Query 045481
Match_columns 177
No_of_seqs 122 out of 1432
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 02:30:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045481.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045481hhsearch_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 6.2E-32 1.3E-36 206.7 5.4 68 1-68 8-77 (195)
2 cd00265 MADS_MEF2_like MEF2 (m 100.0 4E-32 8.6E-37 177.8 3.6 66 1-66 7-72 (77)
3 cd00266 MADS_SRF_like SRF-like 100.0 1.9E-29 4.1E-34 167.5 5.1 68 1-68 7-75 (83)
4 PF00319 SRF-TF: SRF-type tran 100.0 1E-29 2.2E-34 152.4 2.0 51 2-52 1-51 (51)
5 smart00432 MADS MADS domain. 99.9 8.9E-29 1.9E-33 153.1 3.9 53 1-53 7-59 (59)
6 cd00120 MADS MADS: MCM1, Agamo 99.9 3.1E-28 6.7E-33 150.8 3.2 53 1-53 7-59 (59)
7 KOG0015 Regulator of arginine 99.8 3.2E-19 7E-24 140.2 2.6 69 1-69 69-146 (338)
8 COG5068 ARG80 Regulator of arg 99.3 1.2E-12 2.7E-17 107.6 3.5 59 1-59 88-146 (412)
9 PF01486 K-box: K-box region; 98.3 6.7E-06 1.4E-10 56.3 7.8 43 122-164 37-79 (100)
10 PF15079 DUF4546: Domain of un 90.1 2.7 5.8E-05 31.3 7.7 69 86-168 48-116 (205)
11 PF04521 Viral_P18: ssRNA posi 81.0 6.3 0.00014 27.7 5.5 25 10-34 3-27 (120)
12 KOG4252 GTP-binding protein [S 80.1 4.6 9.9E-05 30.8 4.9 29 32-66 91-119 (246)
13 PF10491 Nrf1_DNA-bind: NLS-bi 76.6 6 0.00013 30.5 4.7 51 15-65 30-88 (214)
14 PF10584 Proteasome_A_N: Prote 75.9 0.99 2.1E-05 22.3 0.2 11 38-48 5-15 (23)
15 PF06698 DUF1192: Protein of u 75.4 9 0.0002 23.5 4.4 33 123-155 13-45 (59)
16 cd00187 TOP4c DNA Topoisomeras 74.5 44 0.00095 29.0 10.0 26 37-65 302-327 (445)
17 KOG4302 Microtubule-associated 73.2 55 0.0012 29.9 10.5 50 124-173 150-201 (660)
18 PF05852 DUF848: Gammaherpesvi 67.8 45 0.00098 24.4 7.6 33 128-160 83-115 (146)
19 PHA02592 52 DNA topisomerase I 66.2 61 0.0013 28.1 9.1 42 19-65 285-326 (439)
20 TIGR01916 F420_cofE F420-0:gam 60.1 11 0.00023 30.0 3.1 30 26-55 133-162 (243)
21 PF07106 TBPIP: Tat binding pr 58.8 70 0.0015 23.5 9.6 30 130-159 108-137 (169)
22 PRK09822 lipopolysaccharide co 53.8 12 0.00025 29.7 2.3 39 13-52 119-160 (269)
23 PF08967 DUF1884: Domain of un 52.8 10 0.00022 24.9 1.6 35 141-175 5-39 (85)
24 PRK10803 tol-pal system protei 49.7 73 0.0016 25.5 6.4 16 89-104 58-73 (263)
25 smart00787 Spc7 Spc7 kinetocho 48.7 1.5E+02 0.0033 24.4 10.7 32 126-157 196-227 (312)
26 PF12607 DUF3772: Protein of u 47.3 25 0.00054 21.7 2.7 23 150-175 21-43 (64)
27 COG3883 Uncharacterized protei 46.8 1.5E+02 0.0033 23.9 9.1 26 132-157 78-103 (265)
28 PRK13293 F420-0--gamma-glutamy 46.5 24 0.00051 28.1 3.1 29 27-55 135-163 (245)
29 PF13270 DUF4061: Domain of un 45.9 89 0.0019 20.8 5.4 20 131-150 69-88 (90)
30 KOG1029 Endocytic adaptor prot 45.4 2.7E+02 0.0059 26.3 10.0 32 7-38 435-467 (1118)
31 PF11460 DUF3007: Protein of u 45.3 31 0.00066 23.7 3.1 18 127-144 86-103 (104)
32 PF14257 DUF4349: Domain of un 45.3 1.5E+02 0.0032 23.4 7.6 56 85-152 125-180 (262)
33 PF15233 SYCE1: Synaptonemal c 43.4 1.2E+02 0.0026 21.7 6.2 12 53-64 6-17 (134)
34 PF09151 DUF1936: Domain of un 43.3 22 0.00047 18.8 1.7 27 28-54 3-31 (36)
35 PRK01919 tatB sec-independent 42.7 1.4E+02 0.0031 22.3 8.3 10 36-45 15-24 (169)
36 COG0718 Uncharacterized protei 41.7 61 0.0013 22.3 4.2 31 132-162 63-93 (105)
37 COG4917 EutP Ethanolamine util 40.7 24 0.00052 25.4 2.1 23 28-50 59-81 (148)
38 PF09403 FadA: Adhesion protei 40.6 1.3E+02 0.0029 21.3 10.0 23 134-156 89-111 (126)
39 COG4398 Uncharacterized protei 40.2 43 0.00093 27.5 3.7 38 30-67 317-356 (389)
40 PF04678 DUF607: Protein of un 40.2 1E+02 0.0022 23.1 5.7 46 50-106 32-78 (180)
41 PF08432 Vfa1: AAA-ATPase Vps4 40.1 1.4E+02 0.0029 22.5 6.3 14 32-45 11-24 (182)
42 KOG3366 Mitochondrial F1F0-ATP 38.0 1.7E+02 0.0038 21.9 7.5 15 127-141 129-143 (172)
43 PF07106 TBPIP: Tat binding pr 37.8 1.6E+02 0.0035 21.5 8.2 27 129-155 140-166 (169)
44 PRK00064 recF recombination pr 37.0 1.6E+02 0.0034 24.6 6.9 38 24-65 104-142 (361)
45 PF04873 EIN3: Ethylene insens 37.0 11 0.00024 31.6 0.0 49 8-56 43-92 (354)
46 PRK04863 mukB cell division pr 36.9 3.7E+02 0.008 27.4 10.1 31 126-156 430-460 (1486)
47 PF09941 DUF2173: Uncharacteri 36.0 25 0.00055 24.3 1.6 26 24-50 2-27 (108)
48 PF09278 MerR-DNA-bind: MerR, 35.9 98 0.0021 18.5 4.4 22 137-158 35-56 (65)
49 PRK13729 conjugal transfer pil 35.8 3.1E+02 0.0067 24.2 8.6 22 86-107 70-91 (475)
50 KOG3048 Molecular chaperone Pr 35.5 1E+02 0.0022 22.5 4.7 33 126-158 8-40 (153)
51 KOG0432 Valyl-tRNA synthetase 35.2 62 0.0014 30.6 4.3 19 22-40 879-897 (995)
52 PHA03161 hypothetical protein; 34.2 1.9E+02 0.0041 21.2 7.6 33 132-164 87-119 (150)
53 PRK04098 sec-independent trans 33.9 75 0.0016 23.6 3.9 11 35-45 14-24 (158)
54 PF00843 Arena_nucleocap: Aren 33.2 78 0.0017 27.5 4.3 25 127-151 87-111 (533)
55 KOG0183 20S proteasome, regula 33.2 24 0.00053 27.5 1.2 16 34-49 4-19 (249)
56 KOG0861 SNARE protein YKT6, sy 32.8 1.7E+02 0.0037 22.2 5.6 10 36-45 75-84 (198)
57 cd01363 Motor_domain Myosin an 32.0 42 0.00091 25.0 2.4 24 30-53 19-45 (186)
58 KOG4403 Cell surface glycoprot 31.9 1.3E+02 0.0028 26.2 5.4 16 160-175 326-341 (575)
59 KOG4316 Uncharacterized conser 31.3 23 0.0005 25.9 0.8 42 26-67 43-95 (172)
60 PF14009 DUF4228: Domain of un 31.1 50 0.0011 23.9 2.7 34 32-65 12-46 (181)
61 PF07701 HNOBA: Heme NO bindin 31.1 1.5E+02 0.0032 23.1 5.3 24 39-62 122-146 (219)
62 PF03584 Herpes_ICP4_N: Herpes 30.8 93 0.002 23.3 3.9 32 37-68 15-48 (173)
63 KOG4637 Adaptor for phosphoino 30.7 35 0.00077 28.9 1.9 41 26-66 367-412 (464)
64 PF14282 FlxA: FlxA-like prote 30.5 1.8E+02 0.0038 19.8 8.0 55 85-160 19-73 (106)
65 PF06020 Roughex: Drosophila r 29.7 26 0.00055 28.6 0.9 16 29-44 183-198 (334)
66 PRK04654 sec-independent trans 29.4 1.6E+02 0.0036 22.9 5.2 10 36-45 15-24 (214)
67 PRK09458 pspB phage shock prot 29.3 1.6E+02 0.0035 18.9 4.5 28 129-157 34-61 (75)
68 PF09177 Syntaxin-6_N: Syntaxi 29.2 1.7E+02 0.0038 19.3 7.5 23 130-152 73-95 (97)
69 COG4575 ElaB Uncharacterized c 29.1 1.9E+02 0.0042 19.8 7.1 29 129-157 32-60 (104)
70 PF08557 Lipid_DES: Sphingolip 28.8 39 0.00085 18.9 1.3 21 15-35 16-36 (39)
71 PRK11637 AmiB activator; Provi 28.6 3.7E+02 0.0081 22.9 9.7 31 133-163 109-139 (428)
72 TIGR02420 dksA RNA polymerase- 28.6 1.6E+02 0.0035 20.0 4.7 28 131-158 1-28 (110)
73 COG0099 RpsM Ribosomal protein 28.5 1.6E+02 0.0035 20.8 4.6 33 126-158 43-82 (121)
74 PF09432 THP2: Tho complex sub 28.4 2.2E+02 0.0049 20.3 7.9 12 53-64 38-49 (132)
75 KOG0184 20S proteasome, regula 27.8 32 0.00069 27.0 1.1 21 29-49 3-23 (254)
76 PF06667 PspB: Phage shock pro 27.7 1.7E+02 0.0037 18.8 4.5 29 128-157 33-61 (75)
77 PRK13294 F420-0--gamma-glutamy 27.5 64 0.0014 28.0 3.0 28 26-53 134-161 (448)
78 PF05873 Mt_ATP-synt_D: ATP sy 27.4 2.3E+02 0.0051 20.9 5.6 17 12-28 28-44 (161)
79 PF08317 Spc7: Spc7 kinetochor 27.3 3.5E+02 0.0076 22.2 10.0 31 127-157 202-232 (325)
80 PLN03237 DNA topoisomerase 2; 27.1 6.9E+02 0.015 25.5 11.1 44 18-65 971-1014(1465)
81 COG3883 Uncharacterized protei 26.9 3.4E+02 0.0074 21.9 8.9 31 134-164 87-117 (265)
82 PF01996 F420_ligase: F420-0:G 26.8 18 0.0004 28.3 -0.3 29 26-54 141-169 (228)
83 PF05700 BCAS2: Breast carcino 26.8 3E+02 0.0065 21.3 7.2 28 132-159 137-164 (221)
84 PF04120 Iron_permease: Low af 26.5 2.5E+02 0.0053 20.1 8.0 30 126-155 90-119 (132)
85 COG1938 Archaeal enzymes of AT 26.1 2.2E+02 0.0048 22.7 5.5 10 57-66 194-203 (244)
86 PF11944 DUF3461: Protein of u 26.0 1E+02 0.0022 21.9 3.2 25 133-157 101-125 (125)
87 PRK10132 hypothetical protein; 26.0 2.3E+02 0.0049 19.5 7.1 25 131-155 38-62 (108)
88 TIGR00103 DNA_YbaB_EbfC DNA-bi 25.8 1.2E+02 0.0026 20.5 3.6 35 134-168 64-98 (102)
89 COG4831 Roadblock/LC7 domain [ 25.6 58 0.0013 22.1 1.9 29 23-52 3-31 (109)
90 PF12325 TMF_TATA_bd: TATA ele 25.4 2.4E+02 0.0053 19.8 8.3 27 132-158 94-120 (120)
91 cd00468 HIT_like HIT family: H 25.3 1.3E+02 0.0028 18.7 3.6 26 126-151 30-55 (86)
92 COG5000 NtrY Signal transducti 24.9 50 0.0011 30.0 1.9 22 29-50 374-395 (712)
93 PRK09555 feoA ferrous iron tra 24.7 1E+02 0.0022 19.5 2.9 32 19-50 20-51 (74)
94 PF00383 dCMP_cyt_deam_1: Cyti 24.7 78 0.0017 20.7 2.5 31 20-50 6-40 (102)
95 PTZ00108 DNA topoisomerase 2-l 24.7 7.5E+02 0.016 25.1 10.2 27 37-65 962-988 (1388)
96 PF08796 DUF1797: Protein of u 24.6 51 0.0011 20.8 1.4 19 32-50 24-42 (67)
97 TIGR01478 STEVOR variant surfa 24.6 1.4E+02 0.003 24.4 4.2 42 2-64 27-69 (295)
98 PRK13291 metal-dependent hydro 24.5 1.6E+02 0.0035 21.8 4.4 47 127-176 13-59 (173)
99 COG3411 Ferredoxin [Energy pro 24.5 65 0.0014 20.1 1.8 30 37-66 18-48 (64)
100 PF10046 BLOC1_2: Biogenesis o 24.3 2.3E+02 0.0049 19.0 8.2 25 132-156 74-98 (99)
101 PRK00295 hypothetical protein; 24.2 1.9E+02 0.0041 18.0 4.9 26 83-108 17-42 (68)
102 PRK00736 hypothetical protein; 24.1 1.9E+02 0.0041 18.0 4.9 27 83-109 17-43 (68)
103 cd04751 Commd3 COMM_Domain con 23.7 1.3E+02 0.0027 20.1 3.3 23 130-152 70-92 (95)
104 PRK10722 hypothetical protein; 23.5 3.7E+02 0.008 21.5 6.3 31 86-116 177-207 (247)
105 PF03250 Tropomodulin: Tropomo 23.5 63 0.0014 23.6 1.9 18 128-145 21-38 (147)
106 KOG4797 Transcriptional regula 23.4 2.6E+02 0.0057 19.4 5.6 14 131-144 97-110 (123)
107 PF11232 Med25: Mediator compl 23.2 60 0.0013 23.9 1.7 19 30-48 109-127 (152)
108 TIGR03629 arch_S13P archaeal r 22.7 2.5E+02 0.0055 20.4 5.0 20 126-145 47-66 (144)
109 TIGR03631 bact_S13 30S ribosom 22.7 2.7E+02 0.0058 19.3 4.9 34 126-159 41-81 (113)
110 cd01365 KISc_KIF1A_KIF1B Kines 22.4 1.1E+02 0.0025 25.3 3.5 36 19-54 70-111 (356)
111 TIGR02231 conserved hypothetic 21.9 5.5E+02 0.012 22.5 10.4 16 130-145 123-138 (525)
112 PF13252 DUF4043: Protein of u 21.8 43 0.00094 28.0 0.9 21 26-46 272-292 (341)
113 PRK04406 hypothetical protein; 21.8 2.3E+02 0.0049 18.1 4.9 20 85-104 25-44 (75)
114 COG5179 TAF1 Transcription ini 21.8 58 0.0013 29.7 1.7 44 19-63 446-489 (968)
115 cd01277 HINT_subgroup HINT (hi 21.7 1.6E+02 0.0034 19.2 3.6 27 126-152 46-72 (103)
116 PF04977 DivIC: Septum formati 21.7 2.1E+02 0.0045 17.6 4.9 21 89-109 21-41 (80)
117 PRK04325 hypothetical protein; 21.4 2.3E+02 0.005 18.0 4.9 25 83-107 21-45 (74)
118 PF10168 Nup88: Nuclear pore c 21.3 6.7E+02 0.015 23.4 8.8 67 84-169 564-630 (717)
119 PF11853 DUF3373: Protein of u 21.3 1E+02 0.0022 27.2 3.0 25 86-110 32-56 (489)
120 PF13991 BssS: BssS protein fa 21.2 1.6E+02 0.0035 18.8 3.2 26 127-152 38-63 (73)
121 PRK00587 hypothetical protein; 21.2 1.5E+02 0.0033 20.1 3.3 40 131-170 57-97 (99)
122 PLN03230 acetyl-coenzyme A car 21.1 5.6E+02 0.012 22.3 7.8 12 57-68 59-70 (431)
123 cd07665 BAR_SNX1 The Bin/Amphi 21.1 75 0.0016 25.1 2.1 29 82-110 26-54 (234)
124 PTZ00046 rifin; Provisional 21.0 4.1E+02 0.0088 22.5 6.4 28 30-66 40-68 (358)
125 PF03938 OmpH: Outer membrane 21.0 3.2E+02 0.0068 19.4 8.3 11 54-64 23-33 (158)
126 PF04102 SlyX: SlyX; InterPro 20.6 2.3E+02 0.0049 17.6 5.0 27 83-109 16-42 (69)
127 PF06296 DUF1044: Protein of u 20.5 2.3E+02 0.005 19.9 4.2 35 127-161 81-115 (120)
128 cd02980 TRX_Fd_family Thioredo 20.4 80 0.0017 19.5 1.8 29 32-61 47-76 (77)
129 PRK05179 rpsM 30S ribosomal pr 20.4 3E+02 0.0065 19.3 4.8 33 126-158 43-82 (122)
130 KOG3838 Mannose lectin ERGIC-5 20.2 5.5E+02 0.012 22.2 7.0 42 124-165 309-353 (497)
131 PF06937 EURL: EURL protein; 20.2 2E+02 0.0044 23.3 4.3 30 126-155 214-243 (285)
132 cd08888 SRPBCC_PITPNA-B_like L 20.1 3.2E+02 0.0069 22.0 5.4 26 126-151 232-257 (258)
No 1
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.97 E-value=6.2e-32 Score=206.73 Aligned_cols=68 Identities=51% Similarity=0.863 Sum_probs=65.0
Q ss_pred CcccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCC--hhHHHHHHhhcCCC
Q 045481 1 ISKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPN--VDSILDLYLARNPN 68 (177)
Q Consensus 1 ik~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~ps--v~~Vl~ry~~~~~~ 68 (177)
|++|+|+.+|+|||+|||.||||||+||||||||+||+|||||+|++|.||+|+ |+.|++||......
T Consensus 8 i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~ 77 (195)
T KOG0014|consen 8 IKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEP 77 (195)
T ss_pred eeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhh
Confidence 789999999999999999999999999999999999999999999999999987 99999999987654
No 2
>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.97 E-value=4e-32 Score=177.82 Aligned_cols=66 Identities=45% Similarity=0.805 Sum_probs=64.3
Q ss_pred CcccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCChhHHHHHHhhcC
Q 045481 1 ISKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPNVDSILDLYLARN 66 (177)
Q Consensus 1 ik~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~psv~~Vl~ry~~~~ 66 (177)
|++|+|+.+|++||+||++||||||+|||+||||+||+|||||+|++|+|++|++++||+||++.+
T Consensus 7 i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~ 72 (77)
T cd00265 7 IKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTS 72 (77)
T ss_pred eEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhcc
Confidence 689999999999999999999999999999999999999999999999999999999999999865
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=1.9e-29 Score=167.52 Aligned_cols=68 Identities=46% Similarity=0.755 Sum_probs=64.3
Q ss_pred CcccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCC-hhHHHHHHhhcCCC
Q 045481 1 ISKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPN-VDSILDLYLARNPN 68 (177)
Q Consensus 1 ik~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~ps-v~~Vl~ry~~~~~~ 68 (177)
|++|+|+.+|++||+|||.||||||+||||||||+||+|||||+|+.+.|++++ +..++++|...++.
T Consensus 7 i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~ 75 (83)
T cd00266 7 IKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSAL 75 (83)
T ss_pred eEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHh
Confidence 689999999999999999999999999999999999999999999999998877 99999999987643
No 4
>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=99.95 E-value=1e-29 Score=152.39 Aligned_cols=51 Identities=63% Similarity=0.996 Sum_probs=46.7
Q ss_pred cccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCC
Q 045481 2 SKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGH 52 (177)
Q Consensus 2 k~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~ 52 (177)
|+|+|+..|++||+|||.||||||+|||+||||+||+|||||+|++|+|++
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 689999999999999999999999999999999999999999999999975
No 5
>smart00432 MADS MADS domain.
Probab=99.95 E-value=8.9e-29 Score=153.11 Aligned_cols=53 Identities=60% Similarity=0.978 Sum_probs=51.8
Q ss_pred CcccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCC
Q 045481 1 ISKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHP 53 (177)
Q Consensus 1 ik~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~p 53 (177)
|++|+|+.+|++||+||++||||||+||||||||+||+|||||+|++|.|++|
T Consensus 7 i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~p 59 (59)
T smart00432 7 IKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP 59 (59)
T ss_pred eEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccCC
Confidence 68999999999999999999999999999999999999999999999999987
No 6
>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=99.94 E-value=3.1e-28 Score=150.80 Aligned_cols=53 Identities=57% Similarity=0.891 Sum_probs=51.4
Q ss_pred CcccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCC
Q 045481 1 ISKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHP 53 (177)
Q Consensus 1 ik~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~p 53 (177)
|++|+|+.+|++||+||++||||||+||||||||+||+|||||+|+++.|++|
T Consensus 7 i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~~ 59 (59)
T cd00120 7 IKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS 59 (59)
T ss_pred eEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccCC
Confidence 68999999999999999999999999999999999999999999999999876
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.75 E-value=3.2e-19 Score=140.22 Aligned_cols=69 Identities=36% Similarity=0.592 Sum_probs=63.1
Q ss_pred CcccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCCh---------hHHHHHHhhcCCCC
Q 045481 1 ISKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPNV---------DSILDLYLARNPNP 69 (177)
Q Consensus 1 ik~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~psv---------~~Vl~ry~~~~~~~ 69 (177)
|++|+|+..|.+||+|||.||||||+|||||+|.+|-++|.|++|.+|+|..|.. +.+|...++.+..+
T Consensus 69 ~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~s~~Gk~lIq~cLn~pd~~ 146 (338)
T KOG0015|consen 69 MEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMITSDEGKALIQACLNAPDTP 146 (338)
T ss_pred chhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccccchhhHHHHHHHhcCCCCC
Confidence 6899999999999999999999999999999999999999999999999998854 47788888877654
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.30 E-value=1.2e-12 Score=107.59 Aligned_cols=59 Identities=42% Similarity=0.630 Sum_probs=54.9
Q ss_pred CcccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCChhHHH
Q 045481 1 ISKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPNVDSIL 59 (177)
Q Consensus 1 ik~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~psv~~Vl 59 (177)
|.+|+|+.+|.|||.||+.||+|||.||++|.|.+|.++|.|.+|.+++|+.|....|+
T Consensus 88 is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~ 146 (412)
T COG5068 88 ISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVV 146 (412)
T ss_pred cccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCcccccc
Confidence 67899999999999999999999999999999999999999999999999988655443
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=98.26 E-value=6.7e-06 Score=56.35 Aligned_cols=43 Identities=23% Similarity=0.411 Sum_probs=39.2
Q ss_pred ccccCccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC
Q 045481 122 CWWEAPINELGLHELEQLKTAMEELKKNVEQQANKILIDSKNN 164 (177)
Q Consensus 122 ~~w~~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~~ 164 (177)
+..|+++++|+++||..|+..|+..+..|+.|+.+++.+++..
T Consensus 37 ~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~ 79 (100)
T PF01486_consen 37 HLMGEDLESLSLKELQQLEQQLESALKRVRSRKDQLLMEQIEE 79 (100)
T ss_pred ccccccccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999999999999999999887653
No 10
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=90.09 E-value=2.7 Score=31.32 Aligned_cols=69 Identities=23% Similarity=0.428 Sum_probs=49.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhcccccCccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCC
Q 045481 86 NIRELNMQLTQVLHQLEVEKKHGEVLSEIRKASCRQCWWEAPINELGLHELEQLKTAMEELKKNVEQQANKILIDSKNNP 165 (177)
Q Consensus 86 ~~~~l~~q~~~l~~~le~ekk~~e~l~~~~~~~~~~~~w~~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~~~ 165 (177)
.-++|.+++++...+|. .+.+.+.++. ++-|-+.+-|.+|.....+..+...++++-|+.-+-++-
T Consensus 48 ~T~eLkNeLREVREELk---EKmeEIKQIK-----------diMDKDFDKL~EFVEIMKeMQkDMDEKMDvLiNiQKnnK 113 (205)
T PF15079_consen 48 GTQELKNELREVREELK---EKMEEIKQIK-----------DIMDKDFDKLHEFVEIMKEMQKDMDEKMDVLINIQKNNK 113 (205)
T ss_pred ccHHHHHHHHHHHHHHH---HHHHHHHHHH-----------HHHhhhHHHHHHHHHHHHHHHHhHHHhhhHHhhcccccc
Confidence 44566677766665543 3444555543 233346678889999999999999999999999998888
Q ss_pred CCc
Q 045481 166 SPF 168 (177)
Q Consensus 166 ~~~ 168 (177)
+|+
T Consensus 114 lPl 116 (205)
T PF15079_consen 114 LPL 116 (205)
T ss_pred Ccc
Confidence 776
No 11
>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=81.02 E-value=6.3 Score=27.67 Aligned_cols=25 Identities=28% Similarity=0.296 Sum_probs=19.8
Q ss_pred chhhhhhchhhHHHHHHHHhhhcCC
Q 045481 10 LQVTFSKRRAGVFKKASELSTLCGV 34 (177)
Q Consensus 10 R~~Tf~KRr~GL~KKa~ELs~LC~v 34 (177)
.-.+|+|+|..+++|-.+-.+-|..
T Consensus 3 ~~~~~rk~R~~~y~~lgl~~vkC~L 27 (120)
T PF04521_consen 3 SFRCVRKYRASVYKKLGLSAVKCRL 27 (120)
T ss_pred chHHHHHHHHHHHHHcCCeeeeecC
Confidence 3468999999999999887665543
No 12
>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=80.08 E-value=4.6 Score=30.83 Aligned_cols=29 Identities=21% Similarity=0.446 Sum_probs=22.4
Q ss_pred cCCcEEEEEecCCCCCcccCCCChhHHHHHHhhcC
Q 045481 32 CGVDIALIVFSPANKAFSFGHPNVDSILDLYLARN 66 (177)
Q Consensus 32 C~vev~~Ivfsp~gk~~~f~~psv~~Vl~ry~~~~ 66 (177)
-||.+||+|||.+++ -|.+.+++=|....
T Consensus 91 rgaqa~vLVFSTTDr------~SFea~~~w~~kv~ 119 (246)
T KOG4252|consen 91 RGAQASVLVFSTTDR------YSFEATLEWYNKVQ 119 (246)
T ss_pred ccccceEEEEecccH------HHHHHHHHHHHHHH
Confidence 499999999999885 46677777776543
No 13
>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=76.56 E-value=6 Score=30.53 Aligned_cols=51 Identities=18% Similarity=0.341 Sum_probs=37.0
Q ss_pred hhch-hhHHHH----HHHHhhhcCCcEEEEEecCCCC---CcccCCCChhHHHHHHhhc
Q 045481 15 SKRR-AGVFKK----ASELSTLCGVDIALIVFSPANK---AFSFGHPNVDSILDLYLAR 65 (177)
Q Consensus 15 ~KRr-~GL~KK----a~ELs~LC~vev~~Ivfsp~gk---~~~f~~psv~~Vl~ry~~~ 65 (177)
+||. .-|+.| ..|++|-+|-.|+|+|.+|+-. .-.||.-..+.|+..|+..
T Consensus 30 rkrq~~rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~~ 88 (214)
T PF10491_consen 30 RKRQQTRLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKPV 88 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHHH
Confidence 4443 335555 4799999999999999999743 3447877778888877643
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=75.93 E-value=0.99 Score=22.28 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=8.9
Q ss_pred EEEecCCCCCc
Q 045481 38 LIVFSPANKAF 48 (177)
Q Consensus 38 ~Ivfsp~gk~~ 48 (177)
+.+|||+|+++
T Consensus 5 ~t~FSp~Grl~ 15 (23)
T PF10584_consen 5 ITTFSPDGRLF 15 (23)
T ss_dssp TTSBBTTSSBH
T ss_pred ceeECCCCeEE
Confidence 45899999975
No 15
>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=75.45 E-value=9 Score=23.50 Aligned_cols=33 Identities=18% Similarity=0.136 Sum_probs=25.2
Q ss_pred cccCccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 123 WWEAPINELGLHELEQLKTAMEELKKNVEQQAN 155 (177)
Q Consensus 123 ~w~~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~ 155 (177)
..+.+|+.||++||.+-...|+.=...++..+.
T Consensus 13 ~ig~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~ 45 (59)
T PF06698_consen 13 EIGEDLSLLSVEELEERIALLEAEIARLEAAIA 45 (59)
T ss_pred ccCCCchhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999988888766666655443
No 16
>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=74.45 E-value=44 Score=29.03 Aligned_cols=26 Identities=23% Similarity=0.571 Sum_probs=21.9
Q ss_pred EEEEecCCCCCcccCCCChhHHHHHHhhc
Q 045481 37 ALIVFSPANKAFSFGHPNVDSILDLYLAR 65 (177)
Q Consensus 37 ~~Ivfsp~gk~~~f~~psv~~Vl~ry~~~ 65 (177)
-+++|.++|++..| ++.++|+.|...
T Consensus 302 Nm~~~~~~g~p~~~---~l~~iL~~f~~~ 327 (445)
T cd00187 302 NMVAFDPNGRPKKL---NLKEILQEFLDH 327 (445)
T ss_pred eEEEEecCCeeEEe---CHHHHHHHHHHH
Confidence 78889999998777 789999999754
No 17
>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=73.19 E-value=55 Score=29.91 Aligned_cols=50 Identities=28% Similarity=0.471 Sum_probs=35.2
Q ss_pred ccCccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--hhhccCCCCCcccccc
Q 045481 124 WEAPINELGLHELEQLKTAMEELKKNVEQQANKI--LIDSKNNPSPFFGLGF 173 (177)
Q Consensus 124 w~~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L--~~~~~~~~~~~~~~~~ 173 (177)
...+..+|+.+.|.+|...|..+.+.-..|.+.. +..++....-.+|..|
T Consensus 150 ~~~D~~dlsl~kLeelr~~L~~L~~ek~~Rlekv~~~~~~I~~l~~~Lg~~~ 201 (660)
T KOG4302|consen 150 LIADESDLSLEKLEELREHLNELQKEKSDRLEKVLELKEEIKSLCSVLGLDF 201 (660)
T ss_pred cccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 3446789999999999999999999988888775 3334433333344333
No 18
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=67.76 E-value=45 Score=24.36 Aligned_cols=33 Identities=24% Similarity=0.425 Sum_probs=28.5
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045481 128 INELGLHELEQLKTAMEELKKNVEQQANKILID 160 (177)
Q Consensus 128 l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~ 160 (177)
++--.+++++.|.+.++++...|...++.+...
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 455688999999999999999999999998744
No 19
>PHA02592 52 DNA topisomerase II medium subunit; Provisional
Probab=66.22 E-value=61 Score=28.11 Aligned_cols=42 Identities=14% Similarity=0.234 Sum_probs=27.9
Q ss_pred hhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCChhHHHHHHhhc
Q 045481 19 AGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPNVDSILDLYLAR 65 (177)
Q Consensus 19 ~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~psv~~Vl~ry~~~ 65 (177)
++|+|+- .|.+ -.-+-+++|+++|++..| .++.+||+.|...
T Consensus 285 ~~L~k~~-~L~~--~~~~Nm~~~d~~g~~~~~--~~~~~Il~~f~~~ 326 (439)
T PHA02592 285 EKIMKDF-GLIE--RVSQNITVINENGKLKVY--ENAEDLIRDFVEI 326 (439)
T ss_pred HHHHHhc-Cchh--eeeeeEEEEecCCeeeec--CCHHHHHHHHHHH
Confidence 4666542 2322 335788999999986655 4678888888654
No 20
>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=60.10 E-value=11 Score=30.01 Aligned_cols=30 Identities=30% Similarity=0.530 Sum_probs=25.1
Q ss_pred HHHhhhcCCcEEEEEecCCCCCcccCCCCh
Q 045481 26 SELSTLCGVDIALIVFSPANKAFSFGHPNV 55 (177)
Q Consensus 26 ~ELs~LC~vev~~Ivfsp~gk~~~f~~psv 55 (177)
.+|.-.+|++|+|||+.+.|+++--|.+.+
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~~gv 162 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQVGV 162 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCCCCe
Confidence 356667999999999999999988887754
No 21
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=58.82 E-value=70 Score=23.51 Aligned_cols=30 Identities=23% Similarity=0.222 Sum_probs=18.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045481 130 ELGLHELEQLKTAMEELKKNVEQQANKILI 159 (177)
Q Consensus 130 ~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~ 159 (177)
.++.+||..-...|+.-...+..|+..|..
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 356666666666666666666666666554
No 22
>PRK09822 lipopolysaccharide core biosynthesis protein; Provisional
Probab=53.77 E-value=12 Score=29.68 Aligned_cols=39 Identities=18% Similarity=0.339 Sum_probs=28.7
Q ss_pred hhhhchhhHHHHHHHHhhhcCCc---EEEEEecCCCCCcccCC
Q 045481 13 TFSKRRAGVFKKASELSTLCGVD---IALIVFSPANKAFSFGH 52 (177)
Q Consensus 13 Tf~KRr~GL~KKa~ELs~LC~ve---v~~Ivfsp~gk~~~f~~ 52 (177)
-|++-|.|++||.. +..||+.+ ||-|.||+.++...|+.
T Consensus 119 ~~~~~~~~~~~~~~-~~~L~~~~~~l~~~v~fS~~~r~IGFSk 160 (269)
T PRK09822 119 FYRREKGGFLKKIK-FNILKRVHKALLISVPLSKRGRLAGFCK 160 (269)
T ss_pred hhhhccCchhhhhH-HHHHhhhhhhhEEEeeccccCCceeeee
Confidence 34555788888874 78888654 66677999998877765
No 23
>PF08967 DUF1884: Domain of unknown function (DUF1884); InterPro: IPR014418 This group represents an uncharacterised conserved protein.; PDB: 2PK8_A.
Probab=52.85 E-value=10 Score=24.89 Aligned_cols=35 Identities=14% Similarity=0.232 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCCcccccccc
Q 045481 141 TAMEELKKNVEQQANKILIDSKNNPSPFFGLGFWT 175 (177)
Q Consensus 141 ~~Le~~l~~V~~r~~~L~~~~~~~~~~~~~~~~~~ 175 (177)
..+-+.+..|+..+++|-+++..|-.-++|+.|.-
T Consensus 5 ~~li~il~~ie~~inELk~dG~ePDivL~G~ef~e 39 (85)
T PF08967_consen 5 GDLIRILELIEEKINELKEDGFEPDIVLVGPEFYE 39 (85)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT----EEEE-HHHHH
T ss_pred hhHHHHHHHHHHHHHHHHhcCCCCCEEEEcHHHHH
Confidence 34566778889999999999998889999998863
No 24
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=49.67 E-value=73 Score=25.48 Aligned_cols=16 Identities=19% Similarity=0.275 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHH
Q 045481 89 ELNMQLTQVLHQLEVE 104 (177)
Q Consensus 89 ~l~~q~~~l~~~le~e 104 (177)
+|..|++.++.++..+
T Consensus 58 ~l~~ql~~lq~ev~~L 73 (263)
T PRK10803 58 QLQQQLSDNQSDIDSL 73 (263)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4555555555555443
No 25
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=48.71 E-value=1.5e+02 Score=24.40 Aligned_cols=32 Identities=16% Similarity=0.335 Sum_probs=23.5
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEELKKNVEQQANKI 157 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L 157 (177)
..+++++.++|..+...|......+..+...+
T Consensus 196 ~e~~~~d~~eL~~lk~~l~~~~~ei~~~~~~l 227 (312)
T smart00787 196 DELEDCDPTELDRAKEKLKKLLQEIMIKVKKL 227 (312)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35778888888888888877777776555543
No 26
>PF12607 DUF3772: Protein of unknown function (DUF3772); InterPro: IPR022249 This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with PF00924 from PFAM.
Probab=47.32 E-value=25 Score=21.68 Aligned_cols=23 Identities=13% Similarity=0.391 Sum_probs=11.9
Q ss_pred HHHHHHHHhhhccCCCCCcccccccc
Q 045481 150 VEQQANKILIDSKNNPSPFFGLGFWT 175 (177)
Q Consensus 150 V~~r~~~L~~~~~~~~~~~~~~~~~~ 175 (177)
++++...-+.....| ++++.||.
T Consensus 21 rR~~~~~~L~~r~~S---pL~P~~W~ 43 (64)
T PF12607_consen 21 RRERFTSQLLERSPS---PLNPAFWS 43 (64)
T ss_pred HHHHHHHHHHHcCCC---CCCHHHHH
Confidence 344444434344433 46788885
No 27
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.79 E-value=1.5e+02 Score=23.87 Aligned_cols=26 Identities=23% Similarity=0.466 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 132 GLHELEQLKTAMEELKKNVEQQANKI 157 (177)
Q Consensus 132 s~eeL~~l~~~Le~~l~~V~~r~~~L 157 (177)
+-.++..|...|+.+...|++|.+-|
T Consensus 78 ~~~eik~l~~eI~~~~~~I~~r~~~l 103 (265)
T COG3883 78 SKAEIKKLQKEIAELKENIVERQELL 103 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677777777777776665443
No 28
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=46.53 E-value=24 Score=28.12 Aligned_cols=29 Identities=24% Similarity=0.465 Sum_probs=24.3
Q ss_pred HHhhhcCCcEEEEEecCCCCCcccCCCCh
Q 045481 27 ELSTLCGVDIALIVFSPANKAFSFGHPNV 55 (177)
Q Consensus 27 ELs~LC~vev~~Ivfsp~gk~~~f~~psv 55 (177)
+|.-.||++|+|||....|+++-.|...+
T Consensus 135 ~l~~~~g~~v~VIItDt~gr~~R~G~t~v 163 (245)
T PRK13293 135 GLEELTGKKVGVIITDTNGRPFRKGQRGV 163 (245)
T ss_pred HHHHHHCCCEEEEEEcCCCcccccCCcce
Confidence 45667999999999999999988877654
No 29
>PF13270 DUF4061: Domain of unknown function (DUF4061)
Probab=45.85 E-value=89 Score=20.84 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=12.5
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q 045481 131 LGLHELEQLKTAMEELKKNV 150 (177)
Q Consensus 131 Ls~eeL~~l~~~Le~~l~~V 150 (177)
-+.+.+..|...|+.+-..|
T Consensus 69 ~~~~nm~~L~~~Le~Ls~sI 88 (90)
T PF13270_consen 69 QSDENMDKLFSNLEQLSNSI 88 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 35566666777776665554
No 30
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=45.36 E-value=2.7e+02 Score=26.33 Aligned_cols=32 Identities=19% Similarity=0.168 Sum_probs=22.6
Q ss_pred CCcchhhhhhchhhHHHHHHHHh-hhcCCcEEE
Q 045481 7 KNNLQVTFSKRRAGVFKKASELS-TLCGVDIAL 38 (177)
Q Consensus 7 ~~~R~~Tf~KRr~GL~KKa~ELs-~LC~vev~~ 38 (177)
..++..+..-+-..|--|..+|+ -||||.+.+
T Consensus 435 ~nak~~ql~~eletLn~k~qqls~kl~Dvr~~~ 467 (1118)
T KOG1029|consen 435 LNAKKKQLQQELETLNFKLQQLSGKLQDVRVDI 467 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhheecc
Confidence 34556666666777888888887 588888764
No 31
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=45.33 E-value=31 Score=23.71 Aligned_cols=18 Identities=39% Similarity=0.595 Sum_probs=15.5
Q ss_pred ccCCCCHHHHHHHHHHHH
Q 045481 127 PINELGLHELEQLKTAME 144 (177)
Q Consensus 127 ~l~~Ls~eeL~~l~~~Le 144 (177)
.++.|++||+..|...|+
T Consensus 86 Rle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 86 RLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHhCCHHHHHHHHHHhc
Confidence 578899999999988776
No 32
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=45.27 E-value=1.5e+02 Score=23.43 Aligned_cols=56 Identities=14% Similarity=0.251 Sum_probs=35.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhcccccCccCCCCHHHHHHHHHHHHHHHHHHHH
Q 045481 85 ANIRELNMQLTQVLHQLEVEKKHGEVLSEIRKASCRQCWWEAPINELGLHELEQLKTAMEELKKNVEQ 152 (177)
Q Consensus 85 ~~~~~l~~q~~~l~~~le~ekk~~e~l~~~~~~~~~~~~w~~~l~~Ls~eeL~~l~~~Le~~l~~V~~ 152 (177)
...++...++..+..+++..++..+.+..+.+.. =+.+|+-.++..|.+....|+.
T Consensus 125 ~~~~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka------------~~~~d~l~ie~~L~~v~~eIe~ 180 (262)
T PF14257_consen 125 ISSEDVTEQYVDLEARLKNLEAEEERLLELLEKA------------KTVEDLLEIERELSRVRSEIEQ 180 (262)
T ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhc------------CCHHHHHHHHHHHHHHHHHHHH
Confidence 3455666777777777777766666555544321 1777777777777666666543
No 33
>PF15233 SYCE1: Synaptonemal complex central element protein 1
Probab=43.39 E-value=1.2e+02 Score=21.70 Aligned_cols=12 Identities=8% Similarity=0.459 Sum_probs=6.5
Q ss_pred CChhHHHHHHhh
Q 045481 53 PNVDSILDLYLA 64 (177)
Q Consensus 53 psv~~Vl~ry~~ 64 (177)
|-+..+|.|...
T Consensus 6 P~iE~LInrIne 17 (134)
T PF15233_consen 6 PQIEDLINRINE 17 (134)
T ss_pred chHHHHHHHHHH
Confidence 555555555543
No 34
>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=43.32 E-value=22 Score=18.80 Aligned_cols=27 Identities=26% Similarity=0.512 Sum_probs=18.1
Q ss_pred HhhhcCCcEEEEEecCCCCCccc--CCCC
Q 045481 28 LSTLCGVDIALIVFSPANKAFSF--GHPN 54 (177)
Q Consensus 28 Ls~LC~vev~~Ivfsp~gk~~~f--~~ps 54 (177)
|+--|||-|-+-||...|..-.| ++|.
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrcsnpa 31 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRCSNPA 31 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEES-TT
T ss_pred cCCccCceEEEEeecCCCcEEEEEcCCCc
Confidence 56679999999999999975444 5564
No 35
>PRK01919 tatB sec-independent translocase; Provisional
Probab=42.66 E-value=1.4e+02 Score=22.33 Aligned_cols=10 Identities=40% Similarity=0.843 Sum_probs=8.4
Q ss_pred EEEEEecCCC
Q 045481 36 IALIVFSPAN 45 (177)
Q Consensus 36 v~~Ivfsp~g 45 (177)
||+|||+|..
T Consensus 15 VALiV~GPek 24 (169)
T PRK01919 15 VALVVIGPER 24 (169)
T ss_pred HHHheeCchH
Confidence 7899999964
No 36
>COG0718 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.73 E-value=61 Score=22.32 Aligned_cols=31 Identities=6% Similarity=0.073 Sum_probs=17.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 045481 132 GLHELEQLKTAMEELKKNVEQQANKILIDSK 162 (177)
Q Consensus 132 s~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~ 162 (177)
.++|..-|++.|-...+...+++++...+..
T Consensus 63 dpeD~E~LeDLi~aA~ndA~~kv~e~~~e~m 93 (105)
T COG0718 63 DPEDKEMLEDLILAAFNDAKKKVEETRKEKM 93 (105)
T ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556666666666666666555555443333
No 37
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=40.66 E-value=24 Score=25.44 Aligned_cols=23 Identities=22% Similarity=0.403 Sum_probs=18.9
Q ss_pred HhhhcCCcEEEEEecCCCCCccc
Q 045481 28 LSTLCGVDIALIVFSPANKAFSF 50 (177)
Q Consensus 28 Ls~LC~vev~~Ivfsp~gk~~~f 50 (177)
+.++|||+|-++|-+.+.+...|
T Consensus 59 ~tt~~dadvi~~v~~and~~s~f 81 (148)
T COG4917 59 ITTLQDADVIIYVHAANDPESRF 81 (148)
T ss_pred HHHhhccceeeeeecccCccccC
Confidence 67889999999999988874444
No 38
>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=40.57 E-value=1.3e+02 Score=21.34 Aligned_cols=23 Identities=13% Similarity=0.342 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 045481 134 HELEQLKTAMEELKKNVEQQANK 156 (177)
Q Consensus 134 eeL~~l~~~Le~~l~~V~~r~~~ 156 (177)
++-.+|....+..++.+...|..
T Consensus 89 ~eYk~llk~y~~~~~~L~k~I~~ 111 (126)
T PF09403_consen 89 DEYKELLKKYKDLLNKLDKEIAE 111 (126)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666666666655543
No 39
>COG4398 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.23 E-value=43 Score=27.53 Aligned_cols=38 Identities=26% Similarity=0.475 Sum_probs=31.9
Q ss_pred hhcCCcEEEEEecCCCCCcc-cCCCChh-HHHHHHhhcCC
Q 045481 30 TLCGVDIALIVFSPANKAFS-FGHPNVD-SILDLYLARNP 67 (177)
Q Consensus 30 ~LC~vev~~Ivfsp~gk~~~-f~~psv~-~Vl~ry~~~~~ 67 (177)
-+-+.-|+.++||.+|+.+- ||.|+.+ +.|++|....+
T Consensus 317 e~~~~avGaLmFsC~GRG~~m~G~p~~Ds~~~~~~~~gip 356 (389)
T COG4398 317 ELPGRAVGALLFTCNGRGRRMFGVPDHDASTIEELLGGIP 356 (389)
T ss_pred hCCCccceeEEEEecCccccccCCCCccHHHHHHHhCCCc
Confidence 46789999999999999865 8999986 88999986554
No 40
>PF04678 DUF607: Protein of unknown function, DUF607; InterPro: IPR006769 This entry represents the C-terminal domain of coiled-coil domain containing protein 109.
Probab=40.16 E-value=1e+02 Score=23.06 Aligned_cols=46 Identities=22% Similarity=0.270 Sum_probs=22.2
Q ss_pred cCCCC-hhHHHHHHhhcCCCCCCCCchhHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 045481 50 FGHPN-VDSILDLYLARNPNPPSESSTDRLIEAHRNANIRELNMQLTQVLHQLEVEKK 106 (177)
Q Consensus 50 f~~ps-v~~Vl~ry~~~~~~~~~~~~~~~~~e~~~~~~~~~l~~q~~~l~~~le~ekk 106 (177)
+-.|+ |...+.+-...... +.......+.+..+++.+..+++...+
T Consensus 32 ~L~P~~v~~~v~~~~~~~~~-----------~~~~~~~~~~l~~~l~~~~~el~~le~ 78 (180)
T PF04678_consen 32 YLRPKQVKEAVHRLLPLLNV-----------EEYQNSRERQLRKRLEELRQELAPLEK 78 (180)
T ss_pred eECHHHHHHHHHHHhccccc-----------hhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44564 66666666654422 111223344455555555555544433
No 41
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=40.07 E-value=1.4e+02 Score=22.51 Aligned_cols=14 Identities=14% Similarity=0.484 Sum_probs=11.7
Q ss_pred cCCcEEEEEecCCC
Q 045481 32 CGVDIALIVFSPAN 45 (177)
Q Consensus 32 C~vev~~Ivfsp~g 45 (177)
.++..|.|||-|+.
T Consensus 11 ~~~k~C~IC~Kpst 24 (182)
T PF08432_consen 11 TDAKACFICYKPST 24 (182)
T ss_pred CCCCceeEecCCCc
Confidence 67899999998864
No 42
>KOG3366 consensus Mitochondrial F1F0-ATP synthase, subunit d/ATP7 [Energy production and conversion]
Probab=38.01 E-value=1.7e+02 Score=21.94 Aligned_cols=15 Identities=20% Similarity=0.538 Sum_probs=11.2
Q ss_pred ccCCCCHHHHHHHHH
Q 045481 127 PINELGLHELEQLKT 141 (177)
Q Consensus 127 ~l~~Ls~eeL~~l~~ 141 (177)
+++.|+.+|+.+-.=
T Consensus 129 P~demT~ed~~ea~P 143 (172)
T KOG3366|consen 129 PFDEMTMEDLNEAFP 143 (172)
T ss_pred CcccccHHHHHHhCc
Confidence 688899988876543
No 43
>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=37.82 E-value=1.6e+02 Score=21.55 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 129 NELGLHELEQLKTAMEELKKNVEQQAN 155 (177)
Q Consensus 129 ~~Ls~eeL~~l~~~Le~~l~~V~~r~~ 155 (177)
...+.++...+........+..+.|+.
T Consensus 140 ~~vs~ee~~~~~~~~~~~~k~w~kRKr 166 (169)
T PF07106_consen 140 KPVSPEEKEKLEKEYKKWRKEWKKRKR 166 (169)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 338899999999999999999888875
No 44
>PRK00064 recF recombination protein F; Reviewed
Probab=37.05 E-value=1.6e+02 Score=24.59 Aligned_cols=38 Identities=29% Similarity=0.488 Sum_probs=26.2
Q ss_pred HHHHHhhhcCCcEEEEEecCCCCCcccCCCCh-hHHHHHHhhc
Q 045481 24 KASELSTLCGVDIALIVFSPANKAFSFGHPNV-DSILDLYLAR 65 (177)
Q Consensus 24 Ka~ELs~LC~vev~~Ivfsp~gk~~~f~~psv-~~Vl~ry~~~ 65 (177)
++++|.-+.. +|+|+|.+-....+.|+. ...||++...
T Consensus 104 ~~~~l~~~~~----~v~~~p~~~~l~~~~p~~RR~fLD~~~~~ 142 (361)
T PRK00064 104 KLAELAGLLN----VVLFTPEDLRLVKGGPSERRRFLDRLLFQ 142 (361)
T ss_pred CHHHHhhhcc----EEEEccchhhhhcCCHHHHHHHHHHHHhc
Confidence 4555554433 799999987777788875 4777777653
No 45
>PF04873 EIN3: Ethylene insensitive 3; InterPro: IPR006957 Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses. In the presence of ethylene, dark-grown dicotyledonous seedlings undergo dramatic morphological changes collectively known as the 'triple response'. In Arabidopsis, these changes consist of a radial swelling of the hypocotyl, an exaggeration in the curvature of the apical hook, and the inhibition of cell elongation in the hypocotyl and root.; GO: 0005634 nucleus; PDB: 1WIJ_A.
Probab=37.04 E-value=11 Score=31.58 Aligned_cols=49 Identities=16% Similarity=0.205 Sum_probs=0.0
Q ss_pred CcchhhhhhchhhHHHHHHHHhhhcCCcEEE-EEecCCCCCcccCCCChh
Q 045481 8 NNLQVTFSKRRAGVFKKASELSTLCGVDIAL-IVFSPANKAFSFGHPNVD 56 (177)
Q Consensus 8 ~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~-Ivfsp~gk~~~f~~psv~ 56 (177)
..|+.+=+.=..||+|=+-=..-+|+|..+| -+.+..||+.+|++|+..
T Consensus 43 q~~kr~~s~aqd~ilkym~~~m~~~n~~gfvy~~~~~~~k~~~~~s~slr 92 (354)
T PF04873_consen 43 QIRKRKMSRAQDGILKYMFPEMELCNAPGFVYTIISSSGKPVEGVSPSLR 92 (354)
T ss_dssp --------------------------------------------------
T ss_pred HHHhhhhhhhhhHHHHhhccccccccCceeeecCCCCCCCccCCcCCccc
Confidence 3344444444567777777778999999999 888899999999999875
No 46
>PRK04863 mukB cell division protein MukB; Provisional
Probab=36.87 E-value=3.7e+02 Score=27.38 Aligned_cols=31 Identities=6% Similarity=0.121 Sum_probs=21.0
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEELKKNVEQQANK 156 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~ 156 (177)
+++.+|+.++|.......+............
T Consensus 430 ~~~~~~SdEeLe~~LenF~aklee~e~qL~e 460 (1486)
T PRK04863 430 CGLPDLTADNAEDWLEEFQAKEQEATEELLS 460 (1486)
T ss_pred hCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678899999887777766666555444433
No 47
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=36.01 E-value=25 Score=24.29 Aligned_cols=26 Identities=35% Similarity=0.330 Sum_probs=20.6
Q ss_pred HHHHHhhhcCCcEEEEEecCCCCCccc
Q 045481 24 KASELSTLCGVDIALIVFSPANKAFSF 50 (177)
Q Consensus 24 Ka~ELs~LC~vev~~Ivfsp~gk~~~f 50 (177)
+..+|-.|-||-+| ..||++|++.+|
T Consensus 2 ~l~~Lm~lpGv~AA-g~Fs~~G~l~e~ 27 (108)
T PF09941_consen 2 KLDKLMKLPGVVAA-GEFSDDGKLVEY 27 (108)
T ss_pred cHHHhhcCCCeEEE-EEECCCCeEEee
Confidence 35678888888655 899999998766
No 48
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=35.92 E-value=98 Score=18.47 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 045481 137 EQLKTAMEELKKNVEQQANKIL 158 (177)
Q Consensus 137 ~~l~~~Le~~l~~V~~r~~~L~ 158 (177)
......++..+..|+++++.|-
T Consensus 35 ~~~~~~l~~~~~~i~~~i~~L~ 56 (65)
T PF09278_consen 35 ADRRALLEEKLEEIEEQIAELQ 56 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444778888888888888764
No 49
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=35.82 E-value=3.1e+02 Score=24.17 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=10.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHh
Q 045481 86 NIRELNMQLTQVLHQLEVEKKH 107 (177)
Q Consensus 86 ~~~~l~~q~~~l~~~le~ekk~ 107 (177)
.+.+.+....+++++++.++.+
T Consensus 70 ALteqQ~kasELEKqLaaLrqE 91 (475)
T PRK13729 70 ATTEMQVTAAQMQKQYEEIRRE 91 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444455555555555433
No 50
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=35.53 E-value=1e+02 Score=22.50 Aligned_cols=33 Identities=18% Similarity=0.304 Sum_probs=24.9
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 045481 126 APINELGLHELEQLKTAMEELKKNVEQQANKIL 158 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~ 158 (177)
-++..||+++|.++...+|.-+.-+..-.+.|.
T Consensus 8 idltkLsleQL~~lk~q~dqEl~~lq~Sl~~L~ 40 (153)
T KOG3048|consen 8 IDLTKLSLEQLGALKKQFDQELNFLQDSLNALK 40 (153)
T ss_pred CChhhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468889999999998888877766665555553
No 51
>KOG0432 consensus Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=35.22 E-value=62 Score=30.62 Aligned_cols=19 Identities=26% Similarity=0.303 Sum_probs=12.7
Q ss_pred HHHHHHHhhhcCCcEEEEE
Q 045481 22 FKKASELSTLCGVDIALIV 40 (177)
Q Consensus 22 ~KKa~ELs~LC~vev~~Iv 40 (177)
--.+.++++||..+.--|+
T Consensus 879 ~~~~~~i~~l~~~~~v~i~ 897 (995)
T KOG0432|consen 879 KEFLDEISTLTNLELVSIS 897 (995)
T ss_pred HHHHHHHHHhhccceeEec
Confidence 3456888888877655444
No 52
>PHA03161 hypothetical protein; Provisional
Probab=34.20 E-value=1.9e+02 Score=21.25 Aligned_cols=33 Identities=18% Similarity=0.268 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC
Q 045481 132 GLHELEQLKTAMEELKKNVEQQANKILIDSKNN 164 (177)
Q Consensus 132 s~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~~ 164 (177)
-.+.+..|.+.++++...|.-.++.|-..+.+.
T Consensus 87 kl~~~E~L~drv~eLkeel~~ELe~l~~~q~~~ 119 (150)
T PHA03161 87 KLSAAEDLQDKILELKEDIHFEIEALNHGQPSS 119 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccc
Confidence 456778888999999999999998887554443
No 53
>PRK04098 sec-independent translocase; Provisional
Probab=33.91 E-value=75 Score=23.56 Aligned_cols=11 Identities=27% Similarity=0.606 Sum_probs=8.5
Q ss_pred cEEEEEecCCC
Q 045481 35 DIALIVFSPAN 45 (177)
Q Consensus 35 ev~~Ivfsp~g 45 (177)
=||+|||+|.-
T Consensus 14 vVaLlvfGP~K 24 (158)
T PRK04098 14 VVAIIFLGPDK 24 (158)
T ss_pred HHHHhhcCchH
Confidence 47889999963
No 54
>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=33.25 E-value=78 Score=27.53 Aligned_cols=25 Identities=36% Similarity=0.591 Sum_probs=22.0
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHHHH
Q 045481 127 PINELGLHELEQLKTAMEELKKNVE 151 (177)
Q Consensus 127 ~l~~Ls~eeL~~l~~~Le~~l~~V~ 151 (177)
.+.+|+.+||.+|..-||.++++|.
T Consensus 87 kvG~LskdeLm~LasDLeKLk~Kv~ 111 (533)
T PF00843_consen 87 KVGDLSKDELMELASDLEKLKKKVQ 111 (533)
T ss_dssp EBTTB-HHHHHHHHHHHHHHHHHHH
T ss_pred EecCcCHHHHHHHHHHHHHHHHHHh
Confidence 5789999999999999999999984
No 55
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=33.15 E-value=24 Score=27.51 Aligned_cols=16 Identities=50% Similarity=0.706 Sum_probs=12.3
Q ss_pred CcEEEEEecCCCCCcc
Q 045481 34 VDIALIVFSPANKAFS 49 (177)
Q Consensus 34 vev~~Ivfsp~gk~~~ 49 (177)
-+-|+-||||+|+++.
T Consensus 4 ydraltvFSPDGhL~Q 19 (249)
T KOG0183|consen 4 YDRALTVFSPDGHLFQ 19 (249)
T ss_pred cccceEEECCCCCEEe
Confidence 3567889999998654
No 56
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.79 E-value=1.7e+02 Score=22.19 Aligned_cols=10 Identities=0% Similarity=0.195 Sum_probs=5.0
Q ss_pred EEEEEecCCC
Q 045481 36 IALIVFSPAN 45 (177)
Q Consensus 36 v~~Ivfsp~g 45 (177)
.|.|++..+.
T Consensus 75 L~~V~~~D~e 84 (198)
T KOG0861|consen 75 LCGVLIADDE 84 (198)
T ss_pred eeEEEEecCc
Confidence 3455555543
No 57
>cd01363 Motor_domain Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Probab=32.04 E-value=42 Score=25.04 Aligned_cols=24 Identities=17% Similarity=0.497 Sum_probs=17.6
Q ss_pred hhcCCcEEEEEecCCC--CCcc-cCCC
Q 045481 30 TLCGVDIALIVFSPAN--KAFS-FGHP 53 (177)
Q Consensus 30 ~LC~vev~~Ivfsp~g--k~~~-f~~p 53 (177)
++.|-.+|+++|++.| |-|+ +|.+
T Consensus 19 ~~~G~n~~i~~yG~tGsGKT~Tm~G~~ 45 (186)
T cd01363 19 ALDGYNVCIFAYGQTGSGKTYTMEGKR 45 (186)
T ss_pred HhCCcceeEEEECCCCCcceEecCCCC
Confidence 4579999999999985 5555 3444
No 58
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=31.94 E-value=1.3e+02 Score=26.17 Aligned_cols=16 Identities=19% Similarity=0.318 Sum_probs=10.5
Q ss_pred hccCCCCCcccccccc
Q 045481 160 DSKNNPSPFFGLGFWT 175 (177)
Q Consensus 160 ~~~~~~~~~~~~~~~~ 175 (177)
+.-|+-+|+.++|-|.
T Consensus 326 e~nS~wsaP~aLQ~wL 341 (575)
T KOG4403|consen 326 EANSSWSAPLALQKWL 341 (575)
T ss_pred HhccCCCCcHHHHHHH
Confidence 3344557888888883
No 59
>KOG4316 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.28 E-value=23 Score=25.88 Aligned_cols=42 Identities=21% Similarity=0.214 Sum_probs=24.5
Q ss_pred HHHhhhcCCcEEEEEec----CCC--CCcccCC-----CChhHHHHHHhhcCC
Q 045481 26 SELSTLCGVDIALIVFS----PAN--KAFSFGH-----PNVDSILDLYLARNP 67 (177)
Q Consensus 26 ~ELs~LC~vev~~Ivfs----p~g--k~~~f~~-----psv~~Vl~ry~~~~~ 67 (177)
+++++||++..-+.--. |.. ...-|+. -.|++||+||++..-
T Consensus 43 ~a~~~lcq~p~vla~r~a~~~Ps~~r~~t~Fs~~kGkrktvkaVldRFkRL~~ 95 (172)
T KOG4316|consen 43 SARNLLCQHPSVLANRMAPVLPSVVRSLTYFSARKGKRKTVKAVLDRFKRLHC 95 (172)
T ss_pred hHHHhHhcCcHHHHhccCCCCcchhhhhhhhhhhhcccccHHHHHHHHHhccc
Confidence 67889998765433111 211 1222322 248899999998764
No 60
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=31.14 E-value=50 Score=23.94 Aligned_cols=34 Identities=15% Similarity=0.202 Sum_probs=25.1
Q ss_pred cCCcEEEEEecCCCCCcccCCC-ChhHHHHHHhhc
Q 045481 32 CGVDIALIVFSPANKAFSFGHP-NVDSILDLYLAR 65 (177)
Q Consensus 32 C~vev~~Ivfsp~gk~~~f~~p-sv~~Vl~ry~~~ 65 (177)
|+...++-|..++|++..|..| .+.+|+..|=..
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h 46 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGH 46 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCC
Confidence 4455556666689999999887 588888888544
No 61
>PF07701 HNOBA: Heme NO binding associated; InterPro: IPR011645 The HNOBA (Haem NO Binding) domain is found associated with the HNOB domain and IPR001054 from INTERPRO in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a haem-dependent sensor for gaseous ligands, and transduce diverse downstream signals in both bacteria and animals.; GO: 0004383 guanylate cyclase activity, 0006182 cGMP biosynthetic process; PDB: 2P04_B 2P08_A 3HLS_E.
Probab=31.13 E-value=1.5e+02 Score=23.10 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=11.2
Q ss_pred EEecCCCCCccc-CCCChhHHHHHH
Q 045481 39 IVFSPANKAFSF-GHPNVDSILDLY 62 (177)
Q Consensus 39 Ivfsp~gk~~~f-~~psv~~Vl~ry 62 (177)
++|-|.....-| |+|.|..+=+-+
T Consensus 122 M~y~~e~~~ilFl~sP~v~~l~el~ 146 (219)
T PF07701_consen 122 MVYLEEWDSILFLGSPVVSSLEELR 146 (219)
T ss_dssp EEEETTTTEEEEEEEE---TT----
T ss_pred EEEecCCCeEEEEcccccCCHHHHH
Confidence 567777766555 788765443333
No 62
>PF03584 Herpes_ICP4_N: Herpesvirus ICP4-like protein N-terminal region; InterPro: IPR005206 The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0042025 host cell nucleus
Probab=30.84 E-value=93 Score=23.27 Aligned_cols=32 Identities=9% Similarity=0.137 Sum_probs=25.0
Q ss_pred EEEEecCCC--CCcccCCCChhHHHHHHhhcCCC
Q 045481 37 ALIVFSPAN--KAFSFGHPNVDSILDLYLARNPN 68 (177)
Q Consensus 37 ~~Ivfsp~g--k~~~f~~psv~~Vl~ry~~~~~~ 68 (177)
+-|-|++.| ++--|..|.|.+...||...+.+
T Consensus 15 grv~~Gg~Gd~R~gLwd~peV~~A~~rf~as~~p 48 (173)
T PF03584_consen 15 GRVRYGGSGDSRPGLWDDPEVREAAARFEASPGP 48 (173)
T ss_pred CceeeCCCCCCCccccCCHHHHHHHHHHHhccCC
Confidence 446677777 46668899999999999977654
No 63
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=30.71 E-value=35 Score=28.90 Aligned_cols=41 Identities=15% Similarity=0.297 Sum_probs=26.0
Q ss_pred HHHhhhcCCcEEEEEecCCCCCcccCCC-----ChhHHHHHHhhcC
Q 045481 26 SELSTLCGVDIALIVFSPANKAFSFGHP-----NVDSILDLYLARN 66 (177)
Q Consensus 26 ~ELs~LC~vev~~Ivfsp~gk~~~f~~p-----sv~~Vl~ry~~~~ 66 (177)
.-|||+||-+|---+.-.+...|-|.+| ++++.+..|...+
T Consensus 367 yalSV~~~~~V~HClIy~tatG~GFa~pyn~y~tlk~lV~hY~h~S 412 (464)
T KOG4637|consen 367 YALSVVHDGEVKHCLIYQTATGFGFAEPYNLYSTLKELVLHYQHTS 412 (464)
T ss_pred eEEEEEECCceeeeEEeeccccccccchhHHHHHHHHHHHHHhhhh
Confidence 4589999755533333344455777777 3577888887543
No 64
>PF14282 FlxA: FlxA-like protein
Probab=30.55 E-value=1.8e+02 Score=19.80 Aligned_cols=55 Identities=16% Similarity=0.218 Sum_probs=34.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhcccccCccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 045481 85 ANIRELNMQLTQVLHQLEVEKKHGEVLSEIRKASCRQCWWEAPINELGLHELEQLKTAMEELKKNVEQQANKILID 160 (177)
Q Consensus 85 ~~~~~l~~q~~~l~~~le~ekk~~e~l~~~~~~~~~~~~w~~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~ 160 (177)
..+..|..++..|..++.... .-.+|+.++-..-...|..-+..+...|.++..+
T Consensus 19 ~~I~~L~~Qi~~Lq~ql~~l~---------------------~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q 73 (106)
T PF14282_consen 19 SQIEQLQKQIKQLQEQLQELS---------------------QDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQ 73 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHH---------------------cccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666555322 1145677777777777777777777776666544
No 65
>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=29.71 E-value=26 Score=28.61 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=13.2
Q ss_pred hhhcCCcEEEEEecCC
Q 045481 29 STLCGVDIALIVFSPA 44 (177)
Q Consensus 29 s~LC~vev~~Ivfsp~ 44 (177)
.-+||+|||++||--.
T Consensus 183 ~~~~~~EICLavYek~ 198 (334)
T PF06020_consen 183 GQVSGFEICLAVYEKG 198 (334)
T ss_pred CccccceEEeeehhhh
Confidence 3479999999999754
No 66
>PRK04654 sec-independent translocase; Provisional
Probab=29.39 E-value=1.6e+02 Score=22.88 Aligned_cols=10 Identities=40% Similarity=0.876 Sum_probs=7.6
Q ss_pred EEEEEecCCC
Q 045481 36 IALIVFSPAN 45 (177)
Q Consensus 36 v~~Ivfsp~g 45 (177)
|++|||+|..
T Consensus 15 VALlV~GPer 24 (214)
T PRK04654 15 VALVVLGPER 24 (214)
T ss_pred HHHHhcCchH
Confidence 6788888854
No 67
>PRK09458 pspB phage shock protein B; Provisional
Probab=29.29 E-value=1.6e+02 Score=18.95 Aligned_cols=28 Identities=14% Similarity=0.296 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 129 NELGLHELEQLKTAMEELKKNVEQQANKI 157 (177)
Q Consensus 129 ~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L 157 (177)
.+||.+|.+.|.+ |-+.-++.++|++.|
T Consensus 34 ~~Ls~~d~~~L~~-L~~~A~rm~~RI~tL 61 (75)
T PRK09458 34 QGLSQEEQQRLAQ-LTEKAERMRERIQAL 61 (75)
T ss_pred CCCCHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 5789998866644 444456677888776
No 68
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=29.20 E-value=1.7e+02 Score=19.28 Aligned_cols=23 Identities=13% Similarity=0.364 Sum_probs=17.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Q 045481 130 ELGLHELEQLKTAMEELKKNVEQ 152 (177)
Q Consensus 130 ~Ls~eeL~~l~~~Le~~l~~V~~ 152 (177)
+++..++..-...+......|..
T Consensus 73 ~l~~~Ei~~Rr~fv~~~~~~i~~ 95 (97)
T PF09177_consen 73 NLSEEEISRRRQFVSAIRNQIKQ 95 (97)
T ss_dssp T-HHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHh
Confidence 68899998888888877777653
No 69
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=29.13 E-value=1.9e+02 Score=19.82 Aligned_cols=29 Identities=21% Similarity=0.260 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 129 NELGLHELEQLKTAMEELKKNVEQQANKI 157 (177)
Q Consensus 129 ~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L 157 (177)
.+++-+++..+...++..+++++.|+...
T Consensus 32 g~~a~~e~~~lR~r~~~~Lk~~r~rl~~~ 60 (104)
T COG4575 32 GSLAGDEAEELRSKAESALKEARDRLGDT 60 (104)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34788899999999999999998887654
No 70
>PF08557 Lipid_DES: Sphingolipid Delta4-desaturase (DES); InterPro: IPR013866 Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine []. Some proteins in this entry have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis []. This small protein associates with FA_desaturase IPR005804 from INTERPRO and appears to be specific to sphingolipid delta 4-desaturase. ; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0006633 fatty acid biosynthetic process, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=28.78 E-value=39 Score=18.87 Aligned_cols=21 Identities=38% Similarity=0.631 Sum_probs=18.4
Q ss_pred hhchhhHHHHHHHHhhhcCCc
Q 045481 15 SKRRAGVFKKASELSTLCGVD 35 (177)
Q Consensus 15 ~KRr~GL~KKa~ELs~LC~ve 35 (177)
..||.-+++|=-|+--|+|.+
T Consensus 16 ~~RRk~IL~k~PeIk~L~G~d 36 (39)
T PF08557_consen 16 ASRRKEILKKHPEIKKLMGPD 36 (39)
T ss_pred HHHHHHHHHhChHHHHHhCCC
Confidence 468999999999999999876
No 71
>PRK11637 AmiB activator; Provisional
Probab=28.60 E-value=3.7e+02 Score=22.91 Aligned_cols=31 Identities=6% Similarity=0.125 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 045481 133 LHELEQLKTAMEELKKNVEQQANKILIDSKN 163 (177)
Q Consensus 133 ~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~ 163 (177)
.+++..+...|+.....+..|+..+.+....
T Consensus 109 ~~eI~~~q~~l~~~~~~l~~rlra~Y~~g~~ 139 (428)
T PRK11637 109 NASIAKLEQQQAAQERLLAAQLDAAFRQGEH 139 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 3577788888888888888888888876543
No 72
>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=28.55 E-value=1.6e+02 Score=20.02 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=19.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 045481 131 LGLHELEQLKTAMEELKKNVEQQANKIL 158 (177)
Q Consensus 131 Ls~eeL~~l~~~Le~~l~~V~~r~~~L~ 158 (177)
|+.+++..|...|...+..+..++....
T Consensus 1 M~~~~l~~~k~~L~~~~~~L~~~i~~~~ 28 (110)
T TIGR02420 1 MSEAQLEHFRKILLRWKQELLEEADKTL 28 (110)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777777777777766666554
No 73
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=28.48 E-value=1.6e+02 Score=20.80 Aligned_cols=33 Identities=24% Similarity=0.567 Sum_probs=25.8
Q ss_pred CccCCCCHHHHHHHHHHHH-------HHHHHHHHHHHHHh
Q 045481 126 APINELGLHELEQLKTAME-------ELKKNVEQQANKIL 158 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le-------~~l~~V~~r~~~L~ 158 (177)
..+.+|+.||+..+.+.++ ++...|..-|+.|+
T Consensus 43 ~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkRl~ 82 (121)
T COG0099 43 KRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKRLM 82 (121)
T ss_pred HhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHHHH
Confidence 4578999999999999998 56666776666654
No 74
>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=28.40 E-value=2.2e+02 Score=20.31 Aligned_cols=12 Identities=33% Similarity=0.534 Sum_probs=9.9
Q ss_pred CChhHHHHHHhh
Q 045481 53 PNVDSILDLYLA 64 (177)
Q Consensus 53 psv~~Vl~ry~~ 64 (177)
+.+.+|++.|..
T Consensus 38 ~el~~iLe~y~~ 49 (132)
T PF09432_consen 38 KELQSILEKYNT 49 (132)
T ss_pred HHHHHHHHHHcC
Confidence 358899999986
No 75
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=27.75 E-value=32 Score=27.03 Aligned_cols=21 Identities=33% Similarity=0.551 Sum_probs=16.7
Q ss_pred hhhcCCcEEEEEecCCCCCcc
Q 045481 29 STLCGVDIALIVFSPANKAFS 49 (177)
Q Consensus 29 s~LC~vev~~Ivfsp~gk~~~ 49 (177)
||=.|-|.|.-+|||+|+.|.
T Consensus 3 sIGtGyDls~s~fSpdGrvfQ 23 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQ 23 (254)
T ss_pred cccccccccceeeCCCCceeh
Confidence 455678899999999998654
No 76
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=27.65 E-value=1.7e+02 Score=18.76 Aligned_cols=29 Identities=14% Similarity=0.252 Sum_probs=19.7
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 128 INELGLHELEQLKTAMEELKKNVEQQANKI 157 (177)
Q Consensus 128 l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L 157 (177)
-.+||.+|.+.| ..|-+.-.+.++|++.|
T Consensus 33 ~~gLs~~d~~~L-~~L~~~a~rm~eRI~tL 61 (75)
T PF06667_consen 33 SQGLSEEDEQRL-QELYEQAERMEERIETL 61 (75)
T ss_pred CCCCCHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 356788887555 45555566778888776
No 77
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=27.46 E-value=64 Score=28.03 Aligned_cols=28 Identities=29% Similarity=0.479 Sum_probs=22.4
Q ss_pred HHHhhhcCCcEEEEEecCCCCCcccCCC
Q 045481 26 SELSTLCGVDIALIVFSPANKAFSFGHP 53 (177)
Q Consensus 26 ~ELs~LC~vev~~Ivfsp~gk~~~f~~p 53 (177)
.+|.-.||++|+|||....|+++--|..
T Consensus 134 ~~l~~~~g~~v~vii~Dt~gr~~r~g~~ 161 (448)
T PRK13294 134 AGLRERLGVDVAVVVTDTMGRAWRNGQT 161 (448)
T ss_pred HHHHHHHCCCEEEEEecCCCCccccCcc
Confidence 3566789999999999999977666554
No 78
>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=27.37 E-value=2.3e+02 Score=20.87 Aligned_cols=17 Identities=29% Similarity=0.419 Sum_probs=10.8
Q ss_pred hhhhhchhhHHHHHHHH
Q 045481 12 VTFSKRRAGVFKKASEL 28 (177)
Q Consensus 12 ~Tf~KRr~GL~KKa~EL 28 (177)
..|++|-.++..++..|
T Consensus 28 ~afk~r~d~~~~~v~~~ 44 (161)
T PF05873_consen 28 QAFKKRSDEYKRRVSKL 44 (161)
T ss_dssp HHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 35666766766666654
No 79
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=27.32 E-value=3.5e+02 Score=22.21 Aligned_cols=31 Identities=26% Similarity=0.455 Sum_probs=22.9
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 127 PINELGLHELEQLKTAMEELKKNVEQQANKI 157 (177)
Q Consensus 127 ~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L 157 (177)
.++..+.++|..+...|......|..+...+
T Consensus 202 e~~~~D~~eL~~lr~eL~~~~~~i~~~k~~l 232 (325)
T PF08317_consen 202 EIESCDQEELEALRQELAEQKEEIEAKKKEL 232 (325)
T ss_pred hhhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4777888888888888887777776554443
No 80
>PLN03237 DNA topoisomerase 2; Provisional
Probab=27.11 E-value=6.9e+02 Score=25.53 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=26.4
Q ss_pred hhhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCChhHHHHHHhhc
Q 045481 18 RAGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPNVDSILDLYLAR 65 (177)
Q Consensus 18 r~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~psv~~Vl~ry~~~ 65 (177)
.+||+|+ ..|.+.-++ --+++|.++|+...| .++.+||..|...
T Consensus 971 ~~~L~k~-~kL~~s~~~-~nm~l~d~~G~i~k~--~~~~~Il~~F~~~ 1014 (1465)
T PLN03237 971 QEGLLKK-FKLTTTIST-SNMHLFDSKGVIKKY--DTPEQILEEFFHL 1014 (1465)
T ss_pred HHHHHHh-hcCcceece-eEEEEEcCCCCccee--CCHHHHHHHHHHH
Confidence 4566643 333333222 367889888875544 4667888888753
No 81
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.86 E-value=3.4e+02 Score=21.92 Aligned_cols=31 Identities=16% Similarity=0.350 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhccCC
Q 045481 134 HELEQLKTAMEELKKNVEQQANKILIDSKNN 164 (177)
Q Consensus 134 eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~~ 164 (177)
.++..+...|.+....+..|...+...+.+.
T Consensus 87 ~eI~~~~~~I~~r~~~l~~raRAmq~nG~~t 117 (265)
T COG3883 87 KEIAELKENIVERQELLKKRARAMQVNGTAT 117 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChh
Confidence 3566777778888888888888877766654
No 82
>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=26.81 E-value=18 Score=28.30 Aligned_cols=29 Identities=21% Similarity=0.488 Sum_probs=21.6
Q ss_pred HHHhhhcCCcEEEEEecCCCCCcccCCCC
Q 045481 26 SELSTLCGVDIALIVFSPANKAFSFGHPN 54 (177)
Q Consensus 26 ~ELs~LC~vev~~Ivfsp~gk~~~f~~ps 54 (177)
.+|--.||++|+|||-.++|+++-.|.+.
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 46677899999999999999988887664
No 83
>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=26.79 E-value=3e+02 Score=21.26 Aligned_cols=28 Identities=11% Similarity=0.164 Sum_probs=18.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045481 132 GLHELEQLKTAMEELKKNVEQQANKILI 159 (177)
Q Consensus 132 s~eeL~~l~~~Le~~l~~V~~r~~~L~~ 159 (177)
..+.|..+...++..+..++..++.+-.
T Consensus 137 ~n~~Le~~~~~le~~l~~~k~~ie~vN~ 164 (221)
T PF05700_consen 137 HNEQLEAMLKRLEKELAKLKKEIEEVNR 164 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466677777777777777766666543
No 84
>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=26.46 E-value=2.5e+02 Score=20.15 Aligned_cols=30 Identities=23% Similarity=0.433 Sum_probs=24.6
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEELKKNVEQQAN 155 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~ 155 (177)
-++++++.+||.++...+++.-..-+.+..
T Consensus 90 i~iE~l~~~el~~~~~~~~~~~~~~~~~~~ 119 (132)
T PF04120_consen 90 IDIEDLTEEELEEIRKRYERLAEQARERHD 119 (132)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHHhhhhcc
Confidence 479999999999999999888777665543
No 85
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=26.08 E-value=2.2e+02 Score=22.71 Aligned_cols=10 Identities=30% Similarity=0.315 Sum_probs=5.5
Q ss_pred HHHHHHhhcC
Q 045481 57 SILDLYLARN 66 (177)
Q Consensus 57 ~Vl~ry~~~~ 66 (177)
+++++-.+.+
T Consensus 194 e~lnk~~~l~ 203 (244)
T COG1938 194 EALNKMLGLN 203 (244)
T ss_pred HHHHHHhcCc
Confidence 4556655544
No 86
>PF11944 DUF3461: Protein of unknown function (DUF3461); InterPro: IPR020911 This entry describes proteins of unknown function.
Probab=25.98 E-value=1e+02 Score=21.86 Aligned_cols=25 Identities=20% Similarity=0.426 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 133 LHELEQLKTAMEELKKNVEQQANKI 157 (177)
Q Consensus 133 ~eeL~~l~~~Le~~l~~V~~r~~~L 157 (177)
++||.-|+..+..+...|++.++.|
T Consensus 101 L~dL~HLE~Vv~~KIaEIe~dlekL 125 (125)
T PF11944_consen 101 LDDLRHLEKVVNSKIAEIERDLEKL 125 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 5688889999999999999888753
No 87
>PRK10132 hypothetical protein; Provisional
Probab=25.97 E-value=2.3e+02 Score=19.53 Aligned_cols=25 Identities=16% Similarity=0.121 Sum_probs=16.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 131 LGLHELEQLKTAMEELKKNVEQQAN 155 (177)
Q Consensus 131 Ls~eeL~~l~~~Le~~l~~V~~r~~ 155 (177)
.+-+++..+...++..+...+++..
T Consensus 38 ~~~~~~~~lR~r~~~~L~~ar~~l~ 62 (108)
T PRK10132 38 DAKGEAEAARRKAQALLKETRARMH 62 (108)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4556677777777777777765554
No 88
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=25.75 E-value=1.2e+02 Score=20.49 Aligned_cols=35 Identities=11% Similarity=0.216 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCc
Q 045481 134 HELEQLKTAMEELKKNVEQQANKILIDSKNNPSPF 168 (177)
Q Consensus 134 eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~~~~~~ 168 (177)
++...|++.|-...+....+..+...+......|+
T Consensus 64 ~d~e~LedlI~~A~N~A~~k~~~~~~e~~t~gl~~ 98 (102)
T TIGR00103 64 EDKEALEDMITEALNDAVKKVEETYKELMTSGMPL 98 (102)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence 45556666666666666666665555544444554
No 89
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=25.63 E-value=58 Score=22.05 Aligned_cols=29 Identities=34% Similarity=0.383 Sum_probs=22.1
Q ss_pred HHHHHHhhhcCCcEEEEEecCCCCCcccCC
Q 045481 23 KKASELSTLCGVDIALIVFSPANKAFSFGH 52 (177)
Q Consensus 23 KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~ 52 (177)
-|..||--+-||=+| =.|||+||+-.|-.
T Consensus 3 ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykg 31 (109)
T COG4831 3 EKLDELLQIKGVMAA-GEFSPDGKLVEYKG 31 (109)
T ss_pred hhHHHHhCccceeEe-ceeCCCCceEEeeC
Confidence 467788877787555 67999999887754
No 90
>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=25.42 E-value=2.4e+02 Score=19.75 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 045481 132 GLHELEQLKTAMEELKKNVEQQANKIL 158 (177)
Q Consensus 132 s~eeL~~l~~~Le~~l~~V~~r~~~L~ 158 (177)
-.|+..+|..-|.+++...+..++.|+
T Consensus 94 K~E~veEL~~Dv~DlK~myr~Qi~~lv 120 (120)
T PF12325_consen 94 KSEEVEELRADVQDLKEMYREQIDQLV 120 (120)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 557777888888888888888877653
No 91
>cd00468 HIT_like HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups.
Probab=25.31 E-value=1.3e+02 Score=18.72 Aligned_cols=26 Identities=15% Similarity=0.236 Sum_probs=20.0
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEELKKNVE 151 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~ 151 (177)
.++.+|+.+++.++...+....+.++
T Consensus 30 ~~~~~l~~~~~~~l~~~~~~~~~~l~ 55 (86)
T cd00468 30 ETLPDLDEALLADLVITAQRVAAELE 55 (86)
T ss_pred CChhHCCHHHHHHHHHHHHHHHHHHH
Confidence 36788999999888888777766654
No 92
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=24.89 E-value=50 Score=30.03 Aligned_cols=22 Identities=18% Similarity=0.274 Sum_probs=20.0
Q ss_pred hhhcCCcEEEEEecCCCCCccc
Q 045481 29 STLCGVDIALIVFSPANKAFSF 50 (177)
Q Consensus 29 s~LC~vev~~Ivfsp~gk~~~f 50 (177)
+||.|+.++||+|.++|..+.+
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~ 395 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTV 395 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEee
Confidence 5999999999999999987775
No 93
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=24.73 E-value=1e+02 Score=19.52 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=28.3
Q ss_pred hhHHHHHHHHhhhcCCcEEEEEecCCCCCccc
Q 045481 19 AGVFKKASELSTLCGVDIALIVFSPANKAFSF 50 (177)
Q Consensus 19 ~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f 50 (177)
.++..+..++-++.|++|-++-.+|.|.|..+
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i 51 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHI 51 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEE
Confidence 55889999999999999999999998877655
No 94
>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=24.71 E-value=78 Score=20.71 Aligned_cols=31 Identities=16% Similarity=0.300 Sum_probs=23.0
Q ss_pred hHHHHHHHHhhhc----CCcEEEEEecCCCCCccc
Q 045481 20 GVFKKASELSTLC----GVDIALIVFSPANKAFSF 50 (177)
Q Consensus 20 GL~KKa~ELs~LC----~vev~~Ivfsp~gk~~~f 50 (177)
-+++.|-+++... +..|+.||++|+|+....
T Consensus 6 ~~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~ 40 (102)
T PF00383_consen 6 EFMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIAT 40 (102)
T ss_dssp HHHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEE
T ss_pred HHHHHHHHHHHhccccCCCCEEEEEEeccCccEEE
Confidence 3567777777666 899999999988764433
No 95
>PTZ00108 DNA topoisomerase 2-like protein; Provisional
Probab=24.66 E-value=7.5e+02 Score=25.13 Aligned_cols=27 Identities=15% Similarity=0.317 Sum_probs=19.6
Q ss_pred EEEEecCCCCCcccCCCChhHHHHHHhhc
Q 045481 37 ALIVFSPANKAFSFGHPNVDSILDLYLAR 65 (177)
Q Consensus 37 ~~Ivfsp~gk~~~f~~psv~~Vl~ry~~~ 65 (177)
-+++|.++|+...| .++.+||+.|...
T Consensus 962 Nm~~~d~~g~i~~~--~~~~~Il~~f~~~ 988 (1388)
T PTZ00108 962 NMVLFDENGKIKKY--SDALDILKEFYLV 988 (1388)
T ss_pred eEEEEeCCCCccee--CCHHHHHHHHHHH
Confidence 67889999875544 4566888888653
No 96
>PF08796 DUF1797: Protein of unknown function (DUF1797); InterPro: IPR014904 The function of this protein is unknown. It forms a central anti-parallel beta sheet with flanking alpha helical regions. ; PDB: 2FFG_B.
Probab=24.65 E-value=51 Score=20.76 Aligned_cols=19 Identities=16% Similarity=0.562 Sum_probs=15.5
Q ss_pred cCCcEEEEEecCCCCCccc
Q 045481 32 CGVDIALIVFSPANKAFSF 50 (177)
Q Consensus 32 C~vev~~Ivfsp~gk~~~f 50 (177)
-|+++|.|.|.|....|+.
T Consensus 24 ~G~~~c~V~y~~~t~~F~l 42 (67)
T PF08796_consen 24 EGVEVCTVTYDQETETFEL 42 (67)
T ss_dssp TTEEEEEEEEETTTTEEEE
T ss_pred CCEEEEEEEEECCCCeEEE
Confidence 5899999999998775554
No 97
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=24.62 E-value=1.4e+02 Score=24.40 Aligned_cols=42 Identities=24% Similarity=0.376 Sum_probs=27.8
Q ss_pred cccCCCCcchhhhhhchhhHHHHHHHHhhhcCCcEEEEEecCCCCCccc-CCCChhHHHHHHhh
Q 045481 2 SKIPKKNNLQVTFSKRRAGVFKKASELSTLCGVDIALIVFSPANKAFSF-GHPNVDSILDLYLA 64 (177)
Q Consensus 2 k~I~n~~~R~~Tf~KRr~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f-~~psv~~Vl~ry~~ 64 (177)
-.|.|...|..+=+ | .||..|.+ |.| .| ..|.|++|++.|..
T Consensus 27 ~li~n~tqr~t~~s-R------------~L~Ecel~---~~p-----~Y~nDpEmK~iid~~n~ 69 (295)
T TIGR01478 27 SYIQNNTQMTSTKS-R------------LLAEIQRP---KNP-----HYHNDPELKEIIDKLNE 69 (295)
T ss_pred ecccCccccccccc-e------------ehhhhccc---cCC-----CCCCcHHHHHHHHHHhH
Confidence 35677777666532 2 46877765 444 23 35999999999875
No 98
>PRK13291 metal-dependent hydrolase; Provisional
Probab=24.52 E-value=1.6e+02 Score=21.77 Aligned_cols=47 Identities=15% Similarity=0.327 Sum_probs=28.9
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCccccccccc
Q 045481 127 PINELGLHELEQLKTAMEELKKNVEQQANKILIDSKNNPSPFFGLGFWTL 176 (177)
Q Consensus 127 ~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~~~~~~~~~~~~~~ 176 (177)
..+..+.+++.++...|+.....+..-+..|--++.+.. ++.|-||.
T Consensus 13 ~~~~~~~~~~~~~i~~l~~~~~~l~~~l~~lsee~l~~~---~~~gkWSi 59 (173)
T PRK13291 13 YPEEITEEQIQEWIAEIEALPNELRAAVSGLSDEQLDTP---YREGGWTV 59 (173)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHcCC---CCCCCCcH
Confidence 456667777777777777777777766666554544332 23445653
No 99
>COG3411 Ferredoxin [Energy production and conversion]
Probab=24.50 E-value=65 Score=20.08 Aligned_cols=30 Identities=17% Similarity=0.265 Sum_probs=22.7
Q ss_pred EEEEecCCCCCcccCCC-ChhHHHHHHhhcC
Q 045481 37 ALIVFSPANKAFSFGHP-NVDSILDLYLARN 66 (177)
Q Consensus 37 ~~Ivfsp~gk~~~f~~p-sv~~Vl~ry~~~~ 66 (177)
+++++.|+|-.|....| .++.|++......
T Consensus 18 Pvl~vYpegvWY~~V~p~~a~rIv~~hl~~G 48 (64)
T COG3411 18 PVLVVYPEGVWYTRVDPEDARRIVQSHLLGG 48 (64)
T ss_pred CEEEEecCCeeEeccCHHHHHHHHHHHHhCC
Confidence 46777888988888776 5788888887643
No 100
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=24.35 E-value=2.3e+02 Score=18.96 Aligned_cols=25 Identities=32% Similarity=0.422 Sum_probs=17.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 132 GLHELEQLKTAMEELKKNVEQQANK 156 (177)
Q Consensus 132 s~eeL~~l~~~Le~~l~~V~~r~~~ 156 (177)
+..+|.+....|+..-+.+..|+..
T Consensus 74 ~V~~LE~~v~~LD~ysk~LE~k~k~ 98 (99)
T PF10046_consen 74 QVTELEQTVYELDEYSKELESKFKK 98 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5566777777777777777776653
No 101
>PRK00295 hypothetical protein; Provisional
Probab=24.16 E-value=1.9e+02 Score=18.02 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=13.5
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHhh
Q 045481 83 RNANIRELNMQLTQVLHQLEVEKKHG 108 (177)
Q Consensus 83 ~~~~~~~l~~q~~~l~~~le~ekk~~ 108 (177)
....++.||..+.+.+++++...+..
T Consensus 17 qE~tie~Ln~~v~~Qq~~I~~L~~ql 42 (68)
T PRK00295 17 QDDTIQALNDVLVEQQRVIERLQLQM 42 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556655555555555444433
No 102
>PRK00736 hypothetical protein; Provisional
Probab=24.05 E-value=1.9e+02 Score=18.01 Aligned_cols=27 Identities=26% Similarity=0.329 Sum_probs=14.5
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHhhh
Q 045481 83 RNANIRELNMQLTQVLHQLEVEKKHGE 109 (177)
Q Consensus 83 ~~~~~~~l~~q~~~l~~~le~ekk~~e 109 (177)
....++.||..+.+..++++...++..
T Consensus 17 qe~tie~Ln~~v~~Qq~~i~~L~~ql~ 43 (68)
T PRK00736 17 QEKTIEELSDQLAEQWKTVEQMRKKLD 43 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666665555555555444433
No 103
>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=23.68 E-value=1.3e+02 Score=20.08 Aligned_cols=23 Identities=26% Similarity=0.475 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Q 045481 130 ELGLHELEQLKTAMEELKKNVEQ 152 (177)
Q Consensus 130 ~Ls~eeL~~l~~~Le~~l~~V~~ 152 (177)
.+++++|+.|...|++..+.+..
T Consensus 70 ~c~~e~L~~Li~~Lk~A~~~~e~ 92 (95)
T cd04751 70 TCTLEQLQDLVNKLKDAAKNIER 92 (95)
T ss_pred EeCHHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999988888764
No 104
>PRK10722 hypothetical protein; Provisional
Probab=23.51 E-value=3.7e+02 Score=21.46 Aligned_cols=31 Identities=26% Similarity=0.378 Sum_probs=16.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 045481 86 NIRELNMQLTQVLHQLEVEKKHGEVLSEIRK 116 (177)
Q Consensus 86 ~~~~l~~q~~~l~~~le~ekk~~e~l~~~~~ 116 (177)
.++.+..|...++.+++....++|.|..|.+
T Consensus 177 qlD~lrqq~~~Lq~~L~~t~rKLEnLTdIER 207 (247)
T PRK10722 177 ELDALRQQQQRLQYQLELTTRKLENLTDIER 207 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555555555555555555444
No 105
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=23.47 E-value=63 Score=23.63 Aligned_cols=18 Identities=39% Similarity=0.645 Sum_probs=14.8
Q ss_pred cCCCCHHHHHHHHHHHHH
Q 045481 128 INELGLHELEQLKTAMEE 145 (177)
Q Consensus 128 l~~Ls~eeL~~l~~~Le~ 145 (177)
|..||.+||.+|...|+.
T Consensus 21 L~~LS~EEL~~L~~el~e 38 (147)
T PF03250_consen 21 LAKLSPEELEELENELEE 38 (147)
T ss_pred HHhCCHHHHHHHHHHHHh
Confidence 678999999999977654
No 106
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=23.36 E-value=2.6e+02 Score=19.38 Aligned_cols=14 Identities=21% Similarity=0.299 Sum_probs=9.8
Q ss_pred CCHHHHHHHHHHHH
Q 045481 131 LGLHELEQLKTAME 144 (177)
Q Consensus 131 Ls~eeL~~l~~~Le 144 (177)
.+.|+|.+|...+.
T Consensus 97 ~spe~L~ql~~~~~ 110 (123)
T KOG4797|consen 97 ASPEQLAQLPAQLS 110 (123)
T ss_pred CCHHHHHHHHHhcc
Confidence 47788877766554
No 107
>PF11232 Med25: Mediator complex subunit 25 PTOV activation and synapsin 2; InterPro: IPR021394 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear []. ; PDB: 2KY6_A 2L23_A 2XNF_A 2L6U_A.
Probab=23.16 E-value=60 Score=23.92 Aligned_cols=19 Identities=32% Similarity=0.864 Sum_probs=15.1
Q ss_pred hhcCCcEEEEEecCCCCCc
Q 045481 30 TLCGVDIALIVFSPANKAF 48 (177)
Q Consensus 30 ~LC~vev~~Ivfsp~gk~~ 48 (177)
.-|++.|-+++|||.-+.|
T Consensus 109 p~c~iKvL~LlYs~kk~~f 127 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKAF 127 (152)
T ss_dssp SSSS-SEEEEEEETTTTEE
T ss_pred CCCceEEEEEEEcCCCceE
Confidence 4699999999999988744
No 108
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=22.75 E-value=2.5e+02 Score=20.36 Aligned_cols=20 Identities=35% Similarity=0.466 Sum_probs=15.7
Q ss_pred CccCCCCHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEE 145 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~ 145 (177)
..+.+|+.+|+..|...|+.
T Consensus 47 ~~~~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 47 AKLGYLDDEEIEKLEEAVEN 66 (144)
T ss_pred CCcccCCHHHHHHHHHHHHh
Confidence 45778888888888888865
No 109
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=22.73 E-value=2.7e+02 Score=19.27 Aligned_cols=34 Identities=18% Similarity=0.450 Sum_probs=26.3
Q ss_pred CccCCCCHHHHHHHHHHHH-------HHHHHHHHHHHHHhh
Q 045481 126 APINELGLHELEQLKTAME-------ELKKNVEQQANKILI 159 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le-------~~l~~V~~r~~~L~~ 159 (177)
..+.+|+.+|+..|...|+ ++...+++-|+.|..
T Consensus 41 ~~~~~L~~~qi~~l~~~l~~~~~i~~~L~~~~~~dI~rl~~ 81 (113)
T TIGR03631 41 KRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIKRLMD 81 (113)
T ss_pred cccccCCHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHH
Confidence 4578999999999999994 566667777777643
No 110
>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=22.36 E-value=1.1e+02 Score=25.33 Aligned_cols=36 Identities=22% Similarity=0.540 Sum_probs=23.8
Q ss_pred hhHHHHHH-HH--hhhcCCcEEEEEecCCC--CCcc-cCCCC
Q 045481 19 AGVFKKAS-EL--STLCGVDIALIVFSPAN--KAFS-FGHPN 54 (177)
Q Consensus 19 ~GL~KKa~-EL--s~LC~vev~~Ivfsp~g--k~~~-f~~ps 54 (177)
.-+|+.+. ++ +++-|..+||++|+++| |-|+ ||.+.
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 34555543 22 36789999999999976 5555 46543
No 111
>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=21.85 E-value=5.5e+02 Score=22.54 Aligned_cols=16 Identities=25% Similarity=-0.037 Sum_probs=8.6
Q ss_pred CCCHHHHHHHHHHHHH
Q 045481 130 ELGLHELEQLKTAMEE 145 (177)
Q Consensus 130 ~Ls~eeL~~l~~~Le~ 145 (177)
..+.+++.++...+..
T Consensus 123 ~~~~~~~~~~~~~~~~ 138 (525)
T TIGR02231 123 EPDLKEWFQAFDFNGS 138 (525)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 4456666665544433
No 112
>PF13252 DUF4043: Protein of unknown function (DUF4043)
Probab=21.85 E-value=43 Score=27.97 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=17.0
Q ss_pred HHHhhhcCCcEEEEEecCCCC
Q 045481 26 SELSTLCGVDIALIVFSPANK 46 (177)
Q Consensus 26 ~ELs~LC~vev~~Ivfsp~gk 46 (177)
-.-+.|||+.++++.|+..+.
T Consensus 272 v~ralLlGaQA~~~A~G~~~~ 292 (341)
T PF13252_consen 272 VARALLLGAQALVIAFGKSGS 292 (341)
T ss_pred eeeeeeechhheeeeeeccCC
Confidence 345789999999999998443
No 113
>PRK04406 hypothetical protein; Provisional
Probab=21.80 E-value=2.3e+02 Score=18.09 Aligned_cols=20 Identities=30% Similarity=0.227 Sum_probs=8.3
Q ss_pred hhHHHHHHHHHHHHHHHHHH
Q 045481 85 ANIRELNMQLTQVLHQLEVE 104 (177)
Q Consensus 85 ~~~~~l~~q~~~l~~~le~e 104 (177)
..++.||..+.+.+.+++..
T Consensus 25 ~tIe~LN~~v~~Qq~~I~~L 44 (75)
T PRK04406 25 QTIEELNDALSQQQLLITKM 44 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444333
No 114
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=21.79 E-value=58 Score=29.66 Aligned_cols=44 Identities=25% Similarity=0.414 Sum_probs=36.5
Q ss_pred hhHHHHHHHHhhhcCCcEEEEEecCCCCCcccCCCChhHHHHHHh
Q 045481 19 AGVFKKASELSTLCGVDIALIVFSPANKAFSFGHPNVDSILDLYL 63 (177)
Q Consensus 19 ~GL~KKa~ELs~LC~vev~~Ivfsp~gk~~~f~~psv~~Vl~ry~ 63 (177)
.++++++.||++==-+++.++=||.. .|+.-+.|.|...|.-|-
T Consensus 446 ~e~i~t~~elTvgDtsp~~L~EySEe-~P~~Lsn~GMas~l~nYY 489 (968)
T COG5179 446 QEIIKTAGELTVGDTSPFSLFEYSEE-EPFFLSNPGMASLLNNYY 489 (968)
T ss_pred hhhhccccceeccCCCceeeeeeccc-CceeecCchHHHHHHHHH
Confidence 68999999999999999999999984 566667899877666664
No 115
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=21.67 E-value=1.6e+02 Score=19.17 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=18.9
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEELKKNVEQ 152 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~~ 152 (177)
.++.+|+.+++.+|...+....+.++.
T Consensus 46 ~~~~~l~~~e~~~l~~~~~~v~~~l~~ 72 (103)
T cd01277 46 ENLLDLDPEELAELILAAKKVARALKK 72 (103)
T ss_pred CChhhCCHHHHHHHHHHHHHHHHHHHH
Confidence 368889999888777666665555543
No 116
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=21.65 E-value=2.1e+02 Score=17.61 Aligned_cols=21 Identities=29% Similarity=0.482 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q 045481 89 ELNMQLTQVLHQLEVEKKHGE 109 (177)
Q Consensus 89 ~l~~q~~~l~~~le~ekk~~e 109 (177)
.++.++..+..+++..+++++
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~ 41 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENE 41 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444333
No 117
>PRK04325 hypothetical protein; Provisional
Probab=21.36 E-value=2.3e+02 Score=17.96 Aligned_cols=25 Identities=16% Similarity=0.256 Sum_probs=12.1
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHh
Q 045481 83 RNANIRELNMQLTQVLHQLEVEKKH 107 (177)
Q Consensus 83 ~~~~~~~l~~q~~~l~~~le~ekk~ 107 (177)
....++.|+..+.+.+.+++...+.
T Consensus 21 QE~tIe~LN~vv~~Qq~~I~~L~~q 45 (74)
T PRK04325 21 QEDLIDGLNATVARQQQTLDLLQAQ 45 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345555555555555444444433
No 118
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=21.31 E-value=6.7e+02 Score=23.35 Aligned_cols=67 Identities=16% Similarity=0.258 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhcccccCccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 045481 84 NANIRELNMQLTQVLHQLEVEKKHGEVLSEIRKASCRQCWWEAPINELGLHELEQLKTAMEELKKNVEQQANKILIDSKN 163 (177)
Q Consensus 84 ~~~~~~l~~q~~~l~~~le~ekk~~e~l~~~~~~~~~~~~w~~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~ 163 (177)
...+..+..+.+++..++...+.+.+.+.. +.+.|.+=...+.+..+.+..|++.++..- .
T Consensus 564 ~~rv~~Lk~~~e~Ql~~L~~l~e~~~~l~~------------------~ae~LaeR~e~a~d~Qe~L~~R~~~vl~~l-~ 624 (717)
T PF10168_consen 564 QRRVKLLKQQKEQQLKELQELQEERKSLRE------------------SAEKLAERYEEAKDKQEKLMKRVDRVLQLL-N 624 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-h
Q ss_pred CCCCcc
Q 045481 164 NPSPFF 169 (177)
Q Consensus 164 ~~~~~~ 169 (177)
..+|.+
T Consensus 625 ~~~P~L 630 (717)
T PF10168_consen 625 SQLPVL 630 (717)
T ss_pred ccCCCC
No 119
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=21.26 E-value=1e+02 Score=27.23 Aligned_cols=25 Identities=20% Similarity=0.182 Sum_probs=14.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhH
Q 045481 86 NIRELNMQLTQVLHQLEVEKKHGEV 110 (177)
Q Consensus 86 ~~~~l~~q~~~l~~~le~ekk~~e~ 110 (177)
++++|.+|+++|+++++..+++.++
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v~k 56 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRVDK 56 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccccch
Confidence 5666666666666666654444433
No 120
>PF13991 BssS: BssS protein family
Probab=21.22 E-value=1.6e+02 Score=18.84 Aligned_cols=26 Identities=19% Similarity=0.072 Sum_probs=21.3
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHH
Q 045481 127 PINELGLHELEQLKTAMEELKKNVEQ 152 (177)
Q Consensus 127 ~l~~Ls~eeL~~l~~~Le~~l~~V~~ 152 (177)
..-.|+.+..++|...|++.+.+++.
T Consensus 38 ~~~~lT~e~Ar~Li~~L~~~I~kiE~ 63 (73)
T PF13991_consen 38 RTYWLTTEMARQLISILEAGIDKIES 63 (73)
T ss_pred ceeEecHHHHHHHHHHHHHHHHHHHh
Confidence 34558999999999999998887753
No 121
>PRK00587 hypothetical protein; Provisional
Probab=21.18 E-value=1.5e+02 Score=20.07 Aligned_cols=40 Identities=15% Similarity=0.040 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCC-CCccc
Q 045481 131 LGLHELEQLKTAMEELKKNVEQQANKILIDSKNNP-SPFFG 170 (177)
Q Consensus 131 Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~~~~~~-~~~~~ 170 (177)
+..+|..-|++.|-...+....++++...+..... .++.|
T Consensus 57 ld~eD~E~LeDLI~aA~NdA~~k~~e~~~e~m~~~~~~~~~ 97 (99)
T PRK00587 57 IDPEDKETLQDMLREAINEAISITCKERDAIMNSTIPKGTG 97 (99)
T ss_pred cCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 45567777777777777776666666555544433 34444
No 122
>PLN03230 acetyl-coenzyme A carboxylase carboxyl transferase; Provisional
Probab=21.13 E-value=5.6e+02 Score=22.31 Aligned_cols=12 Identities=17% Similarity=0.277 Sum_probs=8.1
Q ss_pred HHHHHHhhcCCC
Q 045481 57 SILDLYLARNPN 68 (177)
Q Consensus 57 ~Vl~ry~~~~~~ 68 (177)
..+.+|+-....
T Consensus 59 ~~~~~~~~~~~~ 70 (431)
T PLN03230 59 KILNRFKPLKNK 70 (431)
T ss_pred HHHHhcCCCCCC
Confidence 478888766544
No 123
>cd07665 BAR_SNX1 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization
Probab=21.11 E-value=75 Score=25.10 Aligned_cols=29 Identities=10% Similarity=0.103 Sum_probs=19.5
Q ss_pred HhhhhHHHHHHHHHHHHHHHHHHHHhhhH
Q 045481 82 HRNANIRELNMQLTQVLHQLEVEKKHGEV 110 (177)
Q Consensus 82 ~~~~~~~~l~~q~~~l~~~le~ekk~~e~ 110 (177)
.+...+..|..++.++.+.++..-++...
T Consensus 26 ~k~~~ie~LE~qLk~L~k~~~~lv~~r~e 54 (234)
T cd07665 26 EKLQEVECEEQRLRKLHAVVETLVNHRKE 54 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35567778888888877777766554433
No 124
>PTZ00046 rifin; Provisional
Probab=21.04 E-value=4.1e+02 Score=22.51 Aligned_cols=28 Identities=18% Similarity=0.629 Sum_probs=20.2
Q ss_pred hhcCCcEEEEEecCCCCCcccC-CCChhHHHHHHhhcC
Q 045481 30 TLCGVDIALIVFSPANKAFSFG-HPNVDSILDLYLARN 66 (177)
Q Consensus 30 ~LC~vev~~Ivfsp~gk~~~f~-~psv~~Vl~ry~~~~ 66 (177)
+||..|. |+|+ |. .|.|+.|.+.|.+..
T Consensus 40 ~LcECeL----Y~pn-----YDNDPeMK~Vme~F~rqT 68 (358)
T PTZ00046 40 LLCECEL----YSSN-----YDNDPEMKSVMENFDRQT 68 (358)
T ss_pred hhhhhhc----CCCC-----CCCcHHHHHHHHHHhHHH
Confidence 5787775 5552 33 499999999997654
No 125
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=21.03 E-value=3.2e+02 Score=19.44 Aligned_cols=11 Identities=27% Similarity=0.359 Sum_probs=6.9
Q ss_pred ChhHHHHHHhh
Q 045481 54 NVDSILDLYLA 64 (177)
Q Consensus 54 sv~~Vl~ry~~ 64 (177)
+++.|+..|..
T Consensus 23 d~~~v~~~~~~ 33 (158)
T PF03938_consen 23 DVDKVFQESPA 33 (158)
T ss_dssp -HHHHHHHHHH
T ss_pred eHHHHHHhCHH
Confidence 46677777754
No 126
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=20.62 E-value=2.3e+02 Score=17.60 Aligned_cols=27 Identities=22% Similarity=0.276 Sum_probs=14.6
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHhhh
Q 045481 83 RNANIRELNMQLTQVLHQLEVEKKHGE 109 (177)
Q Consensus 83 ~~~~~~~l~~q~~~l~~~le~ekk~~e 109 (177)
....++.|+..+.+...+++..+....
T Consensus 16 qe~~ie~Ln~~v~~Qq~~I~~L~~~l~ 42 (69)
T PF04102_consen 16 QEDTIEELNDVVTEQQRQIDRLQRQLR 42 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444556666655555555555544433
No 127
>PF06296 DUF1044: Protein of unknown function (DUF1044); InterPro: IPR009387 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.47 E-value=2.3e+02 Score=19.90 Aligned_cols=35 Identities=23% Similarity=0.292 Sum_probs=30.2
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 045481 127 PINELGLHELEQLKTAMEELKKNVEQQANKILIDS 161 (177)
Q Consensus 127 ~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~~L~~~~ 161 (177)
.-+++|.+|+..|......++.--.+.++.++...
T Consensus 81 ~~~nis~~El~~lk~la~~l~~~~~~~l~~~i~~g 115 (120)
T PF06296_consen 81 EKANISDKELKALKKLAKELLNLSEEQLETLIANG 115 (120)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHhCHHHHHHHHHcC
Confidence 35899999999999999999999999998887543
No 128
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=20.39 E-value=80 Score=19.46 Aligned_cols=29 Identities=24% Similarity=0.614 Sum_probs=15.7
Q ss_pred cCCcEEEEEecCCCCCcccCCC-ChhHHHHH
Q 045481 32 CGVDIALIVFSPANKAFSFGHP-NVDSILDL 61 (177)
Q Consensus 32 C~vev~~Ivfsp~gk~~~f~~p-sv~~Vl~r 61 (177)
|+-.-.|+|+ |.+..|...+| .+..|++.
T Consensus 47 C~~~P~v~i~-~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 47 CGLAPVVVVY-PDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred ccCCCEEEEe-CCCeEEccCCHHHHHHHHHh
Confidence 5444444444 66665555554 35666654
No 129
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=20.35 E-value=3e+02 Score=19.33 Aligned_cols=33 Identities=15% Similarity=0.517 Sum_probs=24.7
Q ss_pred CccCCCCHHHHHHHHHHHHH-------HHHHHHHHHHHHh
Q 045481 126 APINELGLHELEQLKTAMEE-------LKKNVEQQANKIL 158 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~-------~l~~V~~r~~~L~ 158 (177)
..+.+|+.+|+..|...|++ +...+++-|+.|.
T Consensus 43 ~~~~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~rl~ 82 (122)
T PRK05179 43 TRVKDLTDEELDKIREEIDKNYKVEGDLRREVSMNIKRLM 82 (122)
T ss_pred cccccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHH
Confidence 45789999999999999975 4555666666654
No 130
>KOG3838 consensus Mannose lectin ERGIC-53, involved in glycoprotein traffic [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.22 E-value=5.5e+02 Score=22.25 Aligned_cols=42 Identities=24% Similarity=0.232 Sum_probs=33.1
Q ss_pred ccCccCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHhhhccCCC
Q 045481 124 WEAPINELGLHELEQLKTA---MEELKKNVEQQANKILIDSKNNP 165 (177)
Q Consensus 124 w~~~l~~Ls~eeL~~l~~~---Le~~l~~V~~r~~~L~~~~~~~~ 165 (177)
|++--++++..||++.-.- |..-+.....+.++++..+....
T Consensus 309 ~~~~yEs~~~Relrqi~egQn~i~~~l~ql~rql~~il~~Q~~~~ 353 (497)
T KOG3838|consen 309 LFDLYESLGHRELRQILEGQNAIHKQLAQLERQLDKILGPQARPV 353 (497)
T ss_pred hhhhhhccchHHHHHHHhhhhHHHHHHHHHHHHHHHHhCccccCC
Confidence 3434478899999988776 88888888899999988877664
No 131
>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=20.18 E-value=2e+02 Score=23.29 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=21.5
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEELKKNVEQQAN 155 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~~r~~ 155 (177)
+.+++|+.+||.+|-..|-.....|-+..-
T Consensus 214 EeL~~Mt~~EL~qL~~~L~~qIq~vfeeLt 243 (285)
T PF06937_consen 214 EELNSMTLDELKQLNEKLLQQIQDVFEELT 243 (285)
T ss_pred HHhhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357889999999888887766666544433
No 132
>cd08888 SRPBCC_PITPNA-B_like Lipid-binding SRPBCC domain of mammalian PITPNA, -B, and related proteins (Class I PITPs). This subgroup includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class 1 phosphatidylinositol transfer proteins (PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator, and related proteins. These are single domain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. In addition, PITPNB transfers sphingomyelin in vitro, with a low affinity. PITPNA is found chiefly in the nucleus and cy
Probab=20.11 E-value=3.2e+02 Score=22.02 Aligned_cols=26 Identities=4% Similarity=0.201 Sum_probs=22.3
Q ss_pred CccCCCCHHHHHHHHHHHHHHHHHHH
Q 045481 126 APINELGLHELEQLKTAMEELKKNVE 151 (177)
Q Consensus 126 ~~l~~Ls~eeL~~l~~~Le~~l~~V~ 151 (177)
+.=-+|+++|++.++....+.+++++
T Consensus 232 DeW~gltmedIR~~E~~t~~~l~~~~ 257 (258)
T cd08888 232 DKWHGLTMDDIRRMEDETKKELDEMR 257 (258)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHHhh
Confidence 35667999999999999998888775
Done!