Query 011020
Match_columns 495
No_of_seqs 194 out of 789
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:12:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011020.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011020hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1886 BAH domain proteins [T 100.0 1.4E-48 3.1E-53 407.7 11.4 311 88-458 7-320 (464)
2 cd04713 BAH_plant_3 BAH, or Br 100.0 1.4E-35 2.9E-40 271.3 16.1 146 111-257 1-146 (146)
3 cd04716 BAH_plantDCM_I BAH, or 99.9 1E-26 2.2E-31 207.9 13.2 118 128-248 1-121 (122)
4 cd04717 BAH_polybromo BAH, or 99.9 6.9E-27 1.5E-31 206.2 12.0 117 128-247 1-119 (121)
5 cd04714 BAH_BAHCC1 BAH, or Bro 99.9 1E-26 2.3E-31 206.4 10.6 112 128-242 1-117 (121)
6 cd04715 BAH_Orc1p_like BAH, or 99.9 3.6E-26 7.8E-31 212.6 14.0 138 100-245 4-152 (159)
7 cd04370 BAH BAH, or Bromo Adja 99.9 6E-26 1.3E-30 194.3 12.5 117 128-247 1-122 (123)
8 smart00439 BAH Bromo adjacent 99.9 6.2E-26 1.3E-30 195.0 12.1 116 130-248 1-120 (120)
9 cd04710 BAH_fungalPHD BAH, or 99.9 5.6E-26 1.2E-30 206.2 11.6 116 125-245 6-134 (135)
10 PF01426 BAH: BAH domain; Int 99.9 7.2E-26 1.6E-30 194.7 10.8 115 129-248 1-119 (119)
11 cd04709 BAH_MTA BAH, or Bromo 99.9 2.6E-25 5.6E-30 207.8 12.0 117 128-245 1-137 (164)
12 cd04721 BAH_plant_1 BAH, or Br 99.9 2.3E-24 4.9E-29 194.4 10.8 120 124-247 1-124 (130)
13 cd04708 BAH_plantDCM_II BAH, o 99.9 6.6E-23 1.4E-27 197.0 11.7 124 124-250 1-148 (202)
14 cd04712 BAH_DCM_I BAH, or Brom 99.9 2E-22 4.3E-27 181.8 13.4 114 127-248 2-129 (130)
15 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 1.5E-22 3.3E-27 181.6 10.9 112 128-244 1-123 (124)
16 cd04720 BAH_Orc1p_Yeast BAH, o 99.8 7.8E-20 1.7E-24 172.9 11.9 122 123-245 44-175 (179)
17 cd04719 BAH_Orc1p_animal BAH, 99.8 6.8E-20 1.5E-24 165.4 9.5 113 129-244 2-125 (128)
18 cd04718 BAH_plant_2 BAH, or Br 99.8 1.3E-20 2.8E-25 173.4 1.7 98 145-247 50-147 (148)
19 cd04711 BAH_Dnmt1_II BAH, or B 99.7 3.5E-18 7.6E-23 155.4 7.6 114 134-248 13-136 (137)
20 KOG1827 Chromatin remodeling c 99.5 5.4E-15 1.2E-19 161.1 6.5 116 124-242 184-301 (629)
21 KOG3554 Histone deacetylase co 99.1 1.2E-11 2.6E-16 130.4 -1.7 137 129-268 4-185 (693)
22 PF07500 TFIIS_M: Transcriptio 98.3 1.9E-06 4E-11 76.0 6.4 70 347-458 1-72 (115)
23 smart00510 TFS2M Domain in the 98.1 6.4E-06 1.4E-10 72.1 6.0 68 349-458 1-70 (102)
24 TIGR01385 TFSII transcription 97.4 0.00022 4.9E-09 73.2 6.1 70 346-459 133-206 (299)
25 COG5076 Transcription factor i 94.2 0.0058 1.3E-07 64.0 -2.6 95 123-220 269-363 (371)
26 KOG1105 Transcription elongati 80.6 4 8.7E-05 42.6 6.4 68 345-454 129-196 (296)
27 PTZ00112 origin recognition co 78.3 2.4 5.1E-05 50.5 4.3 132 119-250 441-613 (1164)
28 PF09926 DUF2158: Uncharacteri 77.5 3.2 7E-05 32.8 3.6 38 131-172 1-38 (53)
29 PF10383 Clr2: Transcription-s 57.4 47 0.001 30.8 7.4 52 120-171 2-70 (139)
30 cd05834 HDGF_related The PWWP 57.0 15 0.00032 31.2 3.7 43 130-174 2-44 (83)
31 cd06080 MUM1_like Mutated mela 48.0 26 0.00057 29.9 3.8 39 131-174 1-39 (80)
32 cd05835 Dnmt3b_related The PWW 47.0 22 0.00048 30.2 3.3 40 131-172 1-43 (87)
33 cd05162 PWWP The PWWP domain, 42.1 34 0.00074 28.5 3.6 40 131-172 1-46 (87)
34 PF02459 Adeno_terminal: Adeno 41.3 13 0.00028 41.7 1.3 7 66-72 294-300 (548)
35 PF11302 DUF3104: Protein of u 39.0 63 0.0014 27.6 4.7 29 131-159 6-39 (75)
36 KOG0343 RNA Helicase [RNA proc 36.0 16 0.00035 41.6 1.0 40 73-112 672-715 (758)
37 PF11717 Tudor-knot: RNA bindi 35.4 69 0.0015 24.9 4.2 37 131-170 1-37 (55)
38 PRK13251 transcription attenua 34.9 90 0.0019 26.5 4.9 48 166-216 19-66 (75)
39 cd05840 SPBC215_ISWI_like The 33.3 43 0.00093 29.1 3.0 39 131-171 1-48 (93)
40 KOG1634 Predicted transcriptio 32.8 20 0.00042 42.0 1.0 44 408-454 262-306 (778)
41 smart00293 PWWP domain with co 32.5 59 0.0013 25.8 3.4 40 131-172 1-47 (63)
42 PF12213 Dpoe2NT: DNA polymera 31.7 60 0.0013 27.2 3.5 34 337-370 25-58 (73)
43 KOG1827 Chromatin remodeling c 30.9 33 0.00071 39.4 2.3 89 130-241 375-465 (629)
44 PF08940 DUF1918: Domain of un 30.6 63 0.0014 26.4 3.2 40 132-172 4-43 (58)
45 TIGR03442 conserved hypothetic 30.0 27 0.00058 35.2 1.3 24 470-493 88-111 (251)
46 PRK10708 hypothetical protein; 29.6 1.2E+02 0.0026 24.9 4.6 43 132-176 2-51 (62)
47 PF00855 PWWP: PWWP domain; I 28.6 40 0.00086 27.5 1.9 40 131-172 1-43 (86)
48 PF02081 TrpBP: Tryptophan RNA 28.4 80 0.0017 26.9 3.6 48 166-216 19-66 (75)
49 PF10781 DSRB: Dextransucrase 25.9 1.5E+02 0.0032 24.4 4.6 43 132-176 2-51 (62)
50 COG5475 Uncharacterized small 25.5 1.4E+02 0.003 24.4 4.3 38 128-175 2-40 (60)
51 TIGR02227 sigpep_I_bact signal 24.9 3.3E+02 0.0071 25.4 7.5 96 121-216 42-160 (163)
52 PF00467 KOW: KOW motif; Inte 24.9 1.3E+02 0.0027 21.0 3.6 26 133-160 1-26 (32)
53 PF02183 HALZ: Homeobox associ 24.2 95 0.002 23.8 3.1 27 427-453 11-40 (45)
54 smart00739 KOW KOW (Kyprides, 22.8 1.2E+02 0.0026 19.5 3.0 25 131-157 2-26 (28)
55 PF09871 DUF2098: Uncharacteri 21.6 1.9E+02 0.004 25.5 4.8 44 130-179 2-48 (91)
56 COG4014 Uncharacterized protei 21.4 1.9E+02 0.0041 25.7 4.7 42 132-178 10-54 (97)
57 PF05705 DUF829: Eukaryotic pr 21.4 1.6E+02 0.0035 28.4 4.9 78 408-485 36-130 (240)
58 COG0121 Predicted glutamine am 21.2 38 0.00083 34.5 0.6 37 445-493 62-98 (252)
No 1
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=100.00 E-value=1.4e-48 Score=407.74 Aligned_cols=311 Identities=41% Similarity=0.687 Sum_probs=283.5
Q ss_pred hhhhhhccCCCCCccccccceeecCCCCCcceeeeEEEEcCEEEee-CCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceE
Q 011020 88 EEEEEEEEQPQEDAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYEL-EDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMM 165 (495)
Q Consensus 88 ~~~~~~~~~~~~~a~pIG~pVK~~GKGkk~R~~Y~Sf~~dG~~YkV-GD~VyV~~ed~~e~PyIArI~eIwedkd-G~~~ 165 (495)
+...+.++++.++|.|+|...+..|+|..+++||.+|.+.|..|.. ||.|++.+++++.+||||+|..||.... +.+.
T Consensus 7 ~~~~~~~~~~~~~a~~~g~a~~~qGv~~~k~~h~~t~~~~~g~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k 86 (464)
T KOG1886|consen 7 EPKLKSELRPRDEASSMGDANKEQGVGGVKSLHFETFIYRGGRYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVK 86 (464)
T ss_pred cccccccCCccchhhhhhhhhhhccccccccccccceeeccCcccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcc
Confidence 3455678899999999999999999999999999999999988888 9999999999999999999999998765 5899
Q ss_pred EEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCCCCCCCCceEEEeeeecCCcEEe
Q 011020 166 VTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLW 245 (495)
Q Consensus 166 VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp~~~~pd~FfCr~vYD~~~kKL~ 245 (495)
++|+|||||+|+.....+.|....++|||+|+|+|.+++++|.++|.|++++.|.+++.+..+++|+|+.+||..+.++|
T Consensus 87 ~ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~ 166 (464)
T KOG1886|consen 87 VEVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLR 166 (464)
T ss_pred eecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceeeeccccccccccCCCCCccccccccccccccc
Confidence 99999999999998888888888999999999999999999999999999999999998888999999999999999999
Q ss_pred ecCCchhhccccchhhHHHHHhhhhcCCCCCCCccccccchhhhhhhcccccccCCCCCccccccccccCcccccccccC
Q 011020 246 KLTDKDYEDNKQHEIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAET 325 (495)
Q Consensus 246 ~L~dkDye~~~q~Evd~Ll~Kt~~rlG~L~Di~~~e~~~~~~~d~~~~k~~~r~~~~~~~~~~~~~~~~~~~~~~~k~~t 325 (495)
.+.+.+|....+.++|.++.++..++++++++.... + +..++++|+.++++++ .++|.
T Consensus 167 ~~~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~-t----~~~~~~~~~~~~s~~~--~~~r~--------------- 224 (464)
T KOG1886|consen 167 KLRDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQ-T----LNAAASKRSQQKSEIS--SLSRA--------------- 224 (464)
T ss_pred CccccchhcccccCCccchhhhcccCCCCCCccccc-c----ccccccceeccccccc--ccccc---------------
Confidence 999999999999999999999999999999999988 3 3578889999998887 22222
Q ss_pred CCccCCCCchhHHHHhhhccccCCchhhhHHHHHHHHh-hhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCcccc
Q 011020 326 PGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGL-QYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREK 404 (495)
Q Consensus 326 p~~~~~~~~~~~~~l~~~~~~tg~~~rd~~l~~l~~~i-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 404 (495)
..+.++.||+.|..+||+++|||.|++|++.+ +++|.++..+.+.
T Consensus 225 ------ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~---------------------------- 270 (464)
T KOG1886|consen 225 ------SSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAG---------------------------- 270 (464)
T ss_pred ------ccccccccccCCCCCCCcccccccccccchhhccccccccccCCCc----------------------------
Confidence 34467889999999999999999999999999 9999999877753
Q ss_pred ccCCCCCCCCchhHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhccccccc
Q 011020 405 GQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQKYNQKLRQLLFNLKRAWVGP 458 (495)
Q Consensus 405 ~~~~~~~~~wp~~~v~~v~ale~~~~~~~~~d~~kyn~k~~~l~~n~k~~~~~~ 458 (495)
...+ .|||.+|+.|.|||+++|++|+.|+.|||+|++.|++++|+..+|+
T Consensus 271 ---~~~~-~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~ 320 (464)
T KOG1886|consen 271 ---DQGS-LWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLK 320 (464)
T ss_pred ---cccc-CCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhc
Confidence 2223 8999999999999999999999999999999999999999988876
No 2
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=100.00 E-value=1.4e-35 Score=271.34 Aligned_cols=146 Identities=64% Similarity=1.163 Sum_probs=135.1
Q ss_pred cCCCCCcceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCC
Q 011020 111 SGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDT 190 (495)
Q Consensus 111 ~GKGkk~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~ 190 (495)
+|||+++++||++|.++|++|+|||+|||.+++ +.+||||+|++||++.+|.++|+|+|||||+||.....+.+..+++
T Consensus 1 ~~~~~~~~~~y~s~~~dg~~y~vgD~Vlv~~~~-~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~ 79 (146)
T cd04713 1 TGKGKKKKCHYTSFEKDGNKYRLEDCVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDP 79 (146)
T ss_pred CCCCccceeeeeeEEECCEEEECCCEEEEeCCC-CCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCC
Confidence 489999999999999999999999999999887 4899999999999998899999999999999999766666656689
Q ss_pred CeeEeeCCcccccccceeeecEEEecCccccCCCCCCCCceEEEeeeecCCcEEeecCCchhhcccc
Q 011020 191 RELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLTDKDYEDNKQ 257 (495)
Q Consensus 191 nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp~~~~pd~FfCr~vYD~~~kKL~~L~dkDye~~~q 257 (495)
||||+|.|.|.+|+++|+|||.|++.+++.++|.....++|||++.||..+++||+|+++||+++.|
T Consensus 80 ~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~~~~~~~~~~~~~ 146 (146)
T cd04713 80 RELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLWKLTDQDYEDERQ 146 (146)
T ss_pred CeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEeeccccccccccC
Confidence 9999999999999999999999999999998886666899999999999999999999999998754
No 3
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.94 E-value=1e-26 Score=207.93 Aligned_cols=118 Identities=22% Similarity=0.417 Sum_probs=104.2
Q ss_pred CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (495)
Q Consensus 128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI 207 (495)
|+.|++||+|||.+++ +.++|||+|++||++.+|..+|+|+|||||+||.....+ ..++++|||+|+|+|++|+++|
T Consensus 1 g~~~~lgD~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~--~~~~~rEvFlS~~~D~~pl~~I 77 (122)
T cd04716 1 GITYNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQA--TNHDKKRVFYSEIKNDNPLDCL 77 (122)
T ss_pred CcEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhcccccc--ccCCCceEEEecccCccchhhe
Confidence 6789999999999987 599999999999999999999999999999999974322 4578999999999999999999
Q ss_pred eeecEEEecCccccCC---CCCCCCceEEEeeeecCCcEEeecC
Q 011020 208 MHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKLT 248 (495)
Q Consensus 208 ~GKC~V~~v~ey~qlp---~~~~pd~FfCr~vYD~~~kKL~~L~ 248 (495)
+|||+|++++++..++ ....+++|||++.|+..-.+|..|+
T Consensus 78 ~~Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~~~~ 121 (122)
T cd04716 78 ISKVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQTLR 121 (122)
T ss_pred eeeeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheEeCC
Confidence 9999999999988873 3345799999999999877777664
No 4
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.94 E-value=6.9e-27 Score=206.18 Aligned_cols=117 Identities=25% Similarity=0.420 Sum_probs=103.7
Q ss_pred CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (495)
Q Consensus 128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI 207 (495)
|..|++||+|||.+++.+.++|||+|.+||++.+|..+|+|+|||||+||.+...+.+ ++||||+|.+.+++|+++|
T Consensus 1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~---~~~Evfls~~~d~~~~~~I 77 (121)
T cd04717 1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKF---YKNEVFKSPLYETVPVEEI 77 (121)
T ss_pred CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCcccc---ccCceEEcCccccccHHHh
Confidence 6789999999999987668899999999999988999999999999999988666544 8999999999999999999
Q ss_pred eeecEEEecCccccCC-C-CCCCCceEEEeeeecCCcEEeec
Q 011020 208 MHKCVVHFVPIHKQLP-N-RKQHPGFIVQKVYDTVERKLWKL 247 (495)
Q Consensus 208 ~GKC~V~~v~ey~qlp-~-~~~pd~FfCr~vYD~~~kKL~~L 247 (495)
+|||.||++.+|.+.. . ....+.|+|+..||...+.|..+
T Consensus 78 ~~kc~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~~ 119 (121)
T cd04717 78 VGKCAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKI 119 (121)
T ss_pred cCeeEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEecc
Confidence 9999999999998874 2 22458899999999988777654
No 5
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.94 E-value=1e-26 Score=206.40 Aligned_cols=112 Identities=27% Similarity=0.439 Sum_probs=99.5
Q ss_pred CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (495)
Q Consensus 128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI 207 (495)
|.+|++||+|||.+++.+.+||||+|.+||++.+|.++|+|+|||||+||.+... ..+++||||+|+|.|++|+++|
T Consensus 1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~---~~~~~~EvF~S~~~d~~~~~~I 77 (121)
T cd04714 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRK---PNHGEKELFASDHQDENSVQTI 77 (121)
T ss_pred CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCccc---ccCCCCceEecCCcccccHHHh
Confidence 5789999999999987568899999999999988999999999999999987443 3469999999999999999999
Q ss_pred eeecEEEecCccccCCC-----CCCCCceEEEeeeecCCc
Q 011020 208 MHKCVVHFVPIHKQLPN-----RKQHPGFIVQKVYDTVER 242 (495)
Q Consensus 208 ~GKC~V~~v~ey~qlp~-----~~~pd~FfCr~vYD~~~k 242 (495)
+|||.|+++++|.++.. ....+.|+|+..||+...
T Consensus 78 ~gkc~V~~~~ey~~~~~~~~~~~~~~d~~~Ce~~yn~~~~ 117 (121)
T cd04714 78 EHKCYVLTFAEYERLARVKKKPQDGVDFYYCAGTYNPDTG 117 (121)
T ss_pred CcccEEEehhHheecccccCCCCcCCCEEEEeccCCCCcC
Confidence 99999999999988652 246799999999998753
No 6
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.94 E-value=3.6e-26 Score=212.62 Aligned_cols=138 Identities=25% Similarity=0.388 Sum_probs=114.3
Q ss_pred CccccccceeecCCCCCcceeeeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC--CceEEEEEEeeccccc
Q 011020 100 DAKPVGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD--GSMMVTGQWFYRPEEA 177 (495)
Q Consensus 100 ~a~pIG~pVK~~GKGkk~R~~Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkd--G~~~VrVqWFYRPEET 177 (495)
-++|.|.+.+..+ ++||+++.++|..|++||+|||.+++ .+||||+|.+||+..+ |.++++|+|||||+||
T Consensus 4 ~~~~~g~~~~~~~-----~~~Y~s~~~~g~~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~ 76 (159)
T cd04715 4 WGVKRGEGGKKKD-----GQFYRSFTYDGVEYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEI 76 (159)
T ss_pred cceecccccccCC-----ceEEEEEEECCEEEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHh
Confidence 3567777777654 56999999999999999999999865 8999999999999865 8899999999999999
Q ss_pred ccCCCCCCcCCCCCeeEeeCCc-----ccccccceeeecEEEecCccccCC--CC--CCCCceEEEeeeecCCcEEe
Q 011020 178 DRKGGGNWLSRDTRELFYSFHR-----DEVPAESVMHKCVVHFVPIHKQLP--NR--KQHPGFIVQKVYDTVERKLW 245 (495)
Q Consensus 178 ~~~~~g~f~~~~~nELFlSdh~-----D~~PlesI~GKC~V~~v~ey~qlp--~~--~~pd~FfCr~vYD~~~kKL~ 245 (495)
.+...+. +.+.+||||+|.|. +++|+++|+|||.|+++++|...+ +. .....|++.+.||+..++..
T Consensus 77 ~~~~~~~-~~~~~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~~s~~~~~~~~~~f~~~f~~~~~~~~ 152 (159)
T cd04715 77 RMELKGE-PKRHINEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQPSDGIPTSADFLFPCNFDVGRCVIV 152 (159)
T ss_pred ccccccC-cccCCCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCCCcCCccccCcceeeeEEEecCceec
Confidence 8644333 34689999999986 668999999999999999998754 11 23477888889998876653
No 7
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=99.93 E-value=6e-26 Score=194.34 Aligned_cols=117 Identities=38% Similarity=0.646 Sum_probs=103.7
Q ss_pred CEEEeeCCeEEEcCCCC--CCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccccc
Q 011020 128 GNKYELEDPVLLTPEDT--NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAE 205 (495)
Q Consensus 128 G~~YkVGD~VyV~~ed~--~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~Ple 205 (495)
|.+|++||+|||.+++. ..++|||+|.+||++.+|.++++|+|||||+||.+...+ .+.+||||+|++++++|++
T Consensus 1 g~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~---~~~~~Elf~s~~~~~i~v~ 77 (123)
T cd04370 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSP---FALRRELFLSDHLDEIPVE 77 (123)
T ss_pred CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhcccccc---ccccceeEEecCccccCHH
Confidence 67899999999999874 478999999999999899999999999999999975443 4599999999999999999
Q ss_pred ceeeecEEEecCccccCC---CCCCCCceEEEeeeecCCcEEeec
Q 011020 206 SVMHKCVVHFVPIHKQLP---NRKQHPGFIVQKVYDTVERKLWKL 247 (495)
Q Consensus 206 sI~GKC~V~~v~ey~qlp---~~~~pd~FfCr~vYD~~~kKL~~L 247 (495)
+|+|||.|++..++.+.. ....++.|||++.||..+.++..+
T Consensus 78 ~I~gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~~ 122 (123)
T cd04370 78 SIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKAL 122 (123)
T ss_pred HhccccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEeC
Confidence 999999999999988763 445679999999999988777654
No 8
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.93 E-value=6.2e-26 Score=195.05 Aligned_cols=116 Identities=31% Similarity=0.462 Sum_probs=102.4
Q ss_pred EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc-eEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccccccee
Q 011020 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS-MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVM 208 (495)
Q Consensus 130 ~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~-~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~ 208 (495)
.|++||+|||.+++...++|||+|.+||++.+|. ++++|+|||||+||.+...+. .++||||+|++++++|+++|+
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~---~~~~Elf~s~~~~~i~~~~I~ 77 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAAL---FDKNEVFLSDEYDTVPLSDII 77 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhcccccccc---CCCcceEEEccCccCChHHee
Confidence 4899999999998866889999999999998888 899999999999999755443 489999999999999999999
Q ss_pred eecEEEecCccccCCCCC---CCCceEEEeeeecCCcEEeecC
Q 011020 209 HKCVVHFVPIHKQLPNRK---QHPGFIVQKVYDTVERKLWKLT 248 (495)
Q Consensus 209 GKC~V~~v~ey~qlp~~~---~pd~FfCr~vYD~~~kKL~~L~ 248 (495)
|||.|++.+++...+... .++.|||++.||...++|+.++
T Consensus 78 ~kc~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~~~ 120 (120)
T smart00439 78 GKCNVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKKLP 120 (120)
T ss_pred eEEEEEEcchhcccccccCCCCCCeEEEEEEEccccCcccCCC
Confidence 999999999998765322 4799999999999988887653
No 9
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.93 E-value=5.6e-26 Score=206.21 Aligned_cols=116 Identities=24% Similarity=0.447 Sum_probs=101.8
Q ss_pred EEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC------------CceEEEEEEeecccccccCCCCCCcCCCCCe
Q 011020 125 EFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD------------GSMMVTGQWFYRPEEADRKGGGNWLSRDTRE 192 (495)
Q Consensus 125 ~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkd------------G~~~VrVqWFYRPEET~~~~~g~f~~~~~nE 192 (495)
..+|+.|++||+|||.++++++|+|||+|++|+..++ +..+|+|+|||||+||.... .++++|
T Consensus 6 ~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~-----~~d~re 80 (135)
T cd04710 6 LKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV-----VADSRL 80 (135)
T ss_pred ccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc-----cCCceE
Confidence 4689999999999999998889999999999998543 23689999999999986422 469999
Q ss_pred eEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEe
Q 011020 193 LFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLW 245 (495)
Q Consensus 193 LFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~ 245 (495)
||+|+|.|++|+++|+|||+|++..++..+. ....+++|||.++||++++|++
T Consensus 81 lf~S~h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~ 134 (135)
T cd04710 81 LYASMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYY 134 (135)
T ss_pred EEEEeeEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhcc
Confidence 9999999999999999999999999887765 3445899999999999999886
No 10
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=99.93 E-value=7.2e-26 Score=194.75 Aligned_cols=115 Identities=37% Similarity=0.622 Sum_probs=100.5
Q ss_pred EEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCc--eEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccc
Q 011020 129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS--MMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES 206 (495)
Q Consensus 129 ~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~--~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~Ples 206 (495)
++|++||+|||.+++...++|||+|.+||++.++. ++++|+|||||+||.. +. ...+||||+|++++++|+++
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~---~~--~~~~~Elf~s~~~~~~~~~~ 75 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSL---GK--TFSPRELFLSDHCDDIPVES 75 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTT---GG--HSCTTEEEEEEEEEEEEGGG
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECcccccc---cc--cCCCCEEEEECcEeEEehhh
Confidence 57999999999999878999999999999998877 9999999999999932 21 23569999999999999999
Q ss_pred eeeecEEEecCccccCCCCC--CCCceEEEeeeecCCcEEeecC
Q 011020 207 VMHKCVVHFVPIHKQLPNRK--QHPGFIVQKVYDTVERKLWKLT 248 (495)
Q Consensus 207 I~GKC~V~~v~ey~qlp~~~--~pd~FfCr~vYD~~~kKL~~L~ 248 (495)
|+|||.|++..++.+..... .++.|||++.||+..++|..++
T Consensus 76 I~gkc~V~~~~~~~~~~~~~~~~~~~F~cr~~yd~~~~~f~~~~ 119 (119)
T PF01426_consen 76 IRGKCNVLHLEDYEQARPYGKEEPDTFFCRYAYDPQKKRFKKLP 119 (119)
T ss_dssp EEEEEEEEEHHHHTTGCCHCHHTTTEEEEEEEEETTTTEEEE-S
T ss_pred EEeeeEEEECCccccccccccCCCCEEEEEEEEeCCcCEEeCCC
Confidence 99999999999998765332 6899999999999999998764
No 11
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.92 E-value=2.6e-25 Score=207.84 Aligned_cols=117 Identities=21% Similarity=0.333 Sum_probs=101.3
Q ss_pred CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccC----CCC---------------CCcCC
Q 011020 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK----GGG---------------NWLSR 188 (495)
Q Consensus 128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~----~~g---------------~f~~~ 188 (495)
++.|++||+|||.++. +.++|||+|++||++.+|.++|+|+|||||+||+.. ..+ ..+..
T Consensus 1 ~~~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~ 79 (164)
T cd04709 1 ANMYRVGDYVYFESSP-NNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQL 79 (164)
T ss_pred CcEEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhcc
Confidence 3689999999999884 678889999999999999999999999999998642 111 11345
Q ss_pred CCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEe
Q 011020 189 DTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLW 245 (495)
Q Consensus 189 ~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~ 245 (495)
+.+|||+|.|.+++|+++|+|||.|+++.+|..+. ....+++|||+.+||+.+++|.
T Consensus 80 ~~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~ 137 (164)
T cd04709 80 RHRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLL 137 (164)
T ss_pred CcceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeec
Confidence 89999999999999999999999999999998876 3346899999999999999994
No 12
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.91 E-value=2.3e-24 Score=194.39 Aligned_cols=120 Identities=22% Similarity=0.329 Sum_probs=102.8
Q ss_pred EEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccc
Q 011020 124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP 203 (495)
Q Consensus 124 f~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~P 203 (495)
|..+|.++++||+|||.+++ .++|||+|.+||++.+|.++|+|+||+||+||.+..... .+.+||||+|++.+++|
T Consensus 1 ~~r~~~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~--~~~~~EvFlS~~~d~i~ 76 (130)
T cd04721 1 FCRNGVTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPD--SVNPREIFLSPNLQVIS 76 (130)
T ss_pred CccCCEEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCC--CCCCCeEEEcCCccccc
Confidence 34689999999999999876 778999999999998999999999999999999754433 25999999999999999
Q ss_pred ccceeeecEEEecCccccCCC----CCCCCceEEEeeeecCCcEEeec
Q 011020 204 AESVMHKCVVHFVPIHKQLPN----RKQHPGFIVQKVYDTVERKLWKL 247 (495)
Q Consensus 204 lesI~GKC~V~~v~ey~qlp~----~~~pd~FfCr~vYD~~~kKL~~L 247 (495)
+++|+|||+||+..+|.++.. ....+.|+|++.||....+-+++
T Consensus 77 ~~~I~gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~~~~~fd~ 124 (130)
T cd04721 77 VECIDGLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNNKVKPFDI 124 (130)
T ss_pred hHHeeeeeEECCHHHHhhhhccccCccccccEEEEEEecCCCCceeee
Confidence 999999999999999988641 12367999999999986644443
No 13
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.89 E-value=6.6e-23 Score=197.04 Aligned_cols=124 Identities=27% Similarity=0.382 Sum_probs=104.7
Q ss_pred EEEcCEEEeeCCeEEEcCCC-----------------CCCCCeEEEEeEEeeCCCC------ceEEEEEEeecccccccC
Q 011020 124 FEFDGNKYELEDPVLLTPED-----------------TNQKPYVAIIKEITQSKDG------SMMVTGQWFYRPEEADRK 180 (495)
Q Consensus 124 f~~dG~~YkVGD~VyV~~ed-----------------~~e~PyIArI~eIwedkdG------~~~VrVqWFYRPEET~~~ 180 (495)
|+++|++|++||+|||.++. ...+++||+|.+|+..+++ ..+|+|+|||||+||..
T Consensus 1 f~~~Gv~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~- 79 (202)
T cd04708 1 FVYDGVTYSVGDFLYVSPDAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSP- 79 (202)
T ss_pred CcCCCEEEecCCeEEECcccccccccccccccccccCCCCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCc-
Confidence 56899999999999999981 1357889999999986554 68999999999999853
Q ss_pred CCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEeecCCc
Q 011020 181 GGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWKLTDK 250 (495)
Q Consensus 181 ~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~~L~dk 250 (495)
+...+++.+|||+|++.+++|+++|.|||.|++..++..+. ....++.|||+..||+.++.|.+||..
T Consensus 80 --~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~~lP~~ 148 (202)
T cd04708 80 --EKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLKQLPPN 148 (202)
T ss_pred --ccceecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccCCCCch
Confidence 22235699999999999999999999999999999886653 233489999999999999999888774
No 14
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.88 E-value=2e-22 Score=181.81 Aligned_cols=114 Identities=20% Similarity=0.277 Sum_probs=98.6
Q ss_pred cCEEEeeCCeEEEcCCCCC----------CCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEee
Q 011020 127 DGNKYELEDPVLLTPEDTN----------QKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYS 196 (495)
Q Consensus 127 dG~~YkVGD~VyV~~ed~~----------e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlS 196 (495)
.|..|++||+|+|.++++. .++||++|..||++.+|.+||+|+|||||+||.+.. .+++||||||
T Consensus 2 ~~~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~-----~~~~~ElFLS 76 (130)
T cd04712 2 HGLTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN-----YANERELFLT 76 (130)
T ss_pred CCCEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc-----cCCCceEEEe
Confidence 5778999999999998855 489999999999999999999999999999999854 4699999999
Q ss_pred CCccccccc----ceeeecEEEecCccccCCCCCCCCceEEEeeeecCCcEEeecC
Q 011020 197 FHRDEVPAE----SVMHKCVVHFVPIHKQLPNRKQHPGFIVQKVYDTVERKLWKLT 248 (495)
Q Consensus 197 dh~D~~Ple----sI~GKC~V~~v~ey~qlp~~~~pd~FfCr~vYD~~~kKL~~L~ 248 (495)
+||++++++ .|++||.|++...+.. ...++.|+|+..|++.++.|..|+
T Consensus 77 d~c~~~~~~~~~~~I~~k~~V~~~~~~~~---~~~~~~F~r~syy~~e~~~F~~l~ 129 (130)
T cd04712 77 NECTCLELDLLSTEIKGVHKVDWSGTPWG---KGLPEFFVRQSYYWPERGAFTSLK 129 (130)
T ss_pred ccccccccccccceeEEEEEEEEecCcCC---cCCCCEEEEEEEECccCCceEcCC
Confidence 999999999 9999999998876653 124566777777787888888775
No 15
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.88 E-value=1.5e-22 Score=181.65 Aligned_cols=112 Identities=22% Similarity=0.319 Sum_probs=96.2
Q ss_pred CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccce
Q 011020 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESV 207 (495)
Q Consensus 128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI 207 (495)
|.+|.+||+|+|.++++..+||||+|..||++.+|.+|++|+|||||+||.+... ++++|||+|++|+.+++.+|
T Consensus 1 g~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~-----~~~kEvFlsd~c~d~~l~~I 75 (124)
T cd04760 1 GEELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGET-----SDPLELFLVDECEDMALSSI 75 (124)
T ss_pred CCEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCccccccc-----CCCcEEEeecccCCcchHHh
Confidence 5689999999999988789999999999999999999999999999999997543 69999999999999999999
Q ss_pred eeecEEEecCccc--------cCC---CCCCCCceEEEeeeecCCcEE
Q 011020 208 MHKCVVHFVPIHK--------QLP---NRKQHPGFIVQKVYDTVERKL 244 (495)
Q Consensus 208 ~GKC~V~~v~ey~--------qlp---~~~~pd~FfCr~vYD~~~kKL 244 (495)
.+||+|+..+.-. ..+ ....-.+|||++.||+...++
T Consensus 76 ~~Kv~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf 123 (124)
T cd04760 76 HGKVNVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARF 123 (124)
T ss_pred eeeeEEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhcc
Confidence 9999999987651 111 112348899999999966554
No 16
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.82 E-value=7.8e-20 Score=172.94 Aligned_cols=122 Identities=16% Similarity=0.222 Sum_probs=100.4
Q ss_pred EEEE-cCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC-CceEEEEEEeecccccccCCC-CCCc-----CCCCCeeE
Q 011020 123 AFEF-DGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKD-GSMMVTGQWFYRPEEADRKGG-GNWL-----SRDTRELF 194 (495)
Q Consensus 123 Sf~~-dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkd-G~~~VrVqWFYRPEET~~~~~-g~f~-----~~~~nELF 194 (495)
.... +|.+|++||+|+|.+++ ..++|||+|.+|+.+.. +.+.+.|+|||||.|+..... +.+. ...+||||
T Consensus 44 l~R~~d~~~~~vGD~Vlik~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElf 122 (179)
T cd04720 44 LARDSDGLELSVGDTILVKDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELY 122 (179)
T ss_pred EEEccCCeEEeCCCEEEEeCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEE
Confidence 3344 89999999999999987 48999999999998765 567999999999999964221 1111 23489999
Q ss_pred eeCCcccccccceeeecEEEecCccccCC-C-CCCCCceEEEeeeecCCcEEe
Q 011020 195 YSFHRDEVPAESVMHKCVVHFVPIHKQLP-N-RKQHPGFIVQKVYDTVERKLW 245 (495)
Q Consensus 195 lSdh~D~~PlesI~GKC~V~~v~ey~qlp-~-~~~pd~FfCr~vYD~~~kKL~ 245 (495)
+|.|.+.+++.+|+|||+||...+|.++. . .....+||||++||+.+..|.
T Consensus 123 lT~~~d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~ 175 (179)
T cd04720 123 LTAELSEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFV 175 (179)
T ss_pred EecccceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEc
Confidence 99999999999999999999999998764 2 234689999999999887664
No 17
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.81 E-value=6.8e-20 Score=165.40 Aligned_cols=113 Identities=27% Similarity=0.406 Sum_probs=94.1
Q ss_pred EEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCC---ceEEEEEEeecccccccCC---CCCCcCCCCCeeEeeCCc---
Q 011020 129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDG---SMMVTGQWFYRPEEADRKG---GGNWLSRDTRELFYSFHR--- 199 (495)
Q Consensus 129 ~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG---~~~VrVqWFYRPEET~~~~---~g~f~~~~~nELFlSdh~--- 199 (495)
.+|+|||||+|.+++. .++|||+|++||++.++ ...++|||||||+|+++.. .+. ..+++|||+|+|.
T Consensus 2 ~~i~vGd~VlI~~~d~-~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~--~~~~~EvF~~~~~~~~ 78 (128)
T cd04719 2 LTIEVGDFVLIEGEDA-DGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGR--EPHSQEVFFYSRSSCD 78 (128)
T ss_pred eEEecCCEEEEECCCC-CCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccC--CCCCcEEEEecCcccc
Confidence 4799999999999884 88999999999998765 5699999999999997532 222 3489999999987
Q ss_pred ccccccceeeecEEEecCccccCCC--CCCCCceEEEeeeecCCcEE
Q 011020 200 DEVPAESVMHKCVVHFVPIHKQLPN--RKQHPGFIVQKVYDTVERKL 244 (495)
Q Consensus 200 D~~PlesI~GKC~V~~v~ey~qlp~--~~~pd~FfCr~vYD~~~kKL 244 (495)
+.+++++|.|+|.|+...+|..++. ......||+++.|+....+.
T Consensus 79 ~~i~~etI~gkc~V~~~~~y~~l~~~~~~~~~~~F~r~~~~~k~~~~ 125 (128)
T cd04719 79 NDIDAETIIGKVRVEPVEPKTDLPETKKKTGGPLFVKRYWDTKTFRS 125 (128)
T ss_pred CcEeHHHcccEEEEEEcCCccchhhhccccCceEEEEEEeccccccc
Confidence 4899999999999999999999873 23457899999998765543
No 18
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.79 E-value=1.3e-20 Score=173.44 Aligned_cols=98 Identities=18% Similarity=0.342 Sum_probs=86.8
Q ss_pred CCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEecCccccCCC
Q 011020 145 NQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLPN 224 (495)
Q Consensus 145 ~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp~ 224 (495)
...+|||+|++||++. |..+|+|+|||||+||.++... .++.+|||+|+|.|++++++|+|||.||++.+|.++..
T Consensus 50 ~~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~~---~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~ 125 (148)
T cd04718 50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQP---HNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASN 125 (148)
T ss_pred cCchHHHHHHHHHhcc-CceEEEEEEEeCchhccCcccc---ccccceeeeccccccccHHHHhcccEEcCHHHcccccC
Confidence 3578999999999986 9999999999999999985544 45999999999999999999999999999999988753
Q ss_pred CCCCCceEEEeeeecCCcEEeec
Q 011020 225 RKQHPGFIVQKVYDTVERKLWKL 247 (495)
Q Consensus 225 ~~~pd~FfCr~vYD~~~kKL~~L 247 (495)
. ..++|||+..||...+.|..+
T Consensus 126 ~-g~Dvy~Ce~~Yd~~~~~Fkr~ 147 (148)
T cd04718 126 D-GDDVFLCEYEYDVHWQSFKRL 147 (148)
T ss_pred C-CCceEEEEEEEhhhcCceeec
Confidence 3 478999999999998887654
No 19
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.74 E-value=3.5e-18 Score=155.37 Aligned_cols=114 Identities=18% Similarity=0.228 Sum_probs=88.5
Q ss_pred CCeEEEcCCCCCCCCeEEEEeEEeeCCCC-------ceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccc
Q 011020 134 EDPVLLTPEDTNQKPYVAIIKEITQSKDG-------SMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAES 206 (495)
Q Consensus 134 GD~VyV~~ed~~e~PyIArI~eIwedkdG-------~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~Ples 206 (495)
+|+|-=.+-+.+.+++||||++|...+++ .++|+|+|||||+||..+.... .+.+.||||+|+|.+++|+++
T Consensus 13 ~~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~a-yhsDirevy~Sd~~~~~~~~~ 91 (137)
T cd04711 13 SDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKAT-YHADINMLYWSDEEATVDFSA 91 (137)
T ss_pred ccccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccc-cccceeeEEeecceeecChhh
Confidence 34444445556789999999999876442 4689999999999999632221 245789999999999999999
Q ss_pred eeeecEEEecCcccc-CC--CCCCCCceEEEeeeecCCcEEeecC
Q 011020 207 VMHKCVVHFVPIHKQ-LP--NRKQHPGFIVQKVYDTVERKLWKLT 248 (495)
Q Consensus 207 I~GKC~V~~v~ey~q-lp--~~~~pd~FfCr~vYD~~~kKL~~L~ 248 (495)
|.|||.|++..+... +. ....++.|||+.+||..++.|.++|
T Consensus 92 I~GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d~p 136 (137)
T cd04711 92 VQGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFEDPP 136 (137)
T ss_pred ccceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCcccCCC
Confidence 999999997766542 32 2246899999999999999886654
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.54 E-value=5.4e-15 Score=161.09 Aligned_cols=116 Identities=27% Similarity=0.393 Sum_probs=107.2
Q ss_pred EEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCccccc
Q 011020 124 FEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVP 203 (495)
Q Consensus 124 f~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~P 203 (495)
+.++|..|.+||+||+.+..++..+.|++|.++|+..+|..|+.++|||||++|.|..++.| ..+|+|.|..+.+++
T Consensus 184 ~~i~~~~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F---~k~Evfkt~~~~~~~ 260 (629)
T KOG1827|consen 184 VEIDGTKYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKF---YKQEVFKTSLYRDDL 260 (629)
T ss_pred ccccCcccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccch---hcccceecccccccH
Confidence 78999999999999999988779999999999999999999999999999999999999988 999999999999999
Q ss_pred ccceeeecEEEecCccccCC--CCCCCCceEEEeeeecCCc
Q 011020 204 AESVMHKCVVHFVPIHKQLP--NRKQHPGFIVQKVYDTVER 242 (495)
Q Consensus 204 lesI~GKC~V~~v~ey~qlp--~~~~pd~FfCr~vYD~~~k 242 (495)
+..|+|+|.|+++.+|.... ....-+.|.|+..|+...+
T Consensus 261 ~q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K 301 (629)
T KOG1827|consen 261 VQRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLK 301 (629)
T ss_pred HHHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchh
Confidence 99999999999999997753 3345699999999988653
No 21
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=99.07 E-value=1.2e-11 Score=130.43 Aligned_cols=137 Identities=21% Similarity=0.338 Sum_probs=108.8
Q ss_pred EEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccC-------CCC-----------------C
Q 011020 129 NKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRK-------GGG-----------------N 184 (495)
Q Consensus 129 ~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~-------~~g-----------------~ 184 (495)
..|+|||+||+..+. .+++.|-+|+++.++.+|++..+|..|||..||... ..+ .
T Consensus 4 n~y~vgd~vYf~~ss-s~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e 82 (693)
T KOG3554|consen 4 NMYRVGDYVYFENSS-SNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAE 82 (693)
T ss_pred ccceecceEEEecCC-CChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhh
Confidence 379999999999987 556779999999999999999999999999998741 011 1
Q ss_pred C-----------------cCCCCCeeEeeCCcccccccceeeecEEEecCccccCC-CCCCCCceEEEeeeecCCcEEee
Q 011020 185 W-----------------LSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQLP-NRKQHPGFIVQKVYDTVERKLWK 246 (495)
Q Consensus 185 f-----------------~~~~~nELFlSdh~D~~PlesI~GKC~V~~v~ey~qlp-~~~~pd~FfCr~vYD~~~kKL~~ 246 (495)
+ +....+|||+|.+....|+..|+|||.|....+...+. +....++||+..+||+..++|
T Consensus 83 ~EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTL-- 160 (693)
T KOG3554|consen 83 IEEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTL-- 160 (693)
T ss_pred hhhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhh--
Confidence 1 11357899999999999999999999999887766543 445679999999999998887
Q ss_pred cCCchhh---ccccchhhHHHHHhh
Q 011020 247 LTDKDYE---DNKQHEIDLLVQKTQ 268 (495)
Q Consensus 247 L~dkDye---~~~q~Evd~Ll~Kt~ 268 (495)
|.|+..+ +..|.+|+..+..+.
T Consensus 161 LADkGeIRVG~kYQA~i~e~l~EgE 185 (693)
T KOG3554|consen 161 LADKGEIRVGEKYQADIPEWLEEGE 185 (693)
T ss_pred hccCcceeecccccccchHHHHhcc
Confidence 4565543 456677877776543
No 22
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=98.26 E-value=1.9e-06 Score=75.98 Aligned_cols=70 Identities=33% Similarity=0.406 Sum_probs=57.3
Q ss_pred cCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHHHH
Q 011020 347 TGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALE 426 (495)
Q Consensus 347 tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~ale 426 (495)
|++..||+|.+-|..++....... . . +..+..++..+|
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~~-~---~--------------------------------------~~~~~~lA~~IE 38 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDEQ-D---D--------------------------------------PEDAKELAKEIE 38 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCCC-C---C--------------------------------------TCCHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHHhcCccc-c---c--------------------------------------hhHHHHHHHHHH
Confidence 789999999988888887653221 1 1 568899999999
Q ss_pred HHhhhhhhhhHHHHHHHHHHHHHhhc--cccccc
Q 011020 427 KASHDTLSLDFQKYNQKLRQLLFNLK--RAWVGP 458 (495)
Q Consensus 427 ~~~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~ 458 (495)
.|+|+.++++-.+|++|+|+|.|||| +|+-|.
T Consensus 39 ~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~ 72 (115)
T PF07500_consen 39 EALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLR 72 (115)
T ss_dssp HHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHH
T ss_pred HHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHH
Confidence 99999998899999999999999999 665554
No 23
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=98.08 E-value=6.4e-06 Score=72.14 Aligned_cols=68 Identities=26% Similarity=0.296 Sum_probs=53.9
Q ss_pred CchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHHHHHH
Q 011020 349 ETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKA 428 (495)
Q Consensus 349 ~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~ale~~ 428 (495)
|..||++.+.|..+++..+..... . ..+..+..++|.+
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~--~----------------------------------------~~~~~lA~~IE~~ 38 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEI--E----------------------------------------LDPTELAVQIEAE 38 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcc--c----------------------------------------ccHHHHHHHHHHH
Confidence 467999999999998766543310 0 1355678899999
Q ss_pred hhhhhhhhHHHHHHHHHHHHHhhc--cccccc
Q 011020 429 SHDTLSLDFQKYNQKLRQLLFNLK--RAWVGP 458 (495)
Q Consensus 429 ~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~ 458 (495)
+|+.++.+..+|++|+|+|.|||| +|+-|.
T Consensus 39 lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr 70 (102)
T smart00510 39 MFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLR 70 (102)
T ss_pred HHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHH
Confidence 999999999999999999999999 776444
No 24
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=97.43 E-value=0.00022 Score=73.23 Aligned_cols=70 Identities=21% Similarity=0.235 Sum_probs=55.0
Q ss_pred ccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCch--hHHHHHH
Q 011020 346 LTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPD--TAIAAVT 423 (495)
Q Consensus 346 ~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~--~~v~~v~ 423 (495)
+|||..||++.+-|.+++...+... |+ +...+..
T Consensus 133 ~t~d~~Rdk~r~~L~~aL~~~~~~~--------------------------------------------~~~~~~~~lA~ 168 (299)
T TIGR01385 133 VTNDKVRDKCRELLYDALAKDSDHP--------------------------------------------PQSIDPEAKAI 168 (299)
T ss_pred cCCcHHHHHHHHHHHHHHhhcCCCC--------------------------------------------ccccCHHHHHH
Confidence 6999999999999999987532110 11 2234578
Q ss_pred HHHHHhhhhhhhhHHHHHHHHHHHHHhhc--ccccccc
Q 011020 424 ALEKASHDTLSLDFQKYNQKLRQLLFNLK--RAWVGPG 459 (495)
Q Consensus 424 ale~~~~~~~~~d~~kyn~k~~~l~~n~k--~~~~~~~ 459 (495)
++|.++|+.++.+-.+|+.|+|+|.|||| +|+-|..
T Consensus 169 ~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~ 206 (299)
T TIGR01385 169 QIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRH 206 (299)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHH
Confidence 89999999999999999999999999998 6665543
No 25
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=94.21 E-value=0.0058 Score=63.97 Aligned_cols=95 Identities=11% Similarity=0.007 Sum_probs=82.9
Q ss_pred EEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccc
Q 011020 123 AFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEV 202 (495)
Q Consensus 123 Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~ 202 (495)
+..+.+....+|+++.+.+......|.++.+..+|.+.++..+.-++|||||.++.+.....+ ..+++.+....+.+
T Consensus 269 ~~~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~ 345 (371)
T COG5076 269 SVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLF---FDNCVMYNGEVTDY 345 (371)
T ss_pred hhcccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchh---hhcccccchhhhhh
Confidence 345667799999999999988889999999999999988888889999999998887665544 89999999999999
Q ss_pred cccceeeecEEEecCccc
Q 011020 203 PAESVMHKCVVHFVPIHK 220 (495)
Q Consensus 203 PlesI~GKC~V~~v~ey~ 220 (495)
.+....+.|.|....++.
T Consensus 346 ~~~~~~~~~~~~~~~~~~ 363 (371)
T COG5076 346 YKNANVLEDFVIKKTRLI 363 (371)
T ss_pred hhhccchhhhHhhhhhhh
Confidence 999999999998776654
No 26
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=80.65 E-value=4 Score=42.56 Aligned_cols=68 Identities=26% Similarity=0.324 Sum_probs=51.7
Q ss_pred cccCCchhhhHHHHHHHHhhhhcCCCcccccccCCCCCCCCCCCCCcccccCccCCccccccCCCCCCCCchhHHHHHHH
Q 011020 345 ALTGETHRDKWLERLLQGLQYICNSADSIHADQNGKGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTA 424 (495)
Q Consensus 345 ~~tg~~~rd~~l~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wp~~~v~~v~a 424 (495)
.+|.+.-|+++++.|..++. .+.+. .-.|+ ..-.+.+.
T Consensus 129 ~~~~d~~r~k~~e~l~~al~---~~~~~--------------------------------------~~~~~-~~~~~a~~ 166 (296)
T KOG1105|consen 129 PITNDPVRDKCRELLYAALT---TEDDS--------------------------------------RVTGA-DPLELAVQ 166 (296)
T ss_pred CCCCchHHHHHHHHHHHHhc---ccccc--------------------------------------cccCC-CHHHHHHH
Confidence 56799999999999999987 11111 11122 22334567
Q ss_pred HHHHhhhhhhhhHHHHHHHHHHHHHhhccc
Q 011020 425 LEKASHDTLSLDFQKYNQKLRQLLFNLKRA 454 (495)
Q Consensus 425 le~~~~~~~~~d~~kyn~k~~~l~~n~k~~ 454 (495)
+|.+.|..++.-..||-.++|..+||||..
T Consensus 167 iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~ 196 (296)
T KOG1105|consen 167 IEEAIFEKLGNTDSKYKNRYRSRVSNLKDK 196 (296)
T ss_pred HHHHHHHHhCCCcHHHHHHHHHHhhccCCC
Confidence 899999999999999999999999999854
No 27
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=78.27 E-value=2.4 Score=50.48 Aligned_cols=132 Identities=14% Similarity=0.236 Sum_probs=84.9
Q ss_pred eeeeEEEEcCEEEeeCCeEEEcCCCCC-------------------CCCe---EEEEeEEeeCCC-CceEEEEEEeeccc
Q 011020 119 SHYEAFEFDGNKYELEDPVLLTPEDTN-------------------QKPY---VAIIKEITQSKD-GSMMVTGQWFYRPE 175 (495)
Q Consensus 119 ~~Y~Sf~~dG~~YkVGD~VyV~~ed~~-------------------e~Py---IArI~eIwedkd-G~~~VrVqWFYRPE 175 (495)
..|+++.++++.|.+||.|+|..+..+ ...| =|+|-.|+++.. ..+.+.||.||-..
T Consensus 441 ~iye~~~in~~~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y~d~~ 520 (1164)
T PTZ00112 441 VIYESIQINDVEYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIYYDQH 520 (1164)
T ss_pred eEEEEEEEcceeeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEEEccc
Confidence 479999999999999999999754421 1123 388999988754 46899999999888
Q ss_pred cccc---CC----CC----CC---cCCCCCeeEeeC--CcccccccceeeecEEEecCc-cccCC-CCCCCCceEEEeee
Q 011020 176 EADR---KG----GG----NW---LSRDTRELFYSF--HRDEVPAESVMHKCVVHFVPI-HKQLP-NRKQHPGFIVQKVY 237 (495)
Q Consensus 176 ET~~---~~----~g----~f---~~~~~nELFlSd--h~D~~PlesI~GKC~V~~v~e-y~qlp-~~~~pd~FfCr~vY 237 (495)
|..- +. .+ .| .....++.||-. |.-.+.+.-|..|..|..... |..-. .....+-|.|-+..
T Consensus 521 d~~~i~~~~~~~~~rr~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne~~~~~~d~~~~~g~~kflc~~~~ 600 (1164)
T PTZ00112 521 DAQYIKELEEKQKSRRCKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNEKELYDEDKTAKQGKDKFLCTHYL 600 (1164)
T ss_pred cHHHHHHHHHHHHhhhhhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecchhhcccchhhhcccchhhhhHhh
Confidence 7542 11 01 11 123456666655 345567778888988875543 22111 12234789997766
Q ss_pred ecCCcEEeecCCc
Q 011020 238 DTVERKLWKLTDK 250 (495)
Q Consensus 238 D~~~kKL~~L~dk 250 (495)
-....++..+.++
T Consensus 601 k~~~~~~~~~~~~ 613 (1164)
T PTZ00112 601 KEREERICFIQNS 613 (1164)
T ss_pred hcchhheeeccch
Confidence 5555556655554
No 28
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=77.48 E-value=3.2 Score=32.84 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=26.4
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEee
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFY 172 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFY 172 (495)
|++||.|.++++. ...-|..|..- ......++.++||-
T Consensus 1 f~~GDvV~LKSGG--p~MTV~~v~~~--~~~~~~~v~C~WFd 38 (53)
T PF09926_consen 1 FKIGDVVQLKSGG--PRMTVTEVGPN--AGASGGWVECQWFD 38 (53)
T ss_pred CCCCCEEEEccCC--CCeEEEEcccc--ccCCCCeEEEEeCC
Confidence 5799999999986 44455544332 12345799999995
No 29
>PF10383 Clr2: Transcription-silencing protein Clr2 ; InterPro: IPR018839 Clr2 (cryptic loci regulator) is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast []. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organisation at the cnt domain, the site of kinetochore assembly.
Probab=57.35 E-value=47 Score=30.76 Aligned_cols=52 Identities=19% Similarity=0.251 Sum_probs=38.4
Q ss_pred eeeEEEEcCEEEeeCCeEEEcCCC----------CCCCCeEEEEeEEeeCCCC-------ceEEEEEEe
Q 011020 120 HYEAFEFDGNKYELEDPVLLTPED----------TNQKPYVAIIKEITQSKDG-------SMMVTGQWF 171 (495)
Q Consensus 120 ~Y~Sf~~dG~~YkVGD~VyV~~ed----------~~e~PyIArI~eIwedkdG-------~~~VrVqWF 171 (495)
||..+.++-+.+.+||.|-|.+.. .+....|-.|.+|...... .++|++.=|
T Consensus 2 ~y~GiflGAE~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~lY 70 (139)
T PF10383_consen 2 YYRGIFLGAEMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDLY 70 (139)
T ss_pred eECeEEEeeEEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEec
Confidence 899999999999999999995432 2344578888888765332 466666654
No 30
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=56.97 E-value=15 Score=31.21 Aligned_cols=43 Identities=14% Similarity=0.099 Sum_probs=34.2
Q ss_pred EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecc
Q 011020 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRP 174 (495)
Q Consensus 130 ~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRP 174 (495)
.|++||.|.-+-. +-++|-|+|.+.-........+.|+||-..
T Consensus 2 ~f~~GdlVwaK~k--Gyp~WPa~I~~~~~~~~~~~~~~V~FfGt~ 44 (83)
T cd05834 2 QFKAGDLVFAKVK--GYPAWPARVDEPEDWKPPGKKYPVYFFGTH 44 (83)
T ss_pred CCCCCCEEEEecC--CCCCCCEEEecccccCCCCCEEEEEEeCCC
Confidence 4789999999874 589999999998754344568999999743
No 31
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=48.04 E-value=26 Score=29.91 Aligned_cols=39 Identities=18% Similarity=0.166 Sum_probs=31.1
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecc
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRP 174 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRP 174 (495)
|.+||.|.-.-- +-|+|-|+|.++.. +...+.|.||=-.
T Consensus 1 f~~gdlVWaK~~--g~P~WPa~I~~~~~---~~~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQ--GYPWWPAVIKSISR---KKQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCC--CCCCCCEEEeeecC---CCCEEEEEEeCCC
Confidence 578999998865 48999999999863 3678899998544
No 32
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=47.04 E-value=22 Score=30.18 Aligned_cols=40 Identities=18% Similarity=0.107 Sum_probs=31.2
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCCC---CceEEEEEEee
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKD---GSMMVTGQWFY 172 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIwedkd---G~~~VrVqWFY 172 (495)
|.+||.|..+-. +-++|-|+|.+...... ...++.|+||=
T Consensus 1 f~vGDlVWaK~k--g~pwWP~~V~~~~~~~~~~~~~~~~~V~fFG 43 (87)
T cd05835 1 FNVGDLVWGKIK--GFPWWPGRVVSITVTSKRPPVVGMRWVTWFG 43 (87)
T ss_pred CCCCCEEEEecC--CCCCCCeEEechhhcccccCCCCeEEEEEeC
Confidence 578999999875 48899999999865431 23578999995
No 33
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=42.06 E-value=34 Score=28.47 Aligned_cols=40 Identities=13% Similarity=0.060 Sum_probs=30.9
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCC------CCceEEEEEEee
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSK------DGSMMVTGQWFY 172 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIwedk------dG~~~VrVqWFY 172 (495)
|++||.|..+-.. -+.|-|+|....... .....+.|+||-
T Consensus 1 f~~GdlVwaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg 46 (87)
T cd05162 1 FRPGDLVWAKMKG--YPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFG 46 (87)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEccccccchhhhccCCCCEEEEEEeC
Confidence 5789999999864 789999999987642 223578888885
No 34
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=41.29 E-value=13 Score=41.67 Aligned_cols=7 Identities=29% Similarity=0.506 Sum_probs=3.7
Q ss_pred hhhccCc
Q 011020 66 ERRDKGK 72 (495)
Q Consensus 66 ~~~~~~~ 72 (495)
|||||+.
T Consensus 294 rRrRR~p 300 (548)
T PF02459_consen 294 RRRRRRP 300 (548)
T ss_pred cccCCCC
Confidence 5555554
No 35
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=38.98 E-value=63 Score=27.58 Aligned_cols=29 Identities=10% Similarity=0.194 Sum_probs=23.1
Q ss_pred EeeCCeEEEcCCC-----CCCCCeEEEEeEEeeC
Q 011020 131 YELEDPVLLTPED-----TNQKPYVAIIKEITQS 159 (495)
Q Consensus 131 YkVGD~VyV~~ed-----~~e~PyIArI~eIwed 159 (495)
++.||+|.|..+. .+...|+|+|+.+-..
T Consensus 6 Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg 39 (75)
T PF11302_consen 6 VKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG 39 (75)
T ss_pred cCCCCEEEEecCccccccCCCCcEEEEEEEEecc
Confidence 6899999999765 2456799999988654
No 36
>KOG0343 consensus RNA Helicase [RNA processing and modification]
Probab=35.96 E-value=16 Score=41.58 Aligned_cols=40 Identities=18% Similarity=0.165 Sum_probs=18.1
Q ss_pred cccccCCCCCC-CcchhhhhhhccCCCC---CccccccceeecC
Q 011020 73 VREAEKPRNDG-VEDEEEEEEEEEQPQE---DAKPVGELVRFSG 112 (495)
Q Consensus 73 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~---~a~pIG~pVK~~G 112 (495)
.|++|+.++++ +++++++.-..|.-.+ +.-|.++|-+...
T Consensus 672 rr~aeea~~~e~e~~e~d~~~~~~~gs~dD~d~s~lPd~dk~~k 715 (758)
T KOG0343|consen 672 RRRAEEANEEEAEAEEEDGDFVDWSGSEDDPDISWLPDPDKVRK 715 (758)
T ss_pred HHHHHhcccccccchhccCchhcccCCcccCCcccCCChhhhhh
Confidence 46666655544 2222222222232222 3456777766554
No 37
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=35.42 E-value=69 Score=24.88 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=26.1
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEE
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQW 170 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqW 170 (495)
+.+|+.|++.-. ...+|-|+|+++... .|.....|.+
T Consensus 1 ~~vG~~v~~~~~--~~~~y~A~I~~~r~~-~~~~~YyVHY 37 (55)
T PF11717_consen 1 FEVGEKVLCKYK--DGQWYEAKILDIREK-NGEPEYYVHY 37 (55)
T ss_dssp --TTEEEEEEET--TTEEEEEEEEEEEEC-TTCEEEEEEE
T ss_pred CCcCCEEEEEEC--CCcEEEEEEEEEEec-CCCEEEEEEc
Confidence 468999999873 478899999999884 4444444544
No 38
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=34.94 E-value=90 Score=26.54 Aligned_cols=48 Identities=13% Similarity=0.068 Sum_probs=36.0
Q ss_pred EEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEec
Q 011020 166 VTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216 (495)
Q Consensus 166 VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v 216 (495)
|+|.=+-|..||.-...-+ .+..||.+....+-..+-.|+||+.|+..
T Consensus 19 V~vIgltrg~dtkfhhtEk---LDkGEVmiaqftehtsaiKirGkA~I~t~ 66 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHTEK---LDKGEVMIAQFTEHTSAIKIRGKAEIQTK 66 (75)
T ss_pred eEEEEEecCCCccchhhhh---cCCCcEEEEEeecceeEEEEeceEEEEee
Confidence 4555566777774222222 38999999999999999999999999864
No 39
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=33.28 E-value=43 Score=29.05 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=29.2
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEe---------eCCCCceEEEEEEe
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEIT---------QSKDGSMMVTGQWF 171 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIw---------edkdG~~~VrVqWF 171 (495)
|++||.|..+-.. -++|-|+|..=- ....+...+.|+||
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FF 48 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFF 48 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEe
Confidence 5789999999764 899999998621 11234568888888
No 40
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=32.81 E-value=20 Score=41.96 Aligned_cols=44 Identities=32% Similarity=0.387 Sum_probs=37.1
Q ss_pred CCCCCCCchhHHHHHHHHHHHhhhhhh-hhHHHHHHHHHHHHHhhccc
Q 011020 408 NGKSFIWPDTAIAAVTALEKASHDTLS-LDFQKYNQKLRQLLFNLKRA 454 (495)
Q Consensus 408 ~~~~~~wp~~~v~~v~ale~~~~~~~~-~d~~kyn~k~~~l~~n~k~~ 454 (495)
+.+.+-||..... -.|.-+|-.|+ .=..||-.|+|.|.||||--
T Consensus 262 g~k~~~d~~ll~~---~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDk 306 (778)
T KOG1634|consen 262 GEKQLQDPNLLLE---KIEHELFVLFGLGVNKKYPEKLRSLLFNLKDK 306 (778)
T ss_pred ccccccchhhHhh---hhhhhceeccCCcccccchhhhhhhhhccccc
Confidence 6788899987755 67888888888 66799999999999999854
No 41
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=32.49 E-value=59 Score=25.84 Aligned_cols=40 Identities=10% Similarity=0.028 Sum_probs=30.2
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-------CCceEEEEEEee
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEITQSK-------DGSMMVTGQWFY 172 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIwedk-------dG~~~VrVqWFY 172 (495)
|++||.|..+-.. -+.|-|+|..-.... .....+.|++|-
T Consensus 1 f~~GdlVwaK~~G--~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg 47 (63)
T smart00293 1 FKPGDLVWAKMKG--FPWWPALVVSPKETPDNIRKRKRFENLYPVLFFG 47 (63)
T ss_pred CCCCCEEEEECCC--CCCCCeEEcCcccCChhHhhccCCCCEEEEEEeC
Confidence 5789999999764 789999999886532 224577788874
No 42
>PF12213 Dpoe2NT: DNA polymerases epsilon N terminal; InterPro: IPR024639 This domain is found in the N-terminal of DNA polymerase epsilon subunit B proteins. It contains a single completely conserved phenylalanine residue that may be functionally important. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. The N-terminal domain has close structural relation to AAA+ protein C-terminal domains [].; PDB: 2V6Z_M.
Probab=31.67 E-value=60 Score=27.21 Aligned_cols=34 Identities=21% Similarity=0.361 Sum_probs=23.4
Q ss_pred HHHHhhhccccCCchhhhHHHHHHHHhhhhcCCC
Q 011020 337 YNILSKFKALTGETHRDKWLERLLQGLQYICNSA 370 (495)
Q Consensus 337 ~~~l~~~~~~tg~~~rd~~l~~l~~~i~~~~~~~ 370 (495)
...|+++-..-++..|++||+++++.|+--+-++
T Consensus 25 ~~~l~~~l~~~~~~e~e~~l~~Ii~~v~kq~Lss 58 (73)
T PF12213_consen 25 SKYLAEQLQSLSEEEREDWLDKIIDAVQKQPLSS 58 (73)
T ss_dssp HHHHHHHTTTS-TTTHHHHHHHHHHHHTTS--SS
T ss_pred HHHHHHHHccCCHHHHHHHHHHHHHHHhcCCCCC
Confidence 3445665555678899999999999997655444
No 43
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=30.91 E-value=33 Score=39.38 Aligned_cols=89 Identities=17% Similarity=0.238 Sum_probs=57.6
Q ss_pred EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceee
Q 011020 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMH 209 (495)
Q Consensus 130 ~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~G 209 (495)
.+..|||+++.+.+ .-+-+..+ -.|-..+|..++...|+.|++++.+...+.+ +. .+
T Consensus 375 ~~~~~d~~~~an~~--~~~~~i~~-p~~~~~eg~~~~~t~~~~~~t~t~~s~~~~~---------~~-----------~~ 431 (629)
T KOG1827|consen 375 KLETGDFLLVANSP--LCPRYIIR-PNTPEPEGKNDFSTGWIITSTETTPSEPRKF---------FK-----------YN 431 (629)
T ss_pred cccccceeeecCCC--CCcceeec-cCCCCcccccccccceeccCCCCccCCCccc---------cc-----------cc
Confidence 78899999998854 22223223 3343458999999999999999987443333 22 66
Q ss_pred ecEEEecCccccCC--CCCCCCceEEEeeeecCC
Q 011020 210 KCVVHFVPIHKQLP--NRKQHPGFIVQKVYDTVE 241 (495)
Q Consensus 210 KC~V~~v~ey~qlp--~~~~pd~FfCr~vYD~~~ 241 (495)
.|.++-...+..-+ .....+.+.|...||-..
T Consensus 432 ~~~~~~~~~~~~s~~~~~~~~~~~~~~~~p~~~s 465 (629)
T KOG1827|consen 432 RCSSFVKEAFINSPPHTPLSKPLSPIQQIPDLLS 465 (629)
T ss_pred chHHHHHHHhhcCCCCcccCCCcccccccchHhH
Confidence 66666555544332 122357788888887643
No 44
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=30.56 E-value=63 Score=26.38 Aligned_cols=40 Identities=20% Similarity=0.204 Sum_probs=27.2
Q ss_pred eeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEEEee
Q 011020 132 ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFY 172 (495)
Q Consensus 132 kVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVqWFY 172 (495)
++||.+.+....-+.+...|.|.++.-. +|..=..|+|--
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g~-dG~PPY~VRw~D 43 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRGP-DGSPPYLVRWDD 43 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S-S-SS-S-EEEEETT
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEECC-CCCCCEEEEecC
Confidence 6899999998777788899999999864 777888899963
No 45
>TIGR03442 conserved hypothetical protein TIGR03442. Members of this strictly bacterial protein family show similarity to class II glutamine amidotransferases (see Pfam family pfam00310). They are distinguished by appearing in a genome context with, and usually adjacent to or between, members of families TIGR03438 (an uncharacterized methyltransferase) and TIGR03440 (an uncharacterized protein).
Probab=30.04 E-value=27 Score=35.19 Aligned_cols=24 Identities=38% Similarity=0.661 Sum_probs=21.1
Q ss_pred CcCCccchhhccCCCccccccccc
Q 011020 470 HVRSPTRAFLLSLPTCQPFLSGRL 493 (495)
Q Consensus 470 ~~~~~~~~~~~~~~~~~~~~~~~~ 493 (495)
|||..|....+++-.||||..|++
T Consensus 88 HvR~AT~G~~~~~~N~hPf~~g~~ 111 (251)
T TIGR03442 88 AVRSATVGMAIDESACAPFSDGRW 111 (251)
T ss_pred EeeeCCCCCCcchhcCCCCCcCCE
Confidence 999999987788899999998764
No 46
>PRK10708 hypothetical protein; Provisional
Probab=29.65 E-value=1.2e+02 Score=24.91 Aligned_cols=43 Identities=16% Similarity=0.470 Sum_probs=31.1
Q ss_pred eeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEE-------EEEEeecccc
Q 011020 132 ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMV-------TGQWFYRPEE 176 (495)
Q Consensus 132 kVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~V-------rVqWFYRPEE 176 (495)
+++|.|+|+.+. .+...|.|..+-.=.+|.+++ .+.||+--.+
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG~MyLvaL~dYP~GiWFFNE~~ 51 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEGTMYLVSLEDYPLGIWFFNEAG 51 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCcEEEEEEcCcCCCceEEEeccC
Confidence 688999999875 667778888776556776654 4678876443
No 47
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=28.59 E-value=40 Score=27.48 Aligned_cols=40 Identities=15% Similarity=0.061 Sum_probs=28.7
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEeeC---CCCceEEEEEEee
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEITQS---KDGSMMVTGQWFY 172 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIwed---kdG~~~VrVqWFY 172 (495)
|.+||.|..+-.. -+.|-|+|...... ......+.|.||-
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg 43 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFG 43 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecC
Confidence 6789999998754 78899999988643 2234567777773
No 48
>PF02081 TrpBP: Tryptophan RNA-binding attenuator protein; InterPro: IPR023558 The tryptophan RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in Bacillus sp. by binding to the leader region of the nascent trp operon mRNA []. The crystal structure of the Trp RNA-binding attenuation protein of Bacillus subtilis has been solved []. TRAP forms an oligomeric ring consisting of 11 single-domain subunits, where each subunit adopts a double-stranded beta-helix structure with the appearance of a beta-sandwich of distinct architecture and jelly-roll fold. The 11 subunits are stabilised by 11 inter-subunit strands, forming a beta-wheel with a large central hole. TRAP is activated by binding to tryptophan in clefts between adjacent beta-strands, which induces conformational changes in the protein. Activated TRAP binds an mRNA target sequence consisting of 11 (G/U)AG repeats, separated by 2-3 spacer nucleotides. The spacer nucleotides do not make direct contact with the TRAP protein, but they do influence the conformation of the RNA, which might influence the specificity of TRAP []. This entry represents the structural domain in the TRAP family of proteins.; PDB: 3ZTE_U 1GTN_H 1UTD_D 1GTF_D 1UTF_F 2ZP9_K 1C9S_Q 2EXT_A 3AQD_T 1QAW_C ....
Probab=28.42 E-value=80 Score=26.86 Aligned_cols=48 Identities=15% Similarity=0.051 Sum_probs=32.7
Q ss_pred EEEEEeecccccccCCCCCCcCCCCCeeEeeCCcccccccceeeecEEEec
Q 011020 166 VTGQWFYRPEEADRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFV 216 (495)
Q Consensus 166 VrVqWFYRPEET~~~~~g~f~~~~~nELFlSdh~D~~PlesI~GKC~V~~v 216 (495)
|+|.=+-|..||.-...-+ .+..||.+....+-..+-.|+|++.|+..
T Consensus 19 V~ViGlTRG~dtkfhHtEk---LDkGEVmIaQFTehtsaiKiRGkA~I~t~ 66 (75)
T PF02081_consen 19 VTVIGLTRGTDTKFHHTEK---LDKGEVMIAQFTEHTSAIKIRGKAEILTK 66 (75)
T ss_dssp EEEEEEESSSSSSEEEEEE---E-TT-EEEEE-BSSEEEEEEESSEEEEET
T ss_pred eEEEEEecCCcccchhhhc---cCCCcEEEEEeecceEEEEEeeeEEEEec
Confidence 4455566777765322222 38899999999999999999999999864
No 49
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=25.85 E-value=1.5e+02 Score=24.35 Aligned_cols=43 Identities=19% Similarity=0.518 Sum_probs=30.8
Q ss_pred eeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEE-------EEEEeecccc
Q 011020 132 ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMV-------TGQWFYRPEE 176 (495)
Q Consensus 132 kVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~V-------rVqWFYRPEE 176 (495)
+++|.|+|+.+. .+..-|.|..+-.=.+|.+++ .+.||+--.+
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG~MYLvaL~dYP~GiWFFNE~~ 51 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEGTMYLVALEDYPAGIWFFNEKD 51 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCcEEEEEEcCcCCcceEEEecCC
Confidence 688999999875 666777777776555776654 4678876544
No 50
>COG5475 Uncharacterized small protein [Function unknown]
Probab=25.54 E-value=1.4e+02 Score=24.45 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=25.5
Q ss_pred CEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeCC-CCceEEEEEEeeccc
Q 011020 128 GNKYELEDPVLLTPEDTNQKPYVAIIKEITQSK-DGSMMVTGQWFYRPE 175 (495)
Q Consensus 128 G~~YkVGD~VyV~~ed~~e~PyIArI~eIwedk-dG~~~VrVqWFYRPE 175 (495)
+..|++||.|.|+.+.+ +|.-+. ...-++.++||-+-.
T Consensus 2 ~~~FstgdvV~lKsGGP----------~Mtvs~~ss~Gmy~C~Wf~g~g 40 (60)
T COG5475 2 EMSFSTGDVVTLKSGGP----------RMTVSGYSSDGMYECRWFDGYG 40 (60)
T ss_pred CceeecCcEEEeecCCc----------eEEEeccccCCeEEEEEecCCC
Confidence 35789999999998873 222111 112589999997765
No 51
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=24.94 E-value=3.3e+02 Score=25.39 Aligned_cols=96 Identities=18% Similarity=0.336 Sum_probs=51.9
Q ss_pred eeEEEEcCEEEeeCCeEEEcCCCCCCCCeEEEEeEEeeC----CCCceEEEEEEeecc---cccccCCCC----CC--cC
Q 011020 121 YEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQS----KDGSMMVTGQWFYRP---EEADRKGGG----NW--LS 187 (495)
Q Consensus 121 Y~Sf~~dG~~YkVGD~VyV~~ed~~e~PyIArI~eIwed----kdG~~~VrVqWFYRP---EET~~~~~g----~f--~~ 187 (495)
...+.+....++.||.|.+.........+|-||..+--+ .+|..+++.+-.-.+ .+......+ .. ..
T Consensus 42 v~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 (163)
T TIGR02227 42 VNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVT 121 (163)
T ss_pred EEEeEcCCCCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceE
Confidence 333333345678899999987654566788888877432 245566666544222 110000000 00 01
Q ss_pred CCCCeeEeeCCc----------ccccccceeeecEEEec
Q 011020 188 RDTRELFYSFHR----------DEVPAESVMHKCVVHFV 216 (495)
Q Consensus 188 ~~~nELFlSdh~----------D~~PlesI~GKC~V~~v 216 (495)
.-++++|+-... --++.+.|+|++.....
T Consensus 122 vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~~~ 160 (163)
T TIGR02227 122 VPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVFY 160 (163)
T ss_pred ECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEEEC
Confidence 246667665522 23777888888776654
No 52
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=24.89 E-value=1.3e+02 Score=20.95 Aligned_cols=26 Identities=31% Similarity=0.289 Sum_probs=21.2
Q ss_pred eCCeEEEcCCCCCCCCeEEEEeEEeeCC
Q 011020 133 LEDPVLLTPEDTNQKPYVAIIKEITQSK 160 (495)
Q Consensus 133 VGD~VyV~~ed~~e~PyIArI~eIwedk 160 (495)
+||.|.|..+. ..=.+|+|.+|....
T Consensus 1 ~Gd~V~V~~G~--~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGP--FKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSST--TTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcC--CCCceEEEEEEECCC
Confidence 58999999875 666899999998653
No 53
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=24.19 E-value=95 Score=23.81 Aligned_cols=27 Identities=44% Similarity=0.569 Sum_probs=22.2
Q ss_pred HHhhhhhhhhHH---HHHHHHHHHHHhhcc
Q 011020 427 KASHDTLSLDFQ---KYNQKLRQLLFNLKR 453 (495)
Q Consensus 427 ~~~~~~~~~d~~---kyn~k~~~l~~n~k~ 453 (495)
++.||+|.+|+. +=|++|+..+--|++
T Consensus 11 K~~yd~Lk~~~~~L~~E~~~L~aev~~L~~ 40 (45)
T PF02183_consen 11 KASYDSLKAEYDSLKKENEKLRAEVQELKE 40 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 688999999874 678899988877764
No 54
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=22.83 E-value=1.2e+02 Score=19.53 Aligned_cols=25 Identities=24% Similarity=0.296 Sum_probs=19.5
Q ss_pred EeeCCeEEEcCCCCCCCCeEEEEeEEe
Q 011020 131 YELEDPVLLTPEDTNQKPYVAIIKEIT 157 (495)
Q Consensus 131 YkVGD~VyV~~ed~~e~PyIArI~eIw 157 (495)
+.+||.|.|..+. ..-.+|.|.++.
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~ 26 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVD 26 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEc
Confidence 5689999999864 556788888875
No 55
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=21.61 E-value=1.9e+02 Score=25.49 Aligned_cols=44 Identities=20% Similarity=0.315 Sum_probs=32.6
Q ss_pred EEeeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEE---EEeeccccccc
Q 011020 130 KYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTG---QWFYRPEEADR 179 (495)
Q Consensus 130 ~YkVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrV---qWFYRPEET~~ 179 (495)
.+.+|++|--.+.. -+|.|.+| +..++..|+.+ .-||||.-+..
T Consensus 2 ~I~vGs~VRY~~TG-----T~G~V~di-K~ed~~~wv~LD~t~L~Yr~~~Lev 48 (91)
T PF09871_consen 2 PIKVGSYVRYINTG-----TVGKVVDI-KEEDGETWVLLDSTDLYYRPDYLEV 48 (91)
T ss_pred cceeCCEEEECCCC-----eEEEEEEE-EEeCCCeEEEEccCCceeecceeEE
Confidence 46889988665544 58999999 44577888877 67788887654
No 56
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.40 E-value=1.9e+02 Score=25.72 Aligned_cols=42 Identities=21% Similarity=0.365 Sum_probs=30.1
Q ss_pred eeCCeEEEcCCCCCCCCeEEEEeEEeeCCCCceEEEEE---Eeecccccc
Q 011020 132 ELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQ---WFYRPEEAD 178 (495)
Q Consensus 132 kVGD~VyV~~ed~~e~PyIArI~eIwedkdG~~~VrVq---WFYRPEET~ 178 (495)
.|||.|--.+.+ -+++|..|.++.+|..||..- -+||+.=+.
T Consensus 10 ~VG~avrYvnTg-----TvgrV~dIkkdEdG~~WV~LdstdLwYre~~le 54 (97)
T COG4014 10 KVGDAVRYVNTG-----TVGRVVDIKKDEDGDIWVVLDSTDLWYREHYLE 54 (97)
T ss_pred hhcceEEEeecC-----ceeeEEEEEeecCCceEEEEecCCceeccccee
Confidence 388886555444 589999999999999998763 356665443
No 57
>PF05705 DUF829: Eukaryotic protein of unknown function (DUF829); InterPro: IPR008547 This signature identifies Transmembrane protein 53, that have no known function but are predicted to be integral membrane proteins.
Probab=21.37 E-value=1.6e+02 Score=28.38 Aligned_cols=78 Identities=28% Similarity=0.387 Sum_probs=49.7
Q ss_pred CCCCCCCch-hHHHHHHHHHH------------Hhhhhhhh-hHHHHHHHHHHHHHhhccccccc--ceeeecCCCC-CC
Q 011020 408 NGKSFIWPD-TAIAAVTALEK------------ASHDTLSL-DFQKYNQKLRQLLFNLKRAWVGP--GLFCLSSCPG-PH 470 (495)
Q Consensus 408 ~~~~~~wp~-~~v~~v~ale~------------~~~~~~~~-d~~kyn~k~~~l~~n~k~~~~~~--~~~~~~~~~~-~~ 470 (495)
....++||. .+.+++..|-. .++.+||. =..-|.+-+..+.-+-+...++. ....+-|||| ++
T Consensus 36 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~il~H~FSnGG~~~~~~l~~~~~~~~~~~~~~~~i~g~I~DS~P~~~~ 115 (240)
T PF05705_consen 36 PPADFFWPSKRLAPAADKLLELLSDSQSASPPPILFHSFSNGGSFLYSQLLEAYQSRKKFGKLLPRIKGIIFDSCPGIPT 115 (240)
T ss_pred CHHHHeeeccchHHHHHHHHHHhhhhccCCCCCEEEEEEECchHHHHHHHHHHHHhcccccccccccceeEEeCCCCccc
Confidence 345677883 44444443322 34455665 56677777755554444455553 5567999997 47
Q ss_pred cCCccchhhccCCCc
Q 011020 471 VRSPTRAFLLSLPTC 485 (495)
Q Consensus 471 ~~~~~~~~~~~~~~~ 485 (495)
..+..++|..++|.-
T Consensus 116 ~~~~~~~~~~~~~~~ 130 (240)
T PF05705_consen 116 YSSSARAFSAALPKS 130 (240)
T ss_pred cccHHHHHHHHcCcc
Confidence 778899999998875
No 58
>COG0121 Predicted glutamine amidotransferase [General function prediction only]
Probab=21.23 E-value=38 Score=34.51 Aligned_cols=37 Identities=30% Similarity=0.387 Sum_probs=30.2
Q ss_pred HHHHHhhcccccccceeeecCCCCCCcCCccchhhccCCCccccccccc
Q 011020 445 RQLLFNLKRAWVGPGLFCLSSCPGPHVRSPTRAFLLSLPTCQPFLSGRL 493 (495)
Q Consensus 445 ~~l~~n~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 493 (495)
..|..+||-..|+| |||+-|.. .+|+-.|+||+.+..
T Consensus 62 ~~~~~~i~S~~via-----------HvR~At~G-~vs~~ntHPF~~~~~ 98 (252)
T COG0121 62 LVLAYPIKSELVIA-----------HVRKATQG-EVSLSNTHPFTRELW 98 (252)
T ss_pred hhcccccCccEEEE-----------EEeccCCC-cccccCCCCccccCC
Confidence 44567788776665 99999999 999999999997653
Done!