Query 019534
Match_columns 339
No_of_seqs 216 out of 744
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 02:31:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019534.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019534hhsearch_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 6.2E-15 1.3E-19 111.1 6.1 50 77-126 1-56 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.5 2.3E-14 5.1E-19 102.1 5.9 46 79-124 1-48 (48)
3 KOG0724 Zuotin and related mol 99.4 1.4E-14 3.1E-19 137.7 -3.0 243 62-319 35-311 (335)
4 smart00717 SANT SANT SWI3, AD 99.2 2.1E-11 4.6E-16 82.7 5.3 46 79-124 1-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 4.8E-11 1E-15 80.1 5.5 43 81-123 1-44 (45)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.1 7.6E-11 1.7E-15 86.6 4.8 43 82-124 1-43 (60)
7 KOG0457 Histone acetyltransfer 99.0 5.5E-10 1.2E-14 112.2 7.3 65 62-126 49-120 (438)
8 PLN03212 Transcription repress 98.8 4.5E-09 9.7E-14 99.6 5.8 51 77-127 23-75 (249)
9 PLN03212 Transcription repress 98.8 1.9E-08 4E-13 95.5 8.7 53 77-129 76-128 (249)
10 PLN03091 hypothetical protein; 98.7 9.8E-09 2.1E-13 103.8 5.2 52 75-126 10-63 (459)
11 PLN03091 hypothetical protein; 98.6 5.5E-08 1.2E-12 98.5 7.2 53 77-129 65-117 (459)
12 KOG0048 Transcription factor, 98.6 1.3E-07 2.8E-12 87.7 7.1 53 77-129 60-112 (238)
13 COG5259 RSC8 RSC chromatin rem 98.5 1.1E-07 2.3E-12 97.0 5.2 41 80-120 280-320 (531)
14 KOG0048 Transcription factor, 98.5 7.3E-08 1.6E-12 89.3 3.5 51 79-129 9-61 (238)
15 COG5114 Histone acetyltransfer 98.4 7.7E-07 1.7E-11 87.8 8.3 64 63-126 41-111 (432)
16 KOG1279 Chromatin remodeling f 98.4 5.4E-07 1.2E-11 92.8 5.9 44 77-120 251-294 (506)
17 KOG0049 Transcription factor, 97.7 5.7E-05 1.2E-09 80.2 6.1 53 77-129 358-411 (939)
18 PLN03162 golden-2 like transcr 97.1 0.0039 8.5E-08 63.3 10.1 55 76-130 234-293 (526)
19 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.0027 5.8E-08 49.3 5.1 50 79-128 1-68 (90)
20 KOG0051 RNA polymerase I termi 96.7 0.0017 3.6E-08 68.7 4.8 53 73-126 377-430 (607)
21 KOG4468 Polycomb-group transcr 96.7 0.0063 1.4E-07 64.7 8.4 53 78-130 87-149 (782)
22 KOG0050 mRNA splicing protein 96.4 0.0036 7.8E-08 65.4 4.7 54 75-128 3-57 (617)
23 KOG0049 Transcription factor, 96.4 0.0043 9.4E-08 66.5 5.3 46 78-123 411-457 (939)
24 KOG0051 RNA polymerase I termi 96.3 0.0047 1E-07 65.4 4.6 51 77-127 434-510 (607)
25 COG5147 REB1 Myb superfamily p 95.3 0.011 2.4E-07 61.7 2.7 57 73-129 14-71 (512)
26 KOG4329 DNA-binding protein [G 95.3 0.024 5.2E-07 57.5 4.8 45 79-126 277-322 (445)
27 COG5118 BDP1 Transcription ini 95.0 0.048 1E-06 55.8 6.1 42 78-119 364-405 (507)
28 PF13873 Myb_DNA-bind_5: Myb/S 94.8 0.13 2.8E-06 39.5 6.9 51 79-129 2-74 (78)
29 KOG4167 Predicted DNA-binding 94.6 0.062 1.3E-06 58.5 6.0 45 78-122 618-662 (907)
30 KOG0724 Zuotin and related mol 93.3 0.052 1.1E-06 52.3 2.4 70 77-153 162-238 (335)
31 COG5147 REB1 Myb superfamily p 93.2 0.11 2.3E-06 54.6 4.6 53 77-129 70-122 (512)
32 KOG0050 mRNA splicing protein 93.2 0.09 1.9E-06 55.4 4.0 47 78-125 58-104 (617)
33 KOG3554 Histone deacetylase co 92.8 0.11 2.4E-06 54.4 4.0 44 77-120 283-327 (693)
34 KOG3841 TEF-1 and related tran 92.6 0.57 1.2E-05 48.1 8.6 52 77-129 74-147 (455)
35 KOG1194 Predicted DNA-binding 92.5 0.3 6.6E-06 50.9 6.6 42 79-120 187-228 (534)
36 PF09111 SLIDE: SLIDE; InterP 92.5 0.46 9.9E-06 40.9 6.7 58 72-129 42-115 (118)
37 TIGR02894 DNA_bind_RsfA transc 91.8 0.33 7E-06 44.3 5.2 52 78-130 3-61 (161)
38 PLN03142 Probable chromatin-re 91.7 0.37 8E-06 54.4 6.6 48 80-127 825-873 (1033)
39 PF08914 Myb_DNA-bind_2: Rap1 89.7 0.5 1.1E-05 36.8 3.9 48 79-126 2-59 (65)
40 PF12776 Myb_DNA-bind_3: Myb/S 89.7 1 2.2E-05 35.3 5.8 43 81-123 1-61 (96)
41 smart00426 TEA TEA domain. 89.0 0.5 1.1E-05 37.7 3.5 43 79-121 3-66 (68)
42 PRK13923 putative spore coat p 86.8 0.91 2E-05 41.7 4.2 50 78-127 4-59 (170)
43 KOG4282 Transcription factor G 85.3 12 0.00026 36.5 11.4 51 79-129 54-118 (345)
44 PF04504 DUF573: Protein of un 81.4 5.5 0.00012 33.1 6.3 43 79-121 4-59 (98)
45 PF01285 TEA: TEA/ATTS domain 80.3 1.9 4.2E-05 44.4 4.0 48 76-123 46-112 (431)
46 PF13404 HTH_AsnC-type: AsnC-t 76.4 9.7 0.00021 27.0 5.5 37 85-122 3-40 (42)
47 KOG1194 Predicted DNA-binding 74.6 6 0.00013 41.7 5.6 56 72-127 362-417 (534)
48 KOG2009 Transcription initiati 74.3 2.9 6.3E-05 44.9 3.3 50 78-130 408-457 (584)
49 PF11035 SnAPC_2_like: Small n 71.9 12 0.00027 37.8 6.8 52 78-129 20-75 (344)
50 PF08281 Sigma70_r4_2: Sigma-7 69.4 18 0.00039 25.6 5.6 39 85-124 13-51 (54)
51 PF01388 ARID: ARID/BRIGHT DNA 67.6 12 0.00025 29.6 4.7 38 89-126 40-90 (92)
52 PF02954 HTH_8: Bacterial regu 66.9 15 0.00032 25.7 4.6 25 86-110 6-30 (42)
53 PLN03142 Probable chromatin-re 64.7 17 0.00037 41.5 6.9 55 76-130 923-990 (1033)
54 PRK11179 DNA-binding transcrip 64.3 14 0.00031 31.9 5.0 44 84-132 8-52 (153)
55 smart00501 BRIGHT BRIGHT, ARID 63.5 22 0.00047 28.4 5.6 40 90-129 37-89 (93)
56 KOG2656 DNA methyltransferase 62.5 6.9 0.00015 40.6 3.1 51 79-129 130-186 (445)
57 PRK11169 leucine-responsive tr 61.0 19 0.0004 31.7 5.2 44 84-132 13-57 (164)
58 KOG0493 Transcription factor E 58.8 1.1E+02 0.0024 30.8 10.4 53 78-131 249-305 (342)
59 PF11626 Rap1_C: TRF2-interact 58.5 5.9 0.00013 31.8 1.5 38 77-120 45-82 (87)
60 PF09420 Nop16: Ribosome bioge 57.6 20 0.00042 32.0 4.8 46 78-123 113-162 (164)
61 TIGR02937 sigma70-ECF RNA poly 57.5 36 0.00079 26.8 5.9 47 81-129 110-156 (158)
62 PF06461 DUF1086: Domain of Un 55.8 31 0.00068 31.2 5.7 50 81-130 40-92 (145)
63 PF04545 Sigma70_r4: Sigma-70, 54.6 63 0.0014 22.7 6.1 42 86-128 8-49 (50)
64 PF10561 UPF0565: Uncharacteri 50.8 13 0.00028 37.1 2.7 29 71-99 273-301 (303)
65 KOG1878 Nuclear receptor coreg 50.8 5.4 0.00012 46.9 0.2 48 85-132 360-407 (1672)
66 KOG0385 Chromatin remodeling c 50.6 28 0.00062 39.3 5.5 59 71-130 787-846 (971)
67 smart00344 HTH_ASNC helix_turn 50.6 36 0.00079 27.1 4.9 44 84-132 2-46 (108)
68 PF07750 GcrA: GcrA cell cycle 44.0 37 0.00081 30.6 4.4 37 81-118 2-38 (162)
69 PHA00442 host recBCD nuclease 43.7 13 0.00028 29.0 1.2 32 76-107 9-49 (59)
70 cd06171 Sigma70_r4 Sigma70, re 43.7 91 0.002 20.3 5.4 42 81-124 10-51 (55)
71 PF10440 WIYLD: Ubiquitin-bind 43.4 14 0.00031 29.2 1.5 19 88-106 30-48 (65)
72 PF13325 MCRS_N: N-terminal re 41.2 62 0.0014 30.6 5.5 46 78-123 72-125 (199)
73 smart00595 MADF subfamily of S 41.0 49 0.0011 25.6 4.1 23 100-123 29-51 (89)
74 PRK01905 DNA-binding protein F 38.8 85 0.0018 24.6 5.2 28 83-110 35-62 (77)
75 PRK00430 fis global DNA-bindin 37.1 86 0.0019 25.9 5.2 26 85-110 55-80 (95)
76 PF01527 HTH_Tnp_1: Transposas 36.5 1.1E+02 0.0024 22.7 5.3 46 78-125 3-48 (76)
77 KOG0384 Chromodomain-helicase 36.0 1.2E+02 0.0025 36.1 7.6 54 78-132 1132-1198(1373)
78 KOG1019 Retinoblastoma pathway 35.8 24 0.00052 39.6 2.2 63 56-118 21-84 (837)
79 PRK11924 RNA polymerase sigma 32.7 1.4E+02 0.0031 24.8 6.0 32 96-128 139-170 (179)
80 cd08311 Death_p75NR Death doma 30.8 39 0.00084 27.1 2.1 33 84-118 2-34 (77)
81 cd08780 Death_TRADD Death Doma 30.2 91 0.002 26.3 4.2 24 83-109 1-24 (90)
82 COG1522 Lrp Transcriptional re 30.1 1.4E+02 0.0031 24.9 5.6 44 84-132 7-51 (154)
83 PF10545 MADF_DNA_bdg: Alcohol 29.3 95 0.0021 23.1 3.9 25 99-123 27-52 (85)
84 TIGR02985 Sig70_bacteroi1 RNA 28.9 2.1E+02 0.0046 23.3 6.3 31 97-128 128-158 (161)
85 PF12451 VPS11_C: Vacuolar pro 28.4 53 0.0012 24.2 2.3 28 83-110 17-44 (49)
86 KOG1878 Nuclear receptor coreg 27.6 22 0.00049 42.2 0.3 44 77-120 223-266 (1672)
87 PRK09652 RNA polymerase sigma 27.3 2.1E+02 0.0046 23.8 6.2 31 96-127 142-172 (182)
88 PF06628 Catalase-rel: Catalas 27.3 2.1E+02 0.0046 22.0 5.6 39 81-129 19-57 (68)
89 TIGR02915 PEP_resp_reg putativ 26.5 82 0.0018 31.1 4.0 39 84-131 404-443 (445)
90 PF01410 COLFI: Fibrillar coll 25.9 35 0.00077 31.7 1.3 16 4-19 21-36 (214)
91 PRK09643 RNA polymerase sigma 25.2 2.3E+02 0.0049 25.0 6.2 32 95-127 147-178 (192)
92 PF13384 HTH_23: Homeodomain-l 24.7 1.3E+02 0.0028 20.8 3.7 34 83-118 3-36 (50)
93 PF01726 LexA_DNA_bind: LexA D 24.4 2.3E+02 0.0051 21.8 5.4 39 94-136 19-59 (65)
94 PRK11608 pspF phage shock prot 23.7 99 0.0021 30.1 3.9 38 85-131 286-324 (326)
95 COG3604 FhlA Transcriptional r 23.5 89 0.0019 33.8 3.7 43 81-124 502-544 (550)
96 PRK10365 transcriptional regul 22.6 90 0.0019 30.6 3.4 29 84-112 404-433 (441)
97 TIGR00571 dam DNA adenine meth 22.2 83 0.0018 29.8 3.0 49 69-122 178-237 (266)
98 PF00191 Annexin: Annexin; In 22.0 1.2E+02 0.0025 22.1 3.2 39 88-126 4-42 (66)
99 cd08317 Death_ank Death domain 21.9 75 0.0016 25.1 2.3 23 88-110 5-27 (84)
100 PF11593 Med3: Mediator comple 21.7 1.6E+02 0.0034 30.6 4.9 13 65-77 190-202 (379)
101 PF12181 MogR_DNAbind: DNA bin 21.5 2.4E+02 0.0051 25.7 5.5 64 78-144 59-134 (148)
102 PF09862 DUF2089: Protein of u 21.4 2.8E+02 0.006 24.2 5.7 43 84-127 35-77 (113)
103 PRK05022 anaerobic nitric oxid 20.8 1.3E+02 0.0027 31.2 4.2 40 84-132 467-507 (509)
104 PRK11388 DNA-binding transcrip 20.8 1.4E+02 0.0031 31.5 4.7 42 82-132 588-630 (638)
105 KOG1079 Transcriptional repres 20.3 1.3E+02 0.0028 33.6 4.2 53 70-122 399-452 (739)
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=99.56 E-value=6.2e-15 Score=111.12 Aligned_cols=50 Identities=48% Similarity=0.727 Sum_probs=46.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCh-hH---HHHHHHhC-CC-CHHHHHHHHHHHHHH
Q 019534 77 KSRESWTEQEHDKFLEALQLFDR-DW---KKIEAFIG-SK-TVIQIRSHAQKYFLK 126 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGr-dW---kkIA~~Vg-TR-T~~QIRSHaQKYf~k 126 (339)
|.+..||+|||.+||+||+.||+ +| ++|+++++ ++ |..||++|+||||.+
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 46789999999999999999997 99 99998776 67 999999999999986
No 2
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.51 E-value=2.3e-14 Score=102.13 Aligned_cols=46 Identities=41% Similarity=0.724 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHcChh-HHHHHHHhC-CCCHHHHHHHHHHHH
Q 019534 79 RESWTEQEHDKFLEALQLFDRD-WKKIEAFIG-SKTVIQIRSHAQKYF 124 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyGrd-WkkIA~~Vg-TRT~~QIRSHaQKYf 124 (339)
++.||+||+++|+++|++||.+ |+.||++|+ +||..||++||++|+
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 4789999999999999999986 999999999 999999999999873
No 3
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.40 E-value=1.4e-14 Score=137.74 Aligned_cols=243 Identities=23% Similarity=0.146 Sum_probs=154.9
Q ss_pred CCCCCCCCCCCcccccCCCC-CCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc-CCC---CCC
Q 019534 62 AEDPSKKIRKPYTITKSRES-WTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN-GTS---EHV 136 (339)
Q Consensus 62 ~e~~~~KvrkPytitk~r~~-WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~-g~~---e~i 136 (339)
.++..++|+++|++.+.+.+ ||.+|++.|.++|..|++.|..|-++++.++..|++.|+|+||-++.+. +.. +.+
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 45667899999999997554 9999999999999999889999999999999999999999999998774 222 348
Q ss_pred CCCCCCCCCCCCCCCCCCCCcccccccCCCcCCcccccCCCcccCCCCCCccCCCCCcccCCCCCCCCCCCccccccccc
Q 019534 137 PPPRPKRKAAHPYPQKAPKTVHGVSQFGGQVQSSAALLEPGYIYRPDSSSVLGNPVPVAALSSWSYDSVPPVNVSQVTKD 216 (339)
Q Consensus 137 Pppr~KRks~h~~p~k~~~~~~~~~q~~~~~qss~~~~e~g~~~~~dsss~~~~~~~~~~~~sw~~~~~~~~~~~~~~~~ 216 (339)
|++++++++.|+|+++...+.... ..........+. +++....+..+..+..+.......|..... .
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 999999999999999987643221 111111112222 344444444444444443333222222100 0
Q ss_pred CCCCCCCCCCCCc----ccccCCCCCCC------ccccccccCCCCCCCC---Ce------eeeeccccc-----C----
Q 019534 217 DVGLPGSSNAQNF----CYSSSNDSTLR------TWPVGETIDRGDHGKP---RR------VYSFLGSVF-----D---- 268 (339)
Q Consensus 217 d~~~~g~~~~~n~----~~sss~~s~~~------~~~~~~~~~~~~~~~~---~~------VY~FiGsvF-----d---- 268 (339)
++....-....++ +.. .-++-.. ........+.....+. ++ .+.|.++++ +
T Consensus 182 ~~~~~~~~~~~~~~~~r~~~-~~~s~a~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 260 (335)
T KOG0724|consen 182 DGKIDWRKISQNVEKERTPE-QVASHAQEKAFEKALARQKSGEEEKRRKSIEDITTASEAEDRKKEDEAAKEAKKKPRDT 260 (335)
T ss_pred cccccceechhhhhhhhcch-hhhhhhhhhhhHHHHHHHhhhccccccchhhhhhccchhhhhhcchhhhhhhhcccccc
Confidence 1110000001110 000 0000000 0000001111111111 11 444999999 7
Q ss_pred CCCchhhhhhccCCcchHHHHHHHHH-HHHhhcCCchhHHHHHhhhhccccc
Q 019534 269 PNSTGHIQRLKQMDPINFETVLLLMR-NLAINLTSPEFEDHKRLLSLYDVES 319 (339)
Q Consensus 269 p~~~~hlq~Lk~MdpI~~ETvLLLmr-NLs~NL~sp~fe~~~~lls~y~~~~ 319 (339)
|...+|.+.++.|++++.++.++.|. |+..+|+++.|++++.+++. ....
T Consensus 261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 311 (335)
T KOG0724|consen 261 PSLKSRNKRLKSFDGIAEESSETEDSLELVAALSAPMEEPQWELKAA-AGSN 311 (335)
T ss_pred ccccchhhhcccCCccCCCchhHHHhHHHHHhhhccccccHHHHHhh-cccc
Confidence 88999999999999999999999999 89999999999999777766 5543
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.21 E-value=2.1e-11 Score=82.73 Aligned_cols=46 Identities=24% Similarity=0.539 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC-hhHHHHHHHhCCCCHHHHHHHHHHHH
Q 019534 79 RESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYF 124 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyG-rdWkkIA~~VgTRT~~QIRSHaQKYf 124 (339)
+..||.||+.+|++++.+|| .+|..||+++++||..||+.||..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 46899999999999999999 89999999999999999999987654
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=99.17 E-value=4.8e-11 Score=80.10 Aligned_cols=43 Identities=30% Similarity=0.581 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHHHcC-hhHHHHHHHhCCCCHHHHHHHHHHH
Q 019534 81 SWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKY 123 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqkyG-rdWkkIA~~VgTRT~~QIRSHaQKY 123 (339)
.||.||+.+|+.++.+|| .+|..|++++++||..||+.||+++
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=99.12 E-value=7.6e-11 Score=86.58 Aligned_cols=43 Identities=33% Similarity=0.670 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHH
Q 019534 82 WTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 124 (339)
Q Consensus 82 WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf 124 (339)
||.||+++|++++++||.+|++||+++|.||..||+.||.+++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHL 43 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999987643
No 7
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.01 E-value=5.5e-10 Score=112.19 Aligned_cols=65 Identities=32% Similarity=0.559 Sum_probs=59.7
Q ss_pred CCCCCCCCCCCcccccC------CCCCCHHHHHHHHHHHHHcC-hhHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 019534 62 AEDPSKKIRKPYTITKS------RESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (339)
Q Consensus 62 ~e~~~~KvrkPytitk~------r~~WT~EEh~lFLEaLqkyG-rdWkkIA~~VgTRT~~QIRSHaQKYf~k 126 (339)
+|-+.|+-.+||.+-+. ...||.+|+.+||+|++.|| +||..||+|||+||..+|+.|+.|+|..
T Consensus 49 aE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 49 AETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVN 120 (438)
T ss_pred cccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhc
Confidence 36677899999998876 56999999999999999999 7999999999999999999999999876
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.83 E-value=4.5e-09 Score=99.64 Aligned_cols=51 Identities=16% Similarity=0.296 Sum_probs=46.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhC-CCCHHHHHHHHHHHHHHH
Q 019534 77 KSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~Vg-TRT~~QIRSHaQKYf~kl 127 (339)
..++.||.||+++|++++++||. +|+.||+.++ .||..|||.||.+|+..-
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~ 75 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPS 75 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchh
Confidence 46889999999999999999995 9999999986 899999999999998653
No 9
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.79 E-value=1.9e-08 Score=95.48 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=49.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
.+++.||.||+++|++++..||..|..||++|++||..|||+||..++++..+
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 46899999999999999999999999999999999999999999988877544
No 10
>PLN03091 hypothetical protein; Provisional
Probab=98.73 E-value=9.8e-09 Score=103.84 Aligned_cols=52 Identities=15% Similarity=0.340 Sum_probs=46.3
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhC-CCCHHHHHHHHHHHHHH
Q 019534 75 ITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYFLK 126 (339)
Q Consensus 75 itk~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~Vg-TRT~~QIRSHaQKYf~k 126 (339)
...+++.||.|||++|+++|++||. +|+.||+.++ .||..|||.||.+|+..
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP 63 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRP 63 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCC
Confidence 3456789999999999999999995 9999999887 89999999999987643
No 11
>PLN03091 hypothetical protein; Provisional
Probab=98.64 E-value=5.5e-08 Score=98.54 Aligned_cols=53 Identities=19% Similarity=0.330 Sum_probs=48.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
.+++.||.||+++||+++++||.+|.+||++|+.||..|||+||...++|..+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999987777544
No 12
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.57 E-value=1.3e-07 Score=87.70 Aligned_cols=53 Identities=17% Similarity=0.306 Sum_probs=48.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
.+++.||+|||++++++..+||.+|..||+++++||...||+||.-.++|..+
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~ 112 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLKKKLL 112 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999888766543
No 13
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.51 E-value=1.1e-07 Score=97.02 Aligned_cols=41 Identities=32% Similarity=0.627 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHH
Q 019534 80 ESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (339)
Q Consensus 80 ~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHa 120 (339)
..||.+|..+|||||++||.+|.+||.|||+||++||.-|+
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHF 320 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHH
Confidence 48999999999999999999999999999999999999975
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.50 E-value=7.3e-08 Score=89.28 Aligned_cols=51 Identities=16% Similarity=0.300 Sum_probs=47.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhC-CCCHHHHHHHHHHHHHHHhh
Q 019534 79 RESWTEQEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~Vg-TRT~~QIRSHaQKYf~kl~K 129 (339)
+++||.|||++|++.|++||. +|..|++.+| .|+..|||-||-.|++.-.|
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 799999999999999999995 8999999999 99999999999999876444
No 15
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.41 E-value=7.7e-07 Score=87.84 Aligned_cols=64 Identities=27% Similarity=0.498 Sum_probs=56.0
Q ss_pred CCCCCCCCCCccccc------CCCCCCHHHHHHHHHHHHHcC-hhHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 019534 63 EDPSKKIRKPYTITK------SRESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (339)
Q Consensus 63 e~~~~KvrkPytitk------~r~~WT~EEh~lFLEaLqkyG-rdWkkIA~~VgTRT~~QIRSHaQKYf~k 126 (339)
+.+.+.--++|.|.. ..+.|+.+|+.+|+++++..| ++|..||.|||+|+.+.||+|+.||+..
T Consensus 41 ~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~e 111 (432)
T COG5114 41 ETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYDE 111 (432)
T ss_pred cccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHhh
Confidence 455566777887764 367999999999999999999 6999999999999999999999999874
No 16
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.35 E-value=5.4e-07 Score=92.80 Aligned_cols=44 Identities=34% Similarity=0.632 Sum_probs=41.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHH
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHa 120 (339)
..+..||++|..+|||||++||.+|.+|+.|||+||..||..|.
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 45789999999999999999999999999999999999999974
No 17
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.69 E-value=5.7e-05 Score=80.25 Aligned_cols=53 Identities=21% Similarity=0.376 Sum_probs=47.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 77 KSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
.+.++||.+||.+|+.|+.+||. +|-+|-+.|++|+..|||.+|.+.+..-.|
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K 411 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAK 411 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhc
Confidence 46899999999999999999995 999999999999999999998776655444
No 18
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.05 E-value=0.0039 Score=63.29 Aligned_cols=55 Identities=27% Similarity=0.376 Sum_probs=46.5
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcCh---hHHHHHHHhC--CCCHHHHHHHHHHHHHHHhhc
Q 019534 76 TKSRESWTEQEHDKFLEALQLFDR---DWKKIEAFIG--SKTVIQIRSHAQKYFLKVQKN 130 (339)
Q Consensus 76 tk~r~~WT~EEh~lFLEaLqkyGr---dWkkIA~~Vg--TRT~~QIRSHaQKYf~kl~K~ 130 (339)
.|.|-.||.|=|++|++||++.|. -=|+|=++++ .=|..+|+||.|||...+++.
T Consensus 234 KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l 293 (526)
T PLN03162 234 KKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHL 293 (526)
T ss_pred CCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccc
Confidence 357789999999999999999993 6677877765 578999999999998887643
No 19
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.77 E-value=0.0027 Score=49.28 Aligned_cols=50 Identities=28% Similarity=0.493 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHH------cC--------hhHHHHHHHhC----CCCHHHHHHHHHHHHHHHh
Q 019534 79 RESWTEQEHDKFLEALQL------FD--------RDWKKIEAFIG----SKTVIQIRSHAQKYFLKVQ 128 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqk------yG--------rdWkkIA~~Vg----TRT~~QIRSHaQKYf~kl~ 128 (339)
|..||++|...||+.+.. |+ .-|+.||+.+. .||+.||+.+|.....+-.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 468999999999999876 32 16999997663 5999999999977655543
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.73 E-value=0.0017 Score=68.74 Aligned_cols=53 Identities=25% Similarity=0.493 Sum_probs=46.4
Q ss_pred ccccc-CCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 019534 73 YTITK-SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (339)
Q Consensus 73 ytitk-~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~k 126 (339)
|++-. .++.||+||++.|...+.+.|.+|+.|++.+| |.+.-||.||..|...
T Consensus 377 y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~~~~ 430 (607)
T KOG0051|consen 377 YTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQYVKC 430 (607)
T ss_pred CCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHhhcc
Confidence 33334 89999999999999999999999999999998 6889999999887544
No 21
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=96.66 E-value=0.0063 Score=64.67 Aligned_cols=53 Identities=28% Similarity=0.506 Sum_probs=44.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcChhHHHH----------HHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019534 78 SRESWTEQEHDKFLEALQLFDRDWKKI----------EAFIGSKTVIQIRSHAQKYFLKVQKN 130 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGrdWkkI----------A~~VgTRT~~QIRSHaQKYf~kl~K~ 130 (339)
.+..||..|+.-|..||++||+|+.+| -.-+..||..|+|.||-+...++.|.
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 367999999999999999999999999 33456789999999988776666654
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.41 E-value=0.0036 Score=65.45 Aligned_cols=54 Identities=17% Similarity=0.398 Sum_probs=48.6
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019534 75 ITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (339)
Q Consensus 75 itk~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~ 128 (339)
+-+.++.|+.-||+.+..++.+||. .|.+|+..+..+|..||+.+|.+|.....
T Consensus 3 i~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i 57 (617)
T KOG0050|consen 3 IEIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAI 57 (617)
T ss_pred eEEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHH
Confidence 3457899999999999999999996 99999999999999999999999876543
No 23
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.40 E-value=0.0043 Score=66.51 Aligned_cols=46 Identities=26% Similarity=0.543 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKY 123 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKY 123 (339)
+.++||..||++|+++|++||. .|-+||.++|.||..|.+.+-..+
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 4689999999999999999995 999999999999998877655443
No 24
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.26 E-value=0.0047 Score=65.44 Aligned_cols=51 Identities=24% Similarity=0.502 Sum_probs=43.7
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hc------------------Ch-hHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019534 77 KSRESWTEQEHDKFLEALQ-------LF------------------DR-DWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLq-------ky------------------Gr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl 127 (339)
.+++.||.||+++||..++ +| .. .|..|++.+|||+..|||.||++....-
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 45 11 7999999999999999999998876554
No 25
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=95.28 E-value=0.011 Score=61.68 Aligned_cols=57 Identities=16% Similarity=0.268 Sum_probs=49.7
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 73 YTITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 73 ytitk~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
+......+.|+..||+.++-+++.||. +|.+||..+..|+..||+.||..|.....+
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk 71 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLK 71 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcc
Confidence 555567889999999999999999995 999999988889999999999888766543
No 26
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=95.25 E-value=0.024 Score=57.54 Aligned_cols=45 Identities=27% Similarity=0.566 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHcChhHHHHH-HHhCCCCHHHHHHHHHHHHHH
Q 019534 79 RESWTEQEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSHAQKYFLK 126 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyGrdWkkIA-~~VgTRT~~QIRSHaQKYf~k 126 (339)
-..|+++|=..|.++|+.||+|+..|. .-|.+|++..|..+ ||++
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVey---YYlW 322 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEY---YYLW 322 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHH---HHHh
Confidence 458999999999999999999999997 68999999999985 4554
No 27
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.01 E-value=0.048 Score=55.76 Aligned_cols=42 Identities=24% Similarity=0.533 Sum_probs=39.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSH 119 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSH 119 (339)
...+||.+|-++|..||.++|-++..|+.++++|...||+..
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaK 405 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAK 405 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHH
Confidence 457999999999999999999999999999999999999973
No 28
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.85 E-value=0.13 Score=39.48 Aligned_cols=51 Identities=18% Similarity=0.434 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHc-----C------------hhHHHHHHHh-----CCCCHHHHHHHHHHHHHHHhh
Q 019534 79 RESWTEQEHDKFLEALQLF-----D------------RDWKKIEAFI-----GSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqky-----G------------rdWkkIA~~V-----gTRT~~QIRSHaQKYf~kl~K 129 (339)
...||.+|.+.|++.+++| | +-|..|+..+ +.||..|++..|..+.....+
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 4579999999999999887 2 2799999655 369999999999988776644
No 29
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=94.59 E-value=0.062 Score=58.52 Aligned_cols=45 Identities=27% Similarity=0.389 Sum_probs=41.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQK 122 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQK 122 (339)
....||..|..+|-.||-.|.+|+-.|++.|.+||+.||-.+|-.
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 357999999999999999999999999999999999999987643
No 30
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=93.35 E-value=0.052 Score=52.25 Aligned_cols=70 Identities=27% Similarity=0.354 Sum_probs=56.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCh-hHHHHH-HHhCCCCHHHHHHHHH-----HHHHHHhhcCCCCCCCCCCCCCCCCCCC
Q 019534 77 KSRESWTEQEHDKFLEALQLFDR-DWKKIE-AFIGSKTVIQIRSHAQ-----KYFLKVQKNGTSEHVPPPRPKRKAAHPY 149 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGr-dWkkIA-~~VgTRT~~QIRSHaQ-----KYf~kl~K~g~~e~iPppr~KRks~h~~ 149 (339)
+.+..|+..++.+++.++.+||+ +|..|+ .++..|++.|+.+|+| +|+.+....+. ...|+++|++
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~-------~~~~~s~~~~ 234 (335)
T KOG0724|consen 162 RKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEE-------EKRRKSIEDI 234 (335)
T ss_pred hccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhcc-------ccccchhhhh
Confidence 46789999999999999999997 999998 5777899999999999 88888744432 4556777776
Q ss_pred CCCC
Q 019534 150 PQKA 153 (339)
Q Consensus 150 p~k~ 153 (339)
....
T Consensus 235 ~~~~ 238 (335)
T KOG0724|consen 235 TTAS 238 (335)
T ss_pred hccc
Confidence 6443
No 31
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=93.23 E-value=0.11 Score=54.55 Aligned_cols=53 Identities=13% Similarity=0.364 Sum_probs=47.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
.++..|+.||++.++.+-.++|-.|..|+.+++.||..||..+|..-+....+
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 46789999999999999999999999999999999999999988876665544
No 32
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=93.19 E-value=0.09 Score=55.44 Aligned_cols=47 Identities=19% Similarity=0.471 Sum_probs=43.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 125 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~ 125 (339)
++..|+.||++++|.+.+.+..-|..|+..|| ||..||-.|+++.+-
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ll~ 104 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNLLD 104 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHHHH
Confidence 57899999999999999999999999999998 899999999988543
No 33
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=92.81 E-value=0.11 Score=54.43 Aligned_cols=44 Identities=27% Similarity=0.499 Sum_probs=39.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHH-HHhCCCCHHHHHHHH
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSHA 120 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA-~~VgTRT~~QIRSHa 120 (339)
..-+.|+.-|-.+|.|+|++||+|+..|- +|++=|+...|..+|
T Consensus 283 DemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyY 327 (693)
T KOG3554|consen 283 DEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYY 327 (693)
T ss_pred hhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHH
Confidence 34579999999999999999999999997 799988888888765
No 34
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=92.63 E-value=0.57 Score=48.08 Aligned_cols=52 Identities=25% Similarity=0.411 Sum_probs=42.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHc-----------------ChhHHHHHHHhC-----CCCHHHHHHHHHHHHHHHhh
Q 019534 77 KSRESWTEQEHDKFLEALQLF-----------------DRDWKKIEAFIG-----SKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqky-----------------GrdWkkIA~~Vg-----TRT~~QIRSHaQKYf~kl~K 129 (339)
.-.+.|+++=|+.|+|||..| || =..||.||+ |||..||-+|-|-+-++..+
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGR-NELIarYIKlrtgktRTrKQVSSHIQVlarrk~r 147 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGR-NELIARYIKLRTGKTRTRKQVSSHIQVLARRKLR 147 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccch-HHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHH
Confidence 457899999999999999776 33 366999886 79999999999977666544
No 35
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=92.53 E-value=0.3 Score=50.92 Aligned_cols=42 Identities=21% Similarity=0.459 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHH
Q 019534 79 RESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHa 120 (339)
...||.||-.+|-.+++.||+++.+|-+.++.|+...++-+|
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 469999999999999999999999999999999999988765
No 36
>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=92.46 E-value=0.46 Score=40.95 Aligned_cols=58 Identities=21% Similarity=0.431 Sum_probs=45.2
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHcCh----hHHHHHH------------HhCCCCHHHHHHHHHHHHHHHhh
Q 019534 72 PYTITKSRESWTEQEHDKFLEALQLFDR----DWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 72 Pytitk~r~~WT~EEh~lFLEaLqkyGr----dWkkIA~------------~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
+|..+..+..||+|||.-+|-.+.+||- .|..|-+ |+.+||+..|.-|+.-...-+.|
T Consensus 42 ~y~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 42 NYPPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp SSTSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred ccCCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 4666778899999999999999999995 9999854 45699999999999766665554
No 37
>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=91.78 E-value=0.33 Score=44.32 Aligned_cols=52 Identities=13% Similarity=0.245 Sum_probs=41.5
Q ss_pred CCCCCCHHHHHHHHHHHHHc---Ch----hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019534 78 SRESWTEQEHDKFLEALQLF---DR----DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqky---Gr----dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~ 130 (339)
....||.|||.+|-+.+-+| |+ -+..+++-+ +||..-|.-||+.|.++.-..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 35689999999999999887 42 566666655 499999999999998875443
No 38
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=91.71 E-value=0.37 Score=54.37 Aligned_cols=48 Identities=21% Similarity=0.469 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019534 80 ESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 80 ~~WT~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl 127 (339)
..|+..+=..|+.|..+||+ +...||..|++||..+|+.+++-|+.+.
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 47999999999999999998 9999999999999999999887776553
No 39
>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=89.71 E-value=0.5 Score=36.82 Aligned_cols=48 Identities=21% Similarity=0.284 Sum_probs=31.0
Q ss_pred CCCCCHHHHHHHHHHHHHcC---------hhHHHHHHHhC-CCCHHHHHHHHHHHHHH
Q 019534 79 RESWTEQEHDKFLEALQLFD---------RDWKKIEAFIG-SKTVIQIRSHAQKYFLK 126 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyG---------rdWkkIA~~Vg-TRT~~QIRSHaQKYf~k 126 (339)
|..+|.|||..+++-|..+. .=|+++++.-. ..|..-.|.||.|.+..
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 56789999999999996552 27999996555 78999999998776554
No 40
>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=89.68 E-value=1 Score=35.28 Aligned_cols=43 Identities=23% Similarity=0.371 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHHc---C----------hhHHHHHHHh----C-CCCHHHHHHHHHHH
Q 019534 81 SWTEQEHDKFLEALQLF---D----------RDWKKIEAFI----G-SKTVIQIRSHAQKY 123 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqky---G----------rdWkkIA~~V----g-TRT~~QIRSHaQKY 123 (339)
.||+++++.||+++... | ..|+.|++.+ | ..|..||++|+...
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 59999999999999544 1 1699988433 3 46899999998653
No 41
>smart00426 TEA TEA domain.
Probab=89.02 E-value=0.5 Score=37.69 Aligned_cols=43 Identities=28% Similarity=0.476 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHHHHHcCh--hH--------------HHHHHHhC-----CCCHHHHHHHHH
Q 019534 79 RESWTEQEHDKFLEALQLFDR--DW--------------KKIEAFIG-----SKTVIQIRSHAQ 121 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyGr--dW--------------kkIA~~Vg-----TRT~~QIRSHaQ 121 (339)
...|.++=|..|++||+.|-. .+ .-|++|+- .||..||-||-|
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 468999999999999998852 22 12555553 478888888765
No 42
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=86.76 E-value=0.91 Score=41.72 Aligned_cols=50 Identities=16% Similarity=0.222 Sum_probs=38.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCh-hHHHHHH--HhC---CCCHHHHHHHHHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFDR-DWKKIEA--FIG---SKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~--~Vg---TRT~~QIRSHaQKYf~kl 127 (339)
....||.||+.+|-+.+-.|++ .=.+++. .+| .||..+|..||+.+.++.
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~rt~aac~fRwNs~vrk~ 59 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALKRTAAACGFRWNSVVRKQ 59 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhhhHHHHHhHHHHHHHHH
Confidence 4578999999999999988885 3333442 223 589999999998887764
No 43
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=85.26 E-value=12 Score=36.49 Aligned_cols=51 Identities=18% Similarity=0.347 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHHHc----------ChhHHHHHH---HhC-CCCHHHHHHHHHHHHHHHhh
Q 019534 79 RESWTEQEHDKFLEALQLF----------DRDWKKIEA---FIG-SKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqky----------GrdWkkIA~---~Vg-TRT~~QIRSHaQKYf~kl~K 129 (339)
...|+.+|-..||++.... +..|..||+ ..| -||..||+..+.+...+-++
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 4899999999999988433 126999996 334 59999999998775555443
No 44
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=81.40 E-value=5.5 Score=33.06 Aligned_cols=43 Identities=19% Similarity=0.343 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHHHHc----C----hhHHHHHHHhCCC-----CHHHHHHHHH
Q 019534 79 RESWTEQEHDKFLEALQLF----D----RDWKKIEAFIGSK-----TVIQIRSHAQ 121 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqky----G----rdWkkIA~~VgTR-----T~~QIRSHaQ 121 (339)
...||+|+|..||+||.-| | .+|...-++|... |..|+..-..
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kir 59 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIR 59 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHH
Confidence 4679999999999999888 6 3888877776533 6677765443
No 45
>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=80.29 E-value=1.9 Score=44.41 Aligned_cols=48 Identities=25% Similarity=0.419 Sum_probs=32.6
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcC-----------h---hHHHHHHHhC-----CCCHHHHHHHHHHH
Q 019534 76 TKSRESWTEQEHDKFLEALQLFD-----------R---DWKKIEAFIG-----SKTVIQIRSHAQKY 123 (339)
Q Consensus 76 tk~r~~WT~EEh~lFLEaLqkyG-----------r---dWkkIA~~Vg-----TRT~~QIRSHaQKY 123 (339)
.+..+.|+++=|..|+|||..|- + +=+-|++||. .||..||-+|.|-.
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 45678999999999999998883 1 1134787774 59999999999976
No 46
>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=76.37 E-value=9.7 Score=27.05 Aligned_cols=37 Identities=19% Similarity=0.286 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHH
Q 019534 85 QEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQK 122 (339)
Q Consensus 85 EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQK 122 (339)
+=+.++|..|+.-|+ .|..||+.+|- |...|..+.++
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 557899999999997 99999999996 78888887765
No 47
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=74.61 E-value=6 Score=41.73 Aligned_cols=56 Identities=2% Similarity=-0.014 Sum_probs=48.2
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019534 72 PYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 72 Pytitk~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl 127 (339)
|-.+-+....||.+|..+++.+|++||++...|+-.||.++..|++.....|-++.
T Consensus 362 pes~c~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~ 417 (534)
T KOG1194|consen 362 PESTCRMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQ 417 (534)
T ss_pred CchhhhhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHH
Confidence 44444456899999999999999999999999999999999999999887776654
No 48
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=74.27 E-value=2.9 Score=44.88 Aligned_cols=50 Identities=22% Similarity=0.392 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019534 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~ 130 (339)
....|+.+|-++|-.++..+|-+..-|+.....|...|||. ||-++-.++
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 45899999999999999999999999999999999999996 665554443
No 49
>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=71.85 E-value=12 Score=37.82 Aligned_cols=52 Identities=19% Similarity=0.325 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHc-Ch---hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 78 SRESWTEQEHDKFLEALQLF-DR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqky-Gr---dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
....||..|...||.+|+-- |. |-..|++.+.+|+..+|+..-|+.-.++.+
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 35699999999999999865 43 777889999999999999988877666544
No 50
>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=69.36 E-value=18 Score=25.59 Aligned_cols=39 Identities=5% Similarity=0.142 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHH
Q 019534 85 QEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 124 (339)
Q Consensus 85 EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf 124 (339)
+++...+...-..|..|++||+.+| .|...|+.|.++=.
T Consensus 13 ~~~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 13 ERQREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRRAR 51 (54)
T ss_dssp HHHHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHHHH
Confidence 4556666666777889999999998 68899998765433
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=67.58 E-value=12 Score=29.57 Aligned_cols=38 Identities=26% Similarity=0.540 Sum_probs=26.9
Q ss_pred HHHHHHHHcC--------hhHHHHHHHhCCCC-----HHHHHHHHHHHHHH
Q 019534 89 KFLEALQLFD--------RDWKKIEAFIGSKT-----VIQIRSHAQKYFLK 126 (339)
Q Consensus 89 lFLEaLqkyG--------rdWkkIA~~VgTRT-----~~QIRSHaQKYf~k 126 (339)
+|-.++...| +.|..|++.+|--. ..++|.+|.+|+..
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 3444555555 27999999887432 47899999998764
No 52
>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=66.90 E-value=15 Score=25.70 Aligned_cols=25 Identities=20% Similarity=0.252 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHcChhHHHHHHHhCC
Q 019534 86 EHDKFLEALQLFDRDWKKIEAFIGS 110 (339)
Q Consensus 86 Eh~lFLEaLqkyGrdWkkIA~~VgT 110 (339)
|...+.++|+.+|++..+.|+.+|-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgi 30 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCC
Confidence 7788999999999999999999994
No 53
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=64.67 E-value=17 Score=41.52 Aligned_cols=55 Identities=15% Similarity=0.336 Sum_probs=45.3
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcC-hhHHHHHH------------HhCCCCHHHHHHHHHHHHHHHhhc
Q 019534 76 TKSRESWTEQEHDKFLEALQLFD-RDWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQKN 130 (339)
Q Consensus 76 tk~r~~WT~EEh~lFLEaLqkyG-rdWkkIA~------------~VgTRT~~QIRSHaQKYf~kl~K~ 130 (339)
+.++..||+|||..+|-.+.+|| .+|..|-. |+.+||+..|..|+.-.+..+.|.
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e 990 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKE 990 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHH
Confidence 34566799999999999999999 58999942 456999999999998777777654
No 54
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=64.26 E-value=14 Score=31.95 Aligned_cols=44 Identities=20% Similarity=0.285 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019534 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~g~ 132 (339)
++-|.++|++|++-|+ .|..||+-+|- +...|+.+.++ +...|.
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~r----L~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEK----MKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHH----HHHCCC
Confidence 4678999999999998 99999999985 78888887654 555654
No 55
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=63.50 E-value=22 Score=28.40 Aligned_cols=40 Identities=23% Similarity=0.476 Sum_probs=29.5
Q ss_pred HHHHHHHcCh--------hHHHHHHHhCCC-----CHHHHHHHHHHHHHHHhh
Q 019534 90 FLEALQLFDR--------DWKKIEAFIGSK-----TVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 90 FLEaLqkyGr--------dWkkIA~~VgTR-----T~~QIRSHaQKYf~kl~K 129 (339)
|-.++.+.|+ .|..|++.+|-. ...+++.++++|+....+
T Consensus 37 Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE~ 89 (93)
T smart00501 37 LYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPFER 89 (93)
T ss_pred HHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHHH
Confidence 4445666662 899999988754 368899999999776543
No 56
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=62.51 E-value=6.9 Score=40.59 Aligned_cols=51 Identities=22% Similarity=0.322 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHcChhHHHHHHH-----hCC-CCHHHHHHHHHHHHHHHhh
Q 019534 79 RESWTEQEHDKFLEALQLFDRDWKKIEAF-----IGS-KTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 79 r~~WT~EEh~lFLEaLqkyGrdWkkIA~~-----VgT-RT~~QIRSHaQKYf~kl~K 129 (339)
...||.||.+-|.+..+.|.-+|--|+.- .+. ||++..+.++-...+++.+
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 45799999999999999999999999843 565 9999999988666666655
No 57
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=61.01 E-value=19 Score=31.66 Aligned_cols=44 Identities=14% Similarity=0.219 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019534 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~g~ 132 (339)
++-|.++|.+|++-|+ .|..||+-+|- +...|+.|.++ +.+.|-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~r----L~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVRR----LERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHHH----HHHCCC
Confidence 6789999999999998 99999999985 77788887654 555554
No 58
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=58.76 E-value=1.1e+02 Score=30.79 Aligned_cols=53 Identities=17% Similarity=0.210 Sum_probs=40.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcC----hhHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcC
Q 019534 78 SRESWTEQEHDKFLEALQLFD----RDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNG 131 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyG----rdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~g 131 (339)
.|..+|.|.-.+|..-++.-- ++-..++.-++- +..||+.-+|+-..||+|..
T Consensus 249 PRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgL-NEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 249 PRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGL-NESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred ccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCc-CHHHhhHHhhhhhhhhhhcc
Confidence 478999999888887775533 366778877774 78999998888777776653
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=58.50 E-value=5.9 Score=31.84 Aligned_cols=38 Identities=18% Similarity=0.297 Sum_probs=17.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHH
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHa 120 (339)
...+.||.|+|+.|+.+ +...|.+.+.......|..|.
T Consensus 45 n~~GiWT~eDD~~L~~~------~~~~~~~L~~khG~~~i~~R~ 82 (87)
T PF11626_consen 45 NMPGIWTPEDDEMLRSG------DKDDIERLIKKHGEERIERRK 82 (87)
T ss_dssp T-TT---HHHHHHHTS--------HHHHHHHHHHH-HHHHHHHH
T ss_pred CCCCCcCHHHHHHHHcC------CHHHHHHHHHHhCHHHHHHHH
Confidence 45789999999988544 333344333333344554443
No 60
>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=57.63 E-value=20 Score=31.97 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcChhHHHHHHHhC----CCCHHHHHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIG----SKTVIQIRSHAQKY 123 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~Vg----TRT~~QIRSHaQKY 123 (339)
....=|.+|.+-+..+|++||.|++.++.=.. -.|..||+....+|
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 44567788888888899999999999994333 47999999877666
No 61
>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=57.53 E-value=36 Score=26.79 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
..++.|...|. ..-..|..+..||+.+|. +...|+.+.++-+.++++
T Consensus 110 ~L~~~~~~ii~-~~~~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLV-LRYLEGLSYKEIAEILGI-SVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHh-hHHhcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHh
Confidence 45555555543 332357899999999996 788888877777666643
No 62
>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=55.83 E-value=31 Score=31.25 Aligned_cols=50 Identities=18% Similarity=0.366 Sum_probs=43.8
Q ss_pred CCCHHHHHHHHHHHHHcCh---hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019534 81 SWTEQEHDKFLEALQLFDR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqkyGr---dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~ 130 (339)
-++..+...||.+|-+||- +|+-+-..+..||..+|+.+.--|+..+.-.
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 9999999999999999999987777776543
No 63
>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=54.61 E-value=63 Score=22.67 Aligned_cols=42 Identities=10% Similarity=0.131 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019534 86 EHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (339)
Q Consensus 86 Eh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~ 128 (339)
++..++...-..|..+..||+.+|- |...|+.+-.+-+.+++
T Consensus 8 ~er~vi~~~y~~~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 8 REREVIRLRYFEGLTLEEIAERLGI-SRSTVRRILKRALKKLR 49 (50)
T ss_dssp HHHHHHHHHHTST-SHHHHHHHHTS-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCC-cHHHHHHHHHHHHHHhc
Confidence 3344444443445699999999985 77777776666666654
No 64
>PF10561 UPF0565: Uncharacterised protein family UPF0565; InterPro: IPR018881 This family of proteins has no known function.
Probab=50.85 E-value=13 Score=37.08 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=27.4
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCh
Q 019534 71 KPYTITKSRESWTEQEHDKFLEALQLFDR 99 (339)
Q Consensus 71 kPytitk~r~~WT~EEh~lFLEaLqkyGr 99 (339)
.||++....+.|=..|++.|++.|+++|.
T Consensus 273 TPyQv~D~~RpwI~~E~~~F~~~L~~~~~ 301 (303)
T PF10561_consen 273 TPYQVSDPMRPWIGKEEKKFVKLLKKLGA 301 (303)
T ss_pred CcccccCCCCcHHHHHHHHHHHHHHHhCC
Confidence 59999999999999999999999999984
No 65
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=50.77 E-value=5.4 Score=46.91 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019534 85 QEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 85 EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~g~ 132 (339)
||-+.-..||-.+|++|.+|+..|+++|..||++.+-||-.+...++.
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 455677788888999999999999999999999876677666655544
No 66
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=50.61 E-value=28 Score=39.25 Aligned_cols=59 Identities=19% Similarity=0.400 Sum_probs=50.2
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 019534 71 KPYTITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (339)
Q Consensus 71 kPytitk~r~~WT~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~ 130 (339)
|+--++..-..||..+=..|+.|.++||+ +-..|++-|-. |+..|..++.-+|.++.+.
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 34444556678999999999999999998 99999988877 9999999999888888664
No 67
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=50.58 E-value=36 Score=27.09 Aligned_cols=44 Identities=18% Similarity=0.315 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019534 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~g~ 132 (339)
++.|.++|++|+..|+ .|+.|++.+|- +...|+.|. .++.+.|.
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 3678899999999987 99999999985 777888764 44555554
No 68
>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=43.98 E-value=37 Score=30.60 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHH
Q 019534 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRS 118 (339)
.||+|+.++|.+.. .-|..-.+||+-+|..|...|.-
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViG 38 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIG 38 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhh
Confidence 59998888665554 66889999999999545445544
No 69
>PHA00442 host recBCD nuclease inhibitor
Probab=43.68 E-value=13 Score=28.98 Aligned_cols=32 Identities=25% Similarity=0.591 Sum_probs=25.9
Q ss_pred ccCCCCC--------CHHHHHHHHHHHHHcCh-hHHHHHHH
Q 019534 76 TKSRESW--------TEQEHDKFLEALQLFDR-DWKKIEAF 107 (339)
Q Consensus 76 tk~r~~W--------T~EEh~lFLEaLqkyGr-dWkkIA~~ 107 (339)
+..|..| +-|.+..||++|+..|- +|..+.+.
T Consensus 9 titRd~wnd~q~yidsLek~~~~L~~Lea~GVDNW~Gy~eA 49 (59)
T PHA00442 9 TITRDAWNDMQGYIDSLEKDNEFLKALRACGVDNWDGYMDA 49 (59)
T ss_pred eecHHHHHHHHHHHHHHHHhhHHHHHHHHcCCcchhhHHHH
Confidence 4456778 56788899999999995 99998754
No 70
>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=43.66 E-value=91 Score=20.34 Aligned_cols=42 Identities=12% Similarity=0.170 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHH
Q 019534 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 124 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf 124 (339)
.++.++ ..+++.+-..|..++.||+.+|- +..+|+.+-++..
T Consensus 10 ~l~~~~-~~~~~~~~~~~~~~~~ia~~~~~-s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPERE-REVILLRFGEGLSYEEIAEILGI-SRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHH-HHHHHHHHhcCCCHHHHHHHHCc-CHHHHHHHHHHHH
Confidence 455554 44555555567799999998884 6677776554443
No 71
>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=43.44 E-value=14 Score=29.22 Aligned_cols=19 Identities=32% Similarity=0.677 Sum_probs=15.8
Q ss_pred HHHHHHHHHcChhHHHHHH
Q 019534 88 DKFLEALQLFDRDWKKIEA 106 (339)
Q Consensus 88 ~lFLEaLqkyGrdWkkIA~ 106 (339)
..+.+.|+.||++|.-|.+
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3567788999999999984
No 72
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=41.23 E-value=62 Score=30.59 Aligned_cols=46 Identities=13% Similarity=0.206 Sum_probs=36.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcC---hhHHHHH-----HHhCCCCHHHHHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFD---RDWKKIE-----AFIGSKTVIQIRSHAQKY 123 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyG---rdWkkIA-----~~VgTRT~~QIRSHaQKY 123 (339)
.+..||.+|+++|...-.... ..+++|= -|-.+||+.+...||+-.
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 578999999999998765554 3777762 466789999999999843
No 73
>smart00595 MADF subfamily of SANT domain.
Probab=40.96 E-value=49 Score=25.56 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=20.6
Q ss_pred hHHHHHHHhCCCCHHHHHHHHHHH
Q 019534 100 DWKKIEAFIGSKTVIQIRSHAQKY 123 (339)
Q Consensus 100 dWkkIA~~VgTRT~~QIRSHaQKY 123 (339)
-|..|+.-++. |+.+|+.+|...
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 89999999988 999999998763
No 74
>PRK01905 DNA-binding protein Fis; Provisional
Probab=38.80 E-value=85 Score=24.62 Aligned_cols=28 Identities=7% Similarity=0.061 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHHHHcChhHHHHHHHhCC
Q 019534 83 TEQEHDKFLEALQLFDRDWKKIEAFIGS 110 (339)
Q Consensus 83 T~EEh~lFLEaLqkyGrdWkkIA~~VgT 110 (339)
..-|.+.+.++++.+|.++.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 3457788999999999999999999985
No 75
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=37.09 E-value=86 Score=25.92 Aligned_cols=26 Identities=12% Similarity=0.081 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHcChhHHHHHHHhCC
Q 019534 85 QEHDKFLEALQLFDRDWKKIEAFIGS 110 (339)
Q Consensus 85 EEh~lFLEaLqkyGrdWkkIA~~VgT 110 (339)
-|...|.++++.+|+++.+.|+.+|-
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 76
>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=36.55 E-value=1.1e+02 Score=22.73 Aligned_cols=46 Identities=7% Similarity=0.026 Sum_probs=32.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHH
Q 019534 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 125 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~ 125 (339)
.+..||.|+-..+++.+..-|.....|+.-.|= +..++.. |.+-|.
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 467899999999999998888899999988887 6666654 655554
No 77
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=36.03 E-value=1.2e+02 Score=36.07 Aligned_cols=54 Identities=15% Similarity=0.362 Sum_probs=38.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-hhHHHHH--HHhC----------CCCHHHHHHHHHHHHHHHhhcCC
Q 019534 78 SRESWTEQEHDKFLEALQLFD-RDWKKIE--AFIG----------SKTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLqkyG-rdWkkIA--~~Vg----------TRT~~QIRSHaQKYf~kl~K~g~ 132 (339)
....|..||+..||.||-+|| +.|..|- ..++ --...|...++ .|+..+.+.+.
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~-~yLls~~~~~~ 1198 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRA-DYLLSLLRKHD 1198 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHH-HHHHHHHhhcc
Confidence 457899999999999999999 5999993 1111 12355666665 67777765543
No 78
>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=35.80 E-value=24 Score=39.58 Aligned_cols=63 Identities=17% Similarity=0.297 Sum_probs=51.0
Q ss_pred ccccccCCCCCCCCCCCcccccCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhC-CCCHHHHHH
Q 019534 56 INTMSFAEDPSKKIRKPYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIG-SKTVIQIRS 118 (339)
Q Consensus 56 ~~~~~~~e~~~~KvrkPytitk~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~Vg-TRT~~QIRS 118 (339)
+-.+++.....-+-|++..-.+-.-.|+..|-++|+++..++|+.|+..+..+. +|...++.-
T Consensus 21 sp~~~~~~~sKt~qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~~vel 84 (837)
T KOG1019|consen 21 SPRYDSGSTSKTPQRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSNMVEL 84 (837)
T ss_pred cccccccccccCCCCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhhHHHH
Confidence 445666666666777777777788899999999999999999999999997665 488888764
No 79
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=32.68 E-value=1.4e+02 Score=24.81 Aligned_cols=32 Identities=13% Similarity=0.236 Sum_probs=22.3
Q ss_pred HcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019534 96 LFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (339)
Q Consensus 96 kyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~ 128 (339)
..|..+..||+.+|. +...|+.+..+-..+++
T Consensus 139 ~~~~~~~eIA~~lgi-s~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 139 VEGLSYREIAEILGV-PVGTVKSRLRRARQLLR 170 (179)
T ss_pred HcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
Confidence 346799999999985 56677766655555553
No 80
>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=30.81 E-value=39 Score=27.06 Aligned_cols=33 Identities=27% Similarity=0.445 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHH
Q 019534 84 EQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRS 118 (339)
.||-+++|..= .-|+||+..|..+|- +...|+.
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 46777777521 567899999999996 3455544
No 81
>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=30.20 E-value=91 Score=26.35 Aligned_cols=24 Identities=17% Similarity=0.459 Sum_probs=17.6
Q ss_pred CHHHHHHHHHHHHHcChhHHHHHHHhC
Q 019534 83 TEQEHDKFLEALQLFDRDWKKIEAFIG 109 (339)
Q Consensus 83 T~EEh~lFLEaLqkyGrdWkkIA~~Vg 109 (339)
|.++.+.|-+ ..|++|+.++..+|
T Consensus 1 ~~~~~q~~~~---nvGr~WK~laR~Lg 24 (90)
T cd08780 1 TPADQQHFAK---SVGKKWKPVGRSLQ 24 (90)
T ss_pred CHHHHHHHHH---HHhHHHHHHHHHHc
Confidence 3455555554 45899999999999
No 82
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.08 E-value=1.4e+02 Score=24.92 Aligned_cols=44 Identities=14% Similarity=0.212 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHcCh-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 019534 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGr-dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~g~ 132 (339)
++-+.++|+.|+.-|+ .+..||+.+| -+..-|+.|- .++.+.|.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg-lS~~~v~~Ri----~~L~~~Gi 51 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG-LSPSTVLRRI----KRLEEEGV 51 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC-CCHHHHHHHH----HHHHHCCc
Confidence 4668899999999997 9999999999 5788888764 55666664
No 83
>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=29.25 E-value=95 Score=23.07 Aligned_cols=25 Identities=16% Similarity=0.344 Sum_probs=20.6
Q ss_pred hhHHHHHHHhCC-CCHHHHHHHHHHH
Q 019534 99 RDWKKIEAFIGS-KTVIQIRSHAQKY 123 (339)
Q Consensus 99 rdWkkIA~~VgT-RT~~QIRSHaQKY 123 (339)
+-|..|+..++. -+..+|+.+|+..
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHH
Confidence 489999998885 5788999999874
No 84
>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=28.88 E-value=2.1e+02 Score=23.27 Aligned_cols=31 Identities=19% Similarity=0.333 Sum_probs=23.2
Q ss_pred cChhHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 019534 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (339)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~ 128 (339)
.|..++.||+.+|- +...|+.+...-..+++
T Consensus 128 ~~~~~~eIA~~lgi-s~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 128 EGKSYKEIAEELGI-SVKTVEYHISKALKELR 158 (161)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
Confidence 46799999999885 78888887666555553
No 85
>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=28.45 E-value=53 Score=24.21 Aligned_cols=28 Identities=21% Similarity=0.517 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHcChhHHHHHHHhCC
Q 019534 83 TEQEHDKFLEALQLFDRDWKKIEAFIGS 110 (339)
Q Consensus 83 T~EEh~lFLEaLqkyGrdWkkIA~~VgT 110 (339)
..+.|++|...|+.-....+-||+|+|-
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfGr 44 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFGR 44 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHcc
Confidence 3567999999998877899999999983
No 86
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=27.58 E-value=22 Score=42.17 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=40.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHH
Q 019534 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (339)
Q Consensus 77 k~r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHa 120 (339)
.....|+.+|++.|.+-+.++-++...|+.|+-.||..+|--+|
T Consensus 223 ~~~n~Ws~~Ek~~fk~rf~~H~knf~~~as~~erkSv~d~vlfy 266 (1672)
T KOG1878|consen 223 QRMNEWSPEEKELFKSRFAQHVKNFGLIASFFERKSVSDCVLFY 266 (1672)
T ss_pred HHhhhccccccccccchhhhcCcchhhhhhhhcccchhhceeee
Confidence 47889999999999999999999999999999999999987654
No 87
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=27.33 E-value=2.1e+02 Score=23.84 Aligned_cols=31 Identities=13% Similarity=0.215 Sum_probs=20.1
Q ss_pred HcChhHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019534 96 LFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 96 kyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl 127 (339)
..|..++.||+.+|- +...|+.+...-..++
T Consensus 142 ~~~~s~~eIA~~lgi-s~~tV~~~l~ra~~~L 172 (182)
T PRK09652 142 IEGLSYEEIAEIMGC-PIGTVRSRIFRAREAL 172 (182)
T ss_pred HcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHH
Confidence 356799999999985 5666665544433333
No 88
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=27.32 E-value=2.1e+02 Score=21.96 Aligned_cols=39 Identities=21% Similarity=0.446 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 019534 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl~K 129 (339)
.++++|.+.|++ .|+.+++.=+..+|+.++-.||.++..
T Consensus 19 ~l~~~er~~lv~----------nia~~l~~v~~~~i~~r~l~~f~~vd~ 57 (68)
T PF06628_consen 19 VLSDEERERLVE----------NIAGHLSGVSDEEIQERVLAYFYKVDP 57 (68)
T ss_dssp HSSHHHHHHHHH----------HHHHHHTTSSHHHHHHHHHHHHHHH-H
T ss_pred HCCHHHHHHHHH----------HHHHHHccCChhhHHHHHHHHHHHhCH
Confidence 567888888874 577788877777799999999998743
No 89
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=26.51 E-value=82 Score=31.09 Aligned_cols=39 Identities=15% Similarity=0.371 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHcChhHHHHHHHhC-CCCHHHHHHHHHHHHHHHhhcC
Q 019534 84 EQEHDKFLEALQLFDRDWKKIEAFIG-SKTVIQIRSHAQKYFLKVQKNG 131 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGrdWkkIA~~Vg-TRT~~QIRSHaQKYf~kl~K~g 131 (339)
+-|.+.+.++|+.+|++..+.|+.+| +|+ ..++|+++-|
T Consensus 404 ~~E~~~i~~al~~~~gn~~~aA~~Lgisr~---------tl~rkl~~~~ 443 (445)
T TIGR02915 404 RAEREAVRKAIARVDGNIARAAELLGITRP---------TLYDLMKKHG 443 (445)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHH---------HHHHHHHHhC
Confidence 34778999999999999999999999 454 2455666654
No 90
>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=25.91 E-value=35 Score=31.72 Aligned_cols=16 Identities=25% Similarity=0.657 Sum_probs=14.3
Q ss_pred CCCCCCCCCcccCCCC
Q 019534 4 VNPNPAQGFFFFDPMN 19 (339)
Q Consensus 4 ~~p~~~~~~~~~dp~~ 19 (339)
.+|+.+.|.|++||.+
T Consensus 21 ~~p~~~dG~YwIDPN~ 36 (214)
T PF01410_consen 21 CHPELPDGEYWIDPNG 36 (214)
T ss_pred hCcccCCCcEeECCCC
Confidence 5799999999999984
No 91
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=25.23 E-value=2.3e+02 Score=24.95 Aligned_cols=32 Identities=6% Similarity=0.085 Sum_probs=22.4
Q ss_pred HHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019534 95 QLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 95 qkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl 127 (339)
-..|..++.||+.+|. +...|+.|...-..++
T Consensus 147 ~~~g~s~~EIA~~lg~-s~~tV~~rl~rar~~L 178 (192)
T PRK09643 147 DMQGYSVADAARMLGV-AEGTVKSRCARGRARL 178 (192)
T ss_pred HHcCCCHHHHHHHHCc-CHHHHHHHHHHHHHHH
Confidence 3456799999999885 7778888764444444
No 92
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.74 E-value=1.3e+02 Score=20.82 Aligned_cols=34 Identities=12% Similarity=0.231 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHH
Q 019534 83 TEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (339)
Q Consensus 83 T~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRS 118 (339)
+.++...++..+.. |...++||+.+|- +...|..
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 45556667777777 9999999999983 5555554
No 93
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=24.45 E-value=2.3e+02 Score=21.79 Aligned_cols=39 Identities=10% Similarity=0.171 Sum_probs=27.9
Q ss_pred HHHcCh--hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCCCCCC
Q 019534 94 LQLFDR--DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGTSEHV 136 (339)
Q Consensus 94 LqkyGr--dWkkIA~~VgTRT~~QIRSHaQKYf~kl~K~g~~e~i 136 (339)
++.+|. .-..|++.+|-++..-|.. |+..+.+.|.....
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~~tv~~----~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKSTSTVQR----HLKALERKGYIRRD 59 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSHHHHHH----HHHHHHHTTSEEEG
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHHCcCccCC
Confidence 344564 8899999999998887775 56777777765443
No 94
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=23.72 E-value=99 Score=30.15 Aligned_cols=38 Identities=18% Similarity=0.201 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHcChhHHHHHHHhCC-CCHHHHHHHHHHHHHHHhhcC
Q 019534 85 QEHDKFLEALQLFDRDWKKIEAFIGS-KTVIQIRSHAQKYFLKVQKNG 131 (339)
Q Consensus 85 EEh~lFLEaLqkyGrdWkkIA~~VgT-RT~~QIRSHaQKYf~kl~K~g 131 (339)
-|.+.+.++|+.+|++-.+.|+.+|- |+ ..++|+++.|
T Consensus 286 ~Er~~I~~aL~~~~gn~~~aA~~LGIsR~---------tLyrklk~~g 324 (326)
T PRK11608 286 QEKELLQRSLQQAKFNQKRAAELLGLTYH---------QLRALLKKHQ 324 (326)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCHH---------HHHHHHHHcC
Confidence 47888999999999999999999994 44 3566666655
No 95
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=23.50 E-value=89 Score=33.78 Aligned_cols=43 Identities=16% Similarity=0.180 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHH
Q 019534 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 124 (339)
Q Consensus 81 ~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf 124 (339)
.--+.|.+++.++|++-|.+|.+-|+.+|. ++.|+-+++++|=
T Consensus 502 ~~~~~eR~~I~~aL~~~~~~~a~AAr~LGl-~~~~L~~~~kRlG 544 (550)
T COG3604 502 ATEEFERQLIIAALEETNGNWAGAARRLGL-TRRTLLYRMKRLG 544 (550)
T ss_pred hhHHHHHHHHHHHHHHhCCcHHHHHHHhCC-CHHHHHHHHHHcC
Confidence 333678889999999999999998899996 7888887766653
No 96
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=22.62 E-value=90 Score=30.57 Aligned_cols=29 Identities=21% Similarity=0.288 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHcChhHHHHHHHhC-CCC
Q 019534 84 EQEHDKFLEALQLFDRDWKKIEAFIG-SKT 112 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGrdWkkIA~~Vg-TRT 112 (339)
+-|.+.+.++|+++|++..+.|+.+| +|+
T Consensus 404 ~~e~~~i~~~l~~~~gn~~~aa~~Lgisr~ 433 (441)
T PRK10365 404 EVEKEVILAALEKTGGNKTEAARQLGITRK 433 (441)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence 45778899999999999999999999 354
No 97
>TIGR00571 dam DNA adenine methylase (dam). All proteins in this family for which functions are known are DNA-adenine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The DNA adenine methylase (dam) of E. coli and related species is instrumental in distinguishing the newly synthesized strand during DNA replication for methylation-directed mismatch repair. This family includes several phage methylases and a number of different restriction enzyme chromosomal site-specific modification systems.
Probab=22.19 E-value=83 Score=29.83 Aligned_cols=49 Identities=14% Similarity=0.161 Sum_probs=30.6
Q ss_pred CCCCccccc--------CCCCCCHHHHHHHHHHHHHcCh---hHHHHHHHhCCCCHHHHHHHHHH
Q 019534 69 IRKPYTITK--------SRESWTEQEHDKFLEALQLFDR---DWKKIEAFIGSKTVIQIRSHAQK 122 (339)
Q Consensus 69 vrkPytitk--------~r~~WT~EEh~lFLEaLqkyGr---dWkkIA~~VgTRT~~QIRSHaQK 122 (339)
++.||.... .+..|++|||.+|++.|+.... .|- -.+ -...+|+..+..
T Consensus 178 lDPPY~~~~~~~~f~~y~~~~f~~~dh~~L~~~l~~l~~~~~~~~--lS~---~~~~~i~ely~~ 237 (266)
T TIGR00571 178 CDPPYLPLSATYNFTGYHTNGFDEDEQKRLANFCKSLDERGIKFL--LSN---SDSSFTRELYQG 237 (266)
T ss_pred ECCCCCCCCCCCCccCccCCCCCHHHHHHHHHHHHHHHhCCCEEE--EEe---CCCHHHHHHhcC
Confidence 456886431 1367999999999999988632 221 111 134577776643
No 98
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=21.98 E-value=1.2e+02 Score=22.14 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=31.0
Q ss_pred HHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 019534 88 DKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (339)
Q Consensus 88 ~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~k 126 (339)
++|-++++..|.+=..|-+.+.+|+..|.+.=.+.|...
T Consensus 4 ~~l~~a~~~~g~de~~li~Il~~rs~~ql~~i~~~Y~~~ 42 (66)
T PF00191_consen 4 ELLHAALKGWGTDEDVLIEILCTRSPAQLRAIKQAYKKK 42 (66)
T ss_dssp HHHHHHHSSSSSTHHHHHHHHHHSTHHHHHHHHHHHHHH
T ss_pred HHHHHHccCCCCChhHhhhHHhhhcccccceeehhhhhh
Confidence 377888888897666777788899999998877777554
No 99
>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=21.94 E-value=75 Score=25.10 Aligned_cols=23 Identities=17% Similarity=0.473 Sum_probs=18.2
Q ss_pred HHHHHHHHHcChhHHHHHHHhCC
Q 019534 88 DKFLEALQLFDRDWKKIEAFIGS 110 (339)
Q Consensus 88 ~lFLEaLqkyGrdWkkIA~~VgT 110 (339)
..|...-+..|.+|+++|..+|-
T Consensus 5 ~~l~~ia~~lG~dW~~LAr~Lg~ 27 (84)
T cd08317 5 IRLADISNLLGSDWPQLARELGV 27 (84)
T ss_pred chHHHHHHHHhhHHHHHHHHcCC
Confidence 34555667779999999999984
No 100
>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=21.69 E-value=1.6e+02 Score=30.64 Aligned_cols=13 Identities=46% Similarity=0.549 Sum_probs=8.7
Q ss_pred CCCCCCCCccccc
Q 019534 65 PSKKIRKPYTITK 77 (339)
Q Consensus 65 ~~~KvrkPytitk 77 (339)
..||-|||....|
T Consensus 190 t~KKpRKPRqtKK 202 (379)
T PF11593_consen 190 TAKKPRKPRQTKK 202 (379)
T ss_pred ccCCCCCCCCccc
Confidence 3478888887444
No 101
>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=21.54 E-value=2.4e+02 Score=25.73 Aligned_cols=64 Identities=22% Similarity=0.281 Sum_probs=34.2
Q ss_pred CCCCCCHHHHHHHHHHHH---HcChhHHHHHHHhC-------CCCHHHHHHHHHHHHHHHhhcCCCCCCCC--CCCCCC
Q 019534 78 SRESWTEQEHDKFLEALQ---LFDRDWKKIEAFIG-------SKTVIQIRSHAQKYFLKVQKNGTSEHVPP--PRPKRK 144 (339)
Q Consensus 78 ~r~~WT~EEh~lFLEaLq---kyGrdWkkIA~~Vg-------TRT~~QIRSHaQKYf~kl~K~g~~e~iPp--pr~KRk 144 (339)
+.-.|=.-|-++|-+.++ .+|-+--.|+++|. -||+.|..+-+ |.-....-.-++||. |.||||
T Consensus 59 S~isWLKsELELLy~~YQf~q~h~lni~diSk~~Skn~L~lFpKTeSQLQNTY---YKLKk~~i~fEnI~K~KPGRKrK 134 (148)
T PF12181_consen 59 SNISWLKSELELLYACYQFCQRHGLNILDISKMLSKNDLNLFPKTESQLQNTY---YKLKKEEIPFENIKKNKPGRKRK 134 (148)
T ss_dssp SSEEE-HHHHHHHHHHHHHHHHTT--HHHHHHHHSTTTT-SSSS-HHHHHHHH---HHHHTTSS-SS-EE----S----
T ss_pred hhhHHHHHHHHHHHHHHHHHHHcCCccccHHHHhhhhhhccCCCCHHHHHHHH---HHHHhhhcchhhccccCCCcccc
Confidence 345798999998888774 45668888888876 48999988754 322222223355655 445655
No 102
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.38 E-value=2.8e+02 Score=24.18 Aligned_cols=43 Identities=19% Similarity=0.259 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 019534 84 EQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQKYf~kl 127 (339)
.+|+..|++.+-+..++-+.|++.+|- +.--||++-.+...++
T Consensus 35 ~~E~~~Fi~~Fi~~rGnlKe~e~~lgi-SYPTvR~rLd~ii~~l 77 (113)
T PF09862_consen 35 SPEQLEFIKLFIKNRGNLKEMEKELGI-SYPTVRNRLDKIIEKL 77 (113)
T ss_pred CHHHHHHHHHHHHhcCCHHHHHHHHCC-CcHHHHHHHHHHHHHh
Confidence 578999999999999999999999985 7888999887776665
No 103
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=20.81 E-value=1.3e+02 Score=31.25 Aligned_cols=40 Identities=10% Similarity=0.181 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHcChhHHHHHHHhCC-CCHHHHHHHHHHHHHHHhhcCC
Q 019534 84 EQEHDKFLEALQLFDRDWKKIEAFIGS-KTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 84 ~EEh~lFLEaLqkyGrdWkkIA~~VgT-RT~~QIRSHaQKYf~kl~K~g~ 132 (339)
+-|.+.+.++|+.+|++..+.|+.+|- |+ ..+.|++|-|.
T Consensus 467 ~~Er~~I~~aL~~~~gn~~~aA~~LGisr~---------tL~rklk~~gi 507 (509)
T PRK05022 467 AFQRQLIRQALAQHQGNWAAAARALELDRA---------NLHRLAKRLGL 507 (509)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHH---------HHHHHHHHcCC
Confidence 457889999999999999999999994 43 24566666554
No 104
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=20.78 E-value=1.4e+02 Score=31.50 Aligned_cols=42 Identities=21% Similarity=0.446 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHHcChhHHHHHHHhC-CCCHHHHHHHHHHHHHHHhhcCC
Q 019534 82 WTEQEHDKFLEALQLFDRDWKKIEAFIG-SKTVIQIRSHAQKYFLKVQKNGT 132 (339)
Q Consensus 82 WT~EEh~lFLEaLqkyGrdWkkIA~~Vg-TRT~~QIRSHaQKYf~kl~K~g~ 132 (339)
+-+-|.+.+.++|+.+|++..+.|+.+| +|+ -.++|+++-|.
T Consensus 588 l~~~E~~~i~~al~~~~gn~~~aA~~LGisR~---------TLyrklk~~~i 630 (638)
T PRK11388 588 LAELEKEAIINAAQVCGGRIQEMAALLGIGRT---------TLWRKMKQHGI 630 (638)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHCCCHH---------HHHHHHHHcCC
Confidence 4466888999999999999999999999 455 35677777765
No 105
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=20.33 E-value=1.3e+02 Score=33.61 Aligned_cols=53 Identities=23% Similarity=0.246 Sum_probs=43.5
Q ss_pred CCCcccccC-CCCCCHHHHHHHHHHHHHcChhHHHHHHHhCCCCHHHHHHHHHH
Q 019534 70 RKPYTITKS-RESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQK 122 (339)
Q Consensus 70 rkPytitk~-r~~WT~EEh~lFLEaLqkyGrdWkkIA~~VgTRT~~QIRSHaQK 122 (339)
+.|+...+. ...|+.-|..+|..+...||.+.-.|+..+.+||-.||-.+.++
T Consensus 399 ~~~~~~~~~~~~ew~~~ek~~fr~~~~~~~~n~c~Iar~l~~ktC~~v~~~~~~ 452 (739)
T KOG1079|consen 399 QNPVHGKKDTNVEWNGAEKVLFRVGSTLYGTNRCSIARNLLTKTCRQVYEYEQK 452 (739)
T ss_pred cCcccccCCcccccchhhhHHHHhccccccchhhHHHHHhcchHHHHHHHHhhc
Confidence 334443333 34899999999999999999999999999999999998887664
Done!