Query 045289
Match_columns 71
No_of_seqs 109 out of 213
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 11:43:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045289.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045289hhsearch_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 4.2E-26 9E-31 162.7 5.3 47 10-56 24-70 (168)
2 KOG0871 Class 2 transcription 99.4 2.5E-13 5.5E-18 96.4 5.3 45 13-57 7-51 (156)
3 COG5150 Class 2 transcription 99.0 8.7E-10 1.9E-14 77.7 5.2 46 12-57 5-50 (148)
4 PF00808 CBFD_NFYB_HMF: Histon 98.9 4E-09 8.6E-14 62.4 4.6 38 18-56 2-39 (65)
5 KOG0870 DNA polymerase epsilon 98.8 7.2E-09 1.6E-13 74.7 3.8 45 12-56 4-49 (172)
6 COG2036 HHT1 Histones H3 and H 98.7 6.4E-09 1.4E-13 68.0 2.5 45 10-56 11-55 (91)
7 cd07981 TAF12 TATA Binding Pro 93.9 0.16 3.4E-06 31.0 4.5 36 19-55 2-37 (72)
8 PF09415 CENP-X: CENP-S associ 93.4 0.063 1.4E-06 33.5 2.0 36 20-55 1-37 (72)
9 smart00428 H3 Histone H3. 93.1 0.11 2.5E-06 34.6 3.0 43 13-55 24-71 (105)
10 PF03847 TFIID_20kDa: Transcri 91.0 0.46 1E-05 29.3 3.8 33 22-55 3-35 (68)
11 smart00803 TAF TATA box bindin 90.2 0.87 1.9E-05 27.6 4.5 36 18-55 2-37 (65)
12 cd00076 H4 Histone H4, one of 90.2 0.65 1.4E-05 29.9 4.1 36 18-55 13-48 (85)
13 PLN00035 histone H4; Provision 89.1 0.88 1.9E-05 30.5 4.2 38 16-55 27-64 (103)
14 smart00417 H4 Histone H4. 85.8 2 4.3E-05 27.1 4.2 37 17-55 12-48 (74)
15 PLN00121 histone H3; Provision 84.7 0.94 2E-05 31.6 2.6 44 13-56 57-103 (136)
16 PF00125 Histone: Core histone 84.5 1.8 3.9E-05 25.4 3.4 39 16-54 3-44 (75)
17 PF00356 LacI: Bacterial regul 84.4 2.5 5.4E-05 24.1 3.8 32 18-53 10-41 (46)
18 PTZ00015 histone H4; Provision 83.2 2.6 5.6E-05 28.1 4.1 40 14-55 26-65 (102)
19 PLN00161 histone H3; Provision 83.1 2.2 4.8E-05 29.9 3.9 43 13-55 50-96 (135)
20 COG5208 HAP5 CCAAT-binding fac 81.4 1.5 3.3E-05 33.9 2.7 39 15-55 106-145 (286)
21 cd08048 TAF11 TATA Binding Pro 79.9 4.4 9.5E-05 25.9 4.1 44 18-61 16-65 (85)
22 PLN00160 histone H3; Provision 79.3 2.8 6.1E-05 27.7 3.2 43 13-55 16-62 (97)
23 PTZ00018 histone H3; Provision 77.9 4 8.6E-05 28.5 3.7 43 14-56 58-103 (136)
24 TIGR01481 ccpA catabolite cont 76.7 3.7 8.1E-05 28.7 3.4 32 18-53 12-43 (329)
25 PRK09526 lacI lac repressor; R 73.5 5.6 0.00012 28.0 3.6 32 18-53 16-47 (342)
26 PF04719 TAFII28: hTAFII28-lik 72.1 7.3 0.00016 25.3 3.6 41 18-59 23-71 (90)
27 PRK10727 DNA-binding transcrip 71.0 6.6 0.00014 27.9 3.5 32 18-53 12-43 (343)
28 PRK10703 DNA-binding transcrip 70.2 7.5 0.00016 27.4 3.6 32 18-53 12-43 (341)
29 PRK10423 transcriptional repre 67.6 9.2 0.0002 26.6 3.6 32 18-53 9-40 (327)
30 PF15511 CENP-T: Centromere ki 67.4 7.9 0.00017 30.5 3.6 39 16-54 349-391 (414)
31 smart00354 HTH_LACI helix_turn 67.1 14 0.0003 21.7 3.8 34 17-54 10-43 (70)
32 KOG1657 CCAAT-binding factor, 66.9 5.4 0.00012 29.8 2.5 44 15-59 71-114 (236)
33 PRK09492 treR trehalose repres 64.4 11 0.00023 26.2 3.4 32 18-53 15-46 (315)
34 KOG1142 Transcription initiati 60.6 16 0.00034 28.2 4.0 40 15-55 151-190 (258)
35 TIGR02417 fruct_sucro_rep D-fr 60.4 15 0.00033 25.7 3.6 34 19-53 11-44 (327)
36 PRK10014 DNA-binding transcrip 59.4 16 0.00035 25.7 3.6 32 18-53 17-48 (342)
37 PRK10339 DNA-binding transcrip 59.0 12 0.00027 26.3 3.0 34 18-53 12-45 (327)
38 cd00074 H2A Histone 2A; H2A is 58.2 19 0.00041 24.2 3.7 39 15-55 17-55 (115)
39 PRK10401 DNA-binding transcrip 58.0 16 0.00034 26.0 3.4 32 18-53 12-43 (346)
40 TIGR02405 trehalos_R_Ecol treh 55.8 20 0.00043 25.2 3.6 32 18-53 12-43 (311)
41 PRK14987 gluconate operon tran 55.4 17 0.00037 25.6 3.2 32 18-53 16-47 (331)
42 PRK11303 DNA-binding transcrip 54.0 23 0.00049 24.8 3.7 35 18-53 11-45 (328)
43 KOG0605 NDR and related serine 53.5 15 0.00033 31.0 3.1 35 18-52 391-429 (550)
44 PF09114 MotA_activ: Transcrip 49.9 28 0.00061 23.4 3.4 36 21-56 50-89 (96)
45 PF09339 HTH_IclR: IclR helix- 40.6 20 0.00044 19.7 1.4 15 16-30 27-41 (52)
46 KOG0612 Rho-associated, coiled 40.2 30 0.00066 32.0 3.1 28 22-49 288-319 (1317)
47 PLN00167 aquaporin TIP5; Provi 38.6 26 0.00057 25.9 2.1 28 28-55 1-31 (256)
48 PF02953 zf-Tim10_DDP: Tim10/D 38.5 52 0.0011 19.0 3.0 24 34-57 33-56 (66)
49 COG1609 PurR Transcriptional r 37.4 47 0.001 24.6 3.3 31 19-53 12-42 (333)
50 cd01392 HTH_LacI Helix-turn-he 35.6 72 0.0016 16.8 3.5 33 17-53 7-39 (52)
51 KOG4449 Translocase of outer m 34.8 32 0.00069 21.0 1.7 15 36-50 1-15 (53)
52 KOG3284 Vacuolar sorting prote 30.9 72 0.0016 24.1 3.4 38 22-60 93-137 (213)
53 KOG3489 Mitochondrial import i 30.0 61 0.0013 21.4 2.6 22 34-55 46-67 (86)
54 KOG3219 Transcription initiati 29.7 28 0.0006 25.9 1.0 44 18-61 112-161 (195)
55 PF10380 CRF1: Transcription f 29.4 18 0.00039 25.0 -0.0 21 15-47 6-29 (123)
56 cd00083 HLH Helix-loop-helix d 29.4 1E+02 0.0022 16.7 3.5 32 25-56 23-54 (60)
57 PF15630 CENP-S: Kinetochore c 27.5 1.6E+02 0.0035 18.3 4.1 33 23-55 10-43 (76)
58 cd05492 Bromo_ZMYND11 Bromodom 26.2 97 0.0021 20.4 3.1 30 24-53 71-103 (109)
59 PRK10001 D-alanyl-D-alanine ca 26.1 50 0.0011 26.1 1.9 32 12-43 55-98 (400)
60 KOG1151 Tousled-like protein k 23.6 48 0.001 28.8 1.5 49 19-71 694-742 (775)
61 KOG0425 Ubiquitin-protein liga 22.9 52 0.0011 24.1 1.4 25 8-32 101-125 (171)
62 cd08045 TAF4 TATA Binding Prot 22.3 1.4E+02 0.003 21.1 3.5 40 16-55 42-83 (212)
63 PF10557 Cullin_Nedd8: Cullin 21.3 63 0.0014 19.0 1.3 11 21-31 10-20 (68)
64 cd07153 Fur_like Ferric uptake 21.2 51 0.0011 20.3 1.0 20 13-32 27-46 (116)
65 PF04380 BMFP: Membrane fusoge 21.1 1.6E+02 0.0034 18.1 3.2 38 19-56 6-47 (79)
66 PLN00154 histone H2A; Provisio 21.0 1.7E+02 0.0038 20.5 3.6 40 16-56 36-75 (136)
67 smart00777 Mad3_BUB1_I Mad3/BU 20.3 2.3E+02 0.005 19.0 4.1 41 15-56 19-59 (125)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.92 E-value=4.2e-26 Score=162.69 Aligned_cols=47 Identities=49% Similarity=0.735 Sum_probs=45.1
Q ss_pred CCCCccccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhh
Q 045289 10 SNIQEEDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 10 ~~~reqD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
..+|+|||+||||||+||||++||+++||||||||+|||||||||-|
T Consensus 24 ~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISF 70 (168)
T KOG0869|consen 24 LSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISF 70 (168)
T ss_pred cccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHH
Confidence 35999999999999999999999999999999999999999999976
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.42 E-value=2.5e-13 Score=96.42 Aligned_cols=45 Identities=20% Similarity=0.406 Sum_probs=42.1
Q ss_pred CccccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhhc
Q 045289 13 QEEDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLAR 57 (71)
Q Consensus 13 reqD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~~ 57 (71)
..+|..||.|+|.+|||+.||.++.|+|||||++++||+|||+.-
T Consensus 7 ~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~li 51 (156)
T KOG0871|consen 7 EDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLI 51 (156)
T ss_pred ccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHH
Confidence 347899999999999999999999999999999999999999863
No 3
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=98.98 E-value=8.7e-10 Score=77.71 Aligned_cols=46 Identities=17% Similarity=0.290 Sum_probs=42.5
Q ss_pred CCccccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhhc
Q 045289 12 IQEEDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLAR 57 (71)
Q Consensus 12 ~reqD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~~ 57 (71)
..++..+||+|||.|++...||.+.-++||||++++.||.|||+.-
T Consensus 5 ~~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~l 50 (148)
T COG5150 5 KNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINML 50 (148)
T ss_pred cccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHH
Confidence 4457789999999999999999999999999999999999999864
No 4
>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=98.87 E-value=4e-09 Score=62.43 Aligned_cols=38 Identities=21% Similarity=0.304 Sum_probs=34.1
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhh
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
.||++.|.||||.. |...+||+||.++|+.|+.+||..
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~ 39 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQY 39 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHH
Confidence 69999999999999 999999999999999999999964
No 5
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.76 E-value=7.2e-09 Score=74.73 Aligned_cols=45 Identities=24% Similarity=0.327 Sum_probs=42.3
Q ss_pred CCccccccchHHHHHHHHhhCCCC-CcccHhHHHHHHHHHHHHHhh
Q 045289 12 IQEEDRYLPIANISWIIKKAFPAN-DIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 12 ~reqD~~LPiAnI~RIMK~aLP~~-aKISKeAKe~iqeCvsEFIl~ 56 (71)
-|.+|+.||.|.|+|++|++||.. +.|+|||+.+|++.++-||++
T Consensus 4 eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~ 49 (172)
T KOG0870|consen 4 ERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIF 49 (172)
T ss_pred hhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHH
Confidence 466899999999999999999988 999999999999999999975
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.73 E-value=6.4e-09 Score=67.97 Aligned_cols=45 Identities=20% Similarity=0.176 Sum_probs=41.1
Q ss_pred CCCCccccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhh
Q 045289 10 SNIQEEDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 10 ~~~reqD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
...+..|+.||+|+|.||||++.+. +||.+|++++|+|+.||+..
T Consensus 11 ~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~ 55 (91)
T COG2036 11 RYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEE 55 (91)
T ss_pred hhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHH
Confidence 3457789999999999999999998 99999999999999999853
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=93.94 E-value=0.16 Score=30.99 Aligned_cols=36 Identities=8% Similarity=0.171 Sum_probs=32.1
Q ss_pred cchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 19 LPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 19 LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
|+.-++..++++.=| +..++.+|++.+|+.+.+|+.
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~ 37 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVD 37 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHH
Confidence 567788999999877 589999999999999999985
No 8
>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=93.39 E-value=0.063 Score=33.50 Aligned_cols=36 Identities=17% Similarity=0.240 Sum_probs=28.6
Q ss_pred chHHHHHHHHhhCC-CCCcccHhHHHHHHHHHHHHHh
Q 045289 20 PIANISWIIKKAFP-ANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 20 PiAnI~RIMK~aLP-~~aKISKeAKe~iqeCvsEFIl 55 (71)
|..+|.||++...- +..||+++|-.++++...-||.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~ 37 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVR 37 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHH
Confidence 78899999998774 6789999999999998887774
No 9
>smart00428 H3 Histone H3.
Probab=93.06 E-value=0.11 Score=34.64 Aligned_cols=43 Identities=12% Similarity=0.122 Sum_probs=37.0
Q ss_pred CccccccchHHHHHHHHhhCCC-----CCcccHhHHHHHHHHHHHHHh
Q 045289 13 QEEDRYLPIANISWIIKKAFPA-----NDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 13 reqD~~LPiAnI~RIMK~aLP~-----~aKISKeAKe~iqeCvsEFIl 55 (71)
+..|+.+|++..+|++++.... +.+++.+|.+++|+++-.|+.
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv 71 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLV 71 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHH
Confidence 4568889999999999888753 679999999999999988876
No 10
>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=91.05 E-value=0.46 Score=29.26 Aligned_cols=33 Identities=6% Similarity=0.128 Sum_probs=24.0
Q ss_pred HHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 22 ANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 22 AnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
-++.-+++++= |+.++.+++.+++.+.+.+||-
T Consensus 3 ~~l~~Lv~~iD-p~~~ld~~vee~Ll~laddFv~ 35 (68)
T PF03847_consen 3 RKLQELVKQID-PNEKLDPDVEELLLELADDFVD 35 (68)
T ss_dssp HHHHHHHHCC--SS----HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHH
Confidence 46777888875 5799999999999999999984
No 11
>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=90.21 E-value=0.87 Score=27.57 Aligned_cols=36 Identities=11% Similarity=0.112 Sum_probs=29.0
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
+||.++|.||.+.. +--.||+|+.+.+.+-+..|+.
T Consensus 2 ~~p~~~i~ria~~~--Gi~ris~~a~~~l~~~~e~rl~ 37 (65)
T smart00803 2 WLPKETIKDVAESL--GIGNLSDEAAKLLAEDVEYRIK 37 (65)
T ss_pred CCCHHHHHHHHHHC--CCccccHHHHHHHHHHHHHHHH
Confidence 69999999998875 2235999999988888877763
No 12
>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=90.17 E-value=0.65 Score=29.89 Aligned_cols=36 Identities=11% Similarity=0.009 Sum_probs=31.1
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
.||++.|.||.++.= --+||+++.+-+.++..+|+.
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~ 48 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLE 48 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHH
Confidence 499999999999872 446999999999999998874
No 13
>PLN00035 histone H4; Provisional
Probab=89.06 E-value=0.88 Score=30.47 Aligned_cols=38 Identities=11% Similarity=-0.037 Sum_probs=32.1
Q ss_pred ccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 16 DRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 16 D~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
-..||++.|.||.+++= --+||.++.+.+.+...+|+.
T Consensus 27 i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~ 64 (103)
T PLN00035 27 IQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLE 64 (103)
T ss_pred hccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHH
Confidence 45599999999999873 457999999999999888874
No 14
>smart00417 H4 Histone H4.
Probab=85.80 E-value=2 Score=27.11 Aligned_cols=37 Identities=8% Similarity=0.002 Sum_probs=30.5
Q ss_pred cccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 17 RYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 17 ~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
..||++.|.||.+++ .--+||.++.+-+.+...+|+.
T Consensus 12 ~gI~k~~IrRLaRr~--GvkRIS~~~y~elr~vle~~l~ 48 (74)
T smart00417 12 QGITKPAIRRLARRG--GVKRISGLIYDETRNVLKSFLE 48 (74)
T ss_pred cCCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHH
Confidence 469999999999987 2336999999988888888864
No 15
>PLN00121 histone H3; Provisional
Probab=84.68 E-value=0.94 Score=31.65 Aligned_cols=44 Identities=7% Similarity=0.080 Sum_probs=37.0
Q ss_pred CccccccchHHHHHHHHhhCCC---CCcccHhHHHHHHHHHHHHHhh
Q 045289 13 QEEDRYLPIANISWIIKKAFPA---NDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 13 reqD~~LPiAnI~RIMK~aLP~---~aKISKeAKe~iqeCvsEFIl~ 56 (71)
+..|+.+|.+-.+|+++++... +..+..+|-+++||++--|+.-
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~ 103 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVG 103 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHH
Confidence 3458889999999999988754 6899999999999999888753
No 16
>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=84.45 E-value=1.8 Score=25.38 Aligned_cols=39 Identities=15% Similarity=0.108 Sum_probs=30.5
Q ss_pred ccccchHHHHHHHHhhCCC---CCcccHhHHHHHHHHHHHHH
Q 045289 16 DRYLPIANISWIIKKAFPA---NDIITKNAKQIVQGCSKACS 54 (71)
Q Consensus 16 D~~LPiAnI~RIMK~aLP~---~aKISKeAKe~iqeCvsEFI 54 (71)
++..|..-|.|+.|+..+. ..+||++|-+++|..+-.|+
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~ 44 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLL 44 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhh
Confidence 3567888888888888764 25999999999998766554
No 17
>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=84.36 E-value=2.5 Score=24.06 Aligned_cols=32 Identities=3% Similarity=0.164 Sum_probs=26.9
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
.+.+++|+|++... ..||.+.++-|++.+.|.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 46789999998876 589999999999988763
No 18
>PTZ00015 histone H4; Provisional
Probab=83.25 E-value=2.6 Score=28.12 Aligned_cols=40 Identities=18% Similarity=0.169 Sum_probs=32.7
Q ss_pred ccccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 14 EEDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 14 eqD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
+.-..||++.|.||.+++ .--+||.++.+-+.+...+|+.
T Consensus 26 ~~i~gI~k~~IrRLarr~--GvkRIS~d~y~e~r~vle~~l~ 65 (102)
T PTZ00015 26 DNIRGITKGAIRRLARRG--GVKRISGDIYEEVRGVLKAFLE 65 (102)
T ss_pred hcccCCCHHHHHHHHHHc--CCccchHHHHHHHHHHHHHHHH
Confidence 344569999999999987 2346999999999999888874
No 19
>PLN00161 histone H3; Provisional
Probab=83.12 E-value=2.2 Score=29.90 Aligned_cols=43 Identities=7% Similarity=0.021 Sum_probs=36.3
Q ss_pred CccccccchHHHHHHHHhhC----CCCCcccHhHHHHHHHHHHHHHh
Q 045289 13 QEEDRYLPIANISWIIKKAF----PANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 13 reqD~~LPiAnI~RIMK~aL----P~~aKISKeAKe~iqeCvsEFIl 55 (71)
+..|+.+|.+-.+|+++++. +.+.++..+|-+++||++--|+.
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV 96 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLV 96 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHH
Confidence 44578889999999988875 34689999999999999988886
No 20
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=81.38 E-value=1.5 Score=33.90 Aligned_cols=39 Identities=21% Similarity=0.274 Sum_probs=30.9
Q ss_pred cccccchHHHHHHHHhhCCCCCc-ccHhHHHHHHHHHHHHHh
Q 045289 15 EDRYLPIANISWIIKKAFPANDI-ITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 15 qD~~LPiAnI~RIMK~aLP~~aK-ISKeAKe~iqeCvsEFIl 55 (71)
.|.+||.|-|-|+||-- .++| ||.||--+....+--||.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ 145 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIE 145 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHH
Confidence 46789999999999953 4565 888888888777777774
No 21
>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=79.91 E-value=4.4 Score=25.86 Aligned_cols=44 Identities=18% Similarity=0.153 Sum_probs=30.1
Q ss_pred ccchHHHHHHHHhhCCCCC------cccHhHHHHHHHHHHHHHhhccccc
Q 045289 18 YLPIANISWIIKKAFPAND------IITKNAKQIVQGCSKACSLARDEME 61 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~a------KISKeAKe~iqeCvsEFIl~~~~~~ 61 (71)
.||.+.|-|||...+..+. -++.=||..|.|.+.+-..+.++.+
T Consensus 16 ~f~k~~iKr~~~~~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~ 65 (85)
T cd08048 16 SFPKAAIKRLIQSVTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWG 65 (85)
T ss_pred hccHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3999999999999996322 2455566666666666666655543
No 22
>PLN00160 histone H3; Provisional
Probab=79.32 E-value=2.8 Score=27.75 Aligned_cols=43 Identities=9% Similarity=0.031 Sum_probs=36.2
Q ss_pred CccccccchHHHHHHHHhhCC----CCCcccHhHHHHHHHHHHHHHh
Q 045289 13 QEEDRYLPIANISWIIKKAFP----ANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 13 reqD~~LPiAnI~RIMK~aLP----~~aKISKeAKe~iqeCvsEFIl 55 (71)
+..|+.+|++-.+|++++... .+.++..+|-+++|+++--|+.
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv 62 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLV 62 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHH
Confidence 456888999999999988863 4589999999999999888875
No 23
>PTZ00018 histone H3; Provisional
Probab=77.93 E-value=4 Score=28.54 Aligned_cols=43 Identities=7% Similarity=0.078 Sum_probs=36.3
Q ss_pred ccccccchHHHHHHHHhhCC---CCCcccHhHHHHHHHHHHHHHhh
Q 045289 14 EEDRYLPIANISWIIKKAFP---ANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 14 eqD~~LPiAnI~RIMK~aLP---~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
..|+.+|++-.+|+++++.. .+..+..+|-+++||++-.|+.-
T Consensus 58 st~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~ 103 (136)
T PTZ00018 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVG 103 (136)
T ss_pred cchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHH
Confidence 34888999999999988863 46899999999999999888753
No 24
>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=76.71 E-value=3.7 Score=28.71 Aligned_cols=32 Identities=16% Similarity=0.198 Sum_probs=26.8
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
.+-++||+|+++. ..+||++.|+-|++++.|-
T Consensus 12 gvS~~TVSrvLn~----~~~vs~~tr~rV~~~a~~l 43 (329)
T TIGR01481 12 GVSMATVSRVVNG----NPNVKPATRKKVLEVIKRL 43 (329)
T ss_pred CCCHHHHHHHhCC----CCCCCHHHHHHHHHHHHHH
Confidence 3568999999875 3579999999999999875
No 25
>PRK09526 lacI lac repressor; Reviewed
Probab=73.50 E-value=5.6 Score=27.97 Aligned_cols=32 Identities=6% Similarity=0.194 Sum_probs=26.7
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
-.-++||+|+++. ..+||++.|+-|++++.|-
T Consensus 16 GVS~~TVSrvLn~----~~~vs~~tr~rV~~~a~el 47 (342)
T PRK09526 16 GVSYQTVSRVLNQ----ASHVSAKTREKVEAAMAEL 47 (342)
T ss_pred CCCHHHHHHHhcC----CCCCCHHHHHHHHHHHHHH
Confidence 4668899999875 3579999999999999874
No 26
>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=72.09 E-value=7.3 Score=25.30 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=24.4
Q ss_pred ccchHHHHHHHHhhCCCCCccc--------HhHHHHHHHHHHHHHhhccc
Q 045289 18 YLPIANISWIIKKAFPANDIIT--------KNAKQIVQGCSKACSLARDE 59 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKIS--------KeAKe~iqeCvsEFIl~~~~ 59 (71)
.||+++|-|||+..+. +..++ -=||-.|-|.|.+-..+++|
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 3999999999999995 23444 44566666666665566654
No 27
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=71.02 E-value=6.6 Score=27.89 Aligned_cols=32 Identities=13% Similarity=0.237 Sum_probs=26.6
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
-+-++||+|+++. ..+||.+.|+-|++.+.|.
T Consensus 12 GVS~~TVSrvLn~----~~~Vs~~tr~rV~~~a~el 43 (343)
T PRK10727 12 GVSVATVSRVINN----SPKASEASRLAVHSAMESL 43 (343)
T ss_pred CCCHHHHHHHhCC----CCCCCHHHHHHHHHHHHHH
Confidence 4568999999875 3579999999999999874
No 28
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=70.16 E-value=7.5 Score=27.42 Aligned_cols=32 Identities=16% Similarity=0.274 Sum_probs=26.2
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
.+-++||+|.++. ...||++.|+-|++++.|-
T Consensus 12 gVS~~TVSrvLn~----~~~vs~~tr~~V~~~a~el 43 (341)
T PRK10703 12 GVSTTTVSHVINK----TRFVAEETRNAVWAAIKEL 43 (341)
T ss_pred CCCHHHHHHHHcC----CCCCCHHHHHHHHHHHHHH
Confidence 3567899998864 3479999999999999875
No 29
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=67.63 E-value=9.2 Score=26.63 Aligned_cols=32 Identities=16% Similarity=0.275 Sum_probs=26.1
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
.+-++||+|.++. ...||++.|+-|++.+.|-
T Consensus 9 gVS~~TVSrvLn~----~~~vs~~tr~rV~~~a~~l 40 (327)
T PRK10423 9 GVSTSTVSHVINK----DRFVSEAITAKVEAAIKEL 40 (327)
T ss_pred CCcHHHHHHHhCC----CCCCCHHHHHHHHHHHHHH
Confidence 3567899999875 3479999999999998775
No 30
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=67.45 E-value=7.9 Score=30.49 Aligned_cols=39 Identities=15% Similarity=0.068 Sum_probs=25.4
Q ss_pred ccccchHHHHHHHHhhCC----CCCcccHhHHHHHHHHHHHHH
Q 045289 16 DRYLPIANISWIIKKAFP----ANDIITKNAKQIVQGCSKACS 54 (71)
Q Consensus 16 D~~LPiAnI~RIMK~aLP----~~aKISKeAKe~iqeCvsEFI 54 (71)
--.||-+.|-|+.....- .+.||+|+|-++|.+|..-|.
T Consensus 349 ~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfF 391 (414)
T PF15511_consen 349 YPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFF 391 (414)
T ss_dssp ---S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHH
T ss_pred CCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHH
Confidence 345888888887666654 568999999999999988774
No 31
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=67.07 E-value=14 Score=21.72 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=27.2
Q ss_pred cccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHH
Q 045289 17 RYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACS 54 (71)
Q Consensus 17 ~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFI 54 (71)
..+..++|+|+++. ...|+.+.++-|++.+.|+=
T Consensus 10 ~gvS~~TVSr~ln~----~~~v~~~t~~~i~~~~~~~g 43 (70)
T smart00354 10 AGVSKATVSRVLNG----NGRVSEETREKVLAAMEELG 43 (70)
T ss_pred HCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHHHhC
Confidence 45788999998753 45689999999999998863
No 32
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=66.92 E-value=5.4 Score=29.80 Aligned_cols=44 Identities=20% Similarity=0.212 Sum_probs=35.8
Q ss_pred cccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhhccc
Q 045289 15 EDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLARDE 59 (71)
Q Consensus 15 qD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~~~~ 59 (71)
-...||+|-|-||||.-= .--+|+-||--++-.||-.||+..-.
T Consensus 71 ~~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~ 114 (236)
T KOG1657|consen 71 KNHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTL 114 (236)
T ss_pred hhccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHH
Confidence 356799999999998642 12289999999999999999987654
No 33
>PRK09492 treR trehalose repressor; Provisional
Probab=64.35 E-value=11 Score=26.24 Aligned_cols=32 Identities=6% Similarity=0.171 Sum_probs=26.2
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
-+-++||+|.++. ..+||.+.|+-|.+.+.|-
T Consensus 15 gVS~~TVSrvLn~----~~~vs~~tr~rV~~~a~el 46 (315)
T PRK09492 15 GVGKSTVSRVLNN----ESGVSEETRERVEAVINQH 46 (315)
T ss_pred CCCHHHHhHHhCC----CCCCCHHHHHHHHHHHHHH
Confidence 3567899999875 3579999999999998774
No 34
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=60.61 E-value=16 Score=28.16 Aligned_cols=40 Identities=3% Similarity=0.092 Sum_probs=33.6
Q ss_pred cccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 15 EDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 15 qD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
.++.|=+-.+.-+++++- .+.+|.+|++|++.+.|-.||-
T Consensus 151 ~~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~ 190 (258)
T KOG1142|consen 151 NNPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVS 190 (258)
T ss_pred CCccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHH
Confidence 356677777888899884 5799999999999999999984
No 35
>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=60.41 E-value=15 Score=25.72 Aligned_cols=34 Identities=12% Similarity=0.169 Sum_probs=25.7
Q ss_pred cchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 19 LPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 19 LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
+-++||+|+++.. +....||++.|+-|++.+.|-
T Consensus 11 VS~~TVSrvLn~~-~~~~~vs~~tr~rV~~~a~~l 44 (327)
T TIGR02417 11 VSKTTASYVINGK-AKEYRISQETVERVMAVVREQ 44 (327)
T ss_pred CCHHHHHHHHcCC-CCCCccCHHHHHHHHHHHHHh
Confidence 5578999998652 111259999999999999874
No 36
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=59.42 E-value=16 Score=25.69 Aligned_cols=32 Identities=9% Similarity=0.174 Sum_probs=26.2
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
..-++||+|.++. ..+||.+.++-|++.+.|-
T Consensus 17 gVS~~TVSr~Ln~----~~~vs~~tr~~V~~~a~el 48 (342)
T PRK10014 17 GVSVSTVSLVLSG----KGRISTATGERVNQAIEEL 48 (342)
T ss_pred CCCHHHHHHHHCC----CCCCCHHHHHHHHHHHHHh
Confidence 3567899998864 4579999999999998775
No 37
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=58.97 E-value=12 Score=26.30 Aligned_cols=34 Identities=12% Similarity=0.234 Sum_probs=26.3
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
.+-++||+|.++.. | ...||.+.|+-|++.+-|.
T Consensus 12 gVS~~TVSrvln~~-~-~~~vs~~tr~rV~~~a~~l 45 (327)
T PRK10339 12 GVSLATVSRVLNDD-P-TLNVKEETKHRILEIAEKL 45 (327)
T ss_pred CCCHHhhhhhhcCC-C-CCCcCHHHHHHHHHHHHHh
Confidence 35678999988653 2 2359999999999998775
No 38
>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=58.19 E-value=19 Score=24.19 Aligned_cols=39 Identities=13% Similarity=0.107 Sum_probs=29.3
Q ss_pred cccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHh
Q 045289 15 EDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 15 qD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl 55 (71)
..+.+|++-|.|+||+.-- .-+|+..|...+..+ -|++.
T Consensus 17 agL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAv-LEYL~ 55 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAV-LEYLT 55 (115)
T ss_pred cCccCcHHHHHHHHHcCcc-ccccccchHHHHHHH-HHHHH
Confidence 4688999999999998432 378999998877664 34443
No 39
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=57.97 E-value=16 Score=26.02 Aligned_cols=32 Identities=9% Similarity=0.302 Sum_probs=26.2
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
-.-++||+|.++. ...||++.|+-|.+++.|-
T Consensus 12 GVS~~TVSrvLn~----~~~Vs~~tr~kV~~~a~el 43 (346)
T PRK10401 12 GVSVATVSRVLNN----SALVSADTREAVMKAVSEL 43 (346)
T ss_pred CCCHHHHHHHHCC----CCCCCHHHHHHHHHHHHHH
Confidence 3567899999875 2469999999999999774
No 40
>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=55.84 E-value=20 Score=25.17 Aligned_cols=32 Identities=6% Similarity=0.155 Sum_probs=26.0
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
.+-++||+|+++. ..+||.+.|+-|++.+.|-
T Consensus 12 gVS~sTVSr~Ln~----~~~vs~~tr~rV~~~a~~l 43 (311)
T TIGR02405 12 GVGKSTVSRVLNN----EPKVSIETRERVEQVIQQS 43 (311)
T ss_pred CCCHHHHHHHhCC----CCCCCHHHHHHHHHHHHHH
Confidence 3567899999864 3479999999999998774
No 41
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=55.39 E-value=17 Score=25.58 Aligned_cols=32 Identities=3% Similarity=0.089 Sum_probs=25.6
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
..-++||+|+++. ..+||.+.|+-|++.+.|-
T Consensus 16 gVS~~TVSrvLn~----~~~vs~~tr~rV~~~a~el 47 (331)
T PRK14987 16 GVTKMTVSRFLRN----PEQVSVALRGKIAAALDEL 47 (331)
T ss_pred CCCHHHhhhhhCC----CCCCCHHHHHHHHHHHHHh
Confidence 3567899998864 3579999999999998873
No 42
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=54.03 E-value=23 Score=24.75 Aligned_cols=35 Identities=9% Similarity=0.115 Sum_probs=26.1
Q ss_pred ccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
..-++||+|+++.. |..-.||.+.|+-|++++.|-
T Consensus 11 GVS~~TVSrvLn~~-~~~~~Vs~~tr~rV~~~a~el 45 (328)
T PRK11303 11 GVSRTTASYVINGK-AKQYRVSDKTVEKVMAVVREH 45 (328)
T ss_pred CCCHHHHHHHHcCC-CCCCCcCHHHHHHHHHHHHHh
Confidence 35678999998653 111269999999999999874
No 43
>KOG0605 consensus NDR and related serine/threonine kinases [General function prediction only]
Probab=53.52 E-value=15 Score=30.96 Aligned_cols=35 Identities=14% Similarity=0.153 Sum_probs=29.6
Q ss_pred ccchHHHHHHHHhh--C--CCCCcccHhHHHHHHHHHHH
Q 045289 18 YLPIANISWIIKKA--F--PANDIITKNAKQIVQGCSKA 52 (71)
Q Consensus 18 ~LPiAnI~RIMK~a--L--P~~aKISKeAKe~iqeCvsE 52 (71)
.-|.++-.|||.-- | |..+.+|+|||++|..|..+
T Consensus 391 ~tp~~T~rkI~nwr~~l~fP~~~~~s~eA~DLI~rll~d 429 (550)
T KOG0605|consen 391 ETPQETYRKIVNWRETLKFPEEVDLSDEAKDLITRLLCD 429 (550)
T ss_pred CCHHHHHHHHHHHhhhccCCCcCcccHHHHHHHHHHhcC
Confidence 35889999998755 4 89999999999999999864
No 44
>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=49.86 E-value=28 Score=23.42 Aligned_cols=36 Identities=22% Similarity=0.271 Sum_probs=27.9
Q ss_pred hHHHHHHHHhhCC----CCCcccHhHHHHHHHHHHHHHhh
Q 045289 21 IANISWIIKKAFP----ANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 21 iAnI~RIMK~aLP----~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
-.||++++|+-|= .+.-++.++++++++.+.=|-..
T Consensus 50 ~SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~e 89 (96)
T PF09114_consen 50 NSNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQE 89 (96)
T ss_dssp HHHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHHH
T ss_pred HHhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHhc
Confidence 4689999999993 34569999999999998776543
No 45
>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=40.58 E-value=20 Score=19.72 Aligned_cols=15 Identities=13% Similarity=0.293 Sum_probs=11.6
Q ss_pred ccccchHHHHHHHHh
Q 045289 16 DRYLPIANISWIIKK 30 (71)
Q Consensus 16 D~~LPiAnI~RIMK~ 30 (71)
...+|.++++|+++.
T Consensus 27 ~~gl~~stv~r~L~t 41 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQT 41 (52)
T ss_dssp HHTS-HHHHHHHHHH
T ss_pred HHCcCHHHHHHHHHH
Confidence 456999999999875
No 46
>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]
Probab=40.16 E-value=30 Score=32.04 Aligned_cols=28 Identities=18% Similarity=0.440 Sum_probs=23.6
Q ss_pred HHHHHHHHh----hCCCCCcccHhHHHHHHHH
Q 045289 22 ANISWIIKK----AFPANDIITKNAKQIVQGC 49 (71)
Q Consensus 22 AnI~RIMK~----aLP~~aKISKeAKe~iqeC 49 (71)
.|-+|||.- .+|+..+||++||++|+..
T Consensus 288 eTY~KIm~hk~~l~FP~~~~VSeeakdLI~~l 319 (1317)
T KOG0612|consen 288 ETYGKIMNHKESLSFPDETDVSEEAKDLIEAL 319 (1317)
T ss_pred HHHHHHhchhhhcCCCcccccCHHHHHHHHHH
Confidence 567899976 5698899999999999874
No 47
>PLN00167 aquaporin TIP5; Provisional
Probab=38.59 E-value=26 Score=25.92 Aligned_cols=28 Identities=7% Similarity=0.087 Sum_probs=20.2
Q ss_pred HHhhCCCCCcc-cHh--HHHHHHHHHHHHHh
Q 045289 28 IKKAFPANDII-TKN--AKQIVQGCSKACSL 55 (71)
Q Consensus 28 MK~aLP~~aKI-SKe--AKe~iqeCvsEFIl 55 (71)
|++.+|++... .++ .++.++.+..||+-
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~laEflg 31 (256)
T PLN00167 1 MRKMAPTSLSARFQQSVTRNALRSYLAEFIS 31 (256)
T ss_pred CCcccCCCCcCchhhhccHHHHHHHHHHHHH
Confidence 56777776654 344 68889999999873
No 48
>PF02953 zf-Tim10_DDP: Tim10/DDP family zinc finger; InterPro: IPR004217 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a putative zinc binding domain with four conserved cysteine residues. Members of this family include subunits 8, 9, 10 and 13 of the mitochondrial inner membrane translocase complex, which are involved in mitochondrial protein import [, ]. Defects in TIM8 are the cause of 2 human syndromes: Mohr-Tranebjaerg syndrome (MTS) [MIM:304700]; also known as dystonia-deafness syndrome (DDS) or X-linked progressive deafness type 1 (DFN-1). It is a recessive neurodegenerative syndrome characterised by postlingual progressive sensorineural deafness as the first presenting symptom in early childhood, followed by progressive dystonia, spasticity, dysphagia, mental deterioration, paranoia and cortical blindness. Jensen syndrome [MIM:311150]; also known as opticoacoustic nerve atrophy with dementia. This X-linked disease is characterised by deafness, blindness and muscle weakness. The small alpha helical proteins Tim8 and Tim13 assemble into a hexameric complex which can bind Tim23 as its substrate and chaperone the hydrophobic Tim23 across the aqueous membrane space []. More information on zinc fingers can be found at Protein of the Month: Zinc Fingers [].; GO: 0006626 protein targeting to mitochondrion, 0045039 protein import into mitochondrial inner membrane, 0042719 mitochondrial intermembrane space protein transporter complex; PDB: 2BSK_B 3CJH_A 3DXR_A.
Probab=38.52 E-value=52 Score=18.99 Aligned_cols=24 Identities=4% Similarity=0.210 Sum_probs=18.9
Q ss_pred CCCcccHhHHHHHHHHHHHHHhhc
Q 045289 34 ANDIITKNAKQIVQGCSKACSLAR 57 (71)
Q Consensus 34 ~~aKISKeAKe~iqeCvsEFIl~~ 57 (71)
++.++++..+.||..|+.-|+-+.
T Consensus 33 ~~~~L~~~E~~Ci~~C~~ky~~~~ 56 (66)
T PF02953_consen 33 PSSSLSSKEESCIDNCVDKYIDTN 56 (66)
T ss_dssp SSSS--HHHHHHHHHHHHHHHHHH
T ss_pred CCCCCchhHHHHHHHHHHHHHHHH
Confidence 568899999999999999998653
No 49
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=37.41 E-value=47 Score=24.58 Aligned_cols=31 Identities=13% Similarity=0.261 Sum_probs=24.5
Q ss_pred cchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 19 LPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 19 LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
.-++||+|.++. +.+||.|.|+-|.+.+.|-
T Consensus 12 VS~sTVSrvln~----~~~Vs~eTr~kV~~a~~el 42 (333)
T COG1609 12 VSKATVSRVLNG----SPYVSEETREKVLAAIKEL 42 (333)
T ss_pred CCHHHHHHHHcC----CCCCCHHHHHHHHHHHHHH
Confidence 457788887654 4599999999999988763
No 50
>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=35.59 E-value=72 Score=16.84 Aligned_cols=33 Identities=9% Similarity=0.227 Sum_probs=25.5
Q ss_pred cccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHH
Q 045289 17 RYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 17 ~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEF 53 (71)
..+..++|+|+.+.. ..|+.+.+.-|++.+.++
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 456788999987742 368889998888888775
No 51
>KOG4449 consensus Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.75 E-value=32 Score=20.98 Aligned_cols=15 Identities=7% Similarity=0.031 Sum_probs=12.4
Q ss_pred CcccHhHHHHHHHHH
Q 045289 36 DIITKNAKQIVQGCS 50 (71)
Q Consensus 36 aKISKeAKe~iqeCv 50 (71)
.|+|+|+||-++...
T Consensus 1 mklS~esKerl~k~~ 15 (53)
T KOG4449|consen 1 MKLSEESKERLVKVF 15 (53)
T ss_pred CccCHHHHHHHHHHe
Confidence 378999999998754
No 52
>KOG3284 consensus Vacuolar sorting protein VPS28 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.92 E-value=72 Score=24.13 Aligned_cols=38 Identities=16% Similarity=0.133 Sum_probs=25.6
Q ss_pred HHHHHHHHhhCCCCCcc-------cHhHHHHHHHHHHHHHhhcccc
Q 045289 22 ANISWIIKKAFPANDII-------TKNAKQIVQGCSKACSLARDEM 60 (71)
Q Consensus 22 AnI~RIMK~aLP~~aKI-------SKeAKe~iqeCvsEFIl~~~~~ 60 (71)
|.|.|| ++..|-.++= ++..--+|.+||+-||++-|-.
T Consensus 93 ~Ai~Ri-~~~~piT~e~~ia~s~dk~~~ak~IAe~v~nFIT~mDaL 137 (213)
T KOG3284|consen 93 AAIERI-REGRPITVEDRIAPSADKGNSAKCIAEIVQNFITVMDAL 137 (213)
T ss_pred HHHHHH-HcCCCCcccccccccCCcccHHHHHHHHHHHHHHHHHHH
Confidence 457777 5777755432 2233458999999999987643
No 53
>KOG3489 consensus Mitochondrial import inner membrane translocase, subunit TIM8 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.03 E-value=61 Score=21.40 Aligned_cols=22 Identities=5% Similarity=0.146 Sum_probs=19.3
Q ss_pred CCCcccHhHHHHHHHHHHHHHh
Q 045289 34 ANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 34 ~~aKISKeAKe~iqeCvsEFIl 55 (71)
++.|.+.....|++.||--||-
T Consensus 46 ~~sklds~~e~ClsnCV~RfiD 67 (86)
T KOG3489|consen 46 PGSKLDSSEETCLSNCVNRFID 67 (86)
T ss_pred CcccccchHHHHHHHHHHHHHH
Confidence 3489999999999999999884
No 54
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=29.71 E-value=28 Score=25.87 Aligned_cols=44 Identities=20% Similarity=0.152 Sum_probs=33.7
Q ss_pred ccchHHHHHHHHhhCC----CCCc--ccHhHHHHHHHHHHHHHhhccccc
Q 045289 18 YLPIANISWIIKKAFP----ANDI--ITKNAKQIVQGCSKACSLARDEME 61 (71)
Q Consensus 18 ~LPiAnI~RIMK~aLP----~~aK--ISKeAKe~iqeCvsEFIl~~~~~~ 61 (71)
.||+|+|-|+|....- +++- ++-=||-.|-|.|-|-.-++++..
T Consensus 112 ~f~Ka~iKkL~~~itg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~ 161 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWG 161 (195)
T ss_pred cCCHHHHHHHHHHHhCCccCcceeeeecchhhHhHHHHHHHHHHHHHHhc
Confidence 5999999999998774 3333 455688888888888888777644
No 55
>PF10380 CRF1: Transcription factor CRF1; InterPro: IPR018837 CRF1 is a transcription factor that co-represses ribosomal genes with FHL1 via the TOR signalling pathway and protein kinase A [].
Probab=29.37 E-value=18 Score=25.05 Aligned_cols=21 Identities=38% Similarity=0.619 Sum_probs=14.4
Q ss_pred cccccchHHHHHHHHhhCCCCCc---ccHhHHHHHH
Q 045289 15 EDRYLPIANISWIIKKAFPANDI---ITKNAKQIVQ 47 (71)
Q Consensus 15 qD~~LPiAnI~RIMK~aLP~~aK---ISKeAKe~iq 47 (71)
.|..|| |++.| +++-|||.+.
T Consensus 6 ED~sLP------------~~~~k~k~~~~kAkEVlS 29 (123)
T PF10380_consen 6 EDESLP------------PPSSKSKKGSKKAKEVLS 29 (123)
T ss_pred ccccCC------------CCCccccccCccceeeec
Confidence 688888 44433 7788887753
No 56
>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=29.37 E-value=1e+02 Score=16.67 Aligned_cols=32 Identities=9% Similarity=-0.091 Sum_probs=22.1
Q ss_pred HHHHHhhCCCCCcccHhHHHHHHHHHHHHHhh
Q 045289 25 SWIIKKAFPANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 25 ~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
....+..||......+-.|-.|-+.+.+||..
T Consensus 23 ~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~ 54 (60)
T cd00083 23 FDELRSLLPTLPPSKKLSKAEILRKAVDYIKS 54 (60)
T ss_pred HHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Confidence 34457788877444555556689999999864
No 57
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=27.53 E-value=1.6e+02 Score=18.35 Aligned_cols=33 Identities=3% Similarity=-0.102 Sum_probs=26.1
Q ss_pred HHHHHHHhhC-CCCCcccHhHHHHHHHHHHHHHh
Q 045289 23 NISWIIKKAF-PANDIITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 23 nI~RIMK~aL-P~~aKISKeAKe~iqeCvsEFIl 55 (71)
+|+||..+.. +.+..+|+..--++.|.+-.++.
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~ 43 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLE 43 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHH
Confidence 5788888874 77889999999999988877763
No 58
>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.22 E-value=97 Score=20.38 Aligned_cols=30 Identities=7% Similarity=0.036 Sum_probs=22.0
Q ss_pred HHHHHHhhC---CCCCcccHhHHHHHHHHHHHH
Q 045289 24 ISWIIKKAF---PANDIITKNAKQIVQGCSKAC 53 (71)
Q Consensus 24 I~RIMK~aL---P~~aKISKeAKe~iqeCvsEF 53 (71)
|..|...+. +++..+.+.|++++++|.-|-
T Consensus 71 v~LI~~N~~~yNg~~s~~~~~A~~l~~d~~~el 103 (109)
T cd05492 71 ALLLLHNTAIFHGADSEQYDAARWLYRDTCHDL 103 (109)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Confidence 344444444 677889999999999998763
No 59
>PRK10001 D-alanyl-D-alanine carboxypeptidase fraction C; Provisional
Probab=26.07 E-value=50 Score=26.14 Aligned_cols=32 Identities=19% Similarity=0.107 Sum_probs=22.9
Q ss_pred CCccccccchHHHHHHHHhhC------------CCCCcccHhHH
Q 045289 12 IQEEDRYLPIANISWIIKKAF------------PANDIITKNAK 43 (71)
Q Consensus 12 ~reqD~~LPiAnI~RIMK~aL------------P~~aKISKeAK 43 (71)
-+..|..+|+|.++|||--.| -..++||++|.
T Consensus 55 ~knad~~~~pAS~TKlMTa~v~~e~i~~g~l~ldd~v~vs~~a~ 98 (400)
T PRK10001 55 EGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAW 98 (400)
T ss_pred hcCcCCCcCchHHHHHHHHHHHHHHHHcCCCCCCCEEEECHHHH
Confidence 455688999999999994422 23467888774
No 60
>KOG1151 consensus Tousled-like protein kinase [Signal transduction mechanisms]
Probab=23.62 E-value=48 Score=28.76 Aligned_cols=49 Identities=27% Similarity=0.485 Sum_probs=39.0
Q ss_pred cchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhhcccccccccccccCC
Q 045289 19 LPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLARDEMEFDNEELGCYP 71 (71)
Q Consensus 19 LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~~~~~~~~~~~~~~~~ 71 (71)
|--.+|-+--.-.+|+.--+|.+||..|..|. ..|.|-.||-.+|.|-|
T Consensus 694 LqeNTIlkAtEVqFP~KPvVsseAkaFIRRCL----aYRKeDR~DV~qLA~dp 742 (775)
T KOG1151|consen 694 LQENTILKATEVQFPPKPVVSSEAKAFIRRCL----AYRKEDRIDVQQLACDP 742 (775)
T ss_pred HhhhchhcceeccCCCCCccCHHHHHHHHHHH----HhhhhhhhhHHHHccCc
Confidence 44455555555667988889999999999994 57889899998988865
No 61
>KOG0425 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.88 E-value=52 Score=24.14 Aligned_cols=25 Identities=16% Similarity=0.347 Sum_probs=19.1
Q ss_pred CCCCCCccccccchHHHHHHHHhhC
Q 045289 8 SRSNIQEEDRYLPIANISWIIKKAF 32 (71)
Q Consensus 8 ~~~~~reqD~~LPiAnI~RIMK~aL 32 (71)
+.+.-...||++|.-||--||=.++
T Consensus 101 ~~gyE~~~erW~Pv~tvetIllSiI 125 (171)
T KOG0425|consen 101 PSGYELPSERWLPVQTVETILLSII 125 (171)
T ss_pred cccCCChhhccCCccchhHhHHHHH
Confidence 3344456799999999999987665
No 62
>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=22.33 E-value=1.4e+02 Score=21.15 Aligned_cols=40 Identities=8% Similarity=0.067 Sum_probs=31.9
Q ss_pred ccccchHHHHHHHHhhCCCCC--cccHhHHHHHHHHHHHHHh
Q 045289 16 DRYLPIANISWIIKKAFPAND--IITKNAKQIVQGCSKACSL 55 (71)
Q Consensus 16 D~~LPiAnI~RIMK~aLP~~a--KISKeAKe~iqeCvsEFIl 55 (71)
-.+|....+.+.|.+....+. .|+.|..++|..||-+++.
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr 83 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLR 83 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 467777778887777776433 7999999999999998874
No 63
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=21.28 E-value=63 Score=18.99 Aligned_cols=11 Identities=36% Similarity=0.332 Sum_probs=8.4
Q ss_pred hHHHHHHHHhh
Q 045289 21 IANISWIIKKA 31 (71)
Q Consensus 21 iAnI~RIMK~a 31 (71)
-|.|.||||..
T Consensus 10 ~AaIVrimK~~ 20 (68)
T PF10557_consen 10 DAAIVRIMKQE 20 (68)
T ss_dssp HHHHHHHHHHS
T ss_pred hhheehhhhhc
Confidence 37788999864
No 64
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=21.21 E-value=51 Score=20.25 Aligned_cols=20 Identities=5% Similarity=0.101 Sum_probs=13.7
Q ss_pred CccccccchHHHHHHHHhhC
Q 045289 13 QEEDRYLPIANISWIIKKAF 32 (71)
Q Consensus 13 reqD~~LPiAnI~RIMK~aL 32 (71)
+++...+..+||+|.++.-.
T Consensus 27 ~~~~~~i~~~TVYR~L~~L~ 46 (116)
T cd07153 27 RKKGPSISLATVYRTLELLE 46 (116)
T ss_pred HhcCCCCCHHHHHHHHHHHH
Confidence 34445678899998876544
No 65
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=21.12 E-value=1.6e+02 Score=18.15 Aligned_cols=38 Identities=24% Similarity=0.254 Sum_probs=25.5
Q ss_pred cchHHHHHHHHhhCCCCCc----ccHhHHHHHHHHHHHHHhh
Q 045289 19 LPIANISWIIKKAFPANDI----ITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 19 LPiAnI~RIMK~aLP~~aK----ISKeAKe~iqeCvsEFIl~ 56 (71)
=++..+.+.+..++|+... +.+..|..++...+.+=++
T Consensus 6 ~~~d~~~~~~~~~~~~~~~~~~e~e~~~r~~l~~~l~kldlV 47 (79)
T PF04380_consen 6 KIFDDLAKQISEALPAAQGPREEIEKNIRARLQSALSKLDLV 47 (79)
T ss_pred hHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHCCCC
Confidence 3578899999999996544 4445555666666554444
No 66
>PLN00154 histone H2A; Provisional
Probab=21.04 E-value=1.7e+02 Score=20.54 Aligned_cols=40 Identities=15% Similarity=0.131 Sum_probs=30.5
Q ss_pred ccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhh
Q 045289 16 DRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 16 D~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
.+.+|..-|.|++|+-....-+|+..|--.+. .|-||+.+
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLA-AVLEYLtA 75 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTA-AILEYLTA 75 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHH-HHHHHHHH
Confidence 67899999999999987656789888865543 45566654
No 67
>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.
Probab=20.27 E-value=2.3e+02 Score=19.04 Aligned_cols=41 Identities=7% Similarity=0.082 Sum_probs=28.7
Q ss_pred cccccchHHHHHHHHhhCCCCCcccHhHHHHHHHHHHHHHhh
Q 045289 15 EDRYLPIANISWIIKKAFPANDIITKNAKQIVQGCSKACSLA 56 (71)
Q Consensus 15 qD~~LPiAnI~RIMK~aLP~~aKISKeAKe~iqeCvsEFIl~ 56 (71)
+|...|--.--+=+.++.|.+.+ ...-..++.+|+..|...
T Consensus 19 dDPL~~w~~yI~W~~~~~p~g~~-~s~L~~lLerc~~~f~~~ 59 (125)
T smart00777 19 DDPLDLWLRYIKWTEENYPQGGK-ESGLLTLLERCIRYFEDD 59 (125)
T ss_pred CCChHHHHHHHHHHHHhCCCCCc-hhhHHHHHHHHHHHhhhh
Confidence 45555555545557788997754 456788999999999754
Done!