Query 006139
Match_columns 659
No_of_seqs 193 out of 559
Neff 2.9
Searched_HMMs 46136
Date Thu Mar 28 18:55:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006139.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006139hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01557 myb_SHAQKYF myb-like 99.6 2.9E-15 6.3E-20 121.2 6.1 50 22-71 1-56 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.4 1.2E-12 2.6E-17 100.1 6.3 45 24-68 1-47 (48)
3 smart00717 SANT SANT SWI3, AD 99.0 1E-09 2.2E-14 79.6 5.3 46 24-69 1-47 (49)
4 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 1.4E-09 3.1E-14 78.0 5.5 44 26-69 1-45 (45)
5 KOG0724 Zuotin and related mol 98.9 7.8E-11 1.7E-15 119.8 -2.6 100 6-111 34-134 (335)
6 PF13921 Myb_DNA-bind_6: Myb-l 98.7 1.3E-08 2.8E-13 80.1 4.9 42 27-68 1-42 (60)
7 PLN03212 Transcription repress 98.3 1.5E-06 3.2E-11 88.6 6.7 61 9-69 8-72 (249)
8 PLN03212 Transcription repress 98.2 3.8E-06 8.3E-11 85.7 8.7 53 21-73 75-127 (249)
9 COG5259 RSC8 RSC chromatin rem 98.2 1.3E-06 2.8E-11 95.2 5.3 61 12-76 265-327 (531)
10 PLN03091 hypothetical protein; 98.1 2.1E-06 4.6E-11 93.1 5.3 53 18-70 8-62 (459)
11 KOG1279 Chromatin remodeling f 98.1 5.3E-06 1.1E-10 91.5 6.3 53 20-76 249-301 (506)
12 KOG0457 Histone acetyltransfer 98.1 4.7E-06 1E-10 90.1 5.5 59 13-71 55-120 (438)
13 PLN03091 hypothetical protein; 98.0 1.8E-05 4E-10 86.1 9.0 53 22-74 65-117 (459)
14 KOG0048 Transcription factor, 97.5 0.00012 2.6E-09 72.9 4.5 47 24-70 9-57 (238)
15 COG5114 Histone acetyltransfer 97.4 0.00037 8E-09 74.0 7.3 48 23-70 62-110 (432)
16 KOG0048 Transcription factor, 97.2 0.00095 2E-08 66.6 7.2 47 22-68 60-106 (238)
17 PLN03162 golden-2 like transcr 97.2 0.00097 2.1E-08 72.0 7.5 85 21-105 234-326 (526)
18 KOG4329 DNA-binding protein [G 97.0 0.0031 6.7E-08 68.2 9.4 58 14-74 264-325 (445)
19 KOG0049 Transcription factor, 96.1 0.0082 1.8E-07 68.7 5.7 48 21-68 357-405 (939)
20 KOG4468 Polycomb-group transcr 95.3 0.025 5.5E-07 64.3 5.5 52 24-75 88-149 (782)
21 PF13837 Myb_DNA-bind_4: Myb/S 94.2 0.081 1.8E-06 44.1 4.7 50 24-73 1-68 (90)
22 KOG0049 Transcription factor, 94.1 0.072 1.6E-06 61.4 5.6 46 23-68 411-457 (939)
23 COG5118 BDP1 Transcription ini 94.0 0.094 2E-06 57.4 5.9 50 21-74 362-411 (507)
24 PLN03142 Probable chromatin-re 93.8 0.11 2.3E-06 62.5 6.5 48 25-72 825-873 (1033)
25 KOG4167 Predicted DNA-binding 93.0 0.17 3.7E-06 59.0 6.1 48 23-73 618-665 (907)
26 KOG0051 RNA polymerase I termi 92.1 0.17 3.7E-06 57.9 4.7 48 22-69 434-507 (607)
27 KOG0724 Zuotin and related mol 91.9 0.1 2.2E-06 54.0 2.5 57 21-77 161-224 (335)
28 KOG3841 TEF-1 and related tran 91.6 0.33 7.1E-06 53.3 5.9 55 22-76 74-149 (455)
29 KOG0051 RNA polymerase I termi 91.6 0.24 5.1E-06 56.8 5.0 50 18-68 377-427 (607)
30 PF13873 Myb_DNA-bind_5: Myb/S 91.4 0.96 2.1E-05 37.5 7.2 52 24-75 2-75 (78)
31 KOG0050 mRNA splicing protein 91.3 0.22 4.9E-06 56.2 4.4 50 22-71 5-55 (617)
32 KOG3554 Histone deacetylase co 90.5 0.69 1.5E-05 52.1 7.2 43 22-64 283-326 (693)
33 smart00426 TEA TEA domain. 89.6 0.31 6.8E-06 42.1 2.9 43 24-66 3-66 (68)
34 KOG1194 Predicted DNA-binding 85.9 1.7 3.7E-05 48.9 6.5 43 23-65 186-228 (534)
35 PF01285 TEA: TEA/ATTS domain 83.7 1 2.3E-05 49.8 3.7 48 21-68 46-112 (431)
36 PF11035 SnAPC_2_like: Small n 83.0 7.1 0.00015 42.5 9.3 58 22-79 19-80 (344)
37 PF09111 SLIDE: SLIDE; InterP 81.6 4.1 9E-05 38.0 6.2 57 18-74 43-115 (118)
38 COG5147 REB1 Myb superfamily p 81.4 0.93 2E-05 51.3 2.3 59 16-74 12-71 (512)
39 PF12776 Myb_DNA-bind_3: Myb/S 74.7 13 0.00029 31.4 6.9 43 26-68 1-61 (96)
40 COG5147 REB1 Myb superfamily p 73.9 4.1 8.8E-05 46.4 4.5 53 22-74 70-122 (512)
41 KOG4282 Transcription factor G 64.6 32 0.00069 36.2 8.5 56 24-79 54-123 (345)
42 KOG1194 Predicted DNA-binding 63.7 14 0.00029 42.1 5.8 61 16-76 361-421 (534)
43 KOG0050 mRNA splicing protein 63.3 7.8 0.00017 44.5 3.9 47 23-70 58-104 (617)
44 KOG0385 Chromatin remodeling c 62.6 13 0.00028 44.8 5.7 60 16-76 787-847 (971)
45 KOG2009 Transcription initiati 56.8 7.2 0.00016 45.1 2.3 43 22-64 407-449 (584)
46 PF08914 Myb_DNA-bind_2: Rap1 49.4 33 0.00071 29.2 4.6 47 24-70 2-58 (65)
47 PRK13923 putative spore coat p 48.4 31 0.00068 34.6 4.9 48 23-70 4-57 (170)
48 COG4425 Predicted membrane pro 44.7 22 0.00047 40.8 3.6 50 391-451 87-136 (588)
49 KOG1019 Retinoblastoma pathway 43.2 12 0.00027 44.8 1.5 61 4-64 24-85 (837)
50 TIGR02894 DNA_bind_RsfA transc 43.1 37 0.0008 33.9 4.5 53 23-76 3-62 (161)
51 PLN03142 Probable chromatin-re 42.6 1.2E+02 0.0025 37.8 9.4 55 22-76 924-991 (1033)
52 PF01388 ARID: ARID/BRIGHT DNA 42.1 72 0.0016 27.3 5.6 41 32-72 39-91 (92)
53 COG0315 MoaC Molybdenum cofact 41.7 22 0.00048 35.4 2.7 27 436-462 55-81 (157)
54 cd08780 Death_TRADD Death Doma 41.3 42 0.00092 30.8 4.2 38 28-68 1-42 (90)
55 PF04504 DUF573: Protein of un 40.8 71 0.0015 28.9 5.6 40 25-64 5-57 (98)
56 smart00595 MADF subfamily of S 39.7 66 0.0014 27.0 5.0 25 45-70 29-53 (89)
57 PF06461 DUF1086: Domain of Un 36.7 86 0.0019 31.0 5.8 49 26-74 40-91 (145)
58 PRK12343 putative molybdenum c 33.3 40 0.00087 33.3 3.0 25 438-462 51-75 (151)
59 cd01420 MoaC_PE MoaC family, p 32.7 45 0.00098 32.6 3.2 27 436-462 41-67 (140)
60 PF08281 Sigma70_r4_2: Sigma-7 32.4 1.5E+02 0.0032 22.8 5.5 35 33-68 16-50 (54)
61 PF12451 VPS11_C: Vacuolar pro 31.8 38 0.00082 27.3 2.2 28 28-55 17-44 (49)
62 smart00501 BRIGHT BRIGHT, ARID 30.9 1.4E+02 0.003 26.0 5.7 44 32-75 35-90 (93)
63 TIGR00581 moaC molybdenum cofa 30.7 45 0.00098 32.8 2.9 25 438-462 54-78 (147)
64 cd00528 MoaC MoaC family. Memb 30.4 49 0.0011 32.2 3.1 27 436-462 41-67 (136)
65 TIGR02937 sigma70-ECF RNA poly 29.8 1.7E+02 0.0036 25.0 5.9 47 26-74 110-156 (158)
66 cd01419 MoaC_A MoaC family, ar 26.7 63 0.0014 31.7 3.1 26 437-462 42-67 (141)
67 PRK09364 moaC molybdenum cofac 25.0 68 0.0015 32.0 3.0 24 439-462 58-81 (159)
68 PHA00442 host recBCD nuclease 23.9 42 0.00092 28.6 1.2 32 21-52 9-49 (59)
69 PF03187 Corona_I: Corona nucl 22.0 53 0.0011 33.7 1.7 27 629-656 144-170 (207)
70 PF10545 MADF_DNA_bdg: Alcohol 21.2 1.8E+02 0.0039 23.5 4.4 31 45-75 28-59 (85)
71 PF09420 Nop16: Ribosome bioge 20.6 1.9E+02 0.004 28.0 5.0 46 23-68 113-162 (164)
72 PLN02375 molybderin biosynthes 20.4 83 0.0018 33.7 2.8 27 436-462 167-193 (270)
No 1
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.57 E-value=2.9e-15 Score=121.15 Aligned_cols=50 Identities=42% Similarity=0.651 Sum_probs=46.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hh---HHHHHHhC-CC-CHHHHHHHHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALKLYGR-AW---QRIEEHIG-TK-KAVQIRSHAQKFFSK 71 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGr-dW---KkIAe~Vg-TR-T~~QVRSHAQKYF~K 71 (659)
+.+..||+|||++||+||+.||+ +| ++|+++++ ++ |..||+||+||||+|
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 46789999999999999999999 99 99999765 78 999999999999986
No 2
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.36 E-value=1.2e-12 Score=100.06 Aligned_cols=45 Identities=42% Similarity=0.786 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHhChh-hHHHHHHhC-CCCHHHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKLYGRA-WQRIEEHIG-TKKAVQIRSHAQKF 68 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~YGrd-WKkIAe~Vg-TRT~~QVRSHAQKY 68 (659)
++.||+||+++|++||++||.+ |+.||.+|+ +||..||++|+++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 5789999999999999999997 999999999 99999999999987
No 3
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.96 E-value=1e-09 Score=79.63 Aligned_cols=46 Identities=30% Similarity=0.653 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC-hhhHHHHHHhCCCCHHHHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKLYG-RAWQRIEEHIGTKKAVQIRSHAQKFF 69 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~YG-rdWKkIAe~VgTRT~~QVRSHAQKYF 69 (659)
+..||++|+.+|+.+++.|| .+|..|++++++||..||+.++..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 36799999999999999999 89999999999999999999987764
No 4
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.95 E-value=1.4e-09 Score=78.03 Aligned_cols=44 Identities=34% Similarity=0.686 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHHHhC-hhhHHHHHHhCCCCHHHHHHHHHHHH
Q 006139 26 RWTEEEHNRFLEALKLYG-RAWQRIEEHIGTKKAVQIRSHAQKFF 69 (659)
Q Consensus 26 ~WTeEEHelFLEgLe~YG-rdWKkIAe~VgTRT~~QVRSHAQKYF 69 (659)
.||.+|+++|+.+++.|| .+|..|++++++||..||+.|+++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 79999999999999999999987763
No 5
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.92 E-value=7.8e-11 Score=119.83 Aligned_cols=100 Identities=32% Similarity=0.313 Sum_probs=89.4
Q ss_pred cccccccccCCCcccccCCCC-CCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhhhcCCCCC
Q 006139 6 SGEDLVLKTRKPYTITKQRER-WTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEALSKGVPIG 84 (659)
Q Consensus 6 ~ge~~~~K~RKPytitk~r~~-WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k~~~~~g~~~g 84 (659)
.+++..++++|+|.+...+.+ ||.+||+.|.++|..|++.|++|-+|++.++.+|+|.|+|+||-++.+.. .+
T Consensus 34 ~~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~~------~~ 107 (335)
T KOG0724|consen 34 WTEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKSD------TS 107 (335)
T ss_pred hHHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCccc------cc
Confidence 466778999999999987655 99999999999999998899999999999999999999999999998764 24
Q ss_pred ccccccCCCCCCCCCCCCCCCCCCCCC
Q 006139 85 QAIDIDIPPPRPKRKPRNPYPRKTCTN 111 (659)
Q Consensus 85 ~~~~I~iPpPRPKRkps~PYPrK~~~g 111 (659)
..+.+.+|++++++++.+|||++...+
T Consensus 108 ~~~~~~~~~~~~~~k~~~~y~~~~~~~ 134 (335)
T KOG0724|consen 108 LAEVEEFYNFWPKFKSWRQYPQKDEPD 134 (335)
T ss_pred cccccccCCccccccccccCCCCCCcc
Confidence 556788999999999999999997654
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.74 E-value=1.3e-08 Score=80.13 Aligned_cols=42 Identities=38% Similarity=0.790 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHH
Q 006139 27 WTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKF 68 (659)
Q Consensus 27 WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKY 68 (659)
||+||.++++++++.||.+|+.||+++|.||+.||+.++.++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~ 42 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNH 42 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999997764
No 7
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.26 E-value=1.5e-06 Score=88.55 Aligned_cols=61 Identities=21% Similarity=0.397 Sum_probs=50.5
Q ss_pred ccccccCCCcc--cccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhC-CCCHHHHHHHHHHHH
Q 006139 9 DLVLKTRKPYT--ITKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIG-TKKAVQIRSHAQKFF 69 (659)
Q Consensus 9 ~~~~K~RKPyt--itk~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~Vg-TRT~~QVRSHAQKYF 69 (659)
+.+.+.+.|.- ....+++||.||++++++++++||. +|+.||..++ +||..|||-++.+|+
T Consensus 8 ~~~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 8 KPVSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CCCCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh
Confidence 34555555533 2456889999999999999999996 8999999986 899999999998886
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.23 E-value=3.8e-06 Score=85.65 Aligned_cols=53 Identities=21% Similarity=0.310 Sum_probs=47.3
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHH
Q 006139 21 TKQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLE 73 (659)
Q Consensus 21 tk~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~ 73 (659)
..+++.||+||.+++++..+.||..|..||.+|+.||..||+.|+..++.|..
T Consensus 75 ~I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l 127 (249)
T PLN03212 75 SVKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKL 127 (249)
T ss_pred hcccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHH
Confidence 35688999999999999999999999999999999999999999876655543
No 9
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.22 E-value=1.3e-06 Score=95.22 Aligned_cols=61 Identities=33% Similarity=0.617 Sum_probs=49.6
Q ss_pred cccCCCccccc--CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 006139 12 LKTRKPYTITK--QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (659)
Q Consensus 12 ~K~RKPytitk--~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k~~ 76 (659)
+.--||.++.- ....||.+|-.++|||++.||.+|.+||.||||||+.||.-| |..|.-+.
T Consensus 265 ssDf~~v~~~~~~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~----FL~LPieD 327 (531)
T COG5259 265 SSDFKPVTISLLIRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILH----FLQLPIED 327 (531)
T ss_pred cccchhhhhhcccccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHH----HHcCCcch
Confidence 33445555543 344899999999999999999999999999999999999999 66665443
No 10
>PLN03091 hypothetical protein; Provisional
Probab=98.15 E-value=2.1e-06 Score=93.12 Aligned_cols=53 Identities=19% Similarity=0.515 Sum_probs=46.5
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhC-CCCHHHHHHHHHHHHH
Q 006139 18 YTITKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIG-TKKAVQIRSHAQKFFS 70 (659)
Q Consensus 18 ytitk~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~Vg-TRT~~QVRSHAQKYF~ 70 (659)
|+....+++||.||++++++++++||. +|+.||.+++ +||..|||-++.+|+.
T Consensus 8 ~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLd 62 (459)
T PLN03091 8 YKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLR 62 (459)
T ss_pred cCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccC
Confidence 334556789999999999999999997 8999999886 8999999999988763
No 11
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.06 E-value=5.3e-06 Score=91.50 Aligned_cols=53 Identities=36% Similarity=0.663 Sum_probs=48.2
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 006139 20 ITKQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (659)
Q Consensus 20 itk~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k~~ 76 (659)
....+..||++|-.++|+||+.||.+|.+|+.|||+||..||-.| |++|....
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~k----FL~LPieD 301 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILK----FLRLPIED 301 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHH----HHhcCccc
Confidence 356788999999999999999999999999999999999999999 77776654
No 12
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.05 E-value=4.7e-06 Score=90.13 Aligned_cols=59 Identities=37% Similarity=0.666 Sum_probs=51.1
Q ss_pred ccCCCccccc------CCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHH
Q 006139 13 KTRKPYTITK------QRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSK 71 (659)
Q Consensus 13 K~RKPytitk------~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~K 71 (659)
+.--||.+-. -...||.+|.-+||+|++.||= +|..||+||||||..+|+.|.-|+|..
T Consensus 55 ~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 55 QNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVN 120 (438)
T ss_pred CCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhc
Confidence 4455666533 3568999999999999999997 999999999999999999999999875
No 13
>PLN03091 hypothetical protein; Provisional
Probab=98.01 E-value=1.8e-05 Score=86.06 Aligned_cols=53 Identities=17% Similarity=0.364 Sum_probs=47.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
..++.||.||.+++|+..++||..|.+||.+|+.||..||+.|+...++|..+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999999999999999999999998876665444
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.45 E-value=0.00012 Score=72.86 Aligned_cols=47 Identities=17% Similarity=0.364 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhC-CCCHHHHHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKLYGR-AWQRIEEHIG-TKKAVQIRSHAQKFFS 70 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~YGr-dWKkIAe~Vg-TRT~~QVRSHAQKYF~ 70 (659)
+++||.||++++++-++.||. .|..|+..+| .|+..|||-++-.|+.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLr 57 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLR 57 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccC
Confidence 799999999999999999997 7999999999 9999999999988853
No 15
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.39 E-value=0.00037 Score=74.05 Aligned_cols=48 Identities=29% Similarity=0.613 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHH
Q 006139 23 QRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFS 70 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~ 70 (659)
..+.|+.+|..+|+++++-.|- +|..||.|||.|+...|++|.-||+.
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 3568999999999999999998 99999999999999999999999887
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.18 E-value=0.00095 Score=66.63 Aligned_cols=47 Identities=17% Similarity=0.417 Sum_probs=43.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKF 68 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKY 68 (659)
..++.||+||.++.+++-.+||-.|..||.++++||.-.|+.|+--.
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~ 106 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTH 106 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHH
Confidence 45899999999999999999999999999999999999999998433
No 17
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.17 E-value=0.00097 Score=72.02 Aligned_cols=85 Identities=29% Similarity=0.343 Sum_probs=61.5
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh---hhHHHHHH--hCCCCHHHHHHHHHHHHHHHHHHhhhc---CCCCCccccccCC
Q 006139 21 TKQRERWTEEEHNRFLEALKLYGR---AWQRIEEH--IGTKKAVQIRSHAQKFFSKLEKEALSK---GVPIGQAIDIDIP 92 (659)
Q Consensus 21 tk~r~~WTeEEHelFLEgLe~YGr---dWKkIAe~--VgTRT~~QVRSHAQKYF~KL~k~~~~~---g~~~g~~~~I~iP 92 (659)
.|.|-+||.|=|++|++|++..|- -=|+|-++ |..=|..+|+||-|||...+++..... +.-.........|
T Consensus 234 KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~swt~kr~~~~~P 313 (526)
T PLN03162 234 KKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWTHRRAYTQAP 313 (526)
T ss_pred CCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhccchhhhhhccCC
Confidence 357789999999999999999994 46788876 567899999999999999887543221 1111122223345
Q ss_pred CCCCCCCCCCCCC
Q 006139 93 PPRPKRKPRNPYP 105 (659)
Q Consensus 93 pPRPKRkps~PYP 105 (659)
.+|-+|+..+||-
T Consensus 314 ~~rs~~~~g~p~~ 326 (526)
T PLN03162 314 WPRSSRRDGLPYL 326 (526)
T ss_pred cccCCCCCCCccc
Confidence 6777777777764
No 18
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=97.00 E-value=0.0031 Score=68.18 Aligned_cols=58 Identities=22% Similarity=0.487 Sum_probs=45.8
Q ss_pred cCCCccc---ccCCCCCCHHHHHHHHHHHHHhChhhHHHHH-HhCCCCHHHHHHHHHHHHHHHHH
Q 006139 14 TRKPYTI---TKQRERWTEEEHNRFLEALKLYGRAWQRIEE-HIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 14 ~RKPyti---tk~r~~WTeEEHelFLEgLe~YGrdWKkIAe-~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
.|+++.. +..-..|+++|-+.|.+||++|||++-.|.. -|.||++..|-.+ ||++-+.
T Consensus 264 rr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVey---YYlWKkS 325 (445)
T KOG4329|consen 264 RRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEY---YYLWKKS 325 (445)
T ss_pred HhcCCcceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHH---HHHhhcC
Confidence 3444443 3444589999999999999999999999988 6999999999877 5555433
No 19
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.09 E-value=0.0082 Score=68.69 Aligned_cols=48 Identities=21% Similarity=0.510 Sum_probs=43.2
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHH
Q 006139 21 TKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKF 68 (659)
Q Consensus 21 tk~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKY 68 (659)
....++||++|+-+++.|+.+||. +|-+|-+.|+.|+..|||.++-+.
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 356789999999999999999985 999999999999999999995444
No 20
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=95.26 E-value=0.025 Score=64.33 Aligned_cols=52 Identities=21% Similarity=0.537 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhChhhHHH----------HHHhCCCCHHHHHHHHHHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKLYGRAWQRI----------EEHIGTKKAVQIRSHAQKFFSKLEKE 75 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~YGrdWKkI----------Ae~VgTRT~~QVRSHAQKYF~KL~k~ 75 (659)
+..||-.|.+-|..||++||+|+.+| -.-+..||.-|||.|+-+...++.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~ 149 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKL 149 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhh
Confidence 67999999999999999999999999 33466789999999976555555443
No 21
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.21 E-value=0.081 Score=44.14 Aligned_cols=50 Identities=26% Similarity=0.561 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHHHH------hC---h-----hhHHHHHHhC----CCCHHHHHHHHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKL------YG---R-----AWQRIEEHIG----TKKAVQIRSHAQKFFSKLE 73 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~------YG---r-----dWKkIAe~Vg----TRT~~QVRSHAQKYF~KL~ 73 (659)
|..||++|...||+.+.. |+ . -|+.||+.+. .||+.||+..+.....+-.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 457999999999999887 32 1 5999999653 6999999999665443333
No 22
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=94.15 E-value=0.072 Score=61.39 Aligned_cols=46 Identities=30% Similarity=0.609 Sum_probs=41.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHH
Q 006139 23 QRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKF 68 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKY 68 (659)
..++||-.|++++++++++||. .|-+||.++|.||..|.++.-..+
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~ 457 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRL 457 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHH
Confidence 4679999999999999999999 899999999999999987764433
No 23
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=94.03 E-value=0.094 Score=57.44 Aligned_cols=50 Identities=30% Similarity=0.557 Sum_probs=43.8
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 006139 21 TKQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 21 tk~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
.+...+||.+|-++|..||..+|-++..|+.++++|...||+.. |++-.|
T Consensus 362 ~~~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaK----fi~Eek 411 (507)
T COG5118 362 KKGALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAK----FIKEEK 411 (507)
T ss_pred CCCCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHH----HHHHhh
Confidence 35567999999999999999999999999999999999999876 555444
No 24
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=93.80 E-value=0.11 Score=62.54 Aligned_cols=48 Identities=23% Similarity=0.528 Sum_probs=44.7
Q ss_pred CCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 006139 25 ERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSKL 72 (659)
Q Consensus 25 ~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~KL 72 (659)
..||..+-..|+.|.++||| +..+||..|++||..+|+-|++-|+.+.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~ 873 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERY 873 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhh
Confidence 46999999999999999999 8999999999999999999999888663
No 25
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=92.96 E-value=0.17 Score=59.00 Aligned_cols=48 Identities=19% Similarity=0.378 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHH
Q 006139 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLE 73 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~ 73 (659)
....||..|..+|-+||-.|-+|+..|+..|.+||+.||--+ ||.+-+
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVey---YYtWKK 665 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEY---YYTWKK 665 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHH---HHHHHH
Confidence 456999999999999999999999999999999999999877 555443
No 26
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=92.13 E-value=0.17 Score=57.91 Aligned_cols=48 Identities=27% Similarity=0.542 Sum_probs=41.1
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hh-------C------------hhhHHHHHHhCCCCHHHHHHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALK-------LY-------G------------RAWQRIEEHIGTKKAVQIRSHAQKFF 69 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe-------~Y-------G------------rdWKkIAe~VgTRT~~QVRSHAQKYF 69 (659)
..+++||-||.+++|..++ .| | -.|..|++.+|||+..|||.|+.|..
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~ 507 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLT 507 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHH
Confidence 3789999999999999996 44 2 15999999999999999999987663
No 27
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=91.95 E-value=0.1 Score=53.98 Aligned_cols=57 Identities=28% Similarity=0.379 Sum_probs=50.2
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHH-HhCCCCHHHHHHHHH-----HHHHHHHHHhh
Q 006139 21 TKQRERWTEEEHNRFLEALKLYGR-AWQRIEE-HIGTKKAVQIRSHAQ-----KFFSKLEKEAL 77 (659)
Q Consensus 21 tk~r~~WTeEEHelFLEgLe~YGr-dWKkIAe-~VgTRT~~QVRSHAQ-----KYF~KL~k~~~ 77 (659)
.+.+..|+..+|.+|+.++..||+ +|.+|.+ ++..|++.|+.+|+| +||.+......
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~ 224 (335)
T KOG0724|consen 161 RRKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEE 224 (335)
T ss_pred hhccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhcc
Confidence 355679999999999999999999 9999998 688999999999999 89888855543
No 28
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=91.64 E-value=0.33 Score=53.32 Aligned_cols=55 Identities=27% Similarity=0.382 Sum_probs=43.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHhC---h-------------hhHHHHHHhC-----CCCHHHHHHHHHHHHHHHHHHh
Q 006139 22 KQRERWTEEEHNRFLEALKLYG---R-------------AWQRIEEHIG-----TKKAVQIRSHAQKFFSKLEKEA 76 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YG---r-------------dWKkIAe~Vg-----TRT~~QVRSHAQKYF~KL~k~~ 76 (659)
-..+.|+++=.+.|+|||..|. | +=..||+||. |||..||-||-|=+-++..|.-
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~rei 149 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREI 149 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHH
Confidence 3457999999999999999874 2 2457999985 8999999999997766655543
No 29
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=91.55 E-value=0.24 Score=56.78 Aligned_cols=50 Identities=24% Similarity=0.560 Sum_probs=44.2
Q ss_pred ccccc-CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHH
Q 006139 18 YTITK-QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKF 68 (659)
Q Consensus 18 ytitk-~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKY 68 (659)
|++-. .++.||+||.+.+......+|.+|+.|+..|| |.+.=||.++..|
T Consensus 377 y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~ 427 (607)
T KOG0051|consen 377 YTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQY 427 (607)
T ss_pred CCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHh
Confidence 34444 89999999999999999999999999999998 6788899998876
No 30
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=91.36 E-value=0.96 Score=37.50 Aligned_cols=52 Identities=25% Similarity=0.484 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHHHHh-----C------------hhhHHHHHHh-----CCCCHHHHHHHHHHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKLY-----G------------RAWQRIEEHI-----GTKKAVQIRSHAQKFFSKLEKE 75 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~Y-----G------------rdWKkIAe~V-----gTRT~~QVRSHAQKYF~KL~k~ 75 (659)
...||.+|-+.+++-|+.| | +.|..|+..+ +.||..|++-.++++-..+++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999987 3 1599999843 3699999999998887666654
No 31
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=91.32 E-value=0.22 Score=56.24 Aligned_cols=50 Identities=22% Similarity=0.466 Sum_probs=45.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSK 71 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~K 71 (659)
..++.|+.-|++-+--|+.+||+ .|.+|+..+..+|+.||+..|.+|..-
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp 55 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDP 55 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCH
Confidence 46789999999999999999998 799999999999999999999888643
No 32
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=90.54 E-value=0.69 Score=52.13 Aligned_cols=43 Identities=30% Similarity=0.504 Sum_probs=36.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHH-HhCCCCHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEE-HIGTKKAVQIRSH 64 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGrdWKkIAe-~VgTRT~~QVRSH 64 (659)
-..+-|+..|-.+|.|||++||+|+..|-. |++=|+..-|--+
T Consensus 283 DemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIvey 326 (693)
T KOG3554|consen 283 DEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEY 326 (693)
T ss_pred hhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHH
Confidence 345689999999999999999999999965 8888887666555
No 33
>smart00426 TEA TEA domain.
Probab=89.59 E-value=0.31 Score=42.12 Aligned_cols=43 Identities=30% Similarity=0.455 Sum_probs=34.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCh-h-h--------------HHHHHHhC-----CCCHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKLYGR-A-W--------------QRIEEHIG-----TKKAVQIRSHAQ 66 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~YGr-d-W--------------KkIAe~Vg-----TRT~~QVRSHAQ 66 (659)
.+.|.++=...|++||+.|-. . + .-|++||- .||..||-||-|
T Consensus 3 ~~vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQ 66 (68)
T smart00426 3 EGVWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQ 66 (68)
T ss_pred CCcCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhe
Confidence 468999999999999999864 1 1 24677653 599999999977
No 34
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=85.90 E-value=1.7 Score=48.88 Aligned_cols=43 Identities=16% Similarity=0.436 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHH
Q 006139 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHA 65 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHA 65 (659)
.-..||.||--||..++..||+++.+|-..++-|+..-++-++
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY 228 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH
Confidence 3468999999999999999999999999999999988887664
No 35
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=83.68 E-value=1 Score=49.77 Aligned_cols=48 Identities=27% Similarity=0.407 Sum_probs=32.9
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh----hh----------HHHHHHhC-----CCCHHHHHHHHHHH
Q 006139 21 TKQRERWTEEEHNRFLEALKLYGR----AW----------QRIEEHIG-----TKKAVQIRSHAQKF 68 (659)
Q Consensus 21 tk~r~~WTeEEHelFLEgLe~YGr----dW----------KkIAe~Vg-----TRT~~QVRSHAQKY 68 (659)
....+.|+++=...|++||+.|.. .| +.|++||. +||..||.||-|-.
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 356789999999999999999852 22 35788764 69999999999965
No 36
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=83.01 E-value=7.1 Score=42.47 Aligned_cols=58 Identities=19% Similarity=0.412 Sum_probs=48.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHh-Ch---hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhhhc
Q 006139 22 KQRERWTEEEHNRFLEALKLY-GR---AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEALSK 79 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~Y-Gr---dWKkIAe~VgTRT~~QVRSHAQKYF~KL~k~~~~~ 79 (659)
.....||..|.+.+|.+|+.- |. |-..|+..|.+|+..+|+..-|+.-.++.++.+.+
T Consensus 19 ~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvareaiqk 80 (344)
T PF11035_consen 19 TGPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAREAIQK 80 (344)
T ss_pred CCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 445699999999999999865 55 55567778999999999999998888888887654
No 37
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=81.65 E-value=4.1 Score=38.03 Aligned_cols=57 Identities=21% Similarity=0.498 Sum_probs=43.0
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHhCh----hhHHHHH------------HhCCCCHHHHHHHHHHHHHHHHH
Q 006139 18 YTITKQRERWTEEEHNRFLEALKLYGR----AWQRIEE------------HIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 18 ytitk~r~~WTeEEHelFLEgLe~YGr----dWKkIAe------------~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
|..+..+..||++|+.-.|-.|-+||- .|.+|-+ |+.+||+..|.-++.-...-+.|
T Consensus 43 y~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 43 YPPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp STSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred cCCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 555677889999999999999999997 7999854 35699999999998855444443
No 38
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=81.41 E-value=0.93 Score=51.32 Aligned_cols=59 Identities=14% Similarity=0.267 Sum_probs=49.6
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 006139 16 KPYTITKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 16 KPytitk~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
|++......+.|+..|++..+-+++.||. .|.+||..++.||..||+.|+-.|.....+
T Consensus 12 ~~~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk 71 (512)
T COG5147 12 KLMQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLK 71 (512)
T ss_pred ccccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcc
Confidence 44555667789999999999999999998 899999988889999999999666555443
No 39
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=74.72 E-value=13 Score=31.40 Aligned_cols=43 Identities=26% Similarity=0.495 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHHh---C----------hhhHHHHHHh----C-CCCHHHHHHHHHHH
Q 006139 26 RWTEEEHNRFLEALKLY---G----------RAWQRIEEHI----G-TKKAVQIRSHAQKF 68 (659)
Q Consensus 26 ~WTeEEHelFLEgLe~Y---G----------rdWKkIAe~V----g-TRT~~QVRSHAQKY 68 (659)
.||+++.+.||+.|... | ..|+.|++.+ | ..|..||++|.+.+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999999653 1 1599998743 3 46899999996644
No 40
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=73.86 E-value=4.1 Score=46.38 Aligned_cols=53 Identities=21% Similarity=0.406 Sum_probs=46.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
..+..|+.||.+..+..-+.+|-.|..|+.+|+.||..||-..+.+-+..+..
T Consensus 70 lk~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred cccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 46778999999999999999999999999999999999998887766655554
No 41
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=64.60 E-value=32 Score=36.24 Aligned_cols=56 Identities=23% Similarity=0.462 Sum_probs=44.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC----------hhhHHHHH---HhC-CCCHHHHHHHHHHHHHHHHHHhhhc
Q 006139 24 RERWTEEEHNRFLEALKLYG----------RAWQRIEE---HIG-TKKAVQIRSHAQKFFSKLEKEALSK 79 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~YG----------rdWKkIAe---~Vg-TRT~~QVRSHAQKYF~KL~k~~~~~ 79 (659)
...|+.+|-..||++..... ..|..||+ ..| -||+.||+....+...+.++.....
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~ 123 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKK 123 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 57899999999999877532 25999998 244 5999999999988877777766543
No 42
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=63.74 E-value=14 Score=42.12 Aligned_cols=61 Identities=8% Similarity=0.024 Sum_probs=51.1
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 006139 16 KPYTITKQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (659)
Q Consensus 16 KPytitk~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k~~ 76 (659)
-|-.+-+.+.+||.+|..+.+.+|++||++..-|.-.||.++..|+..-.-.|-++..-.+
T Consensus 361 ipes~c~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~mfea 421 (534)
T KOG1194|consen 361 IPESTCRMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQMFEA 421 (534)
T ss_pred CCchhhhhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHHHHH
Confidence 3444446678999999999999999999999999999999999999988777766655544
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=63.26 E-value=7.8 Score=44.54 Aligned_cols=47 Identities=23% Similarity=0.538 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHH
Q 006139 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFS 70 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~ 70 (659)
++.-|+.||++++|.+.+++..-|..|+..|| ||..||--+..+..-
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ll~ 104 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNLLD 104 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHHHH
Confidence 46789999999999999999999999999987 899999998776543
No 44
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=62.62 E-value=13 Score=44.75 Aligned_cols=60 Identities=23% Similarity=0.467 Sum_probs=50.9
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 006139 16 KPYTITKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (659)
Q Consensus 16 KPytitk~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~KL~k~~ 76 (659)
|+.-.+..-..||+.+-..|+.|-++||| +-..|+.-|-. |+..|..+|.-||.++++..
T Consensus 787 k~~ll~~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~ 847 (971)
T KOG0385|consen 787 KEELLSQGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELS 847 (971)
T ss_pred hhhhhhccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhh
Confidence 33334455567999999999999999999 89999998766 99999999999999988754
No 45
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=56.84 E-value=7.2 Score=45.12 Aligned_cols=43 Identities=21% Similarity=0.407 Sum_probs=39.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHH
Q 006139 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSH 64 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSH 64 (659)
....+|+.+|-++|-.+|..+|-+..-|+...+.|+..|||--
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K 449 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAK 449 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHH
Confidence 3467999999999999999999999999999999999999854
No 46
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=49.36 E-value=33 Score=29.19 Aligned_cols=47 Identities=26% Similarity=0.379 Sum_probs=29.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCh---------hhHHHHHHhC-CCCHHHHHHHHHHHHH
Q 006139 24 RERWTEEEHNRFLEALKLYGR---------AWQRIEEHIG-TKKAVQIRSHAQKFFS 70 (659)
Q Consensus 24 r~~WTeEEHelFLEgLe~YGr---------dWKkIAe~Vg-TRT~~QVRSHAQKYF~ 70 (659)
|...|.||+..+++-|+.+.+ -|+.+++.-. ..|..=.|.|+-|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~ 58 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLR 58 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence 456789999999999976532 4999999544 7888888888655543
No 47
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=48.37 E-value=31 Score=34.57 Aligned_cols=48 Identities=15% Similarity=0.250 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-hhHHHHHH--hC---CCCHHHHHHHHHHHHH
Q 006139 23 QRERWTEEEHNRFLEALKLYGR-AWQRIEEH--IG---TKKAVQIRSHAQKFFS 70 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGr-dWKkIAe~--Vg---TRT~~QVRSHAQKYF~ 70 (659)
....||.||+.++-+-+-.|++ .=.+++.| +| .||+.+|..+|--+..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~rt~aac~fRwNs~vr 57 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALKRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhhhHHHHHhHHHHHHH
Confidence 4568999999999999999987 44455543 33 6999999999955444
No 48
>COG4425 Predicted membrane protein [Function unknown]
Probab=44.72 E-value=22 Score=40.80 Aligned_cols=50 Identities=30% Similarity=0.312 Sum_probs=38.5
Q ss_pred HHHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHc
Q 006139 391 AAHAAASFAATFWPYTNMETSADSPTCPQGGFLSRQMSSPPSMAAIAAATVAAATAWWAAH 451 (659)
Q Consensus 391 AaHAAAsfAASfWP~an~e~s~ds~~~~~~~~~~r~~~SpPSmAAIaAATVAAAsAWWAah 451 (659)
+-|+|+.|+-.-|+|-+...|+.-+ .|-+ =..+|||+|.+|..++|||+|
T Consensus 87 ~Gy~~gv~~~wl~~y~elp~~s~~~--------~R~~---~~~~ai~~~~~a~~fl~qa~~ 136 (588)
T COG4425 87 AGYGAGVFLHWLWRYLELPESSPRP--------PRWA---KPAAAIVGAAGAVGFLVQAAV 136 (588)
T ss_pred hhhHHHHHHHHHHHHhhCCCCCCCC--------cchh---hhHHHHHHHHHHHHHHHHHHH
Confidence 5699999999999999886544332 2222 236899999999999999997
No 49
>KOG1019 consensus Retinoblastoma pathway protein LIN-9/chromatin-associated protein Aly [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=43.22 E-value=12 Score=44.80 Aligned_cols=61 Identities=25% Similarity=0.440 Sum_probs=49.3
Q ss_pred CCcccccccccCCCcccccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHh-CCCCHHHHHHH
Q 006139 4 YSSGEDLVLKTRKPYTITKQRERWTEEEHNRFLEALKLYGRAWQRIEEHI-GTKKAVQIRSH 64 (659)
Q Consensus 4 ~~~ge~~~~K~RKPytitk~r~~WTeEEHelFLEgLe~YGrdWKkIAe~V-gTRT~~QVRSH 64 (659)
++++.-...+-||+....+-.-.|+..|-++|.++..+||+.|++.+..+ ++|...+|..-
T Consensus 24 ~~~~~~sKt~qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~~vell 85 (837)
T KOG1019|consen 24 YDSGSTSKTPQRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSNMVELL 85 (837)
T ss_pred ccccccccCCCCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhhHHHHH
Confidence 34555566677777777777889999999999999999999999999876 45888777643
No 50
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=43.14 E-value=37 Score=33.91 Aligned_cols=53 Identities=21% Similarity=0.297 Sum_probs=40.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-------hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 006139 23 QRERWTEEEHNRFLEALKLYGR-------AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGr-------dWKkIAe~VgTRT~~QVRSHAQKYF~KL~k~~ 76 (659)
....||.||+.++-+.+-.|=| .+..++..+ +||+.=|..+|-.|..|.-..+
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 4568999999999999999854 344444444 5999999999998877654443
No 51
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=42.60 E-value=1.2e+02 Score=37.80 Aligned_cols=55 Identities=15% Similarity=0.348 Sum_probs=45.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hhHHHHH------------HhCCCCHHHHHHHHHHHHHHHHHHh
Q 006139 22 KQRERWTEEEHNRFLEALKLYGR-AWQRIEE------------HIGTKKAVQIRSHAQKFFSKLEKEA 76 (659)
Q Consensus 22 k~r~~WTeEEHelFLEgLe~YGr-dWKkIAe------------~VgTRT~~QVRSHAQKYF~KL~k~~ 76 (659)
.++..||+||++.+|-.|-+||- .|.+|-. |+.+||+..|.-++.-...-+.|+.
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e~ 991 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKEN 991 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHHH
Confidence 34557999999999999999996 7999943 4569999999999987777777663
No 52
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=42.08 E-value=72 Score=27.27 Aligned_cols=41 Identities=22% Similarity=0.501 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhC-------hhhHHHHHHhCCC---C--HHHHHHHHHHHHHHH
Q 006139 32 HNRFLEALKLYG-------RAWQRIEEHIGTK---K--AVQIRSHAQKFFSKL 72 (659)
Q Consensus 32 HelFLEgLe~YG-------rdWKkIAe~VgTR---T--~~QVRSHAQKYF~KL 72 (659)
+.+|....+.-| +.|..|++.+|-- + ..+++.|..+|+...
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~f 91 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLPF 91 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHHH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHhh
Confidence 345554444444 2699999987632 2 478999999987643
No 53
>COG0315 MoaC Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]
Probab=41.75 E-value=22 Score=35.35 Aligned_cols=27 Identities=33% Similarity=0.535 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 436 IAAATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 436 IaAATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
|++|=+|+..|==-+.-|+|||-||+.
T Consensus 55 l~tAriAgimaaKkT~elIPlCHpi~l 81 (157)
T COG0315 55 LATARIAGIMAAKRTSELIPLCHPLPL 81 (157)
T ss_pred HHHHHHHHHHHhhhhhhhCccCCCCcc
Confidence 555666666666677799999999654
No 54
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=41.32 E-value=42 Score=30.80 Aligned_cols=38 Identities=16% Similarity=0.442 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHHHhCC----CCHHHHHHHHHHH
Q 006139 28 TEEEHNRFLEALKLYGRAWQRIEEHIGT----KKAVQIRSHAQKF 68 (659)
Q Consensus 28 TeEEHelFLEgLe~YGrdWKkIAe~VgT----RT~~QVRSHAQKY 68 (659)
|.++.+.|-+. .|++||++++.+|- =|..+|..-+.+|
T Consensus 1 ~~~~~q~~~~n---vGr~WK~laR~Lg~~cral~d~~ID~I~~~y 42 (90)
T cd08780 1 TPADQQHFAKS---VGKKWKPVGRSLQKNCRALRDPAIDNLAYEY 42 (90)
T ss_pred CHHHHHHHHHH---HhHHHHHHHHHHcccccccchhHHHHHHhhc
Confidence 45666666654 48999999999992 2445555554444
No 55
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=40.80 E-value=71 Score=28.86 Aligned_cols=40 Identities=18% Similarity=0.351 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHHHHh----Ch----hhHHHHHHhCCC-----CHHHHHHH
Q 006139 25 ERWTEEEHNRFLEALKLY----GR----AWQRIEEHIGTK-----KAVQIRSH 64 (659)
Q Consensus 25 ~~WTeEEHelFLEgLe~Y----Gr----dWKkIAe~VgTR-----T~~QVRSH 64 (659)
..||+|+.-.+|+||-.| |+ +|..+-++|... |..|+..-
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~K 57 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDK 57 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHH
Confidence 469999999999999998 73 788887777544 55555443
No 56
>smart00595 MADF subfamily of SANT domain.
Probab=39.75 E-value=66 Score=27.02 Aligned_cols=25 Identities=20% Similarity=0.469 Sum_probs=20.8
Q ss_pred hhHHHHHHhCCCCHHHHHHHHHHHHH
Q 006139 45 AWQRIEEHIGTKKAVQIRSHAQKFFS 70 (659)
Q Consensus 45 dWKkIAe~VgTRT~~QVRSHAQKYF~ 70 (659)
.|..|++-+|. |+.+|+.++...-.
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~LR~ 53 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHHHH
Confidence 69999999988 99999988865433
No 57
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=36.67 E-value=86 Score=30.96 Aligned_cols=49 Identities=22% Similarity=0.444 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHHHHHhCh---hhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 006139 26 RWTEEEHNRFLEALKLYGR---AWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 26 ~WTeEEHelFLEgLe~YGr---dWKkIAe~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
-.+..+...||.+|-.||- +|+-+-..+..||...|+.|+--|+..|.-
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~aY~~LFm~HL~E 91 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIRAYGSLFMRHLCE 91 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHHHHHHHHHHHhcC
Confidence 4689999999999999996 899998899999999999999877666643
No 58
>PRK12343 putative molybdenum cofactor biosynthesis protein MoaC; Reviewed
Probab=33.31 E-value=40 Score=33.34 Aligned_cols=25 Identities=32% Similarity=0.484 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 438 AATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 438 AATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
+|-+|+-.|==-+.-|||||-|++.
T Consensus 51 ~AriAgi~aAK~T~~LIPlCHPl~l 75 (151)
T PRK12343 51 TARVAGILAVKKTPELIPMCHPIPI 75 (151)
T ss_pred HHHHHHHHHHHhhhhhccCCCCccc
Confidence 3334444444456689999999655
No 59
>cd01420 MoaC_PE MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=32.67 E-value=45 Score=32.55 Aligned_cols=27 Identities=33% Similarity=0.529 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 436 IAAATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 436 IaAATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
++.|-+|+-.|==-+.-|+|||-|++.
T Consensus 41 l~vAriAgI~aaK~T~~LIPlCHpi~l 67 (140)
T cd01420 41 LAVARIAGIMAAKRTSELIPLCHPLPL 67 (140)
T ss_pred HHHHHHHHHHHHHhhhcccccCCCCcc
Confidence 344555555555567799999999644
No 60
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=32.38 E-value=1.5e+02 Score=22.80 Aligned_cols=35 Identities=11% Similarity=0.237 Sum_probs=21.0
Q ss_pred HHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHH
Q 006139 33 NRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKF 68 (659)
Q Consensus 33 elFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKY 68 (659)
...+.-....|..|+.||+.+| .|...|+.+-++=
T Consensus 16 r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ra 50 (54)
T PF08281_consen 16 REIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRRA 50 (54)
T ss_dssp HHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHHH
Confidence 3334444556789999999987 6777777775543
No 61
>PF12451 VPS11_C: Vacuolar protein sorting protein 11 C terminal; InterPro: IPR024763 Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion. This entry represents the C-terminal domain of vps11.
Probab=31.78 E-value=38 Score=27.32 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=24.1
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHHHhCC
Q 006139 28 TEEEHNRFLEALKLYGRAWQRIEEHIGT 55 (659)
Q Consensus 28 TeEEHelFLEgLe~YGrdWKkIAe~VgT 55 (659)
..+.|++|...|+.-...++-|++|+|-
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfGr 44 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFGR 44 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHcc
Confidence 3567999999998777799999999984
No 62
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=30.92 E-value=1.4e+02 Score=25.96 Aligned_cols=44 Identities=18% Similarity=0.410 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhC-------hhhHHHHHHhCC-----CCHHHHHHHHHHHHHHHHHH
Q 006139 32 HNRFLEALKLYG-------RAWQRIEEHIGT-----KKAVQIRSHAQKFFSKLEKE 75 (659)
Q Consensus 32 HelFLEgLe~YG-------rdWKkIAe~VgT-----RT~~QVRSHAQKYF~KL~k~ 75 (659)
..+|..-.+.=| +.|+.|++.+|= ....+++.+.+||....++.
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE~~ 90 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPFERF 90 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHHHH
Confidence 456665444433 269999997653 34688999999998777654
No 63
>TIGR00581 moaC molybdenum cofactor biosynthesis protein MoaC. MoaC catalyzes an early step in molybdenum cofactor biosynthesis in E. coli. The Arabidopsis homolog Cnx3 complements MoaC deficiency in E. coli (MUID:95197640). Eukarotic members of this family branch within the bacterial branch, with the archaeal members as an apparent outgroup. This protein is absent in a number of the pathogens with smaller genomes, including Mycoplasmas, Chlamydias, and spirochetes, but is found in most other complete genomes to date. The homolog form Synechocystis sp. is fused to a MobA-homologous region and is an outlier to all other bacterial forms by both neighbor-joining and UPGMA analyses. Members of this family are well-conserved. The seed for this model excludes both archaeal sequences and the most divergent bacterial sequences, but still finds all candidate MoaC sequences easily between trusted and noise cutoffs. We suggest that sequences branching outside the set that contains all seed members
Probab=30.69 E-value=45 Score=32.78 Aligned_cols=25 Identities=32% Similarity=0.505 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 438 AATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 438 AATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
.|-||+-.|==-+.-|+|||-|++.
T Consensus 54 ~AriAgi~aaK~T~~lIPlCHpi~l 78 (147)
T TIGR00581 54 TARIAGIMAAKRTGDLIPLCHPLPL 78 (147)
T ss_pred HHHHHHHHHHHhhhhhcCCCCCccc
Confidence 3344444444456689999999654
No 64
>cd00528 MoaC MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=30.36 E-value=49 Score=32.17 Aligned_cols=27 Identities=33% Similarity=0.529 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 436 IAAATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 436 IaAATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
++.|-+|+-.|==-+.-|+|||-|++.
T Consensus 41 l~~AriAgI~aaK~T~~LIPlCHpl~l 67 (136)
T cd00528 41 LAVARIAGIMAAKRTSELIPLCHPLPL 67 (136)
T ss_pred HHHHHHHHHHHHHhcccccccCCCCcc
Confidence 344555555555667899999999654
No 65
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=29.84 E-value=1.7e+02 Score=24.97 Aligned_cols=47 Identities=19% Similarity=0.314 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 006139 26 RWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (659)
Q Consensus 26 ~WTeEEHelFLEgLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~KL~k 74 (659)
.+++.|...|..- -..|..++.||+.+|. +...|+.+-++-..+|++
T Consensus 110 ~L~~~~~~ii~~~-~~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLR-YLEGLSYKEIAEILGI-SVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhH-HhcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHh
Confidence 4555555554322 2347799999998886 666777776666666654
No 66
>cd01419 MoaC_A MoaC family, archaeal. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=26.68 E-value=63 Score=31.72 Aligned_cols=26 Identities=31% Similarity=0.492 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 437 AAATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 437 aAATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
+.|-+|+-.|==-+.-|+|||-|++.
T Consensus 42 ~vAriAgI~aaK~T~~LIPlCHpl~l 67 (141)
T cd01419 42 ATARIAGILAVKKTPELIPMCHPIPI 67 (141)
T ss_pred HHHHHHHHHHHHhhhhhccCCCCccc
Confidence 34445555554566789999999644
No 67
>PRK09364 moaC molybdenum cofactor biosynthesis protein MoaC; Provisional
Probab=25.03 E-value=68 Score=31.97 Aligned_cols=24 Identities=33% Similarity=0.531 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 439 ATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 439 ATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
|-+|+..|==-+.-|||||-|++.
T Consensus 58 AriAgi~aaK~T~~LIPlCHpi~i 81 (159)
T PRK09364 58 ARIAGIMAAKRTSDLIPLCHPLML 81 (159)
T ss_pred HHHHHHHHHHhhhhhcccCCCCcc
Confidence 333333443456689999999554
No 68
>PHA00442 host recBCD nuclease inhibitor
Probab=23.89 E-value=42 Score=28.63 Aligned_cols=32 Identities=34% Similarity=0.695 Sum_probs=24.9
Q ss_pred ccCCCCC--------CHHHHHHHHHHHHHhCh-hhHHHHHH
Q 006139 21 TKQRERW--------TEEEHNRFLEALKLYGR-AWQRIEEH 52 (659)
Q Consensus 21 tk~r~~W--------TeEEHelFLEgLe~YGr-dWKkIAe~ 52 (659)
+.-|..| +-|-...||++|+..|- +|..|.+.
T Consensus 9 titRd~wnd~q~yidsLek~~~~L~~Lea~GVDNW~Gy~eA 49 (59)
T PHA00442 9 TITRDAWNDMQGYIDSLEKDNEFLKALRACGVDNWDGYMDA 49 (59)
T ss_pred eecHHHHHHHHHHHHHHHHhhHHHHHHHHcCCcchhhHHHH
Confidence 3446677 45667889999999997 89988764
No 69
>PF03187 Corona_I: Corona nucleocapsid I protein; InterPro: IPR004876 Members of this family are Coronavirus proteins that are located in the nucleocapsid. They have no known function.
Probab=21.98 E-value=53 Score=33.66 Aligned_cols=27 Identities=37% Similarity=0.429 Sum_probs=21.5
Q ss_pred HhhhhhhhhhhccccchHHHHHHhhhhc
Q 006139 629 EVLVMHVRGGWLFKHSSLERYCLKAFHL 656 (659)
Q Consensus 629 eeGR~AF~aLF~~~~~~~~~~~~~~~~~ 656 (659)
-.|-.+|--||+..- .+-|||||||-|
T Consensus 144 ~~Gtq~~mrLflLG~-R~vRycLka~mL 170 (207)
T PF03187_consen 144 LKGTQVAMRLFLLGF-RLVRYCLKAFML 170 (207)
T ss_pred HHHHHHHHHHHHhhh-hHHHHHHHHHHH
Confidence 368889999998754 478999999854
No 70
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=21.15 E-value=1.8e+02 Score=23.52 Aligned_cols=31 Identities=19% Similarity=0.416 Sum_probs=23.1
Q ss_pred hhHHHHHHhCC-CCHHHHHHHHHHHHHHHHHH
Q 006139 45 AWQRIEEHIGT-KKAVQIRSHAQKFFSKLEKE 75 (659)
Q Consensus 45 dWKkIAe~VgT-RT~~QVRSHAQKYF~KL~k~ 75 (659)
.|..|+..++. -++.+|+.+++....+..++
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~ 59 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYRRE 59 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHHHH
Confidence 69999999885 46788888887665554444
No 71
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=20.61 E-value=1.9e+02 Score=28.04 Aligned_cols=46 Identities=15% Similarity=0.242 Sum_probs=37.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhC----CCCHHHHHHHHHHH
Q 006139 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIG----TKKAVQIRSHAQKF 68 (659)
Q Consensus 23 ~r~~WTeEEHelFLEgLe~YGrdWKkIAe~Vg----TRT~~QVRSHAQKY 68 (659)
...+=|..|.+-....|++||.|++.++.-.. -.|+.||+--..+|
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 34456778888888888999999999998544 48999999887766
No 72
>PLN02375 molybderin biosynthesis protein CNX3
Probab=20.45 E-value=83 Score=33.68 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 006139 436 IAAATVAAATAWWAAHGLLPLCAPFHA 462 (659)
Q Consensus 436 IaAATVAAAsAWWAahGLLPlcaP~~~ 462 (659)
++.|-||+-.|==-|.-|+|||-|++.
T Consensus 167 LavArIAGImAAKkTseLIPLCHPLpL 193 (270)
T PLN02375 167 LGVAKIAGINGAKQTSSLIPLCHNIAL 193 (270)
T ss_pred HHHHHHHHHHHhhccccccccCCCccc
Confidence 445555555555667899999999644
Done!