Query 021972
Match_columns 304
No_of_seqs 210 out of 697
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:02:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021972.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021972hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01557 myb_SHAQKYF myb-like 99.6 2.3E-16 5E-21 117.2 6.1 50 64-113 1-56 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.5 6.6E-14 1.4E-18 98.4 6.1 45 66-110 1-47 (48)
3 KOG0724 Zuotin and related mol 99.4 7.1E-15 1.5E-19 137.7 -5.0 240 49-293 35-295 (335)
4 smart00717 SANT SANT SWI3, AD 99.2 8.4E-11 1.8E-15 78.6 6.0 46 66-111 1-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.1E-10 2.4E-15 77.2 5.5 43 68-110 1-44 (45)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.0 7.4E-10 1.6E-14 80.2 4.9 41 69-109 1-41 (60)
7 COG5259 RSC8 RSC chromatin rem 98.9 7E-10 1.5E-14 111.1 5.3 72 12-107 246-320 (531)
8 KOG0457 Histone acetyltransfer 98.9 2.5E-09 5.5E-14 106.1 6.7 54 61-114 67-121 (438)
9 KOG1279 Chromatin remodeling f 98.7 1.4E-08 3E-13 102.9 5.0 69 14-107 226-294 (506)
10 PLN03212 Transcription repress 98.5 1.4E-07 3E-12 88.5 5.7 50 62-111 21-72 (249)
11 PLN03212 Transcription repress 98.5 6.1E-07 1.3E-11 84.2 9.7 53 63-115 75-127 (249)
12 PLN03091 hypothetical protein; 98.4 2.7E-07 5.8E-12 92.4 5.1 52 60-111 8-61 (459)
13 COG5114 Histone acetyltransfer 98.4 1.1E-06 2.5E-11 85.6 8.0 49 65-113 62-111 (432)
14 PLN03091 hypothetical protein; 98.3 1.3E-06 2.9E-11 87.6 7.3 53 62-114 63-115 (459)
15 KOG0048 Transcription factor, 98.2 3.3E-06 7.2E-11 77.2 6.9 52 62-113 58-109 (238)
16 KOG0048 Transcription factor, 97.8 2.2E-05 4.8E-10 71.8 4.5 46 66-111 9-56 (238)
17 PLN03162 golden-2 like transcr 97.4 0.00074 1.6E-08 67.5 9.5 56 62-117 233-293 (526)
18 KOG0049 Transcription factor, 97.3 0.00034 7.3E-09 73.7 6.2 52 63-114 357-409 (939)
19 KOG4468 Polycomb-group transcr 96.9 0.0019 4.2E-08 67.6 6.4 61 65-125 87-157 (782)
20 KOG4329 DNA-binding protein [G 96.6 0.016 3.5E-07 58.0 10.0 41 67-107 278-319 (445)
21 PF13837 Myb_DNA-bind_4: Myb/S 96.1 0.011 2.5E-07 45.0 5.1 52 66-117 1-70 (90)
22 KOG0724 Zuotin and related mol 95.6 0.0068 1.5E-07 57.4 2.4 73 63-142 161-240 (335)
23 KOG0051 RNA polymerase I termi 95.3 0.02 4.3E-07 60.1 4.7 56 57-113 374-430 (607)
24 KOG0049 Transcription factor, 95.0 0.036 7.7E-07 59.1 5.5 44 65-108 411-455 (939)
25 KOG0051 RNA polymerase I termi 94.9 0.03 6.4E-07 58.8 4.4 50 64-113 434-509 (607)
26 KOG3841 TEF-1 and related tran 94.6 0.19 4.1E-06 50.8 8.9 53 64-116 74-147 (455)
27 KOG0050 mRNA splicing protein 94.3 0.05 1.1E-06 56.5 4.4 51 62-112 3-54 (617)
28 PLN03142 Probable chromatin-re 94.1 0.095 2.1E-06 58.0 6.4 49 67-115 825-874 (1033)
29 KOG3554 Histone deacetylase co 94.0 0.048 1E-06 56.3 3.4 43 65-107 284-327 (693)
30 COG5118 BDP1 Transcription ini 93.4 0.15 3.2E-06 51.7 5.7 42 65-106 364-405 (507)
31 KOG4167 Predicted DNA-binding 93.3 0.14 2.9E-06 55.3 5.6 46 65-110 618-663 (907)
32 smart00426 TEA TEA domain. 92.3 0.13 2.9E-06 40.4 2.8 43 66-108 3-66 (68)
33 KOG1194 Predicted DNA-binding 92.1 0.32 6.8E-06 50.1 6.1 43 65-107 186-228 (534)
34 PF09111 SLIDE: SLIDE; InterP 91.9 0.62 1.3E-05 39.6 6.7 58 59-116 42-115 (118)
35 PF13873 Myb_DNA-bind_5: Myb/S 90.8 1.2 2.6E-05 33.6 6.8 50 67-116 3-74 (78)
36 PF01285 TEA: TEA/ATTS domain 87.3 0.62 1.3E-05 47.2 3.8 48 63-110 46-112 (431)
37 COG5147 REB1 Myb superfamily p 86.3 1 2.2E-05 46.9 4.7 57 59-115 65-121 (512)
38 PF12776 Myb_DNA-bind_3: Myb/S 85.5 2.6 5.7E-05 32.5 5.7 43 68-110 1-61 (96)
39 COG5147 REB1 Myb superfamily p 85.5 0.55 1.2E-05 48.8 2.4 57 57-113 11-68 (512)
40 KOG0050 mRNA splicing protein 83.7 1.2 2.6E-05 46.7 3.9 47 64-111 57-103 (617)
41 KOG4282 Transcription factor G 80.6 15 0.00032 35.3 9.8 52 66-117 54-119 (345)
42 PF11035 SnAPC_2_like: Small n 75.4 9 0.00019 38.2 6.8 50 66-115 21-74 (344)
43 KOG1194 Predicted DNA-binding 73.6 7.1 0.00015 40.7 5.7 59 57-115 360-418 (534)
44 PF04504 DUF573: Protein of un 72.7 15 0.00032 30.1 6.4 42 65-106 3-57 (98)
45 PF06461 DUF1086: Domain of Un 72.1 11 0.00023 33.7 5.8 50 68-117 40-92 (145)
46 PF08914 Myb_DNA-bind_2: Rap1 70.1 7.8 0.00017 29.8 4.0 46 66-111 2-57 (65)
47 TIGR02894 DNA_bind_RsfA transc 69.5 10 0.00022 34.3 5.2 47 66-113 4-57 (161)
48 KOG0385 Chromatin remodeling c 68.1 6.6 0.00014 43.4 4.4 61 57-118 786-847 (971)
49 PF13404 HTH_AsnC-type: AsnC-t 67.8 19 0.00042 25.1 5.3 37 72-109 3-40 (42)
50 PRK13923 putative spore coat p 64.1 10 0.00022 34.5 4.1 48 65-112 4-57 (170)
51 PF08281 Sigma70_r4_2: Sigma-7 62.9 27 0.00058 24.3 5.3 40 72-112 13-52 (54)
52 PF01388 ARID: ARID/BRIGHT DNA 61.8 22 0.00047 27.6 5.1 27 87-113 59-90 (92)
53 KOG2009 Transcription initiati 61.5 8.2 0.00018 41.0 3.5 50 65-117 408-457 (584)
54 PF02954 HTH_8: Bacterial regu 60.1 22 0.00048 24.4 4.4 26 72-97 5-30 (42)
55 PF10141 ssDNA-exonuc_C: Singl 58.5 10 0.00023 33.9 3.2 46 240-285 90-138 (195)
56 smart00501 BRIGHT BRIGHT, ARID 54.5 38 0.00082 26.6 5.5 41 74-115 35-88 (93)
57 PRK11179 DNA-binding transcrip 52.8 27 0.00058 29.8 4.7 43 71-118 8-51 (153)
58 PLN03142 Probable chromatin-re 51.7 39 0.00084 38.2 6.8 54 64-117 924-990 (1033)
59 cd02336 ZZ_RSC8 Zinc finger, Z 47.1 10 0.00022 27.3 1.1 17 11-30 21-38 (45)
60 PHA00442 host recBCD nuclease 46.8 12 0.00025 28.8 1.4 33 62-94 8-49 (59)
61 smart00344 HTH_ASNC helix_turn 46.3 46 0.00099 26.1 4.8 37 71-108 2-39 (108)
62 TIGR02937 sigma70-ECF RNA poly 46.1 69 0.0015 24.8 5.7 47 68-116 110-156 (158)
63 PRK11169 leucine-responsive tr 45.5 37 0.0008 29.3 4.5 43 71-118 13-56 (164)
64 cd06171 Sigma70_r4 Sigma70, re 39.9 1E+02 0.0022 19.8 5.2 42 68-111 10-51 (55)
65 cd08780 Death_TRADD Death Doma 38.6 53 0.0011 27.3 4.1 24 70-96 1-24 (90)
66 KOG1878 Nuclear receptor coreg 38.0 16 0.00036 42.6 1.4 49 72-120 360-408 (1672)
67 PF09420 Nop16: Ribosome bioge 37.7 69 0.0015 28.0 5.0 46 65-110 113-162 (164)
68 cd08311 Death_p75NR Death doma 36.5 41 0.00089 26.5 3.1 34 71-106 2-35 (77)
69 PF04545 Sigma70_r4: Sigma-70, 36.0 1.5E+02 0.0031 20.5 5.7 43 71-115 7-49 (50)
70 PF12451 VPS11_C: Vacuolar pro 35.0 32 0.0007 25.0 2.1 27 70-96 17-43 (49)
71 PRK00430 fis global DNA-bindin 34.1 1E+02 0.0022 25.1 5.0 26 72-97 55-80 (95)
72 PRK01905 DNA-binding protein F 34.0 1.2E+02 0.0027 23.3 5.4 28 70-97 35-62 (77)
73 KOG2656 DNA methyltransferase 34.0 43 0.00092 34.5 3.5 50 67-116 131-186 (445)
74 COG3604 FhlA Transcriptional r 32.1 49 0.0011 35.1 3.7 43 70-113 504-546 (550)
75 PF13384 HTH_23: Homeodomain-l 30.6 82 0.0018 21.4 3.5 39 70-110 3-41 (50)
76 smart00595 MADF subfamily of S 30.4 87 0.0019 23.7 4.0 23 87-110 29-51 (89)
77 PF13325 MCRS_N: N-terminal re 29.6 96 0.0021 28.9 4.7 45 65-109 72-124 (199)
78 PF10440 WIYLD: Ubiquitin-bind 29.5 35 0.00076 26.7 1.6 19 75-93 30-48 (65)
79 PF06628 Catalase-rel: Catalas 27.1 2E+02 0.0044 21.7 5.4 39 68-116 19-57 (68)
80 PF11626 Rap1_C: TRF2-interact 25.7 39 0.00085 26.7 1.3 16 64-79 45-60 (87)
81 PRK11924 RNA polymerase sigma 25.6 2.2E+02 0.0048 23.3 5.8 32 84-116 140-171 (179)
82 PF10561 UPF0565: Uncharacteri 24.5 61 0.0013 31.9 2.6 30 57-86 272-301 (303)
83 cd08777 Death_RIP1 Death Domai 22.4 1.7E+02 0.0037 23.3 4.4 23 82-105 10-32 (86)
84 PF08074 CHDCT2: CHDCT2 (NUC03 21.8 54 0.0012 30.1 1.6 28 66-93 3-31 (173)
85 TIGR00571 dam DNA adenine meth 21.7 1E+02 0.0022 28.8 3.4 49 57-110 179-238 (266)
86 KOG1019 Retinoblastoma pathway 21.6 53 0.0012 36.5 1.8 50 56-105 34-84 (837)
87 PF07750 GcrA: GcrA cell cycle 21.3 1.3E+02 0.0028 26.7 3.8 38 68-106 2-39 (162)
88 PF10545 MADF_DNA_bdg: Alcohol 20.8 1.6E+02 0.0035 21.4 3.8 27 87-113 28-55 (85)
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=99.65 E-value=2.3e-16 Score=117.25 Aligned_cols=50 Identities=48% Similarity=0.716 Sum_probs=46.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hh---HHHHhhcC-CC-CHHHHHHHHHHHHHH
Q 021972 64 KSRESWTEPEHDKFLEALQLFDR-DW---KKIEAFIG-SK-TVIQIRSHAQKYFLK 113 (304)
Q Consensus 64 k~r~~WTeEEh~lFLeaLe~yGr-dW---kkIA~~Vg-TR-T~~QVrSHAQKYf~k 113 (304)
|.|..||+|||.+||+||+.||+ +| ++|+++++ ++ |..||+||+||||++
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 46789999999999999999998 99 99998765 77 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=99.48 E-value=6.6e-14 Score=98.41 Aligned_cols=45 Identities=42% Similarity=0.709 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhChh-hHHHHhhcC-CCCHHHHHHHHHHH
Q 021972 66 RESWTEPEHDKFLEALQLFDRD-WKKIEAFIG-SKTVIQIRSHAQKY 110 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yGrd-WkkIA~~Vg-TRT~~QVrSHAQKY 110 (304)
++.||+||+++|++|+++||.+ |+.||++|+ +||..||++|+++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 4789999999999999999986 999999999 99999999999987
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=7.1e-15 Score=137.68 Aligned_cols=240 Identities=20% Similarity=0.140 Sum_probs=155.1
Q ss_pred CCCCCCCCCCCcccccCCCC-CCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHhhc----CCCCCC
Q 021972 49 SEDPSKKIRKPYTITKSRES-WTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN----GTAEHL 123 (304)
Q Consensus 49 ~ed~~kk~rKPytitk~r~~-WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~k~----g~~~~i 123 (304)
.++..++++|+|++...+.. ||.+||+.|.++|..|++.|+.|-++++.++..|+++|+|+||-++.+. ...+.+
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 46667899999999998655 9999999999999999889999999999999999999999999998874 223458
Q ss_pred CCCCCCCCCCCCcCCcCCCCCCccccccCCCCCCCCCCCCCcccCCCCccccccccccCC-CCCCCC-C--CcccCCCCC
Q 021972 124 PPPRPKRKAAHPYPQKASKNAPMLSQVSGSFQSSSAQLEPGHFLRPDSSSMLMIPMASAA-TSWTNN-V--QTVSLSPAS 199 (304)
Q Consensus 124 P~pr~KRks~h~~p~~~~~~~~~~~q~~~~~qs~~~~~~~g~~~~~dsss~~~~~~~~~~-~sw~~~-~--~~~~~~~~~ 199 (304)
|++++++++.|+|+.+...+.... +... ......+. .++....+..+..++..+... ..|... . +.+......
T Consensus 115 ~~~~~~~k~~~~y~~~~~~~~~~~-~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (335)
T KOG0724|consen 115 YNFWPKFKSWRQYPQKDEPDEEDS-ENRS-QSRYSGGT-QRGKSNAEELRRKGTPVTERERKLVLLALKKDGKIDWRKIS 191 (335)
T ss_pred CCccccccccccCCCCCCcccccc-cchh-hhhhcccc-cccccchhhhhhccchhHHHHHHHHHhhhcccccccceech
Confidence 999999999999999987653322 1110 01112222 444444444333343322222 222111 0 000000000
Q ss_pred CCCcccCCCCCCCCCCCCccccCccccCCCCcccCCCCCCCcccCCChHHHhh--hhhccc-----C----CCcchHHHh
Q 021972 200 KGPEVANNRSNSTDSTPKARVSGELTDQGGELTDQGNNSHPLRVLPDFAQVYT--FIGSVF-----D----PNASDHVQK 268 (304)
Q Consensus 200 ~g~~~~~~~~s~~~s~~~~~~~~~~~~~~~e~~~~~~~~~~l~~~PdFaqVY~--FiGsvF-----d----p~~~~hlqk 268 (304)
.......+..+..+-+...... ....-....+.....+.++.++++.+++. ++++++ + |...+|.++
T Consensus 192 -~~~~~~r~~~~~~s~a~~~~~~-~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 269 (335)
T KOG0724|consen 192 -QNVEKERTPEQVASHAQEKAFE-KALARQKSGEEEKRRKSIEDITTASEAEDRKKEDEAAKEAKKKPRDTPSLKSRNKR 269 (335)
T ss_pred -hhhhhhhcchhhhhhhhhhhhH-HHHHHHhhhccccccchhhhhhccchhhhhhcchhhhhhhhccccccccccchhhh
Confidence 0001111111111111100000 00001123345556678899999999988 999999 8 889999999
Q ss_pred hhcCCcchHHHHHHHHh-hhhhhhhc
Q 021972 269 LKKMDPIDVETVCYIKN-STFFFHSL 293 (304)
Q Consensus 269 Lk~Mdpi~~eTvlllmr-Nl~~~~~~ 293 (304)
++.|++++.++..+.|. |+++..+.
T Consensus 270 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 295 (335)
T KOG0724|consen 270 LKSFDGIAEESSETEDSLELVAALSA 295 (335)
T ss_pred cccCCccCCCchhHHHhHHHHHhhhc
Confidence 99999999999999999 68776653
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.16 E-value=8.4e-11 Score=78.58 Aligned_cols=46 Identities=24% Similarity=0.523 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC-hhhHHHHhhcCCCCHHHHHHHHHHHH
Q 021972 66 RESWTEPEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYF 111 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yG-rdWkkIA~~VgTRT~~QVrSHAQKYf 111 (304)
+..||++|+.+|+++++.|| .+|..|+.++++||..||+.++..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 36899999999999999999 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=99.13 E-value=1.1e-10 Score=77.16 Aligned_cols=43 Identities=30% Similarity=0.564 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhC-hhhHHHHhhcCCCCHHHHHHHHHHH
Q 021972 68 SWTEPEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKY 110 (304)
Q Consensus 68 ~WTeEEh~lFLeaLe~yG-rdWkkIA~~VgTRT~~QVrSHAQKY 110 (304)
.||.+|+.+|+.+++.|| .+|..|++.+++||..||+.|++++
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=98.97 E-value=7.4e-10 Score=80.17 Aligned_cols=41 Identities=34% Similarity=0.686 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHH
Q 021972 69 WTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQK 109 (304)
Q Consensus 69 WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQK 109 (304)
||+||+++++++++.||.+|++||+++|.||+.||+.|+.+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999999999999999999999999876
No 7
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.95 E-value=7e-10 Score=111.13 Aligned_cols=72 Identities=31% Similarity=0.471 Sum_probs=57.3
Q ss_pred cc-cCCCCCCCCCCCCCCCCCCchhHHhhhcCCccccCCCCCCCCCCCCccccc--CCCCCCHHHHHHHHHHHHHhChhh
Q 021972 12 FY-LDPNGMALPGLGPFASSATTPTAAAAAAGTSTVSTSEDPSKKIRKPYTITK--SRESWTEPEHDKFLEALQLFDRDW 88 (304)
Q Consensus 12 ~y-~~p~~~~~pg~~~~~~~~~~~~~~~~~~~~~~~~s~ed~~kk~rKPytitk--~r~~WTeEEh~lFLeaLe~yGrdW 88 (304)
+| +|++|+-+ | +|++..+ +.|+- +-++.- ....||.+|..++||||+.||.||
T Consensus 246 ~~n~C~~C~~q-g--~f~s~~~----------------ssDf~-----~v~~~~~~~dk~WS~qE~~LLLEGIe~ygDdW 301 (531)
T COG5259 246 KYNSCSECYDQ-G--RFPSEFT----------------SSDFK-----PVTISLLIRDKNWSRQELLLLLEGIEMYGDDW 301 (531)
T ss_pred hcccchHHHhc-C--cCCCccc----------------cccch-----hhhhhcccccccccHHHHHHHHHHHHHhhhhH
Confidence 56 79999998 6 8888622 23432 222222 235899999999999999999999
Q ss_pred HHHHhhcCCCCHHHHHHHH
Q 021972 89 KKIEAFIGSKTVIQIRSHA 107 (304)
Q Consensus 89 kkIA~~VgTRT~~QVrSHA 107 (304)
.+||.|||+||.+||.-|+
T Consensus 302 ~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 302 DKVARHVGTKTKEQCILHF 320 (531)
T ss_pred HHHHHHhCCCCHHHHHHHH
Confidence 9999999999999999984
No 8
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.89 E-value=2.5e-09 Score=106.13 Aligned_cols=54 Identities=30% Similarity=0.495 Sum_probs=48.7
Q ss_pred ccccCCCCCCHHHHHHHHHHHHHhC-hhhHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 021972 61 TITKSRESWTEPEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLKV 114 (304)
Q Consensus 61 titk~r~~WTeEEh~lFLeaLe~yG-rdWkkIA~~VgTRT~~QVrSHAQKYf~kl 114 (304)
+-......||.+|+.+||+|++.|| ++|+.||+|||+||.++|+.|+.|+|..-
T Consensus 67 s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 67 SFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhcC
Confidence 3344568999999999999999999 69999999999999999999999998764
No 9
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.70 E-value=1.4e-08 Score=102.86 Aligned_cols=69 Identities=28% Similarity=0.422 Sum_probs=55.6
Q ss_pred cCCCCCCCCCCCCCCCCCCchhHHhhhcCCccccCCCCCCCCCCCCcccccCCCCCCHHHHHHHHHHHHHhChhhHHHHh
Q 021972 14 LDPNGMALPGLGPFASSATTPTAAAAAAGTSTVSTSEDPSKKIRKPYTITKSRESWTEPEHDKFLEALQLFDRDWKKIEA 93 (304)
Q Consensus 14 ~~p~~~~~pg~~~~~~~~~~~~~~~~~~~~~~~~s~ed~~kk~rKPytitk~r~~WTeEEh~lFLeaLe~yGrdWkkIA~ 93 (304)
+|..|+-+ | +++.. +...|+ ...-...+..||++|..++||||+.||.||.+|+.
T Consensus 226 ~c~~c~~~-g--~~~~~----------------~~~~Df------~~~~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~ 280 (506)
T KOG1279|consen 226 LCADCYDQ-G--EFPSE----------------FKKSDF------KVIGESARPNWTEQETLLLLEAIEMYGDDWNKVAD 280 (506)
T ss_pred hhHHHHhc-C--CccCc----------------cccccc------hhccccCCCCccHHHHHHHHHHHHHhcccHHHHHh
Confidence 78888887 5 55554 222343 33344567899999999999999999999999999
Q ss_pred hcCCCCHHHHHHHH
Q 021972 94 FIGSKTVIQIRSHA 107 (304)
Q Consensus 94 ~VgTRT~~QVrSHA 107 (304)
|||+||..||..|.
T Consensus 281 hVg~ks~eqCI~kF 294 (506)
T KOG1279|consen 281 HVGTKSQEQCILKF 294 (506)
T ss_pred ccCCCCHHHHHHHH
Confidence 99999999999983
No 10
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.51 E-value=1.4e-07 Score=88.49 Aligned_cols=50 Identities=16% Similarity=0.321 Sum_probs=45.2
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcC-CCCHHHHHHHHHHHH
Q 021972 62 ITKSRESWTEPEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYF 111 (304)
Q Consensus 62 itk~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~Vg-TRT~~QVrSHAQKYf 111 (304)
....++.||.||++++++++++||. +|+.||..++ .||..|||.+|.+|+
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh
Confidence 3456789999999999999999995 9999999885 899999999999886
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.50 E-value=6.1e-07 Score=84.22 Aligned_cols=53 Identities=23% Similarity=0.244 Sum_probs=48.2
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 021972 63 TKSRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 115 (304)
Q Consensus 63 tk~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~ 115 (304)
..+++.||+||++++++.++.||..|..||.++++||..||+.||..++.+..
T Consensus 75 ~I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l 127 (249)
T PLN03212 75 SVKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKL 127 (249)
T ss_pred hcccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHH
Confidence 45788999999999999999999999999999999999999999987766643
No 12
>PLN03091 hypothetical protein; Provisional
Probab=98.41 E-value=2.7e-07 Score=92.38 Aligned_cols=52 Identities=17% Similarity=0.394 Sum_probs=45.9
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcC-CCCHHHHHHHHHHHH
Q 021972 60 YTITKSRESWTEPEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYF 111 (304)
Q Consensus 60 ytitk~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~Vg-TRT~~QVrSHAQKYf 111 (304)
|+....++.||.||++++++++++||. +|+.||..++ +||..|||.+|.+|+
T Consensus 8 ~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 8 YKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred cCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc
Confidence 345556789999999999999999996 9999999886 899999999998764
No 13
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.36 E-value=1.1e-06 Score=85.64 Aligned_cols=49 Identities=29% Similarity=0.582 Sum_probs=46.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhC-hhhHHHHhhcCCCCHHHHHHHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLK 113 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yG-rdWkkIA~~VgTRT~~QVrSHAQKYf~k 113 (304)
..+.|+.+|+.+|+++++-.| ++|..||+|||+|+.++|++|+-||++.
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~e 111 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYDE 111 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHhh
Confidence 567999999999999999999 6999999999999999999999999873
No 14
>PLN03091 hypothetical protein; Provisional
Probab=98.31 E-value=1.3e-06 Score=87.55 Aligned_cols=53 Identities=17% Similarity=0.289 Sum_probs=48.1
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 021972 62 ITKSRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 114 (304)
Q Consensus 62 itk~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl 114 (304)
...+++.||.||++++|+.+++||..|.+||.+++.||..|||.|+.....|.
T Consensus 63 P~IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 63 PDLKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred CcccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 34567899999999999999999999999999999999999999998776653
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.20 E-value=3.3e-06 Score=77.19 Aligned_cols=52 Identities=17% Similarity=0.316 Sum_probs=46.9
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHH
Q 021972 62 ITKSRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 113 (304)
Q Consensus 62 itk~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~k 113 (304)
+..+++.||+||+++++++..+||..|..||.++++||..+|+.|+.-...|
T Consensus 58 P~ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lkk 109 (238)
T KOG0048|consen 58 PDLKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLKK 109 (238)
T ss_pred CCccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHHH
Confidence 4457899999999999999999999999999999999999999999665444
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.80 E-value=2.2e-05 Score=71.82 Aligned_cols=46 Identities=15% Similarity=0.346 Sum_probs=43.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcC-CCCHHHHHHHHHHHH
Q 021972 66 RESWTEPEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYF 111 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~Vg-TRT~~QVrSHAQKYf 111 (304)
+++||.||++++.+-|++||. +|..|+...| .|+-.+||-++-+|.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyL 56 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYL 56 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhccc
Confidence 699999999999999999995 8999999999 999999999998883
No 17
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.43 E-value=0.00074 Score=67.51 Aligned_cols=56 Identities=25% Similarity=0.299 Sum_probs=47.5
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCh---hhHHHHhhc--CCCCHHHHHHHHHHHHHHHhhc
Q 021972 62 ITKSRESWTEPEHDKFLEALQLFDR---DWKKIEAFI--GSKTVIQIRSHAQKYFLKVQKN 117 (304)
Q Consensus 62 itk~r~~WTeEEh~lFLeaLe~yGr---dWkkIA~~V--gTRT~~QVrSHAQKYf~kl~k~ 117 (304)
..|.|-.||.|=|++|++||++.|- --|+|=+++ ..-|..+|+||-|||+..+++.
T Consensus 233 ~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l 293 (526)
T PLN03162 233 KKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHL 293 (526)
T ss_pred CCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccc
Confidence 3457789999999999999999993 578887655 4789999999999999987753
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.34 E-value=0.00034 Score=73.70 Aligned_cols=52 Identities=17% Similarity=0.355 Sum_probs=46.1
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 021972 63 TKSRESWTEPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKV 114 (304)
Q Consensus 63 tk~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQKYf~kl 114 (304)
..+.++||++|+.+++.|+++||. ||-+|-+.|++|+..|||.+|-+.+..-
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s 409 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRS 409 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHh
Confidence 456799999999999999999995 9999999999999999999987655443
No 19
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=96.88 E-value=0.0019 Score=67.58 Aligned_cols=61 Identities=25% Similarity=0.402 Sum_probs=49.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHH----------HhhcCCCCHHHHHHHHHHHHHHHhhcCCCCCCCC
Q 021972 65 SRESWTEPEHDKFLEALQLFDRDWKKI----------EAFIGSKTVIQIRSHAQKYFLKVQKNGTAEHLPP 125 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGrdWkkI----------A~~VgTRT~~QVrSHAQKYf~kl~k~g~~~~iP~ 125 (304)
.++.||-.|..-|..||++||+|+.+| -.-+-.||..|||.||-+...++.+.-.++.|+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~F~~~l~~ 157 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLLFGPDLSL 157 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhhcccccCc
Confidence 367999999999999999999999999 3345678999999998777777777544444443
No 20
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=96.56 E-value=0.016 Score=58.02 Aligned_cols=41 Identities=24% Similarity=0.494 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHHhChhhHHHH-hhcCCCCHHHHHHHH
Q 021972 67 ESWTEPEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSHA 107 (304)
Q Consensus 67 ~~WTeEEh~lFLeaLe~yGrdWkkIA-~~VgTRT~~QVrSHA 107 (304)
-.|+++|-+.|.+||+.||||+..|. .-|.||+.-+|..+|
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyY 319 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYY 319 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHH
Confidence 58999999999999999999999997 789999999999874
No 21
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.14 E-value=0.011 Score=45.02 Aligned_cols=52 Identities=29% Similarity=0.439 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--h------hhHHHHhhcC----CCCHHHHHHHHHHHHHHHhhc
Q 021972 66 RESWTEPEHDKFLEALQL------FD--R------DWKKIEAFIG----SKTVIQIRSHAQKYFLKVQKN 117 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~------yG--r------dWkkIA~~Vg----TRT~~QVrSHAQKYf~kl~k~ 117 (304)
|..||++|...||+.+.. |+ + -|+.||+.+. .||+.||+..+.....+..+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999877 32 1 5999997663 699999999988766665543
No 22
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=95.64 E-value=0.0068 Score=57.36 Aligned_cols=73 Identities=26% Similarity=0.325 Sum_probs=60.5
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh-hhHHHH-hhcCCCCHHHHHHHHH-----HHHHHHhhcCCCCCCCCCCCCCCCCCC
Q 021972 63 TKSRESWTEPEHDKFLEALQLFDR-DWKKIE-AFIGSKTVIQIRSHAQ-----KYFLKVQKNGTAEHLPPPRPKRKAAHP 135 (304)
Q Consensus 63 tk~r~~WTeEEh~lFLeaLe~yGr-dWkkIA-~~VgTRT~~QVrSHAQ-----KYf~kl~k~g~~~~iP~pr~KRks~h~ 135 (304)
.+.+..|++.+|.+++.++..+|+ +|..|+ .++..|++.|+.+|+| +|+.+....+ ....|+++|+
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~-------~~~~~~s~~~ 233 (335)
T KOG0724|consen 161 RRKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGE-------EEKRRKSIED 233 (335)
T ss_pred hhccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhc-------cccccchhhh
Confidence 346689999999999999999998 999998 6888999999999999 8888875443 2466788888
Q ss_pred cCCcCCC
Q 021972 136 YPQKASK 142 (304)
Q Consensus 136 ~p~~~~~ 142 (304)
++.....
T Consensus 234 ~~~~~~~ 240 (335)
T KOG0724|consen 234 ITTASEA 240 (335)
T ss_pred hhccchh
Confidence 8766543
No 23
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=95.34 E-value=0.02 Score=60.06 Aligned_cols=56 Identities=25% Similarity=0.500 Sum_probs=48.0
Q ss_pred CCCccccc-CCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHH
Q 021972 57 RKPYTITK-SRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 113 (304)
Q Consensus 57 rKPytitk-~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~k 113 (304)
|.-|++=. .++.||+||.+.+-....++|.+|+.|+..+| |.+.-||.|+..|...
T Consensus 374 rR~y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~~~~ 430 (607)
T KOG0051|consen 374 RRAYTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQYVKC 430 (607)
T ss_pred HhcCCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHhhcc
Confidence 34555555 88999999999999999999999999999998 5799999999877443
No 24
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.03 E-value=0.036 Score=59.07 Aligned_cols=44 Identities=27% Similarity=0.545 Sum_probs=39.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQ 108 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQ 108 (304)
+.+.||-.|++.+++++++||. .|.+||.++|.||..|.++.-.
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~ 455 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRL 455 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHH
Confidence 5689999999999999999996 9999999999999988766533
No 25
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.89 E-value=0.03 Score=58.77 Aligned_cols=50 Identities=24% Similarity=0.509 Sum_probs=42.5
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hh------------------Ch-hhHHHHhhcCCCCHHHHHHHHHHHHHH
Q 021972 64 KSRESWTEPEHDKFLEALQ-------LF------------------DR-DWKKIEAFIGSKTVIQIRSHAQKYFLK 113 (304)
Q Consensus 64 k~r~~WTeEEh~lFLeaLe-------~y------------------Gr-dWkkIA~~VgTRT~~QVrSHAQKYf~k 113 (304)
..++.||.||.+++|..++ +| .. .|..|++.+|||+..|||.|+.+...+
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~ 509 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTS 509 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhh
Confidence 3678999999999999995 44 11 699999999999999999998876554
No 26
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=94.59 E-value=0.19 Score=50.75 Aligned_cols=53 Identities=25% Similarity=0.387 Sum_probs=42.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhC---h-------------hhHHHHhhcC-----CCCHHHHHHHHHHHHHHHhh
Q 021972 64 KSRESWTEPEHDKFLEALQLFD---R-------------DWKKIEAFIG-----SKTVIQIRSHAQKYFLKVQK 116 (304)
Q Consensus 64 k~r~~WTeEEh~lFLeaLe~yG---r-------------dWkkIA~~Vg-----TRT~~QVrSHAQKYf~kl~k 116 (304)
...+.|+++=++.|+|||..|- | +=.-||.||+ |||..||.||-|=.-.+..+
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~r 147 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLR 147 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHH
Confidence 3458999999999999999872 1 3467899885 89999999999966555444
No 27
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=94.31 E-value=0.05 Score=56.55 Aligned_cols=51 Identities=18% Similarity=0.438 Sum_probs=46.1
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHHHHH
Q 021972 62 ITKSRESWTEPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFL 112 (304)
Q Consensus 62 itk~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQKYf~ 112 (304)
+-+.++.|+..|++.+-.|+.+||. .|.+|+..+..+|+.||+.+|.+|..
T Consensus 3 i~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ld 54 (617)
T KOG0050|consen 3 IEIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLD 54 (617)
T ss_pred eEEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhC
Confidence 3456789999999999999999997 89999999999999999999987743
No 28
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.13 E-value=0.095 Score=58.03 Aligned_cols=49 Identities=20% Similarity=0.453 Sum_probs=44.8
Q ss_pred CCCCHHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 021972 67 ESWTEPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 115 (304)
Q Consensus 67 ~~WTeEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQKYf~kl~ 115 (304)
..|+..+-..|+.|.++||| |...||..|.+||..+|+.+++-|+.+..
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~ 874 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYK 874 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhh
Confidence 47999999999999999998 99999999999999999999988776644
No 29
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.96 E-value=0.048 Score=56.31 Aligned_cols=43 Identities=28% Similarity=0.509 Sum_probs=38.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHH-hhcCCCCHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSHA 107 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGrdWkkIA-~~VgTRT~~QVrSHA 107 (304)
.-+.|+..|-.+|.|||++||+|+..|. +|++=|+..-|..++
T Consensus 284 emEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyY 327 (693)
T KOG3554|consen 284 EMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYY 327 (693)
T ss_pred hhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHH
Confidence 3468999999999999999999999997 899999988887765
No 30
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=93.43 E-value=0.15 Score=51.66 Aligned_cols=42 Identities=24% Similarity=0.517 Sum_probs=39.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSH 106 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSH 106 (304)
...+||.+|-++|..||..+|-|+.-|+...++|...||+.-
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaK 405 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAK 405 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHH
Confidence 347999999999999999999999999999999999999984
No 31
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=93.32 E-value=0.14 Score=55.28 Aligned_cols=46 Identities=26% Similarity=0.405 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKY 110 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKY 110 (304)
....||..|..+|-.||-.|.+|+..|+..|.+||..||-.+|=.+
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 3469999999999999999999999999999999999999986433
No 32
>smart00426 TEA TEA domain.
Probab=92.25 E-value=0.13 Score=40.38 Aligned_cols=43 Identities=28% Similarity=0.464 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCh--hh--------------HHHHhhcC-----CCCHHHHHHHHH
Q 021972 66 RESWTEPEHDKFLEALQLFDR--DW--------------KKIEAFIG-----SKTVIQIRSHAQ 108 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yGr--dW--------------kkIA~~Vg-----TRT~~QVrSHAQ 108 (304)
...|.++=+..|++||+.|-. .+ .-|++||- .||..||.||-|
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 368999999999999999853 11 22555553 688889988876
No 33
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=92.11 E-value=0.32 Score=50.14 Aligned_cols=43 Identities=21% Similarity=0.410 Sum_probs=39.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 107 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHA 107 (304)
....||.||-.+|-.|++.||+++.+|-..++-|+...++-+|
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY 228 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH
Confidence 3478999999999999999999999999999999988887765
No 34
>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=91.86 E-value=0.62 Score=39.56 Aligned_cols=58 Identities=21% Similarity=0.418 Sum_probs=44.1
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHhCh----hhHHHHh------------hcCCCCHHHHHHHHHHHHHHHhh
Q 021972 59 PYTITKSRESWTEPEHDKFLEALQLFDR----DWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQK 116 (304)
Q Consensus 59 Pytitk~r~~WTeEEh~lFLeaLe~yGr----dWkkIA~------------~VgTRT~~QVrSHAQKYf~kl~k 116 (304)
.|..+..+..||++|++-+|-.+.+||- .|.+|-+ |+.+||+.++.-++.-...-+.|
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 3666677889999999999999999996 8999954 45699999999999855444543
No 35
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=90.79 E-value=1.2 Score=33.56 Aligned_cols=50 Identities=18% Similarity=0.410 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHHh-----C------------hhhHHHHhhc-----CCCCHHHHHHHHHHHHHHHhh
Q 021972 67 ESWTEPEHDKFLEALQLF-----D------------RDWKKIEAFI-----GSKTVIQIRSHAQKYFLKVQK 116 (304)
Q Consensus 67 ~~WTeEEh~lFLeaLe~y-----G------------rdWkkIA~~V-----gTRT~~QVrSHAQKYf~kl~k 116 (304)
..||.+|...|++.+++| | +-|..|+..+ +.||..|++..++++-....+
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 579999999999999987 3 1599998554 379999999999888766654
No 36
>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=87.27 E-value=0.62 Score=47.22 Aligned_cols=48 Identities=25% Similarity=0.388 Sum_probs=32.3
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh----h----------hHHHHhhcC-----CCCHHHHHHHHHHH
Q 021972 63 TKSRESWTEPEHDKFLEALQLFDR----D----------WKKIEAFIG-----SKTVIQIRSHAQKY 110 (304)
Q Consensus 63 tk~r~~WTeEEh~lFLeaLe~yGr----d----------WkkIA~~Vg-----TRT~~QVrSHAQKY 110 (304)
....+.|+++=+..|+|||+.|-. . =+-|++||. .||..||.||.|-.
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 345689999999999999999831 2 235787773 79999999999965
No 37
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=86.29 E-value=1 Score=46.88 Aligned_cols=57 Identities=12% Similarity=0.306 Sum_probs=48.9
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 021972 59 PYTITKSRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 115 (304)
Q Consensus 59 Pytitk~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~ 115 (304)
.-....++..|++||+..++..-..+|-.|..|+.+++.||..||-..|..-+....
T Consensus 65 ~lnp~lk~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~~ 121 (512)
T COG5147 65 HLNPQLKKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDLS 121 (512)
T ss_pred hhchhcccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhhh
Confidence 334455778999999999999999999999999999999999999998876655543
No 38
>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=85.55 E-value=2.6 Score=32.46 Aligned_cols=43 Identities=23% Similarity=0.354 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHHh---C----------hhhHHHHhhc----C-CCCHHHHHHHHHHH
Q 021972 68 SWTEPEHDKFLEALQLF---D----------RDWKKIEAFI----G-SKTVIQIRSHAQKY 110 (304)
Q Consensus 68 ~WTeEEh~lFLeaLe~y---G----------rdWkkIA~~V----g-TRT~~QVrSHAQKY 110 (304)
.||+++++.||+.+... | ..|+.|++-+ | ..|..||++|....
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 59999999999999554 1 1599998433 3 56899999998755
No 39
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=85.48 E-value=0.55 Score=48.76 Aligned_cols=57 Identities=16% Similarity=0.259 Sum_probs=47.0
Q ss_pred CCCcccccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHHHHHH
Q 021972 57 RKPYTITKSRESWTEPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLK 113 (304)
Q Consensus 57 rKPytitk~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQKYf~k 113 (304)
.|++.+....+.|+..|+..++-+++.||- +|.+||..+..||..||+.|+-.|...
T Consensus 11 ~~~~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp 68 (512)
T COG5147 11 IKLMQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNP 68 (512)
T ss_pred cccccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhch
Confidence 344455556789999999999999999996 999999888889999999998655433
No 40
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=83.69 E-value=1.2 Score=46.74 Aligned_cols=47 Identities=19% Similarity=0.469 Sum_probs=42.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHH
Q 021972 64 KSRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 111 (304)
Q Consensus 64 k~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf 111 (304)
.++.-|+.||++++|.+...+---|..|+..|| ||..||-.++++..
T Consensus 57 i~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ll 103 (617)
T KOG0050|consen 57 IKKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNLL 103 (617)
T ss_pred HhhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHHH
Confidence 456799999999999999999999999999987 79999999998753
No 41
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=80.65 E-value=15 Score=35.31 Aligned_cols=52 Identities=19% Similarity=0.362 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHHHHHhC----------hhhHHHHh---hcC-CCCHHHHHHHHHHHHHHHhhc
Q 021972 66 RESWTEPEHDKFLEALQLFD----------RDWKKIEA---FIG-SKTVIQIRSHAQKYFLKVQKN 117 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yG----------rdWkkIA~---~Vg-TRT~~QVrSHAQKYf~kl~k~ 117 (304)
...|+.+|...||++..... ..|..||+ ..| -||..||+.-+.+...+.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Confidence 47999999999999986542 26999996 233 799999999887766665553
No 42
>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=75.44 E-value=9 Score=38.23 Aligned_cols=50 Identities=20% Similarity=0.302 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHh-Ch---hhHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 021972 66 RESWTEPEHDKFLEALQLF-DR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 115 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~y-Gr---dWkkIA~~VgTRT~~QVrSHAQKYf~kl~ 115 (304)
...||..|.+.+|.+|+-- |. |-..|+..|.+|+..||+..-|+.-.++-
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rva 74 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVA 74 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHH
Confidence 4699999999999999876 43 67788889999999999998887655443
No 43
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=73.56 E-value=7.1 Score=40.66 Aligned_cols=59 Identities=3% Similarity=0.028 Sum_probs=49.9
Q ss_pred CCCcccccCCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 021972 57 RKPYTITKSRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 115 (304)
Q Consensus 57 rKPytitk~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~ 115 (304)
+-|..+-+-..+||.+|..+.+.+|++||++..-|+-.||.++..|+....-.|..+..
T Consensus 360 kipes~c~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~m 418 (534)
T KOG1194|consen 360 KIPESTCRMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQM 418 (534)
T ss_pred CCCchhhhhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHH
Confidence 44545555568999999999999999999999999999999999999998777765543
No 44
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=72.74 E-value=15 Score=30.07 Aligned_cols=42 Identities=19% Similarity=0.334 Sum_probs=31.3
Q ss_pred CCCCCCHHHHHHHHHHHHHh----Ch----hhHHHHhhcCCC-----CHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLF----DR----DWKKIEAFIGSK-----TVIQIRSH 106 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~y----Gr----dWkkIA~~VgTR-----T~~QVrSH 106 (304)
....||+|++..+|+||-.| |. ||...-++|... |..|+..=
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~K 57 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDK 57 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHH
Confidence 34689999999999999888 63 787777776533 55665443
No 45
>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=72.10 E-value=11 Score=33.68 Aligned_cols=50 Identities=18% Similarity=0.350 Sum_probs=44.5
Q ss_pred CCCHHHHHHHHHHHHHhCh---hhHHHHhhcCCCCHHHHHHHHHHHHHHHhhc
Q 021972 68 SWTEPEHDKFLEALQLFDR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 117 (304)
Q Consensus 68 ~WTeEEh~lFLeaLe~yGr---dWkkIA~~VgTRT~~QVrSHAQKYf~kl~k~ 117 (304)
-++..+.+.||.++-+||- +|+-.-..+..||..+|+.|+--|..+|...
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 6789999999999999995 8999999999999999999998777777543
No 46
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=70.12 E-value=7.8 Score=29.78 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=29.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC---------hhhHHHHhhcC-CCCHHHHHHHHHHHH
Q 021972 66 RESWTEPEHDKFLEALQLFD---------RDWKKIEAFIG-SKTVIQIRSHAQKYF 111 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yG---------rdWkkIA~~Vg-TRT~~QVrSHAQKYf 111 (304)
|..+|+||+..+++-|..+. +=|+++++.-. ..|-.-.|.|+.|.+
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L 57 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHL 57 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 56889999999999996653 15999996545 788888888865553
No 47
>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=69.47 E-value=10 Score=34.31 Aligned_cols=47 Identities=17% Similarity=0.271 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCh-------hhHHHHhhcCCCCHHHHHHHHHHHHHH
Q 021972 66 RESWTEPEHDKFLEALQLFDR-------DWKKIEAFIGSKTVIQIRSHAQKYFLK 113 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yGr-------dWkkIA~~VgTRT~~QVrSHAQKYf~k 113 (304)
...||.||+.++-|.+-+|=+ .+..++.-+ +||..-|.-+|..|..|
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHH
Confidence 468999999999999988833 455555544 58999999999888665
No 48
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=68.10 E-value=6.6 Score=43.38 Aligned_cols=61 Identities=18% Similarity=0.378 Sum_probs=52.2
Q ss_pred CCCcccccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHHHHHHHhhcC
Q 021972 57 RKPYTITKSRESWTEPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNG 118 (304)
Q Consensus 57 rKPytitk~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQKYf~kl~k~g 118 (304)
+|+.-.+..-..||..+-..|+.|-++||+ |-..|+.-|-. |+++|..++.-||.++++..
T Consensus 786 ~k~~ll~~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~ 847 (971)
T KOG0385|consen 786 EKEELLSQGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELS 847 (971)
T ss_pred hhhhhhhccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhh
Confidence 455555555578999999999999999998 89999987776 99999999999999988754
No 49
>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=67.79 E-value=19 Score=25.12 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHH
Q 021972 72 PEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQK 109 (304)
Q Consensus 72 EEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQK 109 (304)
+-+.++|+.|+.-|+ .|.+|++-+|- |...|..+.++
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 457889999999998 99999999997 78888877654
No 50
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=64.06 E-value=10 Score=34.54 Aligned_cols=48 Identities=15% Similarity=0.204 Sum_probs=35.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-hhHHHHh--hcC---CCCHHHHHHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFDR-DWKKIEA--FIG---SKTVIQIRSHAQKYFL 112 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGr-dWkkIA~--~Vg---TRT~~QVrSHAQKYf~ 112 (304)
....||.||+.++-+.+-.|++ +=.+++. .+| .||..+|..+|..+..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~rt~aac~fRwNs~vr 57 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALKRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhhhHHHHHhHHHHHHH
Confidence 3479999999999999999986 4444542 223 6899999999955543
No 51
>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=62.91 E-value=27 Score=24.30 Aligned_cols=40 Identities=5% Similarity=0.103 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHH
Q 021972 72 PEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 112 (304)
Q Consensus 72 EEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~ 112 (304)
++++..+......|..|++||+.+| .|...|+.|.++=..
T Consensus 13 ~~~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 13 ERQREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRRARK 52 (54)
T ss_dssp HHHHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHHHHh
Confidence 3444455555666789999999998 588999988665433
No 52
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=61.84 E-value=22 Score=27.58 Aligned_cols=27 Identities=30% Similarity=0.672 Sum_probs=20.8
Q ss_pred hhHHHHhhcCCCC-----HHHHHHHHHHHHHH
Q 021972 87 DWKKIEAFIGSKT-----VIQIRSHAQKYFLK 113 (304)
Q Consensus 87 dWkkIA~~VgTRT-----~~QVrSHAQKYf~k 113 (304)
+|..|++-+|--. ..+++.|+++|+..
T Consensus 59 ~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 59 KWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp THHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred hHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 7999998887322 47899999998754
No 53
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=61.47 E-value=8.2 Score=41.01 Aligned_cols=50 Identities=22% Similarity=0.393 Sum_probs=44.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHhhc
Q 021972 65 SRESWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 117 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~k~ 117 (304)
....|+.+|-.+|-.++..+|-+..-|++..+.|+..|||. ||-++-.+.
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 34799999999999999999999999999999999999997 666655443
No 54
>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=60.10 E-value=22 Score=24.37 Aligned_cols=26 Identities=19% Similarity=0.194 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHhChhhHHHHhhcCC
Q 021972 72 PEHDKFLEALQLFDRDWKKIEAFIGS 97 (304)
Q Consensus 72 EEh~lFLeaLe~yGrdWkkIA~~VgT 97 (304)
-|...+.++|+.+|++..+.|+.+|-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lgi 30 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHTS
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCC
Confidence 48889999999999999999999984
No 55
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=58.45 E-value=10 Score=33.92 Aligned_cols=46 Identities=20% Similarity=0.356 Sum_probs=33.5
Q ss_pred CcccCCC---hHHHhhhhhcccCCCcchHHHhhhcCCcchHHHHHHHHh
Q 021972 240 PLRVLPD---FAQVYTFIGSVFDPNASDHVQKLKKMDPIDVETVCYIKN 285 (304)
Q Consensus 240 ~l~~~Pd---FaqVY~FiGsvFdp~~~~hlqkLk~Mdpi~~eTvlllmr 285 (304)
.+..+|+ |+++|+||-..=.=+...|++.|-.-==|+.+++.++++
T Consensus 90 y~~~~P~Re~F~~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~ 138 (195)
T PF10141_consen 90 YFEGMPTREQFKKLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLK 138 (195)
T ss_pred hhcCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHH
Confidence 4678886 999999998752223477888886666678887776654
No 56
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=54.49 E-value=38 Score=26.60 Aligned_cols=41 Identities=22% Similarity=0.409 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhCh--------hhHHHHhhcCCC-----CHHHHHHHHHHHHHHHh
Q 021972 74 HDKFLEALQLFDR--------DWKKIEAFIGSK-----TVIQIRSHAQKYFLKVQ 115 (304)
Q Consensus 74 h~lFLeaLe~yGr--------dWkkIA~~VgTR-----T~~QVrSHAQKYf~kl~ 115 (304)
..+|. ++...|+ .|++|++-+|-. ...+++.|+++|....+
T Consensus 35 ~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE 88 (93)
T smart00501 35 YRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPFE 88 (93)
T ss_pred HHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHH
Confidence 34444 5666663 799999888743 36789999999976654
No 57
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=52.76 E-value=27 Score=29.78 Aligned_cols=43 Identities=21% Similarity=0.284 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHHHHHHHhhcC
Q 021972 71 EPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNG 118 (304)
Q Consensus 71 eEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQKYf~kl~k~g 118 (304)
++.+.++|++|++-|| .|.+||+-+|- |+..|+.+.+ ++...|
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~----rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVE----KMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHH----HHHHCC
Confidence 4678999999999998 99999999986 7888888654 455555
No 58
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=51.72 E-value=39 Score=38.23 Aligned_cols=54 Identities=15% Similarity=0.329 Sum_probs=44.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhC-hhhHHHHh------------hcCCCCHHHHHHHHHHHHHHHhhc
Q 021972 64 KSRESWTEPEHDKFLEALQLFD-RDWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQKN 117 (304)
Q Consensus 64 k~r~~WTeEEh~lFLeaLe~yG-rdWkkIA~------------~VgTRT~~QVrSHAQKYf~kl~k~ 117 (304)
.++..||+||++.+|-.+.+|| .+|.+|-. |+.+||+.++.-++.-....+.+.
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e 990 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKE 990 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHH
Confidence 3456799999999999999999 48999943 456999999999998666666654
No 59
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=47.12 E-value=10 Score=27.33 Aligned_cols=17 Identities=35% Similarity=0.464 Sum_probs=14.3
Q ss_pred Ccc-cCCCCCCCCCCCCCCCC
Q 021972 11 GFY-LDPNGMALPGLGPFASS 30 (304)
Q Consensus 11 ~~y-~~p~~~~~pg~~~~~~~ 30 (304)
.+| |||.||.+ | ++|++
T Consensus 21 ~~~dLC~~CF~~-G--~f~~~ 38 (45)
T cd02336 21 KKYDLCPSCYQE-G--RFPSN 38 (45)
T ss_pred CccccChHHHhC-c--CCCCC
Confidence 368 99999999 7 88875
No 60
>PHA00442 host recBCD nuclease inhibitor
Probab=46.82 E-value=12 Score=28.84 Aligned_cols=33 Identities=24% Similarity=0.582 Sum_probs=26.1
Q ss_pred cccCCCCC--------CHHHHHHHHHHHHHhCh-hhHHHHhh
Q 021972 62 ITKSRESW--------TEPEHDKFLEALQLFDR-DWKKIEAF 94 (304)
Q Consensus 62 itk~r~~W--------TeEEh~lFLeaLe~yGr-dWkkIA~~ 94 (304)
.+.-|..| +-|....||++|+..|- +|..+.+.
T Consensus 8 VtitRd~wnd~q~yidsLek~~~~L~~Lea~GVDNW~Gy~eA 49 (59)
T PHA00442 8 VTITRDAWNDMQGYIDSLEKDNEFLKALRACGVDNWDGYMDA 49 (59)
T ss_pred eeecHHHHHHHHHHHHHHHHhhHHHHHHHHcCCcchhhHHHH
Confidence 44556778 55778899999999995 99988753
No 61
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=46.31 E-value=46 Score=26.07 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHH
Q 021972 71 EPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQ 108 (304)
Q Consensus 71 eEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQ 108 (304)
++.+.++|+.|+..|+ .+++|++.+|- +...|+.+.+
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~ 39 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVK 39 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHH
Confidence 3578899999999987 99999999986 7788888654
No 62
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=46.13 E-value=69 Score=24.77 Aligned_cols=47 Identities=17% Similarity=0.253 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHhh
Q 021972 68 SWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 116 (304)
Q Consensus 68 ~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~k 116 (304)
..++.|...|..- -..|..+++||+.+|. |...|+.+.++-..++++
T Consensus 110 ~L~~~~~~ii~~~-~~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLR-YLEGLSYKEIAEILGI-SVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhH-HhcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHh
Confidence 4556665555322 2347799999999987 888888888777777653
No 63
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=45.50 E-value=37 Score=29.32 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHhCh-hhHHHHhhcCCCCHHHHHHHHHHHHHHHhhcC
Q 021972 71 EPEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNG 118 (304)
Q Consensus 71 eEEh~lFLeaLe~yGr-dWkkIA~~VgTRT~~QVrSHAQKYf~kl~k~g 118 (304)
++-+.++|.+|++-|| .|.+||+-||- +...|+.+.+ ++.+.|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~----rL~~~G 56 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVR----RLERQG 56 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHH----HHHHCC
Confidence 6788999999999998 99999999985 6777877654 455555
No 64
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=39.85 E-value=1e+02 Score=19.77 Aligned_cols=42 Identities=12% Similarity=0.151 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHH
Q 021972 68 SWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 111 (304)
Q Consensus 68 ~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf 111 (304)
.+++++ ..+++.+-.-|..+++||+.+|- +..+|..+-++..
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 44455555567799999988874 6677776655443
No 65
>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=38.63 E-value=53 Score=27.33 Aligned_cols=24 Identities=17% Similarity=0.466 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHhhcC
Q 021972 70 TEPEHDKFLEALQLFDRDWKKIEAFIG 96 (304)
Q Consensus 70 TeEEh~lFLeaLe~yGrdWkkIA~~Vg 96 (304)
|+++...|-+ ..|++|+.++..+|
T Consensus 1 ~~~~~q~~~~---nvGr~WK~laR~Lg 24 (90)
T cd08780 1 TPADQQHFAK---SVGKKWKPVGRSLQ 24 (90)
T ss_pred CHHHHHHHHH---HHhHHHHHHHHHHc
Confidence 3455555554 44899999999998
No 66
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=38.04 E-value=16 Score=42.64 Aligned_cols=49 Identities=20% Similarity=0.188 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHhhcCCC
Q 021972 72 PEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGTA 120 (304)
Q Consensus 72 EEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~k~g~~ 120 (304)
||-+.--.||-.+||+|.+|.-.|+++|..||...+-||-.+++.++..
T Consensus 360 ee~ev~k~Glveh~R~~aai~p~vvt~tes~c~na~a~~~~r~N~d~~l 408 (1672)
T KOG1878|consen 360 EEMEVAKSGLVEHGREWAAILPKVVTKTESQCKNAYAKYKNRHNLDEPL 408 (1672)
T ss_pred hhhhhhhccchhhhhhHHHhcCccceecccchhhHHHhhhhhhcchhhh
Confidence 4555777888899999999999999999999999877887777766543
No 67
>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=37.72 E-value=69 Score=28.04 Aligned_cols=46 Identities=20% Similarity=0.174 Sum_probs=36.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHhhc----CCCCHHHHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFDRDWKKIEAFI----GSKTVIQIRSHAQKY 110 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~V----gTRT~~QVrSHAQKY 110 (304)
....=|+.|..-....|++||.|++.++.=. --.|+.||+--..+|
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 4456678888888888899999999999433 357999999877665
No 68
>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=36.51 E-value=41 Score=26.49 Aligned_cols=34 Identities=26% Similarity=0.409 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHH
Q 021972 71 EPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSH 106 (304)
Q Consensus 71 eEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSH 106 (304)
.||-+++|.+= .-|+||+..|..+|- +..+|+..
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~LG~-~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGELGY-EDEAIDTF 35 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHcCC-CHHHHHHH
Confidence 47777777521 567899999999996 35555543
No 69
>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=35.95 E-value=1.5e+02 Score=20.45 Aligned_cols=43 Identities=12% Similarity=0.123 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 021972 71 EPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 115 (304)
Q Consensus 71 eEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~ 115 (304)
++|...+..-+ .-|..+++||+.+|- |...|+.+-.+-+.+++
T Consensus 7 ~~er~vi~~~y-~~~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 7 PREREVIRLRY-FEGLTLEEIAERLGI-SRSTVRRILKRALKKLR 49 (50)
T ss_dssp HHHHHHHHHHH-TST-SHHHHHHHHTS-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh-cCCCCHHHHHHHHCC-cHHHHHHHHHHHHHHhc
Confidence 34444333332 334599999999986 78888887766666664
No 70
>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=35.00 E-value=32 Score=24.96 Aligned_cols=27 Identities=22% Similarity=0.519 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHhhcC
Q 021972 70 TEPEHDKFLEALQLFDRDWKKIEAFIG 96 (304)
Q Consensus 70 TeEEh~lFLeaLe~yGrdWkkIA~~Vg 96 (304)
..+.|++|...|+.-....+-|++|+|
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfG 43 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFG 43 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHc
Confidence 356799999999888889999999997
No 71
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=34.10 E-value=1e+02 Score=25.13 Aligned_cols=26 Identities=12% Similarity=0.077 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhChhhHHHHhhcCC
Q 021972 72 PEHDKFLEALQLFDRDWKKIEAFIGS 97 (304)
Q Consensus 72 EEh~lFLeaLe~yGrdWkkIA~~VgT 97 (304)
-|...+.++|+.+|+++.+.|+.+|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 57888999999999999999999995
No 72
>PRK01905 DNA-binding protein Fis; Provisional
Probab=34.03 E-value=1.2e+02 Score=23.30 Aligned_cols=28 Identities=7% Similarity=0.057 Sum_probs=24.7
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHhhcCC
Q 021972 70 TEPEHDKFLEALQLFDRDWKKIEAFIGS 97 (304)
Q Consensus 70 TeEEh~lFLeaLe~yGrdWkkIA~~VgT 97 (304)
.+-|...+.++|+.+|.++.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 4568888999999999999999999984
No 73
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=34.01 E-value=43 Score=34.55 Aligned_cols=50 Identities=24% Similarity=0.383 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHhChhhHHHH-hh----cC-CCCHHHHHHHHHHHHHHHhh
Q 021972 67 ESWTEPEHDKFLEALQLFDRDWKKIE-AF----IG-SKTVIQIRSHAQKYFLKVQK 116 (304)
Q Consensus 67 ~~WTeEEh~lFLeaLe~yGrdWkkIA-~~----Vg-TRT~~QVrSHAQKYf~kl~k 116 (304)
..||.+|.+-+.+.-+.|+-+|--|+ .| .+ +||.+..+.++=....++-+
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~k 186 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLK 186 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999998888 32 45 49999999987544555443
No 74
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=32.11 E-value=49 Score=35.11 Aligned_cols=43 Identities=19% Similarity=0.235 Sum_probs=36.7
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHH
Q 021972 70 TEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 113 (304)
Q Consensus 70 TeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~k 113 (304)
-+.|.+++.+||++-|.+|.+-|+.+|. |+.|+-+.+++|=++
T Consensus 504 ~~~eR~~I~~aL~~~~~~~a~AAr~LGl-~~~~L~~~~kRlGI~ 546 (550)
T COG3604 504 EEFERQLIIAALEETNGNWAGAARRLGL-TRRTLLYRMKRLGIK 546 (550)
T ss_pred HHHHHHHHHHHHHHhCCcHHHHHHHhCC-CHHHHHHHHHHcCCC
Confidence 3788999999999999999998899987 889998887766443
No 75
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=30.59 E-value=82 Score=21.45 Aligned_cols=39 Identities=13% Similarity=0.272 Sum_probs=20.4
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHH
Q 021972 70 TEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKY 110 (304)
Q Consensus 70 TeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKY 110 (304)
+.++....++.+.. |...++||+.+|- +...|....+.|
T Consensus 3 ~~~~R~~ii~l~~~-G~s~~~ia~~lgv-s~~Tv~~w~kr~ 41 (50)
T PF13384_consen 3 SEERRAQIIRLLRE-GWSIREIAKRLGV-SRSTVYRWIKRY 41 (50)
T ss_dssp -------HHHHHHH-T--HHHHHHHHTS--HHHHHHHHT--
T ss_pred chhHHHHHHHHHHC-CCCHHHHHHHHCc-CHHHHHHHHHHc
Confidence 45666777777777 9999999999984 666666644444
No 76
>smart00595 MADF subfamily of SANT domain.
Probab=30.43 E-value=87 Score=23.74 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=20.1
Q ss_pred hhHHHHhhcCCCCHHHHHHHHHHH
Q 021972 87 DWKKIEAFIGSKTVIQIRSHAQKY 110 (304)
Q Consensus 87 dWkkIA~~VgTRT~~QVrSHAQKY 110 (304)
.|.+|++-++. |.++|+.++...
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 69999999988 999999888664
No 77
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=29.60 E-value=96 Score=28.91 Aligned_cols=45 Identities=13% Similarity=0.218 Sum_probs=36.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhC---hhhHHH-----HhhcCCCCHHHHHHHHHH
Q 021972 65 SRESWTEPEHDKFLEALQLFD---RDWKKI-----EAFIGSKTVIQIRSHAQK 109 (304)
Q Consensus 65 ~r~~WTeEEh~lFLeaLe~yG---rdWkkI-----A~~VgTRT~~QVrSHAQK 109 (304)
.+..||.+|++++...-.... ..+++| +-|-.+||+.+...|++-
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~l 124 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRL 124 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHH
Confidence 557999999999998766554 378887 346689999999999983
No 78
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=29.52 E-value=35 Score=26.69 Aligned_cols=19 Identities=32% Similarity=0.677 Sum_probs=15.1
Q ss_pred HHHHHHHHHhChhhHHHHh
Q 021972 75 DKFLEALQLFDRDWKKIEA 93 (304)
Q Consensus 75 ~lFLeaLe~yGrdWkkIA~ 93 (304)
.-+.+.|+.||++|.-|++
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3456778999999999983
No 79
>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=27.11 E-value=2e+02 Score=21.72 Aligned_cols=39 Identities=18% Similarity=0.406 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHHHHHHHHHHhh
Q 021972 68 SWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 116 (304)
Q Consensus 68 ~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~k 116 (304)
.++++|.+.|+ +.|+.+++.=+..+|+...-.||.++..
T Consensus 19 ~l~~~er~~lv----------~nia~~l~~v~~~~i~~r~l~~f~~vd~ 57 (68)
T PF06628_consen 19 VLSDEERERLV----------ENIAGHLSGVSDEEIQERVLAYFYKVDP 57 (68)
T ss_dssp HSSHHHHHHHH----------HHHHHHHTTSSHHHHHHHHHHHHHHH-H
T ss_pred HCCHHHHHHHH----------HHHHHHHccCChhhHHHHHHHHHHHhCH
Confidence 56889999888 4578888877777799999999988754
No 80
>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=25.70 E-value=39 Score=26.68 Aligned_cols=16 Identities=13% Similarity=0.335 Sum_probs=9.1
Q ss_pred cCCCCCCHHHHHHHHH
Q 021972 64 KSRESWTEPEHDKFLE 79 (304)
Q Consensus 64 k~r~~WTeEEh~lFLe 79 (304)
-..+.||.|+++.++-
T Consensus 45 n~~GiWT~eDD~~L~~ 60 (87)
T PF11626_consen 45 NMPGIWTPEDDEMLRS 60 (87)
T ss_dssp T-TT---HHHHHHHTS
T ss_pred CCCCCcCHHHHHHHHc
Confidence 3568999999998843
No 81
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=25.57 E-value=2.2e+02 Score=23.29 Aligned_cols=32 Identities=13% Similarity=0.230 Sum_probs=23.9
Q ss_pred hChhhHHHHhhcCCCCHHHHHHHHHHHHHHHhh
Q 021972 84 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 116 (304)
Q Consensus 84 yGrdWkkIA~~VgTRT~~QVrSHAQKYf~kl~k 116 (304)
.|..++.||+.+|. |...|+.+-.+-..++++
T Consensus 140 ~~~~~~eIA~~lgi-s~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 140 EGLSYREIAEILGV-PVGTVKSRLRRARQLLRE 171 (179)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHH
Confidence 46689999998885 677888877666666654
No 82
>PF10561 UPF0565: Uncharacterised protein family UPF0565; InterPro: IPR018881 This family of proteins has no known function.
Probab=24.52 E-value=61 Score=31.91 Aligned_cols=30 Identities=23% Similarity=0.575 Sum_probs=26.7
Q ss_pred CCCcccccCCCCCCHHHHHHHHHHHHHhCh
Q 021972 57 RKPYTITKSRESWTEPEHDKFLEALQLFDR 86 (304)
Q Consensus 57 rKPytitk~r~~WTeEEh~lFLeaLe~yGr 86 (304)
-.||-..-..++|=.+|++.|++-|+.+|-
T Consensus 272 ~TPyQv~D~~RpwI~~E~~~F~~~L~~~~~ 301 (303)
T PF10561_consen 272 VTPYQVSDPMRPWIGKEEKKFVKLLKKLGA 301 (303)
T ss_pred cCcccccCCCCcHHHHHHHHHHHHHHHhCC
Confidence 468888888899999999999999999984
No 83
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=22.40 E-value=1.7e+02 Score=23.33 Aligned_cols=23 Identities=22% Similarity=0.447 Sum_probs=17.2
Q ss_pred HHhChhhHHHHhhcCCCCHHHHHH
Q 021972 82 QLFDRDWKKIEAFIGSKTVIQIRS 105 (304)
Q Consensus 82 e~yGrdWkkIA~~VgTRT~~QVrS 105 (304)
+.-|++|+.++..+|- +..+|..
T Consensus 10 ~~lG~~Wk~lar~LG~-s~~eI~~ 32 (86)
T cd08777 10 ENLGKKWKRCARKLGF-TESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHcCC-CHHHHHH
Confidence 5568999999999995 4455544
No 84
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.81 E-value=54 Score=30.11 Aligned_cols=28 Identities=18% Similarity=0.395 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCh-hhHHHHh
Q 021972 66 RESWTEPEHDKFLEALQLFDR-DWKKIEA 93 (304)
Q Consensus 66 r~~WTeEEh~lFLeaLe~yGr-dWkkIA~ 93 (304)
.+.|-.+-+..+|.|+-.||. +|+.|.+
T Consensus 3 ~~iw~r~hdywll~gi~~hgy~rwqdi~n 31 (173)
T PF08074_consen 3 YEIWHRRHDYWLLAGIVKHGYGRWQDIQN 31 (173)
T ss_pred hhhhhhhhhHHHHhHHhhccchhHHHHhc
Confidence 468988889999999999996 9999973
No 85
>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=21.67 E-value=1e+02 Score=28.80 Aligned_cols=49 Identities=14% Similarity=0.192 Sum_probs=31.6
Q ss_pred CCCccccc--------CCCCCCHHHHHHHHHHHHHhCh---hhHHHHhhcCCCCHHHHHHHHHHH
Q 021972 57 RKPYTITK--------SRESWTEPEHDKFLEALQLFDR---DWKKIEAFIGSKTVIQIRSHAQKY 110 (304)
Q Consensus 57 rKPytitk--------~r~~WTeEEh~lFLeaLe~yGr---dWkkIA~~VgTRT~~QVrSHAQKY 110 (304)
.+||.... .+..|+++||.+|++.|+...+ .|- -.+ -...+|+.++..|
T Consensus 179 DPPY~~~~~~~~f~~y~~~~f~~~dh~~L~~~l~~l~~~~~~~~--lS~---~~~~~i~ely~~~ 238 (266)
T TIGR00571 179 DPPYLPLSATYNFTGYHTNGFDEDEQKRLANFCKSLDERGIKFL--LSN---SDSSFTRELYQGF 238 (266)
T ss_pred CCCCCCCCCCCCccCccCCCCCHHHHHHHHHHHHHHHhCCCEEE--EEe---CCCHHHHHHhcCC
Confidence 78996431 1357999999999999988732 332 111 1345788776544
No 86
>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=21.63 E-value=53 Score=36.47 Aligned_cols=50 Identities=22% Similarity=0.400 Sum_probs=41.8
Q ss_pred CCCCcccccCCCCCCHHHHHHHHHHHHHhChhhHHHHhhcC-CCCHHHHHH
Q 021972 56 IRKPYTITKSRESWTEPEHDKFLEALQLFDRDWKKIEAFIG-SKTVIQIRS 105 (304)
Q Consensus 56 ~rKPytitk~r~~WTeEEh~lFLeaLe~yGrdWkkIA~~Vg-TRT~~QVrS 105 (304)
-|++..-.+-.-.|+..|-.+|+.+..++++.|+..+..+. +|...++.-
T Consensus 34 qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~~vel 84 (837)
T KOG1019|consen 34 QRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSNMVEL 84 (837)
T ss_pred CCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhhHHHH
Confidence 36666666677799999999999999999999999997664 588888765
No 87
>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=21.25 E-value=1.3e+02 Score=26.74 Aligned_cols=38 Identities=13% Similarity=0.181 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHHHhChhhHHHHhhcCCCCHHHHHHH
Q 021972 68 SWTEPEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSH 106 (304)
Q Consensus 68 ~WTeEEh~lFLeaLe~yGrdWkkIA~~VgTRT~~QVrSH 106 (304)
.||+|+.+++.+. -.=|..-.+|++-+|..|...|.-.
T Consensus 2 ~Wtde~~~~L~~l-w~~G~SasqIA~~lg~vsRnAViGk 39 (162)
T PF07750_consen 2 SWTDERVERLRKL-WAEGLSASQIARQLGGVSRNAVIGK 39 (162)
T ss_pred CCCHHHHHHHHHH-HHcCCCHHHHHHHhCCcchhhhhhh
Confidence 5999888865544 4568889999999995565566554
No 88
>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=20.84 E-value=1.6e+02 Score=21.40 Aligned_cols=27 Identities=15% Similarity=0.259 Sum_probs=20.7
Q ss_pred hhHHHHhhcCC-CCHHHHHHHHHHHHHH
Q 021972 87 DWKKIEAFIGS-KTVIQIRSHAQKYFLK 113 (304)
Q Consensus 87 dWkkIA~~VgT-RT~~QVrSHAQKYf~k 113 (304)
-|..|++.++. -+..+|+.+++.....
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 69999988884 4678898888775433
Done!