
T ss_pred hHHHHHHHHhhHHHHHHHHHHHHHHHHhcc
Confidence 568899999999999999999999998653
No 43
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=32.99 E-value=96 Score=24.18 Aligned_cols=26 Identities=23% Similarity=0.290 Sum_probs=19.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHH
Q 039654 140 APIEELNLPQLEQLKMSLEELKKNVG 165 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~~~Le~l~~~V~ 165 (225)
-++..||++||.+|++.+|.=+.-+.
T Consensus 8 idltkLsleQL~~lk~q~dqEl~~lq 33 (153)
T KOG3048|consen 8 IDLTKLSLEQLGALKKQFDQELNFLQ 33 (153)
T ss_pred CChhhCCHHHHHHHHHHHHHHHHHHH
Confidence 57889999999999988874444433
No 44
>KOG0432 consensus Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=31.94 E-value=1e+02 Score=31.11 Aligned_cols=18 Identities=22% Similarity=0.292 Sum_probs=12.4
Q ss_pred HHHHHHhhhccCcEEEEE
Q 039654 39 KKASELCTLCGADIAIIV 56 (225)
Q Consensus 39 KKA~ELs~LC~aeva~Iv 56 (225)
-.+.++++||.++.--|+
T Consensus 880 ~~~~~i~~l~~~~~v~i~ 897 (995)
T KOG0432|consen 880 EFLDEISTLTNLELVSIS 897 (995)
T ss_pred HHHHHHHHhhccceeEec
Confidence 457889999977654433
No 45
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=31.24 E-value=2.8e+02 Score=22.86 Aligned_cols=25 Identities=36% Similarity=0.355 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 039654 110 QVLNQLEIEKKRGEELNQMRKASQA 134 (225)
Q Consensus 110 ~l~~~le~ekk~~e~L~~l~k~~~~ 134 (225)
.+.++|...++..+.+...|+..|.
T Consensus 147 ~le~~l~~~k~~ie~vN~~RK~~Q~ 171 (221)
T PF05700_consen 147 RLEKELAKLKKEIEEVNRERKRRQE 171 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555555566666665543
No 46
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=31.06 E-value=93 Score=28.83 Aligned_cols=26 Identities=35% Similarity=0.510 Sum_probs=22.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHH
Q 039654 141 PIEELNLPQLEQLKMSLEELKKNVGK 166 (225)
Q Consensus 141 ~l~~Ls~eEL~~L~~~Le~l~~~V~~ 166 (225)
.+.+|+-+||..|..-||.++++|.+
T Consensus 87 kvG~LskdeLm~LasDLeKLk~Kv~r 112 (533)
T PF00843_consen 87 KVGDLSKDELMELASDLEKLKKKVQR 112 (533)
T ss_dssp EBTTB-HHHHHHHHHHHHHHHHHHHH
T ss_pred EecCcCHHHHHHHHHHHHHHHHHHhc
Confidence 47899999999999999999999864
No 47
>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=30.85 E-value=2.6e+02 Score=21.83 Aligned_cols=30 Identities=23% Similarity=0.179 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039654 144 ELNLPQLEQLKMSLEELKKNVGKQAEKMLI 173 (225)
Q Consensus 144 ~Ls~eEL~~L~~~Le~l~~~V~~r~~~L~~ 173 (225)
.++.+||..-...|+.-...+..|...|..
T Consensus 108 ~~t~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 108 EPTNEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456777777777777666666666666644
No 48
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=30.63 E-value=3.7e+02 Score=24.77 Aligned_cols=35 Identities=17% Similarity=0.287 Sum_probs=22.3
Q ss_pred ceeeEeeCCCCccchhh----hcccchHHHHHHHHhhhc
Q 039654 14 KVEMVKMPNESNLQVTF----SKRRTGLFKKASELCTLC 48 (225)
Q Consensus 14 Ki~i~~I~n~~~R~vTF----sKRr~GL~KKA~ELs~LC 48 (225)
+..-..-+.++.|+.+- ++||.-|=-+..||+.|-
T Consensus 221 ~~~~~~~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~li 259 (411)
T KOG1318|consen 221 KTDATALERDRRKRDNHNEVERRRRENINDRIKELGQLI 259 (411)
T ss_pred CcccchhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhC
Confidence 33444444444444443 578888888899998875
No 49
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=30.63 E-value=52 Score=24.15 Aligned_cols=18 Identities=39% Similarity=0.588 Sum_probs=15.6
Q ss_pred CCCCCCHHHHHHHHHHHH
Q 039654 141 PIEELNLPQLEQLKMSLE 158 (225)
Q Consensus 141 ~l~~Ls~eEL~~L~~~Le 158 (225)
.++.|+++|++.|...+|
T Consensus 86 Rle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 86 RLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHhCCHHHHHHHHHHhc
Confidence 567899999999998876
No 50
>PRK02224 chromosome segregation protein; Provisional
Probab=30.20 E-value=3.9e+02 Score=26.70 Aligned_cols=12 Identities=0% Similarity=-0.205 Sum_probs=6.5
Q ss_pred Ccchhhhhhhhh
Q 039654 68 HPCVETIVDRYL 79 (225)
Q Consensus 68 ~psv~~Vi~Ry~ 79 (225)
...+..+++.|.
T Consensus 463 ~~~~~~~~~~~~ 474 (880)
T PRK02224 463 GSPHVETIEEDR 474 (880)
T ss_pred CcchhhhHHHHH
Confidence 334456666665
No 51
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=30.18 E-value=3.3e+02 Score=22.85 Aligned_cols=110 Identities=15% Similarity=0.170 Sum_probs=58.2
Q ss_pred chHHHHHHHHhhhccCcEEEEEecC----CCccc---cc--CCcchhhhhhhhhcCCCCCCCcchhhHHhhhhhhHHHHH
Q 039654 35 TGLFKKASELCTLCGADIAIIVFSP----GKKVF---SF--GHPCVETIVDRYLTRNPPQISGTMQLIEAHRNASVRELN 105 (225)
Q Consensus 35 ~GL~KKA~ELs~LC~aeva~Ivfsp----~gk~~---~f--~~psv~~Vi~Ry~~~~~~~~~~~~~~~E~~~~~~i~~l~ 105 (225)
..-.+++.+++.-.|..|+-.-.+- ++... +. +.-.++..++.......- .+++-..++.-
T Consensus 62 ~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g~v----------~~~~~~~~DvT 131 (262)
T PF14257_consen 62 EKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELGKV----------TSRNISSEDVT 131 (262)
T ss_pred HHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccCce----------eeeeccccchH
Confidence 4455667777777777766655541 11111 11 122355666665532210 12233445566
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 039654 106 MQLTQVLNQLEIEKKRGEELNQMRKASQAQCWWEAPIEELNLPQLEQLKMSLEELKKNVGK 166 (225)
Q Consensus 106 ~ql~~l~~~le~ekk~~e~L~~l~k~~~~~~~w~~~l~~Ls~eEL~~L~~~Le~l~~~V~~ 166 (225)
.++..+..+++..++..+.|..+.+. . =+++|+-.++..|......|..
T Consensus 132 ~~y~D~~arl~~l~~~~~rl~~ll~k--------a----~~~~d~l~ie~~L~~v~~eIe~ 180 (262)
T PF14257_consen 132 EQYVDLEARLKNLEAEEERLLELLEK--------A----KTVEDLLEIERELSRVRSEIEQ 180 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh--------c----CCHHHHHHHHHHHHHHHHHHHH
Confidence 67777766666555555544444321 1 1788888888877766555554
No 52
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=29.83 E-value=14 Score=27.05 Aligned_cols=53 Identities=23% Similarity=0.414 Sum_probs=34.6
Q ss_pred ceeeEee-CCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhhhhhhcC
Q 039654 14 KVEMVKM-PNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIVDRYLTR 81 (225)
Q Consensus 14 Ki~i~~I-~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~~~ 81 (225)
+|++|.+ ++.++-.++|.||-.|+-+ +=...+|..--||.--.+.++..|.+.
T Consensus 19 ~ie~K~~~~~RSN~~i~f~KRt~Girq---------------fEi~n~G~~RI~gYk~se~~~~~f~sl 72 (103)
T PF09158_consen 19 KIEVKEIVIDRSNYEIRFKKRTKGIRQ---------------FEIRNKGEFRIFGYKMSEEIIKKFTSL 72 (103)
T ss_dssp T--EEEEEEETTEEEEEEEEEETTEEE---------------EEEETTSEEEEEEES--HHHHHHHHHT
T ss_pred ceeeeeeEeeccceEEeeecccCceeE---------------EEEecCCcEEEEEEcCCHHHHHHHHhc
Confidence 4777766 7889999999999999732 222345666666666667777777653
No 53
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=28.89 E-value=4e+02 Score=25.01 Aligned_cols=29 Identities=31% Similarity=0.428 Sum_probs=17.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 98 NASVRELNMQLTQVLNQLEIEKKRGEELN 126 (225)
Q Consensus 98 ~~~i~~l~~ql~~l~~~le~ekk~~e~L~ 126 (225)
.+.++++..++..+..+.+..+++.+.|.
T Consensus 65 va~~k~~r~~~~~l~~~N~~l~~eN~~L~ 93 (472)
T TIGR03752 65 VAEVKELRKRLAKLISENEALKAENERLQ 93 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666667777777666655555555543
No 54
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=28.66 E-value=11 Score=28.56 Aligned_cols=41 Identities=27% Similarity=0.419 Sum_probs=28.5
Q ss_pred eCCCCccchhhhcccchHHHHHHHHhhhccCcEEEEEecCCCcccc
Q 039654 20 MPNESNLQVTFSKRRTGLFKKASELCTLCGADIAIIVFSPGKKVFS 65 (225)
Q Consensus 20 I~n~~~R~vTFsKRr~GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~ 65 (225)
|.++.....||.=.-..|-++.=+|+.+| ++.|+|.|+-|-
T Consensus 41 v~~k~~ytktF~V~vaN~s~~~idLsk~C-----f~a~~~~gk~f~ 81 (124)
T PF14263_consen 41 VGGKSFYTKTFDVTVANLSDKDIDLSKMC-----FKAYSPDGKEFK 81 (124)
T ss_dssp ETTEEEEEEEEEEEEEE-SSS-EE-TT-E-----EEEEETTS-EEE
T ss_pred ecCccceEEEEEEEEecCCCCccccccch-----hhhccccCCEEE
Confidence 45566667778888888888888999986 999999998653
No 55
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=28.48 E-value=2.4e+02 Score=20.69 Aligned_cols=28 Identities=18% Similarity=0.150 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 144 ELNLPQLEQLKMSLEELKKNVGKQAEKM 171 (225)
Q Consensus 144 ~Ls~eEL~~L~~~Le~l~~~V~~r~~~L 171 (225)
+..-+|+..|...++.+++.++.|+...
T Consensus 33 ~~a~~e~~~lR~r~~~~Lk~~r~rl~~~ 60 (104)
T COG4575 33 SLAGDEAEELRSKAESALKEARDRLGDT 60 (104)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5677888888888888888888877654
No 56
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=28.27 E-value=4.1e+02 Score=23.30 Aligned_cols=19 Identities=21% Similarity=0.403 Sum_probs=9.6
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q 039654 144 ELNLPQLEQLKMSLEELKK 162 (225)
Q Consensus 144 ~Ls~eEL~~L~~~Le~l~~ 162 (225)
+.+..|+..|...++.+..
T Consensus 272 ~~t~~Ev~~Lk~~~~~Le~ 290 (325)
T PF08317_consen 272 GWTRSEVKRLKAKVDALEK 290 (325)
T ss_pred CCCHHHHHHHHHHHHHHHH
Confidence 3455555555555554443
No 57
>PHA02109 hypothetical protein
Probab=27.96 E-value=1.4e+02 Score=24.09 Aligned_cols=28 Identities=29% Similarity=0.461 Sum_probs=13.5
Q ss_pred cCCCCCCC--HHHHHHHHHHHHHHHHHHHH
Q 039654 139 EAPIEELN--LPQLEQLKMSLEELKKNVGK 166 (225)
Q Consensus 139 ~~~l~~Ls--~eEL~~L~~~Le~l~~~V~~ 166 (225)
++.+++|+ ++|+..|+..||.+-....+
T Consensus 182 ~~~L~~~~~~L~~I~~L~~ki~~LS~E~~Q 211 (233)
T PHA02109 182 GENLEGLTDKLKQISELTIKLEALSDEACQ 211 (233)
T ss_pred hhhhhhhhHHHHhhHHHHHHHHHHHHHHHH
Confidence 34444442 45555555555544444333
No 58
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=27.91 E-value=64 Score=27.45 Aligned_cols=29 Identities=21% Similarity=0.361 Sum_probs=23.7
Q ss_pred HHHhhhccCcEEEEEecCCCcccccCCcc
Q 039654 42 SELCTLCGADIAIIVFSPGKKVFSFGHPC 70 (225)
Q Consensus 42 ~ELs~LC~aeva~Ivfsp~gk~~~f~~ps 70 (225)
.+|.-.||++|+|||....|.+|-.|...
T Consensus 134 ~~l~~~~g~~v~VIItDt~gr~~R~G~t~ 162 (245)
T PRK13293 134 EGLEELTGKKVGVIITDTNGRPFRKGQRG 162 (245)
T ss_pred HHHHHHHCCCEEEEEEcCCCcccccCCcc
Confidence 45667899999999999999988776554
No 59
>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=27.72 E-value=5.1e+02 Score=24.24 Aligned_cols=18 Identities=22% Similarity=0.289 Sum_probs=8.9
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 039654 100 SVRELNMQLTQVLNQLEI 117 (225)
Q Consensus 100 ~i~~l~~ql~~l~~~le~ 117 (225)
.+.+|..++.++..++..
T Consensus 72 ~~~~l~~~l~~l~~~~~~ 89 (525)
T TIGR02231 72 RLAELRKQIRELEAELRD 89 (525)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444555555555544443
No 60
>KOG4171 consensus Adenylate/guanylate kinase [Nucleotide transport and metabolism]
Probab=27.58 E-value=2.1e+02 Score=27.97 Aligned_cols=92 Identities=25% Similarity=0.377 Sum_probs=46.8
Q ss_pred EEecCCCccccc-CCcchh---hhhhh--hhcCCCCCCCcchhh--------HHhhhhhhHHHHHHHHHHHHHHHHHHHH
Q 039654 55 IVFSPGKKVFSF-GHPCVE---TIVDR--YLTRNPPQISGTMQL--------IEAHRNASVRELNMQLTQVLNQLEIEKK 120 (225)
Q Consensus 55 Ivfsp~gk~~~f-~~psv~---~Vi~R--y~~~~~~~~~~~~~~--------~E~~~~~~i~~l~~ql~~l~~~le~ekk 120 (225)
++|=|.+.-.-| |+|.|+ ++..+ |++--|+ ++.+..+ .+-..+...+++.++++++.++|+.||+
T Consensus 333 M~~i~e~~sIlflcSP~V~~LdeL~~~GLyLsDipl-HDatRDlILl~~Q~~aq~el~~~lE~~~~~Le~~~~~Le~EKk 411 (671)
T KOG4171|consen 333 MMYIPESDSILFLCSPVVDNLDELTGRGLYLSDIPL-HDATRDLVLLGQQRRAQLELNLELEKLKEKLEKMTRELEEEKK 411 (671)
T ss_pred EEEecCCCeEEEEcCcccCchHHHHhCCceeccCCc-cccchhheecchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445455554444 888765 55544 4443222 2222211 1222334556667778888888888888
Q ss_pred HHHHH-HHHHHHHHh-hccccCCCCCCCH
Q 039654 121 RGEEL-NQMRKASQA-QCWWEAPIEELNL 147 (225)
Q Consensus 121 ~~e~L-~~l~k~~~~-~~~w~~~l~~Ls~ 147 (225)
+...| -.|-...-+ +-|-++.++-...
T Consensus 412 kTd~LLy~mlP~~VA~qLr~g~~v~a~~f 440 (671)
T KOG4171|consen 412 KTDTLLYSMLPRSVAQQLRQGESVDAKEF 440 (671)
T ss_pred hHHHHHHHhCCHHHHHHHHcCCCcCcccc
Confidence 77754 333222111 1244555555433
No 61
>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=26.82 E-value=30 Score=30.04 Aligned_cols=16 Identities=25% Similarity=0.586 Sum_probs=13.4
Q ss_pred hhhccCcEEEEEecCC
Q 039654 45 CTLCGADIAIIVFSPG 60 (225)
Q Consensus 45 s~LC~aeva~Ivfsp~ 60 (225)
.-+||+||||+||--.
T Consensus 183 ~~~~~~EICLavYek~ 198 (334)
T PF06020_consen 183 GQVSGFEICLAVYEKG 198 (334)
T ss_pred CccccceEEeeehhhh
Confidence 3579999999999765
No 62
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=26.79 E-value=42 Score=30.35 Aligned_cols=40 Identities=15% Similarity=0.295 Sum_probs=26.2
Q ss_pred HHHhhhccCcEEEEEecCCCcccccCCcc-----hhhhhhhhhcC
Q 039654 42 SELCTLCGADIAIIVFSPGKKVFSFGHPC-----VETIVDRYLTR 81 (225)
Q Consensus 42 ~ELs~LC~aeva~Ivfsp~gk~~~f~~ps-----v~~Vi~Ry~~~ 81 (225)
+-|||+||-+|--.+.-.+...|-|.+|. +.+.+..|...
T Consensus 367 yalSV~~~~~V~HClIy~tatG~GFa~pyn~y~tlk~lV~hY~h~ 411 (464)
T KOG4637|consen 367 YALSVVHDGEVKHCLIYQTATGFGFAEPYNLYSTLKELVLHYQHT 411 (464)
T ss_pred eEEEEEECCceeeeEEeeccccccccchhHHHHHHHHHHHHHhhh
Confidence 46899998666443333344557777874 67888888753
No 63
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=26.16 E-value=54 Score=25.27 Aligned_cols=23 Identities=30% Similarity=0.382 Sum_probs=18.8
Q ss_pred HhhhccCcEEEEEecCCCccccc
Q 039654 44 LCTLCGADIAIIVFSPGKKVFSF 66 (225)
Q Consensus 44 Ls~LC~aeva~Ivfsp~gk~~~f 66 (225)
+.++|||+|-++|-+.+.+...|
T Consensus 59 ~tt~~dadvi~~v~~and~~s~f 81 (148)
T COG4917 59 ITTLQDADVIIYVHAANDPESRF 81 (148)
T ss_pred HHHhhccceeeeeecccCccccC
Confidence 67899999999999998774444
No 64
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=26.15 E-value=72 Score=23.08 Aligned_cols=28 Identities=32% Similarity=0.404 Sum_probs=21.2
Q ss_pred HHHHHHhhhccCcEEEEEecCCCcccccC
Q 039654 39 KKASELCTLCGADIAIIVFSPGKKVFSFG 67 (225)
Q Consensus 39 KKA~ELs~LC~aeva~Ivfsp~gk~~~f~ 67 (225)
-|-.||--+-||- |.=.|||+||+..|-
T Consensus 3 ekLdeLlqi~Gv~-AAGefs~DGkLv~Yk 30 (109)
T COG4831 3 EKLDELLQIKGVM-AAGEFSPDGKLVEYK 30 (109)
T ss_pred hhHHHHhCcccee-EeceeCCCCceEEee
Confidence 3567787777774 456799999998874
No 65
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=26.09 E-value=1.9e+02 Score=23.30 Aligned_cols=27 Identities=15% Similarity=0.351 Sum_probs=13.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039654 144 ELNLPQLEQLKMSLEELKKNVGKQAEKM 171 (225)
Q Consensus 144 ~Ls~eEL~~L~~~Le~l~~~V~~r~~~L 171 (225)
+|+.+|-.+-+ .|..|.+.|++...+|
T Consensus 138 hMSeeER~Eae-QLQsLR~avRqElqEL 164 (179)
T PF14723_consen 138 HMSEEEREEAE-QLQSLRSAVRQELQEL 164 (179)
T ss_pred cCCHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 45555544333 2444555555555554
No 66
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=26.02 E-value=3e+02 Score=20.99 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=21.0
Q ss_pred CcEEEEEecCCCcccccCCcchhhhhhhhh
Q 039654 50 ADIAIIVFSPGKKVFSFGHPCVETIVDRYL 79 (225)
Q Consensus 50 aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~ 79 (225)
+-+|||+.+| -++-|..|+-+.++.||.
T Consensus 14 ~G~~ii~~G~--~l~~y~tPTeEeL~~r~s 41 (128)
T PF07960_consen 14 AGAVIIGGGP--ALVKYTTPTEEELFKRYS 41 (128)
T ss_pred hcceeEeech--HHheecCCCHHHHHHhcC
Confidence 3456666666 356788999999999996
No 67
>PRK04863 mukB cell division protein MukB; Provisional
Probab=25.91 E-value=6.8e+02 Score=27.22 Aligned_cols=24 Identities=8% Similarity=0.156 Sum_probs=15.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHH
Q 039654 140 APIEELNLPQLEQLKMSLEELKKN 163 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~~~Le~l~~~ 163 (225)
..+.+|+.++|.......+.....
T Consensus 430 ~~~~~~SdEeLe~~LenF~aklee 453 (1486)
T PRK04863 430 CGLPDLTADNAEDWLEEFQAKEQE 453 (1486)
T ss_pred hCCCCCCHHHHHHHHHHHHHHHHH
Confidence 457789999888666655543333
No 68
>PTZ00108 DNA topoisomerase 2-like protein; Provisional
Probab=25.82 E-value=3.4e+02 Score=29.19 Aligned_cols=26 Identities=12% Similarity=0.342 Sum_probs=19.4
Q ss_pred EEEEecCCCcccccCCcchhhhhhhhhc
Q 039654 53 AIIVFSPGKKVFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 53 a~Ivfsp~gk~~~f~~psv~~Vi~Ry~~ 80 (225)
-+++|.++|+...| .++.+||+.|..
T Consensus 962 Nm~~~d~~g~i~~~--~~~~~Il~~f~~ 987 (1388)
T PTZ00108 962 NMVLFDENGKIKKY--SDALDILKEFYL 987 (1388)
T ss_pred eEEEEeCCCCccee--CCHHHHHHHHHH
Confidence 57888998876655 456788888864
No 69
>PRK06851 hypothetical protein; Provisional
Probab=25.65 E-value=5e+02 Score=23.43 Aligned_cols=28 Identities=25% Similarity=0.293 Sum_probs=22.2
Q ss_pred cchHHHHHHHHhhhccCcEEEEEecCCC
Q 039654 34 RTGLFKKASELCTLCGADIAIIVFSPGK 61 (225)
Q Consensus 34 r~GL~KKA~ELs~LC~aeva~Ivfsp~g 61 (225)
|..|+|++.+-..-+|-+|..++++.+.
T Consensus 43 KStl~~~i~~~~~~~g~~Ve~~~~~~d~ 70 (367)
T PRK06851 43 KSTLMKKIGEEFLEKGYDVEFLHCSSDN 70 (367)
T ss_pred HHHHHHHHHHHHHHcCCeEEEEEcCCCC
Confidence 5678888877777789999998888764
No 70
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=25.61 E-value=1.7e+02 Score=21.31 Aligned_cols=29 Identities=28% Similarity=0.346 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 039654 145 LNLPQLEQLKMSLEELKKNVGKQAEKMLI 173 (225)
Q Consensus 145 Ls~eEL~~L~~~Le~l~~~V~~r~~~L~~ 173 (225)
|+.+++..|+..|+..+..+..++.....
T Consensus 1 M~~~~l~~~k~~L~~~~~~L~~~i~~~~~ 29 (110)
T TIGR02420 1 MSEAQLEHFRKILLRWKQELLEEADKTLE 29 (110)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56678888888888887777776666543
No 71
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=25.55 E-value=3.3e+02 Score=21.27 Aligned_cols=33 Identities=24% Similarity=0.375 Sum_probs=27.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 039654 142 IEELNLPQLEQLKMSLEELKKNVGKQAEKMLIQ 174 (225)
Q Consensus 142 l~~Ls~eEL~~L~~~Le~l~~~V~~r~~~L~~q 174 (225)
++.-.++.++.|...+++++..|....+.+...
T Consensus 83 ~d~~kv~~~E~L~d~v~eLkeel~~el~~l~~~ 115 (146)
T PF05852_consen 83 FDRKKVEDLEKLTDRVEELKEELEFELERLQSA 115 (146)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 566678999999999999999999998888544
No 72
>PRK09631 DNA topoisomerase IV subunit A; Provisional
Probab=25.36 E-value=4.9e+02 Score=25.47 Aligned_cols=62 Identities=11% Similarity=0.153 Sum_probs=34.4
Q ss_pred ccceeeEeeCCCCccchhhh---cccc-------hHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhhhhhhc
Q 039654 12 RQKVEMVKMPNESNLQVTFS---KRRT-------GLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 12 R~Ki~i~~I~n~~~R~vTFs---KRr~-------GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~~ 80 (225)
.+||+|+-|.+++++.+.|- ||-. +|+|+ ..|-+--++-.++| +. +++. .-++.+||+.|..
T Consensus 247 ~~ki~I~~i~D~s~~~v~i~i~l~~~~~~~~~~~~Lyk~-t~lq~s~~~n~~~i-~~--~~p~---~~~l~~il~~~~~ 318 (635)
T PRK09631 247 KGKIKISSINDYTAENVEIEIKLPRGVYASEVIEALYAY-TDCEVSISVNLLVI-KD--RYPV---IYTVTDIIKFHAE 318 (635)
T ss_pred cCCCccceeEeCCCCcEEEEEEECCCCCHHHHHHHHHHh-cCceeEeeeeEEEE-EC--CcCc---CCCHHHHHHHHHH
Confidence 34677888988888876553 2321 45433 23333333333333 32 3322 2578899998874
No 73
>PRK00736 hypothetical protein; Provisional
Probab=25.27 E-value=2.1e+02 Score=19.02 Aligned_cols=12 Identities=17% Similarity=0.462 Sum_probs=4.7
Q ss_pred HHHHHHHHHHHH
Q 039654 153 LKMSLEELKKNV 164 (225)
Q Consensus 153 L~~~Le~l~~~V 164 (225)
|...|..+..++
T Consensus 38 L~~ql~~L~~rl 49 (68)
T PRK00736 38 MRKKLDALTERF 49 (68)
T ss_pred HHHHHHHHHHHH
Confidence 333444444433
No 74
>PF04678 DUF607: Protein of unknown function, DUF607; InterPro: IPR006769 This entry represents the C-terminal domain of coiled-coil domain containing protein 109.
Probab=25.17 E-value=3.5e+02 Score=21.52 Aligned_cols=43 Identities=26% Similarity=0.312 Sum_probs=20.9
Q ss_pred cCCcc-hhhhhhhhhcCCCCCCCcchhhHHhhhhhhHHHHHHHHHHHHHHHHH
Q 039654 66 FGHPC-VETIVDRYLTRNPPQISGTMQLIEAHRNASVRELNMQLTQVLNQLEI 117 (225)
Q Consensus 66 f~~ps-v~~Vi~Ry~~~~~~~~~~~~~~~E~~~~~~i~~l~~ql~~l~~~le~ 117 (225)
+-+|+ |...+.+-...... +.+...+.+.+..++..+.++|+.
T Consensus 32 ~L~P~~v~~~v~~~~~~~~~---------~~~~~~~~~~l~~~l~~~~~el~~ 75 (180)
T PF04678_consen 32 YLRPKQVKEAVHRLLPLLNV---------EEYQNSRERQLRKRLEELRQELAP 75 (180)
T ss_pred eECHHHHHHHHHHHhccccc---------hhhhHHHHHHHHHHHHHHHHHHHH
Confidence 44574 66666665543211 222334444555555555555444
No 75
>PF15233 SYCE1: Synaptonemal complex central element protein 1
Probab=24.76 E-value=2.6e+02 Score=21.42 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=7.8
Q ss_pred cchhhhhhhhhc
Q 039654 69 PCVETIVDRYLT 80 (225)
Q Consensus 69 psv~~Vi~Ry~~ 80 (225)
|-++.+|.|...
T Consensus 6 P~iE~LInrIne 17 (134)
T PF15233_consen 6 PQIEDLINRINE 17 (134)
T ss_pred chHHHHHHHHHH
Confidence 666777777653
No 76
>COG0212 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]
Probab=24.74 E-value=33 Score=27.78 Aligned_cols=15 Identities=40% Similarity=1.112 Sum_probs=11.6
Q ss_pred CCCCCCCCCCCCCCC
Q 039654 211 MPHPGYNPGFGHGFY 225 (225)
Q Consensus 211 ~~~~~~~~~~~~~~~ 225 (225)
+..+.|=+|||+|||
T Consensus 128 fd~~G~RLG~GgGyY 142 (191)
T COG0212 128 FDKQGYRLGYGGGYY 142 (191)
T ss_pred ECCCCccccCCCchH
Confidence 345666799999997
No 77
>PRK00295 hypothetical protein; Provisional
Probab=24.11 E-value=2.3e+02 Score=18.90 Aligned_cols=7 Identities=29% Similarity=0.387 Sum_probs=2.5
Q ss_pred HHHHHHH
Q 039654 156 SLEELKK 162 (225)
Q Consensus 156 ~Le~l~~ 162 (225)
.|..+..
T Consensus 41 ql~~L~~ 47 (68)
T PRK00295 41 QMAALIK 47 (68)
T ss_pred HHHHHHH
Confidence 3333333
No 78
>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=23.97 E-value=74 Score=22.27 Aligned_cols=32 Identities=19% Similarity=0.381 Sum_probs=24.0
Q ss_pred hHHHHHHHHhhhc----cCcEEEEEecCCCcccccC
Q 039654 36 GLFKKASELCTLC----GADIAIIVFSPGKKVFSFG 67 (225)
Q Consensus 36 GL~KKA~ELs~LC----~aeva~Ivfsp~gk~~~f~ 67 (225)
-+++.|.+++... ...|+.||++++|+....|
T Consensus 6 ~~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~g 41 (102)
T PF00383_consen 6 EFMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIATG 41 (102)
T ss_dssp HHHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEEE
T ss_pred HHHHHHHHHHHhccccCCCCEEEEEEeccCccEEEE
Confidence 3677777777766 8899999999877655444
No 79
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=23.86 E-value=39 Score=28.29 Aligned_cols=21 Identities=33% Similarity=0.542 Sum_probs=17.5
Q ss_pred hhhccCcEEEEEecCCCcccc
Q 039654 45 CTLCGADIAIIVFSPGKKVFS 65 (225)
Q Consensus 45 s~LC~aeva~Ivfsp~gk~~~ 65 (225)
||=+|-+.|.-+|||+|++|.
T Consensus 3 sIGtGyDls~s~fSpdGrvfQ 23 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQ 23 (254)
T ss_pred cccccccccceeeCCCCceeh
Confidence 455678899999999999875
No 80
>PLN03128 DNA topoisomerase 2; Provisional
Probab=23.77 E-value=4.7e+02 Score=27.48 Aligned_cols=26 Identities=15% Similarity=0.422 Sum_probs=18.4
Q ss_pred EEEEecCCCcccccCCcchhhhhhhhhc
Q 039654 53 AIIVFSPGKKVFSFGHPCVETIVDRYLT 80 (225)
Q Consensus 53 a~Ivfsp~gk~~~f~~psv~~Vi~Ry~~ 80 (225)
-+++|.+.|++..| .++++||+.|..
T Consensus 961 nm~l~d~~~~i~ky--~~~~~il~~f~~ 986 (1135)
T PLN03128 961 NMHLFDKDGKIKKY--DSPEDILEEFFH 986 (1135)
T ss_pred EEEEECCCCcccCC--CCHHHHHHHHHH
Confidence 46778887776554 467888888864
No 81
>PF05873 Mt_ATP-synt_D: ATP synthase D chain, mitochondrial (ATP5H); InterPro: IPR008689 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit D from the F0 complex in F-ATPases found in mitochondria. The D subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit D in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2CLY_E 2WSS_U.
Probab=23.60 E-value=1.8e+02 Score=22.97 Aligned_cols=14 Identities=14% Similarity=0.411 Sum_probs=0.0
Q ss_pred CCCCCCCHHHHHHH
Q 039654 140 APIEELNLPQLEQL 153 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L 153 (225)
.|+++|+++|+..-
T Consensus 126 ~P~e~mT~dd~~~a 139 (161)
T PF05873_consen 126 RPFEQMTVDDYAAA 139 (161)
T ss_dssp --------------
T ss_pred CChHhCCHHHHHHh
Confidence 58889998887543
No 82
>PRK01770 sec-independent translocase; Provisional
Probab=23.05 E-value=1.3e+02 Score=24.21 Aligned_cols=16 Identities=31% Similarity=0.536 Sum_probs=11.2
Q ss_pred HHhhhccCcEEEEEecCC
Q 039654 43 ELCTLCGADIAIIVFSPG 60 (225)
Q Consensus 43 ELs~LC~aeva~Ivfsp~ 60 (225)
||-+++ =||||||+|.
T Consensus 8 ELllI~--vVaLlV~GPe 23 (171)
T PRK01770 8 ELLLVF--VIGLVVLGPQ 23 (171)
T ss_pred HHHHHH--HHHHHhcCch
Confidence 555554 4688999995
No 83
>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=22.89 E-value=75 Score=28.22 Aligned_cols=36 Identities=17% Similarity=0.409 Sum_probs=24.1
Q ss_pred chHHHHHH-HH--hhhccCcEEEEEecCC--Ccccc-cCCcc
Q 039654 35 TGLFKKAS-EL--CTLCGADIAIIVFSPG--KKVFS-FGHPC 70 (225)
Q Consensus 35 ~GL~KKA~-EL--s~LC~aeva~Ivfsp~--gk~~~-f~~ps 70 (225)
.-+|+.+. ++ +++-|..+||++|+++ ||-|+ ||.+.
T Consensus 70 ~~vf~~~~~p~v~~~l~G~n~~i~ayGqtGSGKT~Tm~G~~~ 111 (356)
T cd01365 70 EDVFEDLGRELLDHAFEGYNVCLFAYGQTGSGKSYTMMGYKE 111 (356)
T ss_pred HHHHHHHHHHHHHHHhCCCceEEEEecCCCCCCeEEecCCCC
Confidence 34555553 22 3678999999999996 56665 46543
No 84
>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=22.75 E-value=4.5e+02 Score=22.99 Aligned_cols=11 Identities=9% Similarity=0.374 Sum_probs=7.9
Q ss_pred hccccCCCCCC
Q 039654 135 QCWWEAPIEEL 145 (225)
Q Consensus 135 ~~~w~~~l~~L 145 (225)
..+||.+-++-
T Consensus 176 d~yWgkda~gk 186 (308)
T PF06717_consen 176 DRYWGKDANGK 186 (308)
T ss_pred HhccCCCCCCC
Confidence 35899887765
No 85
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=22.74 E-value=5.6e+02 Score=22.92 Aligned_cols=21 Identities=14% Similarity=0.259 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 039654 151 EQLKMSLEELKKNVGKQAEKM 171 (225)
Q Consensus 151 ~~L~~~Le~l~~~V~~r~~~L 171 (225)
..|...|.+++.+||...+.|
T Consensus 183 ~KF~~vLNeKK~KIR~lq~~L 203 (342)
T PF06632_consen 183 AKFVLVLNEKKAKIRELQRLL 203 (342)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHHHHHHHHHH
Confidence 456667777777777665554
No 86
>PF06694 Plant_NMP1: Plant nuclear matrix protein 1 (NMP1); InterPro: IPR010604 This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm [].
Probab=22.06 E-value=4.5e+02 Score=23.21 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=12.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q 039654 143 EELNLPQLEQLKMSLEELKKNVG 165 (225)
Q Consensus 143 ~~Ls~eEL~~L~~~Le~l~~~V~ 165 (225)
|.-..+-..+|...|+.+...++
T Consensus 203 d~~~~e~~~~Lr~~L~tflq~~~ 225 (325)
T PF06694_consen 203 DEEYVEKESQLRLELETFLQTAA 225 (325)
T ss_pred chhhHHHHHHHHHHHHHHHHHHH
Confidence 44444445556666666555544
No 87
>TIGR03545 conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
Probab=21.99 E-value=5.7e+02 Score=24.50 Aligned_cols=31 Identities=10% Similarity=0.018 Sum_probs=17.2
Q ss_pred cchHHHHHHHHhh--hccCcEEEEEecCCCcccc
Q 039654 34 RTGLFKKASELCT--LCGADIAIIVFSPGKKVFS 65 (225)
Q Consensus 34 r~GL~KKA~ELs~--LC~aeva~Ivfsp~gk~~~ 65 (225)
-.-|+.++=++.. |-|+.+.+....+ |+.|+
T Consensus 88 l~pLL~~~vvI~~l~l~g~~v~l~R~~~-G~~~~ 120 (555)
T TIGR03545 88 WDALLRGKVVIEELAIEGLAFGTERSTS-GAVPE 120 (555)
T ss_pred cHHHhcCCcEEeEEEEecCEEEEEEccC-CCCCC
Confidence 3446666654443 3467777666665 45553
No 88
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=21.92 E-value=5.4e+02 Score=22.46 Aligned_cols=16 Identities=25% Similarity=0.430 Sum_probs=8.1
Q ss_pred hhhHHHHHHHHHHHHH
Q 039654 98 NASVRELNMQLTQVLN 113 (225)
Q Consensus 98 ~~~i~~l~~ql~~l~~ 113 (225)
...|.+|..||.++.+
T Consensus 88 etEI~eLksQL~RMrE 103 (305)
T PF15290_consen 88 ETEIDELKSQLARMRE 103 (305)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3445555555555443
No 89
>PRK04325 hypothetical protein; Provisional
Probab=21.92 E-value=2.7e+02 Score=18.90 Aligned_cols=7 Identities=43% Similarity=0.790 Sum_probs=2.6
Q ss_pred HHHHHHH
Q 039654 101 VRELNMQ 107 (225)
Q Consensus 101 i~~l~~q 107 (225)
|.+|..+
T Consensus 11 i~~LE~k 17 (74)
T PRK04325 11 ITELEIQ 17 (74)
T ss_pred HHHHHHH
Confidence 3333333
No 90
>PF06034 DUF919: Nucleopolyhedrovirus protein of unknown function (DUF919); InterPro: IPR009265 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several short baculovirus proteins of unknown function.
Probab=21.90 E-value=2.5e+02 Score=18.57 Aligned_cols=19 Identities=32% Similarity=0.599 Sum_probs=13.7
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q 039654 146 NLPQLEQLKMSLEELKKNV 164 (225)
Q Consensus 146 s~eEL~~L~~~Le~l~~~V 164 (225)
++.||..+...|.++....
T Consensus 36 ~p~El~~i~~kl~~~R~~F 54 (62)
T PF06034_consen 36 NPKELQEIEKKLQELRQNF 54 (62)
T ss_pred CHHHHHHHHHHHHHHHHHH
Confidence 6778888888877765543
No 91
>PRK10333 5-formyltetrahydrofolate cyclo-ligase family protein; Provisional
Probab=21.86 E-value=38 Score=27.08 Aligned_cols=13 Identities=46% Similarity=0.897 Sum_probs=10.0
Q ss_pred CCCCCCCCCCCCC
Q 039654 213 HPGYNPGFGHGFY 225 (225)
Q Consensus 213 ~~~~~~~~~~~~~ 225 (225)
.+.+=+|||.|||
T Consensus 122 ~~G~RLG~GgGyY 134 (182)
T PRK10333 122 EYGQRLGMGGGFY 134 (182)
T ss_pred CCCCcccCCcchH
Confidence 3444599999998
No 92
>PRK10884 SH3 domain-containing protein; Provisional
Probab=21.75 E-value=4.6e+02 Score=21.57 Aligned_cols=19 Identities=21% Similarity=0.338 Sum_probs=10.6
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q 039654 99 ASVRELNMQLTQVLNQLEI 117 (225)
Q Consensus 99 ~~i~~l~~ql~~l~~~le~ 117 (225)
..+.+++.+++++.++|..
T Consensus 93 ~rlp~le~el~~l~~~l~~ 111 (206)
T PRK10884 93 TRVPDLENQVKTLTDKLNN 111 (206)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4455666666666555533
No 93
>KOG2856 consensus Adaptor protein PACSIN [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=21.74 E-value=6.2e+02 Score=23.11 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 039654 142 IEELNLPQLEQLKMSLEELKKNVGKQA 168 (225)
Q Consensus 142 l~~Ls~eEL~~L~~~Le~l~~~V~~r~ 168 (225)
-..++.++|..|...+|.++..|..-+
T Consensus 171 DsSvspeq~kKlqdrveK~k~evqktk 197 (472)
T KOG2856|consen 171 DSSVSPEQLKKLQDRVEKCKQEVQKTK 197 (472)
T ss_pred CccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999998888875443
No 94
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=21.58 E-value=1.3e+02 Score=21.37 Aligned_cols=23 Identities=30% Similarity=0.439 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Q 039654 144 ELNLPQLEQLKMSLEELKKNVGK 166 (225)
Q Consensus 144 ~Ls~eEL~~L~~~Le~l~~~V~~ 166 (225)
.+++++|+.|...|++..+.+.+
T Consensus 70 ~c~~e~L~~Li~~Lk~A~~~~e~ 92 (95)
T cd04751 70 TCTLEQLQDLVNKLKDAAKNIER 92 (95)
T ss_pred EeCHHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999998888765
No 95
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=21.09 E-value=1.6e+02 Score=25.42 Aligned_cols=28 Identities=21% Similarity=0.302 Sum_probs=21.1
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 039654 139 EAPIEELNLPQLEQLKMSLEELKKNVGK 166 (225)
Q Consensus 139 ~~~l~~Ls~eEL~~L~~~Le~l~~~V~~ 166 (225)
-+.++.|+++||++|...|-.....|-+
T Consensus 213 rEeL~~Mt~~EL~qL~~~L~~qIq~vfe 240 (285)
T PF06937_consen 213 REELNSMTLDELKQLNEKLLQQIQDVFE 240 (285)
T ss_pred HHHhhhCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999998887655555443
No 96
>PHA00727 hypothetical protein
Probab=21.05 E-value=3.9e+02 Score=22.05 Aligned_cols=55 Identities=31% Similarity=0.382 Sum_probs=27.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 039654 100 SVRELNMQLTQVLNQLEIEKKRGEELNQMRKASQAQCWWEAPIEELNLPQLEQLKMSLEELKKNV 164 (225)
Q Consensus 100 ~i~~l~~ql~~l~~~le~ekk~~e~L~~l~k~~~~~~~w~~~l~~Ls~eEL~~L~~~Le~l~~~V 164 (225)
.+++|...+++.+.++.. +..+.++.+.-+.+ --+|-..|.++|+..|+..+++.
T Consensus 19 sleelkqkyee~qkqi~d----gk~lkrlykvyekr------efelk~~qf~qlkael~kkkkk~ 73 (278)
T PHA00727 19 SLEELKQKYEEAQKQIAD----GKTLKRLYKVYEKR------EFELKKQQFEQLKAELSKKKKKF 73 (278)
T ss_pred cHHHHHHHHHHHHHHhhc----cHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHh
Confidence 455666666655544422 22334444332111 11345566677777777655554
No 97
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=21.02 E-value=7e+02 Score=23.44 Aligned_cols=12 Identities=25% Similarity=0.387 Sum_probs=7.5
Q ss_pred Ccchhhhhhhhh
Q 039654 68 HPCVETIVDRYL 79 (225)
Q Consensus 68 ~psv~~Vi~Ry~ 79 (225)
.|+|-.|++.-.
T Consensus 51 ~~~~~~vV~~~F 62 (475)
T PRK13729 51 VPDMTGVVDTTF 62 (475)
T ss_pred CCCccceecchh
Confidence 356667777644
No 98
>PF15119 APOC4: Apolipoprotein C4
Probab=20.85 E-value=52 Score=23.35 Aligned_cols=20 Identities=35% Similarity=0.861 Sum_probs=16.0
Q ss_pred hhcccchHHHHHHHHh--hhcc
Q 039654 30 FSKRRTGLFKKASELC--TLCG 49 (225)
Q Consensus 30 FsKRr~GL~KKA~ELs--~LC~ 49 (225)
...-|..|+.||+-|| .|||
T Consensus 75 l~sSkd~llnk~~sLCPrllC~ 96 (99)
T PF15119_consen 75 LRSSKDSLLNKTHSLCPRLLCG 96 (99)
T ss_pred HHHhHHHHHHHHHhhCchhhcc
Confidence 4556789999999998 5775
No 99
>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=20.81 E-value=1e+02 Score=22.77 Aligned_cols=33 Identities=12% Similarity=0.212 Sum_probs=24.6
Q ss_pred HHHHHHHhhhc------cCcEEEEEecCCCcccccCCcc
Q 039654 38 FKKASELCTLC------GADIAIIVFSPGKKVFSFGHPC 70 (225)
Q Consensus 38 ~KKA~ELs~LC------~aeva~Ivfsp~gk~~~f~~ps 70 (225)
++.|-||+-.+ +..|+.||..++|++..-++..
T Consensus 1 m~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~~g~n~ 39 (115)
T cd01284 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEGYHR 39 (115)
T ss_pred CHHHHHHHHhcccccCCCCCEEEEEEeCCCeEEEEecCC
Confidence 46788888877 7799888888878876655444
No 100
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=20.74 E-value=55 Score=27.30 Aligned_cols=16 Identities=44% Similarity=0.698 Sum_probs=13.3
Q ss_pred CcEEEEEecCCCcccc
Q 039654 50 ADIAIIVFSPGKKVFS 65 (225)
Q Consensus 50 aeva~Ivfsp~gk~~~ 65 (225)
-+-||-||||+|.++.
T Consensus 4 ydraltvFSPDGhL~Q 19 (249)
T KOG0183|consen 4 YDRALTVFSPDGHLFQ 19 (249)
T ss_pred cccceEEECCCCCEEe
Confidence 4668999999999874
No 101
>KOG2662 consensus Magnesium transporters: CorA family [Inorganic ion transport and metabolism]
Probab=20.64 E-value=6.7e+02 Score=23.07 Aligned_cols=36 Identities=36% Similarity=0.452 Sum_probs=27.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHH---HHHHHHHHhhhc
Q 039654 140 APIEELNLPQLEQLKMSLEELKKN---VGKQAEKMLIQS 175 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~~~Le~l~~~---V~~r~~~L~~q~ 175 (225)
.++...+++.|..+++.|-.+.++ |++-+++|+.+.
T Consensus 212 ~~is~~nL~~lr~~k~~Lt~l~~rvqkvRDeLe~LLddd 250 (414)
T KOG2662|consen 212 NKISTLNLERLRILKKRLTELTSRVQKVRDELEELLDDD 250 (414)
T ss_pred hhhhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhcCh
Confidence 567778899999999998866554 677777777554
No 102
>TIGR02727 MTHFS_bact 5,10-methenyltetrahydrofolate synthetase. This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism.
Probab=20.56 E-value=43 Score=26.65 Aligned_cols=13 Identities=46% Similarity=1.242 Sum_probs=9.8
Q ss_pred CCCCCCCCCCCCC
Q 039654 213 HPGYNPGFGHGFY 225 (225)
Q Consensus 213 ~~~~~~~~~~~~~ 225 (225)
.+.+=+|||.|||
T Consensus 128 ~~G~RLG~GgGyY 140 (181)
T TIGR02727 128 RRGYRLGYGGGYY 140 (181)
T ss_pred CCCccccCCcchH
Confidence 3444599999998
No 103
>COG3096 MukB Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=20.41 E-value=9.1e+02 Score=24.52 Aligned_cols=34 Identities=12% Similarity=0.071 Sum_probs=18.2
Q ss_pred hHHHHHHHHhhhccCcEEEEEecCCCcccccCCcchhhhhhhhh
Q 039654 36 GLFKKASELCTLCGADIAIIVFSPGKKVFSFGHPCVETIVDRYL 79 (225)
Q Consensus 36 GL~KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv~~Vi~Ry~ 79 (225)
.-|.||++|..----+ -+-+-.+...+.+|..|-
T Consensus 473 sQF~~AyqLV~~iaGE----------~~RS~A~~~A~~llR~~p 506 (1480)
T COG3096 473 SQFEQAYQLVVAIAGE----------LARSEAWDVARELLREGP 506 (1480)
T ss_pred HHHHHHHHHHHHHhCc----------cchhhHHHHHHHHHHhCh
Confidence 4578888886433111 122333455667776664
No 104
>PRK03918 chromosome segregation protein; Provisional
Probab=20.39 E-value=5.4e+02 Score=25.63 Aligned_cols=21 Identities=29% Similarity=0.207 Sum_probs=10.6
Q ss_pred hhhcccchHHHHHHHHhhhcc
Q 039654 29 TFSKRRTGLFKKASELCTLCG 49 (225)
Q Consensus 29 TFsKRr~GL~KKA~ELs~LC~ 49 (225)
....+..-|-++..+|..-||
T Consensus 416 ~~~~~i~eL~~~l~~L~~~~~ 436 (880)
T PRK03918 416 ELKKEIKELKKAIEELKKAKG 436 (880)
T ss_pred HHHHHHHHHHHHHHHHHhcCC
Confidence 334444445555555565564
No 105
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=20.34 E-value=2.3e+02 Score=17.48 Aligned_cols=23 Identities=35% Similarity=0.460 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 039654 148 PQLEQLKMSLEELKKNVGKQAEK 170 (225)
Q Consensus 148 eEL~~L~~~Le~l~~~V~~r~~~ 170 (225)
.+|.+|...|.+++..++.++.+
T Consensus 8 ~ql~~l~~~l~elk~~l~~Q~kE 30 (45)
T PF11598_consen 8 KQLSELNQMLQELKELLRQQIKE 30 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666677777777666554
No 106
>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=20.26 E-value=40 Score=28.21 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=21.6
Q ss_pred HHHhhhccCcEEEEEecCCCcccccCCcc
Q 039654 42 SELCTLCGADIAIIVFSPGKKVFSFGHPC 70 (225)
Q Consensus 42 ~ELs~LC~aeva~Ivfsp~gk~~~f~~ps 70 (225)
.+|--.||++|+|||-.+.|.+|..|.+.
T Consensus 141 ~~l~~~~g~~v~ViI~Dt~gr~~r~G~~~ 169 (228)
T PF01996_consen 141 EELKERTGKDVGVIITDTNGRPWRLGQTG 169 (228)
T ss_dssp HHHHHHHS---EEEEEEEEEETTEECEEE
T ss_pred HHHHHHHCCceEEEEECCCCcEEecCCcc
Confidence 56777899999999999999888887654
No 107
>PHA00451 protein kinase
Probab=20.13 E-value=5.5e+02 Score=22.53 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=15.3
Q ss_pred ccCcEEEEEecCCCcc-----cccCC
Q 039654 48 CGADIAIIVFSPGKKV-----FSFGH 68 (225)
Q Consensus 48 C~aeva~Ivfsp~gk~-----~~f~~ 68 (225)
.|..-+-|+|+++|++ .+|+|
T Consensus 193 FDmHSGNiMf~~~g~p~ITDPVSFS~ 218 (362)
T PHA00451 193 FDMHSGNIMFDQDGVPYITDPVSFSH 218 (362)
T ss_pred ccccCCceeeCCCCCeEecCCccccC
Confidence 4556678999999974 46764
No 108
>PRK00064 recF recombination protein F; Reviewed
Probab=20.11 E-value=2.5e+02 Score=24.95 Aligned_cols=38 Identities=29% Similarity=0.512 Sum_probs=26.6
Q ss_pred HHHHHHhhhccCcEEEEEecCCCcccccCCcch-hhhhhhhhc
Q 039654 39 KKASELCTLCGADIAIIVFSPGKKVFSFGHPCV-ETIVDRYLT 80 (225)
Q Consensus 39 KKA~ELs~LC~aeva~Ivfsp~gk~~~f~~psv-~~Vi~Ry~~ 80 (225)
|+++||.-+.. +|+|+|.+-....+.|+. ...||++..
T Consensus 103 ~~~~~l~~~~~----~v~~~p~~~~l~~~~p~~RR~fLD~~~~ 141 (361)
T PRK00064 103 RKLAELAGLLN----VVLFTPEDLRLVKGGPSERRRFLDRLLF 141 (361)
T ss_pred cCHHHHhhhcc----EEEEccchhhhhcCCHHHHHHHHHHHHh
Confidence 35566555443 899999887666678876 478888765
No 109
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=20.09 E-value=2.5e+02 Score=21.17 Aligned_cols=36 Identities=17% Similarity=0.415 Sum_probs=28.4
Q ss_pred CCCCCCCHHHHHHHHHHHH-------HHHHHHHHHHHHHhhhc
Q 039654 140 APIEELNLPQLEQLKMSLE-------ELKKNVGKQAEKMLIQS 175 (225)
Q Consensus 140 ~~l~~Ls~eEL~~L~~~Le-------~l~~~V~~r~~~L~~q~ 175 (225)
.-+.+|+.+|+..|...++ ++...|+.-+..|+.-+
T Consensus 43 ~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkRl~~i~ 85 (121)
T COG0099 43 KRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKRLMKIG 85 (121)
T ss_pred HhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHHHHHhh
Confidence 4578999999999999988 67777877777775443
Done!