Query 034435
Match_columns 95
No_of_seqs 103 out of 335
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 02:50:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034435.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034435hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 99.9 1.2E-27 2.5E-32 178.0 8.7 78 2-80 1-81 (168)
2 KOG0871 Class 2 transcription 99.9 1.3E-21 2.9E-26 144.4 6.9 57 24-80 5-61 (156)
3 COG5150 Class 2 transcription 99.7 4.6E-17 1E-21 118.9 7.0 56 25-80 5-60 (148)
4 KOG0870 DNA polymerase epsilon 99.5 8.1E-14 1.8E-18 104.6 5.6 58 25-82 4-62 (172)
5 PF00808 CBFD_NFYB_HMF: Histon 99.4 8.4E-13 1.8E-17 82.4 6.9 50 31-81 2-51 (65)
6 COG2036 HHT1 Histones H3 and H 98.8 5.3E-09 1.1E-13 71.6 4.8 56 23-80 11-66 (91)
7 cd07981 TAF12 TATA Binding Pro 96.9 0.0058 1.3E-07 39.3 6.4 47 32-79 2-48 (72)
8 smart00428 H3 Histone H3. 96.1 0.016 3.4E-07 40.6 5.0 55 25-79 23-82 (105)
9 PF09415 CENP-X: CENP-S associ 96.0 0.015 3.2E-07 38.1 4.3 49 33-81 1-50 (72)
10 PF00125 Histone: Core histone 95.5 0.058 1.3E-06 33.6 5.6 51 30-80 4-57 (75)
11 cd00076 H4 Histone H4, one of 95.4 0.075 1.6E-06 35.9 6.1 47 31-79 13-59 (85)
12 PF03847 TFIID_20kDa: Transcri 95.2 0.092 2E-06 33.9 5.8 46 34-80 2-47 (68)
13 PLN00035 histone H4; Provision 95.0 0.051 1.1E-06 38.1 4.4 54 24-79 22-75 (103)
14 smart00803 TAF TATA box bindin 94.8 0.2 4.3E-06 31.9 6.4 47 31-79 2-48 (65)
15 PTZ00015 histone H4; Provision 94.5 0.17 3.7E-06 35.4 6.0 54 24-79 23-76 (102)
16 smart00417 H4 Histone H4. 94.5 0.2 4.3E-06 33.1 6.1 51 27-79 9-59 (74)
17 cd08048 TAF11 TATA Binding Pro 94.3 0.24 5.2E-06 33.2 6.2 50 31-82 16-65 (85)
18 PLN00121 histone H3; Provision 92.1 0.29 6.2E-06 35.9 4.3 51 26-76 57-110 (136)
19 KOG1142 Transcription initiati 92.0 1.4 3E-05 35.5 8.3 52 27-79 150-201 (258)
20 PLN00161 histone H3; Provision 91.7 0.69 1.5E-05 33.9 5.9 51 26-76 50-104 (135)
21 PF04719 TAFII28: hTAFII28-lik 91.1 0.96 2.1E-05 30.9 5.8 49 31-80 23-71 (90)
22 smart00427 H2B Histone H2B. 91.0 1 2.2E-05 30.9 5.8 44 36-80 6-49 (89)
23 PTZ00018 histone H3; Provision 90.1 0.99 2.1E-05 33.1 5.4 51 26-76 57-110 (136)
24 PLN00160 histone H3; Provision 89.6 1 2.2E-05 31.3 5.0 51 26-76 16-70 (97)
25 PLN00158 histone H2B; Provisio 88.8 1.7 3.8E-05 31.2 5.8 47 33-80 29-75 (116)
26 PTZ00463 histone H2B; Provisio 88.6 1.8 4E-05 31.2 5.8 44 36-80 33-76 (117)
27 KOG1657 CCAAT-binding factor, 88.3 0.57 1.2E-05 36.7 3.4 52 27-79 70-121 (236)
28 KOG1744 Histone H2B [Chromatin 81.9 4 8.7E-05 29.7 5.0 54 24-81 33-86 (127)
29 PF15511 CENP-T: Centromere ki 80.6 3.2 6.9E-05 34.5 4.6 49 23-71 343-395 (414)
30 KOG3219 Transcription initiati 80.4 2 4.3E-05 33.3 3.1 50 31-82 112-161 (195)
31 COG5208 HAP5 CCAAT-binding fac 80.0 3.7 8E-05 33.1 4.6 44 29-74 107-151 (286)
32 cd00074 H2A Histone 2A; H2A is 77.5 9.9 0.00021 26.8 5.7 41 26-67 15-55 (115)
33 PF00356 LacI: Bacterial regul 76.7 5.3 0.00011 23.8 3.6 31 31-65 10-40 (46)
34 TIGR01481 ccpA catabolite cont 67.8 7.3 0.00016 29.0 3.4 35 32-71 13-47 (329)
35 smart00576 BTP Bromodomain tra 67.2 30 0.00064 22.0 6.2 45 34-80 9-53 (77)
36 cd00083 HLH Helix-loop-helix d 66.7 20 0.00042 20.7 4.5 37 37-73 22-58 (60)
37 cd08050 TAF6 TATA Binding Prot 65.3 23 0.00049 28.6 5.9 44 33-79 1-45 (343)
38 cd07978 TAF13 The TATA Binding 64.1 17 0.00037 24.5 4.3 43 36-79 7-49 (92)
39 PRK09526 lacI lac repressor; R 62.7 11 0.00023 28.3 3.4 37 31-72 16-52 (342)
40 PRK10703 DNA-binding transcrip 61.2 13 0.00028 27.9 3.6 32 31-66 12-43 (341)
41 cd08045 TAF4 TATA Binding Prot 60.8 29 0.00063 26.0 5.5 55 26-80 39-95 (212)
42 KOG1658 DNA polymerase epsilon 60.2 14 0.0003 28.1 3.6 45 30-76 58-103 (162)
43 PRK10423 transcriptional repre 60.2 14 0.0003 27.4 3.6 35 32-71 10-44 (327)
44 PHA01399 membrane protein P6 60.2 12 0.00026 29.7 3.4 57 37-93 18-79 (242)
45 PF13690 CheX: Chemotaxis phos 60.0 24 0.00053 22.7 4.4 45 30-78 17-61 (94)
46 TIGR02417 fruct_sucro_rep D-fr 60.0 14 0.0003 27.5 3.6 37 32-70 11-47 (327)
47 PRK10727 DNA-binding transcrip 59.5 12 0.00025 28.3 3.2 36 32-72 13-48 (343)
48 PRK10339 DNA-binding transcrip 59.1 11 0.00024 28.2 3.0 41 31-74 12-52 (327)
49 smart00354 HTH_LACI helix_turn 57.9 19 0.00041 22.2 3.5 41 30-75 10-50 (70)
50 PRK09492 treR trehalose repres 57.2 15 0.00033 27.0 3.4 36 31-71 15-50 (315)
51 PRK11303 DNA-binding transcrip 56.0 18 0.0004 26.8 3.7 33 32-65 12-44 (328)
52 PF09339 HTH_IclR: IclR helix- 53.7 7.1 0.00015 22.8 0.9 18 28-45 26-43 (52)
53 KOG0605 NDR and related serine 53.5 17 0.00037 32.1 3.6 36 31-66 391-430 (550)
54 PF02269 TFIID-18kDa: Transcri 53.2 20 0.00044 24.0 3.2 34 48-81 17-50 (93)
55 PRK10401 DNA-binding transcrip 51.1 22 0.00047 26.9 3.4 34 32-70 13-46 (346)
56 PRK10014 DNA-binding transcrip 50.7 25 0.00053 26.3 3.6 36 31-71 17-52 (342)
57 TIGR02405 trehalos_R_Ecol treh 49.3 27 0.00058 26.0 3.6 36 31-71 12-47 (311)
58 PF09114 MotA_activ: Transcrip 49.2 30 0.00064 24.3 3.6 33 34-66 50-86 (96)
59 PF13713 BRX_N: Transcription 49.1 28 0.00061 20.5 3.0 21 61-81 8-28 (39)
60 PRK14987 gluconate operon tran 45.6 27 0.00059 26.1 3.2 36 31-71 16-51 (331)
61 PLN03085 nucleobase:cation sym 43.6 32 0.0007 27.2 3.4 44 16-61 110-157 (221)
62 COG5262 HTA1 Histone H2A [Chro 43.3 89 0.0019 23.0 5.4 47 27-78 22-68 (132)
63 PF08681 DUF1778: Protein of u 42.2 92 0.002 20.0 5.0 26 48-73 3-35 (80)
64 PF01544 CorA: CorA-like Mg2+ 41.4 54 0.0012 24.0 4.2 41 55-95 211-252 (292)
65 cd01392 HTH_LacI Helix-turn-he 41.1 47 0.001 18.6 3.1 33 30-66 7-39 (52)
66 PF07524 Bromo_TP: Bromodomain 40.9 90 0.0019 19.5 5.0 32 50-81 23-54 (77)
67 cd05022 S-100A13 S-100A13: S-1 36.5 95 0.0021 20.4 4.4 50 27-76 21-79 (89)
68 PF09350 DUF1992: Domain of un 36.3 58 0.0013 20.9 3.3 45 15-60 18-66 (71)
69 PRK10203 hypothetical protein; 34.6 55 0.0012 23.5 3.2 49 15-65 24-79 (122)
70 PF05236 TAF4: Transcription i 34.2 80 0.0017 24.3 4.3 55 25-79 37-93 (264)
71 COG1609 PurR Transcriptional r 34.1 53 0.0011 25.7 3.3 34 32-70 12-45 (333)
72 cd07979 TAF9 TATA Binding Prot 33.5 1.7E+02 0.0036 20.4 6.1 43 36-80 6-48 (117)
73 PLN00154 histone H2A; Provisio 33.2 2E+02 0.0043 21.2 7.2 49 26-78 33-81 (136)
74 COG2512 Predicted membrane-ass 32.1 28 0.00061 27.5 1.5 16 29-44 219-234 (258)
75 PF15630 CENP-S: Kinetochore c 31.7 1.5E+02 0.0033 19.4 6.3 36 36-71 10-46 (76)
76 smart00353 HLH helix loop heli 29.3 1.1E+02 0.0025 17.2 4.3 37 38-74 15-51 (53)
77 KOG0425 Ubiquitin-protein liga 28.4 1.4E+02 0.0031 22.9 4.7 58 13-75 94-161 (171)
78 COG3355 Predicted transcriptio 26.6 1.2E+02 0.0025 21.9 3.8 46 28-73 50-118 (126)
79 COG3311 AlpA Predicted transcr 24.0 1.4E+02 0.0031 19.5 3.5 23 31-53 24-47 (70)
80 PLN00167 aquaporin TIP5; Provi 23.3 63 0.0014 25.2 2.0 27 41-67 1-30 (256)
81 cd07955 Anticodon_Ia_Cys_like 22.4 1.3E+02 0.0027 19.4 3.0 38 27-64 38-77 (81)
82 COG5624 TAF61 Transcription in 21.9 88 0.0019 27.5 2.7 43 29-71 381-423 (505)
83 PF00010 HLH: Helix-loop-helix 21.8 1.5E+02 0.0032 17.1 3.0 33 38-70 20-54 (55)
84 PF12627 PolyA_pol_RNAbd: Prob 21.7 32 0.00069 20.3 0.1 14 50-63 3-16 (64)
85 smart00346 HTH_ICLR helix_turn 21.7 52 0.0011 20.2 1.1 20 28-47 28-47 (91)
86 PF09239 Topo-VIb_trans: Topoi 21.5 1.1E+02 0.0024 23.1 3.0 34 43-76 121-154 (160)
87 cd00823 TopoIIB_Trans TopoIIB_ 21.5 1.6E+02 0.0034 22.1 3.7 33 43-75 112-144 (151)
88 PF02796 HTH_7: Helix-turn-hel 21.4 58 0.0013 18.5 1.1 15 29-43 30-44 (45)
89 cd03197 GST_C_mPGES2 GST_C fam 21.0 1.9E+02 0.0041 21.2 4.1 36 36-71 61-96 (149)
90 PF04439 Adenyl_transf: Strept 20.7 1.8E+02 0.0039 23.0 4.2 64 24-87 97-180 (282)
91 TIGR02431 pcaR_pcaU beta-ketoa 20.1 53 0.0012 24.4 1.0 19 28-46 32-50 (248)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.95 E-value=1.2e-27 Score=177.97 Aligned_cols=78 Identities=64% Similarity=0.904 Sum_probs=65.5
Q ss_pred CCCCCCCCCCCCCCCCCC-CC--CCCCCcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHH
Q 034435 2 AAEAPASPGGGSHESGEQ-SP--RSNVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVV 78 (95)
Q Consensus 2 ~~~~~~~~~~~~~~~g~~-~~--~~~~~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic 78 (95)
|++++..+ .+.|+.|+. .+ ...++++|++||+|||.||||++||+++||+|||||+|||||+|||+|||+||+|+|
T Consensus 1 m~~s~~~~-~~~~e~~g~~~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC 79 (168)
T KOG0869|consen 1 MAESDHDS-GGGDENGGNSSPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKC 79 (168)
T ss_pred CCCCcCCC-CccccCCcccCCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 45556544 444444442 22 247999999999999999999999999999999999999999999999999999999
Q ss_pred HH
Q 034435 79 LF 80 (95)
Q Consensus 79 ~~ 80 (95)
..
T Consensus 80 ~~ 81 (168)
T KOG0869|consen 80 QR 81 (168)
T ss_pred HH
Confidence 86
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.85 E-value=1.3e-21 Score=144.36 Aligned_cols=57 Identities=30% Similarity=0.568 Sum_probs=54.4
Q ss_pred CCCcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 24 ~~~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
+..+||++||+|||+||||++||++++|+|||||+|++||+|||++||||||++|++
T Consensus 5 ~~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~ 61 (156)
T KOG0871|consen 5 GKEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNK 61 (156)
T ss_pred ccccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 346899999999999999999999999999999999999999999999999999986
No 3
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.69 E-value=4.6e-17 Score=118.85 Aligned_cols=56 Identities=23% Similarity=0.386 Sum_probs=53.8
Q ss_pred CCcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 25 VREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 25 ~~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
..+|+++||+|||+||+.++||.+..++|||||++++||.|||+++||+||++|+.
T Consensus 5 ~~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~ 60 (148)
T COG5150 5 KNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEE 60 (148)
T ss_pred cccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999985
No 4
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.46 E-value=8.1e-14 Score=104.56 Aligned_cols=58 Identities=29% Similarity=0.393 Sum_probs=54.9
Q ss_pred CCcccccChhHHHHHHHHhhCCCC-ccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 034435 25 VREQDRYLPIANISRIMKKALPAN-GKIAKDAKETVQECVSEFISFITSEYDVVVLFLF 82 (95)
Q Consensus 25 ~~edD~~LP~A~V~RImKe~LP~~-~kIskdAkeli~eC~sEFI~~vTSeANeic~~~~ 82 (95)
.+.+|+.||+|+|.|++|++||.. +.|+|||+.+|++.++.||+|+|+.||++|..|.
T Consensus 4 eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~ 62 (172)
T KOG0870|consen 4 ERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQK 62 (172)
T ss_pred hhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 467899999999999999999987 9999999999999999999999999999999874
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.41 E-value=8.4e-13 Score=82.37 Aligned_cols=50 Identities=30% Similarity=0.521 Sum_probs=45.7
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLFL 81 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~ 81 (95)
.||++.|.||||.. |+..+||+||.++|++|+.+||.+|+.+|+++|...
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~ 51 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRD 51 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 69999999999999 999999999999999999999999999999999853
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.83 E-value=5.3e-09 Score=71.58 Aligned_cols=56 Identities=27% Similarity=0.377 Sum_probs=52.6
Q ss_pred CCCCcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 23 SNVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 23 ~~~~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
...+..|+.||+++|.||||++.+. +||.+|++.+|+++.||+..|+.+|++.|..
T Consensus 11 ~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~h 66 (91)
T COG2036 11 RYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEH 66 (91)
T ss_pred hhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999999998 9999999999999999999999999999875
No 7
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=96.87 E-value=0.0058 Score=39.28 Aligned_cols=47 Identities=15% Similarity=0.280 Sum_probs=43.6
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
|++.++..++|+.=|. .+++.||.+++++.+.+|+.-++..|...|.
T Consensus 2 ~~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAk 48 (72)
T cd07981 2 LTKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAK 48 (72)
T ss_pred CcHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6788999999999775 8999999999999999999999999999886
No 8
>smart00428 H3 Histone H3.
Probab=96.06 E-value=0.016 Score=40.62 Aligned_cols=55 Identities=11% Similarity=0.235 Sum_probs=47.2
Q ss_pred CCcccccChhHHHHHHHHhhCCC-----CccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 25 VREQDRYLPIANISRIMKKALPA-----NGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 25 ~~edD~~LP~A~V~RImKe~LP~-----~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
.+..|+.+|+..-+|+++|+... +.+++.+|.+++|+++-.|+-=+...||..+.
T Consensus 23 Qkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~ 82 (105)
T smart00428 23 QKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAI 82 (105)
T ss_pred ccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678889999999999998754 68999999999999999999988888887553
No 9
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=96.00 E-value=0.015 Score=38.10 Aligned_cols=49 Identities=20% Similarity=0.202 Sum_probs=38.9
Q ss_pred hhHHHHHHHHhhCC-CCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 034435 33 PIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEYDVVVLFL 81 (95)
Q Consensus 33 P~A~V~RImKe~LP-~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~ 81 (95)
|..+|.||++...- +++||++||..++.+....||.=....|.+.++..
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e 50 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAE 50 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 88999999997773 67999999999999999999987777777766654
No 10
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=95.55 E-value=0.058 Score=33.60 Aligned_cols=51 Identities=18% Similarity=0.221 Sum_probs=43.9
Q ss_pred ccChhHHHHHHHHhhCCC---CccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 30 RYLPIANISRIMKKALPA---NGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 30 ~~LP~A~V~RImKe~LP~---~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
...|+.-|.|+.|+..+. ..+|+++|.++++..+-.|+.=+..+|+..+..
T Consensus 4 ~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~ 57 (75)
T PF00125_consen 4 RLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARH 57 (75)
T ss_dssp HSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhh
Confidence 457888888888888764 269999999999999999999999999988864
No 11
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=95.39 E-value=0.075 Score=35.90 Aligned_cols=47 Identities=9% Similarity=0.182 Sum_probs=42.7
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
.||++.|.||.+.. .--+||.|+.+.+.+...+|+.-|..+|...++
T Consensus 13 gi~k~~I~RLarr~--GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~ 59 (85)
T cd00076 13 GITKPAIRRLARRG--GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTE 59 (85)
T ss_pred cCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 49999999999998 346999999999999999999999999988776
No 12
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=95.21 E-value=0.092 Score=33.94 Aligned_cols=46 Identities=20% Similarity=0.257 Sum_probs=35.8
Q ss_pred hHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 34 IANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 34 ~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
+..++.+++++=| +.++..|+.+++.+.+.+||.=+++.|-.+|.-
T Consensus 2 K~~l~~Lv~~iDp-~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKh 47 (68)
T PF03847_consen 2 KRKLQELVKQIDP-NEKLDPDVEELLLELADDFVDDVVSFACRLAKH 47 (68)
T ss_dssp HHHHHHHHHCC-S-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4567889999865 589999999999999999999999999888864
No 13
>PLN00035 histone H4; Provisional
Probab=94.97 E-value=0.051 Score=38.10 Aligned_cols=54 Identities=11% Similarity=0.138 Sum_probs=46.7
Q ss_pred CCCcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 24 ~~~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
..++.-..||++.|.||.+.. .--+||.|+.+.+.+...+|+.-|..+|...++
T Consensus 22 ~~~d~i~~ipk~~IrRLARr~--GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~ 75 (103)
T PLN00035 22 VLRDNIQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTE 75 (103)
T ss_pred HHHhhhccCCHHHHHHHHHHc--CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555569999999999998 345999999999999999999999999988776
No 14
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=94.76 E-value=0.2 Score=31.89 Aligned_cols=47 Identities=21% Similarity=0.241 Sum_probs=41.4
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
.||+++|.||.+.. .--+|+.|+.+.+.+-+.+++.=|..+|...++
T Consensus 2 ~~p~~~i~ria~~~--Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~ 48 (65)
T smart00803 2 WLPKETIKDVAESL--GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMR 48 (65)
T ss_pred CCCHHHHHHHHHHC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999987 223699999999999999999999999988765
No 15
>PTZ00015 histone H4; Provisional
Probab=94.48 E-value=0.17 Score=35.36 Aligned_cols=54 Identities=17% Similarity=0.274 Sum_probs=46.9
Q ss_pred CCCcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 24 ~~~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
.+++....||++.|.||.+.. .--+||.|+.+.+.+...+|+.-|..+|...++
T Consensus 23 ~~r~~i~gI~k~~IrRLarr~--GvkRIS~d~y~e~r~vle~~l~~I~rdav~~ae 76 (102)
T PTZ00015 23 VLRDNIRGITKGAIRRLARRG--GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTE 76 (102)
T ss_pred HHhhcccCCCHHHHHHHHHHc--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666679999999999998 345999999999999999999999999988775
No 16
>smart00417 H4 Histone H4.
Probab=94.47 E-value=0.2 Score=33.14 Aligned_cols=51 Identities=8% Similarity=0.146 Sum_probs=44.3
Q ss_pred cccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 27 edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
+.-..||++.|.||.+.. .--+||.++.+-+.+...+|+.-|..+|...++
T Consensus 9 d~i~gI~k~~IrRLaRr~--GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ 59 (74)
T smart00417 9 DNIQGITKPAIRRLARRG--GVKRISGLIYDETRNVLKSFLENVVRDAVTYTE 59 (74)
T ss_pred hhhcCCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334469999999999998 335899999999999999999999999988876
No 17
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=94.26 E-value=0.24 Score=33.24 Aligned_cols=50 Identities=18% Similarity=0.147 Sum_probs=45.8
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLFLF 82 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~~ 82 (95)
.||++.|-|+|...+. .+++.+...+|.--+.+||.=|..+|.++-+...
T Consensus 16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~ 65 (85)
T cd08048 16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWG 65 (85)
T ss_pred hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4999999999999997 5999999999999999999999999999987643
No 18
>PLN00121 histone H3; Provisional
Probab=92.15 E-value=0.29 Score=35.86 Aligned_cols=51 Identities=8% Similarity=0.194 Sum_probs=43.0
Q ss_pred CcccccChhHHHHHHHHhhCCC---CccccHhHHHHHHHHHHHHHHHHHhHHHH
Q 034435 26 REQDRYLPIANISRIMKKALPA---NGKIAKDAKETVQECVSEFISFITSEYDV 76 (95)
Q Consensus 26 ~edD~~LP~A~V~RImKe~LP~---~~kIskdAkeli~eC~sEFI~~vTSeANe 76 (95)
+..|+.+|+.--+|+++|+... +.+++.+|.+++|+++-.|+--+-..+|-
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~l 110 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNL 110 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 3458889999999999998854 78999999999999999998777666654
No 19
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.97 E-value=1.4 Score=35.47 Aligned_cols=52 Identities=13% Similarity=0.208 Sum_probs=43.6
Q ss_pred cccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 27 edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
+.+..|=+-.+..+++++-+ +.++.+|++|++.+-|-.||.-|+.-|-.+|.
T Consensus 150 ~~~~il~k~kl~dLvqqId~-~~~LD~dVedlLleiADdFV~sii~~sC~LAK 201 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQIDG-TTKLDDDVEDLLLEIADDFVSSIIHRSCKLAK 201 (258)
T ss_pred CCCccccccchhHHHHhhcC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456777888899999954 58999999999999999999999988877664
No 20
>PLN00161 histone H3; Provisional
Probab=91.69 E-value=0.69 Score=33.95 Aligned_cols=51 Identities=10% Similarity=0.233 Sum_probs=42.7
Q ss_pred CcccccChhHHHHHHHHhhC----CCCccccHhHHHHHHHHHHHHHHHHHhHHHH
Q 034435 26 REQDRYLPIANISRIMKKAL----PANGKIAKDAKETVQECVSEFISFITSEYDV 76 (95)
Q Consensus 26 ~edD~~LP~A~V~RImKe~L----P~~~kIskdAkeli~eC~sEFI~~vTSeANe 76 (95)
+..|+.+|++--+|+++|+. +.+.+++.+|.+++||++-.|+--+-..||-
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~l 104 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNL 104 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677899999999999985 3469999999999999999998777667664
No 21
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=91.12 E-value=0.96 Score=30.86 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=39.2
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
.||+++|-|+|+..+. +..|+....-+|.-.+..||.=|-.+|-++...
T Consensus 23 ~~~k~~ikkli~~~~~-~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~ 71 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG-NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEE 71 (90)
T ss_dssp ---HHHHHHHHHHHHS--S---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4999999999999995 479999999999999999999999999999874
No 22
>smart00427 H2B Histone H2B.
Probab=90.98 E-value=1 Score=30.94 Aligned_cols=44 Identities=18% Similarity=0.320 Sum_probs=39.0
Q ss_pred HHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 36 ~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
-|+|+.|++-|+ ..||+.|...|.--+.....=|++||...+..
T Consensus 6 Yi~kvLKqVhpd-~giS~kam~imnSfvnDiferIa~EAs~L~~~ 49 (89)
T smart00427 6 YIYKVLKQVHPD-TGISSKAMSIMNSFVNDIFERIAAEASKLARY 49 (89)
T ss_pred HHHHHHHHhCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 489999999986 79999999999988888888899999988763
No 23
>PTZ00018 histone H3; Provisional
Probab=90.06 E-value=0.99 Score=33.06 Aligned_cols=51 Identities=8% Similarity=0.200 Sum_probs=42.8
Q ss_pred CcccccChhHHHHHHHHhhCC---CCccccHhHHHHHHHHHHHHHHHHHhHHHH
Q 034435 26 REQDRYLPIANISRIMKKALP---ANGKIAKDAKETVQECVSEFISFITSEYDV 76 (95)
Q Consensus 26 ~edD~~LP~A~V~RImKe~LP---~~~kIskdAkeli~eC~sEFI~~vTSeANe 76 (95)
+..|+.+|+.--+|+++|+.. .+.+++.+|.+++|+++-.|+--+-..+|-
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~l 110 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNL 110 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHH
Confidence 345888999999999999864 478999999999999999999777766654
No 24
>PLN00160 histone H3; Provisional
Probab=89.64 E-value=1 Score=31.29 Aligned_cols=51 Identities=10% Similarity=0.120 Sum_probs=42.2
Q ss_pred CcccccChhHHHHHHHHhhCC----CCccccHhHHHHHHHHHHHHHHHHHhHHHH
Q 034435 26 REQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFITSEYDV 76 (95)
Q Consensus 26 ~edD~~LP~A~V~RImKe~LP----~~~kIskdAkeli~eC~sEFI~~vTSeANe 76 (95)
+..|+.+|++--+|+++|+.. .+.++..+|.+++|+++--|+--+-..+|-
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~l 70 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNL 70 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 456788999999999999864 458999999999999999988766666653
No 25
>PLN00158 histone H2B; Provisional
Probab=88.77 E-value=1.7 Score=31.21 Aligned_cols=47 Identities=15% Similarity=0.254 Sum_probs=40.5
Q ss_pred hhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 33 PIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 33 P~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
-..-|+|+.|++-|+ ..||..|..+|.-.+.....=|++||..++..
T Consensus 29 y~~YI~kVLKQVhPd-~gIS~kaM~ImnSfvnDiferIA~EAs~La~~ 75 (116)
T PLN00158 29 YKIYIYKVLKQVHPD-TGISSKAMSIMNSFINDIFEKIATEAGKLARY 75 (116)
T ss_pred HHHHHHHHHHHhCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345599999999986 78999999999988888888899999998763
No 26
>PTZ00463 histone H2B; Provisional
Probab=88.55 E-value=1.8 Score=31.16 Aligned_cols=44 Identities=14% Similarity=0.277 Sum_probs=38.4
Q ss_pred HHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 36 ~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
-|+|++|++-|+ .-||+.|..+|.-.+.-...=|++||..++..
T Consensus 33 YI~KVLKqVhPd-~gIS~kaM~ImnSfvnDifErIA~EAs~La~~ 76 (117)
T PTZ00463 33 YIFKVLKQVHPD-TGISRKSMNIMNSFLVDTFEKIATEASRLCKY 76 (117)
T ss_pred HHHHHHHhhCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 499999999986 78999999999988888788889999988763
No 27
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=88.32 E-value=0.57 Score=36.71 Aligned_cols=52 Identities=25% Similarity=0.238 Sum_probs=42.2
Q ss_pred cccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 27 edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
.-...||++-|-||||.-= .--+|+-||--++.++|-.||.-+|..|....+
T Consensus 70 ~~~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Te 121 (236)
T KOG1657|consen 70 FKNHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTLRSWVHTE 121 (236)
T ss_pred hhhccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 3345799999999999652 223899999999999999999999998766544
No 28
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=81.92 E-value=4 Score=29.75 Aligned_cols=54 Identities=17% Similarity=0.209 Sum_probs=44.6
Q ss_pred CCCcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 034435 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLFL 81 (95)
Q Consensus 24 ~~~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~ 81 (95)
..+.+.+..+ |+|++|++-|. .-|+.++..++.--..++.--|.+||+..+...
T Consensus 33 ~~~~e~~s~y---v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~ 86 (127)
T KOG1744|consen 33 TRRKESYSEY---VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYN 86 (127)
T ss_pred ccccCceeee---hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence 4444555444 78899999997 789999999999999999999999999988654
No 29
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=80.60 E-value=3.2 Score=34.47 Aligned_cols=49 Identities=20% Similarity=0.220 Sum_probs=30.0
Q ss_pred CCCCcccccChhHHHHHHHHhhCC----CCccccHhHHHHHHHHHHHHHHHHH
Q 034435 23 SNVREQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 23 ~~~~edD~~LP~A~V~RImKe~LP----~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
+..+..--.||.+.|-|+...... .+.||+|||.++|.+|--.|-.-|.
T Consensus 343 Skhgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~ 395 (414)
T PF15511_consen 343 SKHGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLG 395 (414)
T ss_dssp ---------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHH
Confidence 455666667999999999888865 5789999999999999999876554
No 30
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=80.40 E-value=2 Score=33.31 Aligned_cols=50 Identities=14% Similarity=0.107 Sum_probs=43.1
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLFLF 82 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~~ 82 (95)
.||+++|-|+|.++.-.. |+.-+.-+|+--+..||-=|--+|-++|+...
T Consensus 112 ~f~Ka~iKkL~~~itg~~--v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~ 161 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQS--VSENVAIAMAGIAKVFVGEVVEEALDVREEWG 161 (195)
T ss_pred cCCHHHHHHHHHHHhCCc--cCcceeeeecchhhHhHHHHHHHHHHHHHHhc
Confidence 499999999999998653 77777778888899999999999999998764
No 31
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=79.98 E-value=3.7 Score=33.13 Aligned_cols=44 Identities=27% Similarity=0.369 Sum_probs=37.3
Q ss_pred cccChhHHHHHHHHhhCCCCc-cccHhHHHHHHHHHHHHHHHHHhHH
Q 034435 29 DRYLPIANISRIMKKALPANG-KIAKDAKETVQECVSEFISFITSEY 74 (95)
Q Consensus 29 D~~LP~A~V~RImKe~LP~~~-kIskdAkeli~eC~sEFI~~vTSeA 74 (95)
+.+||.|.|.|+||-- .++ .||.||--+..+.|..||.=+|-.|
T Consensus 107 ~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRA 151 (286)
T COG5208 107 DHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRA 151 (286)
T ss_pred hccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHH
Confidence 5679999999999965 344 5899999999999999999888665
No 32
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=77.51 E-value=9.9 Score=26.83 Aligned_cols=41 Identities=17% Similarity=0.241 Sum_probs=30.6
Q ss_pred CcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHH
Q 034435 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFI 67 (95)
Q Consensus 26 ~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI 67 (95)
.-..+.+|.+-|.|+||+.--. -+|+.+|...+..+.-.+.
T Consensus 15 ~ragL~fPV~ri~R~Lk~~~~a-~RVs~~A~VyLaAvLEYL~ 55 (115)
T cd00074 15 ARAGLQFPVGRIHRYLKKGRYA-ERVGAGAPVYLAAVLEYLT 55 (115)
T ss_pred cccCccCcHHHHHHHHHcCccc-cccccchHHHHHHHHHHHH
Confidence 3447899999999999984333 6999999888776544333
No 33
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=76.66 E-value=5.3 Score=23.78 Aligned_cols=31 Identities=16% Similarity=0.421 Sum_probs=26.5
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSE 65 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sE 65 (95)
.+-++||+|++... -+|+.++++-|.+.+.|
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEE 40 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHH
Confidence 46689999999887 48999999999998765
No 34
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=67.83 E-value=7.3 Score=28.96 Aligned_cols=35 Identities=14% Similarity=0.405 Sum_probs=28.1
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
+=++||+|+++.. .+||+++|+-|.+++.| +.|.-
T Consensus 13 vS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~-lgY~p 47 (329)
T TIGR01481 13 VSMATVSRVVNGN----PNVKPATRKKVLEVIKR-LDYRP 47 (329)
T ss_pred CCHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCC
Confidence 4579999999863 47999999999999988 45544
No 35
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=67.19 E-value=30 Score=22.01 Aligned_cols=45 Identities=13% Similarity=0.202 Sum_probs=36.0
Q ss_pred hHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 34 IANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 34 ~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
+-.|.+|.|++ .=-+++.+|.|.+.+-..+|+.-+..++...|+.
T Consensus 9 ~~~Vaqil~~~--Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~ 53 (77)
T smart00576 9 RIAVAQILESA--GFDSFQESALETLTDILQSYIQELGRTAHSYAEL 53 (77)
T ss_pred HHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456666655 1138999999999999999999999999999865
No 36
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=66.71 E-value=20 Score=20.74 Aligned_cols=37 Identities=14% Similarity=0.124 Sum_probs=29.2
Q ss_pred HHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhH
Q 034435 37 ISRIMKKALPANGKIAKDAKETVQECVSEFISFITSE 73 (95)
Q Consensus 37 V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSe 73 (95)
-..-.+..||......+-.|-.|.+.+.++|..+..+
T Consensus 22 ~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~ 58 (60)
T cd00083 22 AFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58 (60)
T ss_pred HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3455678889875567777799999999999998765
No 37
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=65.33 E-value=23 Score=28.56 Aligned_cols=44 Identities=16% Similarity=0.123 Sum_probs=35.0
Q ss_pred hhHHHHHHHHhhCCCCc-cccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 33 PIANISRIMKKALPANG-KIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 33 P~A~V~RImKe~LP~~~-kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
|..+|.-|.+.+ ++ ++++||...+.+.+.+++.-|..+|...++
T Consensus 1 ~~~~i~~ia~~~---Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~ 45 (343)
T cd08050 1 PQESIKLIAESL---GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMR 45 (343)
T ss_pred ChhHHHHHHHHc---CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555554 34 999999999999999999999999988664
No 38
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=64.07 E-value=17 Score=24.49 Aligned_cols=43 Identities=14% Similarity=0.135 Sum_probs=33.3
Q ss_pred HHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 36 ~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
-|..||... .....-..|+.++|.+.+.+||.=++++|.+++.
T Consensus 7 ei~~mmy~~-GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~ 49 (92)
T cd07978 7 EIRQMMYGF-GDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ 49 (92)
T ss_pred HHHHHHHHc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555433 2334567899999999999999999999999995
No 39
>PRK09526 lacI lac repressor; Reviewed
Probab=62.69 E-value=11 Score=28.26 Aligned_cols=37 Identities=16% Similarity=0.501 Sum_probs=29.9
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHh
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITS 72 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTS 72 (95)
..=++||+|++... .+|+.++|+-|++++.| +.|.-.
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 35589999999863 47999999999999999 666543
No 40
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=61.20 E-value=13 Score=27.87 Aligned_cols=32 Identities=16% Similarity=0.363 Sum_probs=26.2
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEF 66 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEF 66 (95)
.+=++||+|.++.. ..||+++|+-|.+.+.|-
T Consensus 12 gVS~~TVSrvLn~~----~~vs~~tr~~V~~~a~el 43 (341)
T PRK10703 12 GVSTTTVSHVINKT----RFVAEETRNAVWAAIKEL 43 (341)
T ss_pred CCCHHHHHHHHcCC----CCCCHHHHHHHHHHHHHH
Confidence 35579999999753 479999999999998873
No 41
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=60.82 E-value=29 Score=25.96 Aligned_cols=55 Identities=11% Similarity=0.215 Sum_probs=43.5
Q ss_pred CcccccChhHHHHHHHHhhCCCCc--cccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 26 REQDRYLPIANISRIMKKALPANG--KIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 26 ~edD~~LP~A~V~RImKe~LP~~~--kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
..+..+|....+.+.|.++...+. .|+.|..++|..+|-+++..|-...-++|+-
T Consensus 39 ~~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~h 95 (212)
T cd08045 39 QKDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEH 95 (212)
T ss_pred cchhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445567777777777777776433 7999999999999999999988888777753
No 42
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=60.24 E-value=14 Score=28.06 Aligned_cols=45 Identities=20% Similarity=0.328 Sum_probs=36.5
Q ss_pred ccChhHHHHHHHHhhCCCCcccc-HhHHHHHHHHHHHHHHHHHhHHHH
Q 034435 30 RYLPIANISRIMKKALPANGKIA-KDAKETVQECVSEFISFITSEYDV 76 (95)
Q Consensus 30 ~~LP~A~V~RImKe~LP~~~kIs-kdAkeli~eC~sEFI~~vTSeANe 76 (95)
..||.+.|..++| |+++...+ +|++.+|.+++--||..|+..++.
T Consensus 58 ~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~ 103 (162)
T KOG1658|consen 58 SRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYT 103 (162)
T ss_pred hhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccch
Confidence 4588888888886 56777765 578999999999999999988765
No 43
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=60.16 E-value=14 Score=27.36 Aligned_cols=35 Identities=11% Similarity=0.366 Sum_probs=27.6
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
+=++||+|.++.. -+|+.++|+-|.+.+.|- .|.-
T Consensus 10 VS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~p 44 (327)
T PRK10423 10 VSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAP 44 (327)
T ss_pred CcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCc
Confidence 4579999999753 479999999999998873 4543
No 44
>PHA01399 membrane protein P6
Probab=60.15 E-value=12 Score=29.75 Aligned_cols=57 Identities=26% Similarity=0.484 Sum_probs=33.1
Q ss_pred HHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHHH-----HHHHhhccccc
Q 034435 37 ISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLFLF-----IFVCFFFPSFF 93 (95)
Q Consensus 37 V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~~-----~~~~~~~~~~~ 93 (95)
|.|++|.++..-++.-|....+|.+-++.-+.|++.-=+.+---+- |+.-||||.|.
T Consensus 18 vvkvvk~vv~~~v~~ika~vk~ikkivsvi~~fiskifs~ig~il~~il~~~~awf~fpa~I 79 (242)
T PHA01399 18 VVKVVKAVVDAIVKAIKAIVKIIKKIVSVILDFISKIFSKIGIILIIILIIIAAWFFFPAFA 79 (242)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Confidence 4455555554444555566666777777766777655555443332 23348899874
No 45
>PF13690 CheX: Chemotaxis phosphatase CheX; PDB: 3HM4_B 3H4Y_A 3H2D_A 3IIC_B.
Probab=60.00 E-value=24 Score=22.72 Aligned_cols=45 Identities=11% Similarity=0.193 Sum_probs=34.1
Q ss_pred ccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHH
Q 034435 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVV 78 (95)
Q Consensus 30 ~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic 78 (95)
+.+|+.+..++.+. |-.+ ..|-.+.++++..|+.++|...+....
T Consensus 17 l~~~~~~a~~la~~-mg~~---~~~~~e~~~da~~El~NiI~G~~~~~l 61 (94)
T PF13690_consen 17 LSFDEELAKKLASA-MGEE---EEEDDEMVQDALGELANIIAGNAKSEL 61 (94)
T ss_dssp EEE-HHHHHHHHHH-HSSS----SSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEECHHHHHHHHHH-hCCC---CcchhHHHHHHHHHHHHHHHHHHHHHc
Confidence 35789999999987 5333 455789999999999999998887443
No 46
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=59.99 E-value=14 Score=27.50 Aligned_cols=37 Identities=16% Similarity=0.251 Sum_probs=27.0
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHH
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFI 70 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~v 70 (95)
.=++||+|++... +...+||.++|+-|.+.+.| +.|.
T Consensus 11 VS~~TVSrvLn~~-~~~~~vs~~tr~rV~~~a~~-lgY~ 47 (327)
T TIGR02417 11 VSKTTASYVINGK-AKEYRISQETVERVMAVVRE-QGYQ 47 (327)
T ss_pred CCHHHHHHHHcCC-CCCCccCHHHHHHHHHHHHH-hCCC
Confidence 4478999999764 11126999999999998877 3443
No 47
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=59.50 E-value=12 Score=28.28 Aligned_cols=36 Identities=17% Similarity=0.437 Sum_probs=28.5
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHh
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITS 72 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTS 72 (95)
+=++||+|++... .+||.++|+-|.+.+.| +.|.-+
T Consensus 13 VS~~TVSrvLn~~----~~Vs~~tr~rV~~~a~e-lgY~pn 48 (343)
T PRK10727 13 VSVATVSRVINNS----PKASEASRLAVHSAMES-LSYHPN 48 (343)
T ss_pred CCHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCCC
Confidence 4579999999764 47999999999999988 455443
No 48
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=59.07 E-value=11 Score=28.16 Aligned_cols=41 Identities=20% Similarity=0.402 Sum_probs=29.6
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEY 74 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeA 74 (95)
.+=++||+|+++.. | ..+||.++|+-|.+.+.|. .|.-+.|
T Consensus 12 gVS~~TVSrvln~~-~-~~~vs~~tr~rV~~~a~~l-gY~pn~~ 52 (327)
T PRK10339 12 GVSLATVSRVLNDD-P-TLNVKEETKHRILEIAEKL-EYKTSSA 52 (327)
T ss_pred CCCHHhhhhhhcCC-C-CCCcCHHHHHHHHHHHHHh-CCCCchh
Confidence 35578999999764 2 2369999999999998883 4443333
No 49
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=57.92 E-value=19 Score=22.23 Aligned_cols=41 Identities=20% Similarity=0.467 Sum_probs=30.3
Q ss_pred ccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHH
Q 034435 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYD 75 (95)
Q Consensus 30 ~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeAN 75 (95)
..+.++||+|+++.. ..|+.++++-|.+.+.|+ .|....++
T Consensus 10 ~gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~-gy~~~~~~ 50 (70)
T smart00354 10 AGVSKATVSRVLNGN----GRVSEETREKVLAAMEEL-GYIPNRVA 50 (70)
T ss_pred HCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh-CCCCCHHH
Confidence 357889999988653 568999999999988874 44444333
No 50
>PRK09492 treR trehalose repressor; Provisional
Probab=57.19 E-value=15 Score=27.04 Aligned_cols=36 Identities=14% Similarity=0.386 Sum_probs=28.1
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
.+=++||+|+++.. .+||.++|+-|.+.+.| +.|.-
T Consensus 15 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~p 50 (315)
T PRK09492 15 GVGKSTVSRVLNNE----SGVSEETRERVEAVINQ-HGFSP 50 (315)
T ss_pred CCCHHHHhHHhCCC----CCCCHHHHHHHHHHHHH-HCCCc
Confidence 35579999999863 47999999999999887 34544
No 51
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=55.98 E-value=18 Score=26.81 Aligned_cols=33 Identities=15% Similarity=0.221 Sum_probs=25.6
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHH
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSE 65 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sE 65 (95)
.=++||+|++... |...+|+.++|+-|.+.+.|
T Consensus 12 VS~~TVSrvLn~~-~~~~~Vs~~tr~rV~~~a~e 44 (328)
T PRK11303 12 VSRTTASYVINGK-AKQYRVSDKTVEKVMAVVRE 44 (328)
T ss_pred CCHHHHHHHHcCC-CCCCCcCHHHHHHHHHHHHH
Confidence 4579999999764 11136999999999999887
No 52
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=53.67 E-value=7.1 Score=22.76 Aligned_cols=18 Identities=17% Similarity=0.399 Sum_probs=13.3
Q ss_pred ccccChhHHHHHHHHhhC
Q 034435 28 QDRYLPIANISRIMKKAL 45 (95)
Q Consensus 28 dD~~LP~A~V~RImKe~L 45 (95)
+...+|+++|+|+++.-.
T Consensus 26 ~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 26 RALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHHTS-HHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHHHHH
Confidence 345799999999998653
No 53
>KOG0605 consensus NDR and related serine/threonine kinases [General function prediction only]
Probab=53.55 E-value=17 Score=32.13 Aligned_cols=36 Identities=17% Similarity=0.306 Sum_probs=30.6
Q ss_pred cChhHHHHHHHHhh--C--CCCccccHhHHHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKA--L--PANGKIAKDAKETVQECVSEF 66 (95)
Q Consensus 31 ~LP~A~V~RImKe~--L--P~~~kIskdAkeli~eC~sEF 66 (95)
.-|.+|-.||+.-. | |.+..++.||+|+|.+|+.+=
T Consensus 391 ~tp~~T~rkI~nwr~~l~fP~~~~~s~eA~DLI~rll~d~ 430 (550)
T KOG0605|consen 391 ETPQETYRKIVNWRETLKFPEEVDLSDEAKDLITRLLCDP 430 (550)
T ss_pred CCHHHHHHHHHHHhhhccCCCcCcccHHHHHHHHHHhcCH
Confidence 46999999999765 4 789999999999999987653
No 54
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=53.16 E-value=20 Score=23.96 Aligned_cols=34 Identities=18% Similarity=0.092 Sum_probs=24.5
Q ss_pred CccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 034435 48 NGKIAKDAKETVQECVSEFISFITSEYDVVVLFL 81 (95)
Q Consensus 48 ~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~ 81 (95)
.-.-..|+..+|.+-+.+||.-+.++|.+++...
T Consensus 17 ~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~r 50 (93)
T PF02269_consen 17 VEEPLPETVDLVEDIVREYIIELCQEAMEVAQRR 50 (93)
T ss_dssp -SS--HHHHHHHHHHHHHHHHHHHHHHHC-----
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3456789999999999999999999999988776
No 55
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=51.08 E-value=22 Score=26.86 Aligned_cols=34 Identities=26% Similarity=0.585 Sum_probs=27.1
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHH
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFI 70 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~v 70 (95)
.=++||+|+++.. -+|+.++|+-|.+.+.|- .|.
T Consensus 13 VS~~TVSrvLn~~----~~Vs~~tr~kV~~~a~el-gY~ 46 (346)
T PRK10401 13 VSVATVSRVLNNS----ALVSADTREAVMKAVSEL-GYR 46 (346)
T ss_pred CCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHH-CCC
Confidence 4578999999763 379999999999999773 443
No 56
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=50.68 E-value=25 Score=26.29 Aligned_cols=36 Identities=19% Similarity=0.493 Sum_probs=27.7
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
..=++||+|.+++. -+||.++|+-|.+.+.|- .|+-
T Consensus 17 gVS~~TVSr~Ln~~----~~vs~~tr~~V~~~a~el-gY~p 52 (342)
T PRK10014 17 GVSVSTVSLVLSGK----GRISTATGERVNQAIEEL-GFVR 52 (342)
T ss_pred CCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh-CCCc
Confidence 45689999998753 479999999999888773 4443
No 57
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=49.30 E-value=27 Score=26.04 Aligned_cols=36 Identities=17% Similarity=0.426 Sum_probs=27.6
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
.+=++||+|+++.. -+||.++|+-|.+.+.|- .|.-
T Consensus 12 gVS~sTVSr~Ln~~----~~vs~~tr~rV~~~a~~l-gY~p 47 (311)
T TIGR02405 12 GVGKSTVSRVLNNE----PKVSIETRERVEQVIQQS-GFVP 47 (311)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCc
Confidence 35579999999752 479999999999988873 3443
No 58
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=49.17 E-value=30 Score=24.29 Aligned_cols=33 Identities=18% Similarity=0.267 Sum_probs=26.4
Q ss_pred hHHHHHHHHhhCC----CCccccHhHHHHHHHHHHHH
Q 034435 34 IANISRIMKKALP----ANGKIAKDAKETVQECVSEF 66 (95)
Q Consensus 34 ~A~V~RImKe~LP----~~~kIskdAkeli~eC~sEF 66 (95)
-+||.++||+-|= ++..++.+++++|++.+.-|
T Consensus 50 ~SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~ 86 (96)
T PF09114_consen 50 NSNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELW 86 (96)
T ss_dssp HHHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHH
T ss_pred HHhHHHHHHcCcccccCCceEEechHHHHHHHHHHHH
Confidence 3578889999883 56789999999999998765
No 59
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=49.10 E-value=28 Score=20.53 Aligned_cols=21 Identities=19% Similarity=0.196 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHhHHHHHHHHH
Q 034435 61 ECVSEFISFITSEYDVVVLFL 81 (95)
Q Consensus 61 eC~sEFI~~vTSeANeic~~~ 81 (95)
..+.|+|..||++-.++++++
T Consensus 8 kaaKe~IKsLt~QlK~maekl 28 (39)
T PF13713_consen 8 KAAKEVIKSLTAQLKDMAEKL 28 (39)
T ss_pred HHHHHHHHHHHHHHHHHHHhC
Confidence 467799999999999999886
No 60
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=45.64 E-value=27 Score=26.06 Aligned_cols=36 Identities=11% Similarity=0.359 Sum_probs=28.0
Q ss_pred cChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 31 ~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
..=++||+|++++. .+|+.++|+-|.+.+.| +.|.-
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~p 51 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIP 51 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCc
Confidence 35578999998753 47999999999998888 55643
No 61
>PLN03085 nucleobase:cation symporter-1; Provisional
Probab=43.64 E-value=32 Score=27.23 Aligned_cols=44 Identities=20% Similarity=0.330 Sum_probs=32.0
Q ss_pred CCCCCCCCCCCcccccChhHH--HHHHHHh--hCCCCccccHhHHHHHHH
Q 034435 16 SGEQSPRSNVREQDRYLPIAN--ISRIMKK--ALPANGKIAKDAKETVQE 61 (95)
Q Consensus 16 ~g~~~~~~~~~edD~~LP~A~--V~RImKe--~LP~~~kIskdAkeli~e 61 (95)
.|.+.|-. .+++..+|... .+||||+ .+|+.+...||..++|.+
T Consensus 110 pG~GKPL~--ldd~p~vp~e~r~~nRILknaG~lPpwIeL~KEI~~~i~~ 157 (221)
T PLN03085 110 PGKGKPLN--LSTNPHADPAEDTLYRILSKNGCAPEWVELNKEIRGQINE 157 (221)
T ss_pred CCCCCCCC--CcccCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence 45554443 45677777655 8999997 589999999999888743
No 62
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=43.32 E-value=89 Score=22.98 Aligned_cols=47 Identities=15% Similarity=0.305 Sum_probs=34.2
Q ss_pred cccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHH
Q 034435 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVV 78 (95)
Q Consensus 27 edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic 78 (95)
...+.+|...|.|+||+. -...+|+++|--.+..|. .|+++|--|.+
T Consensus 22 ~agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~Avl----eYL~aEilelA 68 (132)
T COG5262 22 KAGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVL----EYLAAEILELA 68 (132)
T ss_pred hcCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHH----HHHHHHHHHHh
Confidence 455789999999999943 346899999988777664 46666655443
No 63
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=42.24 E-value=92 Score=19.99 Aligned_cols=26 Identities=23% Similarity=0.367 Sum_probs=17.6
Q ss_pred CccccHhHHHHHHHHH-------HHHHHHHHhH
Q 034435 48 NGKIAKDAKETVQECV-------SEFISFITSE 73 (95)
Q Consensus 48 ~~kIskdAkeli~eC~-------sEFI~~vTSe 73 (95)
+++++.+.|++|.+++ |+||.-...+
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~ 35 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALE 35 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4689999999999986 5777444433
No 64
>PF01544 CorA: CorA-like Mg2+ transporter protein; InterPro: IPR002523 The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli [, ]. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. Transporter ZntB mediates efflux of zinc ions [].; GO: 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 2HN1_A 3NWI_D 3NVO_B 3CK6_A 2IUB_E 2BBJ_E 2HN2_A 2BBH_A.
Probab=41.43 E-value=54 Score=24.02 Aligned_cols=41 Identities=22% Similarity=0.425 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhcc-ccccC
Q 034435 55 AKETVQECVSEFISFITSEYDVVVLFLFIFVCFFFP-SFFCG 95 (95)
Q Consensus 55 Akeli~eC~sEFI~~vTSeANeic~~~~~~~~~~~~-~~~~~ 95 (95)
.++.+..--..+.+.++.+-|+.-..+-++..+|.| +|..|
T Consensus 211 ~~~~~~~l~~~~~~~~~~~~n~~m~~LT~~t~iflPlt~i~g 252 (292)
T PF01544_consen 211 LRERLESLQDLYQSKLSNRQNRVMKVLTIVTAIFLPLTFITG 252 (292)
T ss_dssp HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444445556667777888888888888888888 66554
No 65
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=41.07 E-value=47 Score=18.56 Aligned_cols=33 Identities=18% Similarity=0.434 Sum_probs=26.2
Q ss_pred ccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHH
Q 034435 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEF 66 (95)
Q Consensus 30 ~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEF 66 (95)
..+..+||+|+.+.. ..|+.+.++-|.+.+.++
T Consensus 7 ~gvs~~tvs~~l~g~----~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 7 AGVSVATVSRVLNGK----PRVSEETRERVLAAAEEL 39 (52)
T ss_pred HCcCHHHHHHHHcCC----CCCCHHHHHHHHHHHHHh
Confidence 457789999998854 378899999988887775
No 66
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=40.95 E-value=90 Score=19.49 Aligned_cols=32 Identities=6% Similarity=0.090 Sum_probs=29.2
Q ss_pred cccHhHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 034435 50 KIAKDAKETVQECVSEFISFITSEYDVVVLFL 81 (95)
Q Consensus 50 kIskdAkeli~eC~sEFI~~vTSeANeic~~~ 81 (95)
.++..|.+.+.+-+.+||.-+.+.+...|+..
T Consensus 23 ~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~ 54 (77)
T PF07524_consen 23 SASPSALDTLTDILQRYLQELGRTAKRYAEHA 54 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 79999999999999999999999998888754
No 67
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=36.51 E-value=95 Score=20.43 Aligned_cols=50 Identities=16% Similarity=0.192 Sum_probs=36.9
Q ss_pred cccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHH---------HHHHHHHHhHHHH
Q 034435 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECV---------SEFISFITSEYDV 76 (95)
Q Consensus 27 edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~---------sEFI~~vTSeANe 76 (95)
+.+.+|..+-+.++|++-||..++=.+|.+++|.+.= .||+.++.+-|..
T Consensus 21 ~~~g~i~~~ELk~ll~~elg~~ls~~~~v~~mi~~~D~d~DG~I~F~EF~~l~~~l~~~ 79 (89)
T cd05022 21 GGKESLTASEFQELLTQQLPHLLKDVEGLEEKMKNLDVNQDSKLSFEEFWELIGELAKA 79 (89)
T ss_pred CCCCeECHHHHHHHHHHHhhhhccCHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHH
Confidence 5566899999999999988864332267888886542 5888888877654
No 68
>PF09350 DUF1992: Domain of unknown function (DUF1992); InterPro: IPR018961 This entry represents a family of proteins that may have a role in protein folding or as a chaperone. DnaJ is a member of the J-protein family, which are defined by the presence of a J domain that can regulate the activity of 70kDa heat-shock proteins []. Some of the proteins in this entry contain a J domain.
Probab=36.28 E-value=58 Score=20.87 Aligned_cols=45 Identities=24% Similarity=0.403 Sum_probs=28.8
Q ss_pred CCCCCCCCCCCCcccccChhH--HHHHHHH--hhCCCCccccHhHHHHHH
Q 034435 15 ESGEQSPRSNVREQDRYLPIA--NISRIMK--KALPANGKIAKDAKETVQ 60 (95)
Q Consensus 15 ~~g~~~~~~~~~edD~~LP~A--~V~RImK--e~LP~~~kIskdAkeli~ 60 (95)
-.|.++|-. ..+++..+|.. ..+||+| ..||+.+...||..++-.
T Consensus 18 LpG~GKPL~-~~~~~~~~~~~~~~~~~iLk~~g~lPp~i~l~kei~~l~~ 66 (71)
T PF09350_consen 18 LPGAGKPLP-LDDDNPYWPAEERMANRILKNAGYLPPWIELRKEIEELRE 66 (71)
T ss_pred CCCCCCCCC-CCCCCcCCCHHHHHHHHhhcccCCCCHHHHHHHHHHHHHH
Confidence 345555555 22335778876 5788884 568888888777765443
No 69
>PRK10203 hypothetical protein; Provisional
Probab=34.57 E-value=55 Score=23.46 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=33.5
Q ss_pred CCCCCCCCCCCCcccccChhH--HHHHHHHh--hCCCCccccHhHH---HHHHHHHHH
Q 034435 15 ESGEQSPRSNVREQDRYLPIA--NISRIMKK--ALPANGKIAKDAK---ETVQECVSE 65 (95)
Q Consensus 15 ~~g~~~~~~~~~edD~~LP~A--~V~RImKe--~LP~~~kIskdAk---eli~eC~sE 65 (95)
-.|.+.|-. .++|...|-. .-+||+|+ .||+.+...||+. +++..|..+
T Consensus 24 LpG~GKPL~--~~d~~~~p~e~r~~~rilknag~lP~el~LrKE~~~l~~~l~~~~d~ 79 (122)
T PRK10203 24 LPGSGEPLI--LDDDSHVPPELRAGYRLLKNAGCLPPELEQRREAIQLLDLLKGIRED 79 (122)
T ss_pred CCCCCCCCC--CccCCCCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 345555553 3556667754 45799985 6899999999988 777776543
No 70
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=34.18 E-value=80 Score=24.29 Aligned_cols=55 Identities=11% Similarity=0.160 Sum_probs=35.3
Q ss_pred CCcccccChhHHHHHHHHhhCCCC--ccccHhHHHHHHHHHHHHHHHHHhHHHHHHH
Q 034435 25 VREQDRYLPIANISRIMKKALPAN--GKIAKDAKETVQECVSEFISFITSEYDVVVL 79 (95)
Q Consensus 25 ~~edD~~LP~A~V~RImKe~LP~~--~kIskdAkeli~eC~sEFI~~vTSeANeic~ 79 (95)
...++.+|....+.+-|.++...+ ..|..|..++|.-+|-+.|.-|-..+..+|+
T Consensus 37 ~~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~ 93 (264)
T PF05236_consen 37 SEKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSR 93 (264)
T ss_dssp -------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----
T ss_pred ccccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346677888888888888887543 4799999999999999999888877777664
No 71
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=34.13 E-value=53 Score=25.75 Aligned_cols=34 Identities=18% Similarity=0.453 Sum_probs=27.2
Q ss_pred ChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHH
Q 034435 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFI 70 (95)
Q Consensus 32 LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~v 70 (95)
.-++||+|.++.. .+||.|+|+-|.+.+.| +.|.
T Consensus 12 VS~sTVSrvln~~----~~Vs~eTr~kV~~a~~e-lgY~ 45 (333)
T COG1609 12 VSKATVSRVLNGS----PYVSEETREKVLAAIKE-LGYR 45 (333)
T ss_pred CCHHHHHHHHcCC----CCCCHHHHHHHHHHHHH-HCCC
Confidence 4578999988765 49999999999997766 4555
No 72
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=33.50 E-value=1.7e+02 Score=20.36 Aligned_cols=43 Identities=12% Similarity=0.092 Sum_probs=34.8
Q ss_pred HHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 034435 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVVLF 80 (95)
Q Consensus 36 ~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic~~ 80 (95)
.|.+|+|+. .-.+++.+++..+.|.+-.++.=|..+|...++-
T Consensus 6 ~v~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~h 48 (117)
T cd07979 6 VIAAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEH 48 (117)
T ss_pred HHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467777776 3348999999999999999999999888877653
No 73
>PLN00154 histone H2A; Provisional
Probab=33.24 E-value=2e+02 Score=21.20 Aligned_cols=49 Identities=18% Similarity=0.351 Sum_probs=33.4
Q ss_pred CcccccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHHHH
Q 034435 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEYDVVV 78 (95)
Q Consensus 26 ~edD~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeANeic 78 (95)
.--.+.+|..-|.|++|+-.....+|+..|--.+.-. +-|||+|--|.+
T Consensus 33 ~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAV----LEYLtAEVLELA 81 (136)
T PLN00154 33 SRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAI----LEYLTAEVLELA 81 (136)
T ss_pred cccCccCchHHHHHHHHhhhhhccccccchHHHHHHH----HHHHHHHHHHHH
Confidence 3447889999999999998755568888776544332 345666644443
No 74
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=32.14 E-value=28 Score=27.48 Aligned_cols=16 Identities=25% Similarity=0.374 Sum_probs=13.5
Q ss_pred cccChhHHHHHHHHhh
Q 034435 29 DRYLPIANISRIMKKA 44 (95)
Q Consensus 29 D~~LP~A~V~RImKe~ 44 (95)
++.||++||+||+++-
T Consensus 219 ~lglsktTvsR~L~~L 234 (258)
T COG2512 219 ALGLSKTTVSRILRRL 234 (258)
T ss_pred hhCCChHHHHHHHHHH
Confidence 3469999999999874
No 75
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=31.71 E-value=1.5e+02 Score=19.37 Aligned_cols=36 Identities=8% Similarity=0.177 Sum_probs=29.0
Q ss_pred HHHHHHHhhC-CCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 36 NISRIMKKAL-PANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 36 ~V~RImKe~L-P~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
+|.||..+.. +.+..+|+++-.++.|.+-.++.-++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a 46 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLA 46 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHH
Confidence 6889999884 77899999999999998888776443
No 76
>smart00353 HLH helix loop helix domain.
Probab=29.27 E-value=1.1e+02 Score=17.17 Aligned_cols=37 Identities=19% Similarity=0.205 Sum_probs=25.5
Q ss_pred HHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHHhHH
Q 034435 38 SRIMKKALPANGKIAKDAKETVQECVSEFISFITSEY 74 (95)
Q Consensus 38 ~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vTSeA 74 (95)
....+..||....-.+-.|-.|.+-+.++|..+..+.
T Consensus 15 ~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~ 51 (53)
T smart00353 15 FDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEEL 51 (53)
T ss_pred HHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567888996433444455777888889998887654
No 77
>KOG0425 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.41 E-value=1.4e+02 Score=22.86 Aligned_cols=58 Identities=24% Similarity=0.425 Sum_probs=40.2
Q ss_pred CCCCCCCCCCCCCCcccccChhHHHHHHHHhhC----------CCCccccHhHHHHHHHHHHHHHHHHHhHHH
Q 034435 13 SHESGEQSPRSNVREQDRYLPIANISRIMKKAL----------PANGKIAKDAKETVQECVSEFISFITSEYD 75 (95)
Q Consensus 13 ~~~~g~~~~~~~~~edD~~LP~A~V~RImKe~L----------P~~~kIskdAkeli~eC~sEFI~~vTSeAN 75 (95)
.|..|. .+.+-....|+-+|.-||.-||=.++ |+|+-.+++-||- =.||..-|..++.
T Consensus 94 LH~pgd-D~~gyE~~~erW~Pv~tvetIllSiIsmL~~PN~~SPANVDAa~~~Ren----~~EykkkV~r~vr 161 (171)
T KOG0425|consen 94 LHPPGD-DPSGYELPSERWLPVQTVETILLSIISMLNSPNDESPANVDAAKEWREN----PEEYKKKVRRCVR 161 (171)
T ss_pred ecCCCC-CcccCCChhhccCCccchhHhHHHHHHHHcCCCCCCccchHHHHHHhhC----HHHHHHHHHHHHH
Confidence 678887 35667788899999999999987765 4555555555544 4566666655543
No 78
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=26.60 E-value=1.2e+02 Score=21.92 Aligned_cols=46 Identities=15% Similarity=0.119 Sum_probs=34.4
Q ss_pred ccccChhHHHHHHHHhhCCCCc-----------------------cccHhHHHHHHHHHHHHHHHHHhH
Q 034435 28 QDRYLPIANISRIMKKALPANG-----------------------KIAKDAKETVQECVSEFISFITSE 73 (95)
Q Consensus 28 dD~~LP~A~V~RImKe~LP~~~-----------------------kIskdAkeli~eC~sEFI~~vTSe 73 (95)
+.+.+-++||+|.+++-+-.+. ++.+..+..+.+||..+=..|...
T Consensus 50 e~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l~~w~~~~~~~i~~~ 118 (126)
T COG3355 50 EILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDLDEWYDKMKQLIEEF 118 (126)
T ss_pred HHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999998775432 577777888888888877776543
No 79
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=24.02 E-value=1.4e+02 Score=19.50 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=18.5
Q ss_pred cChhHHHHHHHHh-hCCCCccccH
Q 034435 31 YLPIANISRIMKK-ALPANGKIAK 53 (95)
Q Consensus 31 ~LP~A~V~RImKe-~LP~~~kIsk 53 (95)
.|=++||||+|++ .+|..+++.-
T Consensus 24 GlSrstiYr~i~~~~FPkpvklG~ 47 (70)
T COG3311 24 GLSRSTIYRLIKDGTFPKPVKLGG 47 (70)
T ss_pred CccHHHHHHHHccCCCCCCeecCc
Confidence 4778999999986 5788888773
No 80
>PLN00167 aquaporin TIP5; Provisional
Probab=23.33 E-value=63 Score=25.21 Aligned_cols=27 Identities=22% Similarity=0.466 Sum_probs=18.7
Q ss_pred HHhhCCCCccc-cHh--HHHHHHHHHHHHH
Q 034435 41 MKKALPANGKI-AKD--AKETVQECVSEFI 67 (95)
Q Consensus 41 mKe~LP~~~kI-skd--Akeli~eC~sEFI 67 (95)
|++++|+.... .++ .+++++++..||+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~laEfl 30 (256)
T PLN00167 1 MRKMAPTSLSARFQQSVTRNALRSYLAEFI 30 (256)
T ss_pred CCcccCCCCcCchhhhccHHHHHHHHHHHH
Confidence 45667766554 344 6788888888887
No 81
>cd07955 Anticodon_Ia_Cys_like Anticodon-binding domain of cysteinyl tRNA synthetases and domain found in MshC. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA. The family also includes a domain of MshC, the rate-determining enzyme in the mycothiol biosynthetic pathway, which is specific to actinomycetes. The anticodon-binding site of CysRS lies C-terminal to this model's footprint and is not shared by MshC.
Probab=22.38 E-value=1.3e+02 Score=19.36 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=23.6
Q ss_pred cccccChhH--HHHHHHHhhCCCCccccHhHHHHHHHHHH
Q 034435 27 EQDRYLPIA--NISRIMKKALPANGKIAKDAKETVQECVS 64 (95)
Q Consensus 27 edD~~LP~A--~V~RImKe~LP~~~kIskdAkeli~eC~s 64 (95)
++|++-|.| .+..++|++|+....=..+++++......
T Consensus 38 ~DDLNTp~Ala~L~~l~k~i~~~~~~~~~~~~~~~~~~~~ 77 (81)
T cd07955 38 ADDLDTPKALAALDAWAREALSRGGTDPDAPALVRTAVDA 77 (81)
T ss_pred HhhCChHHHHHHHHHHHHHHHhcCCCCcccHHHHHHHHHH
Confidence 456666654 46777777767655556666666655443
No 82
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=21.88 E-value=88 Score=27.45 Aligned_cols=43 Identities=14% Similarity=0.194 Sum_probs=34.3
Q ss_pred cccChhHHHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 29 D~~LP~A~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
-+.+-+-.+.-+.+..+....||-.|.-|++.+-+.+|+.-+|
T Consensus 381 ~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt 423 (505)
T COG5624 381 WRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVT 423 (505)
T ss_pred hhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccc
Confidence 3456666677777777788889999999999999999886665
No 83
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=21.83 E-value=1.5e+02 Score=17.07 Aligned_cols=33 Identities=18% Similarity=0.312 Sum_probs=23.2
Q ss_pred HHHHHhhCCCC--ccccHhHHHHHHHHHHHHHHHH
Q 034435 38 SRIMKKALPAN--GKIAKDAKETVQECVSEFISFI 70 (95)
Q Consensus 38 ~RImKe~LP~~--~kIskdAkeli~eC~sEFI~~v 70 (95)
..-+++.||.. ..-.+-.|-.|.+-+.+||.++
T Consensus 20 ~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~L 54 (55)
T PF00010_consen 20 FDELRELLPSCSAGSSRKLSKASILQKAIDYIKQL 54 (55)
T ss_dssp HHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHhccchhccccccCCHHHHHHHHHHHHHHh
Confidence 34567888874 2445556688888899998775
No 84
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=21.74 E-value=32 Score=20.33 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=6.7
Q ss_pred cccHhHHHHHHHHH
Q 034435 50 KIAKDAKETVQECV 63 (95)
Q Consensus 50 kIskdAkeli~eC~ 63 (95)
+|.+++..+|++++
T Consensus 3 ~ie~~t~~ai~~~~ 16 (64)
T PF12627_consen 3 KIEPETEEAIKENA 16 (64)
T ss_dssp EE-HHHHHHHHHHG
T ss_pred ccCHHHHHHHHHHH
Confidence 45555555555543
No 85
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=21.74 E-value=52 Score=20.23 Aligned_cols=20 Identities=10% Similarity=0.082 Sum_probs=15.8
Q ss_pred ccccChhHHHHHHHHhhCCC
Q 034435 28 QDRYLPIANISRIMKKALPA 47 (95)
Q Consensus 28 dD~~LP~A~V~RImKe~LP~ 47 (95)
+.+.+|+++|+|+++...-.
T Consensus 28 ~~l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 28 ERLGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred HHhCCCHHHHHHHHHHHHHC
Confidence 44579999999999887543
No 86
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=21.53 E-value=1.1e+02 Score=23.08 Aligned_cols=34 Identities=18% Similarity=0.426 Sum_probs=24.8
Q ss_pred hhCCCCccccHhHHHHHHHHHHHHHHHHHhHHHH
Q 034435 43 KALPANGKIAKDAKETVQECVSEFISFITSEYDV 76 (95)
Q Consensus 43 e~LP~~~kIskdAkeli~eC~sEFI~~vTSeANe 76 (95)
|++-+.--|-+|.|.++|+||.+.=.||+.....
T Consensus 121 eaIa~~pEI~~Ei~lAl~e~~R~L~~yl~rk~~~ 154 (160)
T PF09239_consen 121 EAIADVPEIEKEIRLALQECARKLKKYLSRKRKA 154 (160)
T ss_dssp SSB---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333334688999999999999999999876543
No 87
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=21.52 E-value=1.6e+02 Score=22.07 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=25.3
Q ss_pred hhCCCCccccHhHHHHHHHHHHHHHHHHHhHHH
Q 034435 43 KALPANGKIAKDAKETVQECVSEFISFITSEYD 75 (95)
Q Consensus 43 e~LP~~~kIskdAkeli~eC~sEFI~~vTSeAN 75 (95)
|++-+.--|-+|-|.++|+||.+.=.||+..-.
T Consensus 112 eaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~~ 144 (151)
T cd00823 112 EAIADIPEIEEEIKLALQEVARKLKRYLSKKRK 144 (151)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444468899999999999999999886544
No 88
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.38 E-value=58 Score=18.54 Aligned_cols=15 Identities=13% Similarity=0.160 Sum_probs=10.4
Q ss_pred cccChhHHHHHHHHh
Q 034435 29 DRYLPIANISRIMKK 43 (95)
Q Consensus 29 D~~LP~A~V~RImKe 43 (95)
.+.+.++||+|+.++
T Consensus 30 ~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 30 QFGVSRSTVYRYLNK 44 (45)
T ss_dssp HTTS-HHHHHHHHCC
T ss_pred HHCcCHHHHHHHHhc
Confidence 356788899998764
No 89
>cd03197 GST_C_mPGES2 GST_C family; microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH, or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature, and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated and a C-terminal soluble domain with a GST-like structure. The C-terminus contains two structural domains a N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST active site is located in a cleft between t
Probab=20.98 E-value=1.9e+02 Score=21.19 Aligned_cols=36 Identities=11% Similarity=0.232 Sum_probs=27.1
Q ss_pred HHHHHHHhhCCCCccccHhHHHHHHHHHHHHHHHHH
Q 034435 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (95)
Q Consensus 36 ~V~RImKe~LP~~~kIskdAkeli~eC~sEFI~~vT 71 (95)
.+--++.+.|...--|..|.|+.+.++|.+|+.-+-
T Consensus 61 ~aM~~isk~lkk~~~i~~D~r~~L~~a~~~w~~~~~ 96 (149)
T cd03197 61 AAMYLISKYLKKPRLLQDDVREWLYDALNTWVAALG 96 (149)
T ss_pred HHHHHHHHHhccccCCCchHHHHHHHHHHHHHHHhc
Confidence 333455555666667889999999999999987653
No 90
>PF04439 Adenyl_transf: Streptomycin adenylyltransferase; InterPro: IPR007530 Also known as aminoglycoside 6-adenylyltransferase (2.7.7 from EC), this protein confers resistance to aminoglycoside antibiotics.; PDB: 2PBE_A.
Probab=20.73 E-value=1.8e+02 Score=22.98 Aligned_cols=64 Identities=17% Similarity=0.213 Sum_probs=40.8
Q ss_pred CCCcccccChhHHHHHHHH--hh-----------C---C--C--CccccHhHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 034435 24 NVREQDRYLPIANISRIMK--KA-----------L---P--A--NGKIAKDAKETVQECVSEFISFITSEYDVVVLFLFI 83 (95)
Q Consensus 24 ~~~edD~~LP~A~V~RImK--e~-----------L---P--~--~~kIskdAkeli~eC~sEFI~~vTSeANeic~~~~~ 83 (95)
+.+.|=..+|...+.+.++ +. + | . ...|.+-+..-..+||.||--..+.-|.-+++...+
T Consensus 97 g~rIDltl~~~~~l~~~~~~~d~~~~vLlDKd~~~~~~~~~~~~~y~i~~Ps~~eF~~~cNeFw~~~~~VaKgL~R~El~ 176 (282)
T PF04439_consen 97 GNRIDLTLIPLERLEEYIKESDSLYKVLLDKDGILPKIPPPSDSDYWIKKPSEQEFDDCCNEFWWVSTYVAKGLWRNELW 176 (282)
T ss_dssp S-EEEEEEEEGGGHHHHHH-------EEEESS--S-------GGGTEE----HHHHHHHHHHHHHHHHHHHHHHHTT-HH
T ss_pred CcEEEEEEecHHHHHHHHhhcCcCcEEEEcCCCCcCCCCCCcccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhccHH
Confidence 3444445568888888872 11 1 1 1 236788888999999999998888888888888887
Q ss_pred HHHh
Q 034435 84 FVCF 87 (95)
Q Consensus 84 ~~~~ 87 (95)
++-.
T Consensus 177 yA~~ 180 (282)
T PF04439_consen 177 YAKD 180 (282)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 7643
No 91
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=20.12 E-value=53 Score=24.44 Aligned_cols=19 Identities=16% Similarity=0.118 Sum_probs=15.7
Q ss_pred ccccChhHHHHHHHHhhCC
Q 034435 28 QDRYLPIANISRIMKKALP 46 (95)
Q Consensus 28 dD~~LP~A~V~RImKe~LP 46 (95)
+.+.||++|++|+++...-
T Consensus 32 ~~lglpksT~~RlL~tL~~ 50 (248)
T TIGR02431 32 EATGLTRAAARRFLLTLVE 50 (248)
T ss_pred HHHCcCHHHHHHHHHHHHH
Confidence 4567999999999998654
Done!