Query 038327
Match_columns 91
No_of_seqs 138 out of 1073
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 09:52:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038327hhsearch_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 7.6E-23 1.6E-27 144.5 2.6 54 1-54 8-77 (195)
2 cd00265 MADS_MEF2_like MEF2 (m 99.9 3.6E-23 7.8E-28 131.0 0.8 53 1-53 7-73 (77)
3 cd00266 MADS_SRF_like SRF-like 99.8 1E-20 2.2E-25 121.1 2.2 54 1-54 7-75 (83)
4 smart00432 MADS MADS domain. 99.7 6.6E-19 1.4E-23 107.0 1.0 35 1-35 7-41 (59)
5 cd00120 MADS MADS: MCM1, Agamo 99.7 3E-18 6.6E-23 104.0 0.3 35 1-35 7-41 (59)
6 PF00319 SRF-TF: SRF-type tran 99.7 2.5E-18 5.3E-23 101.9 -2.1 34 2-35 1-34 (51)
7 KOG0015 Regulator of arginine 99.4 2.8E-14 6.1E-19 109.9 0.6 35 1-35 69-103 (338)
8 COG5068 ARG80 Regulator of arg 98.6 7.3E-09 1.6E-13 82.5 0.6 46 1-46 88-147 (412)
9 PF09781 NDUF_B5: NADH:ubiquin 74.9 17 0.00037 26.7 6.5 48 41-88 115-168 (187)
10 PRK14127 cell division protein 73.0 9.6 0.00021 25.6 4.5 34 41-79 28-61 (109)
11 PF04521 Viral_P18: ssRNA posi 71.8 2.9 6.2E-05 28.8 1.8 69 11-79 4-96 (120)
12 cd04772 HTH_TioE_rpt1 First He 70.8 17 0.00037 23.2 5.2 35 42-76 63-97 (99)
13 PF04977 DivIC: Septum formati 66.4 15 0.00033 21.7 4.1 26 55-80 24-49 (80)
14 PF05812 Herpes_BLRF2: Herpesv 64.4 13 0.00029 25.4 3.9 27 56-82 4-30 (118)
15 PF08657 DASH_Spc34: DASH comp 62.8 30 0.00065 26.4 5.9 27 55-81 187-213 (259)
16 PF11943 DUF3460: Protein of u 62.0 4.3 9.3E-05 24.7 1.0 25 66-91 13-37 (60)
17 PHA03162 hypothetical protein; 59.6 19 0.00041 25.2 4.0 27 55-81 13-39 (135)
18 cd01111 HTH_MerD Helix-Turn-He 58.9 47 0.001 21.5 5.9 41 39-79 61-104 (107)
19 PHA03155 hypothetical protein; 58.1 23 0.0005 24.2 4.1 27 55-81 8-34 (115)
20 PF13808 DDE_Tnp_1_assoc: DDE_ 55.2 22 0.00048 22.4 3.5 8 28-35 30-37 (90)
21 PF01486 K-box: K-box region; 54.8 26 0.00056 22.3 3.8 28 55-82 12-39 (100)
22 TIGR02044 CueR Cu(I)-responsiv 54.3 61 0.0013 21.4 6.2 23 57-79 88-110 (127)
23 PF14775 NYD-SP28_assoc: Sperm 53.5 41 0.00088 20.1 4.3 27 55-81 33-59 (60)
24 PRK10227 DNA-binding transcrip 53.1 69 0.0015 21.7 6.0 24 56-79 87-110 (135)
25 cd04785 HTH_CadR-PbrR-like Hel 52.9 64 0.0014 21.3 6.2 24 56-79 87-110 (126)
26 TIGR02976 phageshock_pspB phag 52.5 56 0.0012 20.5 5.0 31 55-86 42-72 (75)
27 PF06667 PspB: Phage shock pro 52.4 57 0.0012 20.5 5.0 31 55-86 42-72 (75)
28 PF04065 Not3: Not1 N-terminal 50.7 55 0.0012 24.7 5.5 51 21-80 13-63 (233)
29 PRK00888 ftsB cell division pr 49.4 39 0.00084 22.1 4.1 25 55-79 34-58 (105)
30 PF03980 Nnf1: Nnf1 ; InterPr 48.9 70 0.0015 20.5 5.5 40 40-79 65-104 (109)
31 cd01109 HTH_YyaN Helix-Turn-He 48.7 71 0.0015 20.5 5.6 23 56-78 80-102 (113)
32 PF12165 DUF3594: Domain of un 47.4 8.6 0.00019 26.9 0.7 28 13-40 9-46 (137)
33 PRK12726 flagellar biosynthesi 45.2 25 0.00054 28.7 3.1 19 61-79 116-134 (407)
34 PRK10803 tol-pal system protei 43.0 50 0.0011 24.8 4.3 25 55-79 61-85 (263)
35 PF10226 DUF2216: Uncharacteri 42.4 29 0.00063 25.7 2.8 54 26-79 3-72 (195)
36 PRK09413 IS2 repressor TnpA; R 42.1 53 0.0012 21.5 3.9 33 56-88 79-111 (121)
37 PF02183 HALZ: Homeobox associ 41.7 65 0.0014 18.1 4.0 24 55-78 12-35 (45)
38 KOG4316 Uncharacterized conser 41.6 34 0.00073 24.6 3.0 14 40-53 82-95 (172)
39 KOG0861 SNARE protein YKT6, sy 41.4 44 0.00095 24.7 3.6 30 39-68 121-150 (198)
40 KOG2150 CCR4-NOT transcription 39.1 88 0.0019 26.7 5.5 40 41-80 24-63 (575)
41 PHA02047 phage lambda Rz1-like 38.6 88 0.0019 20.9 4.4 37 55-91 48-86 (101)
42 PRK02224 chromosome segregatio 38.3 65 0.0014 27.6 4.7 48 25-72 450-499 (880)
43 PF00755 Carn_acyltransf: Chol 37.8 22 0.00048 29.4 1.8 42 39-80 8-56 (591)
44 PF15119 APOC4: Apolipoprotein 37.2 15 0.00033 24.2 0.6 19 16-34 77-97 (99)
45 PTZ00046 rifin; Provisional 36.9 40 0.00087 27.1 3.1 26 29-54 39-70 (358)
46 TIGR02209 ftsL_broad cell divi 36.4 90 0.0019 18.8 4.1 26 55-80 31-56 (85)
47 PF02009 Rifin_STEVOR: Rifin/s 35.8 36 0.00078 26.5 2.6 24 30-53 20-49 (299)
48 PF04423 Rad50_zn_hook: Rad50 35.6 21 0.00046 20.3 1.0 29 21-49 15-43 (54)
49 PRK10265 chaperone-modulator p 35.2 1.2E+02 0.0027 19.4 5.7 27 55-81 71-97 (101)
50 TIGR02047 CadR-PbrR Cd(II)/Pb( 35.0 1.3E+02 0.0029 19.8 6.4 10 40-49 62-71 (127)
51 PRK09458 pspB phage shock prot 34.7 1.2E+02 0.0026 19.1 4.9 31 55-86 42-72 (75)
52 cd04783 HTH_MerR1 Helix-Turn-H 34.6 1.3E+02 0.0029 19.6 6.0 24 56-79 85-108 (126)
53 PF04568 IATP: Mitochondrial A 33.3 76 0.0017 20.9 3.5 22 56-77 73-98 (100)
54 PF13591 MerR_2: MerR HTH fami 32.9 87 0.0019 19.4 3.6 21 55-75 63-83 (84)
55 cd01108 HTH_CueR Helix-Turn-He 32.6 1.5E+02 0.0032 19.5 6.3 11 40-50 62-72 (127)
56 PF08172 CASP_C: CASP C termin 32.0 73 0.0016 24.0 3.7 41 39-79 78-131 (248)
57 KOG2861 Uncharacterized conser 31.8 1.6E+02 0.0035 24.0 5.7 77 9-87 280-374 (399)
58 cd04766 HTH_HspR Helix-Turn-He 30.4 1.1E+02 0.0025 18.8 3.9 25 55-79 65-89 (91)
59 PF06133 DUF964: Protein of un 30.2 62 0.0014 20.3 2.7 30 21-50 2-44 (108)
60 cd04784 HTH_CadR-PbrR Helix-Tu 29.5 1.7E+02 0.0036 19.2 6.3 20 58-77 89-108 (127)
61 PF10398 DUF2443: Protein of u 29.2 1.4E+02 0.0029 19.1 4.0 26 55-80 50-75 (79)
62 cd01282 HTH_MerR-like_sg3 Heli 28.9 1.6E+02 0.0036 18.9 5.9 43 36-78 57-104 (112)
63 PF04210 MtrG: Tetrahydrometha 27.5 1.2E+02 0.0026 18.9 3.5 29 53-81 10-38 (70)
64 PF07716 bZIP_2: Basic region 27.4 1.2E+02 0.0027 17.0 4.2 25 55-79 25-49 (54)
65 PF06156 DUF972: Protein of un 26.9 1.6E+02 0.0035 19.5 4.2 20 59-78 33-52 (107)
66 TIGR02051 MerR Hg(II)-responsi 26.9 1.9E+02 0.0041 19.0 5.2 24 56-79 84-107 (124)
67 PF11853 DUF3373: Protein of u 26.7 83 0.0018 26.3 3.4 22 56-77 32-53 (489)
68 cd04787 HTH_HMRTR_unk Helix-Tu 26.6 2E+02 0.0043 19.1 5.4 10 40-49 62-71 (133)
69 COG1723 Uncharacterized conser 26.3 1.5E+02 0.0033 23.7 4.6 81 7-87 211-307 (331)
70 PF06005 DUF904: Protein of un 26.2 1.7E+02 0.0036 18.0 4.2 15 56-70 19-33 (72)
71 PF09712 PHA_synth_III_E: Poly 26.1 1E+02 0.0022 23.6 3.6 34 42-75 256-292 (293)
72 PHA01548 hypothetical protein 26.1 55 0.0012 23.3 1.9 19 73-91 127-145 (167)
73 PF14193 DUF4315: Domain of un 25.9 1.5E+02 0.0033 18.8 3.8 23 57-79 3-25 (83)
74 TIGR02894 DNA_bind_RsfA transc 25.6 2.6E+02 0.0056 20.1 5.5 20 58-77 114-133 (161)
75 PF15458 NTR2: Nineteen comple 25.3 1.6E+02 0.0035 22.1 4.5 41 38-78 203-252 (254)
76 PF09403 FadA: Adhesion protei 25.1 1.6E+02 0.0034 20.1 4.1 20 33-52 14-33 (126)
77 PF11157 DUF2937: Protein of u 25.1 2.4E+02 0.0053 19.9 5.2 39 36-74 53-97 (167)
78 PRK13752 putative transcriptio 25.0 2.3E+02 0.005 19.3 5.2 11 25-35 10-20 (144)
79 PF11853 DUF3373: Protein of u 24.8 47 0.001 27.8 1.6 25 55-80 25-49 (489)
80 PF11690 DUF3287: Protein of u 24.7 1.5E+02 0.0032 20.0 3.8 34 55-88 49-86 (109)
81 KOG1927 R-kappa-B and related 24.7 58 0.0013 29.8 2.2 39 11-50 111-154 (1274)
82 PRK13169 DNA replication intia 24.7 1.8E+02 0.004 19.4 4.2 22 58-79 32-53 (110)
83 PF06305 DUF1049: Protein of u 23.9 81 0.0018 18.2 2.2 21 58-78 44-64 (68)
84 PF15136 UPF0449: Uncharacteri 23.9 2.2E+02 0.0048 18.8 5.4 13 39-51 14-26 (97)
85 cd04770 HTH_HMRTR Helix-Turn-H 23.8 2.1E+02 0.0045 18.4 5.6 10 40-49 62-71 (123)
86 KOG3718 Carnitine O-acyltransf 23.7 1.3E+02 0.0028 25.7 4.0 42 39-80 26-72 (609)
87 PRK09514 zntR zinc-responsive 23.7 2.4E+02 0.0052 19.0 5.2 16 60-75 86-101 (140)
88 TIGR01477 RIFIN variant surfac 23.5 83 0.0018 25.3 2.7 25 30-54 43-73 (353)
89 PF04999 FtsL: Cell division p 23.4 1.9E+02 0.0042 17.9 4.6 25 55-79 42-66 (97)
90 PF11336 DUF3138: Protein of u 23.1 1.4E+02 0.003 25.1 4.0 28 53-80 23-50 (514)
91 COG3074 Uncharacterized protei 23.0 1.4E+02 0.003 18.9 3.2 22 56-77 19-40 (79)
92 PF10224 DUF2205: Predicted co 23.0 2E+02 0.0043 18.2 4.0 24 55-78 37-60 (80)
93 TIGR02761 TraE_TIGR type IV co 22.7 2E+02 0.0042 20.3 4.3 29 41-69 89-117 (181)
94 PRK13726 conjugal transfer pil 22.0 2.3E+02 0.0049 20.5 4.6 33 38-70 85-118 (188)
95 KOG3717 Carnitine O-acyltransf 21.7 80 0.0017 27.1 2.4 42 38-80 19-67 (612)
96 PF09006 Surfac_D-trimer: Lung 21.7 1.8E+02 0.0038 16.8 3.6 23 58-80 2-24 (46)
97 KOG3156 Uncharacterized membra 21.7 1.8E+02 0.0039 22.0 4.1 26 55-80 116-141 (220)
98 TIGR02043 ZntR Zn(II)-responsi 21.6 2.5E+02 0.0055 18.6 5.6 24 56-79 89-112 (131)
99 PRK11546 zraP zinc resistance 21.5 2.5E+02 0.0055 19.6 4.6 36 41-76 52-110 (143)
100 KOG4557 Origin recognition com 21.3 41 0.00088 25.8 0.6 17 21-37 18-34 (262)
101 PF12833 HTH_18: Helix-turn-he 21.3 99 0.0021 18.1 2.2 27 26-54 49-76 (81)
102 PF14916 CCDC92: Coiled-coil d 21.1 69 0.0015 19.4 1.5 25 55-79 21-45 (60)
103 PF08227 DASH_Hsk3: DASH compl 20.8 1.2E+02 0.0026 17.2 2.4 25 56-80 3-27 (45)
104 KOG3014 Protein involved in es 20.5 1.3E+02 0.0027 23.3 3.1 50 12-61 191-252 (257)
105 COG5665 NOT5 CCR4-NOT transcri 20.4 3.1E+02 0.0066 22.9 5.4 40 40-79 13-52 (548)
106 PF07960 CBP4: CBP4; InterPro 20.4 3E+02 0.0066 19.0 5.7 13 36-48 28-40 (128)
107 PRK15422 septal ring assembly 20.2 2.3E+02 0.0051 18.1 3.8 23 55-77 18-40 (79)
108 PF07195 FliD_C: Flagellar hoo 20.1 3.5E+02 0.0076 19.6 5.7 38 41-78 176-223 (239)
No 1
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.86 E-value=7.6e-23 Score=144.52 Aligned_cols=54 Identities=50% Similarity=0.754 Sum_probs=50.2
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhhhCCC--------------CCCCc--HHHHHHHHhCCChH
Q 038327 1 MKRIENEDDRLITFSKRKSRTYNKASELVTLTGAE--------------IGHPS--IEAVANRFLGQTRR 54 (91)
Q Consensus 1 ik~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~--------------f~~ps--~~~vl~r~~~~~~~ 54 (91)
|++|+|+++|+|||+|||.||||||+||||||||+ |++|+ ++.|+++|.....+
T Consensus 8 i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~ 77 (195)
T KOG0014|consen 8 IKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEP 77 (195)
T ss_pred eeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhh
Confidence 78999999999999999999999999999999999 77887 99999999886654
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=99.86 E-value=3.6e-23 Score=130.99 Aligned_cols=53 Identities=42% Similarity=0.637 Sum_probs=50.2
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhhhCCC--------------CCCCcHHHHHHHHhCCCh
Q 038327 1 MKRIENEDDRLITFSKRKSRTYNKASELVTLTGAE--------------IGHPSIEAVANRFLGQTR 53 (91)
Q Consensus 1 ik~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~--------------f~~ps~~~vl~r~~~~~~ 53 (91)
|++|+|+.+|++||+||+.||||||+|||+|||++ |++|++++||+||+..++
T Consensus 7 i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~~ 73 (77)
T cd00265 7 IKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTSG 73 (77)
T ss_pred eEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhccc
Confidence 68999999999999999999999999999999999 888999999999997654
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=99.80 E-value=1e-20 Score=121.12 Aligned_cols=54 Identities=48% Similarity=0.628 Sum_probs=48.5
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhhhCCC--------------CCCCc-HHHHHHHHhCCChH
Q 038327 1 MKRIENEDDRLITFSKRKSRTYNKASELVTLTGAE--------------IGHPS-IEAVANRFLGQTRR 54 (91)
Q Consensus 1 ik~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~--------------f~~ps-~~~vl~r~~~~~~~ 54 (91)
|++|+|+.+|++||+|||.||||||+|||+|||++ |++++ ++.++++|...+..
T Consensus 7 i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~ 75 (83)
T cd00266 7 IKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSAL 75 (83)
T ss_pred eEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHh
Confidence 68999999999999999999999999999999999 44455 89999999877654
No 4
>smart00432 MADS MADS domain.
Probab=99.73 E-value=6.6e-19 Score=106.95 Aligned_cols=35 Identities=51% Similarity=0.760 Sum_probs=34.3
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhhhCCC
Q 038327 1 MKRIENEDDRLITFSKRKSRTYNKASELVTLTGAE 35 (91)
Q Consensus 1 ik~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~ 35 (91)
|++|+|+..|++||+||+.||||||+|||+|||++
T Consensus 7 i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~ 41 (59)
T smart00432 7 IKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAE 41 (59)
T ss_pred eEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCe
Confidence 68999999999999999999999999999999999
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=99.69 E-value=3e-18 Score=103.99 Aligned_cols=35 Identities=54% Similarity=0.767 Sum_probs=34.2
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhhhCCC
Q 038327 1 MKRIENEDDRLITFSKRKSRTYNKASELVTLTGAE 35 (91)
Q Consensus 1 ik~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~ 35 (91)
|++|+|+..|++||+|||.||||||+|||+|||++
T Consensus 7 i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~ 41 (59)
T cd00120 7 IKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAE 41 (59)
T ss_pred eEEeeCcchhhhhHHHHhchHHHhhhhheeccCCc
Confidence 68999999999999999999999999999999999
No 6
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=99.67 E-value=2.5e-18 Score=101.86 Aligned_cols=34 Identities=59% Similarity=0.811 Sum_probs=30.5
Q ss_pred ccccCCCCcccccccccchhhhhhhhhhhhhCCC
Q 038327 2 KRIENEDDRLITFSKRKSRTYNKASELVTLTGAE 35 (91)
Q Consensus 2 k~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~ 35 (91)
|+|+|++.|++||+|||.||||||+|||+|||++
T Consensus 1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~LC~~~ 34 (51)
T PF00319_consen 1 KRIENKSRRKVTFSKRKKGLFKKASELSTLCGVD 34 (51)
T ss_dssp S--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT-E
T ss_pred CCccchhHhHhHHHHHHhhhhhccceeeeecCCe
Confidence 6899999999999999999999999999999999
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.42 E-value=2.8e-14 Score=109.89 Aligned_cols=35 Identities=54% Similarity=0.679 Sum_probs=34.1
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhhhCCC
Q 038327 1 MKRIENEDDRLITFSKRKSRTYNKASELVTLTGAE 35 (91)
Q Consensus 1 ik~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~ 35 (91)
|++|+|+..|.|||||||.||||||+||++|.|.+
T Consensus 69 ~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtq 103 (338)
T KOG0015|consen 69 MEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQ 103 (338)
T ss_pred chhhcccceeeeeehhhhhhhHHHHHHhhhcccce
Confidence 68999999999999999999999999999999998
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=98.63 E-value=7.3e-09 Score=82.53 Aligned_cols=46 Identities=43% Similarity=0.595 Sum_probs=40.7
Q ss_pred CccccCCCCcccccccccchhhhhhhhhhhhhCCC--------------CCCCcHHHHHH
Q 038327 1 MKRIENEDDRLITFSKRKSRTYNKASELVTLTGAE--------------IGHPSIEAVAN 46 (91)
Q Consensus 1 ik~I~n~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~--------------f~~ps~~~vl~ 46 (91)
|.+|+|+..|.|||+||+.||+|||.||++|.+.+ |+.|....|+.
T Consensus 88 is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~ 147 (412)
T COG5068 88 ISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVK 147 (412)
T ss_pred cccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCccccccc
Confidence 67899999999999999999999999999999988 77777555554
No 9
>PF09781 NDUF_B5: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit; InterPro: IPR019173 Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol [, ].
Probab=74.88 E-value=17 Score=26.72 Aligned_cols=48 Identities=10% Similarity=0.198 Sum_probs=30.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHH------HHHHHHHHHHHhccccCcccc
Q 038327 41 IEAVANRFLGQTRRQMTTLLLVEAQRQ------KERGNFLKQMTKGKETQRWWE 88 (91)
Q Consensus 41 ~~~vl~r~~~~~~~~~~~~l~~el~~~------k~~~~~l~~~~~~~~~~~Ww~ 88 (91)
+..-|.||.-.++.+.|++...-++.+ +....++++.+++.+...||-
T Consensus 115 ItR~iAry~~~spq~~YEk~la~l~~e~ek~~lr~~e~~Vr~lm~eRgD~~~~y 168 (187)
T PF09781_consen 115 ITRWIARYFYPSPQKNYEKMLAYLQIENEKAELRLLEKEVRRLMRERGDYPWYY 168 (187)
T ss_pred HHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcee
Confidence 577888888888888887765544433 333334444444566667774
No 10
>PRK14127 cell division protein GpsB; Provisional
Probab=73.01 E-value=9.6 Score=25.59 Aligned_cols=34 Identities=9% Similarity=0.133 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 41 IEAVANRFLGQTRRQMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 41 ~~~vl~r~~~~~~~~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
|+..|+.-. ..|+.+..++..+++++..|+..+.
T Consensus 28 VD~FLd~V~-----~dye~l~~e~~~Lk~e~~~l~~~l~ 61 (109)
T PRK14127 28 VDKFLDDVI-----KDYEAFQKEIEELQQENARLKAQVD 61 (109)
T ss_pred HHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555555432 3455555555555555555555544
No 11
>PF04521 Viral_P18: ssRNA positive strand viral 18kD cysteine rich protein; InterPro: IPR007609 This family represents the 18kDa cysteine-rich protein from ssRNA positive strand viruses.
Probab=71.82 E-value=2.9 Score=28.76 Aligned_cols=69 Identities=19% Similarity=0.237 Sum_probs=47.1
Q ss_pred ccccccccchhhhhhhhhhhhhCCC------CCCCc--------HHHHHHHHhCCChH----------HHHHHHHHHHHH
Q 038327 11 LITFSKRKSRTYNKASELVTLTGAE------IGHPS--------IEAVANRFLGQTRR----------QMTTLLLVEAQR 66 (91)
Q Consensus 11 ~vTfsKRr~GL~KKA~ELs~Lc~~~------f~~ps--------~~~vl~r~~~~~~~----------~~~~~l~~el~~ 66 (91)
-+.|+|.|..++++-.+-++-|... .|=|. ..-+++.|-+.-.- .++..++.+|+.
T Consensus 4 ~~~~rk~R~~~y~~lgl~~vkC~Ln~~~G~~CGMpaa~~l~~~~~~l~~dgfCGeKH~~~~~Sla~r~~~l~~~~~~L~~ 83 (120)
T PF04521_consen 4 FRCVRKYRASVYKKLGLSAVKCRLNSFCGVSCGMPAAFELEDGHPELPIDGFCGEKHKGLYESLAWRHAQLSDLNLELEK 83 (120)
T ss_pred hHHHHHHHHHHHHHcCCeeeeecCCCCCCcCCCCcceeecCCCCCcccccccccHhHHHHHHHHHHhhhhhhhHHHHHHH
Confidence 4678999999999999988877665 23232 12255666543322 356677788888
Q ss_pred HHHHHHHHHHHHh
Q 038327 67 QKERGNFLKQMTK 79 (91)
Q Consensus 67 ~k~~~~~l~~~~~ 79 (91)
++.+.+.|...+.
T Consensus 84 Le~r~e~Lk~~~~ 96 (120)
T PF04521_consen 84 LERREEQLKTQIQ 96 (120)
T ss_pred HHHHHHHHHHHHH
Confidence 8888888877544
No 12
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=70.80 E-value=17 Score=23.19 Aligned_cols=35 Identities=9% Similarity=-0.016 Sum_probs=17.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 038327 42 EAVANRFLGQTRRQMTTLLLVEAQRQKERGNFLKQ 76 (91)
Q Consensus 42 ~~vl~r~~~~~~~~~~~~l~~el~~~k~~~~~l~~ 76 (91)
..+++.+...+......-|.++.+.+.++.+.|++
T Consensus 63 ~~~~~~~~~~~~~~~~~ll~~~~~~l~~~i~~L~~ 97 (99)
T cd04772 63 QRIMRAVHAGIVASALALVDAAHALLQRYRQQLDQ 97 (99)
T ss_pred HHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444444333334445555555555555555544
No 13
>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=66.38 E-value=15 Score=21.72 Aligned_cols=26 Identities=23% Similarity=0.138 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
.++..++.+++.++++++.|+.++..
T Consensus 24 ~ei~~l~~~i~~l~~e~~~L~~ei~~ 49 (80)
T PF04977_consen 24 QEIAELQKEIEELKKENEELKEEIER 49 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56778888888888888888887664
No 14
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=64.45 E-value=13 Score=25.38 Aligned_cols=27 Identities=19% Similarity=0.122 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccc
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTKGKE 82 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~~~~ 82 (91)
.+++|..+|.+|+-+|..|.+.+++..
T Consensus 4 t~EeLaaeL~kLqmENk~LKkkl~~~~ 30 (118)
T PF05812_consen 4 TMEELAAELQKLQMENKALKKKLRQSV 30 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 478999999999999999999988543
No 15
>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=62.83 E-value=30 Score=26.35 Aligned_cols=27 Identities=7% Similarity=-0.200 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGK 81 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~ 81 (91)
++|..+.+++..++++.+.-+..+...
T Consensus 187 ~~y~~l~~~i~~lE~~VaeQ~~qL~~~ 213 (259)
T PF08657_consen 187 QRYNQLSNSIAYLEAEVAEQEAQLERM 213 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567777777777777776666666533
No 16
>PF11943 DUF3460: Protein of unknown function (DUF3460); InterPro: IPR021853 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.
Probab=61.99 E-value=4.3 Score=24.72 Aligned_cols=25 Identities=16% Similarity=0.345 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHhccccCccccCCC
Q 038327 66 RQKERGNFLKQMTKGKETQRWWETPV 91 (91)
Q Consensus 66 ~~k~~~~~l~~~~~~~~~~~Ww~~~v 91 (91)
.+++++=.|..+.+ .+..-||+.||
T Consensus 13 ~lk~~~Pele~~Q~-~GRallWDk~~ 37 (60)
T PF11943_consen 13 QLKAKHPELEEEQR-AGRALLWDKPQ 37 (60)
T ss_pred HHHHhCCchHHHHH-HhhHHhcCCCC
Confidence 44445555555544 34456999886
No 17
>PHA03162 hypothetical protein; Provisional
Probab=59.56 E-value=19 Score=25.20 Aligned_cols=27 Identities=19% Similarity=0.090 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGK 81 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~ 81 (91)
..+++|..||.+|+-+|..|.+.++..
T Consensus 13 ~tmEeLaaeL~kLqmENK~LKkkl~~~ 39 (135)
T PHA03162 13 PTMEDLAAEIAKLQLENKALKKKIKEG 39 (135)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 347899999999999999999999754
No 18
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=58.94 E-value=47 Score=21.55 Aligned_cols=41 Identities=7% Similarity=0.019 Sum_probs=21.2
Q ss_pred CcHHHHHHHHhCCChH---HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 39 PSIEAVANRFLGQTRR---QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 39 ps~~~vl~r~~~~~~~---~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
+.+..+++.+...... .+...+.++++...+.+..+++.+.
T Consensus 61 ~~I~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~L~~l~~~L~ 104 (107)
T cd01111 61 DELARLCRALDAGDGKQPEACLAQLRQKIEVRRAALNALTTQLA 104 (107)
T ss_pred HHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555433321 3455556666666666666655543
No 19
>PHA03155 hypothetical protein; Provisional
Probab=58.12 E-value=23 Score=24.17 Aligned_cols=27 Identities=22% Similarity=0.038 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGK 81 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~ 81 (91)
..+++|..+|.+|+-+|..|.+.+++.
T Consensus 8 ~tvEeLaaeL~kL~~ENK~LKkkl~~~ 34 (115)
T PHA03155 8 ADVEELEKELQKLKIENKALKKKLLQH 34 (115)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 457899999999999999999998754
No 20
>PF13808 DDE_Tnp_1_assoc: DDE_Tnp_1-associated
Probab=55.25 E-value=22 Score=22.35 Aligned_cols=8 Identities=38% Similarity=0.576 Sum_probs=6.2
Q ss_pred hhhhhCCC
Q 038327 28 LVTLTGAE 35 (91)
Q Consensus 28 Ls~Lc~~~ 35 (91)
+++|||++
T Consensus 30 ~a~l~G~~ 37 (90)
T PF13808_consen 30 CAVLCGAD 37 (90)
T ss_pred HHHHHccc
Confidence 56788888
No 21
>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=54.85 E-value=26 Score=22.32 Aligned_cols=28 Identities=11% Similarity=0.054 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGKE 82 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~~ 82 (91)
..+..++.++..++.+++.|+..+++..
T Consensus 12 ~~~e~~~~e~~~L~~~~~~L~~~~R~~~ 39 (100)
T PF01486_consen 12 SQHEELQQEIAKLRKENESLQKELRHLM 39 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 6788999999999999999999988643
No 22
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=54.35 E-value=61 Score=21.39 Aligned_cols=23 Identities=4% Similarity=0.056 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 038327 57 TTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 57 ~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
...+.+++..+....+.|...+.
T Consensus 88 ~~~l~~~i~~L~~~~~~L~~~~~ 110 (127)
T TIGR02044 88 VAEIERKISELQSMRDQLEALAQ 110 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555555544443
No 23
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=53.51 E-value=41 Score=20.05 Aligned_cols=27 Identities=15% Similarity=0.166 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGK 81 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~ 81 (91)
.+-..+..+.+.++++|.+|+..++++
T Consensus 33 ~~R~~l~~e~~~L~~qN~eLr~lLkqY 59 (60)
T PF14775_consen 33 LDRAALIQEKESLEQQNEELRSLLKQY 59 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344577888899999999998887753
No 24
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=53.13 E-value=69 Score=21.67 Aligned_cols=24 Identities=4% Similarity=-0.011 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
+...+.++++.+....+.|.....
T Consensus 87 ~~~~l~~~i~~L~~~~~~L~~~~~ 110 (135)
T PRK10227 87 KVAEIERHIEELQSMRDQLLALAN 110 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555554443
No 25
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=52.88 E-value=64 Score=21.27 Aligned_cols=24 Identities=13% Similarity=-0.002 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
+...+.+++..++.-...|...+.
T Consensus 87 ~~~~l~~~i~~L~~~~~~L~~~~~ 110 (126)
T cd04785 87 HLADVRARIADLRRLEAELKRMVA 110 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555555554443
No 26
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=52.51 E-value=56 Score=20.45 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccCcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGKETQRW 86 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~~~~~W 86 (91)
+.+++|.++.++++++.+.|+..+. .+...|
T Consensus 42 ~~L~~L~~~a~rm~eRI~tLE~ILd-~e~P~w 72 (75)
T TIGR02976 42 ALLQELYAKADRLEERIDTLERILD-AEHPNW 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCc
Confidence 5678889999999999999988876 344445
No 27
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=52.40 E-value=57 Score=20.48 Aligned_cols=31 Identities=29% Similarity=0.408 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccCcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGKETQRW 86 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~~~~~W 86 (91)
+.+++|.++.+++.++.+.|+..+. .+...|
T Consensus 42 ~~L~~L~~~a~rm~eRI~tLE~ILd-ae~P~w 72 (75)
T PF06667_consen 42 QRLQELYEQAERMEERIETLERILD-AEHPNW 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCc
Confidence 6678999999999999999988885 455556
No 28
>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=50.68 E-value=55 Score=24.65 Aligned_cols=51 Identities=16% Similarity=0.188 Sum_probs=40.5
Q ss_pred hhhhhhhhhhhhCCCCCCCcHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 21 TYNKASELVTLTGAEIGHPSIEAVANRFLGQTRRQMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 21 L~KKA~ELs~Lc~~~f~~ps~~~vl~r~~~~~~~~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
+|||+.|-- -.++.|.+++.+...+.+-+++.+.|.++=+++..++..++.
T Consensus 13 ~lKkv~EG~---------~~F~~i~~K~~~~~n~~QKEK~E~DLKkEIKKLQR~RdQIK~ 63 (233)
T PF04065_consen 13 TLKKVQEGV---------EEFDEIYEKVESATNQNQKEKLEADLKKEIKKLQRLRDQIKT 63 (233)
T ss_pred HHHHHHHHH---------HHHHHHHHHHHcccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466666632 346889999999888888899999998888888888888884
No 29
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=49.42 E-value=39 Score=22.14 Aligned_cols=25 Identities=12% Similarity=0.021 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
.++..+++++++++.+++.|..++.
T Consensus 34 ~q~~~~~~e~~~l~~~n~~L~~eI~ 58 (105)
T PRK00888 34 DQVAAQQQTNAKLKARNDQLFAEID 58 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566667777777777777777665
No 30
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=48.93 E-value=70 Score=20.51 Aligned_cols=40 Identities=15% Similarity=0.119 Sum_probs=31.6
Q ss_pred cHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 40 SIEAVANRFLGQTRRQMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 40 s~~~vl~r~~~~~~~~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
+...+|..++.........+|...+..+.++|+.|...+.
T Consensus 65 ~P~~~i~a~l~~~~~~~~~~L~~~l~~l~~eN~~L~~~i~ 104 (109)
T PF03980_consen 65 TPEEDIRAHLAPYKKKEREQLNARLQELEEENEALAEEIQ 104 (109)
T ss_pred ChHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777766655557888999999999999999988876
No 31
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=48.68 E-value=71 Score=20.52 Aligned_cols=23 Identities=17% Similarity=0.052 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~ 78 (91)
....+.+++..+..+.+.|+..+
T Consensus 80 ~~~~l~~~~~~l~~~i~~l~~~~ 102 (113)
T cd01109 80 RLELLEEHREELEEQIAELQETL 102 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555444
No 32
>PF12165 DUF3594: Domain of unknown function (DUF3594); InterPro: IPR021998 This presumed domain is functionally uncharacterised.This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00628 from PFAM.
Probab=47.44 E-value=8.6 Score=26.91 Aligned_cols=28 Identities=29% Similarity=0.468 Sum_probs=22.1
Q ss_pred ccccccchhhhhh----hhhhhhhCCC------CCCCc
Q 038327 13 TFSKRKSRTYNKA----SELVTLTGAE------IGHPS 40 (91)
Q Consensus 13 TfsKRr~GL~KKA----~ELs~Lc~~~------f~~ps 40 (91)
-|+-||.||++=. .|+.-+||-+ ||+|+
T Consensus 9 df~~RR~g~v~ALT~dve~Fy~~CDP~kenLCLYG~p~ 46 (137)
T PF12165_consen 9 DFSGRRAGIVRALTTDVEEFYQQCDPEKENLCLYGHPD 46 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCccccceEEecCCC
Confidence 4889999988743 6788899887 88764
No 33
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=45.20 E-value=25 Score=28.69 Aligned_cols=19 Identities=11% Similarity=-0.134 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 038327 61 LVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 61 ~~el~~~k~~~~~l~~~~~ 79 (91)
.++++..+.++.+|+..++
T Consensus 116 ~~~~~~~~~~~~~~~~~~~ 134 (407)
T PRK12726 116 EEELSAMRLELAALNRELA 134 (407)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4788888888888888887
No 34
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=43.00 E-value=50 Score=24.81 Aligned_cols=25 Identities=4% Similarity=-0.206 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
.+++.|+.|+..++-+++.+...+.
T Consensus 61 ~ql~~lq~ev~~LrG~~E~~~~~l~ 85 (263)
T PRK10803 61 QQLSDNQSDIDSLRGQIQENQYQLN 85 (263)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 5666777777777766666665544
No 35
>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain. Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.
Probab=42.43 E-value=29 Score=25.67 Aligned_cols=54 Identities=19% Similarity=0.145 Sum_probs=31.5
Q ss_pred hhhhhhhCCCCCCCcHHHHHHHHhCCChH----------------HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 26 SELVTLTGAEIGHPSIEAVANRFLGQTRR----------------QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 26 ~ELs~Lc~~~f~~ps~~~vl~r~~~~~~~----------------~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
.+|+-+.|.++-.-+-..++.|....... .++.....||..+|..|.+|+.++.
T Consensus 3 ~~l~~~sDeell~~skeel~~rLR~~E~ek~~~m~~~g~lm~evNrrlQ~hl~EIR~LKe~NqkLqedNq 72 (195)
T PF10226_consen 3 EDLSKVSDEELLRWSKEELVRRLRRAEAEKMSLMVEHGRLMKEVNRRLQQHLNEIRGLKEVNQKLQEDNQ 72 (195)
T ss_pred cccccCCHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555666554444556666666543221 3445556677777777777776654
No 36
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=42.12 E-value=53 Score=21.51 Aligned_cols=33 Identities=12% Similarity=0.194 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccCcccc
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTKGKETQRWWE 88 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~~~~~~~Ww~ 88 (91)
++.+|..++..++.+++-|.....-.+...|-+
T Consensus 79 ei~~L~~el~~L~~E~diLKKa~~~~~~~~~~~ 111 (121)
T PRK09413 79 QIKELQRLLGKKTMENELLKEAVEYGRAKKWIA 111 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhchhhhhh
Confidence 355666666777777777766666566666654
No 37
>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=41.71 E-value=65 Score=18.13 Aligned_cols=24 Identities=17% Similarity=0.061 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~ 78 (91)
..|+.|..+-+.++++++.|+.++
T Consensus 12 ~~yd~Lk~~~~~L~~E~~~L~aev 35 (45)
T PF02183_consen 12 ASYDSLKAEYDSLKKENEKLRAEV 35 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666666666665554
No 38
>KOG4316 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.62 E-value=34 Score=24.65 Aligned_cols=14 Identities=29% Similarity=0.408 Sum_probs=11.1
Q ss_pred cHHHHHHHHhCCCh
Q 038327 40 SIEAVANRFLGQTR 53 (91)
Q Consensus 40 s~~~vl~r~~~~~~ 53 (91)
.|++||+||....-
T Consensus 82 tvkaVldRFkRL~~ 95 (172)
T KOG4316|consen 82 TVKAVLDRFKRLHC 95 (172)
T ss_pred cHHHHHHHHHhccc
Confidence 38999999987553
No 39
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.41 E-value=44 Score=24.73 Aligned_cols=30 Identities=10% Similarity=0.207 Sum_probs=22.6
Q ss_pred CcHHHHHHHHhCCChHHHHHHHHHHHHHHH
Q 038327 39 PSIEAVANRFLGQTRRQMTTLLLVEAQRQK 68 (91)
Q Consensus 39 ps~~~vl~r~~~~~~~~~~~~l~~el~~~k 68 (91)
|..+..|++|+++.....+.++|+||+.-|
T Consensus 121 ~~L~~~l~kyqdP~ead~l~kvQ~EldETK 150 (198)
T KOG0861|consen 121 PYLDTLLSKYQDPAEADPLLKVQNELDETK 150 (198)
T ss_pred hhHHHHHHHhcChhhhChHHHHHHHHHHHH
Confidence 557888888887666667778888887766
No 40
>KOG2150 consensus CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=39.06 E-value=88 Score=26.75 Aligned_cols=40 Identities=8% Similarity=0.127 Sum_probs=35.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 41 IEAVANRFLGQTRRQMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 41 ~~~vl~r~~~~~~~~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
+++|.+++.+.....|-+++...|.++=+++.+|+..++.
T Consensus 24 Fd~i~ek~~~~~n~sqkeK~e~DLKkEIKKLQRlRdQIKt 63 (575)
T KOG2150|consen 24 FDEIYEKLHSANNVSQKEKLESDLKKEIKKLQRLRDQIKT 63 (575)
T ss_pred HHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4889999999888899999999999999999999998883
No 41
>PHA02047 phage lambda Rz1-like protein
Probab=38.63 E-value=88 Score=20.86 Aligned_cols=37 Identities=22% Similarity=0.271 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc--ccCccccCCC
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGK--ETQRWWETPV 91 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~--~~~~Ww~~~v 91 (91)
.+|..+|.++.+++.+-+.-.++++.. +-..|=+.||
T Consensus 48 ~r~~~~Q~~V~~l~~kae~~t~Ei~~aL~~n~~WaD~PV 86 (101)
T PHA02047 48 VRYATLQRHVQAVEARTNTQRQEVDRALDQNRPWADRPV 86 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCC
Confidence 456677777777776666666665542 2345888886
No 42
>PRK02224 chromosome segregation protein; Provisional
Probab=38.31 E-value=65 Score=27.61 Aligned_cols=48 Identities=10% Similarity=-0.026 Sum_probs=27.4
Q ss_pred hhhhhhhhCCCCCCCcHHHHHHHHhCCChH--HHHHHHHHHHHHHHHHHH
Q 038327 25 ASELVTLTGAEIGHPSIEAVANRFLGQTRR--QMTTLLLVEAQRQKERGN 72 (91)
Q Consensus 25 A~ELs~Lc~~~f~~ps~~~vl~r~~~~~~~--~~~~~l~~el~~~k~~~~ 72 (91)
+..-|.+|+-.|.......+++.|...-.. .....+..+++.++++.+
T Consensus 450 ~~~~Cp~C~r~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~l~~~~~~~e 499 (880)
T PRK02224 450 EAGKCPECGQPVEGSPHVETIEEDRERVEELEAELEDLEEEVEEVEERLE 499 (880)
T ss_pred hcccCCCCCCcCCCcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346788999988877766777766543222 234444444444443333
No 43
>PF00755 Carn_acyltransf: Choline/Carnitine o-acyltransferase; InterPro: IPR000542 A number of eukaryotic acetyltransferases can, on the basis of sequence similarities, be grouped together into a family. These enzymes include: Choline o-acetyltransferase 2.3.1.6 from EC, an enzyme that catalyses the biosynthesis of the neurotransmitter acetylcholine []. Carnitine o-acetyltransferase 2.3.1.7 from EC []. Peroxisomal carnitine octanoyltransferase 2.3.1.137 from EC, a fatty acid beta-oxidation pathway enzyme which is involved in the transport of medium-chain acyl-coenzyme A's from peroxisome to mitochondria []. Mitochondrial carnitine palmitoyltransferases I and II 2.3.1.21 from EC (CPT), enzymes involved in fatty acid metabolism and transport []. Mycoplasma pneumoniae putative acetyltransferase C09_orf600. ; GO: 0016746 transferase activity, transferring acyl groups; PDB: 2DEB_B 2H4T_A 2FW3_A 2RCU_B 2FYO_A 1S5O_A 1NM8_A 1T7Q_B 2H3W_B 1NDI_B ....
Probab=37.78 E-value=22 Score=29.45 Aligned_cols=42 Identities=17% Similarity=0.221 Sum_probs=28.3
Q ss_pred CcHHHHHHHHhCCChH----HHHHHHHHHHHHHHH---HHHHHHHHHhc
Q 038327 39 PSIEAVANRFLGQTRR----QMTTLLLVEAQRQKE---RGNFLKQMTKG 80 (91)
Q Consensus 39 ps~~~vl~r~~~~~~~----~~~~~l~~el~~~k~---~~~~l~~~~~~ 80 (91)
|+++..+++|+....| .++.+..+.++.-.+ ....|++.+..
T Consensus 8 P~L~~Tl~~yL~s~~pl~~~ee~~~t~~~v~~F~~~~~~g~~Lq~~L~~ 56 (591)
T PF00755_consen 8 PSLEDTLDRYLESVKPLLSDEEYEETKEAVEEFLKPGGEGPKLQERLEE 56 (591)
T ss_dssp --HHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHSTTSHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhcccChHHHHHHHHHH
Confidence 7899999999875444 666666666665554 77777777664
No 44
>PF15119 APOC4: Apolipoprotein C4
Probab=37.18 E-value=15 Score=24.22 Aligned_cols=19 Identities=32% Similarity=0.391 Sum_probs=15.5
Q ss_pred cccchhhhhhhhhh--hhhCC
Q 038327 16 KRKSRTYNKASELV--TLTGA 34 (91)
Q Consensus 16 KRr~GL~KKA~ELs--~Lc~~ 34 (91)
.-|.+|++||+.|| +||+-
T Consensus 77 sSkd~llnk~~sLCPrllC~d 97 (99)
T PF15119_consen 77 SSKDSLLNKTHSLCPRLLCGD 97 (99)
T ss_pred HhHHHHHHHHHhhCchhhccC
Confidence 35788999999998 78864
No 45
>PTZ00046 rifin; Provisional
Probab=36.95 E-value=40 Score=27.08 Aligned_cols=26 Identities=27% Similarity=0.368 Sum_probs=19.0
Q ss_pred hhhhCCC-CC-----CCcHHHHHHHHhCCChH
Q 038327 29 VTLTGAE-IG-----HPSIEAVANRFLGQTRR 54 (91)
Q Consensus 29 s~Lc~~~-f~-----~ps~~~vl~r~~~~~~~ 54 (91)
-+||-.+ |. .|.|.+|.+.|...+..
T Consensus 39 R~LcECeLY~pnYDNDPeMK~Vme~F~rqTsQ 70 (358)
T PTZ00046 39 RLLCECELYSSNYDNDPEMKSVMENFDRQTSQ 70 (358)
T ss_pred hhhhhhhcCCCCCCCcHHHHHHHHHHhHHHHH
Confidence 4788777 33 38899999999765543
No 46
>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=36.44 E-value=90 Score=18.77 Aligned_cols=26 Identities=12% Similarity=0.001 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
.++..++.+++.++.+++.|+.+...
T Consensus 31 ~~~~~~~~~~~~l~~en~~L~~ei~~ 56 (85)
T TIGR02209 31 NELQKLQLEIDKLQKEWRDLQLEVAE 56 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677888888888888888777653
No 47
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=35.77 E-value=36 Score=26.51 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=17.9
Q ss_pred hhhCCC-C-----CCCcHHHHHHHHhCCCh
Q 038327 30 TLTGAE-I-----GHPSIEAVANRFLGQTR 53 (91)
Q Consensus 30 ~Lc~~~-f-----~~ps~~~vl~r~~~~~~ 53 (91)
+||-.+ | ..|.|.+|++.|...+.
T Consensus 20 ~LcECely~snYDNDPeMK~Vme~F~rqTs 49 (299)
T PF02009_consen 20 SLCECELYTSNYDNDPEMKSVMENFDRQTS 49 (299)
T ss_pred chhhhcccccCCCCcHHHHHHHHHHHHHHH
Confidence 677777 2 24889999999976553
No 48
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=35.58 E-value=21 Score=20.28 Aligned_cols=29 Identities=10% Similarity=0.239 Sum_probs=16.5
Q ss_pred hhhhhhhhhhhhCCCCCCCcHHHHHHHHh
Q 038327 21 TYNKASELVTLTGAEIGHPSIEAVANRFL 49 (91)
Q Consensus 21 L~KKA~ELs~Lc~~~f~~ps~~~vl~r~~ 49 (91)
.++.+..-|-||+..|+.-..+.++..|.
T Consensus 15 ~l~~~~~~CPlC~r~l~~e~~~~li~~~~ 43 (54)
T PF04423_consen 15 ELKEAKGCCPLCGRPLDEEHRQELIKKYK 43 (54)
T ss_dssp HHTT-SEE-TTT--EE-HHHHHHHHHHHH
T ss_pred HHhcCCCcCCCCCCCCCHHHHHHHHHHHH
Confidence 34455557788888887666777777775
No 49
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=35.17 E-value=1.2e+02 Score=19.41 Aligned_cols=27 Identities=22% Similarity=0.203 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGK 81 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~ 81 (91)
.-.-.|.++++.++.++..|+..++.+
T Consensus 71 alvl~LLd~i~~Lr~el~~L~~~l~~~ 97 (101)
T PRK10265 71 AVALTLLDEIAHLKQENRLLRQRLSRF 97 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556678888888888888888877644
No 50
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=35.00 E-value=1.3e+02 Score=19.80 Aligned_cols=10 Identities=10% Similarity=-0.100 Sum_probs=5.0
Q ss_pred cHHHHHHHHh
Q 038327 40 SIEAVANRFL 49 (91)
Q Consensus 40 s~~~vl~r~~ 49 (91)
.+..+++-+.
T Consensus 62 eI~~~l~~~~ 71 (127)
T TIGR02047 62 EIRQLLRYQD 71 (127)
T ss_pred HHHHHHHhhh
Confidence 4555555443
No 51
>PRK09458 pspB phage shock protein B; Provisional
Probab=34.67 E-value=1.2e+02 Score=19.15 Aligned_cols=31 Identities=29% Similarity=0.402 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccCcc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKGKETQRW 86 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~~~~~~W 86 (91)
+++++|.+..+++.++.+.|+..+. ++...|
T Consensus 42 ~~L~~L~~~A~rm~~RI~tLE~ILD-ae~P~W 72 (75)
T PRK09458 42 QRLAQLTEKAERMRERIQALEAILD-AEHPNW 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHc-ccCCCc
Confidence 5678888999999999999988886 455555
No 52
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=34.59 E-value=1.3e+02 Score=19.63 Aligned_cols=24 Identities=4% Similarity=-0.060 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
+...+.+++..+....+.|...+.
T Consensus 85 ~~~~l~~~i~~L~~~~~~l~~~~~ 108 (126)
T cd04783 85 KLAEVDEKIADLQRMRASLQELVS 108 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555555555554443
No 53
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=33.25 E-value=76 Score=20.93 Aligned_cols=22 Identities=9% Similarity=0.037 Sum_probs=10.8
Q ss_pred HHHHHHHHHHH----HHHHHHHHHHH
Q 038327 56 MTTLLLVEAQR----QKERGNFLKQM 77 (91)
Q Consensus 56 ~~~~l~~el~~----~k~~~~~l~~~ 77 (91)
++.+|.+++.. .+++++.|++.
T Consensus 73 qL~~Lk~kl~~e~~~~~k~i~~le~~ 98 (100)
T PF04568_consen 73 QLKKLKEKLKEEIEHHRKEIDELEKH 98 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44444444444 45555555544
No 54
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=32.94 E-value=87 Score=19.36 Aligned_cols=21 Identities=14% Similarity=0.085 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 038327 55 QMTTLLLVEAQRQKERGNFLK 75 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~ 75 (91)
.-+-.|.++++.+++++..|+
T Consensus 63 ~lil~LLd~i~~L~~el~~L~ 83 (84)
T PF13591_consen 63 ALILDLLDRIEQLRRELRELR 83 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 556678888888888887775
No 55
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=32.58 E-value=1.5e+02 Score=19.53 Aligned_cols=11 Identities=9% Similarity=0.129 Sum_probs=5.4
Q ss_pred cHHHHHHHHhC
Q 038327 40 SIEAVANRFLG 50 (91)
Q Consensus 40 s~~~vl~r~~~ 50 (91)
.+..+++-+..
T Consensus 62 eI~~~l~~~~~ 72 (127)
T cd01108 62 EIRELLALWRD 72 (127)
T ss_pred HHHHHHHHHhC
Confidence 35555554443
No 56
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=32.01 E-value=73 Score=24.04 Aligned_cols=41 Identities=20% Similarity=0.211 Sum_probs=27.6
Q ss_pred CcHHHHH----HHHhCCChH---------HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 39 PSIEAVA----NRFLGQTRR---------QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 39 ps~~~vl----~r~~~~~~~---------~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
.++-.|| |||...... +.+..|+.|++.++.+|-+|=++++
T Consensus 78 ~siLpIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiR 131 (248)
T PF08172_consen 78 SSILPIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIR 131 (248)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555 577653332 4567778888888888888877776
No 57
>KOG2861 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.76 E-value=1.6e+02 Score=24.04 Aligned_cols=77 Identities=14% Similarity=0.201 Sum_probs=48.8
Q ss_pred CcccccccccchhhhhhhhhhhhhCCC-------------CCCCcHHHHH---HHHhCCChHHHHHHHHHHHHHHHHHHH
Q 038327 9 DRLITFSKRKSRTYNKASELVTLTGAE-------------IGHPSIEAVA---NRFLGQTRRQMTTLLLVEAQRQKERGN 72 (91)
Q Consensus 9 ~R~vTfsKRr~GL~KKA~ELs~Lc~~~-------------f~~ps~~~vl---~r~~~~~~~~~~~~l~~el~~~k~~~~ 72 (91)
++.-|++.+|.-++||..+|-.|=..- |..|....+. .+|+... ++.+-|...++-..+-.+
T Consensus 280 a~~gkl~lsr~e~lk~iGkLf~LR~~INL~s~lLdtPdf~W~ep~Le~iY~~~r~yleI~--qRv~vLN~kl~~i~~~~~ 357 (399)
T KOG2861|consen 280 ALGGKLTLSREELLKKIGKLFALRHDINLSSGLLDTPDFYWDEPQLEPIYEATRRYLEIG--QRVNVLNYKLKVIEDLLD 357 (399)
T ss_pred HhcCeecccHHHHHHHHHHHHHHheeeecccccccCcccccCchhHHHHHHHHHHHcccc--hHHHHHHHHHHHHHHHHH
Confidence 445578899999999999999885322 4446555544 4555544 455556666666666666
Q ss_pred HHHHHHhcccc--Cccc
Q 038327 73 FLKQMTKGKET--QRWW 87 (91)
Q Consensus 73 ~l~~~~~~~~~--~~Ww 87 (91)
-|++.+.++.. -.||
T Consensus 358 ~l~e~ln~r~~~~LEWi 374 (399)
T KOG2861|consen 358 ILQENLNERHSERLEWI 374 (399)
T ss_pred HHHHHhhhccccceehh
Confidence 66666554432 2375
No 58
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.41 E-value=1.1e+02 Score=18.78 Aligned_cols=25 Identities=12% Similarity=-0.016 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
..+-.|.++++.++++++.|++.++
T Consensus 65 ~~~l~l~~~~~~l~~~l~~l~~~~~ 89 (91)
T cd04766 65 KRILELEEELAELRAELDELRARLR 89 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5666789999999999999988765
No 59
>PF06133 DUF964: Protein of unknown function (DUF964); InterPro: IPR010368 This entry consists of several relatively short bacterial and archaeal hypothetical sequences. It also includes YlbF and YmcA proteins which are involved in the formation of biofilms []. YlbF regulates sporulation prior to stage II, positively controlling the competence regulator ComK at a post-transcriptional level. It may also modulate the translation, stability or activity of ComS and may work together with YmcA to regulate community development [].; PDB: 2IAZ_C 2OEE_A 2OEQ_D 2PIH_A.
Probab=30.20 E-value=62 Score=20.33 Aligned_cols=30 Identities=27% Similarity=0.491 Sum_probs=21.7
Q ss_pred hhhhhhhhh-hhhCCC------------CCCCcHHHHHHHHhC
Q 038327 21 TYNKASELV-TLTGAE------------IGHPSIEAVANRFLG 50 (91)
Q Consensus 21 L~KKA~ELs-~Lc~~~------------f~~ps~~~vl~r~~~ 50 (91)
|..+|.||+ .++..+ ...|.....++.|+.
T Consensus 2 I~~~a~eL~~~I~~s~ey~~~~~a~~~l~~d~e~~~l~~~f~~ 44 (108)
T PF06133_consen 2 IYDKANELAEAIKESEEYKRYKAAEEALEADPEAQKLIEEFQK 44 (108)
T ss_dssp HHHHHHHHHHHHHTSHHHHHHHHHHHHHHCSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCHHHHHHHHHHHHHHhCHHHHHHHHHHHH
Confidence 567888888 456655 456888888888864
No 60
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.50 E-value=1.7e+02 Score=19.15 Aligned_cols=20 Identities=5% Similarity=0.026 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 038327 58 TLLLVEAQRQKERGNFLKQM 77 (91)
Q Consensus 58 ~~l~~el~~~k~~~~~l~~~ 77 (91)
..+.+++..++.-...|...
T Consensus 89 ~~l~~~i~~L~~~~~~L~~~ 108 (127)
T cd04784 89 AHVRARIAELQALEKQLQAL 108 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444333
No 61
>PF10398 DUF2443: Protein of unknown function (DUF2443); InterPro: IPR019469 This entry represents a small group of highly conserved proteins from bacteria, in particular Helicobacter species. The structure is a bundle of alpha helices. The function is not known. ; PDB: 1ZKE_F.
Probab=29.18 E-value=1.4e+02 Score=19.09 Aligned_cols=26 Identities=19% Similarity=0.215 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
.-+.++-++++++|+..+.|....++
T Consensus 50 ~~~~QideeV~~LKe~IdaLNK~KkE 75 (79)
T PF10398_consen 50 AFLAQIDEEVEKLKEHIDALNKIKKE 75 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66889999999999999999887664
No 62
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.87 E-value=1.6e+02 Score=18.90 Aligned_cols=43 Identities=14% Similarity=0.069 Sum_probs=23.3
Q ss_pred CCCCcHHHHHHHHhCCC-----hHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038327 36 IGHPSIEAVANRFLGQT-----RRQMTTLLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 36 f~~ps~~~vl~r~~~~~-----~~~~~~~l~~el~~~k~~~~~l~~~~ 78 (91)
|+-..+..+++.+.... .+....-+.+++..+..+.+.|+...
T Consensus 57 ~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 104 (112)
T cd01282 57 LTLEEIREFLPCLRGGEPTFRPCPDLLAVLRRELARIDRQIADLTRSR 104 (112)
T ss_pred CCHHHHHHHHHHhhCCCccCCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344566666554432 12344556666666666666665554
No 63
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=27.51 E-value=1.2e+02 Score=18.95 Aligned_cols=29 Identities=7% Similarity=0.058 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 038327 53 RRQMTTLLLVEAQRQKERGNFLKQMTKGK 81 (91)
Q Consensus 53 ~~~~~~~l~~el~~~k~~~~~l~~~~~~~ 81 (91)
++.++.++++.|+.++++.+....+..++
T Consensus 10 ~~~~~~~i~~rLd~iEeKvEf~~~Ei~Qr 38 (70)
T PF04210_consen 10 DPDDFNEIMKRLDEIEEKVEFTNAEIAQR 38 (70)
T ss_pred CHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 45789999999999999988887776543
No 64
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=27.44 E-value=1.2e+02 Score=17.03 Aligned_cols=25 Identities=28% Similarity=0.178 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
..+..|..++..+..++..|...+.
T Consensus 25 ~~~~~le~~~~~L~~en~~L~~~i~ 49 (54)
T PF07716_consen 25 QREEELEQEVQELEEENEQLRQEIA 49 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788888888888888877654
No 65
>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=26.94 E-value=1.6e+02 Score=19.45 Aligned_cols=20 Identities=25% Similarity=0.277 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 038327 59 LLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 59 ~l~~el~~~k~~~~~l~~~~ 78 (91)
.|.+|-..++-+|+.|++.+
T Consensus 33 ~l~EEN~~L~~EN~~Lr~~l 52 (107)
T PF06156_consen 33 ELLEENARLRIENEHLRERL 52 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444443
No 66
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.91 E-value=1.9e+02 Score=18.96 Aligned_cols=24 Identities=4% Similarity=0.016 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
+...+.+++..+..-.+.|.....
T Consensus 84 ~~~~l~~~i~~L~~~~~~L~~~~~ 107 (124)
T TIGR02051 84 KLKSVQAKMADLLRIERLLEELLE 107 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444445544444444444433
No 67
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=26.69 E-value=83 Score=26.34 Aligned_cols=22 Identities=14% Similarity=0.052 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 038327 56 MTTLLLVEAQRQKERGNFLKQM 77 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~ 77 (91)
++++|+.||+.||++.+.+.+.
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~ 53 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDR 53 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccc
Confidence 4555555555555555544443
No 68
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=26.61 E-value=2e+02 Score=19.07 Aligned_cols=10 Identities=10% Similarity=0.096 Sum_probs=4.8
Q ss_pred cHHHHHHHHh
Q 038327 40 SIEAVANRFL 49 (91)
Q Consensus 40 s~~~vl~r~~ 49 (91)
.+..+++.+.
T Consensus 62 eI~~~l~~~~ 71 (133)
T cd04787 62 DIKEILSHAD 71 (133)
T ss_pred HHHHHHhhhc
Confidence 3455555443
No 69
>COG1723 Uncharacterized conserved protein [Function unknown]
Probab=26.29 E-value=1.5e+02 Score=23.69 Aligned_cols=81 Identities=12% Similarity=0.074 Sum_probs=50.6
Q ss_pred CCCcccccccccchhhhhhhhhhhhhCCC-------------CCCCcHHHHHHHHhCCChH-HHHHHHHHHHHHHHHHHH
Q 038327 7 EDDRLITFSKRKSRTYNKASELVTLTGAE-------------IGHPSIEAVANRFLGQTRR-QMTTLLLVEAQRQKERGN 72 (91)
Q Consensus 7 ~~~R~vTfsKRr~GL~KKA~ELs~Lc~~~-------------f~~ps~~~vl~r~~~~~~~-~~~~~l~~el~~~k~~~~ 72 (91)
+-++.-.-+.+|.-|+|+.+.|-.|=..- |.+|....+.......-.. .+++-|...++..-.-.+
T Consensus 211 ~la~~gkvslsr~eilk~iG~LFllR~~iNL~s~IlDtPef~W~ePqleplY~~~~~yLdI~~RvnvLN~Rl~vi~d~l~ 290 (331)
T COG1723 211 ELARTGKVSLSRKEILKQIGKLFLLRVSINLHSDILDTPEFFWSEPQLEPLYLAVREYLDINPRVNVLNRRLEVISDLLD 290 (331)
T ss_pred HHhhcCCccccHHHHHHHHhHHhheeeeeeeeeccccCchhcccCcchhHHHHHHHHHhchhHHHHHHHHHHHHHHHHHH
Confidence 33455566788899999999998775322 6788877666544332222 555666666666666666
Q ss_pred HHHHHHhccc--cCccc
Q 038327 73 FLKQMTKGKE--TQRWW 87 (91)
Q Consensus 73 ~l~~~~~~~~--~~~Ww 87 (91)
.|.+.+.+.. .-.||
T Consensus 291 il~e~ln~~~s~~lEWi 307 (331)
T COG1723 291 ILNEQLNHSHSTRLEWI 307 (331)
T ss_pred HHHHHhhhcccceeEEE
Confidence 6666655433 33475
No 70
>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=26.15 E-value=1.7e+02 Score=18.04 Aligned_cols=15 Identities=33% Similarity=0.461 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHHH
Q 038327 56 MTTLLLVEAQRQKER 70 (91)
Q Consensus 56 ~~~~l~~el~~~k~~ 70 (91)
.+..|+.+++.++++
T Consensus 19 ti~~Lq~e~eeLke~ 33 (72)
T PF06005_consen 19 TIALLQMENEELKEK 33 (72)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 344455555555554
No 71
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=26.12 E-value=1e+02 Score=23.65 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=21.0
Q ss_pred HHHHHHHhC---CChHHHHHHHHHHHHHHHHHHHHHH
Q 038327 42 EAVANRFLG---QTRRQMTTLLLVEAQRQKERGNFLK 75 (91)
Q Consensus 42 ~~vl~r~~~---~~~~~~~~~l~~el~~~k~~~~~l~ 75 (91)
+.|++.++. .|....++.+..+|..++++...|.
T Consensus 256 ~~~~e~~L~~l~lPTr~evd~l~k~l~eLrre~r~Lk 292 (293)
T PF09712_consen 256 QEVVEEYLRSLNLPTRSEVDELYKRLHELRREVRALK 292 (293)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 445554443 2333677778888888877777664
No 72
>PHA01548 hypothetical protein
Probab=26.08 E-value=55 Score=23.33 Aligned_cols=19 Identities=11% Similarity=0.347 Sum_probs=13.3
Q ss_pred HHHHHHhccccCccccCCC
Q 038327 73 FLKQMTKGKETQRWWETPV 91 (91)
Q Consensus 73 ~l~~~~~~~~~~~Ww~~~v 91 (91)
.++..+..-+...||++|+
T Consensus 127 sIQkiisIvGpapwt~EPl 145 (167)
T PHA01548 127 SIQKIISIVGPAPWTDEPL 145 (167)
T ss_pred HHHHHHHHhCCCCCCCCCe
Confidence 3455555667778999995
No 73
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=25.86 E-value=1.5e+02 Score=18.83 Aligned_cols=23 Identities=22% Similarity=0.157 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 038327 57 TTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 57 ~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
++++..++++.+++...++..++
T Consensus 3 leKi~~eieK~k~Kiae~Q~rlK 25 (83)
T PF14193_consen 3 LEKIRAEIEKTKEKIAELQARLK 25 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555544444
No 74
>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=25.58 E-value=2.6e+02 Score=20.10 Aligned_cols=20 Identities=15% Similarity=0.049 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 038327 58 TLLLVEAQRQKERGNFLKQM 77 (91)
Q Consensus 58 ~~l~~el~~~k~~~~~l~~~ 77 (91)
.+|+++++.+.++++.|...
T Consensus 114 ~~l~~~~e~Le~e~~~L~~~ 133 (161)
T TIGR02894 114 ESLQKRNEELEKELEKLRQR 133 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555555443
No 75
>PF15458 NTR2: Nineteen complex-related protein 2
Probab=25.27 E-value=1.6e+02 Score=22.07 Aligned_cols=41 Identities=22% Similarity=0.231 Sum_probs=22.7
Q ss_pred CCcHHHHHHHHhCCChH---------HHHHHHHHHHHHHHHHHHHHHHHH
Q 038327 38 HPSIEAVANRFLGQTRR---------QMTTLLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 38 ~ps~~~vl~r~~~~~~~---------~~~~~l~~el~~~k~~~~~l~~~~ 78 (91)
-|++..++.+....-.. .++..|+.+...+..+...|+..+
T Consensus 203 LP~L~~~~~rL~~~l~~le~~~~~~~~~l~~l~~E~~~I~~re~elq~~l 252 (254)
T PF15458_consen 203 LPSLSECLERLRESLSSLEDSKSQLQQQLESLEKEKEEIEEREKELQELL 252 (254)
T ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 36778888777543322 334455555555555555555544
No 76
>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=25.10 E-value=1.6e+02 Score=20.13 Aligned_cols=20 Identities=5% Similarity=0.056 Sum_probs=6.9
Q ss_pred CCCCCCCcHHHHHHHHhCCC
Q 038327 33 GAEIGHPSIEAVANRFLGQT 52 (91)
Q Consensus 33 ~~~f~~ps~~~vl~r~~~~~ 52 (91)
.+-|+.|+..+|..++.+..
T Consensus 14 s~sfaA~~~~~v~~~l~~LE 33 (126)
T PF09403_consen 14 SISFAATATASVESELNQLE 33 (126)
T ss_dssp ---------HHHHHHHHHHH
T ss_pred HHHHHcccchHHHHHHHHHH
Confidence 34488888677777765443
No 77
>PF11157 DUF2937: Protein of unknown function (DUF2937); InterPro: IPR022584 This family of proteins with unknown function appears to be found mainly in Proteobacteria.
Probab=25.05 E-value=2.4e+02 Score=19.85 Aligned_cols=39 Identities=13% Similarity=0.022 Sum_probs=23.6
Q ss_pred CCCCcHHHHHHHHhCCChH------HHHHHHHHHHHHHHHHHHHH
Q 038327 36 IGHPSIEAVANRFLGQTRR------QMTTLLLVEAQRQKERGNFL 74 (91)
Q Consensus 36 f~~ps~~~vl~r~~~~~~~------~~~~~l~~el~~~k~~~~~l 74 (91)
|...+++..|++|...+.+ .....+.+..+.+......+
T Consensus 53 ~f~~~~~~li~~~~~s~dp~~~~~a~~~~~~~~R~~~L~~~~~~l 97 (167)
T PF11157_consen 53 YFGGDREALIAHYRQSSDPVFRARAESMQATIERYQRLSQQLQAL 97 (167)
T ss_pred HcCCCHHHHHHHHHhCCCHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 4457899999999777765 33444444444444444333
No 78
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=24.98 E-value=2.3e+02 Score=19.31 Aligned_cols=11 Identities=9% Similarity=0.211 Sum_probs=6.0
Q ss_pred hhhhhhhhCCC
Q 038327 25 ASELVTLTGAE 35 (91)
Q Consensus 25 A~ELs~Lc~~~ 35 (91)
.+|+|-+||+.
T Consensus 10 IgevAk~~Gvs 20 (144)
T PRK13752 10 IGVFAKAAGVN 20 (144)
T ss_pred HHHHHHHHCcC
Confidence 34555555555
No 79
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=24.84 E-value=47 Score=27.76 Aligned_cols=25 Identities=20% Similarity=0.118 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
.+.+.+| +|++|++++++|++++..
T Consensus 25 ~~~~~~q-kie~L~kql~~Lk~q~~~ 49 (489)
T PF11853_consen 25 DDIDLLQ-KIEALKKQLEELKAQQDD 49 (489)
T ss_pred hhhHHHH-HHHHHHHHHHHHHHhhcc
Confidence 3344455 999999999999888763
No 80
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=24.66 E-value=1.5e+02 Score=19.95 Aligned_cols=34 Identities=12% Similarity=0.188 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH--HHHHhccccC--cccc
Q 038327 55 QMTTLLLVEAQRQKERGNFL--KQMTKGKETQ--RWWE 88 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l--~~~~~~~~~~--~Ww~ 88 (91)
.++.++..+..++.++.+.| ...++.-+++ .|+.
T Consensus 49 ~qH~~~~~e~r~L~kKi~~l~veRkmr~Les~p~~W~~ 86 (109)
T PF11690_consen 49 DQHQRYCDERRKLRKKIQDLRVERKMRALESHPFDWER 86 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhccCChHHHHH
Confidence 56778888888888888888 6666654444 4754
No 81
>KOG1927 consensus R-kappa-B and related transcription factors [Transcription]
Probab=24.66 E-value=58 Score=29.78 Aligned_cols=39 Identities=15% Similarity=0.228 Sum_probs=29.2
Q ss_pred ccccccccchh-----hhhhhhhhhhhCCCCCCCcHHHHHHHHhC
Q 038327 11 LITFSKRKSRT-----YNKASELVTLTGAEIGHPSIEAVANRFLG 50 (91)
Q Consensus 11 ~vTfsKRr~GL-----~KKA~ELs~Lc~~~f~~ps~~~vl~r~~~ 50 (91)
.-||++|+.|. +.-|.||--+|+-.|++| +....++.+.
T Consensus 111 ~~s~~~~~p~vd~~~~~r~~~~~~~~~~~~f~~~-~~~~~~~~~~ 154 (1274)
T KOG1927|consen 111 RFSLSSYLPDVDQLTFMRTLKELFEGCNFHFGSP-VKKLFDMLKG 154 (1274)
T ss_pred HHhHhhcCCCchHHHHHHHHHHHhhhcccchhhH-HHHHHHHHhc
Confidence 45899999984 778899999999999876 3444444443
No 82
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=24.66 E-value=1.8e+02 Score=19.40 Aligned_cols=22 Identities=18% Similarity=0.172 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 038327 58 TLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 58 ~~l~~el~~~k~~~~~l~~~~~ 79 (91)
..|.+|-..++-+|+.|++.+.
T Consensus 32 ~el~EEN~~L~iEN~~Lr~~l~ 53 (110)
T PRK13169 32 AELLEENTALRLENDKLRERLE 53 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444555544444
No 83
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.91 E-value=81 Score=18.18 Aligned_cols=21 Identities=14% Similarity=0.023 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 038327 58 TLLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 58 ~~l~~el~~~k~~~~~l~~~~ 78 (91)
-++..++.+++++.++++.++
T Consensus 44 ~~~r~~~~~~~k~l~~le~e~ 64 (68)
T PF06305_consen 44 LRLRRRIRRLRKELKKLEKEL 64 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344444444555554444443
No 84
>PF15136 UPF0449: Uncharacterised protein family UPF0449
Probab=23.89 E-value=2.2e+02 Score=18.76 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=8.2
Q ss_pred CcHHHHHHHHhCC
Q 038327 39 PSIEAVANRFLGQ 51 (91)
Q Consensus 39 ps~~~vl~r~~~~ 51 (91)
|++..||+-..+.
T Consensus 14 PTvEqILEDv~~A 26 (97)
T PF15136_consen 14 PTVEQILEDVRGA 26 (97)
T ss_pred CCHHHHHHHHhcC
Confidence 5677777666554
No 85
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.82 E-value=2.1e+02 Score=18.41 Aligned_cols=10 Identities=10% Similarity=-0.107 Sum_probs=4.8
Q ss_pred cHHHHHHHHh
Q 038327 40 SIEAVANRFL 49 (91)
Q Consensus 40 s~~~vl~r~~ 49 (91)
.+..+++...
T Consensus 62 eI~~~l~~~~ 71 (123)
T cd04770 62 EIRELLSLRD 71 (123)
T ss_pred HHHHHHHhhh
Confidence 3455555443
No 86
>KOG3718 consensus Carnitine O-acyltransferase CROT [Lipid transport and metabolism]
Probab=23.73 E-value=1.3e+02 Score=25.67 Aligned_cols=42 Identities=17% Similarity=0.223 Sum_probs=23.7
Q ss_pred CcHHHHHHHHhCCChH----HHHHHHHHHHHHHH-HHHHHHHHHHhc
Q 038327 39 PSIEAVANRFLGQTRR----QMTTLLLVEAQRQK-ERGNFLKQMTKG 80 (91)
Q Consensus 39 ps~~~vl~r~~~~~~~----~~~~~l~~el~~~k-~~~~~l~~~~~~ 80 (91)
|+....|++|+....| .++.+......+-+ --.+.|++.+++
T Consensus 26 PeLeETleKYl~s~~pf~tkeE~a~~ek~a~eFqsg~GaqLh~~Lke 72 (609)
T KOG3718|consen 26 PELEETLEKYLSSIQPFGTKEELAQAEKTADEFQSGVGAQLHEQLKE 72 (609)
T ss_pred chHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 7899999999876554 33333333222222 145556666554
No 87
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=23.65 E-value=2.4e+02 Score=19.00 Aligned_cols=16 Identities=6% Similarity=-0.095 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHHHHH
Q 038327 60 LLVEAQRQKERGNFLK 75 (91)
Q Consensus 60 l~~el~~~k~~~~~l~ 75 (91)
+..+++.++++.+.|+
T Consensus 86 l~~~~~~l~~~i~~L~ 101 (140)
T PRK09514 86 VDEKLAEVEAKIAELQ 101 (140)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444443
No 88
>TIGR01477 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.
Probab=23.47 E-value=83 Score=25.27 Aligned_cols=25 Identities=28% Similarity=0.462 Sum_probs=18.3
Q ss_pred hhhCCC-CC-----CCcHHHHHHHHhCCChH
Q 038327 30 TLTGAE-IG-----HPSIEAVANRFLGQTRR 54 (91)
Q Consensus 30 ~Lc~~~-f~-----~ps~~~vl~r~~~~~~~ 54 (91)
+||-.+ |. .|.|.+|.+.|...+..
T Consensus 43 ~LcECeLy~~nYDNDPeMK~Vm~nF~rqTsQ 73 (353)
T TIGR01477 43 SLCECELYSSNYDNDPEMKSVMEQFDRQTSQ 73 (353)
T ss_pred hhhhhhcccccCCCcHHHHHHHHHHhHHHHH
Confidence 677777 33 48899999999765543
No 89
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=23.38 E-value=1.9e+02 Score=17.88 Aligned_cols=25 Identities=16% Similarity=0.032 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
.++.+++.+.++++.+++.|.-+..
T Consensus 42 ~~l~~l~~~~~~l~~e~~~L~lE~~ 66 (97)
T PF04999_consen 42 YELQQLEKEIDQLQEENERLRLEIA 66 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677888888888888888776654
No 90
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=23.09 E-value=1.4e+02 Score=25.11 Aligned_cols=28 Identities=14% Similarity=0.087 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 53 RRQMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 53 ~~~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
...+++.|+.||..|+++..+|+..+..
T Consensus 23 ~a~~i~~L~~ql~aLq~~v~eL~~~laa 50 (514)
T PF11336_consen 23 TADQIKALQAQLQALQDQVNELRAKLAA 50 (514)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3478999999999999999999998873
No 91
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.03 E-value=1.4e+02 Score=18.94 Aligned_cols=22 Identities=41% Similarity=0.430 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 038327 56 MTTLLLVEAQRQKERGNFLKQM 77 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~ 77 (91)
.+.-||-+++.+|+++..|.++
T Consensus 19 TI~LLQmEieELKEknn~l~~e 40 (79)
T COG3074 19 TITLLQMEIEELKEKNNSLSQE 40 (79)
T ss_pred HHHHHHHHHHHHHHHhhHhHHH
Confidence 3556677777777777766554
No 92
>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=23.01 E-value=2e+02 Score=18.20 Aligned_cols=24 Identities=13% Similarity=0.221 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~ 78 (91)
.+++..+.+.++++.+|+-|+.=+
T Consensus 37 ~Rve~Vk~E~~kL~~EN~~Lq~YI 60 (80)
T PF10224_consen 37 DRVEEVKEENEKLESENEYLQQYI 60 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555443
No 93
>TIGR02761 TraE_TIGR type IV conjugative transfer system protein TraE. TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA. The function of the TraE protein is unknown.
Probab=22.66 E-value=2e+02 Score=20.34 Aligned_cols=29 Identities=21% Similarity=0.207 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHHHH
Q 038327 41 IEAVANRFLGQTRRQMTTLLLVEAQRQKE 69 (91)
Q Consensus 41 ~~~vl~r~~~~~~~~~~~~l~~el~~~k~ 69 (91)
++...+..+...+|..|.+++.+|.++-+
T Consensus 89 vd~~~~~Ll~~v~p~~~~~~k~~L~~~a~ 117 (181)
T TIGR02761 89 ADAQHNALLGYVEPQNYGQIKSRLAKEAE 117 (181)
T ss_pred hhHHHHHHHhhcChhhHHHHHHHHHHHHH
Confidence 55555555555566777777777776644
No 94
>PRK13726 conjugal transfer pilus assembly protein TraE; Provisional
Probab=22.03 E-value=2.3e+02 Score=20.47 Aligned_cols=33 Identities=18% Similarity=0.258 Sum_probs=22.6
Q ss_pred CCc-HHHHHHHHhCCChHHHHHHHHHHHHHHHHH
Q 038327 38 HPS-IEAVANRFLGQTRRQMTTLLLVEAQRQKER 70 (91)
Q Consensus 38 ~ps-~~~vl~r~~~~~~~~~~~~l~~el~~~k~~ 70 (91)
+|. ++...+..+...+|..|.+++.+|.++-++
T Consensus 85 TP~nVd~~~~~LL~~v~p~~~~~lk~~L~~~a~~ 118 (188)
T PRK13726 85 SPETVDASHQALLQYIRPGAQNQMKVILAEEAKR 118 (188)
T ss_pred ChhhHHHHHHHHHhhCCHHHHHHHHHHHHHHHHH
Confidence 353 666666666666777888888888777543
No 95
>KOG3717 consensus Carnitine O-acyltransferase CRAT [Lipid transport and metabolism]
Probab=21.69 E-value=80 Score=27.11 Aligned_cols=42 Identities=19% Similarity=0.277 Sum_probs=24.4
Q ss_pred CCcHHHHHHHHhCCChH-------HHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 38 HPSIEAVANRFLGQTRR-------QMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 38 ~ps~~~vl~r~~~~~~~-------~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
-|..++.|++|+..-.+ ++.+++.++-.+-.- ...|++.+.+
T Consensus 19 VP~L~~TL~~yl~~~~pl~s~~ef~~tk~i~~~F~~~~g-g~~LQ~~L~e 67 (612)
T KOG3717|consen 19 VPPLQQTLDHYLQALQPLVSEEEFARTKQLVNEFQAKGG-GERLQKLLLE 67 (612)
T ss_pred CCcHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHhhcCC-chHHHHHHHH
Confidence 37799999999875544 333444444433332 3556655543
No 96
>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=21.66 E-value=1.8e+02 Score=16.78 Aligned_cols=23 Identities=9% Similarity=-0.015 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Q 038327 58 TLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 58 ~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
+.|.++++.++.+...|+.....
T Consensus 2 ~aLrqQv~aL~~qv~~Lq~~fs~ 24 (46)
T PF09006_consen 2 NALRQQVEALQGQVQRLQAAFSQ 24 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677777777777777766553
No 97
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=21.66 E-value=1.8e+02 Score=21.95 Aligned_cols=26 Identities=19% Similarity=0.061 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
++...+++|.++++.++++++..+++
T Consensus 116 sEF~~lr~e~EklkndlEk~ks~lr~ 141 (220)
T KOG3156|consen 116 SEFANLRAENEKLKNDLEKLKSSLRH 141 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34557788888888888888887774
No 98
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.58 E-value=2.5e+02 Score=18.56 Aligned_cols=24 Identities=13% Similarity=0.084 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
+...+.+++..+....+.|...+.
T Consensus 89 ~~~~l~~~i~~L~~~~~~L~~~~~ 112 (131)
T TIGR02043 89 KLELVDEKINELTKIRRSLKKLSD 112 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444433
No 99
>PRK11546 zraP zinc resistance protein; Provisional
Probab=21.46 E-value=2.5e+02 Score=19.63 Aligned_cols=36 Identities=17% Similarity=0.189 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChH-----------------------HHHHHHHHHHHHHHHHHHHHHH
Q 038327 41 IEAVANRFLGQTRR-----------------------QMTTLLLVEAQRQKERGNFLKQ 76 (91)
Q Consensus 41 ~~~vl~r~~~~~~~-----------------------~~~~~l~~el~~~k~~~~~l~~ 76 (91)
++.|.+.|.....+ ..+.++..|+..++.++..++-
T Consensus 52 ~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r~ 110 (143)
T PRK11546 52 WQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELRV 110 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67788888754433 4466666777777666554443
No 100
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=21.26 E-value=41 Score=25.76 Aligned_cols=17 Identities=29% Similarity=0.368 Sum_probs=15.0
Q ss_pred hhhhhhhhhhhhCCCCC
Q 038327 21 TYNKASELVTLTGAEIG 37 (91)
Q Consensus 21 L~KKA~ELs~Lc~~~f~ 37 (91)
++.||.|+--||++.|.
T Consensus 18 ~lrKa~E~~RL~~~~~~ 34 (262)
T KOG4557|consen 18 LLRKAAEIRRLCDAQFD 34 (262)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 48999999999999953
No 101
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=21.25 E-value=99 Score=18.05 Aligned_cols=27 Identities=22% Similarity=0.396 Sum_probs=15.4
Q ss_pred hhhhhhhCCCCCCCc-HHHHHHHHhCCChH
Q 038327 26 SELVTLTGAEIGHPS-IEAVANRFLGQTRR 54 (91)
Q Consensus 26 ~ELs~Lc~~~f~~ps-~~~vl~r~~~~~~~ 54 (91)
.|++..|| |++++ +...+.++.+.+|.
T Consensus 49 ~~ia~~~G--f~~~~~f~~~fk~~~g~tP~ 76 (81)
T PF12833_consen 49 AEIAEECG--FSSQSHFSRAFKRYFGMTPS 76 (81)
T ss_dssp HHHHHHTT---SSHHHHHHHHHHHHSS-HH
T ss_pred HHHHHHcC--CCCHHHHHHHHHHHHCcCHH
Confidence 34444444 66655 77778888777664
No 102
>PF14916 CCDC92: Coiled-coil domain of unknown function
Probab=21.10 E-value=69 Score=19.38 Aligned_cols=25 Identities=24% Similarity=0.097 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
.-+..|-.||+++++++.+|.=++-
T Consensus 21 ~tL~~LH~EIe~Lq~~~~dL~~kL~ 45 (60)
T PF14916_consen 21 QTLKGLHAEIERLQKRNKDLTFKLI 45 (60)
T ss_pred HHHHHHHHHHHHHHHhccccceeee
Confidence 4466778888888888888876654
No 103
>PF08227 DASH_Hsk3: DASH complex subunit Hsk3 like; InterPro: IPR013183 This is a family of fungal proteins of unknown function.
Probab=20.82 E-value=1.2e+02 Score=17.24 Aligned_cols=25 Identities=4% Similarity=-0.116 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Q 038327 56 MTTLLLVEAQRQKERGNFLKQMTKG 80 (91)
Q Consensus 56 ~~~~l~~el~~~k~~~~~l~~~~~~ 80 (91)
+|..|..+++.+...+....+.++.
T Consensus 3 q~s~L~~qL~qL~aNL~~t~~~l~~ 27 (45)
T PF08227_consen 3 QYSHLASQLAQLQANLADTENLLEM 27 (45)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 6777888888888777777776664
No 104
>KOG3014 consensus Protein involved in establishing cohesion between sister chromatids during DNA replication [Replication, recombination and repair]
Probab=20.46 E-value=1.3e+02 Score=23.29 Aligned_cols=50 Identities=12% Similarity=0.171 Sum_probs=33.5
Q ss_pred cccccccchhhhhhhhhhhhhCCC----------CCCCc--HHHHHHHHhCCChHHHHHHHH
Q 038327 12 ITFSKRKSRTYNKASELVTLTGAE----------IGHPS--IEAVANRFLGQTRRQMTTLLL 61 (91)
Q Consensus 12 vTfsKRr~GL~KKA~ELs~Lc~~~----------f~~ps--~~~vl~r~~~~~~~~~~~~l~ 61 (91)
|.-++||.|+..+--+-+.=|.+- |++|+ -..+..+|.+......|..+.
T Consensus 191 V~s~~Rr~gIAs~lldva~~~~~~g~~isr~~iAfs~PTddGk~lAt~~~~t~~~~~~~~~~ 252 (257)
T KOG3014|consen 191 VSSLRRRKGIASLLLDVARCNFVYGEVISREEIAFSDPTDDGKKLATKYCGTRNFLTYNFLL 252 (257)
T ss_pred eehhhhhhhhHHHHHHHHHHhhhhhcccchhheEecCCCchhHHHHHHHhCccchhhhhhhh
Confidence 455789999998887765444332 88886 567778888766554444443
No 105
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=20.40 E-value=3.1e+02 Score=22.94 Aligned_cols=40 Identities=10% Similarity=0.156 Sum_probs=32.2
Q ss_pred cHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038327 40 SIEAVANRFLGQTRRQMTTLLLVEAQRQKERGNFLKQMTK 79 (91)
Q Consensus 40 s~~~vl~r~~~~~~~~~~~~l~~el~~~k~~~~~l~~~~~ 79 (91)
.++.|.++|.......+-++|...|..+=+++.+++..++
T Consensus 13 ~fd~iyek~~~s~~~s~~ekle~dlk~~ikklq~~rdqik 52 (548)
T COG5665 13 DFDDIYEKFQSTDNSSHREKLESDLKREIKKLQKHRDQIK 52 (548)
T ss_pred hHHHHHHHHhccCchhHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 4689999999888888888888887777777777777766
No 106
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=20.37 E-value=3e+02 Score=18.98 Aligned_cols=13 Identities=23% Similarity=0.462 Sum_probs=11.5
Q ss_pred CCCCcHHHHHHHH
Q 038327 36 IGHPSIEAVANRF 48 (91)
Q Consensus 36 f~~ps~~~vl~r~ 48 (91)
|..|+-..++.+|
T Consensus 28 y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 28 YTTPTEEELFKRY 40 (128)
T ss_pred ecCCCHHHHHHhc
Confidence 6789999999998
No 107
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=20.20 E-value=2.3e+02 Score=18.06 Aligned_cols=23 Identities=39% Similarity=0.424 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 038327 55 QMTTLLLVEAQRQKERGNFLKQM 77 (91)
Q Consensus 55 ~~~~~l~~el~~~k~~~~~l~~~ 77 (91)
..+.-|+-+++.+|+++..|.++
T Consensus 18 dtI~LLqmEieELKekn~~L~~e 40 (79)
T PRK15422 18 DTITLLQMEIEELKEKNNSLSQE 40 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567788888888888877775
No 108
>PF07195 FliD_C: Flagellar hook-associated protein 2 C-terminus; InterPro: IPR010809 The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria []. This alignment covers the C-terminal region of the flagellar hook-associated protein 2.; GO: 0007155 cell adhesion, 0009288 bacterial-type flagellum
Probab=20.10 E-value=3.5e+02 Score=19.61 Aligned_cols=38 Identities=11% Similarity=0.095 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCC-hH---------HHHHHHHHHHHHHHHHHHHHHHHH
Q 038327 41 IEAVANRFLGQT-RR---------QMTTLLLVEAQRQKERGNFLKQMT 78 (91)
Q Consensus 41 ~~~vl~r~~~~~-~~---------~~~~~l~~el~~~k~~~~~l~~~~ 78 (91)
+..+|+.|.... ++ .++..+.++++.++++++..++.+
T Consensus 176 l~~~l~~~~~~~~G~i~~~~~~l~~~~~~~~~~i~~~~~rl~~~~~~l 223 (239)
T PF07195_consen 176 LNDYLDSYTGSSTGSITSRIDSLNSQIKSLDKQIEDLEERLESKEERL 223 (239)
T ss_pred HHHHHHHHhCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677788887665 33 344455555555555555544443
Done!