Query 036514
Match_columns 328
No_of_seqs 157 out of 178
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 02:48:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036514.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036514hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12767 SAGA-Tad1: Transcript 100.0 2.2E-53 4.7E-58 398.1 20.0 249 1-280 1-252 (252)
2 PF05236 TAF4: Transcription i 96.9 0.0012 2.7E-08 62.6 4.9 62 224-286 37-99 (264)
3 smart00803 TAF TATA box bindin 96.6 0.011 2.4E-07 44.9 7.0 56 241-301 8-64 (65)
4 cd08045 TAF4 TATA Binding Prot 96.4 0.014 3E-07 53.8 7.9 75 227-301 40-116 (212)
5 PF02969 TAF: TATA box binding 95.4 0.09 1.9E-06 40.3 7.4 56 241-301 9-65 (66)
6 smart00576 BTP Bromodomain tra 95.3 0.15 3.3E-06 39.6 8.7 64 236-304 7-71 (77)
7 cd00076 H4 Histone H4, one of 95.2 0.093 2E-06 42.1 7.2 61 240-305 18-79 (85)
8 PLN00035 histone H4; Provision 95.2 0.093 2E-06 43.6 7.3 59 241-304 35-94 (103)
9 PTZ00015 histone H4; Provision 95.1 0.12 2.7E-06 42.8 7.8 61 240-305 35-96 (102)
10 PF00808 CBFD_NFYB_HMF: Histon 94.2 0.3 6.5E-06 36.4 7.4 59 238-301 5-65 (65)
11 cd07981 TAF12 TATA Binding Pro 93.4 0.3 6.5E-06 37.7 6.3 54 249-307 17-70 (72)
12 PF07524 Bromo_TP: Bromodomain 93.2 0.78 1.7E-05 35.4 8.5 64 235-303 6-70 (77)
13 COG2036 HHT1 Histones H3 and H 92.0 0.6 1.3E-05 38.0 6.5 57 242-303 26-83 (91)
14 cd07979 TAF9 TATA Binding Prot 91.8 0.86 1.9E-05 38.5 7.6 66 240-310 6-73 (117)
15 PF00125 Histone: Core histone 91.8 0.6 1.3E-05 35.4 6.1 49 250-303 26-74 (75)
16 smart00417 H4 Histone H4. 91.7 0.45 9.7E-06 37.3 5.3 55 239-298 17-72 (74)
17 cd08050 TAF6 TATA Binding Prot 91.3 0.71 1.5E-05 45.7 7.5 58 241-303 5-63 (343)
18 PF03847 TFIID_20kDa: Transcri 89.5 1.3 2.9E-05 34.0 6.1 49 251-304 17-65 (68)
19 PF12174 RST: RCD1-SRO-TAF4 (R 87.4 2.4 5.3E-05 32.8 6.4 56 10-72 9-64 (70)
20 KOG3423 Transcription initiati 87.1 2.4 5.3E-05 38.1 7.0 71 231-306 87-167 (176)
21 PF03540 TFIID_30kDa: Transcri 86.5 2.6 5.6E-05 30.8 5.7 42 242-283 9-51 (51)
22 PF02269 TFIID-18kDa: Transcri 81.0 1.7 3.8E-05 35.1 3.2 55 251-310 19-73 (93)
23 PF15630 CENP-S: Kinetochore c 71.7 15 0.00032 28.9 6.0 67 236-307 6-76 (76)
24 PF02291 TFIID-31kDa: Transcri 70.7 23 0.00051 30.5 7.6 59 240-303 17-76 (129)
25 PF12583 TPPII_N: Tripeptidyl 70.1 3.5 7.5E-05 36.0 2.3 51 25-75 69-124 (139)
26 cd07978 TAF13 The TATA Binding 69.1 29 0.00063 28.1 7.4 64 240-309 7-72 (92)
27 KOG1659 Class 2 transcription 63.4 22 0.00048 33.3 6.3 62 240-306 18-81 (224)
28 smart00427 H2B Histone H2B. 63.3 28 0.0006 28.3 6.1 49 250-303 18-66 (89)
29 cd00074 H2A Histone 2A; H2A is 60.8 28 0.0006 29.5 6.0 64 239-307 24-89 (115)
30 PLN00158 histone H2B; Provisio 58.9 33 0.00071 29.2 6.1 50 249-303 43-92 (116)
31 KOG1142 Transcription initiati 54.1 14 0.0003 35.6 3.4 64 235-306 158-222 (258)
32 PTZ00463 histone H2B; Provisio 53.8 43 0.00093 28.6 5.9 50 249-303 44-93 (117)
33 PRK08084 DNA replication initi 53.0 42 0.0009 31.0 6.4 70 231-303 166-235 (235)
34 PRK09087 hypothetical protein; 52.4 67 0.0015 29.7 7.7 71 230-303 151-221 (226)
35 PF01402 RHH_1: Ribbon-helix-h 51.3 45 0.00098 21.8 4.7 32 235-270 8-39 (39)
36 PHA01513 mnt Mnt 50.8 19 0.00041 28.9 3.2 31 235-265 14-44 (82)
37 COG5247 BUR6 Class 2 transcrip 49.7 51 0.0011 27.6 5.6 62 240-306 28-91 (113)
38 PHA01623 hypothetical protein 48.3 50 0.0011 24.3 4.9 32 235-270 22-53 (56)
39 PRK08727 hypothetical protein; 48.2 53 0.0011 30.3 6.3 69 230-304 160-231 (233)
40 PF11880 DUF3400: Domain of un 46.8 4.8 0.0001 28.7 -0.7 17 298-314 13-29 (45)
41 KOG2549 Transcription initiati 45.7 71 0.0015 34.0 7.3 60 239-303 15-75 (576)
42 smart00428 H3 Histone H3. 40.0 96 0.0021 25.9 5.9 51 249-304 51-101 (105)
43 PRK06585 holA DNA polymerase I 39.0 96 0.0021 29.9 6.8 50 232-281 142-191 (343)
44 PRK12422 chromosomal replicati 38.6 78 0.0017 32.5 6.4 68 231-302 270-341 (445)
45 PF13151 DUF3990: Protein of u 38.1 31 0.00066 30.5 2.9 51 22-72 101-151 (154)
46 PF12213 Dpoe2NT: DNA polymera 35.2 1.4E+02 0.003 23.2 5.8 65 234-301 2-70 (73)
47 PHA01748 hypothetical protein 35.0 1.2E+02 0.0026 22.5 5.3 42 235-280 11-53 (60)
48 KOG1744 Histone H2B [Chromatin 34.9 1.4E+02 0.0029 26.0 6.2 49 250-303 54-102 (127)
49 PF14410 GH-E: HNH/ENDO VII su 34.5 77 0.0017 24.4 4.3 31 23-53 21-51 (70)
50 KOG1942 DNA helicase, TBP-inte 33.4 1.1E+02 0.0023 30.9 6.0 69 231-304 366-438 (456)
51 PRK06893 DNA replication initi 33.3 1.2E+02 0.0025 27.9 6.1 72 228-302 157-228 (229)
52 PF02671 PAH: Paired amphipath 32.9 63 0.0014 22.3 3.3 33 26-58 2-34 (47)
53 COG1224 TIP49 DNA helicase TIP 32.0 1.3E+02 0.0028 30.9 6.5 66 234-304 363-432 (450)
54 COG5248 TAF19 Transcription in 31.8 3.2E+02 0.007 23.2 7.8 66 239-311 13-80 (126)
55 PRK08903 DnaA regulatory inact 31.5 2.5E+02 0.0055 25.1 8.0 69 227-302 153-224 (227)
56 TIGR01128 holA DNA polymerase 31.3 2.4E+02 0.0051 26.3 7.9 48 231-278 110-160 (302)
57 COG1466 HolA DNA polymerase II 30.8 1.8E+02 0.0038 28.4 7.2 65 232-301 140-204 (334)
58 PRK00149 dnaA chromosomal repl 29.7 96 0.0021 31.5 5.3 71 230-303 278-348 (450)
59 PRK06620 hypothetical protein; 29.6 1.6E+02 0.0035 26.9 6.3 68 230-301 145-213 (214)
60 TIGR02397 dnaX_nterm DNA polym 29.4 1.5E+02 0.0033 28.3 6.5 45 231-275 175-219 (355)
61 PRK14086 dnaA chromosomal repl 27.6 1.5E+02 0.0033 32.0 6.5 69 231-302 445-513 (617)
62 PF03869 Arc: Arc-like DNA bin 27.0 99 0.0022 22.1 3.5 31 235-265 13-43 (50)
63 COG5095 TAF6 Transcription ini 26.3 2.1E+02 0.0045 28.8 6.6 57 241-302 11-68 (450)
64 PRK00440 rfc replication facto 25.4 2.1E+02 0.0045 26.7 6.5 64 231-301 160-223 (319)
65 COG5162 Transcription initiati 25.3 2.2E+02 0.0049 25.8 6.1 61 244-304 97-186 (197)
66 PRK05574 holA DNA polymerase I 24.8 3.2E+02 0.007 25.9 7.7 50 231-280 145-194 (340)
67 PF12674 Zn_ribbon_2: Putative 24.3 1.4E+02 0.0031 23.6 4.3 58 200-258 7-67 (81)
68 PF00515 TPR_1: Tetratricopept 24.1 65 0.0014 19.8 1.9 18 289-306 16-33 (34)
69 PF00308 Bac_DnaA: Bacterial d 23.8 1.2E+02 0.0026 27.8 4.3 52 224-276 159-210 (219)
70 COG4545 Glutaredoxin-related p 23.5 49 0.0011 26.4 1.5 20 32-51 38-57 (85)
71 PRK04195 replication factor C 23.3 2.1E+02 0.0046 29.4 6.5 47 231-277 159-205 (482)
72 PRK14088 dnaA chromosomal repl 23.1 1.9E+02 0.0042 29.5 6.1 69 230-302 261-330 (440)
73 smart00414 H2A Histone 2A. 22.8 2E+02 0.0043 24.0 5.1 64 239-307 13-78 (106)
74 PRK12402 replication factor C 22.6 2.5E+02 0.0054 26.5 6.5 46 231-276 183-228 (337)
75 PRK14962 DNA polymerase III su 22.3 2.5E+02 0.0055 29.1 6.8 67 231-306 175-244 (472)
76 PF11537 DUF3227: Protein of u 22.3 2E+02 0.0043 24.0 4.8 48 11-58 45-99 (102)
77 KOG3467 Histone H4 [Chromatin 22.2 2.4E+02 0.0052 23.1 5.1 40 241-280 35-75 (103)
78 PF08369 PCP_red: Proto-chloro 22.0 92 0.002 21.9 2.5 24 235-258 18-42 (45)
No 1
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=100.00 E-value=2.2e-53 Score=398.07 Aligned_cols=249 Identities=39% Similarity=0.509 Sum_probs=178.8
Q ss_pred CCCCCccccccHHHHHHHHHHHhCCccHHHHHHHHHHHHhccCCHHHHHHHHHhhcCCCcccccHHHHHHHHHhhhcCCC
Q 036514 1 MPADRHFMRLDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSIIQNACLSKT 80 (328)
Q Consensus 1 m~~~~~~~RiDl~~lk~~L~~~LG~~~~~~Y~~~l~~fl~gklsk~Efd~~~~~~L~~e~i~LHN~lilsIl~Na~~~~~ 80 (328)
|++ ++++||||.++|++|+++||+++|++||++|++||.|||||+|||++|+.+||+||+||||+||+|||+||+...
T Consensus 1 ~~~-~~~~Ridl~~lk~~l~~~LG~~~~~~Y~~~l~~fl~~klsk~Efd~~~~~~L~~~~~~LHN~li~sIl~na~~~~- 78 (252)
T PF12767_consen 1 MSQ-QQNSRIDLEELKSQLQKRLGPDRWKKYFQSLKRFLSGKLSKEEFDKECRRILGRENVHLHNQLILSILKNALAKS- 78 (252)
T ss_pred CCC-CcccccCHHHHHHHHHHHHChHHHHHHHHHHHHHHHhccCHHHHHHHHHHHhChhHHHHHHHHHHHHHHHHhhcC-
Confidence 555 899999999999999999999999999999999999999999999999999999999999999999999995554
Q ss_pred CCCCCCCCCCCcccccCCCccccccccccCCCCCCccCCCCccccccccc-CCCCCCCCCCCCCcccccCCchhh-Hhhh
Q 036514 81 PPPKEPKVDGFERGKVPNGYQRSCLQSLCKDIPQSSRKGMTPALRDCKLK-DFPSPLGPRGKSHSIACQDSVPKI-QEQL 158 (328)
Q Consensus 81 pp~~~~~~~~s~~~~~~~g~~~~~~q~l~~~~~~~prk~rs~~~rdrr~k-d~~~~lgp~gk~~s~~~~~~~~~~-q~~~ 158 (328)
||+..+.+.++.. ...+.......+..+.++.++++.++...+++.+. +.+++.+++++.... +.+.... ....
T Consensus 79 p~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~k~~~~~~~~~~r~r~~~~~~~--~~~~~~~~~~~~ 154 (252)
T PF12767_consen 79 PPPSSASGPPSSV--KSWVKANGKPSSNQGAKPVSPRKSRSSRRLKRKVMSLPPRERGRLKKIETK--ESGKRQSPDEPS 154 (252)
T ss_pred CCccCcccccccc--cccccccCCCcccccccCCCCccchhHHHHhhhhccCCccccccccccccc--ccccccCCCCcc
Confidence 5543332211100 00011111112233456777877777655666555 555555666654100 0000000 0000
Q ss_pred hhhhhccCCCCCCCCccchhhhhhhcCCCCccCCCCccCCCCCCCCCCCCCcccccCCCCcccchhHhhhCCCCCHHhHH
Q 036514 159 STNELFSLGSRPPGSVEDGEEVDQAAGSPSIYSRSPVKAPLGIPINGKGTPKLLHKSSTDAYYTGICQNHGELPDAYSLR 238 (328)
Q Consensus 159 ~~~e~~~~~~~~p~sve~~ee~~q~~~~~~~~s~spv~aPlgip~~~~s~g~~~~~~~~~~~~~~~c~esgeLPDt~sL~ 238 (328)
++....+.+.....+++++++++|. + ..|+++ +.+.+..++|+++|+|||+++|+
T Consensus 155 ~~~~~~~~~~~~~~~~~~~e~~~~~--~-~~~s~~----------------------~~~~~~~~lc~es~~LPD~~~L~ 209 (252)
T PF12767_consen 155 SLLQTRSKQPPEIPSVEDGEEVEQI--N-SNWSRS----------------------VSSGYQSPLCSESGELPDTQSLR 209 (252)
T ss_pred ccccccccccccCCcccCccccccc--c-cccccc----------------------cccCCCCccHHHhCcCCCHHHHH
Confidence 0001111122223688999999866 3 566654 12346788999999999999999
Q ss_pred HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036514 239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAG 280 (328)
Q Consensus 239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~ 280 (328)
+||+.||||+|| ||+++||++||+|||+|||+||++||++||
T Consensus 210 ~Rm~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~r 252 (252)
T PF12767_consen 210 KRMEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDLVR 252 (252)
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 999999999999 999999999999999999999999999986
No 2
>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=96.89 E-value=0.0012 Score=62.56 Aligned_cols=62 Identities=23% Similarity=0.319 Sum_probs=41.3
Q ss_pred hHhhhCCCCCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC
Q 036514 224 ICQNHGELPDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHK 286 (328)
Q Consensus 224 ~c~esgeLPDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~ 286 (328)
.|.+ --|-++..|.+||..|+..+|+ .++.|.++||+.|++.||++||+.++.+++.|....
T Consensus 37 ~~~~-~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~ 99 (264)
T PF05236_consen 37 SEKE-EPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSS 99 (264)
T ss_dssp --------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------
T ss_pred cccc-ccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence 3444 3377899999999999999999 999999999999999999999999999999888653
No 3
>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=96.55 E-value=0.011 Score=44.95 Aligned_cols=56 Identities=18% Similarity=0.297 Sum_probs=49.2
Q ss_pred HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514 241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT 301 (328)
Q Consensus 241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am 301 (328)
+..+|+..|. .|+.|++..|..-++.|+++|++.++.+++. .++..++..|+..|+
T Consensus 8 i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~h-----akRktlt~~DI~~Al 64 (65)
T smart00803 8 IKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRH-----SKRTTLTTSDIDSAL 64 (65)
T ss_pred HHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCeecHHHHHHHh
Confidence 5678899999 8999999999999999999999999999874 235569999998886
No 4
>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=96.37 E-value=0.014 Score=53.79 Aligned_cols=75 Identities=17% Similarity=0.263 Sum_probs=60.2
Q ss_pred hhCCCCCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC-CCCccchHhhHHHHH
Q 036514 227 NHGELPDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHK-HSSFSASILDFQVAT 301 (328)
Q Consensus 227 esgeLPDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~-~~~~~~Sl~Df~~am 301 (328)
...-|-+...|.++|..++.++|+ +++.|..++|+.|++.||++||+-.+.+++-|.... ....+.-..|.+..|
T Consensus 40 ~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL 116 (212)
T cd08045 40 KDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQL 116 (212)
T ss_pred chhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHH
Confidence 344577889999999999999999 999999999999999999999999999999886542 123333344555443
No 5
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=95.42 E-value=0.09 Score=40.31 Aligned_cols=56 Identities=16% Similarity=0.242 Sum_probs=44.2
Q ss_pred HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514 241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT 301 (328)
Q Consensus 241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am 301 (328)
+..+|+.-|+ .++.||+..|..=+++-||+||..++.+.+- ..+..++..|+-.|+
T Consensus 9 vk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~h-----skR~~Lt~~Di~~AL 65 (66)
T PF02969_consen 9 VKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRH-----SKRTKLTTDDINSAL 65 (66)
T ss_dssp HHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TT-SSB-HHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCCCCHHHHHHHh
Confidence 4568999999 9999999999999999999999999999873 124458899998886
No 6
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=95.34 E-value=0.15 Score=39.63 Aligned_cols=64 Identities=19% Similarity=0.184 Sum_probs=53.5
Q ss_pred hHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514 236 SLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN 304 (328)
Q Consensus 236 sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln 304 (328)
.|+.=+.+||+..|. .+++.+.+.|-..++.|+.+|.+.+...+..- ++...++.|+..||+-.
T Consensus 7 ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~a-----gR~~~~~~Dv~~Al~~~ 71 (77)
T smart00576 7 LLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELA-----GRTEPNLGDVVLALENL 71 (77)
T ss_pred HHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCCCCHHHHHHHHHHh
Confidence 355558899999999 99999999999999999999999999998531 12335699999999753
No 7
>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=95.20 E-value=0.093 Score=42.14 Aligned_cols=61 Identities=11% Similarity=0.205 Sum_probs=52.7
Q ss_pred HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCC
Q 036514 240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNP 305 (328)
Q Consensus 240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP 305 (328)
=+..+|+-.|. -||.++.+-+...|+.||++|++-++.++.. .+...++..|...||+.-.
T Consensus 18 ~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~H-----a~RKTVt~~DV~~alkr~g 79 (85)
T cd00076 18 AIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEH-----AKRKTVTAMDVVYALKRQG 79 (85)
T ss_pred HHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCcCcHHHHHHHHHHCC
Confidence 35678889999 8999999999999999999999999999885 3455699999999987543
No 8
>PLN00035 histone H4; Provisional
Probab=95.17 E-value=0.093 Score=43.62 Aligned_cols=59 Identities=12% Similarity=0.186 Sum_probs=52.1
Q ss_pred HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514 241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN 304 (328)
Q Consensus 241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln 304 (328)
+..+|+..|. -||.++.+-+...|+.||+.|++-++.++.. .....++..|...|++.-
T Consensus 35 IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~H-----A~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH-----ARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCcCcHHHHHHHHHHc
Confidence 5678889999 8999999999999999999999999999986 345569999999998754
No 9
>PTZ00015 histone H4; Provisional
Probab=95.07 E-value=0.12 Score=42.81 Aligned_cols=61 Identities=11% Similarity=0.184 Sum_probs=52.7
Q ss_pred HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCC
Q 036514 240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNP 305 (328)
Q Consensus 240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP 305 (328)
=+..+|+-.|. -||.++.+-+...|+.||++|++-++.++..- ....++.+|...|+..--
T Consensus 35 ~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA-----~RKTVt~~DV~~AlKr~g 96 (102)
T PTZ00015 35 AIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA-----RRKTVTAMDVVYALKRQG 96 (102)
T ss_pred HHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCCcccHHHHHHHHHhcC
Confidence 35678889999 89999999999999999999999999999863 355699999999987543
No 10
>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=94.17 E-value=0.3 Score=36.42 Aligned_cols=59 Identities=17% Similarity=0.264 Sum_probs=47.9
Q ss_pred HHHHHHHHHHh-CC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514 238 RKRLEKKLEME-GL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT 301 (328)
Q Consensus 238 ~~RM~~ia~e~-GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am 301 (328)
..|+..|+.+. +. .|+.|++.+|+.+.+.|+..|.+.+.+.+... +...|+-.|+..|+
T Consensus 5 ~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~-----~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 5 LARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRD-----KRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----TSSEE-HHHHHHHH
T ss_pred hHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-----CCCccCHHHHHHHC
Confidence 35777788877 55 79999999999999999999999999998852 35579999998875
No 11
>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=93.44 E-value=0.3 Score=37.67 Aligned_cols=54 Identities=24% Similarity=0.271 Sum_probs=47.5
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514 249 GLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI 307 (328)
Q Consensus 249 GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l 307 (328)
|..+++++.++|...+|.|+-++++.+..+|+-|..+ .+...|++.++|-+-.+
T Consensus 17 ~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~-----tv~~~Di~l~l~r~~~~ 70 (72)
T cd07981 17 REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSD-----TLEVKDVQLHLERNWNI 70 (72)
T ss_pred CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-----CCCHHHHHHHHHHhcCC
Confidence 3479999999999999999999999999999976553 49999999999987654
No 12
>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=93.24 E-value=0.78 Score=35.41 Aligned_cols=64 Identities=19% Similarity=0.243 Sum_probs=53.0
Q ss_pred HhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 235 YSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
..|+.=+.+++...|. +++..+.+.|..-+..||.+|-+.+-..+.. .++...++.|+..||+-
T Consensus 6 ~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~-----~gRt~~~~~Dv~~al~~ 70 (77)
T PF07524_consen 6 SLLRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEH-----AGRTEPNLQDVEQALEE 70 (77)
T ss_pred HHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCCCCHHHHHHHHHH
Confidence 3566777889999999 9999999999999999999999999888752 12334569999999864
No 13
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=91.96 E-value=0.6 Score=38.02 Aligned_cols=57 Identities=19% Similarity=0.307 Sum_probs=48.3
Q ss_pred HHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 242 EKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 242 ~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
..++...|- .|+.+|.+.|+.+++.|+..|.+-..++|.. .++..|.-.|+..|+..
T Consensus 26 ~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~h-----a~RKTV~~~DI~la~~~ 83 (91)
T COG2036 26 RRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEH-----AKRKTVKAEDIKLALKR 83 (91)
T ss_pred HHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCeecHHHHHHHHHH
Confidence 455666666 8999999999999999999999999999986 34567889999998853
No 14
>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=91.84 E-value=0.86 Score=38.51 Aligned_cols=66 Identities=9% Similarity=0.039 Sum_probs=53.7
Q ss_pred HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc-cccC
Q 036514 240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ-ILGN 310 (328)
Q Consensus 240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~-lLg~ 310 (328)
-|..|+...|. .+++++++.|.--+..|..+|++-...+++- .+...|+..|++.|++.-=. ..+.
T Consensus 6 ~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~h-----A~r~tV~~eDV~lAi~~r~~~~f~~ 73 (117)
T cd07979 6 VIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEH-----AGKANIDADDVKLAIQSRVDYSFTS 73 (117)
T ss_pred HHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCCCCHHHHHHHHHHHhccCCCC
Confidence 35667778899 8999999999999999999999999999874 23567999999999765332 4444
No 15
>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=91.78 E-value=0.6 Score=35.44 Aligned_cols=49 Identities=16% Similarity=0.236 Sum_probs=44.2
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 250 LKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 250 LgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
+.++.++..+|+.++|.|+-+|++.+..++.. ++...|+-.|+..|+.+
T Consensus 26 ~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~-----~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 26 YRISSEALVALQSVLEYLLVEILEEAGNLARH-----AKRKTITPRDIQLAVRI 74 (75)
T ss_dssp SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTBSEEGHHHHHHHHHH
T ss_pred cccccccchhhhhhhhhhhhhhhhHHHHHHhh-----cCCcEecHHHHHHHHhc
Confidence 57999999999999999999999999999986 44677999999999865
No 16
>smart00417 H4 Histone H4.
Probab=91.70 E-value=0.45 Score=37.31 Aligned_cols=55 Identities=11% Similarity=0.193 Sum_probs=46.0
Q ss_pred HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHH
Q 036514 239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQ 298 (328)
Q Consensus 239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~ 298 (328)
.=+..+|.-.|. -||.++.+-+...|+.||.+|++-++.++... +...++..|..
T Consensus 17 ~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha-----~RKTV~~~DV~ 72 (74)
T smart00417 17 PAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHA-----RRKTVTAMDVV 72 (74)
T ss_pred HHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCCcccHHHhe
Confidence 346778889999 89999999999999999999999999999863 34457777753
No 17
>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=91.28 E-value=0.71 Score=45.67 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=50.9
Q ss_pred HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
+..+|+..|. .|+.|++..|..-++.++++|++.++.+++- .++..++..|+..|+++
T Consensus 5 i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~h-----skR~~l~~~Di~~Al~~ 63 (343)
T cd08050 5 IKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRH-----SKRRKLTTSDVNHALRL 63 (343)
T ss_pred HHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCCcCCHHHHHHHHHH
Confidence 4578999999 8999999999999999999999999999873 22456899999999876
No 18
>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=89.51 E-value=1.3 Score=33.99 Aligned_cols=49 Identities=27% Similarity=0.289 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514 251 KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN 304 (328)
Q Consensus 251 gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln 304 (328)
.+++++.++|..-.|.|+-+++.....+|+.|.. ..+.+.|+...+|-|
T Consensus 17 ~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s-----~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 17 KLDPDVEELLLELADDFVDDVVSFACRLAKHRKS-----STLEVKDVQLHLERN 65 (68)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------SEE-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-----CCCCHHHHHHHHHhh
Confidence 7999999999999999999999999999999765 469999999998864
No 19
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=87.43 E-value=2.4 Score=32.77 Aligned_cols=56 Identities=29% Similarity=0.357 Sum_probs=45.9
Q ss_pred ccHHHHHHHHHHHhCCccHHHHHHHHHHHHhccCCHHHHHHHHHhhcCCCcccccHHHHHHHH
Q 036514 10 LDILEIKSHIERKLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSII 72 (328)
Q Consensus 10 iDl~~lk~~L~~~LG~~~~~~Y~~~l~~fl~gklsk~Efd~~~~~~L~~e~i~LHN~lilsIl 72 (328)
+=...|-..|.+.|++++...-..+-..|=.+||||+||-+..+.+.| .++|.+++
T Consensus 9 ~~F~~L~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVG-------D~lL~s~I 64 (70)
T PF12174_consen 9 MPFPMLFSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVG-------DQLLRSAI 64 (70)
T ss_pred ccHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-------HHHHHHHH
Confidence 446678888999999888777777777888999999999999999999 34566666
No 20
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=87.13 E-value=2.4 Score=38.14 Aligned_cols=71 Identities=15% Similarity=0.225 Sum_probs=59.2
Q ss_pred CCCHHhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC---------CCCccchHhhHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHK---------HSSFSASILDFQVA 300 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~---------~~~~~~Sl~Df~~a 300 (328)
+||.-.. -++...|+ .+++...-|+..|.+.|+-.|+..++...|.|.+.. ...+.++|.||.-|
T Consensus 87 IPDavt~-----~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~A 161 (176)
T KOG3423|consen 87 IPDAVTD-----HYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPA 161 (176)
T ss_pred CcHHHHH-----HHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHH
Confidence 5665443 36778999 999999999999999999999999999999998421 57889999999999
Q ss_pred HHhCCc
Q 036514 301 TELNPQ 306 (328)
Q Consensus 301 mElnP~ 306 (328)
++=...
T Consensus 162 L~EyGi 167 (176)
T KOG3423|consen 162 LAEYGI 167 (176)
T ss_pred HHHhCc
Confidence 875433
No 21
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=86.54 E-value=2.6 Score=30.84 Aligned_cols=42 Identities=14% Similarity=0.264 Sum_probs=38.0
Q ss_pred HHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 036514 242 EKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRS 283 (328)
Q Consensus 242 ~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~ 283 (328)
.-++...|+ ..++.++-|++.|.+.|+-+|+..++...+.|.
T Consensus 9 ~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r~ 51 (51)
T PF03540_consen 9 DYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIRT 51 (51)
T ss_pred HHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 456788999 899999999999999999999999999988773
No 22
>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=81.03 E-value=1.7 Score=35.15 Aligned_cols=55 Identities=16% Similarity=0.259 Sum_probs=23.7
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCccccC
Q 036514 251 KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGN 310 (328)
Q Consensus 251 gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg~ 310 (328)
.-.+|++++|-.-|-.|+-.++..+...|..|. +..+++.||.-+|--+|.-|+.
T Consensus 19 ~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg-----~~~i~~eDl~F~lR~D~~Kl~R 73 (93)
T PF02269_consen 19 EPLPETVDLVEDIVREYIIELCQEAMEVAQRRG-----SKKIKVEDLLFLLRKDPKKLAR 73 (93)
T ss_dssp S--HHHHHHHHHHHHHHHHHHHHHHHC---------------------------------
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccc-----cCcCcHHHHHHHHhcCHHHHHH
Confidence 467899999999999999999999999987753 4469999999999999987775
No 23
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=71.70 E-value=15 Score=28.89 Aligned_cols=67 Identities=19% Similarity=0.165 Sum_probs=50.4
Q ss_pred hHHHHHHHHHHHhCC----CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514 236 SLRKRLEKKLEMEGL----KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI 307 (328)
Q Consensus 236 sL~~RM~~ia~e~GL----gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l 307 (328)
.|+-....||+|++. .+|++.+..|.--+=.+++++-+-.-.+|+= .++..|++.|++...-=||+|
T Consensus 6 al~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkH-----A~R~tI~~dDV~Ll~Rrn~~L 76 (76)
T PF15630_consen 6 ALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKH-----AGRSTINMDDVKLLARRNPSL 76 (76)
T ss_dssp HHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TT-SEE-HHHHHHHTTT-HHH
T ss_pred HHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCeecHHHHHHHhhcCCCC
Confidence 466677899999976 4899999999988888888887777666653 246779999999998888764
No 24
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 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 []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=70.67 E-value=23 Score=30.52 Aligned_cols=59 Identities=12% Similarity=0.058 Sum_probs=46.5
Q ss_pred HHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 240 RLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 240 RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
-|..|+.+.|+ ...+.+++.|.-=.-.|...||+-+...+... +...|++.|.+.|.++
T Consensus 17 ~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA-----~~~~i~~~DVrLAi~~ 76 (129)
T PF02291_consen 17 VIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHA-----GRSTIDADDVRLAIQS 76 (129)
T ss_dssp HHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHT-----T-SSB-HHHHHHHHHH
T ss_pred HHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----ccccCChHHHHHHHHH
Confidence 46788999999 89999999999989999999999998888753 2456889999999984
No 25
>PF12583 TPPII_N: Tripeptidyl peptidase II N terminal; InterPro: IPR022232 This entry represents a region of approximately 190 amino acids in length and is found in association with PF00082 from PFAM. The members are serine peptidases belonging to MEROPS peptidase family S8A, tripeptidyl peptidase II (TPPII), clan SB. They are a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. ; PDB: 3LXU_X.
Probab=70.06 E-value=3.5 Score=35.97 Aligned_cols=51 Identities=16% Similarity=0.208 Sum_probs=36.1
Q ss_pred CccHHHHHHHHHHHHhccCCHHHHH---HHHHhhcC--CCcccccHHHHHHHHHhh
Q 036514 25 AAKSDKYFSLLTRYLSLKISKSEFD---RLCIGTIG--RENVRLHNRLLRSIIQNA 75 (328)
Q Consensus 25 ~~~~~~Y~~~l~~fl~gklsk~Efd---~~~~~~L~--~e~i~LHN~lilsIl~Na 75 (328)
..+|+.|-+.|..|-.+.|+|-|.+ ..=..++. ++.+..|=++|-.|=.+-
T Consensus 69 ktk~DeY~EaLRDfq~~~iaKle~e~Ae~vY~el~~~~P~HLpaHla~i~~lDS~~ 124 (139)
T PF12583_consen 69 KTKWDEYSEALRDFQCSWIAKLEPENAEQVYEELLEAHPDHLPAHLAMIQNLDSPE 124 (139)
T ss_dssp ---HHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH-TT-THHHHHHHHHHHHHS
T ss_pred cccHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHCcchHHHHHHHHHccCcHH
Confidence 4689999999999999999999984 22233333 788999999998886443
No 26
>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=69.09 E-value=29 Score=28.13 Aligned_cols=64 Identities=17% Similarity=0.226 Sum_probs=50.5
Q ss_pred HHHHHHHHhCC--CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcccc
Q 036514 240 RLEKKLEMEGL--KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILG 309 (328)
Q Consensus 240 RM~~ia~e~GL--gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg 309 (328)
=+...++..|= .-.+|.+++|---+-.||-.|+..+...|..|.+ .+++.||.-+|--+|-=||
T Consensus 7 ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~------k~~~eD~~FliR~D~~Kl~ 72 (92)
T cd07978 7 EIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRG------KVKVEDLIFLLRKDPKKLA 72 (92)
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC------CCCHHHHHHHHhcCHHHHH
Confidence 34556666665 4688999999999999999999999999973222 2599999999988886554
No 27
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=63.44 E-value=22 Score=33.32 Aligned_cols=62 Identities=26% Similarity=0.493 Sum_probs=48.8
Q ss_pred HHHHHHH-HhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc
Q 036514 240 RLEKKLE-MEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ 306 (328)
Q Consensus 240 RM~~ia~-e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~ 306 (328)
|+-+|+. .+-+ .|..-+.-++.-|||-||..|+....+.++.|+.+ .+|-.=++-|+|..|+
T Consensus 18 RiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aK-----t~s~~hlkq~v~~~~~ 81 (224)
T KOG1659|consen 18 RIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAK-----TVSSSHLKQAVESDPK 81 (224)
T ss_pred HHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCcc-----ccCHHHHHHHHhccch
Confidence 5555554 3445 47788888999999999999999999999987654 4777788888887776
No 28
>smart00427 H2B Histone H2B.
Probab=63.27 E-value=28 Score=28.35 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=42.5
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 250 LKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 250 LgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
+|++..+..+||+-+.....+|....-.++++. ...+|+-.|+.+|+.|
T Consensus 18 ~giS~kam~imnSfvnDiferIa~EAs~L~~~n-----kr~TltsreIqtAvrl 66 (89)
T smart00427 18 TGISSKAMSIMNSFVNDIFERIAAEASKLARYN-----KKSTLSSREIQTAVRL 66 (89)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-----CCCcCCHHHHHHHHHH
Confidence 389999999999999999999999998998874 3567999999999875
No 29
>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=60.84 E-value=28 Score=29.47 Aligned_cols=64 Identities=13% Similarity=0.141 Sum_probs=50.4
Q ss_pred HHHHHHHHH-hCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514 239 KRLEKKLEM-EGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI 307 (328)
Q Consensus 239 ~RM~~ia~e-~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l 307 (328)
.|+..++.+ .+- -|+.+++-+|.-.||++.-+|++-+...++. .....|+-+|+..|+.-+..|
T Consensus 24 ~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~-----~k~krItp~hi~lAi~nD~EL 89 (115)
T cd00074 24 GRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARD-----NKKKRITPRHLQLAVRNDEEL 89 (115)
T ss_pred HHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCeEcHHHHHHHHhccHHH
Confidence 466666665 333 6999999999999999999999988887764 235679999999999776544
No 30
>PLN00158 histone H2B; Provisional
Probab=58.94 E-value=33 Score=29.23 Aligned_cols=50 Identities=14% Similarity=0.191 Sum_probs=42.8
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 249 GLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 249 GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
++|++-.+..+||+-+.....+|....-.++++. ...+||-.|+.+|+.|
T Consensus 43 d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~n-----kr~TltsrEIqtAvrL 92 (116)
T PLN00158 43 DTGISSKAMSIMNSFINDIFEKIATEAGKLARYN-----KKPTVTSREIQTAVRL 92 (116)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-----CCCcCCHHHHHHHHHH
Confidence 3388999999999999999999999888888874 4677999999999976
No 31
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=54.11 E-value=14 Score=35.55 Aligned_cols=64 Identities=25% Similarity=0.320 Sum_probs=50.3
Q ss_pred HhHHHHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc
Q 036514 235 YSLRKRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ 306 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~ 306 (328)
..|..-|..| -|= .++.|+-+||.-=.|.|+-.||...-.||+.|... .|.+.|++..+|-|=+
T Consensus 158 ~kl~dLvqqI---d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsd-----tlEvrDIqLhLEr~~N 222 (258)
T KOG1142|consen 158 RKLDDLVQQI---DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSD-----TVEVRDIQLHLERNFN 222 (258)
T ss_pred cchhHHHHhh---cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC-----ccchhheeeeeecccc
Confidence 3444455555 233 58899999999999999999999999999997765 4788999988886633
No 32
>PTZ00463 histone H2B; Provisional
Probab=53.82 E-value=43 Score=28.59 Aligned_cols=50 Identities=18% Similarity=0.130 Sum_probs=42.2
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 249 GLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 249 GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
+.|+|-.+..+||+-+....-+|-...-.++++. ...+||-.|+.+|+.|
T Consensus 44 d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~n-----kr~TltsrEIQtAvrL 93 (117)
T PTZ00463 44 DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYT-----RRDTLSSREIQTAIRL 93 (117)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCCcCCHHHHHHHHhh
Confidence 3389999999999988888888888888888874 4667999999999975
No 33
>PRK08084 DNA replication initiation factor; Provisional
Probab=53.05 E-value=42 Score=31.02 Aligned_cols=70 Identities=16% Similarity=0.114 Sum_probs=47.4
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
-||.+.+...+...|.+.|+.++.|++++|..-.+.=+..++...-.+.++.-.. ...||+.-.+.++.+
T Consensus 166 ~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~l~~---~~~it~~~~k~~l~~ 235 (235)
T PRK08084 166 PLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITA---QRKLTIPFVKEILKL 235 (235)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhc---CCCCCHHHHHHHHcC
Confidence 3567777788888899999999999999999888865555555444333221110 122778877777653
No 34
>PRK09087 hypothetical protein; Validated
Probab=52.42 E-value=67 Score=29.67 Aligned_cols=71 Identities=11% Similarity=-0.088 Sum_probs=56.1
Q ss_pred CCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 230 ELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 230 eLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
+-||.+.+..-+...+...|+.++.|++++|..-.+.=+..+++..-.+.++... ....+|+..++.+++.
T Consensus 151 ~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~---~~~~it~~~~~~~l~~ 221 (226)
T PRK09087 151 GEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMERSLFAAQTIVDRLDRLALE---RKSRITRALAAEVLNE 221 (226)
T ss_pred CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH---hCCCCCHHHHHHHHHh
Confidence 4588999999999999999999999999999999998888888866555432211 1234889889988864
No 35
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=51.31 E-value=45 Score=21.80 Aligned_cols=32 Identities=19% Similarity=0.355 Sum_probs=26.5
Q ss_pred HhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHH
Q 036514 235 YSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKR 270 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~ 270 (328)
+.+..++...|.+.|++. .+++..|++.||++
T Consensus 8 ~~~~~~l~~~a~~~g~s~----s~~ir~ai~~~l~~ 39 (39)
T PF01402_consen 8 DELYERLDELAKELGRSR----SELIREAIREYLER 39 (39)
T ss_dssp HHHHHHHHHHHHHHTSSH----HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCcCH----HHHHHHHHHHHHhC
Confidence 567899999999999654 47889999999875
No 36
>PHA01513 mnt Mnt
Probab=50.75 E-value=19 Score=28.85 Aligned_cols=31 Identities=16% Similarity=0.538 Sum_probs=29.0
Q ss_pred HhHHHHHHHHHHHhCCCCChhHHHHHHHHHH
Q 036514 235 YSLRKRLEKKLEMEGLKVSVDCANLLNNGLD 265 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd 265 (328)
+.|+.|+...|.++|.+++.+++.+|..+|+
T Consensus 14 ~eLk~rL~~aA~~nGRSmNaeIv~~Le~al~ 44 (82)
T PHA01513 14 YELKEKLKQRAKANGRSLNAELVQIVQDALS 44 (82)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence 5799999999999999999999999999985
No 37
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=49.66 E-value=51 Score=27.58 Aligned_cols=62 Identities=24% Similarity=0.313 Sum_probs=45.8
Q ss_pred HHHHHHH-HhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc
Q 036514 240 RLEKKLE-MEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ 306 (328)
Q Consensus 240 RM~~ia~-e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~ 306 (328)
|+-.|+. .+-+ .|+.-..-++.-|||-||-.||+-....||-. .+..+|..=++-|.|..++
T Consensus 28 r~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~-----~skR~t~e~lk~a~~sdek 91 (113)
T COG5247 28 RLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKK-----SSKRMTSEFLKRATESDEK 91 (113)
T ss_pred HHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhc-----cchhhHHHHHHHHHhhhHH
Confidence 4444443 3455 47777778899999999999999998888753 3456777778888887665
No 38
>PHA01623 hypothetical protein
Probab=48.31 E-value=50 Score=24.31 Aligned_cols=32 Identities=13% Similarity=0.339 Sum_probs=28.0
Q ss_pred HhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHH
Q 036514 235 YSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKR 270 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~ 270 (328)
+.|..+|...|.++|+. ..+++..|++.||..
T Consensus 22 eel~~~Ld~y~~~~g~~----rSe~IreAI~~yL~~ 53 (56)
T PHA01623 22 KDLKTRLKVYCAKNNLQ----LTQAIEEAIKEYLQK 53 (56)
T ss_pred HHHHHHHHHHHHHcCCC----HHHHHHHHHHHHHHH
Confidence 57899999999999873 789999999999975
No 39
>PRK08727 hypothetical protein; Validated
Probab=48.24 E-value=53 Score=30.30 Aligned_cols=69 Identities=10% Similarity=0.011 Sum_probs=51.5
Q ss_pred CCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHH---HHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514 230 ELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRL---IKPCLELAGSRSGHKHSSFSASILDFQVATELN 304 (328)
Q Consensus 230 eLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~L---I~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln 304 (328)
.=||.+.+...+...|...|+.++.+++++|..-.+--+..+ ++.....+.+. + ..+|+..++.+++.+
T Consensus 160 ~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~rd~r~~l~~L~~l~~~~~~~-~-----~~it~~~~~~~l~~~ 231 (233)
T PRK08727 160 PVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALLDRLDRESLAA-K-----RRVTVPFLRRVLEEG 231 (233)
T ss_pred cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHh-C-----CCCCHHHHHHHHhhc
Confidence 345999999999999999999999999999998888555555 54443222221 1 148999999988765
No 40
>PF11880 DUF3400: Domain of unknown function (DUF3400); InterPro: IPR021817 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with PF02754 from PFAM, PF02913 from PFAM, PF01565 from PFAM.
Probab=46.84 E-value=4.8 Score=28.69 Aligned_cols=17 Identities=24% Similarity=0.757 Sum_probs=14.3
Q ss_pred HHHHHhCCccccCCCch
Q 036514 298 QVATELNPQILGNDWPS 314 (328)
Q Consensus 298 ~~amElnP~lLg~d~p~ 314 (328)
+.++|+.-++|||||--
T Consensus 13 YIVVEmA~~lLGe~W~~ 29 (45)
T PF11880_consen 13 YIVVEMARHLLGENWQQ 29 (45)
T ss_pred eehHHHHHHHhhhhHHH
Confidence 35789999999999954
No 41
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=45.66 E-value=71 Score=34.03 Aligned_cols=60 Identities=13% Similarity=0.182 Sum_probs=49.1
Q ss_pred HHHHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 239 KRLEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 239 ~RM~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
.=|..+|+.-|+ .+++|+|.+|..=++.=+|+|+.-....-.. .++..+|+.|+--|+-+
T Consensus 15 Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~h-----skR~kLtv~DV~~ALr~ 75 (576)
T KOG2549|consen 15 ESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVH-----SKRTKLTVDDVDYALRS 75 (576)
T ss_pred HHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhc-----CCCCcCcHHHHHHHHhh
Confidence 347789999999 7999999999999999999999887766432 34566899999877754
No 42
>smart00428 H3 Histone H3.
Probab=40.03 E-value=96 Score=25.91 Aligned_cols=51 Identities=16% Similarity=0.175 Sum_probs=43.2
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514 249 GLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN 304 (328)
Q Consensus 249 GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln 304 (328)
++-++.+|...|..|.|.||-.+.+.+...+.. .+...+...|++.|.-+-
T Consensus 51 ~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~H-----AkRvTl~~kDi~La~rir 101 (105)
T smart00428 51 DLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIH-----AKRVTIMPKDIQLARRIR 101 (105)
T ss_pred CceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCccCcHhhHHHHHHHh
Confidence 457999999999999999999999999888765 346678889999987543
No 43
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=39.00 E-value=96 Score=29.95 Aligned_cols=50 Identities=22% Similarity=0.151 Sum_probs=41.1
Q ss_pred CCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 036514 232 PDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGS 281 (328)
Q Consensus 232 PDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~ 281 (328)
|+...|...+...|.++|+.++.+++++|...+..=|-.+...+=.++-|
T Consensus 142 ~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly 191 (343)
T PRK06585 142 DDERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALY 191 (343)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence 88999999999999999999999999999999888555555554444444
No 44
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=38.61 E-value=78 Score=32.51 Aligned_cols=68 Identities=19% Similarity=0.176 Sum_probs=54.3
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHh---h-ccCCCCCCCccchHhhHHHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELA---G-SRSGHKHSSFSASILDFQVATE 302 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~---~-~R~~~~~~~~~~Sl~Df~~amE 302 (328)
-||.+.+..-+...|...|+.++.+++++|......=+.+|+...-.++ . ++-. ...+++.+.+.++.
T Consensus 270 ~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~dir~L~g~l~~l~~~~a~~~~~----~~~i~~~~~~~~l~ 341 (445)
T PRK12422 270 PLTKEGLRSFLERKAEALSIRIEETALDFLIEALSSNVKSLLHALTLLAKRVAYKKLS----HQLLYVDDIKALLH 341 (445)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHhh----CCCCCHHHHHHHHH
Confidence 3899999999999999999999999999998888877877777777663 2 2222 34588888888875
No 45
>PF13151 DUF3990: Protein of unknown function (DUF3990)
Probab=38.15 E-value=31 Score=30.47 Aligned_cols=51 Identities=14% Similarity=0.095 Sum_probs=39.4
Q ss_pred HhCCccHHHHHHHHHHHHhccCCHHHHHHHHHhhcCCCcccccHHHHHHHH
Q 036514 22 KLGAAKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGRENVRLHNRLLRSII 72 (328)
Q Consensus 22 ~LG~~~~~~Y~~~l~~fl~gklsk~Efd~~~~~~L~~e~i~LHN~lilsIl 72 (328)
.+||--=+.+|+.+..|+.|.||++++-++...---..++-+|++-.+..|
T Consensus 101 V~GpiADd~v~~~i~~y~~g~is~e~~~~~L~~~~~~~Q~~f~tekai~~L 151 (154)
T PF13151_consen 101 VIGPIADDRVFQTINLYINGEISKEQALERLKFKKLGNQYCFKTEKAIDCL 151 (154)
T ss_pred EEecccCChHHHHHHHHHcCCCCHHHHHHHhccCCCCcEEEEeCHHHHhhc
Confidence 356544468999999999999999998887765444677889988766544
No 46
>PF12213 Dpoe2NT: DNA polymerases epsilon N terminal; InterPro: IPR024639 This domain is found in the N-terminal of DNA polymerase epsilon subunit B proteins. It contains a single completely conserved phenylalanine residue that may be functionally important. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. The N-terminal domain has close structural relation to AAA+ protein C-terminal domains [].; PDB: 2V6Z_M.
Probab=35.24 E-value=1.4e+02 Score=23.24 Aligned_cols=65 Identities=18% Similarity=0.281 Sum_probs=42.8
Q ss_pred HHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHH----HHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514 234 AYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVF----MKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT 301 (328)
Q Consensus 234 t~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~y----LK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am 301 (328)
.+-||+++......+||.+..|+..++...|..+ ++.+|..+++.+..-. -.+..++..-++.|+
T Consensus 2 ~~~lrk~I~~~FkL~Gl~Lr~eA~~~l~~~l~~~~~~e~e~~l~~Ii~~v~kq~---Lss~~v~~~~ie~Av 70 (73)
T PF12213_consen 2 AAKLRKKIVKAFKLRGLSLRSEASKYLAEQLQSLSEEEREDWLDKIIDAVQKQP---LSSSIVDKEHIESAV 70 (73)
T ss_dssp HHHHHHHHHHHHHHTT-EE-HHHHHHHHHHTTTS-TTTHHHHHHHHHHHHTTS-----SSSEE-HHHHHHHH
T ss_pred hHHHHHHHHHHhhhccceecHHHHHHHHHHHccCCHHHHHHHHHHHHHHHhcCC---CCCCccCHHHHHHHH
Confidence 4578999999999999999999999998887543 5666777777664211 224445555555444
No 47
>PHA01748 hypothetical protein
Probab=35.02 E-value=1.2e+02 Score=22.51 Aligned_cols=42 Identities=19% Similarity=0.281 Sum_probs=34.1
Q ss_pred HhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHH-HHHHHHHHhh
Q 036514 235 YSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKR-LIKPCLELAG 280 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~-LI~s~i~l~~ 280 (328)
+.|..+|...|..+|+ .-.+++..|++.|+++ ..+.++++.+
T Consensus 11 ~el~~eld~~a~~~g~----~RSE~Ir~Ai~~~~~~~~~~~~~~~~~ 53 (60)
T PHA01748 11 EDLLELLDRYAIKHGL----NRSEAIRKAIEKMVKDELKKETVPVAK 53 (60)
T ss_pred HHHHHHHHHHHHHhCC----CHHHHHHHHHHHHHHHHHHhcccchhh
Confidence 5688999999999986 3789999999999986 6777766643
No 48
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=34.87 E-value=1.4e+02 Score=25.96 Aligned_cols=49 Identities=20% Similarity=0.222 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 250 LKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 250 LgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
+|++-++..+||.=+..++-+|+...=.++.|+ +...||-.++.+|++|
T Consensus 54 ~gis~~a~~vmnsf~ndife~iA~ea~rla~y~-----krstisSreiqta~rL 102 (127)
T KOG1744|consen 54 LGISSKAMGVMNSFVNDIFERIASEAGRLAHYN-----KRSTISSREIQTAVRL 102 (127)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhc-----CCCcccHHHHHHHHHH
Confidence 478889999999888888888888777777764 4566999999999987
No 49
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=34.46 E-value=77 Score=24.37 Aligned_cols=31 Identities=23% Similarity=0.294 Sum_probs=27.0
Q ss_pred hCCccHHHHHHHHHHHHhccCCHHHHHHHHH
Q 036514 23 LGAAKSDKYFSLLTRYLSLKISKSEFDRLCI 53 (328)
Q Consensus 23 LG~~~~~~Y~~~l~~fl~gklsk~Efd~~~~ 53 (328)
+|+.-...||.....+..+.+++.||-....
T Consensus 21 mgH~~~~e~~~~~~~~~~~~~t~ke~~d~~n 51 (70)
T PF14410_consen 21 MGHKPGVEYWRLVGRAEEGGITRKEFLDWYN 51 (70)
T ss_pred ccCchHHHHHHHHHHHHhcCCCHHHHHHHHh
Confidence 4665678999999999999999999988775
No 50
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=33.37 E-value=1.1e+02 Score=30.87 Aligned_cols=69 Identities=26% Similarity=0.373 Sum_probs=51.5
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHH-HHH---HHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNN-GLD---VFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN 304 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~-aLd---~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln 304 (328)
.-|.+.++.-+...|.++||.++.+|-++|.- |.. .|-=+||.+|--+++. ++...|+..|...+-+|.
T Consensus 366 ~y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~-----~g~~~i~v~dvee~~~Lf 438 (456)
T KOG1942|consen 366 PYDEEEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKT-----NGRKEISVEDVEEVTELF 438 (456)
T ss_pred cCCHHHHHHHHHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHH-----cCCceeecccHHHHHHHH
Confidence 34567788888888999999999999998864 222 3555788887777775 345678888888777664
No 51
>PRK06893 DNA replication initiation factor; Validated
Probab=33.25 E-value=1.2e+02 Score=27.88 Aligned_cols=72 Identities=17% Similarity=0.027 Sum_probs=52.0
Q ss_pred hCCCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514 228 HGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE 302 (328)
Q Consensus 228 sgeLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE 302 (328)
.-+-||.+....-+...|...|+.++.|++++|..-.+.=+..|+...-.+.++--. ....+|+...+.++.
T Consensus 157 ~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~~~---~~~~it~~~v~~~L~ 228 (229)
T PRK06893 157 QLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQ---AQRKLTIPFVKEILG 228 (229)
T ss_pred eCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHh---cCCCCCHHHHHHHhc
Confidence 367799999999999999999999999999999988876555555554444322111 012488888887764
No 52
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=32.89 E-value=63 Score=22.27 Aligned_cols=33 Identities=18% Similarity=0.240 Sum_probs=27.9
Q ss_pred ccHHHHHHHHHHHHhccCCHHHHHHHHHhhcCC
Q 036514 26 AKSDKYFSLLTRYLSLKISKSEFDRLCIGTIGR 58 (328)
Q Consensus 26 ~~~~~Y~~~l~~fl~gklsk~Efd~~~~~~L~~ 58 (328)
+....+-..|+.|-.+++|++|.-.++..+|+.
T Consensus 2 ~~Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~ 34 (47)
T PF02671_consen 2 EVYNEFLKILNDYKKGRISRSEVIEEVSELLRG 34 (47)
T ss_dssp HHHHHHHHHHHHHHCTCSCHHHHHHHHHHHTTT
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcc
Confidence 345567788999999999999999999999873
No 53
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=32.04 E-value=1.3e+02 Score=30.91 Aligned_cols=66 Identities=21% Similarity=0.301 Sum_probs=52.8
Q ss_pred HHhHHHHHHHHHHHhCCCCChhHHHHHH-HHHHH---HHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhC
Q 036514 234 AYSLRKRLEKKLEMEGLKVSVDCANLLN-NGLDV---FMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELN 304 (328)
Q Consensus 234 t~sL~~RM~~ia~e~GLgVs~~ca~lLn-~aLd~---yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEln 304 (328)
.+-++.=+.-.|.|+++-++.+|.++|. .|.+. |-=+||.+|.-+|..|.+ ..+.+.|..-|-|++
T Consensus 363 ~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~-----~~V~~~dVe~a~~lF 432 (450)
T COG1224 363 REEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGS-----KRVEVEDVERAKELF 432 (450)
T ss_pred HHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCC-----CeeehhHHHHHHHHH
Confidence 4667888888899999999999999885 44443 556899999999977544 458899999888875
No 54
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=31.77 E-value=3.2e+02 Score=23.23 Aligned_cols=66 Identities=24% Similarity=0.253 Sum_probs=52.8
Q ss_pred HHHHHHHHHhCC--CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCccccCC
Q 036514 239 KRLEKKLEMEGL--KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQILGND 311 (328)
Q Consensus 239 ~RM~~ia~e~GL--gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~lLg~d 311 (328)
+-+...+|.-|= .--.+.|++|---+-.||-.+..-+...|+-|.+-. +.||+-|+.-.|--||.-
T Consensus 13 KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK~k-------~eDfkfaLr~DpkKlgRv 80 (126)
T COG5248 13 KDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTK-------TEDFKFALRRDPKKLGRV 80 (126)
T ss_pred HHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcccch-------HHHHHHHHhhChHHHhHH
Confidence 334445666676 556788888888888899999999999999776644 999999999999988863
No 55
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=31.52 E-value=2.5e+02 Score=25.13 Aligned_cols=69 Identities=12% Similarity=0.083 Sum_probs=47.0
Q ss_pred hhCCCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHH---HHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514 227 NHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLD---VFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE 302 (328)
Q Consensus 227 esgeLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd---~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE 302 (328)
+-..|.+. .....+..++...|++++.++.++|..-.. ..|+++|+..-..+... ...||+...+.+|+
T Consensus 153 ~l~pl~~~-~~~~~l~~~~~~~~v~l~~~al~~L~~~~~gn~~~l~~~l~~l~~~~~~~------~~~i~~~~~~~~l~ 224 (227)
T PRK08903 153 ELKPLSDA-DKIAALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQ------KRPVTLPLLREMLA 224 (227)
T ss_pred EecCCCHH-HHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHh------CCCCCHHHHHHHHh
Confidence 33444443 466677788888999999999999988665 35666777643333221 23588888888876
No 56
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=31.28 E-value=2.4e+02 Score=26.26 Aligned_cols=48 Identities=17% Similarity=0.275 Sum_probs=38.1
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHH---HHHHHHHHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVF---MKRLIKPCLEL 278 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~y---LK~LI~s~i~l 278 (328)
-|+...+...+...+.++|+.++.++++.|...+..= +.+.|+-..-.
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~ 160 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALY 160 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhh
Confidence 4789999999999999999999999999998877643 44445544433
No 57
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=30.75 E-value=1.8e+02 Score=28.39 Aligned_cols=65 Identities=18% Similarity=0.198 Sum_probs=50.5
Q ss_pred CCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514 232 PDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT 301 (328)
Q Consensus 232 PDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am 301 (328)
+|...+.+.+...+.+.||.++.+++++|..++..=+--|-..+=.++-+-..+ .|+..|...++
T Consensus 140 ~~~~~l~~~i~~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~-----~I~~~~V~~~v 204 (334)
T COG1466 140 LDEAELPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDK-----EITLEDVEEVV 204 (334)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCC-----cCCHHHHHHHH
Confidence 677789999999999999999999999999999988777777766666554432 45555555443
No 58
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=29.68 E-value=96 Score=31.49 Aligned_cols=71 Identities=18% Similarity=0.120 Sum_probs=54.7
Q ss_pred CCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHh
Q 036514 230 ELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATEL 303 (328)
Q Consensus 230 eLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amEl 303 (328)
+-||.+.+..-+...|...|+.++.|++++|......=+..|+..+..+..+-... ...+++...+.+++-
T Consensus 278 ~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~---~~~it~~~~~~~l~~ 348 (450)
T PRK00149 278 EPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEGALNRLIAYASLT---GKPITLELAKEALKD 348 (450)
T ss_pred cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHH
Confidence 57999999999999999999999999999999888776666666655554432111 234888888888874
No 59
>PRK06620 hypothetical protein; Validated
Probab=29.60 E-value=1.6e+02 Score=26.92 Aligned_cols=68 Identities=12% Similarity=0.075 Sum_probs=44.6
Q ss_pred CCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhh-ccCCCCCCCccchHhhHHHHH
Q 036514 230 ELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAG-SRSGHKHSSFSASILDFQVAT 301 (328)
Q Consensus 230 eLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~-~R~~~~~~~~~~Sl~Df~~am 301 (328)
+-||.+.+...+...+.+.|+.++.+++++|..-.+.=+..++...-.+.. +... ...|++..++.++
T Consensus 145 ~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~~~~----~~~it~~~~~~~l 213 (214)
T PRK06620 145 NSPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPREYSKIIEILENINYFALIS----KRKITISLVKEVL 213 (214)
T ss_pred CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHHh
Confidence 457888888888899988999999999999988776544444433322211 1111 1236777666654
No 60
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=29.45 E-value=1.5e+02 Score=28.30 Aligned_cols=45 Identities=20% Similarity=0.273 Sum_probs=35.3
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPC 275 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~ 275 (328)
-|+.+.+...+..++.++|+.++.++++.+....+.-+..++..+
T Consensus 175 ~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~l 219 (355)
T TIGR02397 175 RIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLL 219 (355)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHH
Confidence 477899999999999999999999999888776655444444433
No 61
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=27.58 E-value=1.5e+02 Score=32.03 Aligned_cols=69 Identities=12% Similarity=0.083 Sum_probs=51.8
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE 302 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE 302 (328)
-||-+....-+...|...||.++.|++++|..-+..-+..|...+..+..+-... ...|++...+.++.
T Consensus 445 ~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~LegaL~rL~a~a~~~---~~~itl~la~~vL~ 513 (617)
T PRK14086 445 PPELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELEGALIRVTAFASLN---RQPVDLGLTEIVLR 513 (617)
T ss_pred CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHH
Confidence 4999999999999999999999999999999888866777666665554422211 23367777776665
No 62
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=26.96 E-value=99 Score=22.12 Aligned_cols=31 Identities=19% Similarity=0.383 Sum_probs=25.2
Q ss_pred HhHHHHHHHHHHHhCCCCChhHHHHHHHHHH
Q 036514 235 YSLRKRLEKKLEMEGLKVSVDCANLLNNGLD 265 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd 265 (328)
+.|+.++...|.++|-.++.+.+..|-.+|+
T Consensus 13 ~~l~~~lk~~A~~~gRS~NsEIv~~L~~~l~ 43 (50)
T PF03869_consen 13 EELKEKLKERAEENGRSMNSEIVQRLEEALK 43 (50)
T ss_dssp HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCChHHHHHHHHHHHHh
Confidence 3799999999999999999988777766654
No 63
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=26.28 E-value=2.1e+02 Score=28.84 Aligned_cols=57 Identities=18% Similarity=0.169 Sum_probs=46.3
Q ss_pred HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHH
Q 036514 241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATE 302 (328)
Q Consensus 241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amE 302 (328)
+-..|+.-|+ ++++|++..|..-||.-+|++++....+-.- .++--+|+.|..-|+.
T Consensus 11 ~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvh-----SKRtvLt~dDis~ALr 68 (450)
T COG5095 11 LKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVH-----SKRTVLTIDDISYALR 68 (450)
T ss_pred HHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhc-----ccceeeeHHhHHHHHH
Confidence 3467999999 8999999999999999999999988766432 2345678888888875
No 64
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=25.37 E-value=2.1e+02 Score=26.73 Aligned_cols=64 Identities=16% Similarity=0.077 Sum_probs=47.0
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVAT 301 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~am 301 (328)
.++.+.+...+..+|..+|+.++.++++.+......-+..++..+-..+.+. ..|+..|.+.++
T Consensus 160 ~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~~-------~~it~~~v~~~~ 223 (319)
T PRK00440 160 PLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAATG-------KEVTEEAVYKIT 223 (319)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcC-------CCCCHHHHHHHh
Confidence 3678889999999999999999999999998887777777766664443331 235555555443
No 65
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=25.34 E-value=2.2e+02 Score=25.84 Aligned_cols=61 Identities=18% Similarity=0.205 Sum_probs=50.1
Q ss_pred HHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC----------------------------CCCccchH
Q 036514 244 KLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHK----------------------------HSSFSASI 294 (328)
Q Consensus 244 ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~----------------------------~~~~~~Sl 294 (328)
.+...|+ -+++.+-.||..+...|+-.|-....+..|-|...- ++...+++
T Consensus 97 yl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv 176 (197)
T COG5162 97 YLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTV 176 (197)
T ss_pred HHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeee
Confidence 4567899 788899999999999999999999999988776221 46677899
Q ss_pred hhHHHHHHhC
Q 036514 295 LDFQVATELN 304 (328)
Q Consensus 295 ~Df~~amEln 304 (328)
.|+..|+|-.
T Consensus 177 ~DLs~Al~Ey 186 (197)
T COG5162 177 VDLSKALEEY 186 (197)
T ss_pred hHHHHHHHHh
Confidence 9999998753
No 66
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=24.79 E-value=3.2e+02 Score=25.86 Aligned_cols=50 Identities=20% Similarity=0.307 Sum_probs=40.2
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAG 280 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~ 280 (328)
-++...+...+...|.++|+.++.++++.|...+..=+..+...+=.++-
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l 194 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLAL 194 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHh
Confidence 36788999999999999999999999999999887655555554444443
No 67
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=24.27 E-value=1.4e+02 Score=23.58 Aligned_cols=58 Identities=14% Similarity=0.170 Sum_probs=33.7
Q ss_pred CCCCCCCCCCcccccCCCCcccchhHhhhCCCCC---HHhHHHHHHHHHHHhCCCCChhHHH
Q 036514 200 GIPINGKGTPKLLHKSSTDAYYTGICQNHGELPD---AYSLRKRLEKKLEMEGLKVSVDCAN 258 (328)
Q Consensus 200 gip~~~~s~g~~~~~~~~~~~~~~~c~esgeLPD---t~sL~~RM~~ia~e~GLgVs~~ca~ 258 (328)
|.|+......|....-..+.++...||+.|++=. .+.+-.++.+.+.+.+- ++.+-|.
T Consensus 7 GMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~~~t~eemie~~~~~~~~~~~-~~~~~a~ 67 (81)
T PF12674_consen 7 GMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQDITMEEMIEFCVPFMDEFNG-MTPEEAR 67 (81)
T ss_pred cCccCCccccccccCCCCchhHHHHHhcCCceeecCCHHHHHHHHHHHHHHhCC-CCHHHHH
Confidence 5555444434433333556778899999999987 34444555555544442 5554443
No 68
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=24.06 E-value=65 Score=19.82 Aligned_cols=18 Identities=28% Similarity=0.543 Sum_probs=14.5
Q ss_pred CccchHhhHHHHHHhCCc
Q 036514 289 SFSASILDFQVATELNPQ 306 (328)
Q Consensus 289 ~~~~Sl~Df~~amElnP~ 306 (328)
...-++.+|+-|++++|+
T Consensus 16 ~~~~A~~~~~~al~~~p~ 33 (34)
T PF00515_consen 16 DYEEALEYYQRALELDPD 33 (34)
T ss_dssp -HHHHHHHHHHHHHHSTT
T ss_pred CchHHHHHHHHHHHHCcC
Confidence 556678999999999995
No 69
>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.
Probab=23.77 E-value=1.2e+02 Score=27.81 Aligned_cols=52 Identities=17% Similarity=0.229 Sum_probs=35.3
Q ss_pred hHhhhCCCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHH
Q 036514 224 ICQNHGELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCL 276 (328)
Q Consensus 224 ~c~esgeLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i 276 (328)
++++- +-||-+..+.-+...|.+.|+.++.|++++|..-++.=+..|...+-
T Consensus 159 l~~~l-~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~~~r~L~~~l~ 210 (219)
T PF00308_consen 159 LVVEL-QPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFRRDVRELEGALN 210 (219)
T ss_dssp EEEEE-----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTSSHHHHHHHHH
T ss_pred chhhc-CCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcCCHHHHHHHHH
Confidence 34444 67899999999999999999999999999999887766655555443
No 70
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=23.47 E-value=49 Score=26.41 Aligned_cols=20 Identities=40% Similarity=0.718 Sum_probs=17.8
Q ss_pred HHHHHHHHhccCCHHHHHHH
Q 036514 32 FSLLTRYLSLKISKSEFDRL 51 (328)
Q Consensus 32 ~~~l~~fl~gklsk~Efd~~ 51 (328)
-.+|++||..+=|+.|||+-
T Consensus 38 m~NlKrFl~lRDs~~~Fd~v 57 (85)
T COG4545 38 MANLKRFLHLRDSRPEFDEV 57 (85)
T ss_pred hhhHHHHHhhhccchhHHhh
Confidence 45799999999999999974
No 71
>PRK04195 replication factor C large subunit; Provisional
Probab=23.31 E-value=2.1e+02 Score=29.36 Aligned_cols=47 Identities=11% Similarity=0.059 Sum_probs=38.1
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLE 277 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~ 277 (328)
-|+...+..++..+|..+|+.++.++.+.|.....--|..+|...-.
T Consensus 159 ~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ain~Lq~ 205 (482)
T PRK04195 159 RLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQA 205 (482)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 46888999999999999999999999999887766666666654433
No 72
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=23.15 E-value=1.9e+02 Score=29.48 Aligned_cols=69 Identities=19% Similarity=0.214 Sum_probs=53.1
Q ss_pred CCCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhc-cCCCCCCCccchHhhHHHHHH
Q 036514 230 ELPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCLELAGS-RSGHKHSSFSASILDFQVATE 302 (328)
Q Consensus 230 eLPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~-R~~~~~~~~~~Sl~Df~~amE 302 (328)
+-||.+.+..-+...|...|+.++.|++++|..-...-+..|...+..+..+ +.. ...+++...+.++.
T Consensus 261 ~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~l~~l~~~~~~~----~~~it~~~a~~~L~ 330 (440)
T PRK14088 261 EPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETT----GEEVDLKEAILLLK 330 (440)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHHH
Confidence 4599999999999999999999999999999998887777777776666542 222 23477777777765
No 73
>smart00414 H2A Histone 2A.
Probab=22.83 E-value=2e+02 Score=23.95 Aligned_cols=64 Identities=13% Similarity=0.149 Sum_probs=46.5
Q ss_pred HHHHHHHHHhCC--CCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCcc
Q 036514 239 KRLEKKLEMEGL--KVSVDCANLLNNGLDVFMKRLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQI 307 (328)
Q Consensus 239 ~RM~~ia~e~GL--gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~l 307 (328)
.|+...+.+... -|+..++-+|.-.||+..-+|++-+...++. .....|+-+|+..|+.-+..+
T Consensus 13 gRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~-----~k~~rItp~hi~lAi~nD~EL 78 (106)
T smart00414 13 GRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARD-----NKKRRITPRHLQLAIRNDEEL 78 (106)
T ss_pred HHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHh-----cCCCccchHHHhhhccCCHHH
Confidence 466666655544 6999999999999999888888766555543 235568899999888665543
No 74
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=22.59 E-value=2.5e+02 Score=26.49 Aligned_cols=46 Identities=22% Similarity=0.153 Sum_probs=37.4
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHHHHHHHHH
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMKRLIKPCL 276 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK~LI~s~i 276 (328)
-|+.+.+...+..++..+|+.++.++++.|.....-=+..++...-
T Consensus 183 ~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~ 228 (337)
T PRK12402 183 APTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQ 228 (337)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3777889999999999999999999999988777666666665443
No 75
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.34 E-value=2.5e+02 Score=29.10 Aligned_cols=67 Identities=13% Similarity=0.180 Sum_probs=48.3
Q ss_pred CCCHHhHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHHH---HHHHHHHHHhhccCCCCCCCccchHhhHHHHHHhCCc
Q 036514 231 LPDAYSLRKRLEKKLEMEGLKVSVDCANLLNNGLDVFMK---RLIKPCLELAGSRSGHKHSSFSASILDFQVATELNPQ 306 (328)
Q Consensus 231 LPDt~sL~~RM~~ia~e~GLgVs~~ca~lLn~aLd~yLK---~LI~s~i~l~~~R~~~~~~~~~~Sl~Df~~amElnP~ 306 (328)
-++.+.+..++..+|..+|+.++.++++.+....+-=+. ++|+.++..+ . ..|+..|.+.++...+.
T Consensus 175 ~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~----~-----~~It~e~V~~~l~~~~~ 244 (472)
T PRK14962 175 NISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFS----E-----GKITLETVHEALGLIPI 244 (472)
T ss_pred CccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhc----C-----CCCCHHHHHHHHcCCCH
Confidence 366788999999999999999999999999886654333 4444433221 1 12888888888876654
No 76
>PF11537 DUF3227: Protein of unknown function (DUF3227); InterPro: IPR021609 This archaeal family of proteins has no known function. ; PDB: 2P9X_C.
Probab=22.29 E-value=2e+02 Score=23.98 Aligned_cols=48 Identities=15% Similarity=0.161 Sum_probs=37.4
Q ss_pred cHHHHHHHHHHHhCCccHHHHHHHHHHHHhccC-------CHHHHHHHHHhhcCC
Q 036514 11 DILEIKSHIERKLGAAKSDKYFSLLTRYLSLKI-------SKSEFDRLCIGTIGR 58 (328)
Q Consensus 11 Dl~~lk~~L~~~LG~~~~~~Y~~~l~~fl~gkl-------sk~Efd~~~~~~L~~ 58 (328)
|-...|..+.+..|.-.++-+...|-.||.+++ +.+++.++++.+-|-
T Consensus 45 DP~~F~~avsklfGe~sA~l~~~~ii~~l~~~~~~~~ei~~le~~ve~~kk~~g~ 99 (102)
T PF11537_consen 45 DPKKFYEAVSKLFGEYSARLFEMMIINELKLKVGKEEEIEDLEELVEELKKIYGV 99 (102)
T ss_dssp -HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHC-TT---SSHHHHHHHHHHHCT-
T ss_pred ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcccccccHhhHHHHHHHHHHHhCc
Confidence 556789999999996666777888999999999 677888888888773
No 77
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=22.17 E-value=2.4e+02 Score=23.06 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=34.5
Q ss_pred HHHHHHHhCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 036514 241 LEKKLEMEGL-KVSVDCANLLNNGLDVFMKRLIKPCLELAG 280 (328)
Q Consensus 241 M~~ia~e~GL-gVs~~ca~lLn~aLd~yLK~LI~s~i~l~~ 280 (328)
+..+|+-.|+ -|+--|-+=.++++.+||.+.|.-.+-.+-
T Consensus 35 IRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~ 75 (103)
T KOG3467|consen 35 IRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE 75 (103)
T ss_pred HHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4567888999 899999999999999999999997766553
No 78
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=22.03 E-value=92 Score=21.88 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=19.1
Q ss_pred HhHHHHHHHHHHHhCC-CCChhHHH
Q 036514 235 YSLRKRLEKKLEMEGL-KVSVDCAN 258 (328)
Q Consensus 235 ~sL~~RM~~ia~e~GL-gVs~~ca~ 258 (328)
..++++.|..|.+.|. -|+.+..+
T Consensus 18 ~~~r~~~E~~Ar~~G~~~IT~e~v~ 42 (45)
T PF08369_consen 18 KKLRDAAEKYARERGYDEITVEVVD 42 (45)
T ss_dssp HHHHHHHHHHHHHCT-SEE-HHHHH
T ss_pred HHHHHHHHHHHHHcCCCeECHHHHH
Confidence 6789999999999999 89988754
Done!