Query 033891
Match_columns 109
No_of_seqs 95 out of 106
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:27:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033891.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033891hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09415 CENP-X: CENP-S associ 99.9 2.5E-28 5.4E-33 163.3 4.1 61 49-109 11-72 (72)
2 PF00808 CBFD_NFYB_HMF: Histon 97.2 0.0018 4E-08 41.0 5.9 49 54-102 17-65 (65)
3 cd07981 TAF12 TATA Binding Pro 96.7 0.0091 2E-07 39.3 6.2 48 55-102 17-64 (72)
4 PF03847 TFIID_20kDa: Transcri 96.5 0.011 2.5E-07 39.0 6.1 56 40-102 7-62 (68)
5 smart00803 TAF TATA box bindin 94.3 0.2 4.3E-06 32.6 5.7 46 57-102 19-64 (65)
6 COG2036 HHT1 Histones H3 and H 94.1 0.21 4.5E-06 35.0 6.0 48 57-104 36-83 (91)
7 PF02269 TFIID-18kDa: Transcri 93.5 0.12 2.6E-06 35.6 3.8 45 55-99 17-61 (93)
8 PF00125 Histone: Core histone 92.4 0.7 1.5E-05 29.4 6.0 46 56-101 26-71 (75)
9 cd08048 TAF11 TATA Binding Pro 91.6 0.76 1.6E-05 31.5 5.7 47 56-102 32-81 (85)
10 cd00076 H4 Histone H4, one of 89.1 1.5 3.2E-05 30.3 5.5 47 56-102 29-75 (85)
11 cd00074 H2A Histone 2A; H2A is 89.0 0.95 2.1E-05 32.7 4.6 46 56-101 37-82 (115)
12 KOG1142 Transcription initiati 88.4 0.83 1.8E-05 37.5 4.5 46 54-99 169-214 (258)
13 PLN00035 histone H4; Provision 88.1 1.8 3.9E-05 31.0 5.5 59 36-102 33-91 (103)
14 PTZ00015 histone H4; Provision 86.8 6 0.00013 28.2 7.6 64 30-101 28-91 (102)
15 smart00417 H4 Histone H4. 86.0 2.2 4.8E-05 28.8 4.8 59 32-98 13-71 (74)
16 PF04719 TAFII28: hTAFII28-lik 85.2 3.7 7.9E-05 28.6 5.7 49 56-104 40-89 (90)
17 smart00576 BTP Bromodomain tra 83.5 5.5 0.00012 26.0 5.8 47 57-103 23-69 (77)
18 cd07978 TAF13 The TATA Binding 81.3 7.6 0.00017 26.8 6.0 45 57-102 20-64 (92)
19 PF07524 Bromo_TP: Bromodomain 80.7 13 0.00027 24.0 6.9 48 58-105 24-71 (77)
20 PF02969 TAF: TATA box binding 78.4 11 0.00024 24.8 5.8 47 56-102 19-65 (66)
21 cd08050 TAF6 TATA Binding Prot 78.0 7.1 0.00015 32.2 5.9 48 56-103 15-62 (343)
22 smart00414 H2A Histone 2A. 76.6 6.2 0.00013 28.1 4.5 45 57-101 27-71 (106)
23 COG5247 BUR6 Class 2 transcrip 74.8 5.2 0.00011 29.3 3.8 45 57-101 41-85 (113)
24 PF08369 PCP_red: Proto-chloro 71.0 5.9 0.00013 24.1 2.9 40 60-100 3-43 (45)
25 PLN00153 histone H2A; Provisio 68.0 11 0.00023 28.1 4.3 45 57-101 42-86 (129)
26 PTZ00017 histone H2A; Provisio 66.6 10 0.00022 28.3 3.9 45 57-101 45-89 (134)
27 PRK00411 cdc6 cell division co 65.7 22 0.00047 28.5 5.9 49 57-105 228-282 (394)
28 PLN00156 histone H2AX; Provisi 64.6 14 0.00031 27.8 4.4 45 57-101 47-91 (139)
29 PLN00157 histone H2A; Provisio 63.5 14 0.0003 27.6 4.1 46 56-101 43-88 (132)
30 KOG1659 Class 2 transcription 63.1 17 0.00036 29.5 4.7 45 57-101 31-75 (224)
31 TIGR02928 orc1/cdc6 family rep 63.0 31 0.00068 27.2 6.3 49 57-105 220-274 (365)
32 cd07979 TAF9 TATA Binding Prot 62.0 52 0.0011 23.5 6.7 44 56-99 17-60 (117)
33 KOG1657 CCAAT-binding factor, 54.3 25 0.00055 28.2 4.5 82 13-101 50-136 (236)
34 PF02861 Clp_N: Clp amino term 53.0 9.3 0.0002 22.1 1.4 21 81-101 1-21 (53)
35 COG5262 HTA1 Histone H2A [Chro 48.3 29 0.00064 26.0 3.7 48 53-100 40-87 (132)
36 smart00428 H3 Histone H3. 45.5 72 0.0016 22.8 5.2 45 55-99 51-95 (105)
37 TIGR02902 spore_lonB ATP-depen 41.1 54 0.0012 28.6 4.7 50 54-104 279-331 (531)
38 PTZ00252 histone H2A; Provisio 39.2 64 0.0014 24.3 4.3 46 56-101 42-89 (134)
39 KOG0870 DNA polymerase epsilon 38.9 1.1E+02 0.0025 23.9 5.7 48 55-102 28-75 (172)
40 COG5208 HAP5 CCAAT-binding fac 37.7 36 0.00078 28.2 3.0 43 57-99 127-169 (286)
41 PLN00154 histone H2A; Provisio 37.3 83 0.0018 23.7 4.6 45 56-100 56-100 (136)
42 smart00054 EFh EF-hand, calciu 37.0 37 0.00081 15.5 1.9 23 83-105 7-29 (29)
43 PF15511 CENP-T: Centromere ki 34.3 36 0.00078 29.0 2.6 24 54-77 371-394 (414)
44 KOG0869 CCAAT-binding factor, 33.0 1.4E+02 0.003 23.4 5.3 50 55-104 49-98 (168)
45 KOG1756 Histone 2A [Chromatin 32.9 1.5E+02 0.0033 22.3 5.4 45 56-100 44-88 (131)
46 PF00036 EF-hand_1: EF hand; 32.6 45 0.00097 18.1 2.0 26 80-105 4-29 (29)
47 PF02575 YbaB_DNA_bd: YbaB/Ebf 32.2 38 0.00083 22.2 2.0 35 53-87 42-77 (93)
48 TIGR03015 pepcterm_ATPase puta 31.3 1.3E+02 0.0029 22.4 5.0 52 54-105 212-266 (269)
49 PRK02910 light-independent pro 30.8 1.2E+02 0.0025 26.4 5.2 54 48-102 460-514 (519)
50 PF03000 NPH3: NPH3 family; I 30.4 81 0.0018 25.6 3.9 56 5-78 139-194 (258)
51 PF13202 EF-hand_5: EF hand; P 25.8 68 0.0015 16.7 1.9 20 83-102 6-25 (25)
52 PF13405 EF-hand_6: EF-hand do 24.7 78 0.0017 16.7 2.0 21 84-104 8-28 (31)
53 PF12836 HHH_3: Helix-hairpin- 24.2 53 0.0011 20.5 1.5 33 69-101 16-49 (65)
54 KOG2549 Transcription initiati 23.7 2E+02 0.0043 26.4 5.5 48 56-103 27-74 (576)
55 COG1474 CDC6 Cdc6-related prot 23.6 2.1E+02 0.0046 24.0 5.3 48 54-101 208-261 (366)
56 PRK00153 hypothetical protein; 23.5 81 0.0018 21.7 2.4 39 49-87 46-85 (104)
57 PF03979 Sigma70_r1_1: Sigma-7 23.5 96 0.0021 20.3 2.7 32 75-108 6-37 (82)
58 PTZ00463 histone H2B; Provisio 23.4 3.1E+02 0.0067 20.2 5.6 43 54-100 43-89 (117)
59 PF11640 TAN: Telomere-length 23.3 2.9E+02 0.0063 19.9 5.5 62 5-81 39-100 (155)
60 PHA01632 hypothetical protein 22.9 29 0.00063 23.1 0.1 18 92-109 27-44 (64)
61 smart00427 H2B Histone H2B. 22.1 2.9E+02 0.0062 19.3 6.1 43 54-100 16-62 (89)
62 TIGR00764 lon_rel lon-related 22.0 2.3E+02 0.0051 25.4 5.6 45 57-101 330-387 (608)
63 TIGR00103 DNA_YbaB_EbfC DNA-bi 20.5 1.4E+02 0.003 20.7 3.1 38 50-87 49-86 (102)
No 1
>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=99.95 E-value=2.5e-28 Score=163.29 Aligned_cols=61 Identities=59% Similarity=0.785 Sum_probs=55.0
Q ss_pred CccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc-cccchHHHhhhhhhcCC
Q 033891 49 TSKKNRPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSK-IEATHLERILPQLLLDF 109 (109)
Q Consensus 49 ~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~-levehLEKIlPQLLLDF 109 (109)
.+|++++||||+||++++++||++||+||++||+++|+++|++. |+++|||||+|||||||
T Consensus 11 ~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pqLlLDf 72 (72)
T PF09415_consen 11 EHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQLLLDF 72 (72)
T ss_dssp TTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHCHHCHT
T ss_pred HHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHhcCC
Confidence 36899999999999999999999999999999999999999887 99999999999999999
No 2
>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=97.15 E-value=0.0018 Score=41.01 Aligned_cols=49 Identities=12% Similarity=0.165 Sum_probs=43.0
Q ss_pred CCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 54 RPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
+..+||+||..++++-...|+.+-...|...++..+...|..+|+.+.+
T Consensus 17 ~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 17 DVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp TTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 3457999999999999999999999999999999999999999998754
No 3
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=96.65 E-value=0.0091 Score=39.26 Aligned_cols=48 Identities=19% Similarity=0.269 Sum_probs=44.5
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 55 PTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 55 ~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
.++++++|..++.++.+-|+...+..|+..|+-.|...|+++|++-.+
T Consensus 17 ~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l 64 (72)
T cd07981 17 REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHL 64 (72)
T ss_pred CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 368999999999999999999999999999999999999999997654
No 4
>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=96.54 E-value=0.011 Score=39.03 Aligned_cols=56 Identities=23% Similarity=0.250 Sum_probs=43.8
Q ss_pred HHhhhccCCCccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 40 FLLHQAGAGTSKKNRPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 40 ~~~~~~~~~~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
.|..++++ +.++.+++-.++.++.+-||...+.+|+..|+-.+++.|++.|++-+|
T Consensus 7 ~Lv~~iDp-------~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~L 62 (68)
T PF03847_consen 7 ELVKQIDP-------NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHL 62 (68)
T ss_dssp HHHHCC-S-------S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHH
T ss_pred HHHHHcCC-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHH
Confidence 46666754 458899999999999999999999999999999999999999988665
No 5
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=94.26 E-value=0.2 Score=32.63 Aligned_cols=46 Identities=20% Similarity=0.227 Sum_probs=41.6
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
+||.|+...++++++.++.|-+.-|+..++--+-..|+.+|+...|
T Consensus 19 ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Al 64 (65)
T smart00803 19 NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64 (65)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHh
Confidence 6999999999999999999999999999887777889999987654
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=94.15 E-value=0.21 Score=35.00 Aligned_cols=48 Identities=19% Similarity=0.268 Sum_probs=44.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhhhh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERILPQ 104 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIlPQ 104 (109)
|++.+|...+++.++-|..+-...|...|.-.|-..|..+|++..+-.
T Consensus 36 Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~ 83 (91)
T COG2036 36 RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKR 83 (91)
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999986644
No 7
>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=93.50 E-value=0.12 Score=35.63 Aligned_cols=45 Identities=22% Similarity=0.352 Sum_probs=24.7
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHH
Q 033891 55 PTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLE 99 (109)
Q Consensus 55 ~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLE 99 (109)
...-.++++.++-+++.-++.+-+.+|...|...|++.|.+|||.
T Consensus 17 ~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~ 61 (93)
T PF02269_consen 17 VEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLL 61 (93)
T ss_dssp -SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHH
Confidence 335689999999999999999999999999999999999999985
No 8
>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=92.41 E-value=0.7 Score=29.36 Aligned_cols=46 Identities=15% Similarity=0.185 Sum_probs=42.2
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
.+|+++|+..+..+++.|+.+-+..|...|..-+-..|.++|++-.
T Consensus 26 ~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A 71 (75)
T PF00125_consen 26 YRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLA 71 (75)
T ss_dssp SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHH
T ss_pred cccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHH
Confidence 7999999999999999999999999999998888888999998754
No 9
>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=91.59 E-value=0.76 Score=31.52 Aligned_cols=47 Identities=26% Similarity=0.372 Sum_probs=40.9
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC---CccccchHHHhh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGV---SKIEATHLERIL 102 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~---~~levehLEKIl 102 (109)
++++++.+..++-+-++||-|-+..|....+..+. +-|.++||.+-.
T Consensus 32 ~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~ 81 (85)
T cd08048 32 QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAY 81 (85)
T ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHH
Confidence 57899999999999999999999999998766554 789999998643
No 10
>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=89.05 E-value=1.5 Score=30.25 Aligned_cols=47 Identities=11% Similarity=0.195 Sum_probs=41.6
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
.|||+|+...+.++++.|..+-+..|+..++-.+-..|+.+|+.-.+
T Consensus 29 kRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~al 75 (85)
T cd00076 29 KRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYAL 75 (85)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHH
Confidence 47999999999999999999999999999887787889999986443
No 11
>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=88.98 E-value=0.95 Score=32.73 Aligned_cols=46 Identities=20% Similarity=0.222 Sum_probs=42.1
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
.||+.+|..-++..|+.++.|-...|...|+.-+...|.++||+-.
T Consensus 37 ~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lA 82 (115)
T cd00074 37 ERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLA 82 (115)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHH
Confidence 4899999999999999999999999999998888889999999753
No 12
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=88.43 E-value=0.83 Score=37.52 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=42.8
Q ss_pred CCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHH
Q 033891 54 RPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLE 99 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLE 99 (109)
.+|+|.+|+-.++.+|.+=||---+.||+..|+-..++.||+.|++
T Consensus 169 ~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIq 214 (258)
T KOG1142|consen 169 GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQ 214 (258)
T ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhhee
Confidence 5678999999999999999999999999999999999999998875
No 13
>PLN00035 histone H4; Provisional
Probab=88.10 E-value=1.8 Score=31.05 Aligned_cols=59 Identities=14% Similarity=0.182 Sum_probs=47.2
Q ss_pred hHHHHHhhhccCCCccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 36 MESEFLLHQAGAGTSKKNRPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 36 ~~~e~~~~~~~~~~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
....+|....| -.|||.++...+.++++.|..+.+..|+..++--+-..|+.+|+.=.+
T Consensus 33 ~~IrRLARr~G--------vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Al 91 (103)
T PLN00035 33 PAIRRLARRGG--------VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
T ss_pred HHHHHHHHHcC--------cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHH
Confidence 34555555554 347999999999999999999999999999877777789999986443
No 14
>PTZ00015 histone H4; Provisional
Probab=86.81 E-value=6 Score=28.24 Aligned_cols=64 Identities=14% Similarity=0.159 Sum_probs=50.3
Q ss_pred cCCCChhHHHHHhhhccCCCccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 30 NGGTDAMESEFLLHQAGAGTSKKNRPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 30 ~~~~~~~~~e~~~~~~~~~~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
..+..-....+|....|+ .|||.|+...+.++|+.|..+-+..|+..++--+-..|+.+|++-.
T Consensus 28 i~gI~k~~IrRLarr~Gv--------kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~A 91 (102)
T PTZ00015 28 IRGITKGAIRRLARRGGV--------KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYA 91 (102)
T ss_pred ccCCCHHHHHHHHHHcCC--------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHH
Confidence 334445556666666543 3699999999999999999999999999887777778999998644
No 15
>smart00417 H4 Histone H4.
Probab=86.02 E-value=2.2 Score=28.77 Aligned_cols=59 Identities=15% Similarity=0.211 Sum_probs=45.5
Q ss_pred CCChhHHHHHhhhccCCCccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchH
Q 033891 32 GTDAMESEFLLHQAGAGTSKKNRPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHL 98 (109)
Q Consensus 32 ~~~~~~~e~~~~~~~~~~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehL 98 (109)
+..-....+|....|+ -+||.++..-+.++|+.|..+-+..|+..++-.+-..|+.+|+
T Consensus 13 gI~k~~IrRLaRr~Gv--------kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV 71 (74)
T smart00417 13 GITKPAIRRLARRGGV--------KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDV 71 (74)
T ss_pred CCCHHHHHHHHHHcCc--------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHh
Confidence 3344445555555542 3799999999999999999999999999987777777887775
No 16
>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=85.17 E-value=3.7 Score=28.63 Aligned_cols=49 Identities=22% Similarity=0.348 Sum_probs=35.5
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHh-hCCCccccchHHHhhhh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEA-EGVSKIEATHLERILPQ 104 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~-Eg~~~levehLEKIlPQ 104 (109)
..+++..+.+++-+-++||-|-|..|....+. .+.+-|.+.||.+..-.
T Consensus 40 qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rr 89 (90)
T PF04719_consen 40 QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRR 89 (90)
T ss_dssp S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHH
T ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHh
Confidence 46899999999999999999999999987543 34668999999876543
No 17
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=83.45 E-value=5.5 Score=26.05 Aligned_cols=47 Identities=21% Similarity=0.248 Sum_probs=41.0
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhhh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERILP 103 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIlP 103 (109)
+++++|+..+++++.-|+.+-...+..-++.-|-..+++.|++..+-
T Consensus 23 ~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~ 69 (77)
T smart00576 23 SFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALE 69 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 47999999999999999999999999998777778888999886553
No 18
>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=81.32 E-value=7.6 Score=26.84 Aligned_cols=45 Identities=18% Similarity=0.306 Sum_probs=38.3
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
.-.++++.++-+++.-|+.|-+..|...|. .+.+.+.+|||.=.+
T Consensus 20 ~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~Fli 64 (92)
T cd07978 20 NPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLL 64 (92)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHH
Confidence 357899999999999999999999999987 556667999986543
No 19
>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=80.73 E-value=13 Score=24.04 Aligned_cols=48 Identities=23% Similarity=0.339 Sum_probs=42.0
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhhhhh
Q 033891 58 ANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERILPQL 105 (109)
Q Consensus 58 Is~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIlPQL 105 (109)
+++.|+..+++.+.-|+.+-...+...|+..|-....+.|+...+-.+
T Consensus 24 ~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~ 71 (77)
T PF07524_consen 24 ASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEM 71 (77)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 789999999999999999999999988877787888899988776544
No 20
>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=78.36 E-value=11 Score=24.81 Aligned_cols=47 Identities=17% Similarity=0.181 Sum_probs=37.7
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
+.++.++.+.+++=++.-++|-+.-|....+.-.-..++.+|++..|
T Consensus 19 ~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~AL 65 (66)
T PF02969_consen 19 SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSAL 65 (66)
T ss_dssp --B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 35899999999999999999999999998876667889999998754
No 21
>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=78.02 E-value=7.1 Score=32.24 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=43.7
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhhh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERILP 103 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIlP 103 (109)
++++.||.+.+++.++-++++-+.-|...++.-+...|..+|++..+-
T Consensus 15 ~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~ 62 (343)
T cd08050 15 DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALR 62 (343)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence 359999999999999999999999999999888889999999987653
No 22
>smart00414 H2A Histone 2A.
Probab=76.60 E-value=6.2 Score=28.08 Aligned_cols=45 Identities=20% Similarity=0.225 Sum_probs=39.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
||+..|.--++..|+.++.|-...|-..|++-+...|.++|++..
T Consensus 27 Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lA 71 (106)
T smart00414 27 RVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLA 71 (106)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhh
Confidence 788889999999999999999999999888777778999999864
No 23
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=74.81 E-value=5.2 Score=29.27 Aligned_cols=45 Identities=18% Similarity=0.277 Sum_probs=38.3
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
||+..+=-...+-|+.|+.|-|.-+..+|+..+...++.|+|-+-
T Consensus 41 KV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a 85 (113)
T COG5247 41 KVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRA 85 (113)
T ss_pred hhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHH
Confidence 455555567788899999999999999999999999999999873
No 24
>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=71.02 E-value=5.9 Score=24.09 Aligned_cols=40 Identities=20% Similarity=0.232 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH-HHhhCCCccccchHHH
Q 033891 60 ANALKLSCELLRVFVTEAVQRAAAI-AEAEGVSKIEATHLER 100 (109)
Q Consensus 60 ~dAl~L~aeyL~iFV~EAv~RA~~e-A~~Eg~~~levehLEK 100 (109)
+||...+.++ =.||+--+.+.++. |+..|...|+++++..
T Consensus 3 ~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~ 43 (45)
T PF08369_consen 3 DEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDA 43 (45)
T ss_dssp HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHH
T ss_pred HHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHh
Confidence 4455555553 56899777777775 6678889999999875
No 25
>PLN00153 histone H2A; Provisional
Probab=68.02 E-value=11 Score=28.10 Aligned_cols=45 Identities=18% Similarity=0.205 Sum_probs=40.0
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
||+..|.-.++..|+.++.|-...|-..|+..+...|.++||+-.
T Consensus 42 Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lA 86 (129)
T PLN00153 42 RIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLA 86 (129)
T ss_pred ccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhh
Confidence 788889999999999999999999998888888888999998754
No 26
>PTZ00017 histone H2A; Provisional
Probab=66.62 E-value=10 Score=28.35 Aligned_cols=45 Identities=18% Similarity=0.225 Sum_probs=40.0
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
||+..|.-.++..|+.++.|-...|-..|++.+...|.++||+-.
T Consensus 45 RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lA 89 (134)
T PTZ00017 45 RVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLA 89 (134)
T ss_pred cccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhh
Confidence 788889999999999999999999999988877788999998754
No 27
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=65.74 E-value=22 Score=28.50 Aligned_cols=49 Identities=22% Similarity=0.346 Sum_probs=37.4
Q ss_pred ccchHHHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCccccchHHHhhhhh
Q 033891 57 SANANALKLSCELLRV------FVTEAVQRAAAIAEAEGVSKIEATHLERILPQL 105 (109)
Q Consensus 57 kIs~dAl~L~aeyL~i------FV~EAv~RA~~eA~~Eg~~~levehLEKIlPQL 105 (109)
.++++++.+++++..- .+...+.+|...|..++...|+.+|+++.+.++
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 4789999999887743 223456677777777888899999999888764
No 28
>PLN00156 histone H2AX; Provisional
Probab=64.60 E-value=14 Score=27.84 Aligned_cols=45 Identities=18% Similarity=0.209 Sum_probs=39.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
||+..|--.++..|+.++.|....|-..|+......|.++||+-.
T Consensus 47 RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lA 91 (139)
T PLN00156 47 RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLA 91 (139)
T ss_pred ccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhh
Confidence 788889999999999999999999998888777788999998764
No 29
>PLN00157 histone H2A; Provisional
Probab=63.50 E-value=14 Score=27.62 Aligned_cols=46 Identities=22% Similarity=0.235 Sum_probs=40.0
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
-||+..|.-.++..|+.++.|-...|-..|+..+...|.++||+-.
T Consensus 43 ~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lA 88 (132)
T PLN00157 43 TRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLA 88 (132)
T ss_pred hhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhc
Confidence 3788889999999999999999999998888877888999998753
No 30
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=63.13 E-value=17 Score=29.54 Aligned_cols=45 Identities=16% Similarity=0.353 Sum_probs=39.5
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
||..-.=-++.+-|++|+.+-+.++.++++..+...|+.+||.++
T Consensus 31 KvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~ 75 (224)
T KOG1659|consen 31 KVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQA 75 (224)
T ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHH
Confidence 455556667889999999999999999999999999999999884
No 31
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=63.05 E-value=31 Score=27.23 Aligned_cols=49 Identities=20% Similarity=0.346 Sum_probs=36.0
Q ss_pred ccchHHHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCccccchHHHhhhhh
Q 033891 57 SANANALKLSCELLRV------FVTEAVQRAAAIAEAEGVSKIEATHLERILPQL 105 (109)
Q Consensus 57 kIs~dAl~L~aeyL~i------FV~EAv~RA~~eA~~Eg~~~levehLEKIlPQL 105 (109)
.++.+++.++++.... .+...+.+|...|..++...|+.+|+++...++
T Consensus 220 ~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~ 274 (365)
T TIGR02928 220 VLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI 274 (365)
T ss_pred CCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 4788888888776542 234455677777777888899999999987765
No 32
>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=61.99 E-value=52 Score=23.46 Aligned_cols=44 Identities=18% Similarity=0.293 Sum_probs=39.6
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHH
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLE 99 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLE 99 (109)
++.++++...+.+++.-++.+-+.-|...|+--|...|+.+|+.
T Consensus 17 ~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~ 60 (117)
T cd07979 17 TEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVK 60 (117)
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHH
Confidence 35799999999999999999999999999887788899999984
No 33
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=54.32 E-value=25 Score=28.24 Aligned_cols=82 Identities=18% Similarity=0.256 Sum_probs=53.6
Q ss_pred HHHHHHHhhhhhhhhhhcCCCChhHHHHHhhhccCCCccCCC-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033891 13 HAIFKHIWTRRSLERERNGGTDAMESEFLLHQAGAGTSKKNR-----PTSANANALKLSCELLRVFVTEAVQRAAAIAEA 87 (109)
Q Consensus 13 ~~ifk~~w~~~~~~~~~~~~~~~~~~e~~~~~~~~~~s~k~~-----~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~ 87 (109)
++-++..|....-+-+ ...++.-|.++-+--+|-- -..|+.+|.-|.++-.++|+.|-..||...++.
T Consensus 50 ~~~l~~fw~~~~~e~e-------~~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee 122 (236)
T KOG1657|consen 50 RQQLQSFWSKQAIEKE-------GQLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEE 122 (236)
T ss_pred hHHHHhhhhccccccc-------cccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcc
Confidence 7789999998752211 1233444555544333322 237999999999999999999999998877654
Q ss_pred hCCCccccchHHHh
Q 033891 88 EGVSKIEATHLERI 101 (109)
Q Consensus 88 Eg~~~levehLEKI 101 (109)
.....+...||--+
T Consensus 123 ~~rrtl~~sdia~a 136 (236)
T KOG1657|consen 123 NKRRTLQKSDIAAA 136 (236)
T ss_pred cccccchHHHHHHH
Confidence 44444555555443
No 34
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=52.97 E-value=9.3 Score=22.07 Aligned_cols=21 Identities=29% Similarity=0.311 Sum_probs=15.4
Q ss_pred HHHHHHhhCCCccccchHHHh
Q 033891 81 AAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 81 A~~eA~~Eg~~~levehLEKI 101 (109)
|...|+..+..+|+++||=..
T Consensus 1 A~~~A~~~~~~~i~~eHlL~a 21 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLA 21 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHH
Confidence 456677889999999998653
No 35
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=48.32 E-value=29 Score=26.00 Aligned_cols=48 Identities=21% Similarity=0.193 Sum_probs=38.9
Q ss_pred CCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHH
Q 033891 53 NRPTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLER 100 (109)
Q Consensus 53 ~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEK 100 (109)
+-.+||+++|.-.++..|+.++.|-..-|-.-|+..+-..|.+.||.-
T Consensus 40 ~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlql 87 (132)
T COG5262 40 NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQL 87 (132)
T ss_pred ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHH
Confidence 356789999999888888888888888888777777777788888764
No 36
>smart00428 H3 Histone H3.
Probab=45.47 E-value=72 Score=22.79 Aligned_cols=45 Identities=9% Similarity=0.065 Sum_probs=37.9
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHH
Q 033891 55 PTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLE 99 (109)
Q Consensus 55 ~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLE 99 (109)
+-+++++|+.++.+..+.|..+-+.-|..-|.--+-..|.++|+.
T Consensus 51 ~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~ 95 (105)
T smart00428 51 DLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQ 95 (105)
T ss_pred CceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHH
Confidence 469999999999999999999999988877765566677778874
No 37
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=41.09 E-value=54 Score=28.64 Aligned_cols=50 Identities=32% Similarity=0.274 Sum_probs=35.5
Q ss_pred CCCccchHHHHHHHHHHHHHHHHH---HHHHHHHHHhhCCCccccchHHHhhhh
Q 033891 54 RPTSANANALKLSCELLRVFVTEA---VQRAAAIAEAEGVSKIEATHLERILPQ 104 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~iFV~EA---v~RA~~eA~~Eg~~~levehLEKIlPQ 104 (109)
.+..++++++.++..|-. =.||+ +.+|+..|..++...|+.+|++.++.+
T Consensus 279 ~~i~is~~al~~I~~y~~-n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 279 IGINLEKHALELIVKYAS-NGREAVNIVQLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred cCCCcCHHHHHHHHHhhh-hHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 345789999999888875 23554 334444555566678999999999863
No 38
>PTZ00252 histone H2A; Provisional
Probab=39.22 E-value=64 Score=24.25 Aligned_cols=46 Identities=9% Similarity=0.115 Sum_probs=37.5
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhh--CCCccccchHHHh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAE--GVSKIEATHLERI 101 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~E--g~~~levehLEKI 101 (109)
-||+..|---++..|+.++.|-...|-..|+.. ....|.++||+-.
T Consensus 42 ~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lA 89 (134)
T PTZ00252 42 RRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLA 89 (134)
T ss_pred cccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhh
Confidence 388888999999999999999999999887653 3467888888753
No 39
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=38.92 E-value=1.1e+02 Score=23.92 Aligned_cols=48 Identities=21% Similarity=0.144 Sum_probs=39.9
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhh
Q 033891 55 PTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 55 ~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIl 102 (109)
+..|+++|+.+++.--.+||.=...-|.+.|+...-..+.++|.=+-|
T Consensus 28 ~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL 75 (172)
T KOG0870|consen 28 NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKAL 75 (172)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHH
Confidence 578999999999999999999999999999987766667766655443
No 40
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=37.66 E-value=36 Score=28.15 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=34.5
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHH
Q 033891 57 SANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLE 99 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLE 99 (109)
-|+.+|=-|.++.-++|+.|-..||.-.|+......|...||-
T Consensus 127 MisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia 169 (286)
T COG5208 127 MISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIA 169 (286)
T ss_pred heecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHH
Confidence 4689999999999999999999999998865544555555543
No 41
>PLN00154 histone H2A; Provisional
Probab=37.25 E-value=83 Score=23.71 Aligned_cols=45 Identities=20% Similarity=0.275 Sum_probs=38.2
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHH
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLER 100 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEK 100 (109)
-||+..|---++..|+.++.|...-|-..|++.....|.+.||.-
T Consensus 56 ~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~l 100 (136)
T PLN00154 56 GRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQL 100 (136)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhh
Confidence 488899999999999999999888888888877777888888754
No 42
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=36.99 E-value=37 Score=15.51 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=15.3
Q ss_pred HHHHhhCCCccccchHHHhhhhh
Q 033891 83 AIAEAEGVSKIEATHLERILPQL 105 (109)
Q Consensus 83 ~eA~~Eg~~~levehLEKIlPQL 105 (109)
......+.+.|+..++..+++.+
T Consensus 7 ~~~d~~~~g~i~~~e~~~~~~~~ 29 (29)
T smart00054 7 RLFDKDGDGKIDFEEFKDLLKAL 29 (29)
T ss_pred HHHCCCCCCcEeHHHHHHHHHhC
Confidence 33334556788888888877653
No 43
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=34.26 E-value=36 Score=29.04 Aligned_cols=24 Identities=13% Similarity=0.070 Sum_probs=17.5
Q ss_pred CCCccchHHHHHHHHHHHHHHHHH
Q 033891 54 RPTSANANALKLSCELLRVFVTEA 77 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~iFV~EA 77 (109)
.|+||+++|++.+.+-+++|-.=.
T Consensus 371 sK~kiskdal~aleqasdwfFeQl 394 (414)
T PF15511_consen 371 SKMKISKDALEALEQASDWFFEQL 394 (414)
T ss_dssp --S-B-HHHHHHHHHHHHHHHHHH
T ss_pred cCCccCHHHHHHHHHHHHHHHHHH
Confidence 789999999999999999996533
No 44
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=33.00 E-value=1.4e+02 Score=23.37 Aligned_cols=50 Identities=14% Similarity=0.129 Sum_probs=32.5
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhhhh
Q 033891 55 PTSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERILPQ 104 (109)
Q Consensus 55 ~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIlPQ 104 (109)
+-||++||-.-+.|-+--|+.=-..+|.+.++.|--..|+.|||---+.-
T Consensus 49 naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t 98 (168)
T KOG0869|consen 49 NAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST 98 (168)
T ss_pred ccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence 45799999888776666665544455555555555567888887554443
No 45
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=32.95 E-value=1.5e+02 Score=22.26 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=35.5
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHH
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLER 100 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEK 100 (109)
-+|+.+|...++..|+.+..|...-|-..|+...-..|.+.||..
T Consensus 44 ~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~l 88 (131)
T KOG1756|consen 44 QRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQL 88 (131)
T ss_pred hhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHH
Confidence 357777777888888888888888888887777777888888864
No 46
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=32.62 E-value=45 Score=18.11 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=19.0
Q ss_pred HHHHHHHhhCCCccccchHHHhhhhh
Q 033891 80 RAAAIAEAEGVSKIEATHLERILPQL 105 (109)
Q Consensus 80 RA~~eA~~Eg~~~levehLEKIlPQL 105 (109)
++.......++|+|+.+.+-.++-.|
T Consensus 4 ~~F~~~D~d~dG~I~~~Ef~~~~~~L 29 (29)
T PF00036_consen 4 EAFREFDKDGDGKIDFEEFKEMMKKL 29 (29)
T ss_dssp HHHHHHSTTSSSEEEHHHHHHHHHHT
T ss_pred HHHHHHCCCCCCcCCHHHHHHHHHhC
Confidence 34444556789999999998887654
No 47
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=32.19 E-value=38 Score=22.22 Aligned_cols=35 Identities=29% Similarity=0.264 Sum_probs=27.9
Q ss_pred CCCCccchHHHH-HHHHHHHHHHHHHHHHHHHHHHh
Q 033891 53 NRPTSANANALK-LSCELLRVFVTEAVQRAAAIAEA 87 (109)
Q Consensus 53 ~~~TkIs~dAl~-L~aeyL~iFV~EAv~RA~~eA~~ 87 (109)
=.+.+|+++++. +-.+-|.-.|.+|+.+|...++.
T Consensus 42 v~~i~i~~~~~~~~~~~~L~~~I~~A~n~A~~~a~~ 77 (93)
T PF02575_consen 42 VVDIEIDPSALRPLDPEELEDLIVEAVNDAQKKARE 77 (93)
T ss_dssp EEEEEE-GGGGCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEehHhhccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 356678999998 88899999999999999988754
No 48
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=31.27 E-value=1.3e+02 Score=22.40 Aligned_cols=52 Identities=12% Similarity=0.124 Sum_probs=37.3
Q ss_pred CCCccchHHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCccccchHHHhhhhh
Q 033891 54 RPTSANANALKLSCELLRV---FVTEAVQRAAAIAEAEGVSKIEATHLERILPQL 105 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~i---FV~EAv~RA~~eA~~Eg~~~levehLEKIlPQL 105 (109)
....+++++++.+.++-.= .++..+.++...|-..+...|+.++++.++-++
T Consensus 212 ~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~ 266 (269)
T TIGR03015 212 DAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEI 266 (269)
T ss_pred CCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 3456899998888876542 355556666665556778899999999987664
No 49
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=30.82 E-value=1.2e+02 Score=26.44 Aligned_cols=54 Identities=17% Similarity=0.129 Sum_probs=42.6
Q ss_pred CCccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHH-HHhhCCCccccchHHHhh
Q 033891 48 GTSKKNRPTSANANALKLSCELLRVFVTEAVQRAAAI-AEAEGVSKIEATHLERIL 102 (109)
Q Consensus 48 ~~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~e-A~~Eg~~~levehLEKIl 102 (109)
..+..+....=+++|.+.+.+ +=.|||--+.|.+++ |+..|...|++|+++..-
T Consensus 460 ~~~~~~~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~ 514 (519)
T PRK02910 460 KAAAADSELVWTPEAEAELKK-IPFFVRGKVRRNTEKFARERGLPEITLEVLYDAK 514 (519)
T ss_pred CCCCCCCCCCCCHHHHHHHhh-CChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHH
Confidence 333444555669999999965 888999999999987 677899999999998653
No 50
>PF03000 NPH3: NPH3 family; InterPro: IPR004249 The RPT2 protein is a signal transducer of the phototropic response in Arabidopsis thaliana. The RPT2 gene is light inducible; encodes a novel protein with putative phosphorylation sites, a nuclear localization signal, a BTB/POZ domain (IPR000210 from INTERPRO), and a coiled-coil domain. RPT2 belongs to a large gene family that includes the recently isolated NPH3 gene []. The NPH3 protein is a NPH1 photoreceptor-interacting protein that is essential for phototropism. Phototropism of A. thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase []. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay []. Many of the proteins in this group also contain the BTB/POZ domain (IPR000210 from INTERPRO) at the N-terminal.; GO: 0004871 signal transducer activity, 0009416 response to light stimulus
Probab=30.41 E-value=81 Score=25.58 Aligned_cols=56 Identities=20% Similarity=0.345 Sum_probs=37.2
Q ss_pred cCCCHHHHHHHHHHHhhhhhhhhhhcCCCChhHHHHHhhhccCCCccCCCCCccchHHHHHHHHHHHHHHHHHH
Q 033891 5 TTFDSDLIHAIFKHIWTRRSLERERNGGTDAMESEFLLHQAGAGTSKKNRPTSANANALKLSCELLRVFVTEAV 78 (109)
Q Consensus 5 ~tf~~~li~~ifk~~w~~~~~~~~~~~~~~~~~~e~~~~~~~~~~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv 78 (109)
..||.|+++.|+++.-.......... ... ....-..+..++..++++++-|..|..
T Consensus 139 t~yDVd~V~riv~~Fl~~~~~~~~~~-----~~~-------------~~~~~~~~~~~~~~VakLvD~YLaEiA 194 (258)
T PF03000_consen 139 TLYDVDLVQRIVEHFLSQEEEAGEEE-----ESE-------------SESGSSPSSSSLVKVAKLVDGYLAEIA 194 (258)
T ss_pred chhhHHHHHHHHHHHHhccccccccc-----ccc-------------cccccCCChHHHHHHHHHHHHHHHHhc
Confidence 56999999999999987642111000 000 012223577899999999999998863
No 51
>PF13202 EF-hand_5: EF hand; PDB: 3DD4_A 2Q4U_A 2BE4_A 1UHJ_B 1UHI_A 1UHH_B 1EJ3_B 1UHK_A 2ZFD_A 1UHN_A ....
Probab=25.78 E-value=68 Score=16.73 Aligned_cols=20 Identities=20% Similarity=0.403 Sum_probs=15.1
Q ss_pred HHHHhhCCCccccchHHHhh
Q 033891 83 AIAEAEGVSKIEATHLERIL 102 (109)
Q Consensus 83 ~eA~~Eg~~~levehLEKIl 102 (109)
......++|.|+.+.+.+++
T Consensus 6 ~~~D~d~DG~is~~E~~~~~ 25 (25)
T PF13202_consen 6 QQFDTDGDGKISFEEFQRLV 25 (25)
T ss_dssp HHHTTTSSSEEEHHHHHHHH
T ss_pred HHHcCCCCCcCCHHHHHHHC
Confidence 34455789999999998853
No 52
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=24.69 E-value=78 Score=16.67 Aligned_cols=21 Identities=24% Similarity=0.368 Sum_probs=15.9
Q ss_pred HHHhhCCCccccchHHHhhhh
Q 033891 84 IAEAEGVSKIEATHLERILPQ 104 (109)
Q Consensus 84 eA~~Eg~~~levehLEKIlPQ 104 (109)
.-..+++++|+.++|.+++-+
T Consensus 8 ~~D~d~dG~I~~~el~~~l~~ 28 (31)
T PF13405_consen 8 MFDKDGDGFIDFEELRAILRK 28 (31)
T ss_dssp HH-TTSSSEEEHHHHHHHHHH
T ss_pred HHCCCCCCcCcHHHHHHHHHH
Confidence 334578899999999998763
No 53
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=24.19 E-value=53 Score=20.55 Aligned_cols=33 Identities=9% Similarity=-0.008 Sum_probs=20.5
Q ss_pred HHHH-HHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 69 LLRV-FVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 69 yL~i-FV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
+..+ .+.+..++++-.-+.+.+.+-++++|.+|
T Consensus 16 L~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v 49 (65)
T PF12836_consen 16 LQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEV 49 (65)
T ss_dssp HHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGS
T ss_pred HHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhC
Confidence 3444 56677777777767777788888888876
No 54
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=23.75 E-value=2e+02 Score=26.42 Aligned_cols=48 Identities=25% Similarity=0.206 Sum_probs=38.8
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCccccchHHHhhh
Q 033891 56 TSANANALKLSCELLRVFVTEAVQRAAAIAEAEGVSKIEATHLERILP 103 (109)
Q Consensus 56 TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~Eg~~~levehLEKIlP 103 (109)
+.|+.||.+++++-++.=++|.+.-|++.-.----..++++|+..-|-
T Consensus 27 ~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr 74 (576)
T KOG2549|consen 27 TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALR 74 (576)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHh
Confidence 569999999999999999999998888774433446788888887553
No 55
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=23.64 E-value=2.1e+02 Score=23.98 Aligned_cols=48 Identities=27% Similarity=0.406 Sum_probs=37.6
Q ss_pred CCCccchHHHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 54 RPTSANANALKLSCELLRV------FVTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~i------FV~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
....++.+++.+++...-- +..-...+|.+.|+.++++.++.+|.++.
T Consensus 208 ~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a 261 (366)
T COG1474 208 SAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREA 261 (366)
T ss_pred cCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHH
Confidence 3446788888888865432 45667789999999999999999999886
No 56
>PRK00153 hypothetical protein; Validated
Probab=23.54 E-value=81 Score=21.67 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=30.2
Q ss_pred CccCCCCCccchHHH-HHHHHHHHHHHHHHHHHHHHHHHh
Q 033891 49 TSKKNRPTSANANAL-KLSCELLRVFVTEAVQRAAAIAEA 87 (109)
Q Consensus 49 ~s~k~~~TkIs~dAl-~L~aeyL~iFV~EAv~RA~~eA~~ 87 (109)
-..+-.+.+|+++++ ..=.+.|.-.|.+|+.+|...++.
T Consensus 46 G~~~v~~i~Id~~ll~~~d~e~LedlI~~A~n~A~~~~~~ 85 (104)
T PRK00153 46 GKKEVKRVKIDPSLVDPEDVEMLEDLILAAFNDALRKAEE 85 (104)
T ss_pred cCceEEEEEECHHHcCCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 344556778899988 477888888999999999887654
No 57
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=23.49 E-value=96 Score=20.33 Aligned_cols=32 Identities=19% Similarity=0.287 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHhhCCCccccchHHHhhhhhhcC
Q 033891 75 TEAVQRAAAIAEAEGVSKIEATHLERILPQLLLD 108 (109)
Q Consensus 75 ~EAv~RA~~eA~~Eg~~~levehLEKIlPQLLLD 108 (109)
++++.+-+..++.. |+|+.++|...+|+-.+|
T Consensus 6 ~~~i~~Li~~gK~~--G~lT~~eI~~~L~~~~~~ 37 (82)
T PF03979_consen 6 EEAIKKLIEKGKKK--GYLTYDEINDALPEDDLD 37 (82)
T ss_dssp HHHHHHHHHHHHHH--SS-BHHHHHHH-S-S---
T ss_pred HHHHHHHHHHHhhc--CcCCHHHHHHHcCccCCC
Confidence 34555555555544 578888988888865443
No 58
>PTZ00463 histone H2B; Provisional
Probab=23.37 E-value=3.1e+02 Score=20.22 Aligned_cols=43 Identities=7% Similarity=0.208 Sum_probs=26.1
Q ss_pred CCCccchHHHHHHHHHHHHHHHHHHHHHHHH----HHhhCCCccccchHHH
Q 033891 54 RPTSANANALKLSCELLRVFVTEAVQRAAAI----AEAEGVSKIEATHLER 100 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~e----A~~Eg~~~levehLEK 100 (109)
+.|.||..|+..+. .||.--+.|-+.+ ++-..-..|+..+++-
T Consensus 43 Pd~gIS~kaM~Imn----SfvnDifErIA~EAs~La~~nkr~TltsrEIQt 89 (117)
T PTZ00463 43 PDTGISRKSMNIMN----SFLVDTFEKIATEASRLCKYTRRDTLSSREIQT 89 (117)
T ss_pred CCCCccHHHHHHHH----HHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHH
Confidence 45578999997765 4555544444444 4434556677776654
No 59
>PF11640 TAN: Telomere-length maintenance and DNA damage repair; InterPro: IPR021668 ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage []. It is classified as an 2.7.11.1 from EC. ; GO: 0004674 protein serine/threonine kinase activity
Probab=23.31 E-value=2.9e+02 Score=19.88 Aligned_cols=62 Identities=19% Similarity=0.319 Sum_probs=35.6
Q ss_pred cCCCHHHHHHHHHHHhhhhhhhhhhcCCCChhHHHHHhhhccCCCccCCCCCccchHHHHHHHHHHHHHHHHHHHHH
Q 033891 5 TTFDSDLIHAIFKHIWTRRSLERERNGGTDAMESEFLLHQAGAGTSKKNRPTSANANALKLSCELLRVFVTEAVQRA 81 (109)
Q Consensus 5 ~tf~~~li~~ifk~~w~~~~~~~~~~~~~~~~~~e~~~~~~~~~~s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA 81 (109)
...+.-..|.||+.+++-=..|.+.= ..+.+..+.+......=+..++..||.||.-++.|.
T Consensus 39 ~~l~~k~~~~ifeaL~~~i~~Ek~~y---------------~~~~~~~~s~~~~~~~RL~~~a~~lR~~ve~~~~~~ 100 (155)
T PF11640_consen 39 DSLNDKQWHSIFEALFRCIEKEKEAY---------------SRKKSSSASTATTAESRLSSCASALRLFVEKSNSRL 100 (155)
T ss_pred ccCCcchHHHHHHHHHHHHHHHHHHH---------------hcCCCcccchHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34556677888888887543333220 011111111222344557888999999998777654
No 60
>PHA01632 hypothetical protein
Probab=22.87 E-value=29 Score=23.06 Aligned_cols=18 Identities=33% Similarity=0.715 Sum_probs=14.6
Q ss_pred ccccchHHHhhhhhhcCC
Q 033891 92 KIEATHLERILPQLLLDF 109 (109)
Q Consensus 92 ~levehLEKIlPQLLLDF 109 (109)
.-+-|.|.|+||.+|-||
T Consensus 27 kpteeelrkvlpkilkdy 44 (64)
T PHA01632 27 KPTEEELRKVLPKILKDY 44 (64)
T ss_pred CCCHHHHHHHHHHHHHHH
Confidence 345688999999999885
No 61
>smart00427 H2B Histone H2B.
Probab=22.09 E-value=2.9e+02 Score=19.34 Aligned_cols=43 Identities=21% Similarity=0.292 Sum_probs=26.5
Q ss_pred CCCccchHHHHHHHHHHHHHHHHHHHHHHHH----HHhhCCCccccchHHH
Q 033891 54 RPTSANANALKLSCELLRVFVTEAVQRAAAI----AEAEGVSKIEATHLER 100 (109)
Q Consensus 54 ~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~e----A~~Eg~~~levehLEK 100 (109)
+.+.|+..|+..+. .||..-+.|-+.+ ++-..-..|+..+++-
T Consensus 16 pd~giS~kam~imn----SfvnDiferIa~EAs~L~~~nkr~TltsreIqt 62 (89)
T smart00427 16 PDTGISSKAMSIMN----SFVNDIFERIAAEASKLARYNKKSTLSSREIQT 62 (89)
T ss_pred CCccccHHHHHHHH----HHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHH
Confidence 45578999987665 4555555555544 3334455677777764
No 62
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=22.05 E-value=2.3e+02 Score=25.35 Aligned_cols=45 Identities=18% Similarity=0.162 Sum_probs=29.0
Q ss_pred ccchHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhhCCCccccchHHHh
Q 033891 57 SANANALKLSCELLRVF-------------VTEAVQRAAAIAEAEGVSKIEATHLERI 101 (109)
Q Consensus 57 kIs~dAl~L~aeyL~iF-------------V~EAv~RA~~eA~~Eg~~~levehLEKI 101 (109)
.++++|+..+.+|..-. +..-+..|...|+.+++..|+.+|+++.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~A 387 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKA 387 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHH
Confidence 68888888887664421 1112222333466678889999999874
No 63
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=20.50 E-value=1.4e+02 Score=20.68 Aligned_cols=38 Identities=21% Similarity=0.214 Sum_probs=30.7
Q ss_pred ccCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033891 50 SKKNRPTSANANALKLSCELLRVFVTEAVQRAAAIAEA 87 (109)
Q Consensus 50 s~k~~~TkIs~dAl~L~aeyL~iFV~EAv~RA~~eA~~ 87 (109)
..+-.+.+|+++++..=.+.|.-.|.+|+-+|...++.
T Consensus 49 ~~~v~~v~Id~~~l~~d~e~LedlI~~A~N~A~~k~~~ 86 (102)
T TIGR00103 49 NLELKSIEIDPSLLEEDKEALEDMITEALNDAVKKVEE 86 (102)
T ss_pred CceEEEEEECHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34556788999999877888888999999999887654
Done!