Query 019067
Match_columns 346
No_of_seqs 214 out of 728
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:24:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019067.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019067hhsearch_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 1.9E-15 4.1E-20 114.2 6.1 50 77-126 1-56 (57)
2 KOG0724 Zuotin and related mol 99.5 2.7E-16 6E-21 149.8 -2.6 250 62-326 35-311 (335)
3 PF00249 Myb_DNA-binding: Myb- 99.5 3.5E-14 7.7E-19 101.5 6.4 46 79-124 1-48 (48)
4 smart00717 SANT SANT SWI3, AD 99.2 5.4E-11 1.2E-15 81.0 6.0 46 79-124 1-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 6.5E-11 1.4E-15 79.7 5.5 43 81-123 1-44 (45)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.1 1.7E-10 3.7E-15 85.0 4.9 42 82-123 1-42 (60)
7 KOG0457 Histone acetyltransfer 98.9 2.2E-09 4.8E-14 108.2 7.4 66 62-127 49-121 (438)
8 PLN03212 Transcription repress 98.8 7.9E-09 1.7E-13 98.2 7.1 65 63-127 7-75 (249)
9 PLN03091 hypothetical protein; 98.7 1.2E-08 2.6E-13 103.5 5.2 54 73-126 8-63 (459)
10 PLN03212 Transcription repress 98.7 7.7E-08 1.7E-12 91.6 9.7 53 77-129 76-128 (249)
11 PLN03091 hypothetical protein; 98.5 1.9E-07 4.1E-12 95.0 7.3 53 77-129 65-117 (459)
12 KOG0048 Transcription factor, 98.4 1.8E-07 3.8E-12 87.0 4.4 49 79-127 9-59 (238)
13 COG5259 RSC8 RSC chromatin rem 98.4 2.3E-07 5E-12 94.8 5.2 42 79-120 279-320 (531)
14 COG5114 Histone acetyltransfer 98.3 2.1E-06 4.5E-11 85.1 8.3 65 62-126 40-111 (432)
15 KOG0048 Transcription factor, 98.3 1.8E-06 3.8E-11 80.4 7.2 54 76-129 59-112 (238)
16 KOG1279 Chromatin remodeling f 98.3 1E-06 2.2E-11 91.1 6.0 44 77-120 251-294 (506)
17 KOG0049 Transcription factor, 97.6 8.3E-05 1.8E-09 79.3 6.2 51 77-127 358-409 (939)
18 PLN03162 golden-2 like transcr 97.6 0.00036 7.8E-09 70.7 10.2 56 75-130 233-293 (526)
19 KOG4468 Polycomb-group transcr 96.9 0.003 6.4E-08 67.2 8.3 53 78-130 87-149 (782)
20 KOG0051 RNA polymerase I termi 96.9 0.0012 2.6E-08 69.9 4.8 54 73-127 377-431 (607)
21 PF13837 Myb_DNA-bind_4: Myb/S 96.5 0.0056 1.2E-07 47.6 5.0 51 79-129 1-69 (90)
22 KOG0051 RNA polymerase I termi 96.4 0.003 6.4E-08 67.1 4.1 51 77-127 434-510 (607)
23 KOG0050 mRNA splicing protein 96.3 0.0045 9.7E-08 64.9 4.7 52 75-126 3-55 (617)
24 KOG0049 Transcription factor, 96.0 0.0097 2.1E-07 64.1 5.4 46 78-123 411-457 (939)
25 KOG4329 DNA-binding protein [G 95.9 0.01 2.2E-07 60.3 4.9 57 68-127 263-323 (445)
26 COG5118 BDP1 Transcription ini 95.3 0.035 7.6E-07 56.8 6.1 44 75-118 361-404 (507)
27 COG5147 REB1 Myb superfamily p 95.0 0.015 3.2E-07 61.0 2.7 59 71-129 12-71 (512)
28 KOG4167 Predicted DNA-binding 94.8 0.048 1E-06 59.5 5.8 42 79-120 619-660 (907)
29 KOG0724 Zuotin and related mol 94.2 0.03 6.4E-07 54.1 2.4 70 77-153 162-238 (335)
30 PF13873 Myb_DNA-bind_5: Myb/S 93.9 0.25 5.4E-06 38.0 6.7 51 79-129 2-74 (78)
31 PF11035 SnAPC_2_like: Small n 93.8 5 0.00011 40.6 17.0 52 78-129 20-75 (344)
32 KOG1194 Predicted DNA-binding 93.1 0.22 4.8E-06 52.1 6.5 42 79-120 187-228 (534)
33 PLN03142 Probable chromatin-re 91.8 0.34 7.3E-06 54.8 6.4 48 80-127 825-873 (1033)
34 KOG3841 TEF-1 and related tran 91.5 0.9 2E-05 46.8 8.6 54 77-130 74-148 (455)
35 smart00426 TEA TEA domain. 91.5 0.24 5.2E-06 39.6 3.6 43 79-121 3-66 (68)
36 KOG3554 Histone deacetylase co 91.2 0.23 4.9E-06 52.3 4.0 43 77-119 283-326 (693)
37 COG5147 REB1 Myb superfamily p 90.8 0.28 6.1E-06 51.7 4.3 53 77-129 70-122 (512)
38 KOG0050 mRNA splicing protein 90.8 0.26 5.6E-06 52.3 4.0 48 77-125 57-104 (617)
39 TIGR02894 DNA_bind_RsfA transc 90.1 0.6 1.3E-05 42.7 5.3 48 79-127 4-58 (161)
40 PF09111 SLIDE: SLIDE; InterP 90.0 1.2 2.5E-05 38.6 6.8 59 71-129 41-115 (118)
41 PF12776 Myb_DNA-bind_3: Myb/S 88.2 1.6 3.4E-05 34.4 5.8 43 81-123 1-61 (96)
42 PF08914 Myb_DNA-bind_2: Rap1 86.0 1.3 2.8E-05 34.7 4.1 48 79-126 2-59 (65)
43 PRK13923 putative spore coat p 85.0 1.3 2.8E-05 40.9 4.2 49 78-126 4-58 (170)
44 PF01285 TEA: TEA/ATTS domain 84.2 1.2 2.5E-05 46.1 4.1 48 76-123 46-112 (431)
45 KOG4282 Transcription factor G 83.7 16 0.00034 35.8 11.5 51 79-129 54-118 (345)
46 PF04504 DUF573: Protein of un 77.5 8.9 0.00019 31.9 6.4 40 79-118 4-56 (98)
47 KOG2009 Transcription initiati 75.0 2.6 5.6E-05 45.3 3.2 50 78-130 408-457 (584)
48 PF13404 HTH_AsnC-type: AsnC-t 75.0 11 0.00023 27.0 5.4 37 85-122 3-40 (42)
49 KOG1194 Predicted DNA-binding 67.1 12 0.00025 39.8 5.8 57 72-128 362-418 (534)
50 PF02954 HTH_8: Bacterial regu 63.7 19 0.0004 25.2 4.6 33 85-118 5-37 (42)
51 PF01388 ARID: ARID/BRIGHT DNA 63.1 18 0.00038 28.6 4.9 38 89-126 40-90 (92)
52 PRK11179 DNA-binding transcrip 62.8 15 0.00033 31.9 4.9 44 84-132 8-52 (153)
53 KOG1878 Nuclear receptor coreg 59.2 3.7 8.1E-05 48.3 0.6 48 85-132 360-407 (1672)
54 PF10141 ssDNA-exonuc_C: Singl 59.2 9.5 0.00021 34.9 3.1 46 256-301 90-138 (195)
55 PRK11169 leucine-responsive tr 57.7 19 0.00042 31.6 4.8 44 84-132 13-57 (164)
56 smart00501 BRIGHT BRIGHT, ARID 57.5 33 0.00072 27.4 5.7 41 89-129 36-89 (93)
57 PLN03142 Probable chromatin-re 55.7 32 0.0007 39.5 7.1 58 72-130 920-990 (1033)
58 PF08281 Sigma70_r4_2: Sigma-7 55.4 43 0.00093 23.7 5.4 37 85-122 13-49 (54)
59 PF11626 Rap1_C: TRF2-interact 52.7 8.6 0.00019 31.0 1.6 18 76-93 44-61 (87)
60 KOG0385 Chromatin remodeling c 49.4 31 0.00066 39.1 5.5 59 71-130 787-846 (971)
61 PF06461 DUF1086: Domain of Un 49.0 48 0.001 30.2 5.8 50 81-130 40-92 (145)
62 PF10561 UPF0565: Uncharacteri 48.6 15 0.00031 36.8 2.7 30 70-99 272-301 (303)
63 PF09420 Nop16: Ribosome bioge 48.4 34 0.00073 30.6 4.8 46 78-123 113-162 (164)
64 smart00344 HTH_ASNC helix_turn 47.9 42 0.00091 26.8 4.9 44 84-132 2-46 (108)
65 TIGR02937 sigma70-ECF RNA poly 46.8 71 0.0015 25.2 6.0 47 81-129 110-156 (158)
66 PF04545 Sigma70_r4: Sigma-70, 43.2 1.2E+02 0.0025 21.4 6.0 43 84-128 7-49 (50)
67 PHA00442 host recBCD nuclease 42.4 15 0.00033 28.7 1.4 33 75-107 8-49 (59)
68 KOG0493 Transcription factor E 42.1 2.4E+02 0.0052 28.6 9.9 68 62-130 226-304 (342)
69 cd06171 Sigma70_r4 Sigma70, re 39.7 1.1E+02 0.0023 20.0 5.4 42 81-124 10-51 (55)
70 PRK01905 DNA-binding protein F 38.7 89 0.0019 24.6 5.3 28 83-110 35-62 (77)
71 smart00595 MADF subfamily of S 38.5 58 0.0012 25.2 4.2 22 100-122 29-50 (89)
72 PF13325 MCRS_N: N-terminal re 37.7 73 0.0016 30.2 5.4 46 78-123 72-125 (199)
73 PRK00430 fis global DNA-bindin 36.9 90 0.002 25.9 5.3 26 85-110 55-80 (95)
74 PF01527 HTH_Tnp_1: Transposas 32.9 1.4E+02 0.003 22.2 5.4 46 78-125 3-48 (76)
75 PF07750 GcrA: GcrA cell cycle 32.4 66 0.0014 29.1 4.1 37 81-118 2-38 (162)
76 cd08311 Death_p75NR Death doma 31.8 35 0.00076 27.4 2.0 33 84-118 2-34 (77)
77 KOG1019 Retinoblastoma pathway 30.9 27 0.00059 39.3 1.7 56 63-118 28-84 (837)
78 cd08780 Death_TRADD Death Doma 30.9 85 0.0019 26.6 4.2 24 83-109 1-24 (90)
79 PF12451 VPS11_C: Vacuolar pro 30.0 50 0.0011 24.4 2.4 28 83-110 17-44 (49)
80 PF10440 WIYLD: Ubiquitin-bind 29.9 32 0.0007 27.3 1.5 19 88-106 30-48 (65)
81 PF11593 Med3: Mediator comple 28.4 1E+02 0.0022 32.1 5.0 13 65-77 190-202 (379)
82 PF10545 MADF_DNA_bdg: Alcohol 28.0 1E+02 0.0023 22.9 4.0 25 100-124 28-53 (85)
83 KOG2656 DNA methyltransferase 27.9 50 0.0011 34.6 2.8 51 79-129 130-186 (445)
84 PRK11924 RNA polymerase sigma 27.3 2.1E+02 0.0045 23.9 6.1 32 97-129 140-171 (179)
85 COG3604 FhlA Transcriptional r 26.2 75 0.0016 34.4 3.8 46 80-126 501-546 (550)
86 KOG1878 Nuclear receptor coreg 25.0 27 0.00059 41.6 0.4 50 70-119 216-265 (1672)
87 PF12181 MogR_DNAbind: DNA bin 24.9 1.9E+02 0.0042 26.3 5.6 64 78-144 59-134 (148)
88 KOG0487 Transcription factor A 24.8 55 0.0012 32.9 2.5 58 64-130 233-293 (308)
89 PF01410 COLFI: Fibrillar coll 24.5 39 0.00084 31.5 1.3 16 4-19 21-36 (214)
90 PF13384 HTH_23: Homeodomain-l 23.5 1.5E+02 0.0031 20.6 3.8 34 83-118 3-36 (50)
91 cd08317 Death_ank Death domain 22.0 75 0.0016 25.2 2.3 23 88-110 5-27 (84)
92 TIGR03238 dnd_assoc_3 dnd syst 21.5 1.1E+02 0.0024 32.9 4.0 52 273-324 243-296 (504)
93 KOG0384 Chromodomain-helicase 21.2 57 0.0012 38.5 2.0 53 78-131 1132-1197(1373)
94 TIGR02985 Sig70_bacteroi1 RNA 20.6 3.9E+02 0.0085 21.8 6.4 31 97-128 128-158 (161)
95 PRK09643 RNA polymerase sigma 20.6 2.8E+02 0.0062 24.4 5.9 31 97-128 149-179 (192)
96 smart00005 DEATH DEATH domain, 20.1 95 0.0021 23.9 2.5 23 88-110 6-29 (88)
97 PF08074 CHDCT2: CHDCT2 (NUC03 20.0 64 0.0014 30.2 1.7 28 78-105 2-30 (173)
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=99.59 E-value=1.9e-15 Score=114.17 Aligned_cols=50 Identities=48% Similarity=0.727 Sum_probs=46.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCc-hH---HHHHHHhC-CC-CHHHHHHHHHHHHHH
Q 019067 77 KSRESWTEQEHDKFLEALQLFDR-DW---KKIEAFIG-SK-TVIQIRSHAQKYFLK 126 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGr-dW---kkIA~~Vg-TR-T~~QcRSHaQKYF~k 126 (346)
|.|..||+|||.+||+||+.||+ +| ++|+++++ ++ |..||++|+||||++
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 46789999999999999999998 99 99998776 67 999999999999986
No 2
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.54 E-value=2.7e-16 Score=149.81 Aligned_cols=250 Identities=22% Similarity=0.145 Sum_probs=170.7
Q ss_pred CCCCCCCCCCCcccccCCCC-CCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc-CC---CCCC
Q 019067 62 AEDPSKKIRKPYTITKSRES-WTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN-GT---SEHV 136 (346)
Q Consensus 62 ~e~~~kKirkPy~i~k~r~~-WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~-g~---~~~i 136 (346)
.++..++++++|.+.+.+.+ ||.+||++|.++|..|++.|..|-++++.++..|++.|+|+||.++.+. +. .+.+
T Consensus 35 ~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~~~~~~~~~~~ 114 (335)
T KOG0724|consen 35 TEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKSDTSLAEVEEF 114 (335)
T ss_pred HHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCcccccccccccc
Confidence 46667899999999987555 9999999999999999889999999999999999999999999999874 22 2348
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcccccccCCccCccccCCCCcccCCCCCCccCCCCCcccCCCCCCCCCCCccccccccC
Q 019067 137 PPPRPKRKAAHPYPQKAPKTVHGVSQFGGQVQSSAALLEPGYIYRPDSSSVLGNPVPVAALSSWSYDSVPPVNVSQVTKD 216 (346)
Q Consensus 137 P~pr~KRks~h~yp~~~~~~~~~~~q~~~~~qss~~~~~pg~~~~~dsssv~~~~~~~~~~~sw~~~~~~~~~~~~~~~~ 216 (346)
|++++++++.|+|+.+...+.... ..........+. +++....+..+..+..+.......|....- .
T Consensus 115 ~~~~~~~k~~~~y~~~~~~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~ 181 (335)
T KOG0724|consen 115 YNFWPKFKSWRQYPQKDEPDEEDS--ENRSQSRYSGGT-QRGKSNAEELRRKGTPVTERERKLVLLALK----------K 181 (335)
T ss_pred CCccccccccccCCCCCCcccccc--cchhhhhhcccc-cccccchhhhhhccchhHHHHHHHHHhhhc----------c
Confidence 999999999999999987653322 111111112222 344444444444444444333222222110 0
Q ss_pred CCCCCCCCCCCc----ccccCCCCCCC------CccccccccCCCCCCCCCccCCChHHHHh--hhhccc-----C----
Q 019067 217 DVGLPGSSNAQN----FCYSSSNDSTL------RTWPVGETIDRGDHGKPRRVMPDFAQVYS--FLGSVF-----D---- 275 (346)
Q Consensus 217 d~~~~g~~~~~~----~~~~s~~~s~~------~~~~~~~~~~q~~~~~~l~~~PdFaqVY~--FigsvF-----d---- 275 (346)
++....-....+ .+.. ..++-. +........+.....+.++.++++.+++. |.++++ +
T Consensus 182 ~~~~~~~~~~~~~~~~r~~~-~~~s~a~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 260 (335)
T KOG0724|consen 182 DGKIDWRKISQNVEKERTPE-QVASHAQEKAFEKALARQKSGEEEKRRKSIEDITTASEAEDRKKEDEAAKEAKKKPRDT 260 (335)
T ss_pred cccccceechhhhhhhhcch-hhhhhhhhhhhHHHHHHHhhhccccccchhhhhhccchhhhhhcchhhhhhhhcccccc
Confidence 111000000111 0100 000100 11112223445667788899999999988 999999 7
Q ss_pred CCchhhHHhhccCCchhHHHHHHHHH-HHHhhcCChhhHHHHHHHhhhcccc
Q 019067 276 PNSTGHIQRLKQMDPINFETVLLLMR-NLAINLTSPEFEDHKRLLSLYDVES 326 (346)
Q Consensus 276 p~~~~hlq~Lk~MdpId~ETvLLLmr-NLs~NL~sp~fe~~~~llssy~~~~ 326 (346)
|...+|.+.++.|++++.++.++.|. |+..+|+++.|+.++.+++. ....
T Consensus 261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 311 (335)
T KOG0724|consen 261 PSLKSRNKRLKSFDGIAEESSETEDSLELVAALSAPMEEPQWELKAA-AGSN 311 (335)
T ss_pred ccccchhhhcccCCccCCCchhHHHhHHHHHhhhccccccHHHHHhh-cccc
Confidence 88899999999999999999999999 89999999999999777766 5543
No 3
>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=99.51 E-value=3.5e-14 Score=101.47 Aligned_cols=46 Identities=41% Similarity=0.724 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHcCch-HHHHHHHhC-CCCHHHHHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFDRD-WKKIEAFIG-SKTVIQIRSHAQKYF 124 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyGrd-WkkIA~~Vg-TRT~~QcRSHaQKYF 124 (346)
++.||+||+++|+++|++||.+ |+.||++|+ +||..||++||++|.
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5789999999999999999986 999999999 999999999999873
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.18 E-value=5.4e-11 Score=80.95 Aligned_cols=46 Identities=24% Similarity=0.539 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYF 124 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyG-rdWkkIA~~VgTRT~~QcRSHaQKYF 124 (346)
+..||+||+.+|++++.+|| .+|..|++++++||..||+.||.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 46899999999999999999 89999999999999999999887654
No 5
>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=99.16 E-value=6.5e-11 Score=79.67 Aligned_cols=43 Identities=30% Similarity=0.581 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHH
Q 019067 81 SWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKY 123 (346)
Q Consensus 81 ~WTeEEh~lFLeaLekyG-rdWkkIA~~VgTRT~~QcRSHaQKY 123 (346)
.||.||+.+|+.++.+|| .+|..|++.+++||..||+.||+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999998765
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=99.07 E-value=1.7e-10 Score=84.97 Aligned_cols=42 Identities=33% Similarity=0.670 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHH
Q 019067 82 WTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKY 123 (346)
Q Consensus 82 WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKY 123 (346)
||+||+++|++++++||.+|++||+++|.||..||+.||.++
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 999999999999999999999999999999999999998764
No 7
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.91 E-value=2.2e-09 Score=108.17 Aligned_cols=66 Identities=32% Similarity=0.546 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCcccccC------CCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019067 62 AEDPSKKIRKPYTITKS------RESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 62 ~e~~~kKirkPy~i~k~------r~~WTeEEh~lFLeaLekyG-rdWkkIA~~VgTRT~~QcRSHaQKYF~kl 127 (346)
.|.+.|+..+||.+-+. ...||.+|+.+||+|++.|| ++|..||+|||+||..+|+.|+.|+|..-
T Consensus 49 aE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 49 AETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred cccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhcC
Confidence 47788999999988765 57999999999999999999 79999999999999999999999998763
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.82 E-value=7.9e-09 Score=98.21 Aligned_cols=65 Identities=17% Similarity=0.321 Sum_probs=52.7
Q ss_pred CCCCCCCCCCcc--cccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhC-CCCHHHHHHHHHHHHHHH
Q 019067 63 EDPSKKIRKPYT--ITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 63 e~~~kKirkPy~--i~k~r~~WTeEEh~lFLeaLekyGr-dWkkIA~~Vg-TRT~~QcRSHaQKYF~kl 127 (346)
++...+.+-|+- ....++.||.||+++|++++++||. +|+.||+.++ .||..|||.||.+|+..-
T Consensus 7 ~~~~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~ 75 (249)
T PLN03212 7 KKPVSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPS 75 (249)
T ss_pred CCCCCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchh
Confidence 344444455543 3356899999999999999999995 9999999886 899999999999998553
No 9
>PLN03091 hypothetical protein; Provisional
Probab=98.72 E-value=1.2e-08 Score=103.50 Aligned_cols=54 Identities=17% Similarity=0.376 Sum_probs=47.4
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhC-CCCHHHHHHHHHHHHHH
Q 019067 73 YTITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYFLK 126 (346)
Q Consensus 73 y~i~k~r~~WTeEEh~lFLeaLekyGr-dWkkIA~~Vg-TRT~~QcRSHaQKYF~k 126 (346)
|+....++.||.|||++|+++|++||. +|+.||+.++ +||..|||.||.+|+..
T Consensus 8 ~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP 63 (459)
T PLN03091 8 YKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRP 63 (459)
T ss_pred cCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCC
Confidence 344567889999999999999999996 9999999887 89999999999987643
No 10
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.70 E-value=7.7e-08 Score=91.57 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=48.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
.+++.||+||++++++++..||..|..||++|+.||..|||+||..++.+..+
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHH
Confidence 46899999999999999999999999999999999999999999888776544
No 11
>PLN03091 hypothetical protein; Provisional
Probab=98.52 E-value=1.9e-07 Score=94.96 Aligned_cols=53 Identities=19% Similarity=0.330 Sum_probs=48.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
.+++.||.||+++|++.+++||.+|.+||++|+.||..|||+||...++|..+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999877666444
No 12
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.44 E-value=1.8e-07 Score=86.99 Aligned_cols=49 Identities=14% Similarity=0.301 Sum_probs=46.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhC-CCCHHHHHHHHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyGr-dWkkIA~~Vg-TRT~~QcRSHaQKYF~kl 127 (346)
+++||.|||++|++.|++||. +|..|++..| .|+..|||.+|-+|+..-
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ 59 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPD 59 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCC
Confidence 799999999999999999995 8999999999 999999999999997653
No 13
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.42 E-value=2.3e-07 Score=94.83 Aligned_cols=42 Identities=31% Similarity=0.610 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHa 120 (346)
...||.+|..+|||||+.||.+|.+||.|||+||++||..|+
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHF 320 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHH
Confidence 348999999999999999999999999999999999999874
No 14
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.30 E-value=2.1e-06 Score=85.11 Aligned_cols=65 Identities=26% Similarity=0.487 Sum_probs=57.7
Q ss_pred CCCCCCCCCCCccccc------CCCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 019067 62 AEDPSKKIRKPYTITK------SRESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (346)
Q Consensus 62 ~e~~~kKirkPy~i~k------~r~~WTeEEh~lFLeaLekyG-rdWkkIA~~VgTRT~~QcRSHaQKYF~k 126 (346)
.+.+.+..-++|.|.. ..+.|+.+|+.+|+++++-.| ++|..||.|||+|+.+.||+|+-||+..
T Consensus 40 ~~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~e 111 (432)
T COG5114 40 IETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYDE 111 (432)
T ss_pred ccccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHhh
Confidence 4666778888887753 367999999999999999999 6999999999999999999999999874
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.29 E-value=1.8e-06 Score=80.39 Aligned_cols=54 Identities=17% Similarity=0.300 Sum_probs=48.4
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 76 TKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 76 ~k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
..+++.||+||+++++++-.+||.+|..||+++++||...|++||.-...|..+
T Consensus 59 ~ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~ 112 (238)
T KOG0048|consen 59 DLKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLKKKLL 112 (238)
T ss_pred CccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHHHHHH
Confidence 346999999999999999999999999999999999999999999777655433
No 16
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.28 E-value=1e-06 Score=91.07 Aligned_cols=44 Identities=34% Similarity=0.632 Sum_probs=41.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 019067 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHa 120 (346)
..+..||++|..+||+||+.||.+|.+|+.|||+||..||..|.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kF 294 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKF 294 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHH
Confidence 45789999999999999999999999999999999999999973
No 17
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.63 E-value=8.3e-05 Score=79.26 Aligned_cols=51 Identities=20% Similarity=0.371 Sum_probs=45.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019067 77 KSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl 127 (346)
.+.++||.+|+.+|+.|+.+||. +|-+|-+.|++|+..|||.++-+.+..-
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s 409 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRS 409 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHh
Confidence 47899999999999999999995 9999999999999999999876655443
No 18
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.62 E-value=0.00036 Score=70.69 Aligned_cols=56 Identities=27% Similarity=0.357 Sum_probs=48.2
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCc---hHHHHHHHhC--CCCHHHHHHHHHHHHHHHhhc
Q 019067 75 ITKSRESWTEQEHDKFLEALQLFDR---DWKKIEAFIG--SKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 75 i~k~r~~WTeEEh~lFLeaLekyGr---dWkkIA~~Vg--TRT~~QcRSHaQKYF~kl~k~ 130 (346)
..|.|-.||.|=|++|++||++.|- --|+|=++++ .=|..+|+||.|||...+++.
T Consensus 233 ~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l 293 (526)
T PLN03162 233 KKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHL 293 (526)
T ss_pred CCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccc
Confidence 3467889999999999999999993 6788887755 679999999999999988753
No 19
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=96.92 E-value=0.003 Score=67.20 Aligned_cols=53 Identities=28% Similarity=0.506 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHH----------HHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019067 78 SRESWTEQEHDKFLEALQLFDRDWKKI----------EAFIGSKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyGrdWkkI----------A~~VgTRT~~QcRSHaQKYF~kl~k~ 130 (346)
.+..||-.|++-|..||++||+|+.+| -.-+..||..|||.||-+-..++.+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~ 149 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKL 149 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhh
Confidence 378999999999999999999999998 23356789999999876555555553
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.85 E-value=0.0012 Score=69.90 Aligned_cols=54 Identities=24% Similarity=0.464 Sum_probs=47.0
Q ss_pred ccccc-CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019067 73 YTITK-SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 73 y~i~k-~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl 127 (346)
|++-. .++.||+||++.+...+.++|.+|+.|++.+| |.+.-||.||..|...-
T Consensus 377 y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 377 YTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQYVKCG 431 (607)
T ss_pred CCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHhhccc
Confidence 33444 89999999999999999999999999999998 68999999998885443
No 21
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.46 E-value=0.0056 Score=47.60 Aligned_cols=51 Identities=29% Similarity=0.480 Sum_probs=34.6
Q ss_pred CCCCCHHHHHHHHHHHHH------cC--c------hHHHHHHHhC----CCCHHHHHHHHHHHHHHHhh
Q 019067 79 RESWTEQEHDKFLEALQL------FD--R------DWKKIEAFIG----SKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLek------yG--r------dWkkIA~~Vg----TRT~~QcRSHaQKYF~kl~k 129 (346)
|..||++|...||+.+.. |+ + -|+.||+.+. .||+.||+..|..-...-.+
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 468999999999998876 31 1 5999997653 59999999998765555433
No 22
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.41 E-value=0.003 Score=67.06 Aligned_cols=51 Identities=24% Similarity=0.502 Sum_probs=43.0
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hc------------------Cc-hHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019067 77 KSRESWTEQEHDKFLEALQ-------LF------------------DR-DWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLe-------ky------------------Gr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl 127 (346)
.++++||.||+++||+.++ +| .. .|..|++.+|||+..|||.||++-...-
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~ 510 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSP 510 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhH
Confidence 3789999999999999995 44 11 6999999999999999999987765544
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.32 E-value=0.0045 Score=64.94 Aligned_cols=52 Identities=17% Similarity=0.425 Sum_probs=47.8
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 019067 75 ITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (346)
Q Consensus 75 i~k~r~~WTeEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~k 126 (346)
+-+.++.|+..|++.+..++.+||. .|.+|+..+..+|+.||+.+|.+|...
T Consensus 3 i~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp 55 (617)
T KOG0050|consen 3 IEIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDP 55 (617)
T ss_pred eEEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCH
Confidence 4467899999999999999999997 899999999999999999999988765
No 24
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.98 E-value=0.0097 Score=64.09 Aligned_cols=46 Identities=26% Similarity=0.543 Sum_probs=40.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHH
Q 019067 78 SRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKY 123 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKY 123 (346)
+.++||-.|++.|+++|++||. .|-+||.++|.||..|.+.+-..+
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 4689999999999999999996 999999999999998877654443
No 25
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=95.91 E-value=0.01 Score=60.33 Aligned_cols=57 Identities=23% Similarity=0.478 Sum_probs=45.5
Q ss_pred CCCCCcccc---cCCCCCCHHHHHHHHHHHHHcCchHHHHH-HHhCCCCHHHHHHHHHHHHHHH
Q 019067 68 KIRKPYTIT---KSRESWTEQEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 68 KirkPy~i~---k~r~~WTeEEh~lFLeaLekyGrdWkkIA-~~VgTRT~~QcRSHaQKYF~kl 127 (346)
+.|+++... ..-..|+++|=..|.++|+.||+|+..|. .-|.||++..|..+ ||+..
T Consensus 263 lrr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVey---YYlWK 323 (445)
T KOG4329|consen 263 LRRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEY---YYLWK 323 (445)
T ss_pred HHhcCCcceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHH---HHHhh
Confidence 444444332 34468999999999999999999999997 57999999999974 66665
No 26
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.29 E-value=0.035 Score=56.81 Aligned_cols=44 Identities=25% Similarity=0.514 Sum_probs=40.8
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 019067 75 ITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (346)
Q Consensus 75 i~k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRS 118 (346)
..+...+||.+|-++|..||..+|-|+..|+.++++|...||+.
T Consensus 361 ~~~~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKa 404 (507)
T COG5118 361 KKKGALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKA 404 (507)
T ss_pred CCCCCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHH
Confidence 34456799999999999999999999999999999999999997
No 27
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=95.03 E-value=0.015 Score=60.96 Aligned_cols=59 Identities=17% Similarity=0.264 Sum_probs=50.7
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 71 KPYTITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 71 kPy~i~k~r~~WTeEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
|++......+.|+..|++.++-+++.||- +|.+||..++.|+..||+.||..|.....+
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 34556667889999999999999999995 999999988889999999999877666533
No 28
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=94.81 E-value=0.048 Score=59.47 Aligned_cols=42 Identities=29% Similarity=0.426 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHa 120 (346)
...||..|..+|-+||-.|.+|+..|+++|.+||+.||-.++
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyY 660 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYY 660 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHH
Confidence 458999999999999999999999999999999999999754
No 29
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=94.19 E-value=0.03 Score=54.09 Aligned_cols=70 Identities=27% Similarity=0.354 Sum_probs=57.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCc-hHHHHH-HHhCCCCHHHHHHHHH-----HHHHHHhhcCCCCCCCCCCCCCCCCCCC
Q 019067 77 KSRESWTEQEHDKFLEALQLFDR-DWKKIE-AFIGSKTVIQIRSHAQ-----KYFLKVQKNGTSEHVPPPRPKRKAAHPY 149 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGr-dWkkIA-~~VgTRT~~QcRSHaQ-----KYF~kl~k~g~~~~iP~pr~KRks~h~y 149 (346)
+.+..|+..++.+++.++.++|+ +|..|+ .++..|++.|+.+|+| +|+.+....+. ...|+++|++
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~-------~~~~~s~~~~ 234 (335)
T KOG0724|consen 162 RKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEE-------EKRRKSIEDI 234 (335)
T ss_pred hccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhcc-------ccccchhhhh
Confidence 56789999999999999999998 999998 6778899999999999 88888744432 3456777877
Q ss_pred CCCC
Q 019067 150 PQKA 153 (346)
Q Consensus 150 p~~~ 153 (346)
+-..
T Consensus 235 ~~~~ 238 (335)
T KOG0724|consen 235 TTAS 238 (335)
T ss_pred hccc
Confidence 6554
No 30
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.93 E-value=0.25 Score=38.02 Aligned_cols=51 Identities=18% Similarity=0.434 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHc-----C------------chHHHHHHHh-----CCCCHHHHHHHHHHHHHHHhh
Q 019067 79 RESWTEQEHDKFLEALQLF-----D------------RDWKKIEAFI-----GSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLeky-----G------------rdWkkIA~~V-----gTRT~~QcRSHaQKYF~kl~k 129 (346)
...||.+|.+.|++.+++| | +-|..|+..+ +.||..|++..|+++-...++
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3579999999999999987 3 1599998543 269999999999888776654
No 31
>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=93.85 E-value=5 Score=40.61 Aligned_cols=52 Identities=19% Similarity=0.325 Sum_probs=42.1
Q ss_pred CCCCCCHHHHHHHHHHHHHc-Cc---hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 78 SRESWTEQEHDKFLEALQLF-DR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLeky-Gr---dWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
....||..|...+|.+|+-- |. |-..|++.+.+|+..+|+...|+.-.++-+
T Consensus 20 gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvar 75 (344)
T PF11035_consen 20 GPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAR 75 (344)
T ss_pred CcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHH
Confidence 45799999999999999866 43 677788999999999999988776555433
No 32
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=93.07 E-value=0.22 Score=52.06 Aligned_cols=42 Identities=21% Similarity=0.459 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHa 120 (346)
...||.||-.+|-++++.||+++++|...++.|+..-++-++
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY 228 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH
Confidence 368999999999999999999999999999999988887653
No 33
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=91.76 E-value=0.34 Score=54.78 Aligned_cols=48 Identities=21% Similarity=0.469 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019067 80 ESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 80 ~~WTeEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl 127 (346)
..|+..+=..|+.|.++||| +...||..|++||..+|+.+++-|+.+.
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 46999999999999999998 9999999999999999999887776553
No 34
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=91.54 E-value=0.9 Score=46.78 Aligned_cols=54 Identities=24% Similarity=0.395 Sum_probs=42.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHcC---c-------------hHHHHHHHhC-----CCCHHHHHHHHHHHHHHHhhc
Q 019067 77 KSRESWTEQEHDKFLEALQLFD---R-------------DWKKIEAFIG-----SKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyG---r-------------dWkkIA~~Vg-----TRT~~QcRSHaQKYF~kl~k~ 130 (346)
.-.+.|+++=++.|+|||..|- | +=.-||.||+ |||..||-+|-|=.-+++.|.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999998872 1 2356898876 799999999998776665543
No 35
>smart00426 TEA TEA domain.
Probab=91.48 E-value=0.24 Score=39.61 Aligned_cols=43 Identities=28% Similarity=0.476 Sum_probs=31.7
Q ss_pred CCCCCHHHHHHHHHHHHHcCc--hH--------------HHHHHHhC-----CCCHHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFDR--DW--------------KKIEAFIG-----SKTVIQIRSHAQ 121 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyGr--dW--------------kkIA~~Vg-----TRT~~QcRSHaQ 121 (346)
...|.++=+..|++||+.|-. .+ .-|++|+- .||..||-||-|
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 468999999999999999842 11 12565544 488888888866
No 36
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=91.17 E-value=0.23 Score=52.33 Aligned_cols=43 Identities=28% Similarity=0.528 Sum_probs=37.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHH-HHhCCCCHHHHHHH
Q 019067 77 KSRESWTEQEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSH 119 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGrdWkkIA-~~VgTRT~~QcRSH 119 (346)
..-+.|+..|-.+|.+||++||+|+..|- +|++=|+..-|..+
T Consensus 283 DemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIvey 326 (693)
T KOG3554|consen 283 DEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEY 326 (693)
T ss_pred hhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHH
Confidence 34579999999999999999999999997 89998887776654
No 37
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=90.78 E-value=0.28 Score=51.66 Aligned_cols=53 Identities=13% Similarity=0.364 Sum_probs=46.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
.++..|+.||++.++..-.++|-.|..|+.+++.||..||..+|.+-+....+
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 46889999999999999999999999999999999999999987766555433
No 38
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=90.76 E-value=0.26 Score=52.27 Aligned_cols=48 Identities=19% Similarity=0.447 Sum_probs=43.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHH
Q 019067 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 125 (346)
Q Consensus 77 k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~ 125 (346)
.++.-|+.||++++|.+...+..-|..|+..|| ||..||-.|+++.+-
T Consensus 57 i~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ll~ 104 (617)
T KOG0050|consen 57 IKKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNLLD 104 (617)
T ss_pred HhhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHHHH
Confidence 357899999999999999999999999999998 899999999987543
No 39
>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=90.05 E-value=0.6 Score=42.74 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=38.7
Q ss_pred CCCCCHHHHHHHHHHHHHc---Cc----hHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLF---DR----DWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLeky---Gr----dWkkIA~~VgTRT~~QcRSHaQKYF~kl 127 (346)
...||.||+.+|-+.+-+| |+ -+..+++-+ +||..-|.-||+.|..+.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHH
Confidence 4689999999999999888 32 455555554 499999999999998764
No 40
>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=90.04 E-value=1.2 Score=38.60 Aligned_cols=59 Identities=20% Similarity=0.412 Sum_probs=43.9
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCc----hHHHHHH------------HhCCCCHHHHHHHHHHHHHHHhh
Q 019067 71 KPYTITKSRESWTEQEHDKFLEALQLFDR----DWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 71 kPy~i~k~r~~WTeEEh~lFLeaLekyGr----dWkkIA~------------~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
-.|....++..||+|||.-+|-.+.+||- .|..|-+ |+.+||+..+.-|+.--..-+.|
T Consensus 41 i~y~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 41 INYPPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp -SSTSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred eccCCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 34666778899999999999999999995 8999853 36699999999998655544443
No 41
>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=88.20 E-value=1.6 Score=34.38 Aligned_cols=43 Identities=26% Similarity=0.392 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHHc---C-c---------hHHHHHHH----hC-CCCHHHHHHHHHHH
Q 019067 81 SWTEQEHDKFLEALQLF---D-R---------DWKKIEAF----IG-SKTVIQIRSHAQKY 123 (346)
Q Consensus 81 ~WTeEEh~lFLeaLeky---G-r---------dWkkIA~~----Vg-TRT~~QcRSHaQKY 123 (346)
.||+++++.||+.+... | + .|..|++. .| ..|..||++|+...
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 59999999999988554 1 1 59998743 33 36899999997653
No 42
>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=85.97 E-value=1.3 Score=34.68 Aligned_cols=48 Identities=21% Similarity=0.284 Sum_probs=30.4
Q ss_pred CCCCCHHHHHHHHHHHHHcC---------chHHHHHHHhC-CCCHHHHHHHHHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLFD---------RDWKKIEAFIG-SKTVIQIRSHAQKYFLK 126 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyG---------rdWkkIA~~Vg-TRT~~QcRSHaQKYF~k 126 (346)
|..+|.|||..+++.|..+. +=|+.+++.-. ..|..--|.||.|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~ 59 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRG 59 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT--
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence 56789999999999996653 15999997655 78888899987666544
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=84.95 E-value=1.3 Score=40.91 Aligned_cols=49 Identities=16% Similarity=0.236 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcCc-hHHHHHH--HhC---CCCHHHHHHHHHHHHHH
Q 019067 78 SRESWTEQEHDKFLEALQLFDR-DWKKIEA--FIG---SKTVIQIRSHAQKYFLK 126 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyGr-dWkkIA~--~Vg---TRT~~QcRSHaQKYF~k 126 (346)
....||.||+.++-+.+..|++ .=.+++. .+| .||..+|..+|..+..+
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~rt~aac~fRwNs~vrk 58 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALKRTAAACGFRWNSVVRK 58 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhhhHHHHHhHHHHHHHH
Confidence 4578999999999999999986 3333442 233 58999999999776554
No 44
>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=84.24 E-value=1.2 Score=46.11 Aligned_cols=48 Identities=27% Similarity=0.435 Sum_probs=32.1
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcC---c-h--------H--HHHHHHhC-----CCCHHHHHHHHHHH
Q 019067 76 TKSRESWTEQEHDKFLEALQLFD---R-D--------W--KKIEAFIG-----SKTVIQIRSHAQKY 123 (346)
Q Consensus 76 ~k~r~~WTeEEh~lFLeaLekyG---r-d--------W--kkIA~~Vg-----TRT~~QcRSHaQKY 123 (346)
.+..+.|+++=|..|++||+.|- + . | +-|++||. .||..||-+|.|-.
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 45678999999999999999983 1 1 1 23777765 59999999999866
No 45
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=83.73 E-value=16 Score=35.77 Aligned_cols=51 Identities=20% Similarity=0.377 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC----------chHHHHHH---HhC-CCCHHHHHHHHHHHHHHHhh
Q 019067 79 RESWTEQEHDKFLEALQLFD----------RDWKKIEA---FIG-SKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyG----------rdWkkIA~---~Vg-TRT~~QcRSHaQKYF~kl~k 129 (346)
...|+.+|-..||++..... ..|..||+ ..| -||..||+..+.+...+.++
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 58999999999999875431 26999996 344 49999999998765555444
No 46
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=77.46 E-value=8.9 Score=31.91 Aligned_cols=40 Identities=20% Similarity=0.387 Sum_probs=30.3
Q ss_pred CCCCCHHHHHHHHHHHHHc----Cc----hHHHHHHHhCCC-----CHHHHHH
Q 019067 79 RESWTEQEHDKFLEALQLF----DR----DWKKIEAFIGSK-----TVIQIRS 118 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLeky----Gr----dWkkIA~~VgTR-----T~~QcRS 118 (346)
...||+|++..+|+||..| |. ||...-++|... |..|+..
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~ 56 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYD 56 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHH
Confidence 4679999999999999888 63 787776666533 5667654
No 47
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=74.99 E-value=2.6 Score=45.34 Aligned_cols=50 Identities=22% Similarity=0.392 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019067 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~ 130 (346)
....|+.+|-++|..++..+|-+..-|+.....|+..|||. ||-++-.|+
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~---K~~~eE~r~ 457 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKA---KFKKEEKRN 457 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHH---HHhhhhhcc
Confidence 46899999999999999999999999999999999999996 776665554
No 48
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=74.97 E-value=11 Score=26.95 Aligned_cols=37 Identities=19% Similarity=0.286 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHH
Q 019067 85 QEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQK 122 (346)
Q Consensus 85 EEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQK 122 (346)
+=+.++|..|+.-|+ .|..||+.+|- |...|..+.++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 557889999999997 99999999996 78888887664
No 49
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=67.05 E-value=12 Score=39.77 Aligned_cols=57 Identities=2% Similarity=-0.020 Sum_probs=48.1
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019067 72 PYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (346)
Q Consensus 72 Py~i~k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~ 128 (346)
|...-+...+||.+|..+++.+|++||++...|+-.||.++..|++.-...|-.+..
T Consensus 362 pes~c~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~m 418 (534)
T KOG1194|consen 362 PESTCRMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQM 418 (534)
T ss_pred CchhhhhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHH
Confidence 333344568999999999999999999999999999999999999997777755543
No 50
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=63.72 E-value=19 Score=25.23 Aligned_cols=33 Identities=15% Similarity=0.145 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 019067 85 QEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (346)
Q Consensus 85 EEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRS 118 (346)
=|...+.++|+.+|++..+.|+.+|- +...+..
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lgi-sr~tL~~ 37 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLGI-SRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHTS--HHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCC-CHHHHHH
Confidence 37788999999999999999999995 3334433
No 51
>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=63.13 E-value=18 Score=28.63 Aligned_cols=38 Identities=26% Similarity=0.540 Sum_probs=27.0
Q ss_pred HHHHHHHHcC--------chHHHHHHHhCCCC-----HHHHHHHHHHHHHH
Q 019067 89 KFLEALQLFD--------RDWKKIEAFIGSKT-----VIQIRSHAQKYFLK 126 (346)
Q Consensus 89 lFLeaLekyG--------rdWkkIA~~VgTRT-----~~QcRSHaQKYF~k 126 (346)
+|-.++.++| +.|..|++.+|--. ..++|.|+.+|+..
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 4445566666 26999999887422 47899999998754
No 52
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=62.79 E-value=15 Score=31.86 Aligned_cols=44 Identities=20% Similarity=0.251 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019067 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (346)
Q Consensus 84 eEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~g~ 132 (346)
++.+.++|++|++-|| .|..||+.+|. +...|+.+. .++...|-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri----~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRV----EKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHH----HHHHHCCC
Confidence 5678999999999998 99999999996 888888865 45556654
No 53
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=59.24 E-value=3.7 Score=48.27 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019067 85 QEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (346)
Q Consensus 85 EEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~g~ 132 (346)
||.+.-..||..+||+|.+|+..|+++|..||++.+-||-.++..++.
T Consensus 360 ee~ev~k~Glveh~R~~aai~p~vvt~tes~c~na~a~~~~r~N~d~~ 407 (1672)
T KOG1878|consen 360 EEMEVAKSGLVEHGREWAAILPKVVTKTESQCKNAYAKYKNRHNLDEP 407 (1672)
T ss_pred hhhhhhhccchhhhhhHHHhcCccceecccchhhHHHhhhhhhcchhh
Confidence 455677788999999999999999999999999855555555544443
No 54
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=59.17 E-value=9.5 Score=34.85 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=33.9
Q ss_pred CCccCCC---hHHHHhhhhcccCCCchhhHHhhccCCchhHHHHHHHHH
Q 019067 256 PRRVMPD---FAQVYSFLGSVFDPNSTGHIQRLKQMDPINFETVLLLMR 301 (346)
Q Consensus 256 ~l~~~Pd---FaqVY~FigsvFdp~~~~hlq~Lk~MdpId~ETvLLLmr 301 (346)
.+.++|+ |+++|+||-..=.-+...|++.|-.-==|+.+++.++++
T Consensus 90 y~~~~P~Re~F~~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~ 138 (195)
T PF10141_consen 90 YFEGMPTREQFKKLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLK 138 (195)
T ss_pred hhcCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHH
Confidence 3567886 999999998862223467888886666688888777765
No 55
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=57.73 E-value=19 Score=31.63 Aligned_cols=44 Identities=14% Similarity=0.191 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019067 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (346)
Q Consensus 84 eEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~g~ 132 (346)
++-+.++|.+|++-|| .|..||+-+|- +...|+.|. .++.+.|-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri----~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERV----RRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHH----HHHHHCCC
Confidence 6789999999999998 99999999995 777888765 44555553
No 56
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=57.55 E-value=33 Score=27.45 Aligned_cols=41 Identities=22% Similarity=0.486 Sum_probs=29.7
Q ss_pred HHHHHHHHcCc--------hHHHHHHHhCCC-----CHHHHHHHHHHHHHHHhh
Q 019067 89 KFLEALQLFDR--------DWKKIEAFIGSK-----TVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 89 lFLeaLekyGr--------dWkkIA~~VgTR-----T~~QcRSHaQKYF~kl~k 129 (346)
+|-.++.+.|+ .|..|++.+|-. ...+++.|+++|+....+
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE~ 89 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPFER 89 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHHH
Confidence 34446777763 799999888754 357899999999776543
No 57
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=55.71 E-value=32 Score=39.51 Aligned_cols=58 Identities=16% Similarity=0.356 Sum_probs=45.9
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHcC-chHHHHHH------------HhCCCCHHHHHHHHHHHHHHHhhc
Q 019067 72 PYTITKSRESWTEQEHDKFLEALQLFD-RDWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 72 Py~i~k~r~~WTeEEh~lFLeaLekyG-rdWkkIA~------------~VgTRT~~QcRSHaQKYF~kl~k~ 130 (346)
.|. +.++..||+||+..+|-.+.+|| .+|.+|-. |+.+||+..+.-|+.-....+.|.
T Consensus 920 ~~~-~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e 990 (1033)
T PLN03142 920 QYG-QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKE 990 (1033)
T ss_pred ecC-CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHH
Confidence 343 34566799999999999999999 58999842 356999999999997766666554
No 58
>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=55.37 E-value=43 Score=23.71 Aligned_cols=37 Identities=5% Similarity=0.198 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHH
Q 019067 85 QEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQK 122 (346)
Q Consensus 85 EEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQK 122 (346)
+++...+...-..|..|+.||+.+| .|...|+.|.++
T Consensus 13 ~~~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~r 49 (54)
T PF08281_consen 13 ERQREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRR 49 (54)
T ss_dssp HHHHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHH
Confidence 3444455555566789999999998 588889887654
No 59
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=52.68 E-value=8.6 Score=30.99 Aligned_cols=18 Identities=11% Similarity=0.348 Sum_probs=10.0
Q ss_pred ccCCCCCCHHHHHHHHHH
Q 019067 76 TKSRESWTEQEHDKFLEA 93 (346)
Q Consensus 76 ~k~r~~WTeEEh~lFLea 93 (346)
....+.||+|+++.|+.+
T Consensus 44 ~n~~GiWT~eDD~~L~~~ 61 (87)
T PF11626_consen 44 DNMPGIWTPEDDEMLRSG 61 (87)
T ss_dssp TT-TT---HHHHHHHTS-
T ss_pred CCCCCCcCHHHHHHHHcC
Confidence 346789999999988443
No 60
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=49.44 E-value=31 Score=39.11 Aligned_cols=59 Identities=19% Similarity=0.400 Sum_probs=49.6
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019067 71 KPYTITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 71 kPy~i~k~r~~WTeEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~ 130 (346)
|+.-....-..||..+=..|+.|.++||+ |-..|++-|-. |++.|..++.-+|.++.+.
T Consensus 787 k~~ll~~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el 846 (971)
T KOG0385|consen 787 KEELLSQGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEEL 846 (971)
T ss_pred hhhhhhccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHh
Confidence 34444455668999999999999999998 89999988777 9999999999888887664
No 61
>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=49.04 E-value=48 Score=30.19 Aligned_cols=50 Identities=18% Similarity=0.366 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHHHHHcCc---hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019067 81 SWTEQEHDKFLEALQLFDR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 81 ~WTeEEh~lFLeaLekyGr---dWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~ 130 (346)
-++..+...||.+|-+||- +|+-.-..+..||...++.++--|+.++.-.
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~aY~~LFm~HL~E~ 92 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIRAYGSLFMRHLCEP 92 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHHHHHHHHHHHhcCC
Confidence 5789999999999999994 8999888889999999999987777777543
No 62
>PF10561 UPF0565: Uncharacterised protein family UPF0565; InterPro: IPR018881 This family of proteins has no known function.
Probab=48.56 E-value=15 Score=36.78 Aligned_cols=30 Identities=23% Similarity=0.598 Sum_probs=27.7
Q ss_pred CCCcccccCCCCCCHHHHHHHHHHHHHcCc
Q 019067 70 RKPYTITKSRESWTEQEHDKFLEALQLFDR 99 (346)
Q Consensus 70 rkPy~i~k~r~~WTeEEh~lFLeaLekyGr 99 (346)
-.||++....++|=.+|+++|++.|+++|-
T Consensus 272 ~TPyQv~D~~RpwI~~E~~~F~~~L~~~~~ 301 (303)
T PF10561_consen 272 VTPYQVSDPMRPWIGKEEKKFVKLLKKLGA 301 (303)
T ss_pred cCcccccCCCCcHHHHHHHHHHHHHHHhCC
Confidence 359999999999999999999999999984
No 63
>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=48.39 E-value=34 Score=30.58 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=36.1
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhC----CCCHHHHHHHHHHH
Q 019067 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIG----SKTVIQIRSHAQKY 123 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyGrdWkkIA~~Vg----TRT~~QcRSHaQKY 123 (346)
....=|..|.+-+...|++||.|++.++.=.. -.|+.||+-...+|
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 45567788888888889999999999994322 47999999876665
No 64
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=47.87 E-value=42 Score=26.83 Aligned_cols=44 Identities=18% Similarity=0.315 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019067 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (346)
Q Consensus 84 eEEh~lFLeaLekyGr-dWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~g~ 132 (346)
++.|.++|++|++.|+ .|+.|++.+|- +...|+.|. .++.+.|.
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l----~~L~~~g~ 46 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRV----KRLEEEGV 46 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHH----HHHHHCCC
Confidence 3678899999999997 99999999985 777888754 45555554
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=46.75 E-value=71 Score=25.21 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 81 ~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
..++.|...|... -..|..+..||+.+|. +...|+.+.++-..++++
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 4556665555332 2347799999999997 788888877776666643
No 66
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; 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: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=43.19 E-value=1.2e+02 Score=21.39 Aligned_cols=43 Identities=12% Similarity=0.142 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019067 84 EQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (346)
Q Consensus 84 eEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~ 128 (346)
++|.+.+..-+ ..|..+..||+.+|- +...|+.+-.+=+.+++
T Consensus 7 ~~er~vi~~~y-~~~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 7 PREREVIRLRY-FEGLTLEEIAERLGI-SRSTVRRILKRALKKLR 49 (50)
T ss_dssp HHHHHHHHHHH-TST-SHHHHHHHHTS-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh-cCCCCHHHHHHHHCC-cHHHHHHHHHHHHHHhc
Confidence 34444433333 335699999999996 77778776666566654
No 67
>PHA00442 host recBCD nuclease inhibitor
Probab=42.42 E-value=15 Score=28.71 Aligned_cols=33 Identities=24% Similarity=0.605 Sum_probs=26.1
Q ss_pred cccCCCCC--------CHHHHHHHHHHHHHcCc-hHHHHHHH
Q 019067 75 ITKSRESW--------TEQEHDKFLEALQLFDR-DWKKIEAF 107 (346)
Q Consensus 75 i~k~r~~W--------TeEEh~lFLeaLekyGr-dWkkIA~~ 107 (346)
.+..|..| +-|.+..||++|+..|- +|..+.+.
T Consensus 8 VtitRd~wnd~q~yidsLek~~~~L~~Lea~GVDNW~Gy~eA 49 (59)
T PHA00442 8 VTITRDAWNDMQGYIDSLEKDNEFLKALRACGVDNWDGYMDA 49 (59)
T ss_pred eeecHHHHHHHHHHHHHHHHhhHHHHHHHHcCCcchhhHHHH
Confidence 34556778 56778899999999995 99998643
No 68
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=42.09 E-value=2.4e+02 Score=28.55 Aligned_cols=68 Identities=18% Similarity=0.240 Sum_probs=46.4
Q ss_pred CCCCCCCCCCCcccc-------cCCCCCCHHHHHHHHHHHHHcC----chHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019067 62 AEDPSKKIRKPYTIT-------KSRESWTEQEHDKFLEALQLFD----RDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 62 ~e~~~kKirkPy~i~-------k~r~~WTeEEh~lFLeaLekyG----rdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~ 130 (346)
--..+.+-|||.+.. ..|..+|.|.-.+|..-++.-- ++-..++.-+| -+..||+.-+|+-..||+|.
T Consensus 226 RPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELg-LNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 226 RPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELG-LNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred CCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhC-cCHHHhhHHhhhhhhhhhhc
Confidence 344445666665543 2478999999888877665432 35566777666 48999999888877777664
No 69
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=39.67 E-value=1.1e+02 Score=20.04 Aligned_cols=42 Identities=12% Similarity=0.177 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHH
Q 019067 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 124 (346)
Q Consensus 81 ~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF 124 (346)
.+++++. .++..+-..|..++.||+.+|- +..+|+.+.++..
T Consensus 10 ~l~~~~~-~~~~~~~~~~~~~~~ia~~~~~-s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPERER-EVILLRFGEGLSYEEIAEILGI-SRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHH-HHHHHHHhcCCCHHHHHHHHCc-CHHHHHHHHHHHH
Confidence 4555554 4444444567799999998884 6677776655443
No 70
>PRK01905 DNA-binding protein Fis; Provisional
Probab=38.65 E-value=89 Score=24.58 Aligned_cols=28 Identities=7% Similarity=0.061 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhCC
Q 019067 83 TEQEHDKFLEALQLFDRDWKKIEAFIGS 110 (346)
Q Consensus 83 TeEEh~lFLeaLekyGrdWkkIA~~VgT 110 (346)
.+-|...+.++|+.+|.++.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 4557888999999999999999999995
No 71
>smart00595 MADF subfamily of SANT domain.
Probab=38.47 E-value=58 Score=25.24 Aligned_cols=22 Identities=18% Similarity=0.435 Sum_probs=19.9
Q ss_pred hHHHHHHHhCCCCHHHHHHHHHH
Q 019067 100 DWKKIEAFIGSKTVIQIRSHAQK 122 (346)
Q Consensus 100 dWkkIA~~VgTRT~~QcRSHaQK 122 (346)
-|..|+.-+|. |+.+|+.+|..
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~ 50 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKN 50 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHH
Confidence 69999999998 99999999865
No 72
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=37.67 E-value=73 Score=30.23 Aligned_cols=46 Identities=13% Similarity=0.206 Sum_probs=36.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcC---chHHHHH-----HHhCCCCHHHHHHHHHHH
Q 019067 78 SRESWTEQEHDKFLEALQLFD---RDWKKIE-----AFIGSKTVIQIRSHAQKY 123 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyG---rdWkkIA-----~~VgTRT~~QcRSHaQKY 123 (346)
.+..||.+|+++|........ ..+++|= .|-.+||+.+...||+--
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lm 125 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLM 125 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHH
Confidence 578999999999999765554 3777762 456789999999999843
No 73
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=36.85 E-value=90 Score=25.87 Aligned_cols=26 Identities=12% Similarity=0.081 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCC
Q 019067 85 QEHDKFLEALQLFDRDWKKIEAFIGS 110 (346)
Q Consensus 85 EEh~lFLeaLekyGrdWkkIA~~VgT 110 (346)
-|...+.++|+.+|.++.+.|+.+|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 47788999999999999999999995
No 74
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=32.90 E-value=1.4e+02 Score=22.24 Aligned_cols=46 Identities=7% Similarity=0.026 Sum_probs=32.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHH
Q 019067 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 125 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~ 125 (346)
.+..||+|+-...+..+..-|.....|+.-.|= ++.++.. |.+-|.
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi-~~~~l~~-W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREYGI-SPSTLYN-WRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS--HHHHHH-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeeccccc-ccccccH-HHHHHh
Confidence 567899999999999998888899999988786 6666664 555554
No 75
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=32.37 E-value=66 Score=29.13 Aligned_cols=37 Identities=16% Similarity=0.247 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 019067 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (346)
Q Consensus 81 ~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRS 118 (346)
.||+|+-++|.+ |-.-|..-.+|++-+|..|...|.-
T Consensus 2 ~Wtde~~~~L~~-lw~~G~SasqIA~~lg~vsRnAViG 38 (162)
T PF07750_consen 2 SWTDERVERLRK-LWAEGLSASQIARQLGGVSRNAVIG 38 (162)
T ss_pred CCCHHHHHHHHH-HHHcCCCHHHHHHHhCCcchhhhhh
Confidence 599988886554 4567888999999999444444443
No 76
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. 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 adaptor
Probab=31.84 E-value=35 Score=27.40 Aligned_cols=33 Identities=27% Similarity=0.445 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 019067 84 EQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (346)
Q Consensus 84 eEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRS 118 (346)
.||-+++|..= ..|+||+..|..+|- +...|+.
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~LG~-~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGELGY-EDEAIDT 34 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHcCC-CHHHHHH
Confidence 47777777521 567899999999995 3444443
No 77
>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=30.93 E-value=27 Score=39.26 Aligned_cols=56 Identities=20% Similarity=0.363 Sum_probs=43.4
Q ss_pred CCCCCCCCCCcccccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhC-CCCHHHHHH
Q 019067 63 EDPSKKIRKPYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIG-SKTVIQIRS 118 (346)
Q Consensus 63 e~~~kKirkPy~i~k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~Vg-TRT~~QcRS 118 (346)
....-+-|++..-.+-.-.|+..|-++|+++..++|++|++.+..+- +|...++.-
T Consensus 28 ~~sKt~qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~~vel 84 (837)
T KOG1019|consen 28 STSKTPQRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSNMVEL 84 (837)
T ss_pred ccccCCCCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhhHHHH
Confidence 33333555666656677899999999999999999999999986654 488877764
No 78
>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=30.87 E-value=85 Score=26.59 Aligned_cols=24 Identities=17% Similarity=0.459 Sum_probs=17.6
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhC
Q 019067 83 TEQEHDKFLEALQLFDRDWKKIEAFIG 109 (346)
Q Consensus 83 TeEEh~lFLeaLekyGrdWkkIA~~Vg 109 (346)
|+++...|-+ ..|++|++++..+|
T Consensus 1 ~~~~~q~~~~---nvGr~WK~laR~Lg 24 (90)
T cd08780 1 TPADQQHFAK---SVGKKWKPVGRSLQ 24 (90)
T ss_pred CHHHHHHHHH---HHhHHHHHHHHHHc
Confidence 4455555554 45899999999999
No 79
>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=30.04 E-value=50 Score=24.43 Aligned_cols=28 Identities=21% Similarity=0.517 Sum_probs=23.7
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhCC
Q 019067 83 TEQEHDKFLEALQLFDRDWKKIEAFIGS 110 (346)
Q Consensus 83 TeEEh~lFLeaLekyGrdWkkIA~~VgT 110 (346)
..+.|++|...|+.-....+-||+|+|-
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfGr 44 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFGR 44 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHcc
Confidence 3567999999997777799999999983
No 80
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=29.92 E-value=32 Score=27.35 Aligned_cols=19 Identities=32% Similarity=0.677 Sum_probs=15.5
Q ss_pred HHHHHHHHHcCchHHHHHH
Q 019067 88 DKFLEALQLFDRDWKKIEA 106 (346)
Q Consensus 88 ~lFLeaLekyGrdWkkIA~ 106 (346)
..+.+.|+.||++|.-|.+
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3566788999999999984
No 81
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=28.35 E-value=1e+02 Score=32.05 Aligned_cols=13 Identities=46% Similarity=0.549 Sum_probs=9.2
Q ss_pred CCCCCCCCccccc
Q 019067 65 PSKKIRKPYTITK 77 (346)
Q Consensus 65 ~~kKirkPy~i~k 77 (346)
..||.|||+..+|
T Consensus 190 t~KKpRKPRqtKK 202 (379)
T PF11593_consen 190 TAKKPRKPRQTKK 202 (379)
T ss_pred ccCCCCCCCCccc
Confidence 3488888887555
No 82
>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=28.02 E-value=1e+02 Score=22.90 Aligned_cols=25 Identities=16% Similarity=0.296 Sum_probs=20.4
Q ss_pred hHHHHHHHhCC-CCHHHHHHHHHHHH
Q 019067 100 DWKKIEAFIGS-KTVIQIRSHAQKYF 124 (346)
Q Consensus 100 dWkkIA~~VgT-RT~~QcRSHaQKYF 124 (346)
-|..|+..++. -+..+|+.+|+...
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHH
Confidence 69999988885 47889999997753
No 83
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=27.92 E-value=50 Score=34.65 Aligned_cols=51 Identities=22% Similarity=0.322 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHHcCchHHHHHHH-----hCC-CCHHHHHHHHHHHHHHHhh
Q 019067 79 RESWTEQEHDKFLEALQLFDRDWKKIEAF-----IGS-KTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 79 r~~WTeEEh~lFLeaLekyGrdWkkIA~~-----VgT-RT~~QcRSHaQKYF~kl~k 129 (346)
...||.||.+-|.+..+.|.-+|--|++- .+. ||.+..+.++=....++-+
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~k 186 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLK 186 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHH
Confidence 35799999999999999999989888843 565 9999999976333444433
No 84
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.26 E-value=2.1e+02 Score=23.90 Aligned_cols=32 Identities=13% Similarity=0.230 Sum_probs=23.7
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019067 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (346)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k 129 (346)
.|..+..||+.+|. +...|+.+..+-..++++
T Consensus 140 ~~~~~~eIA~~lgi-s~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 140 EGLSYREIAEILGV-PVGTVKSRLRRARQLLRE 171 (179)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHH
Confidence 46789999999985 677777777666666644
No 85
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=26.24 E-value=75 Score=34.38 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 019067 80 ESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (346)
Q Consensus 80 ~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSHaQKYF~k 126 (346)
..--+.|.+++.++|++.|.+|.+-|+.+|. ++.|+-+.+++|=++
T Consensus 501 ~~~~~~eR~~I~~aL~~~~~~~a~AAr~LGl-~~~~L~~~~kRlGI~ 546 (550)
T COG3604 501 EATEEFERQLIIAALEETNGNWAGAARRLGL-TRRTLLYRMKRLGIK 546 (550)
T ss_pred hhhHHHHHHHHHHHHHHhCCcHHHHHHHhCC-CHHHHHHHHHHcCCC
Confidence 3344778889999999999999998899996 788988877666333
No 86
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=24.98 E-value=27 Score=41.61 Aligned_cols=50 Identities=16% Similarity=0.262 Sum_probs=42.2
Q ss_pred CCCcccccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHH
Q 019067 70 RKPYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSH 119 (346)
Q Consensus 70 rkPy~i~k~r~~WTeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRSH 119 (346)
.|+|+.......|+++|++.|..-+.++-++...|+.|+--||..+|--+
T Consensus 216 nkv~k~~~~~n~Ws~~Ek~~fk~rf~~H~knf~~~as~~erkSv~d~vlf 265 (1672)
T KOG1878|consen 216 NKVHKDRQRMNEWSPEEKELFKSRFAQHVKNFGLIASFFERKSVSDCVLF 265 (1672)
T ss_pred ccccchHHHhhhccccccccccchhhhcCcchhhhhhhhcccchhhceee
Confidence 34444444778999999999999999999999999999999999998764
No 87
>PF12181 MogR_DNAbind: DNA binding domain of the motility gene repressor (MogR); InterPro: IPR021009 This domain family is found in bacteria, and is approximately 150 amino acids in length. MogR is involved in the transcriptional repressor of flagellar motility genes, such as flaA, during extracellular growth at 37 degrees Celsius and during intracellular infection. It binds directly to gene promoter region and probably prevents RNA polymerase binding. At low temperatures, MogR repression activity is modulated by the DegU response regulator in an unknown mechanism. MogR is required for full virulence []. MogR binds AT rich flagellar gene promoter regions upstream of the flagellar gene. These regions follow the pattern 5'-TTTTNNNNNAAAA-3'. This domain is the DNA binding domain of MogR []. ; PDB: 3FDQ_B.
Probab=24.92 E-value=1.9e+02 Score=26.34 Aligned_cols=64 Identities=23% Similarity=0.333 Sum_probs=34.4
Q ss_pred CCCCCCHHHHHHHHHHHH---HcCchHHHHHHHhC-------CCCHHHHHHHHHHHHHHHhhcCCCCCCCC--CCCCCC
Q 019067 78 SRESWTEQEHDKFLEALQ---LFDRDWKKIEAFIG-------SKTVIQIRSHAQKYFLKVQKNGTSEHVPP--PRPKRK 144 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLe---kyGrdWkkIA~~Vg-------TRT~~QcRSHaQKYF~kl~k~g~~~~iP~--pr~KRk 144 (346)
..-.|=.-|-++|-+.++ .+|-+--.|+++|. -||+.|..+- ||.-.+..-..++||. |.||||
T Consensus 59 S~isWLKsELELLy~~YQf~q~h~lni~diSk~~Skn~L~lFpKTeSQLQNT---YYKLKk~~i~fEnI~K~KPGRKrK 134 (148)
T PF12181_consen 59 SNISWLKSELELLYACYQFCQRHGLNILDISKMLSKNDLNLFPKTESQLQNT---YYKLKKEEIPFENIKKNKPGRKRK 134 (148)
T ss_dssp SSEEE-HHHHHHHHHHHHHHHHTT--HHHHHHHHSTTTT-SSSS-HHHHHHH---HHHHHTTSS-SS-EE----S----
T ss_pred hhhHHHHHHHHHHHHHHHHHHHcCCccccHHHHhhhhhhccCCCCHHHHHHH---HHHHHhhhcchhhccccCCCcccc
Confidence 344798889888887664 45667777888866 5899998873 4433333334566665 445654
No 88
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=24.79 E-value=55 Score=32.94 Aligned_cols=58 Identities=22% Similarity=0.311 Sum_probs=36.1
Q ss_pred CCCCCCCCCcccccCCCCCCHHHHHHHHHHHHHc---CchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019067 64 DPSKKIRKPYTITKSRESWTEQEHDKFLEALQLF---DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (346)
Q Consensus 64 ~~~kKirkPy~i~k~r~~WTeEEh~lFLeaLeky---GrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~k~ 130 (346)
..++|-|+||+. .=|.|=|+-|| +.+| .|+|. |++.+- =|..||+.-+|+-..|.+|.
T Consensus 233 ~~~RKKRcPYTK-----~QtlELEkEFl--fN~YitkeKR~E-lSr~lN-LTeRQVKIWFQNRRMK~KK~ 293 (308)
T KOG0487|consen 233 RRGRKKRCPYTK-----HQTLELEKEFL--FNMYITKEKRLE-LSRTLN-LTERQVKIWFQNRRMKEKKV 293 (308)
T ss_pred cccccccCCchH-----HHHHHHHHHHH--HHHHHhHHHHHH-HHHhcc-cchhheeeeehhhhhHHhhh
Confidence 345677778872 22344444444 2333 34665 888775 48999999777776666664
No 89
>PF01410 COLFI: Fibrillar collagen C-terminal domain; InterPro: IPR000885 Collagens contain a large number of globular domains in between the regions of triple helical repeats IPR008160 from INTERPRO. These domains are involved in binding diverse substrates. One of these domains is found at the C terminus of fibrillar collagens. The exact function of this domain is unknown.; GO: 0005201 extracellular matrix structural constituent, 0005581 collagen
Probab=24.51 E-value=39 Score=31.54 Aligned_cols=16 Identities=25% Similarity=0.657 Sum_probs=14.3
Q ss_pred CCCCCCCCCcccCCCC
Q 019067 4 VNPNPAQGFFFFDPMN 19 (346)
Q Consensus 4 ~~p~~~~~~~~~dp~~ 19 (346)
.+|+.+.|.|++||.+
T Consensus 21 ~~p~~~dG~YwIDPN~ 36 (214)
T PF01410_consen 21 CHPELPDGEYWIDPNG 36 (214)
T ss_pred hCcccCCCcEeECCCC
Confidence 5799999999999984
No 90
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.52 E-value=1.5e+02 Score=20.61 Aligned_cols=34 Identities=12% Similarity=0.231 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 019067 83 TEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (346)
Q Consensus 83 TeEEh~lFLeaLekyGrdWkkIA~~VgTRT~~QcRS 118 (346)
+.++....++.+.. |...+.||+.+|- +...|..
T Consensus 3 ~~~~R~~ii~l~~~-G~s~~~ia~~lgv-s~~Tv~~ 36 (50)
T PF13384_consen 3 SEERRAQIIRLLRE-GWSIREIAKRLGV-SRSTVYR 36 (50)
T ss_dssp -------HHHHHHH-T--HHHHHHHHTS--HHHHHH
T ss_pred chhHHHHHHHHHHC-CCCHHHHHHHHCc-CHHHHHH
Confidence 44556667777777 8899999999984 5555554
No 91
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=22.03 E-value=75 Score=25.18 Aligned_cols=23 Identities=17% Similarity=0.473 Sum_probs=18.0
Q ss_pred HHHHHHHHHcCchHHHHHHHhCC
Q 019067 88 DKFLEALQLFDRDWKKIEAFIGS 110 (346)
Q Consensus 88 ~lFLeaLekyGrdWkkIA~~VgT 110 (346)
..|...-+..|++|+++|..+|-
T Consensus 5 ~~l~~ia~~lG~dW~~LAr~Lg~ 27 (84)
T cd08317 5 IRLADISNLLGSDWPQLARELGV 27 (84)
T ss_pred chHHHHHHHHhhHHHHHHHHcCC
Confidence 34555667779999999999984
No 92
>TIGR03238 dnd_assoc_3 dnd system-associated protein 3. cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.
Probab=21.51 E-value=1.1e+02 Score=32.86 Aligned_cols=52 Identities=23% Similarity=0.477 Sum_probs=41.0
Q ss_pred ccCCCchhhHHhhccCCchhHHH--HHHHHHHHHhhcCChhhHHHHHHHhhhcc
Q 019067 273 VFDPNSTGHIQRLKQMDPINFET--VLLLMRNLAINLTSPEFEDHKRLLSLYDV 324 (346)
Q Consensus 273 vFdp~~~~hlq~Lk~MdpId~ET--vLLLmrNLs~NL~sp~fe~~~~llssy~~ 324 (346)
+|-++.+.=+.+|.+|||++.-| +--+.=+++.||-.|.|.+-...|..|+.
T Consensus 243 lf~~~~s~L~~~i~~~DP~~~r~~~iD~fIl~~~l~i~d~~~~~f~~~l~~~g~ 296 (504)
T TIGR03238 243 LFSKERSELLKFLHELDPVHRRTSKIDQFIIDLSLNLPDQEFNEFKTVLNRLGC 296 (504)
T ss_pred CCCccccHHHHHhhhcCchhhcchhHhHHHHHhhccCCchhHHHHHHHHHhccc
Confidence 44467788999999999999866 33355566999999999998888888654
No 93
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=21.24 E-value=57 Score=38.54 Aligned_cols=53 Identities=15% Similarity=0.306 Sum_probs=37.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-chHHHHH--------HHhC----CCCHHHHHHHHHHHHHHHhhcC
Q 019067 78 SRESWTEQEHDKFLEALQLFD-RDWKKIE--------AFIG----SKTVIQIRSHAQKYFLKVQKNG 131 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyG-rdWkkIA--------~~Vg----TRT~~QcRSHaQKYF~kl~k~g 131 (346)
-..-|..||+..||.||-+|| +.|..|- +-+. --...|...++ .|+..+.+.+
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~-~yLls~~~~~ 1197 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRA-DYLLSLLRKH 1197 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHH-HHHHHHHhhc
Confidence 456899999999999999999 5999993 1111 12345666655 6888776654
No 94
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=20.61 E-value=3.9e+02 Score=21.76 Aligned_cols=31 Identities=19% Similarity=0.333 Sum_probs=22.8
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019067 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (346)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~ 128 (346)
.|..++.||+.+|- +...|+.+...-..+++
T Consensus 128 ~~~~~~eIA~~lgi-s~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 128 EGKSYKEIAEELGI-SVKTVEYHISKALKELR 158 (161)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
Confidence 36689999999885 88888887655555553
No 95
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.60 E-value=2.8e+02 Score=24.43 Aligned_cols=31 Identities=6% Similarity=0.045 Sum_probs=22.2
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019067 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (346)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYF~kl~ 128 (346)
.|..++.||+.+|. +...|++|...=..+++
T Consensus 149 ~g~s~~EIA~~lg~-s~~tV~~rl~rar~~Lr 179 (192)
T PRK09643 149 QGYSVADAARMLGV-AEGTVKSRCARGRARLA 179 (192)
T ss_pred cCCCHHHHHHHHCc-CHHHHHHHHHHHHHHHH
Confidence 46689999999885 77888887644444443
No 96
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=20.11 E-value=95 Score=23.89 Aligned_cols=23 Identities=22% Similarity=0.560 Sum_probs=17.6
Q ss_pred HHHHHHHHH-cCchHHHHHHHhCC
Q 019067 88 DKFLEALQL-FDRDWKKIEAFIGS 110 (346)
Q Consensus 88 ~lFLeaLek-yGrdWkkIA~~VgT 110 (346)
..|...++. .|.+|+.++..+|-
T Consensus 6 ~~~~~l~~~~~g~~W~~la~~Lg~ 29 (88)
T smart00005 6 EKLAKLLDHPLGLDWRELARKLGL 29 (88)
T ss_pred HHHHHHHcCccchHHHHHHHHcCC
Confidence 445555555 79999999999995
No 97
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.01 E-value=64 Score=30.20 Aligned_cols=28 Identities=18% Similarity=0.430 Sum_probs=24.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCc-hHHHHH
Q 019067 78 SRESWTEQEHDKFLEALQLFDR-DWKKIE 105 (346)
Q Consensus 78 ~r~~WTeEEh~lFLeaLekyGr-dWkkIA 105 (346)
-.+-|-.+-|..||.|+..||- +|..|.
T Consensus 2 ~~~iw~r~hdywll~gi~~hgy~rwqdi~ 30 (173)
T PF08074_consen 2 EYEIWHRRHDYWLLAGIVKHGYGRWQDIQ 30 (173)
T ss_pred hhhhhhhhhhHHHHhHHhhccchhHHHHh
Confidence 3567999999999999999994 999996
Done!