Query 043113
Match_columns 172
No_of_seqs 116 out of 1180
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 12:59:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043113.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043113hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0014 MADS box transcription 99.9 2.9E-25 6.3E-30 169.7 4.3 60 7-66 1-78 (195)
2 cd00265 MADS_MEF2_like MEF2 (m 99.9 1.3E-24 2.8E-29 142.6 2.6 57 8-64 1-73 (77)
3 cd00266 MADS_SRF_like SRF-like 99.8 1.9E-21 4.2E-26 129.3 2.6 58 8-65 1-75 (83)
4 smart00432 MADS MADS domain. 99.8 2.3E-20 4.9E-25 115.9 1.8 37 8-44 1-37 (59)
5 cd00120 MADS MADS: MCM1, Agamo 99.7 2.6E-19 5.5E-24 111.2 1.4 37 8-44 1-37 (59)
6 KOG0015 Regulator of arginine 99.7 5.7E-18 1.2E-22 133.5 0.3 64 3-66 58-146 (338)
7 PF00319 SRF-TF: SRF-type tran 99.5 5E-16 1.1E-20 93.4 -1.6 30 15-44 1-30 (51)
8 COG5068 ARG80 Regulator of arg 99.0 3.8E-11 8.3E-16 99.0 0.5 39 6-44 80-118 (412)
9 PF01486 K-box: K-box region; 98.5 8.9E-07 1.9E-11 60.8 8.3 62 90-157 15-76 (100)
10 PF07106 TBPIP: Tat binding pr 85.8 12 0.00026 27.6 9.9 66 81-156 73-138 (169)
11 KOG4302 Microtubule-associated 81.5 21 0.00046 32.5 10.3 73 82-154 112-184 (660)
12 PF06698 DUF1192: Protein of u 80.6 6.5 0.00014 24.2 4.9 37 119-155 13-49 (59)
13 PF07820 TraC: TraC-like prote 80.4 5.2 0.00011 26.8 4.7 60 82-151 4-64 (92)
14 PF05873 Mt_ATP-synt_D: ATP sy 77.3 7 0.00015 29.0 5.2 13 123-135 127-139 (161)
15 KOG4603 TBP-1 interacting prot 76.1 31 0.00068 26.0 9.9 67 80-156 79-145 (201)
16 PF04065 Not3: Not1 N-terminal 75.5 36 0.00079 26.9 9.0 24 34-64 13-36 (233)
17 PRK00736 hypothetical protein; 73.7 20 0.00043 22.6 5.9 37 76-112 15-51 (68)
18 KOG3838 Mannose lectin ERGIC-5 73.4 25 0.00054 30.1 7.9 75 81-158 273-350 (497)
19 PRK00295 hypothetical protein; 72.7 21 0.00045 22.5 6.0 37 76-112 15-51 (68)
20 KOG3366 Mitochondrial F1F0-ATP 72.5 18 0.00038 27.2 6.1 15 123-137 129-143 (172)
21 PRK04406 hypothetical protein; 72.4 21 0.00045 23.0 5.8 34 77-110 22-55 (75)
22 PRK04325 hypothetical protein; 71.7 23 0.00049 22.7 5.9 36 76-111 19-54 (74)
23 PRK02119 hypothetical protein; 71.3 24 0.00051 22.6 5.9 35 77-111 20-54 (73)
24 PF01166 TSC22: TSC-22/dip/bun 71.1 17 0.00037 22.2 4.8 30 81-110 15-44 (59)
25 PRK02793 phi X174 lysis protei 68.1 28 0.00062 22.1 5.9 35 77-111 19-53 (72)
26 PF04102 SlyX: SlyX; InterPro 66.8 22 0.00047 22.4 5.0 35 77-111 15-49 (69)
27 PF14193 DUF4315: Domain of un 66.3 35 0.00075 22.5 6.3 17 125-141 46-62 (83)
28 PRK00846 hypothetical protein; 66.1 33 0.00072 22.2 5.8 26 79-104 26-51 (77)
29 PF04977 DivIC: Septum formati 64.6 27 0.00059 21.9 5.3 30 82-111 19-48 (80)
30 TIGR02231 conserved hypothetic 63.3 97 0.0021 27.2 10.0 70 81-150 72-147 (525)
31 KOG0972 Huntingtin interacting 60.4 96 0.0021 25.6 9.7 31 135-165 306-336 (384)
32 PF15079 DUF4546: Domain of un 55.8 79 0.0017 23.8 6.9 60 83-157 50-109 (205)
33 PF05812 Herpes_BLRF2: Herpesv 55.1 72 0.0016 22.5 8.4 55 89-145 5-59 (118)
34 COG3883 Uncharacterized protei 54.9 1.1E+02 0.0024 24.7 8.3 28 129-156 79-106 (265)
35 KOG3048 Molecular chaperone Pr 54.3 41 0.0009 24.6 5.1 36 122-157 8-43 (153)
36 PF10498 IFT57: Intra-flagella 53.7 1.4E+02 0.003 25.2 9.2 34 80-113 259-292 (359)
37 KOG0995 Centromere-associated 53.5 1.2E+02 0.0027 27.1 8.7 30 81-110 295-324 (581)
38 smart00787 Spc7 Spc7 kinetocho 53.2 1.3E+02 0.0028 24.8 8.9 32 123-154 197-228 (312)
39 PF14257 DUF4349: Domain of un 53.0 1.1E+02 0.0024 24.1 8.5 58 83-153 128-185 (262)
40 PF08317 Spc7: Spc7 kinetochor 52.4 1.3E+02 0.0029 24.7 9.4 32 123-154 202-233 (325)
41 COG3883 Uncharacterized protei 52.4 1.2E+02 0.0027 24.4 8.7 63 81-158 53-115 (265)
42 PRK00888 ftsB cell division pr 52.3 51 0.0011 22.6 5.2 30 82-111 29-58 (105)
43 PHA03162 hypothetical protein; 51.8 87 0.0019 22.5 8.3 54 90-145 16-69 (135)
44 PF08262 Lem_TRP: Leucophaea m 51.4 8.1 0.00018 15.0 0.6 7 164-170 1-7 (10)
45 PF15372 DUF4600: Domain of un 49.2 96 0.0021 22.2 9.0 28 124-151 48-75 (129)
46 PF06005 DUF904: Protein of un 49.1 68 0.0015 20.4 9.3 16 139-154 51-66 (72)
47 PRK07720 fliJ flagellar biosyn 48.8 96 0.0021 22.1 8.7 69 84-154 20-88 (146)
48 PF09403 FadA: Adhesion protei 48.4 97 0.0021 22.0 8.9 94 45-151 15-110 (126)
49 PF04120 Iron_permease: Low af 47.0 1.1E+02 0.0023 22.1 7.2 29 123-151 91-119 (132)
50 PF11172 DUF2959: Protein of u 45.9 61 0.0013 25.0 5.1 52 52-111 44-95 (201)
51 TIGR03752 conj_TIGR03752 integ 45.5 1.9E+02 0.0042 25.4 8.6 28 81-108 67-94 (472)
52 PF04912 Dynamitin: Dynamitin 44.8 52 0.0011 27.8 5.2 20 25-44 264-283 (388)
53 PF14282 FlxA: FlxA-like prote 44.8 99 0.0021 21.1 8.5 55 81-157 20-74 (106)
54 COG4575 ElaB Uncharacterized c 44.3 1E+02 0.0022 21.2 7.5 29 125-153 32-60 (104)
55 PHA03161 hypothetical protein; 42.6 1.4E+02 0.0029 22.0 9.7 29 128-156 87-115 (150)
56 KOG4797 Transcriptional regula 40.7 1.2E+02 0.0027 21.0 6.0 26 81-106 68-93 (123)
57 PF12325 TMF_TATA_bd: TATA ele 40.7 1.3E+02 0.0028 21.2 8.8 25 129-153 95-119 (120)
58 PF04521 Viral_P18: ssRNA posi 39.8 36 0.00078 24.0 2.8 21 23-43 3-23 (120)
59 COG0718 Uncharacterized protei 38.9 1.3E+02 0.0028 20.7 7.5 42 127-169 62-104 (105)
60 KOG4005 Transcription factor X 38.4 2.1E+02 0.0045 22.9 8.9 36 79-114 89-124 (292)
61 PF06937 EURL: EURL protein; 38.2 37 0.00081 27.4 3.1 39 121-159 213-251 (285)
62 TIGR02209 ftsL_broad cell divi 37.9 1.1E+02 0.0023 19.5 5.5 29 83-111 27-55 (85)
63 TIGR03545 conserved hypothetic 37.6 2.7E+02 0.0059 25.0 8.7 20 129-148 211-230 (555)
64 PHA03155 hypothetical protein; 37.0 1.5E+02 0.0032 20.8 8.1 50 90-145 11-60 (115)
65 KOG1029 Endocytic adaptor prot 36.6 3.8E+02 0.0082 25.5 9.8 71 81-157 487-558 (1118)
66 PF14267 DUF4357: Domain of un 36.1 14 0.00031 22.3 0.3 21 32-52 7-30 (55)
67 PRK05689 fliJ flagellar biosyn 36.0 1.6E+02 0.0034 20.9 8.8 69 84-154 20-88 (147)
68 PRK04863 mukB cell division pr 35.4 3.5E+02 0.0075 27.5 9.7 32 123-154 431-462 (1486)
69 COG1579 Zn-ribbon protein, pos 34.9 2.3E+02 0.005 22.5 8.3 18 131-148 139-156 (239)
70 PF07139 DUF1387: Protein of u 33.7 42 0.00091 27.6 2.7 17 124-140 237-253 (302)
71 KOG4286 Dystrophin-like protei 33.6 1.2E+02 0.0025 28.4 5.7 65 81-146 214-278 (966)
72 PRK13848 conjugal transfer pro 33.5 1.3E+02 0.0027 20.3 4.5 55 84-148 7-62 (98)
73 PF05852 DUF848: Gammaherpesvi 33.4 1.9E+02 0.0042 21.1 8.4 33 124-156 83-115 (146)
74 KOG4286 Dystrophin-like protei 33.2 2.2E+02 0.0047 26.8 7.3 127 27-157 190-335 (966)
75 TIGR02420 dksA RNA polymerase- 32.7 1.6E+02 0.0035 20.0 5.4 30 127-156 1-30 (110)
76 PF02183 HALZ: Homeobox associ 32.6 1E+02 0.0022 17.7 4.6 28 83-110 8-35 (45)
77 PF11800 RP-C_C: Replication p 32.4 1.4E+02 0.0031 22.7 5.5 30 126-155 20-49 (207)
78 PF10224 DUF2205: Predicted co 32.4 1.5E+02 0.0032 19.4 5.6 10 148-157 58-67 (80)
79 TIGR00103 DNA_YbaB_EbfC DNA-bi 32.1 1.1E+02 0.0024 20.8 4.3 28 130-157 64-91 (102)
80 PF09789 DUF2353: Uncharacteri 32.0 3E+02 0.0065 22.9 9.3 32 80-111 79-110 (319)
81 PRK13729 conjugal transfer pil 31.7 2.7E+02 0.0058 24.6 7.4 21 81-101 70-90 (475)
82 TIGR02473 flagell_FliJ flagell 31.7 1.8E+02 0.0039 20.2 8.6 69 83-153 16-84 (141)
83 TIGR03853 matur_matur probable 31.4 1.1E+02 0.0024 19.8 3.9 20 118-137 36-55 (77)
84 PF00038 Filament: Intermediat 29.2 3E+02 0.0065 22.1 7.5 30 82-111 218-247 (312)
85 PRK10722 hypothetical protein; 29.0 3E+02 0.0065 22.0 8.4 52 52-103 125-185 (247)
86 PF14916 CCDC92: Coiled-coil d 28.9 1.1E+02 0.0024 18.9 3.4 27 80-106 10-40 (60)
87 COG5509 Uncharacterized small 28.7 1.5E+02 0.0032 18.3 3.9 21 81-101 26-46 (65)
88 COG2433 Uncharacterized conser 28.4 4.6E+02 0.01 24.0 10.3 30 81-110 430-459 (652)
89 COG5248 TAF19 Transcription in 28.0 34 0.00073 23.8 1.1 18 30-49 6-24 (126)
90 PF10186 Atg14: UV radiation r 27.9 3E+02 0.0065 21.6 7.8 31 80-110 70-100 (302)
91 PF07058 Myosin_HC-like: Myosi 27.7 2.3E+02 0.005 23.5 6.0 22 91-112 11-32 (351)
92 PRK13729 conjugal transfer pil 27.4 4.3E+02 0.0094 23.3 10.0 16 82-97 78-93 (475)
93 TIGR02894 DNA_bind_RsfA transc 26.8 2.7E+02 0.0059 20.7 8.1 25 84-108 108-132 (161)
94 PF07438 DUF1514: Protein of u 26.6 1.7E+02 0.0037 18.3 5.1 44 91-147 22-65 (66)
95 COG2882 FliJ Flagellar biosynt 26.6 2.6E+02 0.0057 20.5 7.9 71 82-154 18-88 (148)
96 PF10828 DUF2570: Protein of u 26.4 2.2E+02 0.0047 19.5 10.1 37 129-165 62-98 (110)
97 PF09006 Surfac_D-trimer: Lung 25.9 1.4E+02 0.0031 17.3 4.8 21 83-103 2-22 (46)
98 PF00843 Arena_nucleocap: Aren 25.9 1.5E+02 0.0033 25.9 4.8 26 123-148 87-112 (533)
99 PRK11637 AmiB activator; Provi 25.8 4.2E+02 0.0091 22.6 9.7 25 131-155 111-135 (428)
100 PF07412 Geminin: Geminin; In 25.6 1.7E+02 0.0038 22.5 4.7 19 130-148 156-174 (200)
101 KOG2861 Uncharacterized conser 25.5 1.4E+02 0.003 25.6 4.6 40 21-60 279-333 (399)
102 PF11944 DUF3461: Protein of u 25.1 1.1E+02 0.0023 21.8 3.2 25 129-153 101-125 (125)
103 PF05957 DUF883: Bacterial pro 25.1 2.1E+02 0.0044 18.8 5.9 22 131-152 28-49 (94)
104 PF03233 Cauli_AT: Aphid trans 25.0 3E+02 0.0064 20.6 6.3 27 128-154 136-162 (163)
105 PF05700 BCAS2: Breast carcino 25.0 3.3E+02 0.0071 21.1 7.4 66 82-155 99-164 (221)
106 COG2433 Uncharacterized conser 24.4 4.4E+02 0.0095 24.1 7.5 30 80-109 436-465 (652)
107 PF11460 DUF3007: Protein of u 24.3 1.1E+02 0.0023 21.1 3.0 18 123-140 86-103 (104)
108 PRK10132 hypothetical protein; 24.3 2.4E+02 0.0053 19.4 7.2 26 126-151 37-62 (108)
109 PF06717 DUF1202: Protein of u 23.5 4.2E+02 0.009 21.8 7.7 35 89-129 154-188 (308)
110 PF00816 Histone_HNS: H-NS his 22.8 1.3E+02 0.0028 19.7 3.2 17 84-100 2-18 (93)
111 COG3096 MukB Uncharacterized p 22.5 6.9E+02 0.015 23.9 10.4 62 82-153 515-576 (1480)
112 PRK14127 cell division protein 22.4 2.7E+02 0.0059 19.2 5.5 22 86-107 43-64 (109)
113 PF10678 DUF2492: Protein of u 21.8 2.2E+02 0.0047 18.5 4.0 20 118-137 38-57 (78)
114 PF09158 MotCF: Bacteriophage 21.8 29 0.00063 23.8 -0.1 49 11-63 19-73 (103)
115 PF02050 FliJ: Flagellar FliJ 21.8 2.4E+02 0.0053 18.4 9.0 30 125-154 40-69 (123)
116 PF00804 Syntaxin: Syntaxin; 21.8 2.3E+02 0.005 18.1 7.8 65 86-156 6-71 (103)
117 PF06156 DUF972: Protein of un 21.7 2.8E+02 0.006 19.1 5.4 30 82-111 24-53 (107)
118 PF10018 Med4: Vitamin-D-recep 21.3 3.6E+02 0.0078 20.2 9.0 64 81-144 30-98 (188)
119 PF09278 MerR-DNA-bind: MerR, 21.3 1.9E+02 0.0042 17.1 4.4 23 133-155 35-57 (65)
120 PF02646 RmuC: RmuC family; I 21.2 4.5E+02 0.0099 21.3 10.1 38 129-166 267-304 (304)
121 PLN02678 seryl-tRNA synthetase 21.2 5.6E+02 0.012 22.4 9.4 70 82-155 35-106 (448)
122 PF10498 IFT57: Intra-flagella 21.1 5.1E+02 0.011 21.9 9.1 9 52-60 200-208 (359)
123 PF04728 LPP: Lipoprotein leuc 20.9 2.1E+02 0.0046 17.3 4.9 19 82-100 5-23 (56)
124 PF01519 DUF16: Protein of unk 20.8 2.9E+02 0.0063 18.9 8.3 48 87-153 53-100 (102)
125 PRK09039 hypothetical protein; 20.7 5E+02 0.011 21.6 9.9 63 79-156 136-198 (343)
126 PF02256 Fe_hyd_SSU: Iron hydr 20.6 57 0.0012 19.8 1.1 37 28-64 8-44 (60)
127 PF10112 Halogen_Hydrol: 5-bro 20.5 1.4E+02 0.0029 22.6 3.4 15 50-64 136-150 (199)
128 PF06305 DUF1049: Protein of u 20.2 1.4E+02 0.0031 18.0 2.9 18 85-102 46-63 (68)
129 KOG0639 Transducin-like enhanc 20.1 6.5E+02 0.014 22.7 7.7 18 82-99 32-49 (705)
130 PF05983 Med7: MED7 protein; 20.1 3.7E+02 0.008 19.8 5.7 21 82-102 133-153 (162)
No 1
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.91 E-value=2.9e-25 Score=169.72 Aligned_cols=60 Identities=43% Similarity=0.666 Sum_probs=56.6
Q ss_pred CCccccceeeecCCcccchhhccccchhhhhhhhhhhc----------------cccCccc--HHHHHHHHhCCCccC
Q 043113 7 KRRQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEA----------------IHLCQPS--VKAIANRFLGMSQLH 66 (172)
Q Consensus 7 m~R~Ki~i~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L----------------~sfg~Ps--v~~Vl~ry~~~~~~~ 66 (172)
|||+||+|++|+|++.|||||+|||.||||||+||||| |+||+|+ |..|+++|.......
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 78 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEPS 78 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhhh
Confidence 89999999999999999999999999999999999999 7899987 999999999877654
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=99.90 E-value=1.3e-24 Score=142.61 Aligned_cols=57 Identities=42% Similarity=0.617 Sum_probs=54.9
Q ss_pred CccccceeeecCCcccchhhccccchhhhhhhhhhhc----------------cccCcccHHHHHHHHhCCCc
Q 043113 8 RRQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEA----------------IHLCQPSVKAIANRFLGMSQ 64 (172)
Q Consensus 8 ~R~Ki~i~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L----------------~sfg~Psv~~Vl~ry~~~~~ 64 (172)
||+||+|++|+|+..|++||+||+.||||||+|||+| |+|++|++++||+||+..+.
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~~ 73 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTSG 73 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhccc
Confidence 8999999999999999999999999999999999999 78999999999999998765
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=99.83 E-value=1.9e-21 Score=129.34 Aligned_cols=58 Identities=43% Similarity=0.642 Sum_probs=53.4
Q ss_pred CccccceeeecCCcccchhhccccchhhhhhhhhhhc----------------cccCccc-HHHHHHHHhCCCcc
Q 043113 8 RRQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEA----------------IHLCQPS-VKAIANRFLGMSQL 65 (172)
Q Consensus 8 ~R~Ki~i~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L----------------~sfg~Ps-v~~Vl~ry~~~~~~ 65 (172)
||+||+|++|+|+..|++||+||+.||||||+||||| |.|++|+ +..+|++|...+..
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~ 75 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSAL 75 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHh
Confidence 7999999999999999999999999999999999999 5577666 99999999988754
No 4
>smart00432 MADS MADS domain.
Probab=99.79 E-value=2.3e-20 Score=115.87 Aligned_cols=37 Identities=51% Similarity=0.793 Sum_probs=36.7
Q ss_pred CccccceeeecCCcccchhhccccchhhhhhhhhhhc
Q 043113 8 RRQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEA 44 (172)
Q Consensus 8 ~R~Ki~i~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L 44 (172)
||+||+|++|+|+..|++||+||+.||||||+|||||
T Consensus 1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~L 37 (59)
T smart00432 1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVL 37 (59)
T ss_pred CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhc
Confidence 8999999999999999999999999999999999999
No 5
>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.75 E-value=2.6e-19 Score=111.21 Aligned_cols=37 Identities=54% Similarity=0.776 Sum_probs=36.6
Q ss_pred CccccceeeecCCcccchhhccccchhhhhhhhhhhc
Q 043113 8 RRQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEA 44 (172)
Q Consensus 8 ~R~Ki~i~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L 44 (172)
||+||+|++|+|+..|++||+||+.||||||+|||||
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~L 37 (59)
T cd00120 1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVL 37 (59)
T ss_pred CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheec
Confidence 7999999999999999999999999999999999999
No 6
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.67 E-value=5.7e-18 Score=133.53 Aligned_cols=64 Identities=42% Similarity=0.523 Sum_probs=56.9
Q ss_pred CCCCCCccccceeeecCCcccchhhccccchhhhhhhhhhhc----------------cccCccc---------HHHHHH
Q 043113 3 GKKTKRRQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEA----------------IHLCQPS---------VKAIAN 57 (172)
Q Consensus 3 ~k~~m~R~Ki~i~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L----------------~sfg~Ps---------v~~Vl~ 57 (172)
+|++.||+||+|++|+|+..|.||||||+.||||||+||||| |.|+.|- -+++|.
T Consensus 58 ~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~s~~Gk~lIq 137 (338)
T KOG0015|consen 58 GKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMITSDEGKALIQ 137 (338)
T ss_pred CccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccccchhhHHHHH
Confidence 588999999999999999999999999999999999999999 8898763 377888
Q ss_pred HHhCCCccC
Q 043113 58 RFLGMSQLH 66 (172)
Q Consensus 58 ry~~~~~~~ 66 (172)
..++.+..+
T Consensus 138 ~cLn~pd~~ 146 (338)
T KOG0015|consen 138 ACLNAPDTP 146 (338)
T ss_pred HHhcCCCCC
Confidence 888877543
No 7
>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=99.53 E-value=5e-16 Score=93.40 Aligned_cols=30 Identities=53% Similarity=0.781 Sum_probs=27.5
Q ss_pred eeecCCcccchhhccccchhhhhhhhhhhc
Q 043113 15 KKIENEDDRLITFSKRGSGIYKKASEIWEA 44 (172)
Q Consensus 15 ~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L 44 (172)
++|+|+..|++||+||+.||||||+|||+|
T Consensus 1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~L 30 (51)
T PF00319_consen 1 KRIENKSRRKVTFSKRKKGLFKKASELSTL 30 (51)
T ss_dssp S--SSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCccchhHhHhHHHHHHhhhhhccceeeee
Confidence 589999999999999999999999999999
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.04 E-value=3.8e-11 Score=99.03 Aligned_cols=39 Identities=41% Similarity=0.476 Sum_probs=38.3
Q ss_pred CCCccccceeeecCCcccchhhccccchhhhhhhhhhhc
Q 043113 6 TKRRQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEA 44 (172)
Q Consensus 6 ~m~R~Ki~i~~I~n~~~R~vTfsKRr~GL~KKa~ELs~L 44 (172)
+|||+||.|.+|+|+..|.|||+||+.||+|||.||++|
T Consensus 80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvL 118 (412)
T COG5068 80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVL 118 (412)
T ss_pred ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhc
Confidence 689999999999999999999999999999999999999
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=98.51 E-value=8.9e-07 Score=60.78 Aligned_cols=62 Identities=13% Similarity=0.283 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 90 NDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 90 ~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~ 157 (172)
..+..++..++..++.|+..++ ++.|+++++|+++||..|+..|+.++..|+.|+.+++.+.
T Consensus 15 e~~~~e~~~L~~~~~~L~~~~R------~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~ 76 (100)
T PF01486_consen 15 EELQQEIAKLRKENESLQKELR------HLMGEDLESLSLKELQQLEQQLESALKRVRSRKDQLLMEQ 76 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh------ccccccccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHH
Confidence 3344444444444445555666 3445699999999999999999999999999999998765
No 10
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=85.80 E-value=12 Score=27.65 Aligned_cols=66 Identities=17% Similarity=0.188 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
.+..+..++..|++++..++.....+....... ...++.+||......|..-...+..|+..|..+
T Consensus 73 el~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L----------~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~ 138 (169)
T PF07106_consen 73 ELAELDAEIKELREELAELKKEVKSLEAELASL----------SSEPTNEELREEIEELEEEIEELEEKLEKLRSG 138 (169)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 466778888888888888888777777666532 256789999999999999999999999988874
No 11
>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=81.50 E-value=21 Score=32.50 Aligned_cols=73 Identities=15% Similarity=0.225 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
+..|..++.+-.+++..+..+.+.+...+.+..+-....-.|..+|+++.|.+|...|..+.+....|++...
T Consensus 112 le~lr~qk~eR~~ef~el~~qie~l~~~l~g~~~~~~~~~~D~~dlsl~kLeelr~~L~~L~~ek~~Rlekv~ 184 (660)
T KOG4302|consen 112 LEGLRKQKDERRAEFKELYHQIEKLCEELGGPEDLPSFLIADESDLSLEKLEELREHLNELQKEKSDRLEKVL 184 (660)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCCcccccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555555544444444432211113345577999999999999999999999888887765
No 12
>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=80.64 E-value=6.5 Score=24.19 Aligned_cols=37 Identities=19% Similarity=0.120 Sum_probs=29.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043113 119 WWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTA 155 (172)
Q Consensus 119 ~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~ 155 (172)
..+.+|+.||++||.+....|+.=..+++.-+.....
T Consensus 13 ~ig~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~~K~a 49 (59)
T PF06698_consen 13 EIGEDLSLLSVEELEERIALLEAEIARLEAAIAKKSA 49 (59)
T ss_pred ccCCCchhcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999888888777776665543
No 13
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=80.36 E-value=5.2 Score=26.83 Aligned_cols=60 Identities=10% Similarity=0.310 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQ-QNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKIN 151 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~-~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~ 151 (172)
+..+..++.+|++++.....+ .+.+-... ....|.+|.++| .+|...++++..+++.-..
T Consensus 4 ~s~I~~eIekLqe~lk~~e~keaERigr~A---------lKaGL~eieI~d-~eL~~~FeeIa~RFrk~~~ 64 (92)
T PF07820_consen 4 SSKIREEIEKLQEQLKQAETKEAERIGRIA---------LKAGLGEIEISD-AELQAAFEEIAARFRKGKK 64 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHcccccccCCH-HHHHHHHHHHHHHHhcccc
Confidence 346778888888888766442 22222221 112555555554 2455555555555555443
No 14
>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=77.26 E-value=7 Score=29.02 Aligned_cols=13 Identities=8% Similarity=0.480 Sum_probs=0.0
Q ss_pred CCCCCCHHHHHHH
Q 043113 123 PVDELNLQELLQM 135 (172)
Q Consensus 123 ~l~~Ls~~eL~~l 135 (172)
++++|+++|+...
T Consensus 127 P~e~mT~dd~~~a 139 (161)
T PF05873_consen 127 PFEQMTVDDYAAA 139 (161)
T ss_dssp -------------
T ss_pred ChHhCCHHHHHHh
Confidence 7888998887654
No 15
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=76.06 E-value=31 Score=26.01 Aligned_cols=67 Identities=7% Similarity=0.109 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 80 ARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 80 ~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
...+.|...+..|.+++..++....-+...++... ..|+++|+++=...|.+-...-+.|+..+..+
T Consensus 79 eel~~ld~~i~~l~ek~q~l~~t~s~veaEik~L~----------s~Lt~eemQe~i~~L~kev~~~~erl~~~k~g 145 (201)
T KOG4603|consen 79 EELQVLDGKIVALTEKVQSLQQTCSYVEAEIKELS----------SALTTEEMQEEIQELKKEVAGYRERLKNIKAG 145 (201)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HhcChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45666777777777777777766665555555322 45788888888888888888888888777654
No 16
>PF04065 Not3: Not1 N-terminal domain, CCR4-Not complex component ; InterPro: IPR007207 The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID []. This domain is the N-terminal region of the Not proteins.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=75.49 E-value=36 Score=26.87 Aligned_cols=24 Identities=17% Similarity=0.106 Sum_probs=15.8
Q ss_pred hhhhhhhhhhccccCcccHHHHHHHHhCCCc
Q 043113 34 IYKKASEIWEAIHLCQPSVKAIANRFLGMSQ 64 (172)
Q Consensus 34 L~KKa~ELs~L~sfg~Psv~~Vl~ry~~~~~ 64 (172)
+|||+.|-- -.++.|.++|.+..+
T Consensus 13 ~lKkv~EG~-------~~F~~i~~K~~~~~n 36 (233)
T PF04065_consen 13 TLKKVQEGV-------EEFDEIYEKVESATN 36 (233)
T ss_pred HHHHHHHHH-------HHHHHHHHHHHcccC
Confidence 567777743 346778888887543
No 17
>PRK00736 hypothetical protein; Provisional
Probab=73.71 E-value=20 Score=22.59 Aligned_cols=37 Identities=16% Similarity=0.225 Sum_probs=25.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043113 76 AYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRRV 112 (172)
Q Consensus 76 ~~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~ 112 (172)
+|+...++.||..+.+.+.+|+.++++...|.+.++.
T Consensus 15 afqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~ 51 (68)
T PRK00736 15 AEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLS 51 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555677788888888877787777766666555543
No 18
>KOG3838 consensus Mannose lectin ERGIC-53, involved in glycoprotein traffic [Intracellular trafficking, secretion, and vesicular transport]
Probab=73.43 E-value=25 Score=30.07 Aligned_cols=75 Identities=11% Similarity=0.102 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHhhh
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSA---VDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~---Le~~l~~V~~r~~~l~~~~ 157 (172)
..+.+.++++..+.++++.+.. ..+.+....++.--|.+--++++-.||.++-.- |..-+.....++++++..+
T Consensus 273 ek~kyqeEfe~~q~elek~k~e---fkk~hpd~~~e~ee~~~~yEs~~~Relrqi~egQn~i~~~l~ql~rql~~il~~Q 349 (497)
T KOG3838|consen 273 EKAKYQEEFEWAQLELEKRKDE---FKKSHPDAQGEGEELFDLYESLGHRELRQILEGQNAIHKQLAQLERQLDKILGPQ 349 (497)
T ss_pred HHHHHHHHHHHHHHHHhhhHhh---hccCCchhhcchhhhhhhhhccchHHHHHHHhhhhHHHHHHHHHHHHHHHHhCcc
Confidence 3445566666666667665442 222222222221123333477888888887666 8888888999999999765
Q ss_pred h
Q 043113 158 A 158 (172)
Q Consensus 158 ~ 158 (172)
.
T Consensus 350 ~ 350 (497)
T KOG3838|consen 350 A 350 (497)
T ss_pred c
Confidence 4
No 19
>PRK00295 hypothetical protein; Provisional
Probab=72.74 E-value=21 Score=22.47 Aligned_cols=37 Identities=19% Similarity=0.203 Sum_probs=25.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043113 76 AYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRRV 112 (172)
Q Consensus 76 ~~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~ 112 (172)
+|+...++.||..+.+.+.+++.++.....+....+.
T Consensus 15 a~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~ 51 (68)
T PRK00295 15 AFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEE 51 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555677788888888887887777766666555543
No 20
>KOG3366 consensus Mitochondrial F1F0-ATP synthase, subunit d/ATP7 [Energy production and conversion]
Probab=72.46 E-value=18 Score=27.18 Aligned_cols=15 Identities=27% Similarity=0.543 Sum_probs=12.1
Q ss_pred CCCCCCHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDS 137 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~ 137 (172)
+++.++++|+.+..=
T Consensus 129 P~demT~ed~~ea~P 143 (172)
T KOG3366|consen 129 PFDEMTMEDLNEAFP 143 (172)
T ss_pred CcccccHHHHHHhCc
Confidence 789999999987543
No 21
>PRK04406 hypothetical protein; Provisional
Probab=72.39 E-value=21 Score=23.00 Aligned_cols=34 Identities=15% Similarity=0.192 Sum_probs=18.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 77 YSHARINELNQQHNDLLRQLDEEKEQQNMLKQMR 110 (172)
Q Consensus 77 ~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~ 110 (172)
|+...|+.||..+...+.+++.++.....|.+..
T Consensus 22 fQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl 55 (75)
T PRK04406 22 FQEQTIEELNDALSQQQLLITKMQDQMKYVVGKV 55 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555566666555555555555544444333
No 22
>PRK04325 hypothetical protein; Provisional
Probab=71.74 E-value=23 Score=22.71 Aligned_cols=36 Identities=28% Similarity=0.277 Sum_probs=22.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 76 AYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 76 ~~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
+|+...|+.||..+.+.+.+++.+++....|...++
T Consensus 19 AfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~ 54 (74)
T PRK04325 19 AFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMR 54 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556777777777777777766666555544444
No 23
>PRK02119 hypothetical protein; Provisional
Probab=71.32 E-value=24 Score=22.57 Aligned_cols=35 Identities=17% Similarity=0.198 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 77 YSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 77 ~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
|+...++.||..+.+.+.+++.++.....+.+.++
T Consensus 20 ~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~~rl~ 54 (73)
T PRK02119 20 FQENLLEELNQALIEQQFVIDKMQVQLRYMANKLK 54 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456666666666666666666665555544444
No 24
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=71.14 E-value=17 Score=22.23 Aligned_cols=30 Identities=27% Similarity=0.360 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMR 110 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~ 110 (172)
.++.|+.+|.+|..++..++.+|..|+...
T Consensus 15 EVevLK~~I~eL~~~n~~Le~EN~~Lk~~~ 44 (59)
T PF01166_consen 15 EVEVLKEQIAELEERNSQLEEENNLLKQNA 44 (59)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 477899999999999999998888776654
No 25
>PRK02793 phi X174 lysis protein; Provisional
Probab=68.05 E-value=28 Score=22.12 Aligned_cols=35 Identities=14% Similarity=0.258 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 77 YSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 77 ~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
|+...++.||..+...+.+++.++.....|...++
T Consensus 19 fQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~ 53 (72)
T PRK02793 19 FQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLK 53 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455666666666666666665555554444443
No 26
>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=66.84 E-value=22 Score=22.37 Aligned_cols=35 Identities=29% Similarity=0.446 Sum_probs=21.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 77 YSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 77 ~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
|+...++.||..+...+.+++.++.....|...++
T Consensus 15 ~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~ 49 (69)
T PF04102_consen 15 FQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLR 49 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45556677777777777777776666555554444
No 27
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=66.27 E-value=35 Score=22.48 Aligned_cols=17 Identities=18% Similarity=0.188 Sum_probs=12.4
Q ss_pred CCCCHHHHHHHHHHHHH
Q 043113 125 DELNLQELLQMDSAVDD 141 (172)
Q Consensus 125 ~~Ls~~eL~~l~~~Le~ 141 (172)
-.|+.++|..|......
T Consensus 46 ~~mtp~eL~~~L~~~~~ 62 (83)
T PF14193_consen 46 MKMTPEELAAFLRAMKS 62 (83)
T ss_pred cCCCHHHHHHHHHHHHh
Confidence 45788988888776654
No 28
>PRK00846 hypothetical protein; Provisional
Probab=66.15 E-value=33 Score=22.24 Aligned_cols=26 Identities=15% Similarity=0.084 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 79 HARINELNQQHNDLLRQLDEEKEQQN 104 (172)
Q Consensus 79 ~~~~~~L~~~~~kl~~~l~~~k~~~~ 104 (172)
...++.||..+...+.+++.++....
T Consensus 26 e~tIe~LN~~v~~qq~~I~~L~~ql~ 51 (77)
T PRK00846 26 EQALTELSEALADARLTGARNAELIR 51 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444444333
No 29
>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=64.64 E-value=27 Score=21.87 Aligned_cols=30 Identities=27% Similarity=0.398 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
...+++++..++.+++.++.+++.|+..+.
T Consensus 19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~ 48 (80)
T PF04977_consen 19 YYQLNQEIAELQKEIEELKKENEELKEEIE 48 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445667777777777777777777766654
No 30
>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=63.26 E-value=97 Score=27.22 Aligned_cols=70 Identities=20% Similarity=0.228 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCC----CC--CCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWW----ET--PVDELNLQELLQMDSAVDDLHQTFLAKI 150 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~----~~--~l~~Ls~~eL~~l~~~Le~~l~~V~~r~ 150 (172)
.+..|+.++.+++.++...+.+...++..+.....-...+ .. ..+..++.++.++...+..-+..+..++
T Consensus 72 ~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 147 (525)
T TIGR02231 72 RLAELRKQIRELEAELRDLEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTED 147 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555666666666665555554444433332111100001 01 1235577777777655555544443333
No 31
>KOG0972 consensus Huntingtin interacting protein 1 (Hip1) interactor Hippi [Signal transduction mechanisms]
Probab=60.42 E-value=96 Score=25.57 Aligned_cols=31 Identities=19% Similarity=0.179 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCCC
Q 043113 135 MDSAVDDLHQTFLAKINEKTAAAAASSSVAP 165 (172)
Q Consensus 135 l~~~Le~~l~~V~~r~~~l~~~~~~~s~~~~ 165 (172)
--..|++.+..+...+.++-.+++.+|..+|
T Consensus 306 rT~~L~eVm~e~E~~KqemEe~G~~msDGap 336 (384)
T KOG0972|consen 306 RTETLDEVMDEIEQLKQEMEEQGAKMSDGAP 336 (384)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccCCch
Confidence 3445666677777777777777666666665
No 32
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=55.81 E-value=79 Score=23.76 Aligned_cols=60 Identities=13% Similarity=0.300 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 83 NELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 83 ~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~ 157 (172)
++|..++-+.+++|.. +.+++.+. + ++=|-+.+-|.+|...+-+..+...++++-|+.-+
T Consensus 50 ~eLkNeLREVREELkE---KmeEIKQI-K-----------diMDKDFDKL~EFVEIMKeMQkDMDEKMDvLiNiQ 109 (205)
T PF15079_consen 50 QELKNELREVREELKE---KMEEIKQI-K-----------DIMDKDFDKLHEFVEIMKEMQKDMDEKMDVLINIQ 109 (205)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHH-H-----------HHHhhhHHHHHHHHHHHHHHHHhHHHhhhHHhhcc
Confidence 4566666555555533 22333332 2 33444688999999999999999999999988644
No 33
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=55.14 E-value=72 Score=22.48 Aligned_cols=55 Identities=13% Similarity=0.012 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q 043113 89 HNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQT 145 (172)
Q Consensus 89 ~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~ 145 (172)
+++|.++|.+++-+|..|++.++...| .--..+..-|+..+=+.+....-..+..
T Consensus 5 ~EeLaaeL~kLqmENk~LKkkl~~~~~--p~~~p~~~~LTp~qKe~~I~s~~~~Lss 59 (118)
T PF05812_consen 5 MEELAAELQKLQMENKALKKKLRQSVG--PGPSPDDEVLTPAQKEAMITSAVSKLSS 59 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTT-----S-TT--B--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccCC--CCCCCCccccChHHHHHHHHHHHHHHHH
Confidence 567778888888888888888875443 0011256788888888777766655544
No 34
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.93 E-value=1.1e+02 Score=24.66 Aligned_cols=28 Identities=7% Similarity=0.220 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 129 LQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 129 ~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
-.++..|+..|..+...|..|-+-|-..
T Consensus 79 ~~eik~l~~eI~~~~~~I~~r~~~l~~r 106 (265)
T COG3883 79 KAEIKKLQKEIAELKENIVERQELLKKR 106 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567778888888888888877665543
No 35
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=54.30 E-value=41 Score=24.57 Aligned_cols=36 Identities=17% Similarity=0.220 Sum_probs=31.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 122 TPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 122 ~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~ 157 (172)
.++..||+++|.++...++-=+..+.+-++.|..-.
T Consensus 8 idltkLsleQL~~lk~q~dqEl~~lq~Sl~~L~~aq 43 (153)
T KOG3048|consen 8 IDLTKLSLEQLGALKKQFDQELNFLQDSLNALKGAQ 43 (153)
T ss_pred CChhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999998888888887543
No 36
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=53.67 E-value=1.4e+02 Score=25.25 Aligned_cols=34 Identities=12% Similarity=0.249 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 80 ARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVK 113 (172)
Q Consensus 80 ~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~ 113 (172)
.+..++|.+++.+..+....+.+...+++..++.
T Consensus 259 sREk~iN~qle~l~~eYr~~~~~ls~~~~~y~~~ 292 (359)
T PF10498_consen 259 SREKYINNQLEPLIQEYRSAQDELSEVQEKYKQA 292 (359)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555666666666666666666655555555544
No 37
>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=53.51 E-value=1.2e+02 Score=27.14 Aligned_cols=30 Identities=10% Similarity=0.271 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMR 110 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~ 110 (172)
.+..++.++++-..+++.++..+..|+..+
T Consensus 295 ~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~I 324 (581)
T KOG0995|consen 295 KLEMLKSEIEEKEEEIEKLQKENDELKKQI 324 (581)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566666666666666666666665555
No 38
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=53.16 E-value=1.3e+02 Score=24.83 Aligned_cols=32 Identities=16% Similarity=0.277 Sum_probs=26.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
.++.++.++|..+...|......|......+.
T Consensus 197 e~~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~ 228 (312)
T smart00787 197 ELEDCDPTELDRAKEKLKKLLQEIMIKVKKLE 228 (312)
T ss_pred HHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888999999999999888888877666554
No 39
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=52.96 E-value=1.1e+02 Score=24.09 Aligned_cols=58 Identities=12% Similarity=0.239 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 83 NELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEK 153 (172)
Q Consensus 83 ~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l 153 (172)
+.+-.+|..++.+++.++...+.|.+..... + +++|+..++..|.+....|..-.-++
T Consensus 128 ~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka-----------~--~~~d~l~ie~~L~~v~~eIe~~~~~~ 185 (262)
T PF14257_consen 128 EDVTEQYVDLEARLKNLEAEEERLLELLEKA-----------K--TVEDLLEIERELSRVRSEIEQLEGQL 185 (262)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----------C--CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456677778888887777666666665421 1 79999999999887777765544444
No 40
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=52.41 E-value=1.3e+02 Score=24.72 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=25.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
.++.++.++|..+...|......|..+...+-
T Consensus 202 e~~~~D~~eL~~lr~eL~~~~~~i~~~k~~l~ 233 (325)
T PF08317_consen 202 EIESCDQEELEALRQELAEQKEEIEAKKKELA 233 (325)
T ss_pred hhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47888999999999999888888876555443
No 41
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.36 E-value=1.2e+02 Score=24.41 Aligned_cols=63 Identities=11% Similarity=0.230 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAAAA 158 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~~ 158 (172)
.++.|..++.+++.+++..++++..++..++... .++..++..|.+....+..|...+-..++
T Consensus 53 ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~---------------~eI~~~~~~I~~r~~~l~~raRAmq~nG~ 115 (265)
T COG3883 53 EIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQ---------------KEIAELKENIVERQELLKKRARAMQVNGT 115 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4555666666666666666666666655555432 34556677777777777777776665554
No 42
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=52.29 E-value=51 Score=22.55 Aligned_cols=30 Identities=13% Similarity=-0.014 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
...+++++..+++++++++.+|..|...+.
T Consensus 29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~ 58 (105)
T PRK00888 29 YWRVNDQVAAQQQTNAKLKARNDQLFAEID 58 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446777788888888888877777776664
No 43
>PHA03162 hypothetical protein; Provisional
Probab=51.82 E-value=87 Score=22.48 Aligned_cols=54 Identities=13% Similarity=-0.002 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q 043113 90 NDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQT 145 (172)
Q Consensus 90 ~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~ 145 (172)
++|.++|.+++-+|..|.+.++...+. .... .-..|+..+=+.+.......+..
T Consensus 16 EeLaaeL~kLqmENK~LKkkl~~~~~~-~~~p-~d~~LTp~qKea~I~s~v~~Lts 69 (135)
T PHA03162 16 EDLAAEIAKLQLENKALKKKIKEGTDD-DPLP-GDPILTPAAKEAMIGAATAALTR 69 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCC-CCCC-CCccCCHHHHHHHHHHHHHHHHH
Confidence 366677777777788888787654332 0000 02358888887777666555544
No 44
>PF08262 Lem_TRP: Leucophaea maderae tachykinin-related peptide ; InterPro: IPR013206 These peptides are designated Leucophaea maderae (Madeira cockroach) tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific. The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae []. They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of Locusta migratoria (Migratory locust). They stimulate visceral muscle contractions of the oviduct and the foregut of L. migratoria [].
Probab=51.39 E-value=8.1 Score=15.01 Aligned_cols=7 Identities=71% Similarity=1.127 Sum_probs=5.3
Q ss_pred CCCCCCC
Q 043113 164 APPMYFH 170 (172)
Q Consensus 164 ~~~~~~~ 170 (172)
+|.|||+
T Consensus 1 apsmgf~ 7 (10)
T PF08262_consen 1 APSMGFH 7 (10)
T ss_pred CCccccc
Confidence 4778887
No 45
>PF15372 DUF4600: Domain of unknown function (DUF4600)
Probab=49.24 E-value=96 Score=22.21 Aligned_cols=28 Identities=7% Similarity=0.274 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 124 VDELNLQELLQMDSAVDDLHQTFLAKIN 151 (172)
Q Consensus 124 l~~Ls~~eL~~l~~~Le~~l~~V~~r~~ 151 (172)
.+.|+.+.|..+...|++-...+...+.
T Consensus 48 ye~Ms~~~l~~llkqLEkeK~~Le~qlk 75 (129)
T PF15372_consen 48 YEQMSVESLNQLLKQLEKEKRSLENQLK 75 (129)
T ss_pred HhhccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3888999999999999988777665544
No 46
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=49.13 E-value=68 Score=20.44 Aligned_cols=16 Identities=0% Similarity=0.146 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 043113 139 VDDLHQTFLAKINEKT 154 (172)
Q Consensus 139 Le~~l~~V~~r~~~l~ 154 (172)
|..-...+..|++.|+
T Consensus 51 L~~e~~~~~~rl~~LL 66 (72)
T PF06005_consen 51 LKQERNAWQERLRSLL 66 (72)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3334444444444443
No 47
>PRK07720 fliJ flagellar biosynthesis chaperone; Validated
Probab=48.83 E-value=96 Score=22.10 Aligned_cols=69 Identities=14% Similarity=0.067 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 84 ELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 84 ~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
....++.+....++..+.+...|......+... |-...-.++++.+|..+...|+.+-..|......+.
T Consensus 20 ~a~~~L~~a~~~~~~~~~~L~~L~~~~~~~~~~--~~~~~~~g~~~~~l~~~~~fl~~L~~~i~~q~~~v~ 88 (146)
T PRK07720 20 KALGEYEEAVSRFEQVAEKLYELLKQKEDLEQA--KEEKLQSGLSIQEIRHYQQFVTNLERTIDHYQLLVM 88 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445555555555555444444444433221 112234788999999999888888888766554443
No 48
>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=48.41 E-value=97 Score=22.04 Aligned_cols=94 Identities=17% Similarity=0.233 Sum_probs=39.8
Q ss_pred cccCcccHHHHHHHHhCCCccCCCCCcchHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--hcCCCCCCC
Q 043113 45 IHLCQPSVKAIANRFLGMSQLHNDNIHPLVKAYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVK--ETQPRWWET 122 (172)
Q Consensus 45 ~sfg~Psv~~Vl~ry~~~~~~~~~~~~~~~e~~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~--~~~~~~~~~ 122 (172)
.+|+.|...+|..++.+.... ...+.+--..+-....++.+.+.++|..+.+....+.+..... ...-.|+.
T Consensus 15 ~sfaA~~~~~v~~~l~~LEae-----~q~L~~kE~~r~~~~k~~ae~a~~~L~~~~~~~~~i~e~~~kl~~~~~~r~yk- 88 (126)
T PF09403_consen 15 ISFAATATASVESELNQLEAE-----YQQLEQKEEARYNEEKQEAEAAEAELAELKELYAEIEEKIEKLKQDSKVRWYK- 88 (126)
T ss_dssp --------HHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTTH-
T ss_pred HHHHcccchHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhcchhHHH-
Confidence 778888877788877654321 0111111123344445555566666665554333333333211 11113333
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDSAVDDLHQTFLAKIN 151 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~ 151 (172)
++-.+|.......++.+...+.
T Consensus 89 -------~eYk~llk~y~~~~~~L~k~I~ 110 (126)
T PF09403_consen 89 -------DEYKELLKKYKDLLNKLDKEIA 110 (126)
T ss_dssp -------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred -------HHHHHHHHHHHHHHHHHHHHHH
Confidence 5555666666666666555543
No 49
>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=46.99 E-value=1.1e+02 Score=22.05 Aligned_cols=29 Identities=14% Similarity=0.275 Sum_probs=24.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDSAVDDLHQTFLAKIN 151 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~ 151 (172)
++++|+.+||..+...+++.-..-+.+..
T Consensus 91 ~iE~l~~~el~~~~~~~~~~~~~~~~~~~ 119 (132)
T PF04120_consen 91 DIEDLTEEELEEIRKRYERLAEQARERHD 119 (132)
T ss_pred CcccCCHHHHHHHHHHHHHHHHHhhhhcc
Confidence 89999999999999999988777665543
No 50
>PF11172 DUF2959: Protein of unknown function (DUF2959); InterPro: IPR021342 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=45.88 E-value=61 Score=25.00 Aligned_cols=52 Identities=13% Similarity=0.252 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCccCCCCCcchHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 52 VKAIANRFLGMSQLHNDNIHPLVKAYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 52 v~~Vl~ry~~~~~~~~~~~~~~~e~~~~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
+.+.+++|......+.. .+-. .-+.|+.+|+.....-+....+...++....
T Consensus 44 F~sALe~f~sl~~~~gg---dLe~-----~Y~~ln~~ye~s~~~A~~V~~RI~~vE~Va~ 95 (201)
T PF11172_consen 44 FKSALEQFKSLVNFDGG---DLED-----KYNALNDEYESSEDAAEEVSDRIDAVEDVAD 95 (201)
T ss_pred HHHHHHHHHHhhCCCCC---cHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677788776654321 1111 2234666666666555555555555544433
No 51
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=45.54 E-value=1.9e+02 Score=25.36 Aligned_cols=28 Identities=18% Similarity=0.364 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQ 108 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~ 108 (172)
.+..++.++..+..+.+.++++|+.|++
T Consensus 67 ~~k~~r~~~~~l~~~N~~l~~eN~~L~~ 94 (472)
T TIGR03752 67 EVKELRKRLAKLISENEALKAENERLQK 94 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666777777777777666666654
No 52
>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []. It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex
Probab=44.85 E-value=52 Score=27.79 Aligned_cols=20 Identities=15% Similarity=0.194 Sum_probs=12.3
Q ss_pred hhhccccchhhhhhhhhhhc
Q 043113 25 ITFSKRGSGIYKKASEIWEA 44 (172)
Q Consensus 25 vTfsKRr~GL~KKa~ELs~L 44 (172)
-.+.+|-..|.+++.+|+-.
T Consensus 264 d~i~~rl~~L~~~~~~l~~~ 283 (388)
T PF04912_consen 264 DSIERRLKSLLSELEELAEK 283 (388)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 35566666666666666544
No 53
>PF14282 FlxA: FlxA-like protein
Probab=44.76 E-value=99 Score=21.08 Aligned_cols=55 Identities=22% Similarity=0.250 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~ 157 (172)
.|..|+.++..|+++|..+.. -.+|+.++-..-...|..-+..|...|.++..+.
T Consensus 20 ~I~~L~~Qi~~Lq~ql~~l~~----------------------~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~ 74 (106)
T PF14282_consen 20 QIEQLQKQIKQLQEQLQELSQ----------------------DSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQ 74 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHc----------------------ccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466677777777666655422 1556777777777777777777777777766544
No 54
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=44.33 E-value=1e+02 Score=21.18 Aligned_cols=29 Identities=10% Similarity=0.136 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 125 DELNLQELLQMDSAVDDLHQTFLAKINEK 153 (172)
Q Consensus 125 ~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l 153 (172)
.+++-+++.++...++.+++.++.|+...
T Consensus 32 g~~a~~e~~~lR~r~~~~Lk~~r~rl~~~ 60 (104)
T COG4575 32 GSLAGDEAEELRSKAESALKEARDRLGDT 60 (104)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 55678999999999999999999998766
No 55
>PHA03161 hypothetical protein; Provisional
Probab=42.64 E-value=1.4e+02 Score=22.03 Aligned_cols=29 Identities=10% Similarity=0.172 Sum_probs=25.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 128 NLQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 128 s~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
-++.+..|.+.++++...|.-.++.+-..
T Consensus 87 kl~~~E~L~drv~eLkeel~~ELe~l~~~ 115 (150)
T PHA03161 87 KLSAAEDLQDKILELKEDIHFEIEALNHG 115 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 37788899999999999999999988854
No 56
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=40.75 E-value=1.2e+02 Score=21.02 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNML 106 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l 106 (172)
.++-|+.+|.+|.+++..++.+|..|
T Consensus 68 EVe~Lk~qI~eL~er~~~Le~EN~lL 93 (123)
T KOG4797|consen 68 EVEVLKEQIRELEERNSALERENSLL 93 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555444444333
No 57
>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=40.67 E-value=1.3e+02 Score=21.20 Aligned_cols=25 Identities=20% Similarity=0.429 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 129 LQELLQMDSAVDDLHQTFLAKINEK 153 (172)
Q Consensus 129 ~~eL~~l~~~Le~~l~~V~~r~~~l 153 (172)
.++..+|..-|.+++.-.+..++.+
T Consensus 95 ~E~veEL~~Dv~DlK~myr~Qi~~l 119 (120)
T PF12325_consen 95 SEEVEELRADVQDLKEMYREQIDQL 119 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5666667777777776666666654
No 58
>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=39.78 E-value=36 Score=23.98 Aligned_cols=21 Identities=19% Similarity=0.115 Sum_probs=17.9
Q ss_pred cchhhccccchhhhhhhhhhh
Q 043113 23 RLITFSKRGSGIYKKASEIWE 43 (172)
Q Consensus 23 R~vTfsKRr~GL~KKa~ELs~ 43 (172)
.-++|+|+|..++++-.+-.+
T Consensus 3 ~~~~~rk~R~~~y~~lgl~~v 23 (120)
T PF04521_consen 3 SFRCVRKYRASVYKKLGLSAV 23 (120)
T ss_pred chHHHHHHHHHHHHHcCCeee
Confidence 346899999999999988766
No 59
>COG0718 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.89 E-value=1.3e+02 Score=20.73 Aligned_cols=42 Identities=17% Similarity=0.210 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh-cCCCCCCCCCC
Q 043113 127 LNLQELLQMDSAVDDLHQTFLAKINEKTAAAA-ASSSVAPPMYF 169 (172)
Q Consensus 127 Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~~-~~s~~~~~~~~ 169 (172)
+..+|-.-|++.|-.+.+....++++...+.- ...+.+|| ||
T Consensus 62 ~dpeD~E~LeDLi~aA~ndA~~kv~e~~~e~m~~~t~gm~P-G~ 104 (105)
T COG0718 62 LDPEDKEMLEDLILAAFNDAKKKVEETRKEKMGALTGGMPP-GF 104 (105)
T ss_pred cCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC-CC
Confidence 34667888888888888888777776664432 34455556 76
No 60
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=38.37 E-value=2.1e+02 Score=22.91 Aligned_cols=36 Identities=17% Similarity=0.280 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 79 HARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKE 114 (172)
Q Consensus 79 ~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~ 114 (172)
++++.++..++..|.++.+.++.+|+.|+...+...
T Consensus 89 KaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~ 124 (292)
T KOG4005|consen 89 KARMEEMEYEIKDLTEENEILQNENDSLRAINESLL 124 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888888888888888888888888887776443
No 61
>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=38.24 E-value=37 Score=27.39 Aligned_cols=39 Identities=13% Similarity=0.282 Sum_probs=32.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 043113 121 ETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAAAAA 159 (172)
Q Consensus 121 ~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~~~ 159 (172)
.+.+..|+++||.+|-..|......|-.-+...+.+...
T Consensus 213 rEeL~~Mt~~EL~qL~~~L~~qIq~vfeeLt~~vQEKDs 251 (285)
T PF06937_consen 213 REELNSMTLDELKQLNEKLLQQIQDVFEELTQQVQEKDS 251 (285)
T ss_pred HHHhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346889999999999999999888888888777766553
No 62
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=37.85 E-value=1.1e+02 Score=19.49 Aligned_cols=29 Identities=17% Similarity=0.204 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 83 NELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 83 ~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
..+..++..++.+++.++.++..|+..+.
T Consensus 27 ~~~~~~~~~~~~~~~~l~~en~~L~~ei~ 55 (85)
T TIGR02209 27 RQLNNELQKLQLEIDKLQKEWRDLQLEVA 55 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666666666666666665555543
No 63
>TIGR03545 conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
Probab=37.64 E-value=2.7e+02 Score=24.96 Aligned_cols=20 Identities=25% Similarity=0.222 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 043113 129 LQELLQMDSAVDDLHQTFLA 148 (172)
Q Consensus 129 ~~eL~~l~~~Le~~l~~V~~ 148 (172)
+.++......++++.+.++.
T Consensus 211 p~~i~~~~~e~d~lk~e~~~ 230 (555)
T TIGR03545 211 PLELQKIKEEFDKLKKEGKA 230 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44444555555544444443
No 64
>PHA03155 hypothetical protein; Provisional
Probab=37.04 E-value=1.5e+02 Score=20.80 Aligned_cols=50 Identities=12% Similarity=0.063 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q 043113 90 NDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQT 145 (172)
Q Consensus 90 ~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~ 145 (172)
++|.++|.+++-+|..|.+.++...+ .+-.-|+..+=+.+.......+..
T Consensus 11 EeLaaeL~kL~~ENK~LKkkl~~~~~------p~d~~LT~~qKea~I~s~v~~Lt~ 60 (115)
T PHA03155 11 EELEKELQKLKIENKALKKKLLQHGN------PEDELLTPAQKDAIINSLVNKLTK 60 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC------CCccccCHHHHHHHHHHHHHHHHH
Confidence 36666777777777777777764321 233668888887777666555544
No 65
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=36.65 E-value=3.8e+02 Score=25.46 Aligned_cols=71 Identities=14% Similarity=0.221 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELN-LQELLQMDSAVDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls-~~eL~~l~~~Le~~l~~V~~r~~~l~~~~ 157 (172)
.+..|.+++.++++.+.++--....|...++..... ...+-+ ..+|......=+.+...|++.+++|-.+.
T Consensus 487 ei~qlqarikE~q~kl~~l~~Ekq~l~~qlkq~q~a------~~~~~~~~s~L~aa~~~ke~irq~ikdqldelskE~ 558 (1118)
T KOG1029|consen 487 EIDQLQARIKELQEKLQKLAPEKQELNHQLKQKQSA------HKETTQRKSELEAARRKKELIRQAIKDQLDELSKET 558 (1118)
T ss_pred HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhh------ccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355566666666666655543333444444433221 222223 66676666666666666666666665543
No 66
>PF14267 DUF4357: Domain of unknown function (DUF4357)
Probab=36.06 E-value=14 Score=22.26 Aligned_cols=21 Identities=14% Similarity=0.153 Sum_probs=15.1
Q ss_pred chhhhhhhhhhhc---cccCcccH
Q 043113 32 SGIYKKASEIWEA---IHLCQPSV 52 (172)
Q Consensus 32 ~GL~KKa~ELs~L---~sfg~Psv 52 (172)
.|++..-.+..++ |.|.+||.
T Consensus 7 ~G~l~~~~~~~~f~~d~~F~SPS~ 30 (55)
T PF14267_consen 7 DGVLVPDGGRLVFTQDYLFSSPSA 30 (55)
T ss_pred CCCEEecCCcEEEecCeEcCChHH
Confidence 4566665666666 89999984
No 67
>PRK05689 fliJ flagellar biosynthesis chaperone; Validated
Probab=36.00 E-value=1.6e+02 Score=20.91 Aligned_cols=69 Identities=13% Similarity=0.138 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 84 ELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 84 ~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
.....+...+.+++..+.+...|......+... |-.....++++.+|..+...|..+-..|......+.
T Consensus 20 ~a~~~la~a~~~~~~~~~~L~~L~~y~~~y~~~--~~~~~~~g~~~~~l~~~~~fi~~L~~~I~~q~~~v~ 88 (147)
T PRK05689 20 QAALQLGQARQELQQAEQQLKMLEDYRLEYRQQ--LNDRGSAGMTSSWWINYQQFLQQLEKAITQQRQQLT 88 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555555555454444322211 111235788999998888888887777766554443
No 68
>PRK04863 mukB cell division protein MukB; Provisional
Probab=35.39 E-value=3.5e+02 Score=27.54 Aligned_cols=32 Identities=6% Similarity=-0.035 Sum_probs=23.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
.+.+|+.++|......++..+......+..+-
T Consensus 431 ~~~~~SdEeLe~~LenF~aklee~e~qL~elE 462 (1486)
T PRK04863 431 GLPDLTADNAEDWLEEFQAKEQEATEELLSLE 462 (1486)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67889999998887777777776666555544
No 69
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=34.94 E-value=2.3e+02 Score=22.50 Aligned_cols=18 Identities=6% Similarity=0.165 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 043113 131 ELLQMDSAVDDLHQTFLA 148 (172)
Q Consensus 131 eL~~l~~~Le~~l~~V~~ 148 (172)
++.+.+..++.....+++
T Consensus 139 ~~~e~~~~~e~e~~~i~e 156 (239)
T COG1579 139 NLAEAEARLEEEVAEIRE 156 (239)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 334444444444444444
No 70
>PF07139 DUF1387: Protein of unknown function (DUF1387); InterPro: IPR009816 This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.
Probab=33.70 E-value=42 Score=27.57 Aligned_cols=17 Identities=6% Similarity=0.354 Sum_probs=11.5
Q ss_pred CCCCCHHHHHHHHHHHH
Q 043113 124 VDELNLQELLQMDSAVD 140 (172)
Q Consensus 124 l~~Ls~~eL~~l~~~Le 140 (172)
...|+-++|.+|...|-
T Consensus 237 A~~MsE~Ql~ELRadIK 253 (302)
T PF07139_consen 237 ASQMSEEQLAELRADIK 253 (302)
T ss_pred HhhcCHHHHHHHHHHHH
Confidence 36677778877776553
No 71
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=33.64 E-value=1.2e+02 Score=28.43 Aligned_cols=65 Identities=22% Similarity=0.318 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTF 146 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V 146 (172)
....|+.++.+..++|..++...+++.-..++..+...-|. ++++|-+++|.+-...+....++|
T Consensus 214 ~~~~w~k~v~~~le~l~elq~a~~el~~~l~~ae~~~~~w~-pvgdl~idsl~~h~e~~~~~~~ei 278 (966)
T KOG4286|consen 214 HSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ-PVGDLLIDSLQDHLEKVKALRGEI 278 (966)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHhhhhccc-cHHHHHHhHHHHHHHHHHHHHhhc
Confidence 34556667777777777777666666655555544444565 788888888887766666555544
No 72
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=33.55 E-value=1.3e+02 Score=20.34 Aligned_cols=55 Identities=15% Similarity=0.390 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 043113 84 ELNQQHNDLLRQLDEEKE-QQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLA 148 (172)
Q Consensus 84 ~L~~~~~kl~~~l~~~k~-~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~ 148 (172)
.+..++++|++++..... ..+.+-... ....|.+|.++|- +|...++++-.+++.
T Consensus 7 ~I~~eI~kLqe~lk~~e~keAERigRiA---------lKAGLgeieI~d~-eL~~aFeeiAaRFR~ 62 (98)
T PRK13848 7 KIREEIAKLQEQLKQAETREAERIGRIA---------LKAGLGEIEIEEA-ELQAAFEELAKRFRG 62 (98)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHcCccccccCHH-HHHHHHHHHHHHHhc
Confidence 466788888888875543 222222221 1125666655552 344445544444443
No 73
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=33.42 E-value=1.9e+02 Score=21.13 Aligned_cols=33 Identities=15% Similarity=0.346 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 124 VDELNLQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 124 l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
++--.++++..|.+.+.++...|...++.+...
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 455579999999999999999999999999754
No 74
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=33.22 E-value=2.2e+02 Score=26.78 Aligned_cols=127 Identities=14% Similarity=0.139 Sum_probs=63.5
Q ss_pred hccccchhhhhhhhhhhccc-cC------cccHHHHHHHHhCCCccCC--CCCcc-------hHHhhhHHHHHHHHHH--
Q 043113 27 FSKRGSGIYKKASEIWEAIH-LC------QPSVKAIANRFLGMSQLHN--DNIHP-------LVKAYSHARINELNQQ-- 88 (172)
Q Consensus 27 fsKRr~GL~KKa~ELs~L~s-fg------~Psv~~Vl~ry~~~~~~~~--~~~~~-------~~e~~~~~~~~~L~~~-- 88 (172)
--+|+.||.|-|.|+..+|+ .+ +--|+..++|.+.....-. +.... ..+...+--++.|...
T Consensus 190 ~q~~~r~~~kqa~~~~~~we~l~~~~~~w~k~v~~~le~l~elq~a~~el~~~l~~ae~~~~~w~pvgdl~idsl~~h~e 269 (966)
T KOG4286|consen 190 AQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLE 269 (966)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHhhhhccccHHHHHHhHHHHHHH
Confidence 35788999999999999944 11 2337777777754432210 00000 0000011123333322
Q ss_pred -HHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 89 -HNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 89 -~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~~ 157 (172)
+..+.+++.-.+.....+....+... -.+-.++.-+...|..+...-..+...|..|+.+|...+
T Consensus 270 ~~~~~~~ei~p~~~~v~~vndla~ql~----~~d~~ls~~~~~~le~~n~rwk~Lq~SV~~rl~qlrna~ 335 (966)
T KOG4286|consen 270 KVKALRGEIAPLKENVSHVNDLARQLT----TLDIQLSPYNLSTLEDLNTRWKLLQVSVPDRLTQLRNAH 335 (966)
T ss_pred HHHHHHhhcchHhhchhhHHHHHHHhh----hcccCCChhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22223333333322222222222111 112234555566777777777788889999999888654
No 75
>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=32.74 E-value=1.6e+02 Score=20.04 Aligned_cols=30 Identities=10% Similarity=0.149 Sum_probs=19.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 127 LNLQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 127 Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
|+-+++..|...|.+.+..+..++.....+
T Consensus 1 M~~~~l~~~k~~L~~~~~~L~~~i~~~~~~ 30 (110)
T TIGR02420 1 MSEAQLEHFRKILLRWKQELLEEADKTLEH 30 (110)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677777777777777776666655443
No 76
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=32.56 E-value=1e+02 Score=17.68 Aligned_cols=28 Identities=18% Similarity=0.256 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 83 NELNQQHNDLLRQLDEEKEQQNMLKQMR 110 (172)
Q Consensus 83 ~~L~~~~~kl~~~l~~~k~~~~~l~~~~ 110 (172)
..|+..|..|..+.+.++..++.|+..+
T Consensus 8 ~~LK~~yd~Lk~~~~~L~~E~~~L~aev 35 (45)
T PF02183_consen 8 DALKASYDSLKAEYDSLKKENEKLRAEV 35 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666666666666666655554444
No 77
>PF11800 RP-C_C: Replication protein C C-terminal region; InterPro: IPR021760 Replication protein C is involved in the early stages of viral DNA replication.
Probab=32.41 E-value=1.4e+02 Score=22.71 Aligned_cols=30 Identities=10% Similarity=0.192 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043113 126 ELNLQELLQMDSAVDDLHQTFLAKINEKTA 155 (172)
Q Consensus 126 ~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~ 155 (172)
.+++++|..+...|+.++..|...++....
T Consensus 20 ~~~~~~L~~l~~~L~~l~~~v~~~le~~~~ 49 (207)
T PF11800_consen 20 KASLADLEALLDELEALLEEVENALESQEK 49 (207)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 468999999999999999999998876553
No 78
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=32.35 E-value=1.5e+02 Score=19.40 Aligned_cols=10 Identities=10% Similarity=0.122 Sum_probs=3.9
Q ss_pred HHHHHHHhhh
Q 043113 148 AKINEKTAAA 157 (172)
Q Consensus 148 ~r~~~l~~~~ 157 (172)
.-|..|+..+
T Consensus 58 ~YI~nLm~~s 67 (80)
T PF10224_consen 58 QYIGNLMSSS 67 (80)
T ss_pred HHHHHHHHhh
Confidence 3333344433
No 79
>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=32.07 E-value=1.1e+02 Score=20.76 Aligned_cols=28 Identities=7% Similarity=0.175 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043113 130 QELLQMDSAVDDLHQTFLAKINEKTAAA 157 (172)
Q Consensus 130 ~eL~~l~~~Le~~l~~V~~r~~~l~~~~ 157 (172)
+|...|++.|-.+.+....+..+...+.
T Consensus 64 ~d~e~LedlI~~A~N~A~~k~~~~~~e~ 91 (102)
T TIGR00103 64 EDKEALEDMITEALNDAVKKVEETYKEL 91 (102)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5777888888888888887777776663
No 80
>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function.
Probab=32.01 E-value=3e+02 Score=22.89 Aligned_cols=32 Identities=16% Similarity=0.341 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 80 ARINELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 80 ~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
.....|..++..|++++...+-.+..|++.+.
T Consensus 79 e~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~la 110 (319)
T PF09789_consen 79 EQNKKLKEEVEELRQKLNEAQGDIKLLREKLA 110 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHhchHHHHHHHHH
Confidence 34555666777777777777666666666554
No 81
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=31.70 E-value=2.7e+02 Score=24.55 Aligned_cols=21 Identities=14% Similarity=0.287 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKE 101 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~ 101 (172)
.+.+-+....+|+++|+.++.
T Consensus 70 ALteqQ~kasELEKqLaaLrq 90 (475)
T PRK13729 70 ATTEMQVTAAQMQKQYEEIRR 90 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344444455566666665543
No 82
>TIGR02473 flagell_FliJ flagellar export protein FliJ. Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.
Probab=31.68 E-value=1.8e+02 Score=20.19 Aligned_cols=69 Identities=16% Similarity=0.097 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 83 NELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEK 153 (172)
Q Consensus 83 ~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l 153 (172)
+....++.....+++........+.......... |-.....++++.++..+...+..+...|......+
T Consensus 16 d~a~~~la~~~~~~~~~~~~l~~l~~~~~~~~~~--~~~~~~~g~~~~~l~~~~~f~~~l~~~i~~q~~~l 84 (141)
T TIGR02473 16 EQAKLELAKAQAEFERLETQLQQLIKYREEYEQQ--ALEKVGAGTSALELSNYQRFIRQLDQRIQQQQQEL 84 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555555554444444444443322110 11113456788888888777777777765554433
No 83
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=31.41 E-value=1.1e+02 Score=19.85 Aligned_cols=20 Identities=25% Similarity=0.370 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCHHHHHHHHH
Q 043113 118 RWWETPVDELNLQELLQMDS 137 (172)
Q Consensus 118 ~~~~~~l~~Ls~~eL~~l~~ 137 (172)
.+.-++.++|++++|.+|-.
T Consensus 36 rFhTCSa~~m~a~~Li~FL~ 55 (77)
T TIGR03853 36 RFHTCSAEGMTADELLQFLL 55 (77)
T ss_pred eEeecccccCCHHHHHHHHH
Confidence 56678999999999998754
No 84
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=29.24 E-value=3e+02 Score=22.06 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
+..+..++..|+.+++.++..+..|...+.
T Consensus 218 ~~~~r~~~~~l~~el~~l~~~~~~Le~~l~ 247 (312)
T PF00038_consen 218 LKELRRQIQSLQAELESLRAKNASLERQLR 247 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhhhhHhhhhhhccccchhhhhhhHH
Confidence 344455556666666666655555555554
No 85
>PRK10722 hypothetical protein; Provisional
Probab=29.02 E-value=3e+02 Score=21.98 Aligned_cols=52 Identities=23% Similarity=0.302 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCccCCCCCcchHHhhhH-----HHHHHHHHHHHHH----HHHHHHHHHHH
Q 043113 52 VKAIANRFLGMSQLHNDNIHPLVKAYSH-----ARINELNQQHNDL----LRQLDEEKEQQ 103 (172)
Q Consensus 52 v~~Vl~ry~~~~~~~~~~~~~~~e~~~~-----~~~~~L~~~~~kl----~~~l~~~k~~~ 103 (172)
-..++++....+......-.++...+.. -.+..-+.+|.+| .++++.+....
T Consensus 125 rr~~l~rl~~~~~~~p~~lrPL~qlwr~~Q~l~l~LaeEr~Ry~rLQq~sD~qlD~lrqq~ 185 (247)
T PRK10722 125 RRQIVERLNAYSLQIPAQVRPLYQLWRDGQALQLALAEERQRYQKLQQSSDSELDALRQQQ 185 (247)
T ss_pred HHHHHHHHhhcccccchhhhHHHHHHHHhhHHHHhHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 5677888777665544444454333221 1233334455566 34444444433
No 86
>PF14916 CCDC92: Coiled-coil domain of unknown function
Probab=28.85 E-value=1.1e+02 Score=18.86 Aligned_cols=27 Identities=22% Similarity=0.320 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHH----HHHHHHHHHHHHH
Q 043113 80 ARINELNQQHNDLL----RQLDEEKEQQNML 106 (172)
Q Consensus 80 ~~~~~L~~~~~kl~----~~l~~~k~~~~~l 106 (172)
..|.+|+++...+. ++|+.++.++..|
T Consensus 10 ~~i~FLq~eH~~tL~~LH~EIe~Lq~~~~dL 40 (60)
T PF14916_consen 10 KSILFLQQEHAQTLKGLHAEIERLQKRNKDL 40 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 46788888766544 4455555544433
No 87
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=28.72 E-value=1.5e+02 Score=18.32 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKE 101 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~ 101 (172)
.+.+|+++|.-|+.+++.++.
T Consensus 26 sV~El~eRIalLq~EIeRlkA 46 (65)
T COG5509 26 SVAELEERIALLQAEIERLKA 46 (65)
T ss_pred hHHHHHHHHHHHHHHHHHHHH
Confidence 466777777777777776654
No 88
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=28.40 E-value=4.6e+02 Score=23.95 Aligned_cols=30 Identities=23% Similarity=0.415 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMR 110 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~ 110 (172)
.+..|..++..|+..++.+++.+++|+...
T Consensus 430 ~ve~l~~e~~~L~~~~ee~k~eie~L~~~l 459 (652)
T COG2433 430 TVERLEEENSELKRELEELKREIEKLESEL 459 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566666666666666666555554443
No 89
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=27.97 E-value=34 Score=23.76 Aligned_cols=18 Identities=17% Similarity=0.232 Sum_probs=14.1
Q ss_pred ccchhhhhhhhhhhc-cccCc
Q 043113 30 RGSGIYKKASEIWEA-IHLCQ 49 (172)
Q Consensus 30 Rr~GL~KKa~ELs~L-~sfg~ 49 (172)
||..||-| ++++| |.||.
T Consensus 6 rr~nLF~K--DikslmYayGD 24 (126)
T COG5248 6 RRVNLFMK--DIKSLMYAYGD 24 (126)
T ss_pred HHHHHHHH--HHHHHHHHhCC
Confidence 56677776 78888 99986
No 90
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=27.85 E-value=3e+02 Score=21.62 Aligned_cols=31 Identities=16% Similarity=0.421 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 80 ARINELNQQHNDLLRQLDEEKEQQNMLKQMR 110 (172)
Q Consensus 80 ~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~ 110 (172)
.++..+..++..+.++++..+++...++..+
T Consensus 70 ~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l 100 (302)
T PF10186_consen 70 ERLERLRERIERLRKRIEQKRERLEELRESL 100 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555555555555555444443333
No 91
>PF07058 Myosin_HC-like: Myosin II heavy chain-like; InterPro: IPR009768 This family represents a conserved region within a number of myosin II heavy chain-like proteins that seem to be specific to Arabidopsis thaliana.
Probab=27.69 E-value=2.3e+02 Score=23.51 Aligned_cols=22 Identities=27% Similarity=0.601 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 043113 91 DLLRQLDEEKEQQNMLKQMRRV 112 (172)
Q Consensus 91 kl~~~l~~~k~~~~~l~~~~~~ 112 (172)
+|..|++--++.|.-|..++++
T Consensus 11 EL~kQiEIcqEENkiLdK~hRQ 32 (351)
T PF07058_consen 11 ELMKQIEICQEENKILDKMHRQ 32 (351)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444444443
No 92
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=27.44 E-value=4.3e+02 Score=23.29 Aligned_cols=16 Identities=25% Similarity=0.530 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLD 97 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~ 97 (172)
..+|+++++.++.+++
T Consensus 78 asELEKqLaaLrqElq 93 (475)
T PRK13729 78 AAQMQKQYEEIRRELD 93 (475)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444443333
No 93
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=26.75 E-value=2.7e+02 Score=20.73 Aligned_cols=25 Identities=24% Similarity=0.397 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 84 ELNQQHNDLLRQLDEEKEQQNMLKQ 108 (172)
Q Consensus 84 ~L~~~~~kl~~~l~~~k~~~~~l~~ 108 (172)
.|..+..+|+++++.++.+++.|.+
T Consensus 108 ~l~~e~~~l~~~~e~Le~e~~~L~~ 132 (161)
T TIGR02894 108 RLKNQNESLQKRNEELEKELEKLRQ 132 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444455555554444444433
No 94
>PF07438 DUF1514: Protein of unknown function (DUF1514); InterPro: IPR009999 This entry is represented by Bacteriophage phi PVL, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Staphylococcus aureus and related bacteriophage proteins of around 65 residues in length. The function of this family is unknown.
Probab=26.61 E-value=1.7e+02 Score=18.31 Aligned_cols=44 Identities=14% Similarity=0.261 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 043113 91 DLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFL 147 (172)
Q Consensus 91 kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~ 147 (172)
.+..+++.++-.|.-|.... +.+-+.++|.+++..+++..+.+.
T Consensus 22 ~lr~eiealkY~N~yL~~~~-------------v~~~g~~gl~~~~~e~~r~~~~~k 65 (66)
T PF07438_consen 22 ELRKEIEALKYMNDYLFDQF-------------VRDNGYEGLEEYEIEIERIKKDFK 65 (66)
T ss_pred HHHHHHHHHHHHHHHHHHHH-------------hhccCcchHHHHHHHHHHHHHHhc
Confidence 55567777776666554443 334457888888888888877654
No 95
>COG2882 FliJ Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=26.56 E-value=2.6e+02 Score=20.47 Aligned_cols=71 Identities=13% Similarity=0.114 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
+..+..++.++....+.......+|......+.-+ |-..-..+++..+...+...|..+-..|......+-
T Consensus 18 ~e~a~~el~k~~~~~~~~~~qL~~l~~y~~ey~q~--~~~k~~~G~s~~q~~nyq~fI~~Le~~I~q~~~~~~ 88 (148)
T COG2882 18 EEEAAIELSKIRSEKENAEEQLKMLSGYRNEYEQN--LNEKLKSGVSAAQWQNYQQFISQLEVAIDQQQSQLS 88 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666666666665555555444444333221 111135788898888887777777777766665554
No 96
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=26.37 E-value=2.2e+02 Score=19.45 Aligned_cols=37 Identities=8% Similarity=0.159 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCC
Q 043113 129 LQELLQMDSAVDDLHQTFLAKINEKTAAAAASSSVAP 165 (172)
Q Consensus 129 ~~eL~~l~~~Le~~l~~V~~r~~~l~~~~~~~s~~~~ 165 (172)
+.+....+..+..--...++.+...+.+..-+..++|
T Consensus 62 ~~~~~~~~qq~r~~~e~~~e~ik~~lk~d~Ca~~~~P 98 (110)
T PF10828_consen 62 VEEQQKREQQLRQQSEERRESIKTALKDDPCANTAVP 98 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHccCccccCCCC
Confidence 5556666666666666677777777766643433343
No 97
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=25.95 E-value=1.4e+02 Score=17.30 Aligned_cols=21 Identities=29% Similarity=0.243 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 043113 83 NELNQQHNDLLRQLDEEKEQQ 103 (172)
Q Consensus 83 ~~L~~~~~kl~~~l~~~k~~~ 103 (172)
..|+++++.|+.++..++..-
T Consensus 2 ~aLrqQv~aL~~qv~~Lq~~f 22 (46)
T PF09006_consen 2 NALRQQVEALQGQVQRLQAAF 22 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHH
Confidence 457888888888888877643
No 98
>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=25.94 E-value=1.5e+02 Score=25.89 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=22.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDSAVDDLHQTFLA 148 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~~Le~~l~~V~~ 148 (172)
.+.+|+-+||.+|..-||++++.|..
T Consensus 87 kvG~LskdeLm~LasDLeKLk~Kv~r 112 (533)
T PF00843_consen 87 KVGDLSKDELMELASDLEKLKKKVQR 112 (533)
T ss_dssp EBTTB-HHHHHHHHHHHHHHHHHHHH
T ss_pred EecCcCHHHHHHHHHHHHHHHHHHhc
Confidence 46999999999999999999999854
No 99
>PRK11637 AmiB activator; Provisional
Probab=25.78 E-value=4.2e+02 Score=22.57 Aligned_cols=25 Identities=4% Similarity=0.165 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 043113 131 ELLQMDSAVDDLHQTFLAKINEKTA 155 (172)
Q Consensus 131 eL~~l~~~Le~~l~~V~~r~~~l~~ 155 (172)
++..++..|+.....+..++...-.
T Consensus 111 eI~~~q~~l~~~~~~l~~rlra~Y~ 135 (428)
T PRK11637 111 SIAKLEQQQAAQERLLAAQLDAAFR 135 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555555555555555444
No 100
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=25.61 E-value=1.7e+02 Score=22.54 Aligned_cols=19 Identities=11% Similarity=0.202 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 043113 130 QELLQMDSAVDDLHQTFLA 148 (172)
Q Consensus 130 ~eL~~l~~~Le~~l~~V~~ 148 (172)
+.++.|...|+.+....-.
T Consensus 156 e~~~~la~~ie~l~~~~~~ 174 (200)
T PF07412_consen 156 EHVQYLAEVIERLTGQELD 174 (200)
T ss_dssp HHHHHHHHHHHHCC-----
T ss_pred HHHHHHHHHHHHHhccCcc
Confidence 3444444555544444333
No 101
>KOG2861 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.49 E-value=1.4e+02 Score=25.62 Aligned_cols=40 Identities=10% Similarity=0.043 Sum_probs=29.1
Q ss_pred cccchhhccccchhhhhhhhhhhc---------------cccCcccHHHHHHHHh
Q 043113 21 DDRLITFSKRGSGIYKKASEIWEA---------------IHLCQPSVKAIANRFL 60 (172)
Q Consensus 21 ~~R~vTfsKRr~GL~KKa~ELs~L---------------~sfg~Psv~~Vl~ry~ 60 (172)
-++--||+.+|.-+|||..+|-.| |-|.-|...++.+...
T Consensus 279 la~~gkl~lsr~e~lk~iGkLf~LR~~INL~s~lLdtPdf~W~ep~Le~iY~~~r 333 (399)
T KOG2861|consen 279 LALGGKLTLSREELLKKIGKLFALRHDINLSSGLLDTPDFYWDEPQLEPIYEATR 333 (399)
T ss_pred HHhcCeecccHHHHHHHHHHHHHHheeeecccccccCcccccCchhHHHHHHHHH
Confidence 344557889999999999999999 3355677666655443
No 102
>PF11944 DUF3461: Protein of unknown function (DUF3461); InterPro: IPR020911 This entry describes proteins of unknown function.
Probab=25.12 E-value=1.1e+02 Score=21.78 Aligned_cols=25 Identities=12% Similarity=0.251 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 129 LQELLQMDSAVDDLHQTFLAKINEK 153 (172)
Q Consensus 129 ~~eL~~l~~~Le~~l~~V~~r~~~l 153 (172)
++||.-|+..+.....+|+..++.|
T Consensus 101 L~dL~HLE~Vv~~KIaEIe~dlekL 125 (125)
T PF11944_consen 101 LDDLRHLEKVVNSKIAEIERDLEKL 125 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7889999999999999999988753
No 103
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=25.08 E-value=2.1e+02 Score=18.75 Aligned_cols=22 Identities=0% Similarity=0.012 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 043113 131 ELLQMDSAVDDLHQTFLAKINE 152 (172)
Q Consensus 131 eL~~l~~~Le~~l~~V~~r~~~ 152 (172)
....+...+.+.+..++.+...
T Consensus 28 ~~~~~r~~~~~~~~~a~~~~~~ 49 (94)
T PF05957_consen 28 KADEARDRAEEALDDARDRAED 49 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444433
No 104
>PF03233 Cauli_AT: Aphid transmission protein; InterPro: IPR004917 This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus []. This protein interacts with the PIII protein []. ; GO: 0019089 transmission of virus
Probab=24.99 E-value=3e+02 Score=20.57 Aligned_cols=27 Identities=11% Similarity=0.085 Sum_probs=20.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 128 NLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 128 s~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
+..++.++...+++.++.|++.+-.+.
T Consensus 136 ~~~~i~e~IKd~de~L~~I~d~iK~Ii 162 (163)
T PF03233_consen 136 TEKLIEELIKDFDERLKEIRDKIKKII 162 (163)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 567788888888888888888775543
No 105
>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=24.97 E-value=3.3e+02 Score=21.06 Aligned_cols=66 Identities=12% Similarity=0.247 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTA 155 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~ 155 (172)
+..|+.-+.....+++....+...|+-+.+ .+.. .|. ...+.|..+...|+..+..++..++.+-.
T Consensus 99 ~~~w~~al~na~a~lehq~~R~~NLeLl~~-~g~n-aW~------~~n~~Le~~~~~le~~l~~~k~~ie~vN~ 164 (221)
T PF05700_consen 99 VEAWKEALDNAYAQLEHQRLRLENLELLSK-YGEN-AWL------IHNEQLEAMLKRLEKELAKLKKEIEEVNR 164 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhHH-HHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456777777777777777666665643332 2221 332 23578888888888888888888777653
No 106
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=24.39 E-value=4.4e+02 Score=24.09 Aligned_cols=30 Identities=13% Similarity=0.323 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 80 ARINELNQQHNDLLRQLDEEKEQQNMLKQM 109 (172)
Q Consensus 80 ~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~ 109 (172)
..+..|...+.+++.++++++.+.+.+...
T Consensus 436 ~e~~~L~~~~ee~k~eie~L~~~l~~~~r~ 465 (652)
T COG2433 436 EENSELKRELEELKREIEKLESELERFRRE 465 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666666666665554444333
No 107
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=24.33 E-value=1.1e+02 Score=21.14 Aligned_cols=18 Identities=22% Similarity=0.495 Sum_probs=14.8
Q ss_pred CCCCCCHHHHHHHHHHHH
Q 043113 123 PVDELNLQELLQMDSAVD 140 (172)
Q Consensus 123 ~l~~Ls~~eL~~l~~~Le 140 (172)
.+++|+.+|+..|...++
T Consensus 86 Rle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 86 RLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHhCCHHHHHHHHHHhc
Confidence 467889999999888776
No 108
>PRK10132 hypothetical protein; Provisional
Probab=24.32 E-value=2.4e+02 Score=19.37 Aligned_cols=26 Identities=12% Similarity=-0.008 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 126 ELNLQELLQMDSAVDDLHQTFLAKIN 151 (172)
Q Consensus 126 ~Ls~~eL~~l~~~Le~~l~~V~~r~~ 151 (172)
+.+-+++..+...++..++..+.++.
T Consensus 37 ~~~~~~~~~lR~r~~~~L~~ar~~l~ 62 (108)
T PRK10132 37 SDAKGEAEAARRKAQALLKETRARMH 62 (108)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34567778888888888888877665
No 109
>PF06717 DUF1202: Protein of unknown function (DUF1202); InterPro: IPR009592 This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.
Probab=23.53 E-value=4.2e+02 Score=21.76 Aligned_cols=35 Identities=17% Similarity=0.289 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCH
Q 043113 89 HNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNL 129 (172)
Q Consensus 89 ~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~ 129 (172)
+..|++++.+++.+.--+.+.+. .+||.+-++=.+
T Consensus 154 I~~L~~qisaLdkqi~ai~Kkid------~yWgkda~gk~~ 188 (308)
T PF06717_consen 154 IPGLNKQISALDKQIVAINKKID------RYWGKDANGKQL 188 (308)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH------hccCCCCCCCcc
Confidence 44444444444443333333443 578877655433
No 110
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=22.79 E-value=1.3e+02 Score=19.72 Aligned_cols=17 Identities=29% Similarity=0.591 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 043113 84 ELNQQHNDLLRQLDEEK 100 (172)
Q Consensus 84 ~L~~~~~kl~~~l~~~k 100 (172)
+|..++.+++.+++...
T Consensus 2 eL~~~~~~l~~~~~~~~ 18 (93)
T PF00816_consen 2 ELEAQIKELEKEIEERR 18 (93)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 45556666666665543
No 111
>COG3096 MukB Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=22.48 E-value=6.9e+02 Score=23.90 Aligned_cols=62 Identities=13% Similarity=0.313 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEK 153 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l 153 (172)
+..|..+..+|..++...+.-.+.+.+..+. .-..|..++|..+...++.++..+.......
T Consensus 515 ~~~lr~~l~eLEqr~~qQqsa~~Ll~~f~kr----------~~~~l~ae~lE~~~~e~eal~E~ls~~~s~~ 576 (1480)
T COG3096 515 VQPLRMRLSELEQRLRQQQSAERLLADFCKR----------QGKNLDAEELEALHQELEALIESLSDSVSNA 576 (1480)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------hcccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666667766666655544444444432 1134458888888888888777766555443
No 112
>PRK14127 cell division protein GpsB; Provisional
Probab=22.43 E-value=2.7e+02 Score=19.24 Aligned_cols=22 Identities=18% Similarity=0.213 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 043113 86 NQQHNDLLRQLDEEKEQQNMLK 107 (172)
Q Consensus 86 ~~~~~kl~~~l~~~k~~~~~l~ 107 (172)
..++..|++++..++.+...++
T Consensus 43 ~~e~~~Lk~e~~~l~~~l~e~~ 64 (109)
T PRK14127 43 QKEIEELQQENARLKAQVDELT 64 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444443333
No 113
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=21.84 E-value=2.2e+02 Score=18.52 Aligned_cols=20 Identities=15% Similarity=0.342 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCHHHHHHHHH
Q 043113 118 RWWETPVDELNLQELLQMDS 137 (172)
Q Consensus 118 ~~~~~~l~~Ls~~eL~~l~~ 137 (172)
.+.-++.++|++++|.+|-.
T Consensus 38 rFhTCSae~m~a~eLv~FL~ 57 (78)
T PF10678_consen 38 RFHTCSAEGMTADELVDFLE 57 (78)
T ss_pred eEEecCCCCCCHHHHHHHHH
Confidence 45678999999999998754
No 114
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=21.83 E-value=29 Score=23.79 Aligned_cols=49 Identities=24% Similarity=0.301 Sum_probs=29.9
Q ss_pred cccee-eecCCcccchhhccccchhhhhhhhhhhc-----cccCcccHHHHHHHHhCCC
Q 043113 11 KIEMK-KIENEDDRLITFSKRGSGIYKKASEIWEA-----IHLCQPSVKAIANRFLGMS 63 (172)
Q Consensus 11 Ki~i~-~I~n~~~R~vTfsKRr~GL~KKa~ELs~L-----~sfg~Psv~~Vl~ry~~~~ 63 (172)
+|+++ -++|-++-.++|.||-.|+-+ +=++ --||.--.+.++..|.+..
T Consensus 19 ~ie~K~~~~~RSN~~i~f~KRt~Girq----fEi~n~G~~RI~gYk~se~~~~~f~slG 73 (103)
T PF09158_consen 19 KIEVKEIVIDRSNYEIRFKKRTKGIRQ----FEIRNKGEFRIFGYKMSEEIIKKFTSLG 73 (103)
T ss_dssp T--EEEEEEETTEEEEEEEEEETTEEE----EEEETTSEEEEEEES--HHHHHHHHHTT
T ss_pred ceeeeeeEeeccceEEeeecccCceeE----EEEecCCcEEEEEEcCCHHHHHHHHhcC
Confidence 46676 457888899999999988743 2233 1144444577788886544
No 115
>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.
Probab=21.77 E-value=2.4e+02 Score=18.40 Aligned_cols=30 Identities=13% Similarity=0.211 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 125 DELNLQELLQMDSAVDDLHQTFLAKINEKT 154 (172)
Q Consensus 125 ~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~ 154 (172)
.+.++.++..+...+..+...|..-...+.
T Consensus 40 ~~~s~~~~~~~~~~~~~l~~~i~~~~~~~~ 69 (123)
T PF02050_consen 40 QGVSVAQLRNYQRYISALEQAIQQQQQELE 69 (123)
T ss_dssp SGGGHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 577888888888887777777665554443
No 116
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=21.76 E-value=2.3e+02 Score=18.11 Aligned_cols=65 Identities=15% Similarity=0.264 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 86 NQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVD-ELNLQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 86 ~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~-~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
-.++..+...+...+.....+...+...... ... .-.-+++..+...+......|..++..+-..
T Consensus 6 ~~~v~~i~~~i~~i~~~~~~l~~l~~~~l~~------~~~d~~~~~el~~l~~~i~~~~~~~~~~lk~l~~~ 71 (103)
T PF00804_consen 6 FDEVQEIREDIDKIKEKLNELRKLHKKILSS------PDQDSELKRELDELTDEIKQLFQKIKKRLKQLSKD 71 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS------SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345555555555555555555555433221 111 1234566677777777777777777776655
No 117
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=21.75 E-value=2.8e+02 Score=19.05 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRR 111 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~ 111 (172)
+..|+.++..|.++...++..|..|++.+.
T Consensus 24 ~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~ 53 (107)
T PF06156_consen 24 LEELKKQLQELLEENARLRIENEHLRERLE 53 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455555555555555555555544443
No 118
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=21.34 E-value=3.6e+02 Score=20.21 Aligned_cols=64 Identities=16% Similarity=0.203 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh--cC---CCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q 043113 81 RINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKE--TQ---PRWWETPVDELNLQELLQMDSAVDDLHQ 144 (172)
Q Consensus 81 ~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~--~~---~~~~~~~l~~Ls~~eL~~l~~~Le~~l~ 144 (172)
+|..|..++..+..++....+.....+..+.... +. ...-...-..++.++|..+...|...-.
T Consensus 30 ~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~YA~rISk~t~ 98 (188)
T PF10018_consen 30 RIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRPVDYEELLSYAHRISKFTS 98 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCHHHHHHHHHHHHHhcC
Confidence 4555555555555554444333333333322111 00 0122234567778888888777665433
No 119
>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=21.26 E-value=1.9e+02 Score=17.10 Aligned_cols=23 Identities=13% Similarity=0.143 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 043113 133 LQMDSAVDDLHQTFLAKINEKTA 155 (172)
Q Consensus 133 ~~l~~~Le~~l~~V~~r~~~l~~ 155 (172)
......+...+..|..++..+-.
T Consensus 35 ~~~~~~l~~~~~~i~~~i~~L~~ 57 (65)
T PF09278_consen 35 ADRRALLEEKLEEIEEQIAELQA 57 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34446788888888888877653
No 120
>PF02646 RmuC: RmuC family; InterPro: IPR003798 This protein contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures []. Proteins in this family are predicted to contain a central endonuclease-like fold domain, surrounded by coiled coils, consistent with a direct role in DNA cleavage [, ].
Probab=21.23 E-value=4.5e+02 Score=21.35 Aligned_cols=38 Identities=16% Similarity=0.213 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCC
Q 043113 129 LQELLQMDSAVDDLHQTFLAKINEKTAAAAASSSVAPP 166 (172)
Q Consensus 129 ~~eL~~l~~~Le~~l~~V~~r~~~l~~~~~~~s~~~~~ 166 (172)
.+...++...++.....+..+++.+...+...+.++||
T Consensus 267 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 304 (304)
T PF02646_consen 267 VKSYNKAVGSLEKRVGNIARRIEKLKELGAKSSKELPP 304 (304)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHhhcchhhhcCCCC
Confidence 55667788888888888889999888888778777775
No 121
>PLN02678 seryl-tRNA synthetase
Probab=21.20 E-value=5.6e+02 Score=22.35 Aligned_cols=70 Identities=17% Similarity=0.141 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043113 82 INELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDEL--NLQELLQMDSAVDDLHQTFLAKINEKTA 155 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~L--s~~eL~~l~~~Le~~l~~V~~r~~~l~~ 155 (172)
+-.+.++..+++.+++.++.+...+.+.+...... +++.+.+ -+.+|.+=...|+..+..+...+.+++.
T Consensus 35 il~ld~~~r~l~~~~e~lr~erN~~sk~I~~~k~~----~~~~~~l~~~~~~Lk~ei~~le~~~~~~~~~l~~~~~ 106 (448)
T PLN02678 35 VIALDKEWRQRQFELDSLRKEFNKLNKEVAKLKIA----KEDATELIAETKELKKEITEKEAEVQEAKAALDAKLK 106 (448)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC----CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55667777788888888777666666655532211 0122222 1233333334445555555566655554
No 122
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=21.14 E-value=5.1e+02 Score=21.86 Aligned_cols=9 Identities=11% Similarity=0.239 Sum_probs=4.6
Q ss_pred HHHHHHHHh
Q 043113 52 VKAIANRFL 60 (172)
Q Consensus 52 v~~Vl~ry~ 60 (172)
|+.|+-+.+
T Consensus 200 vERV~PqLK 208 (359)
T PF10498_consen 200 VERVLPQLK 208 (359)
T ss_pred HHHHhhhhe
Confidence 455555553
No 123
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=20.86 E-value=2.1e+02 Score=17.35 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEK 100 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k 100 (172)
++.|..++..|..+++.+.
T Consensus 5 id~Ls~dVq~L~~kvdqLs 23 (56)
T PF04728_consen 5 IDQLSSDVQTLNSKVDQLS 23 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444443
No 124
>PF01519 DUF16: Protein of unknown function DUF16; InterPro: IPR002862 Proteins that contain this domain are of unknown function. It appears to be confined to proteins from Mycoplasma pneumoniae [].; PDB: 2BA2_C.
Probab=20.81 E-value=2.9e+02 Score=18.93 Aligned_cols=48 Identities=17% Similarity=0.219 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043113 87 QQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEK 153 (172)
Q Consensus 87 ~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l 153 (172)
.++.+|.+.++++-+....+...++ .+...| ..+...+..|..|++.+
T Consensus 53 eqI~kL~e~V~~QGEqIkel~~e~k------------------~qgktL-~~I~~~L~~inkRLD~~ 100 (102)
T PF01519_consen 53 EQINKLTEKVDKQGEQIKELQVEQK------------------AQGKTL-QLILKTLQSINKRLDKM 100 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH------------------HHHHHH-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------------------HHHHHH-HHHHHHHHHHHHHHhhc
Confidence 4555666666666665555555554 223344 66777778888888765
No 125
>PRK09039 hypothetical protein; Validated
Probab=20.74 E-value=5e+02 Score=21.62 Aligned_cols=63 Identities=17% Similarity=0.178 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043113 79 HARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWETPVDELNLQELLQMDSAVDDLHQTFLAKINEKTAA 156 (172)
Q Consensus 79 ~~~~~~L~~~~~kl~~~l~~~k~~~~~l~~~~~~~~~~~~~~~~~l~~Ls~~eL~~l~~~Le~~l~~V~~r~~~l~~~ 156 (172)
...+..|++|++.|+.++..++.....+++..... -..+..|...|+..+..=-..+..+..+
T Consensus 136 ~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~---------------~~~i~~L~~~L~~a~~~~~~~l~~~~~~ 198 (343)
T PRK09039 136 LAQVELLNQQIAALRRQLAALEAALDASEKRDRES---------------QAKIADLGRRLNVALAQRVQELNRYRSE 198 (343)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHhHHH
No 126
>PF02256 Fe_hyd_SSU: Iron hydrogenase small subunit; InterPro: IPR003149 Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases (1.12.7.2 from EC) show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters []. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold [].; PDB: 3LX4_A 1C4C_A 1FEH_A 3C8Y_A 1C4A_A 1HFE_S 1GX7_D 1E08_D.
Probab=20.62 E-value=57 Score=19.83 Aligned_cols=37 Identities=24% Similarity=0.305 Sum_probs=26.5
Q ss_pred ccccchhhhhhhhhhhccccCcccHHHHHHHHhCCCc
Q 043113 28 SKRGSGIYKKASEIWEAIHLCQPSVKAIANRFLGMSQ 64 (172)
Q Consensus 28 sKRr~GL~KKa~ELs~L~sfg~Psv~~Vl~ry~~~~~ 64 (172)
.+|-.||++--....+-.+.-+|.|..+.+.|+..+.
T Consensus 8 ~~R~~~LY~~d~~~~~r~s~eNp~v~~lY~~~lg~p~ 44 (60)
T PF02256_consen 8 LKRAEGLYNIDKSSPLRKSHENPEVQELYKEFLGGPG 44 (60)
T ss_dssp HHHHHHHHHHHHHTSB-SGGG-HHHHHHHHHTTSSTT
T ss_pred HHHHHHHHHHHhcCCCCCCCcCHHHHHHHHHHhCCCC
Confidence 3566777776666654477778999999999999664
No 127
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=20.54 E-value=1.4e+02 Score=22.58 Aligned_cols=15 Identities=7% Similarity=0.414 Sum_probs=12.5
Q ss_pred ccHHHHHHHHhCCCc
Q 043113 50 PSVKAIANRFLGMSQ 64 (172)
Q Consensus 50 Psv~~Vl~ry~~~~~ 64 (172)
|++..++++|.....
T Consensus 136 p~~~~l~~kY~~l~~ 150 (199)
T PF10112_consen 136 PTAVKLLEKYAELES 150 (199)
T ss_pred hHHHHHHHHHHHHHh
Confidence 899999999977654
No 128
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.17 E-value=1.4e+02 Score=18.00 Aligned_cols=18 Identities=17% Similarity=0.340 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 043113 85 LNQQHNDLLRQLDEEKEQ 102 (172)
Q Consensus 85 L~~~~~kl~~~l~~~k~~ 102 (172)
++.++.++++++++.+++
T Consensus 46 ~r~~~~~~~k~l~~le~e 63 (68)
T PF06305_consen 46 LRRRIRRLRKELKKLEKE 63 (68)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344455555555554443
No 129
>KOG0639 consensus Transducin-like enhancer of split protein (contains WD40 repeats) [Chromatin structure and dynamics]
Probab=20.10 E-value=6.5e+02 Score=22.69 Aligned_cols=18 Identities=17% Similarity=0.104 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEE 99 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~ 99 (172)
.++|+.||..++-+.+++
T Consensus 32 fqflqaqyhslkleceKl 49 (705)
T KOG0639|consen 32 FQFLQAQYHSLKLECEKL 49 (705)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344555555444444443
No 130
>PF05983 Med7: MED7 protein; InterPro: IPR009244 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3FBI_C 3FBN_A 1YKH_A 1YKE_A.
Probab=20.10 E-value=3.7e+02 Score=19.82 Aligned_cols=21 Identities=14% Similarity=0.259 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 043113 82 INELNQQHNDLLRQLDEEKEQ 102 (172)
Q Consensus 82 ~~~L~~~~~kl~~~l~~~k~~ 102 (172)
+..+..|+.+.+++++..+..
T Consensus 133 i~~me~Ql~~kr~~i~~i~~~ 153 (162)
T PF05983_consen 133 IMMMEEQLEEKREEIEEIRKV 153 (162)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444433
Done!