Query 005739
Match_columns 680
No_of_seqs 126 out of 216
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 13:02:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005739.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005739hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04715 BAH_Orc1p_like BAH, or 100.0 4.4E-41 9.5E-46 319.7 14.8 156 11-167 1-159 (159)
2 cd04713 BAH_plant_3 BAH, or Br 100.0 9.4E-29 2E-33 231.5 15.7 125 28-161 9-135 (146)
3 cd04716 BAH_plantDCM_I BAH, or 100.0 3.3E-28 7.1E-33 223.1 12.9 119 37-161 1-119 (122)
4 cd04714 BAH_BAHCC1 BAH, or Bro 99.9 1.8E-25 3.8E-30 203.1 11.0 114 37-157 1-117 (121)
5 cd04717 BAH_polybromo BAH, or 99.9 2.6E-25 5.6E-30 200.2 11.6 114 37-159 1-116 (121)
6 cd04370 BAH BAH, or Bromo Adja 99.9 2.8E-24 6E-29 186.5 11.7 117 37-160 1-120 (123)
7 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 2.2E-24 4.7E-29 199.1 10.1 116 37-160 1-124 (124)
8 cd04721 BAH_plant_1 BAH, or Br 99.9 4.3E-24 9.4E-29 197.3 10.2 116 33-155 1-117 (130)
9 smart00439 BAH Bromo adjacent 99.9 1.1E-23 2.3E-28 183.9 11.6 116 39-161 1-118 (120)
10 PF01426 BAH: BAH domain; Int 99.9 1.6E-23 3.5E-28 182.9 9.4 114 38-161 1-117 (119)
11 cd04710 BAH_fungalPHD BAH, or 99.9 9.1E-22 2E-26 183.3 10.9 116 33-161 5-135 (135)
12 cd04709 BAH_MTA BAH, or Bromo 99.9 1.2E-21 2.7E-26 187.9 11.4 116 38-161 2-138 (164)
13 cd04712 BAH_DCM_I BAH, or Brom 99.8 5.9E-20 1.3E-24 169.9 12.6 110 36-161 2-127 (130)
14 cd04708 BAH_plantDCM_II BAH, o 99.8 2.8E-20 6.1E-25 183.8 10.7 125 33-167 1-149 (202)
15 cd04720 BAH_Orc1p_Yeast BAH, o 99.8 1.3E-19 2.8E-24 175.5 13.4 120 35-161 48-176 (179)
16 cd04719 BAH_Orc1p_animal BAH, 99.7 2.1E-17 4.6E-22 153.4 9.4 117 38-158 2-124 (128)
17 cd04718 BAH_plant_2 BAH, or Br 99.6 4.1E-17 8.8E-22 155.0 0.9 93 54-159 51-144 (148)
18 KOG1886 BAH domain proteins [T 99.6 9.8E-16 2.1E-20 166.0 7.3 135 16-161 28-167 (464)
19 cd04711 BAH_Dnmt1_II BAH, or B 99.4 1.4E-13 3E-18 129.7 6.2 100 54-162 25-135 (137)
20 KOG1827 Chromatin remodeling c 99.1 4.3E-11 9.4E-16 134.3 5.8 123 29-159 179-303 (629)
21 PF00076 RRM_1: RNA recognitio 98.2 2.6E-06 5.6E-11 66.8 5.2 69 518-592 1-69 (70)
22 PLN03134 glycine-rich RNA-bind 97.5 0.00036 7.9E-09 65.9 7.8 97 503-604 22-118 (144)
23 KOG3554 Histone deacetylase co 97.3 2.4E-05 5.1E-10 86.3 -3.2 113 39-160 5-161 (693)
24 smart00362 RRM_2 RNA recogniti 97.2 0.0016 3.4E-08 49.6 7.0 69 518-593 2-70 (72)
25 cd00590 RRM RRM (RNA recogniti 97.0 0.0032 7E-08 48.1 7.5 72 518-595 2-73 (74)
26 smart00360 RRM RNA recognition 97.0 0.0026 5.7E-08 48.0 6.5 69 520-593 1-69 (71)
27 TIGR01628 PABP-1234 polyadenyl 96.7 0.0051 1.1E-07 68.2 8.2 82 512-599 282-363 (562)
28 TIGR01659 sex-lethal sex-letha 96.5 0.013 2.9E-07 62.8 10.0 109 513-630 105-215 (346)
29 TIGR01659 sex-lethal sex-letha 96.5 0.008 1.7E-07 64.5 8.0 81 516-599 194-274 (346)
30 TIGR01648 hnRNP-R-Q heterogene 96.2 0.02 4.4E-07 65.6 9.3 108 512-628 55-162 (578)
31 TIGR01648 hnRNP-R-Q heterogene 95.9 0.021 4.6E-07 65.4 7.9 75 514-601 232-308 (578)
32 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.9 0.027 5.8E-07 58.1 8.0 83 513-600 267-349 (352)
33 KOG0533 RRM motif-containing p 95.7 0.031 6.7E-07 58.1 7.6 95 512-612 79-198 (243)
34 TIGR01642 U2AF_lg U2 snRNP aux 95.6 0.037 8E-07 60.2 8.3 81 510-595 170-255 (509)
35 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.5 0.069 1.5E-06 55.1 9.2 96 515-615 3-100 (352)
36 TIGR01622 SF-CC1 splicing fact 95.4 0.039 8.5E-07 59.3 7.5 79 515-598 186-264 (457)
37 TIGR01642 U2AF_lg U2 snRNP aux 95.1 0.09 2E-06 57.2 9.1 81 513-598 293-373 (509)
38 TIGR01649 hnRNP-L_PTB hnRNP-L/ 95.1 0.054 1.2E-06 59.9 7.5 74 516-598 3-76 (481)
39 PF14259 RRM_6: RNA recognitio 95.1 0.03 6.6E-07 44.9 4.0 66 518-592 1-69 (70)
40 TIGR01649 hnRNP-L_PTB hnRNP-L/ 94.8 0.08 1.7E-06 58.6 7.7 77 512-598 272-349 (481)
41 PLN03120 nucleic acid binding 94.8 0.079 1.7E-06 55.7 7.2 75 515-598 4-78 (260)
42 TIGR01628 PABP-1234 polyadenyl 94.6 0.081 1.8E-06 58.9 7.3 75 518-597 3-77 (562)
43 smart00361 RRM_1 RNA recogniti 94.6 0.081 1.8E-06 43.7 5.4 58 535-595 4-70 (70)
44 TIGR01645 half-pint poly-U bin 94.4 0.12 2.5E-06 60.0 8.0 81 514-599 203-283 (612)
45 PF13893 RRM_5: RNA recognitio 94.2 0.071 1.5E-06 41.7 4.1 35 559-596 21-55 (56)
46 TIGR01622 SF-CC1 splicing fact 94.0 0.24 5.1E-06 53.4 8.9 100 510-615 84-197 (457)
47 COG0724 RNA-binding proteins ( 93.3 0.33 7.1E-06 45.1 7.5 80 515-599 115-194 (306)
48 KOG0117 Heterogeneous nuclear 92.5 0.23 4.9E-06 55.8 6.0 108 513-628 81-188 (506)
49 PLN03121 nucleic acid binding 92.3 0.39 8.5E-06 50.2 7.2 72 513-593 3-74 (243)
50 TIGR01645 half-pint poly-U bin 91.5 0.49 1.1E-05 55.0 7.6 82 509-595 101-182 (612)
51 KOG0131 Splicing factor 3b, su 87.8 0.9 1.9E-05 46.3 5.2 79 513-598 7-87 (203)
52 KOG0110 RNA-binding protein (R 86.1 2.8 6E-05 49.6 8.6 118 518-644 518-653 (725)
53 KOG4206 Spliceosomal protein s 84.5 0.77 1.7E-05 47.5 2.9 61 518-580 12-73 (221)
54 KOG0123 Polyadenylate-binding 83.2 2.2 4.7E-05 46.8 5.9 72 518-597 79-150 (369)
55 KOG0123 Polyadenylate-binding 82.5 1.5 3.3E-05 48.0 4.3 88 505-598 259-347 (369)
56 COG5076 Transcription factor i 80.1 0.28 6.1E-06 52.8 -2.2 92 30-127 267-359 (371)
57 PF02617 ClpS: ATP-dependent C 78.1 0.88 1.9E-05 39.4 0.6 75 517-596 8-82 (82)
58 PF09926 DUF2158: Uncharacteri 75.8 3.2 6.9E-05 34.4 3.2 42 40-84 1-42 (53)
59 KOG0148 Apoptosis-promoting RN 72.9 17 0.00037 39.4 8.5 90 501-604 150-242 (321)
60 KOG4207 Predicted splicing fac 70.5 6.1 0.00013 41.4 4.5 79 517-602 15-98 (256)
61 KOG0153 Predicted RNA-binding 68.9 11 0.00024 41.8 6.2 74 516-599 229-302 (377)
62 PF11608 Limkain-b1: Limkain b 68.1 16 0.00034 33.7 6.0 71 516-596 3-73 (90)
63 KOG0114 Predicted RNA-binding 66.4 19 0.00042 34.4 6.5 76 512-595 15-90 (124)
64 PRK00033 clpS ATP-dependent Cl 66.0 7.9 0.00017 35.7 3.9 69 517-596 29-97 (100)
65 KOG0107 Alternative splicing f 59.6 13 0.00029 38.0 4.4 73 514-595 9-90 (195)
66 KOG0122 Translation initiation 58.9 17 0.00037 38.8 5.3 62 517-581 191-253 (270)
67 PLN03213 repressor of silencin 56.7 33 0.00071 40.0 7.3 94 513-631 8-103 (759)
68 PF08777 RRM_3: RNA binding mo 55.3 14 0.00031 33.8 3.5 60 515-582 1-60 (105)
69 PF03467 Smg4_UPF3: Smg-4/UPF3 54.1 7.5 0.00016 38.5 1.7 71 512-582 4-78 (176)
70 KOG0127 Nucleolar protein fibr 53.8 42 0.00091 39.5 7.6 89 508-599 285-377 (678)
71 KOG4212 RNA-binding protein hn 50.2 41 0.00089 38.7 6.7 73 517-594 46-118 (608)
72 KOG1548 Transcription elongati 48.6 20 0.00043 39.9 4.0 76 515-596 265-348 (382)
73 KOG0117 Heterogeneous nuclear 45.9 46 0.001 38.3 6.3 79 512-604 256-335 (506)
74 PTZ00112 origin recognition co 45.5 19 0.00042 44.7 3.6 57 28-84 441-521 (1164)
75 COG5175 MOT2 Transcriptional r 45.3 29 0.00063 38.7 4.6 82 514-598 113-201 (480)
76 KOG0108 mRNA cleavage and poly 44.4 33 0.00071 39.0 5.0 71 516-595 19-93 (435)
77 PF08075 NOPS: NOPS (NUC059) d 44.4 11 0.00024 31.5 1.0 19 630-648 33-51 (52)
78 KOG2133 Transcriptional corepr 41.5 14 0.00031 45.5 1.7 128 35-167 141-288 (1229)
79 PRK10708 hypothetical protein; 40.4 53 0.0011 28.3 4.4 43 41-84 2-51 (62)
80 KOG0131 Splicing factor 3b, su 37.3 67 0.0015 33.3 5.4 75 518-601 99-178 (203)
81 KOG4209 Splicing factor RNPS1, 37.1 51 0.0011 34.3 4.7 81 515-604 101-184 (231)
82 PF10781 DSRB: Dextransucrase 36.6 67 0.0015 27.7 4.4 44 41-85 2-52 (62)
83 KOG0147 Transcriptional coacti 36.2 20 0.00044 41.6 1.8 59 536-597 466-525 (549)
84 COG5475 Uncharacterized small 35.9 75 0.0016 27.4 4.6 37 38-83 3-40 (60)
85 PF11717 Tudor-knot: RNA bindi 35.8 88 0.0019 25.4 4.9 37 40-78 1-37 (55)
86 cd05834 HDGF_related The PWWP 32.4 60 0.0013 28.7 3.8 45 39-84 2-46 (83)
87 KOG0121 Nuclear cap-binding pr 32.0 1.9E+02 0.0041 28.9 7.3 96 492-596 15-112 (153)
88 PF12083 DUF3560: Domain of un 30.8 1E+02 0.0022 29.8 5.2 59 601-662 39-118 (126)
89 PF04059 RRM_2: RNA recognitio 30.7 1.6E+02 0.0034 27.2 6.2 68 516-583 2-69 (97)
90 KOG0127 Nucleolar protein fibr 27.8 86 0.0019 37.1 4.9 78 519-602 121-198 (678)
91 cd05835 Dnmt3b_related The PWW 27.2 66 0.0014 28.5 3.1 42 40-82 1-45 (87)
92 PF10383 Clr2: Transcription-s 26.2 2.7E+02 0.0058 26.9 7.3 41 28-68 1-52 (139)
93 cd06080 MUM1_like Mutated mela 25.9 88 0.0019 28.0 3.6 39 40-82 1-39 (80)
94 cd06530 S26_SPase_I The S26 Ty 25.2 1.6E+02 0.0034 24.8 5.0 41 28-68 20-61 (85)
95 KOG0120 Splicing factor U2AF, 24.3 1.1E+02 0.0023 35.7 4.9 65 528-596 415-488 (500)
96 KOG0110 RNA-binding protein (R 22.5 79 0.0017 38.1 3.4 76 514-594 612-687 (725)
97 PRK03187 tgl transglutaminase; 22.2 44 0.00095 36.0 1.3 19 34-52 160-178 (272)
98 KOG2202 U2 snRNP splicing fact 21.3 60 0.0013 34.9 2.0 48 550-600 101-148 (260)
99 cd05162 PWWP The PWWP domain, 21.1 1.2E+02 0.0025 26.3 3.4 40 40-80 1-46 (87)
100 PF13041 PPR_2: PPR repeat fam 20.9 1.1E+02 0.0023 23.4 2.8 30 637-666 1-30 (50)
101 KOG0145 RNA-binding protein EL 20.6 1.7E+02 0.0037 32.1 5.1 65 515-581 127-191 (360)
No 1
>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=100.00 E-value=4.4e-41 Score=319.72 Aligned_cols=156 Identities=60% Similarity=0.991 Sum_probs=145.3
Q ss_pred eeeeccccCCCCCCCcceeEEEEEECCEEEEeCceEEEeeCCCCCCeEEEEEEEEeeCC--CceEEEEEeecChhccccc
Q 005739 11 DFKWGKKRGIGGKKKDVQFYQSFTYDGVEYTLYDCVYLYKEGDAEPHVGKLIKIWENAD--KAKKVKLLWFFRPSDISNF 88 (680)
Q Consensus 11 ~fKWGkkrGvgGKkkd~~fYeSft~dG~tYrLGDCVyVkseg~~ePYIGRIvemWE~~D--Gek~VkVqWFyRPEEI~~~ 88 (680)
+||||+++|.|||+++++||+|+.++|.+|+|||||||++++ .+||||+|++||++.+ |.++|+|+|||||+||...
T Consensus 1 ~~~~~~~~g~~~~~~~~~~Y~s~~~~g~~y~lGD~Vlv~s~~-~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~ 79 (159)
T cd04715 1 EFKWGVKRGEGGKKKDGQFYRSFTYDGVEYRLYDDVYVHNGD-SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRME 79 (159)
T ss_pred CcccceecccccccCCceEEEEEEECCEEEeCCCEEEEeCCC-CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccc
Confidence 599999999999999999999999999999999999999855 7999999999999876 8999999999999998754
Q ss_pred CCC-ccCCCCceEEecCCCCcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEehhhhhh
Q 005739 89 LGN-VQTLENELILACGEGVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLDKIDEKI 167 (680)
Q Consensus 89 lg~-~~~~pNELFLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD~f~dkI 167 (680)
+.+ ..+++||||||+|.+.++.|+|||+||+|||+|++++++.++++||+..++.++|+|+|.||++.+..++.|+|+|
T Consensus 80 ~~~~~~~~~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~~s~~~~~~~~~~f~~~f~~~~~~~~~~~~d~~ 159 (159)
T cd04715 80 LKGEPKRHINEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQPSDGIPTSADFLFPCNFDVGRCVIVDKYDDKI 159 (159)
T ss_pred cccCcccCCCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCCCcCCccccCcceeeeEEEecCceecccccCCC
Confidence 433 3688999999999888889999999999999999999999999999999999999999999999999999999987
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=99.96 E-value=9.4e-29 Score=231.45 Aligned_cols=125 Identities=28% Similarity=0.490 Sum_probs=107.1
Q ss_pred eeEEEEEECCEEEEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCc--cCCCCceEEecCC
Q 005739 28 QFYQSFTYDGVEYTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNV--QTLENELILACGE 105 (680)
Q Consensus 28 ~fYeSft~dG~tYrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~--~~~pNELFLSsge 105 (680)
+||++|.++|.+|+|||||||.+++..+||||+|.+||++.+|.++|+|+|||||+||....++. .+++||||+|.+
T Consensus 9 ~~y~s~~~dg~~y~vgD~Vlv~~~~~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~~ElF~S~~- 87 (146)
T cd04713 9 CHYTSFEKDGNKYRLEDCVLLVPEDDQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDPRELFYSFH- 87 (146)
T ss_pred eeeeeEEECCEEEECCCEEEEeCCCCCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCCCeEEEeCC-
Confidence 99999999999999999999999877889999999999998899999999999999996533322 346899999984
Q ss_pred CCcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEe
Q 005739 106 GVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 106 g~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD 161 (680)
.|+||++||+|||+|++.+++...+.++ ...+|||++.||+...++.+
T Consensus 88 ----~d~~~~~~I~gkc~V~~~~~~~~~~~~~----~~~~F~cr~~yD~~~~~~~~ 135 (146)
T cd04713 88 ----RDEVPAESVLHPCKVAFVPKGKQIPLRK----GHSGFIVRRVYDNVNKKLWK 135 (146)
T ss_pred ----CCcCCHHHCcceeEEEECCccccCCccC----CCCeEEEEEEEcCCCCcEee
Confidence 8999999999999999887655333332 35689999999999998865
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=99.95 E-value=3.3e-28 Score=223.10 Aligned_cols=119 Identities=18% Similarity=0.326 Sum_probs=100.7
Q ss_pred CEEEEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCCCcccccCccc
Q 005739 37 GVEYTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNINPLE 116 (680)
Q Consensus 37 G~tYrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~DdNPLe 116 (680)
|..|+|||||||.++++.+||||||++|||+.+|..+|+++|||||+|+........++++|||||. ++|+||++
T Consensus 1 g~~~~lgD~V~v~~~~~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~-----~~D~~pl~ 75 (122)
T cd04716 1 GITYNLGDDAYVQGGEGEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNHDKKRVFYSE-----IKNDNPLD 75 (122)
T ss_pred CcEEEcCCEEEEECCCCCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccccccccCCCceEEEec-----ccCccchh
Confidence 6789999999999987788999999999999999999999999999997442112468899999997 59999999
Q ss_pred eeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEe
Q 005739 117 AIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 117 ~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD 161 (680)
||.|||+|++++++...+ ........+||||+|.|++.+.+|..
T Consensus 76 ~I~~Kc~V~~~~~~~~~~-~~~~~~~~~df~c~~~Y~~~~~tF~~ 119 (122)
T cd04716 76 CLISKVKILQVPPNVGTK-RKKPNSEKCDYYYDMEYCVPYSTFQT 119 (122)
T ss_pred heeeeeEEEEeCCCCCcc-cccccCCCceEEEeeEeccchhheEe
Confidence 999999999987766331 12234468899999999999999864
No 4
>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=99.92 E-value=1.8e-25 Score=203.11 Aligned_cols=114 Identities=19% Similarity=0.336 Sum_probs=91.6
Q ss_pred CEEEEeCceEEEeeCCC-CCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCCCcccccCcc
Q 005739 37 GVEYTLYDCVYLYKEGD-AEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNINPL 115 (680)
Q Consensus 37 G~tYrLGDCVyVkseg~-~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~DdNPL 115 (680)
|++|++||||||.+++. .+||||||++||++.+|+++|+++|||||+||.... ...++++|||+|. +.|+||+
T Consensus 1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~-~~~~~~~EvF~S~-----~~d~~~~ 74 (121)
T cd04714 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGR-KPNHGEKELFASD-----HQDENSV 74 (121)
T ss_pred CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcc-cccCCCCceEecC-----CcccccH
Confidence 57899999999999876 689999999999999999999999999999996422 2358999999998 4899999
Q ss_pred ceeecceEEEecCCCcCCCCCCC-ccCCCC-cEEEEeeeeCcce
Q 005739 116 EAIAGKCNVVCTSKDARNPQPSD-EELQIS-DFIFCRTFDVGLR 157 (680)
Q Consensus 116 e~I~GKC~VVsiskD~rn~rPS~-~ei~~a-DFYf~R~YDv~t~ 157 (680)
+||.|||.|++++.+.. .++.. ...+.. .|+|...||+...
T Consensus 75 ~~I~gkc~V~~~~ey~~-~~~~~~~~~~~~d~~~Ce~~yn~~~~ 117 (121)
T cd04714 75 QTIEHKCYVLTFAEYER-LARVKKKPQDGVDFYYCAGTYNPDTG 117 (121)
T ss_pred HHhCcccEEEehhHhee-cccccCCCCcCCCEEEEeccCCCCcC
Confidence 99999999998765542 22211 123344 4666679999864
No 5
>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=99.92 E-value=2.6e-25 Score=200.21 Aligned_cols=114 Identities=24% Similarity=0.514 Sum_probs=95.7
Q ss_pred CEEEEeCceEEEeeCCC-CCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCCCcccccCcc
Q 005739 37 GVEYTLYDCVYLYKEGD-AEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNINPL 115 (680)
Q Consensus 37 G~tYrLGDCVyVkseg~-~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~DdNPL 115 (680)
|..|++||||||.+++. .+||||+|.+||++.+|.++|+++|||||+||....+ ..+++||||+|. +.|+||+
T Consensus 1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~-~~~~~~Evfls~-----~~d~~~~ 74 (121)
T cd04717 1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPT-RKFYKNEVFKSP-----LYETVPV 74 (121)
T ss_pred CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCc-cccccCceEEcC-----ccccccH
Confidence 57899999999999876 7899999999999999999999999999999964333 478999999997 5999999
Q ss_pred ceeecceEEEecCCCcCCCCCCCccCCCCc-EEEEeeeeCcceEE
Q 005739 116 EAIAGKCNVVCTSKDARNPQPSDEELQISD-FIFCRTFDVGLRKV 159 (680)
Q Consensus 116 e~I~GKC~VVsiskD~rn~rPS~~ei~~aD-FYf~R~YDv~t~Ri 159 (680)
++|+|||+|++...+. ..+|.+ .+.+| |+|.+.||+....|
T Consensus 75 ~~I~~kc~Vl~~~~y~-~~~p~~--~~~~dvy~ce~~y~~~~~~~ 116 (121)
T cd04717 75 EEIVGKCAVMDVKDYI-KGRPTE--ISEEDVYVCESRYNESAKSF 116 (121)
T ss_pred HHhcCeeEEEehHHHh-cCCCCC--CCCCCEEEEeEEECcccccE
Confidence 9999999999876554 455653 33445 77888999987654
No 6
>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=99.91 E-value=2.8e-24 Score=186.54 Aligned_cols=117 Identities=26% Similarity=0.539 Sum_probs=96.4
Q ss_pred CEEEEeCceEEEeeCCC---CCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCCCcccccC
Q 005739 37 GVEYTLYDCVYLYKEGD---AEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNIN 113 (680)
Q Consensus 37 G~tYrLGDCVyVkseg~---~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~DdN 113 (680)
|.+|++||||||.+++. .++|||+|.+||++.++.++++++|||||+||...... .+.+||||+|. ++|++
T Consensus 1 g~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~-~~~~~Elf~s~-----~~~~i 74 (123)
T cd04370 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSP-FALRRELFLSD-----HLDEI 74 (123)
T ss_pred CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhcccccc-ccccceeEEec-----Ccccc
Confidence 67899999999999875 68999999999999999999999999999999753332 58899999997 48999
Q ss_pred ccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEE
Q 005739 114 PLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVL 160 (680)
Q Consensus 114 PLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~Riv 160 (680)
|+++|.|||.|++...+... .|........+|||++.||+.+..|.
T Consensus 75 ~v~~I~gkc~V~~~~~~~~~-~~~~~~~~~~~f~~r~~yd~~~~~fk 120 (123)
T cd04370 75 PVESIIGKCKVLFVSEFEGL-KQRPNKIDTDDFFCRLAYDPTTKEFK 120 (123)
T ss_pred CHHHhccccEEEechHhhcc-ccccccCCCCeEEEEEEECcCcceEE
Confidence 99999999999987655422 21222334678999999999877663
No 7
>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=99.91 E-value=2.2e-24 Score=199.12 Aligned_cols=116 Identities=22% Similarity=0.318 Sum_probs=97.2
Q ss_pred CEEEEeCceEEEeeCCC-CCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCCCcccccCcc
Q 005739 37 GVEYTLYDCVYLYKEGD-AEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNINPL 115 (680)
Q Consensus 37 G~tYrLGDCVyVkseg~-~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~DdNPL 115 (680)
|.+|.+||||+|.+++. .+||||+|++|||+.+|+++||++|||||+|+ .+++ .+.++|||||. +|++|+|
T Consensus 1 g~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dT--VlG~-~~~~kEvFlsd-----~c~d~~l 72 (124)
T cd04760 1 GEELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDT--VLGE-TSDPLELFLVD-----ECEDMAL 72 (124)
T ss_pred CCEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCcc--cccc-cCCCcEEEeec-----ccCCcch
Confidence 56899999999998755 57899999999999999999999999999998 5564 68999999997 5999999
Q ss_pred ceeecceEEEecC--CCcC-----CCCCCCccCCCCcEEEEeeeeCcceEEE
Q 005739 116 EAIAGKCNVVCTS--KDAR-----NPQPSDEELQISDFIFCRTFDVGLRKVL 160 (680)
Q Consensus 116 e~I~GKC~VVsis--kD~r-----n~rPS~~ei~~aDFYf~R~YDv~t~Riv 160 (680)
+||.+||+|+.++ .+|+ ...-...+.+..+|||+++||+..+||+
T Consensus 73 ~~I~~Kv~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf~ 124 (124)
T cd04760 73 SSIHGKVNVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARFE 124 (124)
T ss_pred HHheeeeEEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhccC
Confidence 9999999999874 3443 1112223456779999999999999874
No 8
>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=99.90 E-value=4.3e-24 Score=197.30 Aligned_cols=116 Identities=21% Similarity=0.354 Sum_probs=95.2
Q ss_pred EEECCEEEEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCCCccccc
Q 005739 33 FTYDGVEYTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNI 112 (680)
Q Consensus 33 ft~dG~tYrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~Dd 112 (680)
|.+||++|++||||||++++ ..+|||+|.+||++.+|.++|+|+||+||+|+...+....+.+||||+|+ +.|+
T Consensus 1 ~~r~~~~i~vGD~V~v~~~~-~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~-----~~d~ 74 (130)
T cd04721 1 FCRNGVTISVHDFVYVLSEE-EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSP-----NLQV 74 (130)
T ss_pred CccCCEEEECCCEEEEeCCC-CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcC-----Cccc
Confidence 57899999999999999877 67899999999999999999999999999999765454338999999998 4899
Q ss_pred CccceeecceEEEecCCCcCCCCCCCcc-CCCCcEEEEeeeeCc
Q 005739 113 NPLEAIAGKCNVVCTSKDARNPQPSDEE-LQISDFIFCRTFDVG 155 (680)
Q Consensus 113 NPLe~I~GKC~VVsiskD~rn~rPS~~e-i~~aDFYf~R~YDv~ 155 (680)
||++||.|||+|++...+. ...+.... ....+|+|++.||-.
T Consensus 75 i~~~~I~gk~~Vls~~~y~-k~~~~~~~~~~~~~f~C~~~~d~~ 117 (130)
T cd04721 75 ISVECIDGLATVLTREHYE-KFQSVPKNSSELQAYFCYRQIDNN 117 (130)
T ss_pred cchHHeeeeeEECCHHHHh-hhhccccCccccccEEEEEEecCC
Confidence 9999999999999864333 22222111 235589999999875
No 9
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.90 E-value=1.1e-23 Score=183.89 Aligned_cols=116 Identities=22% Similarity=0.336 Sum_probs=95.2
Q ss_pred EEEeCceEEEeeCCC-CCCeEEEEEEEEeeCCCc-eEEEEEeecChhcccccCCCccCCCCceEEecCCCCcccccCccc
Q 005739 39 EYTLYDCVYLYKEGD-AEPHVGKLIKIWENADKA-KKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNINPLE 116 (680)
Q Consensus 39 tYrLGDCVyVkseg~-~ePYIGRIvemWE~~DGe-k~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~DdNPLe 116 (680)
+|++||||||.+++. .++|||+|.+||++.++. ++++++|||||+||..... ..+++||||+|.+ +|++|++
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~-~~~~~~Elf~s~~-----~~~i~~~ 74 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKA-ALFDKNEVFLSDE-----YDTVPLS 74 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhcccccc-ccCCCcceEEEcc-----CccCChH
Confidence 479999999999874 579999999999998888 8999999999999965333 3578999999984 7999999
Q ss_pred eeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEe
Q 005739 117 AIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 117 ~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD 161 (680)
+|.|||+|++.+... ..+|.........|||++.||+.+.+|.+
T Consensus 75 ~I~~kc~V~~~~~~~-~~~~~~~~~~~~~f~cr~~yd~~~~~f~~ 118 (120)
T smart00439 75 DIIGKCNVLSKSDYP-GLRPEGKIGEPDVFFCESLYDPEKGAFKK 118 (120)
T ss_pred HeeeEEEEEEcchhc-ccccccCCCCCCeEEEEEEEccccCcccC
Confidence 999999999876554 23333222246789999999999888854
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=99.89 E-value=1.6e-23 Score=182.92 Aligned_cols=114 Identities=31% Similarity=0.537 Sum_probs=93.4
Q ss_pred EEEEeCceEEEeeCC-CCCCeEEEEEEEEeeCCCc--eEEEEEeecChhcccccCCCccCCCCceEEecCCCCcccccCc
Q 005739 38 VEYTLYDCVYLYKEG-DAEPHVGKLIKIWENADKA--KKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVGLTNINP 114 (680)
Q Consensus 38 ~tYrLGDCVyVkseg-~~ePYIGRIvemWE~~DGe--k~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g~~DdNP 114 (680)
++|++||||||.+++ ..++|||+|.+||++.++. ++++|+|||||+|| .. .....+||||+|. +++++|
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~--~~-~~~~~~~Elf~s~-----~~~~~~ 72 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDT--SL-GKTFSPRELFLSD-----HCDDIP 72 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGS--TT-GGHSCTTEEEEEE-----EEEEEE
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECcccc--cc-cccCCCCEEEEEC-----cEeEEe
Confidence 589999999999987 4678999999999998887 99999999999999 22 2356679999997 499999
Q ss_pred cceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEe
Q 005739 115 LEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 115 Le~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD 161 (680)
+++|.|||.|++..... ...+.... ....|||++.||+...+|.+
T Consensus 73 ~~~I~gkc~V~~~~~~~-~~~~~~~~-~~~~F~cr~~yd~~~~~f~~ 117 (119)
T PF01426_consen 73 VESIRGKCNVLHLEDYE-QARPYGKE-EPDTFFCRYAYDPQKKRFKK 117 (119)
T ss_dssp GGGEEEEEEEEEHHHHT-TGCCHCHH-TTTEEEEEEEEETTTTEEEE
T ss_pred hhhEEeeeEEEECCccc-cccccccC-CCCEEEEEEEEeCCcCEEeC
Confidence 99999999999864332 22222112 46689999999999999875
No 11
>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=99.86 E-value=9.1e-22 Score=183.35 Aligned_cols=116 Identities=25% Similarity=0.433 Sum_probs=92.7
Q ss_pred EEECCEEEEeCceEEEeeCCCC-CCeEEEEEEEEeeCCCc------------eEEEEEeecChhcccccCCCccCCCCce
Q 005739 33 FTYDGVEYTLYDCVYLYKEGDA-EPHVGKLIKIWENADKA------------KKVKLLWFFRPSDISNFLGNVQTLENEL 99 (680)
Q Consensus 33 ft~dG~tYrLGDCVyVkseg~~-ePYIGRIvemWE~~DGe------------k~VkVqWFyRPEEI~~~lg~~~~~pNEL 99 (680)
+..+|..|++||||||.+++.+ |.|||||++||...++. .+|+|+|||||+||.. +...+.+||
T Consensus 5 ~~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~---~~~~d~rel 81 (135)
T cd04710 5 VLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISR---RVVADSRLL 81 (135)
T ss_pred EccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCC---cccCCceEE
Confidence 3568999999999999998764 56899999999965333 5899999999999854 224789999
Q ss_pred EEecCCCCcccccCccceeecceEEEecCCCcCCCCCCCcc--CCCCcEEEEeeeeCcceEEEe
Q 005739 100 ILACGEGVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEE--LQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 100 FLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~e--i~~aDFYf~R~YDv~t~RivD 161 (680)
|+|. +.|++|+++|.|||+|.+.... |+..+ .....|||.+.||+.+.||-|
T Consensus 82 f~S~-----h~d~~p~~si~gKC~V~~~~di-----~~l~~~~~~~~~Fyf~~lyD~~~~r~~~ 135 (135)
T cd04710 82 YASM-----HSDICPIGSVRGKCTVRHRDQI-----PDLEEYKKRPNHFYFDQLFDRYILRYYD 135 (135)
T ss_pred EEEe-----eEeeechHHEEeEEEEEEeccc-----chhhhhccCCCEEEEEeeeCcchhhccC
Confidence 9998 4899999999999999986422 22212 235689999999999998743
No 12
>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=99.86 E-value=1.2e-21 Score=187.94 Aligned_cols=116 Identities=20% Similarity=0.307 Sum_probs=91.6
Q ss_pred EEEEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEeecChhcccccC---------------------CCccCCC
Q 005739 38 VEYTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFL---------------------GNVQTLE 96 (680)
Q Consensus 38 ~tYrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~l---------------------g~~~~~p 96 (680)
..|++||||||.++...++|||||++||++.+|...|+|+|||||+||...+ .++.+..
T Consensus 2 ~~yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~~ 81 (164)
T cd04709 2 NMYRVGDYVYFESSPNNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLRH 81 (164)
T ss_pred cEEecCCEEEEECCCCCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccCc
Confidence 5799999999998744456799999999999999999999999999985421 1233578
Q ss_pred CceEEecCCCCcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEe
Q 005739 97 NELILACGEGVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 97 NELFLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD 161 (680)
+|||+|. +.|.+|+++|.|||.|+++.... .. ..-......|||...|||.+.++.-
T Consensus 82 rELF~S~-----~~d~~p~~~IrGKC~V~~~~d~~-~l--~~~~~~~d~Ff~~~~YDP~~k~l~~ 138 (164)
T cd04709 82 RELFLSR-----QVETLPATHIRGKCSVTLLNDTE-SA--RSYLAREDTFFYSLVYDPEQKTLLA 138 (164)
T ss_pred ceeEEec-----ccccccHHHeeeeEEEEEehhhh-hh--hhccCCCCEEEEEEEECCCCCeecc
Confidence 9999997 58999999999999999864332 21 0111245689999999999988753
No 13
>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=99.82 E-value=5.9e-20 Score=169.93 Aligned_cols=110 Identities=21% Similarity=0.262 Sum_probs=90.3
Q ss_pred CCEEEEeCceEEEeeCCCC-----------CCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecC
Q 005739 36 DGVEYTLYDCVYLYKEGDA-----------EPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACG 104 (680)
Q Consensus 36 dG~tYrLGDCVyVkseg~~-----------ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsg 104 (680)
.|..|++||||+|.+++.. +|||++|..||++.+|+++||++|||||+|+ .+++ .+.++|||||.
T Consensus 2 ~~~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eT--v~g~-~~~~~ElFLSd- 77 (130)
T cd04712 2 HGLTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDT--VLGN-YANERELFLTN- 77 (130)
T ss_pred CCCEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhc--cccc-cCCCceEEEec-
Confidence 5678999999999998754 7899999999999999999999999999998 5565 89999999997
Q ss_pred CCCcccccCccc----eeecceEEEecCCCcCCCCCCCccCCCCcEEEEe-eeeCcceEEEe
Q 005739 105 EGVGLTNINPLE----AIAGKCNVVCTSKDARNPQPSDEELQISDFIFCR-TFDVGLRKVLD 161 (680)
Q Consensus 105 eg~g~~DdNPLe----~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R-~YDv~t~RivD 161 (680)
++|++|++ +|.+||.|...+. |.+ -...+||||. .|++..+.|+.
T Consensus 78 ----~c~~~~~~~~~~~I~~k~~V~~~~~------~~~--~~~~~~F~r~syy~~e~~~F~~ 127 (130)
T cd04712 78 ----ECTCLELDLLSTEIKGVHKVDWSGT------PWG--KGLPEFFVRQSYYWPERGAFTS 127 (130)
T ss_pred ----cccccccccccceeEEEEEEEEecC------cCC--cCCCCEEEEEEEECccCCceEc
Confidence 59999999 9999999985432 221 1234566665 55558888865
No 14
>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=99.82 E-value=2.8e-20 Score=183.85 Aligned_cols=125 Identities=25% Similarity=0.367 Sum_probs=97.9
Q ss_pred EEECCEEEEeCceEEEeeC------------------CCCCCeEEEEEEEEeeCCC------ceEEEEEeecChhccccc
Q 005739 33 FTYDGVEYTLYDCVYLYKE------------------GDAEPHVGKLIKIWENADK------AKKVKLLWFFRPSDISNF 88 (680)
Q Consensus 33 ft~dG~tYrLGDCVyVkse------------------g~~ePYIGRIvemWE~~DG------ek~VkVqWFyRPEEI~~~ 88 (680)
|+++|++|++||+|||.++ +..+.+||||.+|++..++ ..+|+|+|||||+||..
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 5789999999999999998 4446689999999997655 67999999999999843
Q ss_pred CCCccCCCCceEEecCCCCcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEehhhhhh
Q 005739 89 LGNVQTLENELILACGEGVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLDKIDEKI 167 (680)
Q Consensus 89 lg~~~~~pNELFLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD~f~dkI 167 (680)
...+..+.+|||+|. +.++||+++|.|||+|+.. .|.-.... ......+|||...||+.++.|.+ .|-.+
T Consensus 80 ~~~y~sd~rely~Sd-----e~~~~~~~~I~GKC~V~~~-~d~~~~~~--~~~~~~~Ffc~~~Yd~~tg~f~~-lP~~~ 149 (202)
T cd04708 80 EKAYASDIREVYYSE-----DTLTVPVEAVEGKCEVRKK-SDLPDSDA--PVIFEHVFFCELLYDPAKGSLKQ-LPPNI 149 (202)
T ss_pred ccceecCceeEEEec-----cceeechhHcceEEEEEec-Ccchhhhc--cccCCCceEEEEEEcCCCCccCC-CCchh
Confidence 234456899999997 4899999999999999975 33311111 01235689999999999999876 45444
No 15
>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=99.81 E-value=1.3e-19 Score=175.52 Aligned_cols=120 Identities=21% Similarity=0.193 Sum_probs=95.4
Q ss_pred ECCEEEEeCceEEEeeCCCCCCeEEEEEEEEeeCC-CceEEEEEeecChhcccccCCCccCC--------CCceEEecCC
Q 005739 35 YDGVEYTLYDCVYLYKEGDAEPHVGKLIKIWENAD-KAKKVKLLWFFRPSDISNFLGNVQTL--------ENELILACGE 105 (680)
Q Consensus 35 ~dG~tYrLGDCVyVkseg~~ePYIGRIvemWE~~D-Gek~VkVqWFyRPEEI~~~lg~~~~~--------pNELFLSsge 105 (680)
-||.+|++||||+|++++..+||||+|.+|++... +...++|+|||||.|+........++ +||||||.|
T Consensus 48 ~d~~~~~vGD~Vlik~~~~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~- 126 (179)
T cd04720 48 SDGLELSVGDTILVKDDVANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAE- 126 (179)
T ss_pred cCCeEEeCCCEEEEeCCCCCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEecc-
Confidence 39999999999999998778899999999999765 56799999999999985422111233 799999984
Q ss_pred CCcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEe
Q 005739 106 GVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 106 g~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD 161 (680)
.|.+++.+|+|||+|++...+. ...+.+ ...+.+|||+++||+.++.|+.
T Consensus 127 ----~d~i~l~~Ii~k~~Vls~~ef~-~~~~~~-~~~~~~F~cR~~~d~~~~~F~~ 176 (179)
T cd04720 127 ----LSEIKLKDIIDKANVLSESEFN-DLSTDD-KNGERTFFCRYACEPDGEEFVW 176 (179)
T ss_pred ----cceEEhhheeeeEEEecHHHhh-hhcccc-cCCCceEEEEEEEeCCCCeEcc
Confidence 8999999999999999864433 223331 1246799999999999997764
No 16
>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=99.71 E-value=2.1e-17 Score=153.45 Aligned_cols=117 Identities=20% Similarity=0.317 Sum_probs=88.6
Q ss_pred EEEEeCceEEEeeCCCCCCeEEEEEEEEeeCCC---ceEEEEEeecChhcccc---cCCCccCCCCceEEecCCCCcccc
Q 005739 38 VEYTLYDCVYLYKEGDAEPHVGKLIKIWENADK---AKKVKLLWFFRPSDISN---FLGNVQTLENELILACGEGVGLTN 111 (680)
Q Consensus 38 ~tYrLGDCVyVkseg~~ePYIGRIvemWE~~DG---ek~VkVqWFyRPEEI~~---~lg~~~~~pNELFLSsgeg~g~~D 111 (680)
.+|++||||+|.+++..+||||+|.+||++.++ ...++|||||||+|+.. ...++.+.++|||++.+- ...|
T Consensus 2 ~~i~vGd~VlI~~~d~~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~~~~~~EvF~~~~~--~~~~ 79 (128)
T cd04719 2 LTIEVGDFVLIEGEDADGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGREPHSQEVFFYSRS--SCDN 79 (128)
T ss_pred eEEecCCEEEEECCCCCCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccCCCCCcEEEEecCc--cccC
Confidence 479999999999988678899999999998765 46899999999999853 122245788999999851 0116
Q ss_pred cCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceE
Q 005739 112 INPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRK 158 (680)
Q Consensus 112 dNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~R 158 (680)
+-+++||.|||.|+...++..-+. .....+..||++++++...-+
T Consensus 80 ~i~~etI~gkc~V~~~~~y~~l~~--~~~~~~~~~F~r~~~~~k~~~ 124 (128)
T cd04719 80 DIDAETIIGKVRVEPVEPKTDLPE--TKKKTGGPLFVKRYWDTKTFR 124 (128)
T ss_pred cEeHHHcccEEEEEEcCCccchhh--hccccCceEEEEEEecccccc
Confidence 889999999999998765542221 111246789999999876543
No 17
>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=99.63 E-value=4.1e-17 Score=154.99 Aligned_cols=93 Identities=22% Similarity=0.374 Sum_probs=75.6
Q ss_pred CCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCC-ccCCCCceEEecCCCCcccccCccceeecceEEEecCCCcC
Q 005739 54 AEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGN-VQTLENELILACGEGVGLTNINPLEAIAGKCNVVCTSKDAR 132 (680)
Q Consensus 54 ~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~-~~~~pNELFLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~r 132 (680)
+.+|||||++||++. |+.+|+++|||||+|+.. ++ ..++.+|||||+ +.|+||+++|+|||.|++. ++++
T Consensus 51 ~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~--gr~~~~~~kEvFlS~-----~~d~~~~~~I~gkC~V~~~-keY~ 121 (148)
T cd04718 51 GDLWLARIEKLWEEN-GTYWYAARWYTLPEETHM--GRQPHNLRRELYLTN-----DFADIEMECILRHCSVKCP-KEFR 121 (148)
T ss_pred CchHHHHHHHHHhcc-CceEEEEEEEeCchhccC--ccccccccceeeecc-----ccccccHHHHhcccEEcCH-HHcc
Confidence 479999999999976 999999999999999954 43 358899999998 5999999999999999976 4443
Q ss_pred CCCCCCccCCCCcEEEEeeeeCcceEE
Q 005739 133 NPQPSDEELQISDFIFCRTFDVGLRKV 159 (680)
Q Consensus 133 n~rPS~~ei~~aDFYf~R~YDv~t~Ri 159 (680)
...+. ...+|||.-.||...++|
T Consensus 122 k~e~~----g~Dvy~Ce~~Yd~~~~~F 144 (148)
T cd04718 122 DASND----GDDVFLCEYEYDVHWQSF 144 (148)
T ss_pred cccCC----CCceEEEEEEEhhhcCce
Confidence 22222 234677778999998876
No 18
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.60 E-value=9.8e-16 Score=165.98 Aligned_cols=135 Identities=26% Similarity=0.414 Sum_probs=108.8
Q ss_pred cccCCCCCCCcceeEEEEEECCEEEEe-CceEEEeeCCC-CCCeEEEEEEEEeeCC-CceEEEEEeecChhcccccCCCc
Q 005739 16 KKRGIGGKKKDVQFYQSFTYDGVEYTL-YDCVYLYKEGD-AEPHVGKLIKIWENAD-KAKKVKLLWFFRPSDISNFLGNV 92 (680)
Q Consensus 16 kkrGvgGKkkd~~fYeSft~dG~tYrL-GDCVyVkseg~-~ePYIGRIvemWE~~D-Gek~VkVqWFyRPEEI~~~lg~~ 92 (680)
...|++|+++ .||.++.+.|-.|.+ ||+|++.+++. .+||||+|..||.... +.+++.|+|||||+|+..-....
T Consensus 28 ~~qGv~~~k~--~h~~t~~~~~g~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~ 105 (464)
T KOG1886|consen 28 KEQGVGGVKS--LHFETFIYRGGRYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGK 105 (464)
T ss_pred hhcccccccc--ccccceeeccCcccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCC
Confidence 4578877665 799999999998888 99999999985 6899999999999865 58999999999999975422221
Q ss_pred --cCCCCceEEecCCCCcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEEEe
Q 005739 93 --QTLENELILACGEGVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKVLD 161 (680)
Q Consensus 93 --~~~pNELFLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~RivD 161 (680)
.-+++|||||+| +|.++.++|.++|.|.+++.+.+.+ +. ....+|+|++.||..+.++.-
T Consensus 106 ~~a~~~relF~SfH-----~De~~A~ti~~rC~V~fvp~~kqlp--~~--~~~~~f~~r~vYd~~~~~~~~ 167 (464)
T KOG1886|consen 106 WGAKQPRELFLSFH-----EDEAFAETILHRCKVHFVPAYKQLP--NR--VGHESFICRRVYDAVTSKLRK 167 (464)
T ss_pred cccCCCcccccccc-----ccchhhhhhcccceeeecccccccc--cc--CCCCCcccccccccccccccC
Confidence 135679999985 8999999999999999887665322 21 235699999999999988754
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=99.43 E-value=1.4e-13 Score=129.66 Aligned_cols=100 Identities=18% Similarity=0.271 Sum_probs=74.2
Q ss_pred CCCeEEEEEEEEeeCCC-------ceEEEEEeecChhcccccCCC-ccCCCCceEEecCCCCcccccCccceeecceEEE
Q 005739 54 AEPHVGKLIKIWENADK-------AKKVKLLWFFRPSDISNFLGN-VQTLENELILACGEGVGLTNINPLEAIAGKCNVV 125 (680)
Q Consensus 54 ~ePYIGRIvemWE~~DG-------ek~VkVqWFyRPEEI~~~lg~-~~~~pNELFLSsgeg~g~~DdNPLe~I~GKC~VV 125 (680)
.|.|||||++|.-..++ .-+|+|.|||||+||+.-... +-.+-+|||+|.| .++.|+++|.|||+|.
T Consensus 25 ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~ayhsDirevy~Sd~-----~~~~~~~~I~GKC~V~ 99 (137)
T cd04711 25 EPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDE-----EATVDFSAVQGRCTVE 99 (137)
T ss_pred CCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccccccceeeEEeecc-----eeecChhhccceEEEE
Confidence 46689999999986543 247999999999999762211 2245699999984 8999999999999999
Q ss_pred ecCCCcCCCCCCCcc---CCCCcEEEEeeeeCcceEEEeh
Q 005739 126 CTSKDARNPQPSDEE---LQISDFIFCRTFDVGLRKVLDK 162 (680)
Q Consensus 126 siskD~rn~rPS~~e---i~~aDFYf~R~YDv~t~RivD~ 162 (680)
+.. +.-. +-.+ -...+|||...||..|+.|+|+
T Consensus 100 ~~~-di~~---s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d~ 135 (137)
T cd04711 100 YGE-DLPE---SVQEYSGGGPDRFYFLEAYNAKTKSFEDP 135 (137)
T ss_pred ecc-ccch---hHHHHhcCCCcceEEhhhhccccCcccCC
Confidence 531 1100 0111 1245899999999999999985
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.13 E-value=4.3e-11 Score=134.27 Aligned_cols=123 Identities=20% Similarity=0.360 Sum_probs=101.3
Q ss_pred eEEE-EEECCEEEEeCceEEEeeCCC-CCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCC
Q 005739 29 FYQS-FTYDGVEYTLYDCVYLYKEGD-AEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEG 106 (680)
Q Consensus 29 fYeS-ft~dG~tYrLGDCVyVkseg~-~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg 106 (680)
++.. +.+||..|.+||.||+..... ..|.|++|..+|++.+|+++..++|||||+++.+..+ +.|+++|+|.+.
T Consensus 179 ~~~~~~~i~~~~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~-r~F~k~Evfkt~--- 254 (629)
T KOG1827|consen 179 HELGPVEIDGTKYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRAD-RKFYKQEVFKTS--- 254 (629)
T ss_pred ccCCCccccCcccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccc-cchhcccceecc---
Confidence 3344 789999999999999998776 6899999999999999999999999999999866544 589999999986
Q ss_pred CcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeCcceEE
Q 005739 107 VGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDVGLRKV 159 (680)
Q Consensus 107 ~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv~t~Ri 159 (680)
...+.+++-|.|+|.|+.+..+.+ ..|+. ......|.|...|++....|
T Consensus 255 --~~~~~~~q~l~g~c~v~~~~~yi~-~~p~~-ls~~dv~lcesRyn~~~K~f 303 (629)
T KOG1827|consen 255 --LYRDDLVQRLLGKCYVMKPTEYIS-GDPEN-LSEEDVFLCESRYNEQLKKF 303 (629)
T ss_pred --cccccHHHHhhcceEEeehhHhhh-cCccc-ccccceeeEEeeeccchhhh
Confidence 799999999999999998766653 33442 22344577777799887655
No 21
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=98.19 E-value=2.6e-06 Score=66.83 Aligned_cols=69 Identities=28% Similarity=0.375 Sum_probs=62.5
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
|+|.||+|.+|..++.+++.+ |-.-+.++|+.. .+..+.|-|||.|.+++.|+.|+..|+.--+ +||+|
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~-~g~i~~~~~~~~--~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~---~~~~i 69 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQ-FGKIESIKVMRN--SSGKSKGYAFVEFESEEDAEKALEELNGKKI---NGRKI 69 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHT-TSTEEEEEEEEE--TTSSEEEEEEEEESSHHHHHHHHHHHTTEEE---TTEEE
T ss_pred cEEcCCCCcCCHHHHHHHHHH-hhhccccccccc--ccccccceEEEEEcCHHHHHHHHHHcCCCEE---CccCc
Confidence 689999999999999999999 888899999987 6777889999999999999999999999655 78775
No 22
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=97.48 E-value=0.00036 Score=65.86 Aligned_cols=97 Identities=19% Similarity=0.178 Sum_probs=71.4
Q ss_pred ChHHHHHhhhccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccc
Q 005739 503 PWEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 582 (680)
Q Consensus 503 Pwee~~~~a~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~eg 582 (680)
|--...-.+-.-++-|++.||++..|..+|++++.+ |-.-...+++. ...+.-+-|-|||.|.+.++|+.||..|+..
T Consensus 22 ~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~-~G~I~~v~i~~-d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~ 99 (144)
T PLN03134 22 PVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAH-FGDVVDAKVIV-DRETGRSRGFGFVNFNDEGAATAAISEMDGK 99 (144)
T ss_pred ccccccccccCCCCEEEEeCCCCCCCHHHHHHHHhc-CCCeEEEEEEe-cCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence 333333445567888999999999999999888854 44444555432 2334446789999999999999999999855
Q ss_pred eeeecCCceeeeecCCCccCCC
Q 005739 583 CLLLSNGRPLLGSIGTPCFTGK 604 (680)
Q Consensus 583 cl~ls~gRpl~~s~~~~~~p~k 604 (680)
-| +||+|.-+.+.+..+..
T Consensus 100 ~i---~Gr~l~V~~a~~~~~~~ 118 (144)
T PLN03134 100 EL---NGRHIRVNPANDRPSAP 118 (144)
T ss_pred EE---CCEEEEEEeCCcCCCCC
Confidence 33 89999999887665443
No 23
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=97.27 E-value=2.4e-05 Score=86.31 Aligned_cols=113 Identities=22% Similarity=0.363 Sum_probs=82.6
Q ss_pred EEEeCceEEEeeCCCCCCe-EEEEEEEEeeCCCceEEEEEeecChhcccccC-------CC-------------------
Q 005739 39 EYTLYDCVYLYKEGDAEPH-VGKLIKIWENADKAKKVKLLWFFRPSDISNFL-------GN------------------- 91 (680)
Q Consensus 39 tYrLGDCVyVkseg~~ePY-IGRIvemWE~~DGek~VkVqWFyRPEEI~~~l-------g~------------------- 91 (680)
.|++||.|||..+... || |-||+++-.+.+|+.-.+|.-|||-.||...| .+
T Consensus 5 ~y~vgd~vYf~~sss~-PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e~ 83 (693)
T KOG3554|consen 5 MYRVGDYVYFENSSSN-PYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAEI 83 (693)
T ss_pred cceecceEEEecCCCC-hHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhhh
Confidence 7999999999887655 66 99999999999999999999999988864210 00
Q ss_pred -----------------ccCCCCceEEecCCCCcccccCccceeecceEEEecCCCcCCCCCCCccCCCCcEEEEeeeeC
Q 005739 92 -----------------VQTLENELILACGEGVGLTNINPLEAIAGKCNVVCTSKDARNPQPSDEELQISDFIFCRTFDV 154 (680)
Q Consensus 92 -----------------~~~~pNELFLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~~ei~~aDFYf~R~YDv 154 (680)
+.--..|||||- ..+..|...|.|||.|+-..+-.. . ..-...+.+|||.-.|||
T Consensus 84 EEe~e~p~~vdlt~~qrhqLrhrElFlsR-----Q~EsLPAthIRGKCsV~LLnete~-~--~~YL~~eDtFfySLVyDP 155 (693)
T KOG3554|consen 84 EEESECPAPVDLTEKQRHQLRHRELFLSR-----QSESLPATHIRGKCSVTLLNETES-L--QSYLEKEDTFFYSLVYDP 155 (693)
T ss_pred hhhccCCCcCCCCHHHHHHHHHHHHHHhh-----hhccCchhhhccceeEEEecChHH-H--HhhccccceeEEEeeecc
Confidence 000137899986 588999999999999986522110 0 001123457888889999
Q ss_pred cceEEE
Q 005739 155 GLRKVL 160 (680)
Q Consensus 155 ~t~Riv 160 (680)
...+++
T Consensus 156 ~~kTLL 161 (693)
T KOG3554|consen 156 NQKTLL 161 (693)
T ss_pred chhhhh
Confidence 987764
No 24
>smart00362 RRM_2 RNA recognition motif.
Probab=97.20 E-value=0.0016 Score=49.56 Aligned_cols=69 Identities=30% Similarity=0.381 Sum_probs=52.7
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceee
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 593 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~ 593 (680)
|+|.||.+..+..+|.+++.. +-.-...+|+... ..+.|.|||-|.+.++|+.|+..|+.. .+ +|++|.
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~-~g~v~~~~~~~~~---~~~~~~~~v~f~~~~~a~~a~~~~~~~--~~-~~~~i~ 70 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSK-FGPIESVKIPKDT---GKSKGFAFVEFESEEDAEKAIEALNGT--KL-GGRPLR 70 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHh-cCCEEEEEEecCC---CCCCceEEEEeCCHHHHHHHHHHhCCc--EE-CCEEEe
Confidence 679999999999999988753 3333445555444 456799999999999999999999862 22 677764
No 25
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=97.04 E-value=0.0032 Score=48.06 Aligned_cols=72 Identities=25% Similarity=0.271 Sum_probs=55.4
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeee
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 595 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s 595 (680)
|+|.||++..+..+|.+++... -.-+..+|...... ...|-|||-|+|.++|..|+.+++..= -+|+++..+
T Consensus 2 i~i~~l~~~~~~~~i~~~~~~~-g~i~~~~~~~~~~~--~~~~~~~v~f~s~~~a~~a~~~~~~~~---~~~~~~~v~ 73 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFSKF-GKVESVRIVRDKDT--KSKGFAFVEFEDEEDAEKALEALNGKE---LGGRPLRVE 73 (74)
T ss_pred EEEeCCCCccCHHHHHHHHHhc-CCEEEEEEeeCCCC--CcceEEEEEECCHHHHHHHHHHhCCCe---ECCeEEEEe
Confidence 6799999999999999888763 44556666644333 448899999999999999999988753 267776543
No 26
>smart00360 RRM RNA recognition motif.
Probab=96.99 E-value=0.0026 Score=48.01 Aligned_cols=69 Identities=30% Similarity=0.406 Sum_probs=50.2
Q ss_pred EecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceee
Q 005739 520 LENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 593 (680)
Q Consensus 520 lqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~ 593 (680)
|.||++.+|..+|.+++.. |-.-...+++... .+..+.|.|||-|.|.+.|..|+..|+ ++.+ +|++|.
T Consensus 1 i~~l~~~~~~~~l~~~f~~-~g~v~~~~i~~~~-~~~~~~~~a~v~f~~~~~a~~a~~~~~-~~~~--~~~~~~ 69 (71)
T smart00360 1 VGNLPPDVTEEELRELFSK-FGKIESVRLVRDK-DTGKSKGFAFVEFESEEDAEKALEALN-GKEL--DGRPLK 69 (71)
T ss_pred CCCCCcccCHHHHHHHHHh-hCCEeEEEEEeCC-CCCCCCceEEEEeCCHHHHHHHHHHcC-CCee--CCcEEE
Confidence 4689999999999887753 3333344554432 245567899999999999999999998 5553 677764
No 27
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=96.66 E-value=0.0051 Score=68.23 Aligned_cols=82 Identities=27% Similarity=0.333 Sum_probs=66.3
Q ss_pred hccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCce
Q 005739 512 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 591 (680)
Q Consensus 512 ~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRp 591 (680)
..+|+-|++.||+++.|..++.+++- .|-+-+.++++.. -....-|-|||.|.|.+.|+.||..|+..-| +|||
T Consensus 282 ~~~~~~l~V~nl~~~~~~~~L~~~F~-~~G~i~~~~i~~d--~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~---~gk~ 355 (562)
T TIGR01628 282 KAQGVNLYVKNLDDTVTDEKLRELFS-ECGEITSAKVMLD--EKGVSRGFGFVCFSNPEEANRAVTEMHGRML---GGKP 355 (562)
T ss_pred ccCCCEEEEeCCCCccCHHHHHHHHH-hcCCeEEEEEEEC--CCCCcCCeEEEEeCCHHHHHHHHHHhcCCee---CCce
Confidence 44677899999999999999998875 4677777887765 2344568999999999999999999997433 8999
Q ss_pred eeeecCCC
Q 005739 592 LLGSIGTP 599 (680)
Q Consensus 592 l~~s~~~~ 599 (680)
|.-.++..
T Consensus 356 l~V~~a~~ 363 (562)
T TIGR01628 356 LYVALAQR 363 (562)
T ss_pred eEEEeccC
Confidence 98776653
No 28
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=96.52 E-value=0.013 Score=62.82 Aligned_cols=109 Identities=15% Similarity=0.177 Sum_probs=78.6
Q ss_pred ccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 513 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 513 e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
..+|-|++-||.+..|..+|.+|+.. |-.-..++++... .+--+-|-|||-|.+.++|+.||..|+.--| .||||
T Consensus 105 ~~~~~LfVgnLp~~~te~~L~~lF~~-~G~V~~v~i~~d~-~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l---~gr~i 179 (346)
T TIGR01659 105 NSGTNLIVNYLPQDMTDRELYALFRT-IGPINTCRIMRDY-KTGYSFGYAFVDFGSEADSQRAIKNLNGITV---RNKRL 179 (346)
T ss_pred CCCcEEEEeCCCCCCCHHHHHHHHHh-cCCEEEEEEEecC-CCCccCcEEEEEEccHHHHHHHHHHcCCCcc---CCcee
Confidence 36789999999999999999999875 4445566765422 1223458899999999999999999987544 79999
Q ss_pred eeecCCCccC--CCCCceeeeeeehhHHHHHHHHHHhhhc
Q 005739 593 LGSIGTPCFT--GKQSKFVGHLALDKLKFQMQREMREAVS 630 (680)
Q Consensus 593 ~~s~~~~~~p--~k~~~f~GH~~i~k~~~~~qremr~avs 630 (680)
.-+++.|... .....|+|.|.-+= .++++++..+
T Consensus 180 ~V~~a~p~~~~~~~~~lfV~nLp~~v----tee~L~~~F~ 215 (346)
T TIGR01659 180 KVSYARPGGESIKDTNLYVTNLPRTI----TDDQLDTIFG 215 (346)
T ss_pred eeecccccccccccceeEEeCCCCcc----cHHHHHHHHH
Confidence 9988876432 23346888775542 3455665543
No 29
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=96.48 E-value=0.008 Score=64.52 Aligned_cols=81 Identities=17% Similarity=0.243 Sum_probs=57.4
Q ss_pred cEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeee
Q 005739 516 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 595 (680)
Q Consensus 516 ~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s 595 (680)
+-|+|.||+++.|..++.+++. -|-+-..++++... .+--.-|-|||-|.+++.|+.||..|+.-.| .-.++||...
T Consensus 194 ~~lfV~nLp~~vtee~L~~~F~-~fG~V~~v~i~~d~-~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~-~g~~~~l~V~ 270 (346)
T TIGR01659 194 TNLYVTNLPRTITDDQLDTIFG-KYGQIVQKNILRDK-LTGTPRGVAFVRFNKREEAQEAISALNNVIP-EGGSQPLTVR 270 (346)
T ss_pred ceeEEeCCCCcccHHHHHHHHH-hcCCEEEEEEeecC-CCCccceEEEEEECCHHHHHHHHHHhCCCcc-CCCceeEEEE
Confidence 4589999999999999888873 33444455655322 1222248899999999999999999995433 3345788766
Q ss_pred cCCC
Q 005739 596 IGTP 599 (680)
Q Consensus 596 ~~~~ 599 (680)
++..
T Consensus 271 ~a~~ 274 (346)
T TIGR01659 271 LAEE 274 (346)
T ss_pred ECCc
Confidence 5543
No 30
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=96.16 E-value=0.02 Score=65.59 Aligned_cols=108 Identities=19% Similarity=0.205 Sum_probs=83.4
Q ss_pred hccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCce
Q 005739 512 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 591 (680)
Q Consensus 512 ~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRp 591 (680)
-+.|+-|++-||+++.|..++.+++-. |-.-.++|++-. .+--+-|=|||-|.+.|+|+.||..|+...| .+||.
T Consensus 55 p~~~~~lFVgnLp~~~tEd~L~~~F~~-~G~I~~vrl~~D--~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i--~~Gr~ 129 (578)
T TIGR01648 55 PGRGCEVFVGKIPRDLYEDELVPLFEK-AGPIYELRLMMD--FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEI--RPGRL 129 (578)
T ss_pred CCCCCEEEeCCCCCCCCHHHHHHHHHh-hCCEEEEEEEEC--CCCCccceEEEEeCCHHHHHHHHHHcCCCee--cCCcc
Confidence 457899999999999999999998865 556666776655 5667788999999999999999999998765 47887
Q ss_pred eeeecCCCccCCCCCceeeeeeehhHHHHHHHHHHhh
Q 005739 592 LLGSIGTPCFTGKQSKFVGHLALDKLKFQMQREMREA 628 (680)
Q Consensus 592 l~~s~~~~~~p~k~~~f~GH~~i~k~~~~~qremr~a 628 (680)
|...... ..+..|+|-|.-+..+-+..+|+.+.
T Consensus 130 l~V~~S~----~~~rLFVgNLP~~~TeeeL~eeFskv 162 (578)
T TIGR01648 130 LGVCISV----DNCRLFVGGIPKNKKREEILEEFSKV 162 (578)
T ss_pred ccccccc----cCceeEeecCCcchhhHHHHHHhhcc
Confidence 6443322 35778998887776665666666653
No 31
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=95.89 E-value=0.021 Score=65.44 Aligned_cols=75 Identities=23% Similarity=0.260 Sum_probs=60.1
Q ss_pred cccEEEEecCCCCCchhHHHHHHHHHH--hccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCce
Q 005739 514 HGTLVVLENLDPSYTSTVVEDLVWHAF--KENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 591 (680)
Q Consensus 514 ~G~lvllqNLdps~ts~eVedlv~~a~--ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRp 591 (680)
..+.|+|.||+.+.|..+|++++-+ | -+-+..++| .|-|||-|.+++.|+.||..|+..-| +||+
T Consensus 232 ~~k~LfVgNL~~~~tee~L~~~F~~-f~~G~I~rV~~~---------rgfAFVeF~s~e~A~kAi~~lnG~~i---~Gr~ 298 (578)
T TIGR01648 232 KVKILYVRNLMTTTTEEIIEKSFSE-FKPGKVERVKKI---------RDYAFVHFEDREDAVKAMDELNGKEL---EGSE 298 (578)
T ss_pred cccEEEEeCCCCCCCHHHHHHHHHh-cCCCceEEEEee---------cCeEEEEeCCHHHHHHHHHHhCCCEE---CCEE
Confidence 3478999999999998888877753 4 333344443 46899999999999999999997754 9999
Q ss_pred eeeecCCCcc
Q 005739 592 LLGSIGTPCF 601 (680)
Q Consensus 592 l~~s~~~~~~ 601 (680)
|..+++.|..
T Consensus 299 I~V~~Akp~~ 308 (578)
T TIGR01648 299 IEVTLAKPVD 308 (578)
T ss_pred EEEEEccCCC
Confidence 9999998854
No 32
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.89 E-value=0.027 Score=58.09 Aligned_cols=83 Identities=24% Similarity=0.234 Sum_probs=64.4
Q ss_pred ccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 513 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 513 e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
..|..|++-||.+..|..++.+++- .|-.--.++++.. ..+...-|-|||-|.+.+.|..||..|+.-.| +||+|
T Consensus 267 ~~~~~lfV~NL~~~~~e~~L~~~F~-~fG~v~~v~i~~d-~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~---~gr~i 341 (352)
T TIGR01661 267 GAGYCIFVYNLSPDTDETVLWQLFG-PFGAVQNVKIIRD-LTTNQCKGYGFVSMTNYDEAAMAILSLNGYTL---GNRVL 341 (352)
T ss_pred CCCcEEEEeCCCCCCCHHHHHHHHH-hCCCeEEEEEeEc-CCCCCccceEEEEECCHHHHHHHHHHhCCCEE---CCeEE
Confidence 5677899999999988888777764 3555556776643 22344568899999999999999999998655 89999
Q ss_pred eeecCCCc
Q 005739 593 LGSIGTPC 600 (680)
Q Consensus 593 ~~s~~~~~ 600 (680)
--++.+..
T Consensus 342 ~V~~~~~~ 349 (352)
T TIGR01661 342 QVSFKTNK 349 (352)
T ss_pred EEEEccCC
Confidence 88887653
No 33
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=95.72 E-value=0.031 Score=58.09 Aligned_cols=95 Identities=26% Similarity=0.275 Sum_probs=70.8
Q ss_pred hccc-cEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCc
Q 005739 512 HEHG-TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 590 (680)
Q Consensus 512 ~e~G-~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gR 590 (680)
++.| +-|++.|||..++..+|++|+-+=- --.+.+=|---+.+-.|.|-|+|.+++-|+.||.+++- +.| +|+
T Consensus 79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~---~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~g--v~l-dG~ 152 (243)
T KOG0533|consen 79 NETRSTKVNVSNLPYGVIDADLKELFAEFG---ELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG--VAL-DGR 152 (243)
T ss_pred cCCCcceeeeecCCcCcchHHHHHHHHHhc---cceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC--ccc-CCc
Confidence 4556 8899999999999999999976432 22344445555666779999999999999999999998 444 888
Q ss_pred ee---------------ee---------ecCCCccCCCCCceeeee
Q 005739 591 PL---------------LG---------SIGTPCFTGKQSKFVGHL 612 (680)
Q Consensus 591 pl---------------~~---------s~~~~~~p~k~~~f~GH~ 612 (680)
|+ ++ +...|.++++...+.||-
T Consensus 153 ~mk~~~i~~~~~~~r~~~~~~~~~r~~~~~r~~~~~~~~~~~~~~~ 198 (243)
T KOG0533|consen 153 PMKIEIISSPSQSKRLPVGATKPLRAPNSNRTPARVSRGDKASGAS 198 (243)
T ss_pred eeeeEEecCccccccccccccccccccccccccccccCCCCccCcc
Confidence 72 11 444566667777777776
No 34
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=95.64 E-value=0.037 Score=60.16 Aligned_cols=81 Identities=16% Similarity=0.146 Sum_probs=59.9
Q ss_pred hhhccccEEEEecCCCCCchhHHHHHHHHHHhcccccee-----ccCCCCCCCCCceeEEEEeehhHHHHHHHhhcccee
Q 005739 510 VAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKM-----IPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCL 584 (680)
Q Consensus 510 ~a~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~Akm-----I~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl 584 (680)
.|..+.+-|++-||++..|..++.+++.+.|....-..+ |... .....-|.|||-|.|.|.|..|| .|+.- +
T Consensus 170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~-~~~~~kg~afVeF~~~e~A~~Al-~l~g~-~ 246 (509)
T TIGR01642 170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSV-NINKEKNFAFLEFRTVEEATFAM-ALDSI-I 246 (509)
T ss_pred cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEE-EECCCCCEEEEEeCCHHHHhhhh-cCCCe-E
Confidence 566677889999999999999999999988765543221 1111 12345689999999999999999 58753 2
Q ss_pred eecCCceeeee
Q 005739 585 LLSNGRPLLGS 595 (680)
Q Consensus 585 ~ls~gRpl~~s 595 (680)
-+|+||.-.
T Consensus 247 --~~g~~l~v~ 255 (509)
T TIGR01642 247 --YSNVFLKIR 255 (509)
T ss_pred --eeCceeEec
Confidence 267887543
No 35
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.48 E-value=0.069 Score=55.09 Aligned_cols=96 Identities=21% Similarity=0.219 Sum_probs=72.2
Q ss_pred ccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeee
Q 005739 515 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 594 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~ 594 (680)
-+-|++-||.+..|-.|+++++-. |-.-..++++.. ..+-.+-|=|||-|.+.+.|+.||..|+...| .||+|.-
T Consensus 3 ~~~l~V~nLp~~~~e~~l~~~F~~-~G~i~~v~i~~d-~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l---~g~~i~v 77 (352)
T TIGR01661 3 KTNLIVNYLPQTMTQEEIRSLFTS-IGEIESCKLVRD-KVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL---QNKTIKV 77 (352)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHHc-cCCEEEEEEEEc-CCCCccceEEEEEECcHHHHHHHHhhcccEEE---CCeeEEE
Confidence 356899999999999999998876 555566666532 11233557899999999999999999998655 7999988
Q ss_pred ecCCCccC--CCCCceeeeeeeh
Q 005739 595 SIGTPCFT--GKQSKFVGHLALD 615 (680)
Q Consensus 595 s~~~~~~p--~k~~~f~GH~~i~ 615 (680)
.++.|... .....|+|++.-+
T Consensus 78 ~~a~~~~~~~~~~~l~v~~l~~~ 100 (352)
T TIGR01661 78 SYARPSSDSIKGANLYVSGLPKT 100 (352)
T ss_pred EeecccccccccceEEECCcccc
Confidence 88877653 2345677766444
No 36
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=95.45 E-value=0.039 Score=59.28 Aligned_cols=79 Identities=18% Similarity=0.155 Sum_probs=60.2
Q ss_pred ccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeee
Q 005739 515 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 594 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~ 594 (680)
.+-|+|.||.+..|..+|.+++- .|-.-...+++ +....-...|-|||-|.+.+.|..|+..|+...| +||||.-
T Consensus 186 ~~~l~v~nl~~~~te~~l~~~f~-~~G~i~~v~~~-~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i---~g~~i~v 260 (457)
T TIGR01622 186 FLKLYVGNLHFNITEQELRQIFE-PFGDIEDVQLH-RDPETGRSKGFGFIQFHDAEEAKEALEVMNGFEL---AGRPIKV 260 (457)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHH-hcCCeEEEEEE-EcCCCCccceEEEEEECCHHHHHHHHHhcCCcEE---CCEEEEE
Confidence 46789999999999999988774 34443444444 2223335568999999999999999999997333 8999999
Q ss_pred ecCC
Q 005739 595 SIGT 598 (680)
Q Consensus 595 s~~~ 598 (680)
+++.
T Consensus 261 ~~a~ 264 (457)
T TIGR01622 261 GYAQ 264 (457)
T ss_pred EEcc
Confidence 9875
No 37
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=95.13 E-value=0.09 Score=57.22 Aligned_cols=81 Identities=14% Similarity=0.149 Sum_probs=62.6
Q ss_pred ccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 513 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 513 e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
+.++-|+|.||.+..|..+|.+|+-. |-.-..++++.. ..+-.+-|-|||-|.+-++|+.||..|+.--| +|++|
T Consensus 293 ~~~~~l~v~nlp~~~~~~~l~~~f~~-~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~---~~~~l 367 (509)
T TIGR01642 293 DSKDRIYIGNLPLYLGEDQIKELLES-FGDLKAFNLIKD-IATGLSKGYAFCEYKDPSVTDVAIAALNGKDT---GDNKL 367 (509)
T ss_pred CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEEEec-CCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE---CCeEE
Confidence 45678999999999999999988854 544444555432 23445678999999999999999999987655 89998
Q ss_pred eeecCC
Q 005739 593 LGSIGT 598 (680)
Q Consensus 593 ~~s~~~ 598 (680)
.-.++.
T Consensus 368 ~v~~a~ 373 (509)
T TIGR01642 368 HVQRAC 373 (509)
T ss_pred EEEECc
Confidence 877664
No 38
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=95.12 E-value=0.054 Score=59.86 Aligned_cols=74 Identities=20% Similarity=0.227 Sum_probs=59.9
Q ss_pred cEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeee
Q 005739 516 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 595 (680)
Q Consensus 516 ~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s 595 (680)
++|++-||+++.|..|+.+++.. |-.-..++|+. .-|+|||=|.+.|.|+.||..|+..-+.+ +||||.-.
T Consensus 3 ~vv~V~nLp~~~te~~L~~~f~~-fG~V~~v~i~~-------~k~~afVef~~~e~A~~Ai~~~~~~~~~l-~g~~l~v~ 73 (481)
T TIGR01649 3 PVVHVRNLPQDVVEADLVEALIP-FGPVSYVMMLP-------GKRQALVEFEDEESAKACVNFATSVPIYI-RGQPAFFN 73 (481)
T ss_pred cEEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEEC-------CCCEEEEEeCchHHHHHHHHHhhcCCceE-cCeEEEEE
Confidence 68999999999999999998864 66666777874 35899999999999999999875333333 89999876
Q ss_pred cCC
Q 005739 596 IGT 598 (680)
Q Consensus 596 ~~~ 598 (680)
++.
T Consensus 74 ~s~ 76 (481)
T TIGR01649 74 YST 76 (481)
T ss_pred ecC
Confidence 654
No 39
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=95.06 E-value=0.03 Score=44.86 Aligned_cols=66 Identities=29% Similarity=0.385 Sum_probs=44.8
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccc---cceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENC---SAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c---~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
|+|.||.|+.|..++.++ |..-+ ..+|+.... --..|.|||=|.|.+.|..|+..++ |.. -+||.|
T Consensus 1 v~i~nlp~~~~~~~l~~~----f~~~g~v~~v~~~~~~~--~~~~~~a~v~f~~~~~a~~al~~~~-~~~--~~g~~l 69 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNF----FSRFGPVEKVRLIKNKD--GQSRGFAFVEFSSEEDAKRALELLN-GKE--IDGRKL 69 (70)
T ss_dssp EEEESSTTT--HHHHHHH----CTTSSBEEEEEEEESTT--SSEEEEEEEEESSHHHHHHHHHHHT-TEE--ETTEEE
T ss_pred CEEeCCCCCCCHHHHHHH----HHhcCCcceEEEEeeec--cccCCEEEEEeCCHHHHHHHHHHCC-CcE--ECCEEc
Confidence 689999999887666655 44433 234443322 2346899999999999999999987 433 277775
No 40
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=94.80 E-value=0.08 Score=58.58 Aligned_cols=77 Identities=16% Similarity=0.179 Sum_probs=61.5
Q ss_pred hccccEEEEecCCC-CCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCc
Q 005739 512 HEHGTLVVLENLDP-SYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 590 (680)
Q Consensus 512 ~e~G~lvllqNLdp-s~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gR 590 (680)
...++.|++-||++ ..|..++.+|+-. |-.-..+|++.. .-|.|||-|.+.+.|+.||..|+...| +||
T Consensus 272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~-yG~V~~vki~~~------~~g~afV~f~~~~~A~~Ai~~lng~~l---~g~ 341 (481)
T TIGR01649 272 GGPGSVLMVSGLHQEKVNCDRLFNLFCV-YGNVERVKFMKN------KKETALIEMADPYQAQLALTHLNGVKL---FGK 341 (481)
T ss_pred CCCCCEEEEeCCCCCCCCHHHHHHHHHh-cCCeEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEE---CCc
Confidence 45789999999999 5888888888753 444445566542 259999999999999999999998776 899
Q ss_pred eeeeecCC
Q 005739 591 PLLGSIGT 598 (680)
Q Consensus 591 pl~~s~~~ 598 (680)
+|.-++..
T Consensus 342 ~l~v~~s~ 349 (481)
T TIGR01649 342 PLRVCPSK 349 (481)
T ss_pred eEEEEEcc
Confidence 99887763
No 41
>PLN03120 nucleic acid binding protein; Provisional
Probab=94.78 E-value=0.079 Score=55.68 Aligned_cols=75 Identities=15% Similarity=0.093 Sum_probs=58.9
Q ss_pred ccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeee
Q 005739 515 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 594 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~ 594 (680)
++-|++.||+|+-|..+|.+++-. +-+-...+|+... ...|-|||-|.+.++|+.|| .|+ ||.| +||+|.-
T Consensus 4 ~rtVfVgNLs~~tTE~dLrefFS~-~G~I~~V~I~~d~----~~~GfAFVtF~d~eaAe~Al-lLn-G~~l--~gr~V~V 74 (260)
T PLN03120 4 VRTVKVSNVSLKATERDIKEFFSF-SGDIEYVEMQSEN----ERSQIAYVTFKDPQGAETAL-LLS-GATI--VDQSVTI 74 (260)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEEeecC----CCCCEEEEEeCcHHHHHHHH-Hhc-CCee--CCceEEE
Confidence 577999999999999999988744 4555567775432 25799999999999999999 476 6764 6999877
Q ss_pred ecCC
Q 005739 595 SIGT 598 (680)
Q Consensus 595 s~~~ 598 (680)
....
T Consensus 75 t~a~ 78 (260)
T PLN03120 75 TPAE 78 (260)
T ss_pred Eecc
Confidence 7663
No 42
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=94.61 E-value=0.081 Score=58.91 Aligned_cols=75 Identities=21% Similarity=0.251 Sum_probs=54.4
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeeecC
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIG 597 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~~ 597 (680)
|++-||+++.|-.+|.+++-.. -.--..++ .+...+-..-|-|||-|.+.+.|+.|+..|+-..| +|||+.-...
T Consensus 3 l~VgnLp~~vte~~L~~~F~~~-G~v~~v~v-~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i---~gk~i~i~~s 77 (562)
T TIGR01628 3 LYVGDLDPDVTEAKLYDLFKPF-GPVLSVRV-CRDSVTRRSLGYGYVNFQNPADAERALETMNFKRL---GGKPIRIMWS 77 (562)
T ss_pred EEEeCCCCCCCHHHHHHHHHhc-CCEEEEEE-EecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE---CCeeEEeecc
Confidence 7899999999988888775432 12112333 33333344569999999999999999999998766 7999766443
No 43
>smart00361 RRM_1 RNA recognition motif.
Probab=94.56 E-value=0.081 Score=43.68 Aligned_cols=58 Identities=19% Similarity=0.298 Sum_probs=40.5
Q ss_pred HHHHHHhccccc-------e--eccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeee
Q 005739 535 LVWHAFKENCSA-------K--MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 595 (680)
Q Consensus 535 lv~~a~ke~c~A-------k--mI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s 595 (680)
-++.-|.+-|+. . +|++.+...-.-|-|||=|.+.+.|..|+..|+.+=+ +||+|.++
T Consensus 4 ~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~---~gr~l~~~ 70 (70)
T smart00361 4 DFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYF---DGRTVKAE 70 (70)
T ss_pred hHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEE---CCEEEEeC
Confidence 344555555543 2 3455432122358999999999999999999998744 89999764
No 44
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=94.38 E-value=0.12 Score=59.96 Aligned_cols=81 Identities=12% Similarity=0.121 Sum_probs=67.4
Q ss_pred cccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceee
Q 005739 514 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 593 (680)
Q Consensus 514 ~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~ 593 (680)
..+-|++-||+|.++..++.+++- .|-+-..++++... ....+-|-|||-|.+.+.|..||..||.--| +||+|-
T Consensus 203 ~~~rLfVgnLp~~vteedLk~lFs-~FG~I~svrl~~D~-~tgksKGfGFVeFe~~e~A~kAI~amNg~el---gGr~Lr 277 (612)
T TIGR01645 203 KFNRIYVASVHPDLSETDIKSVFE-AFGEIVKCQLARAP-TGRGHKGYGFIEYNNLQSQSEAIASMNLFDL---GGQYLR 277 (612)
T ss_pred ccceEEeecCCCCCCHHHHHHHHh-hcCCeeEEEEEecC-CCCCcCCeEEEEECCHHHHHHHHHHhCCCee---CCeEEE
Confidence 345699999999999999999986 58888888877543 3456889999999999999999999996655 899988
Q ss_pred eecCCC
Q 005739 594 GSIGTP 599 (680)
Q Consensus 594 ~s~~~~ 599 (680)
-.++.+
T Consensus 278 V~kAi~ 283 (612)
T TIGR01645 278 VGKCVT 283 (612)
T ss_pred EEecCC
Confidence 777754
No 45
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=94.16 E-value=0.071 Score=41.71 Aligned_cols=35 Identities=37% Similarity=0.463 Sum_probs=30.3
Q ss_pred CceeEEEEeehhHHHHHHHhhccceeeecCCceeeeec
Q 005739 559 FGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 596 (680)
Q Consensus 559 ~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~ 596 (680)
.|.|||=|.+.++|+.|++.|+...+ +||||..++
T Consensus 21 ~~~a~V~f~~~~~A~~a~~~l~~~~~---~g~~l~V~~ 55 (56)
T PF13893_consen 21 RGFAFVEFASVEDAQKAIEQLNGRQF---NGRPLKVSY 55 (56)
T ss_dssp TTEEEEEESSHHHHHHHHHHHTTSEE---TTEEEEEEE
T ss_pred CCEEEEEECCHHHHHHHHHHhCCCEE---CCcEEEEEE
Confidence 59999999999999999999985554 999987654
No 46
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=93.97 E-value=0.24 Score=53.39 Aligned_cols=100 Identities=16% Similarity=0.137 Sum_probs=68.3
Q ss_pred hhhccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCC
Q 005739 510 VAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNG 589 (680)
Q Consensus 510 ~a~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~g 589 (680)
.+....+-|++.||.+..|..+|.+++-+ +-.--..+||- ...+-..-|-|||-|.+.+.|+.||. |+..-| .|
T Consensus 84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~-~G~v~~v~i~~-d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~---~g 157 (457)
T TIGR01622 84 EAERDDRTVFVLQLALKARERDLYEFFSK-VGKVRDVQCIK-DRNSRRSKGVAYVEFYDVESVIKALA-LTGQML---LG 157 (457)
T ss_pred ccccCCcEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEEee-cCCCCCcceEEEEEECCHHHHHHHHH-hCCCEE---CC
Confidence 45566788999999999999999888755 33333455553 22344556899999999999999996 665443 58
Q ss_pred ceeeeecC--------------CCccCCCCCceeeeeeeh
Q 005739 590 RPLLGSIG--------------TPCFTGKQSKFVGHLALD 615 (680)
Q Consensus 590 Rpl~~s~~--------------~~~~p~k~~~f~GH~~i~ 615 (680)
+||..... ....|.....|+|.|.-+
T Consensus 158 ~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~ 197 (457)
T TIGR01622 158 RPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFN 197 (457)
T ss_pred eeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCC
Confidence 88764321 111234456788887644
No 47
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=93.33 E-value=0.33 Score=45.08 Aligned_cols=80 Identities=24% Similarity=0.261 Sum_probs=62.7
Q ss_pred ccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeee
Q 005739 515 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 594 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~ 594 (680)
.+-|++.||.+.+|..++.+++-+...- ..++|. +-...-..-|-|||-|.+-+.|..|+..++..=| .||+|.-
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~-~~~~~~-~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~---~~~~~~v 189 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGPV-KRVRLV-RDRETGKSRGFAFVEFESEESAEKAIEELNGKEL---EGRPLRV 189 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCce-eEEEee-eccccCccCceEEEEecCHHHHHHHHHHcCCCeE---CCceeEe
Confidence 5788999999999999999988765543 233332 2225566789999999999999999999995533 8999998
Q ss_pred ecCCC
Q 005739 595 SIGTP 599 (680)
Q Consensus 595 s~~~~ 599 (680)
....+
T Consensus 190 ~~~~~ 194 (306)
T COG0724 190 QKAQP 194 (306)
T ss_pred ecccc
Confidence 88665
No 48
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=92.46 E-value=0.23 Score=55.78 Aligned_cols=108 Identities=19% Similarity=0.214 Sum_probs=81.1
Q ss_pred ccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 513 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 513 e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
.+|+=|+|--|--..+..|+-.|+-.+= +--+-|| =.-.+|--+-|-|||-|.|||+|..||..||.-=+ ..|++|
T Consensus 81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG-~I~elRL-MmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Ei--r~GK~i 156 (506)
T KOG0117|consen 81 PRGCEVFVGKIPRDVFEDELVPLFEKIG-KIYELRL-MMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEI--RPGKLL 156 (506)
T ss_pred CCCceEEecCCCccccchhhHHHHHhcc-ceeeEEE-eecccCCCCcceEEEEeecHHHHHHHHHHhhCccc--cCCCEe
Confidence 8899999999988888888888775542 2223332 23345666667899999999999999999998876 799998
Q ss_pred eeecCCCccCCCCCceeeeeeehhHHHHHHHHHHhh
Q 005739 593 LGSIGTPCFTGKQSKFVGHLALDKLKFQMQREMREA 628 (680)
Q Consensus 593 ~~s~~~~~~p~k~~~f~GH~~i~k~~~~~qremr~a 628 (680)
=++.- -.+++.|+|-+-=+|.|-+...||++.
T Consensus 157 gvc~S----van~RLFiG~IPK~k~keeIlee~~kV 188 (506)
T KOG0117|consen 157 GVCVS----VANCRLFIGNIPKTKKKEEILEEMKKV 188 (506)
T ss_pred EEEEe----eecceeEeccCCccccHHHHHHHHHhh
Confidence 66543 467999999887777766666666653
No 49
>PLN03121 nucleic acid binding protein; Provisional
Probab=92.30 E-value=0.39 Score=50.23 Aligned_cols=72 Identities=24% Similarity=0.251 Sum_probs=54.8
Q ss_pred ccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 513 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 513 e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
..|.-|++-||.|+=|..+|.+++-+ +-+--..+||... -..|-|||-|+..++|+.|+ .|+ |+.| .|+|+
T Consensus 3 ~~g~TV~V~NLS~~tTE~dLrefFS~-~G~I~~V~I~~D~----et~gfAfVtF~d~~aaetAl-lLn-Ga~l--~d~~I 73 (243)
T PLN03121 3 PGGYTAEVTNLSPKATEKDVYDFFSH-CGAIEHVEIIRSG----EYACTAYVTFKDAYALETAV-LLS-GATI--VDQRV 73 (243)
T ss_pred CCceEEEEecCCCCCCHHHHHHHHHh-cCCeEEEEEecCC----CcceEEEEEECCHHHHHHHH-hcC-CCee--CCceE
Confidence 36889999999999999999999877 5544455677552 22378999999999999999 454 5554 46665
Q ss_pred e
Q 005739 593 L 593 (680)
Q Consensus 593 ~ 593 (680)
.
T Consensus 74 ~ 74 (243)
T PLN03121 74 C 74 (243)
T ss_pred E
Confidence 3
No 50
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=91.54 E-value=0.49 Score=55.03 Aligned_cols=82 Identities=17% Similarity=0.131 Sum_probs=60.9
Q ss_pred HhhhccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecC
Q 005739 509 RVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSN 588 (680)
Q Consensus 509 ~~a~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~ 588 (680)
..|....+-|++-||++..|..++.+++-. |-.--..+|+. -..+.-+-|-|||-|.+.++|+.||..|| |+. -+
T Consensus 101 ~~a~~~~~rLfVGnLp~~~tEe~Lr~lF~~-fG~I~sV~I~~-D~~TgkskGfAFVeF~s~e~A~~Ai~~ln-G~~--i~ 175 (612)
T TIGR01645 101 QQALAIMCRVYVGSISFELREDTIRRAFDP-FGPIKSINMSW-DPATGKHKGFAFVEYEVPEAAQLALEQMN-GQM--LG 175 (612)
T ss_pred hhhhcCCCEEEEcCCCCCCCHHHHHHHHHc-cCCEEEEEEee-cCCCCCcCCeEEEEeCcHHHHHHHHHhcC-CeE--Ee
Confidence 346666778999999999999999888754 44433455543 23344578999999999999999999997 444 37
Q ss_pred Cceeeee
Q 005739 589 GRPLLGS 595 (680)
Q Consensus 589 gRpl~~s 595 (680)
||+|--.
T Consensus 176 GR~IkV~ 182 (612)
T TIGR01645 176 GRNIKVG 182 (612)
T ss_pred cceeeec
Confidence 9987543
No 51
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=87.83 E-value=0.9 Score=46.31 Aligned_cols=79 Identities=23% Similarity=0.344 Sum_probs=62.0
Q ss_pred ccccEEEEecCCCCCchhHHHHHHHHHHhcc--ccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCc
Q 005739 513 EHGTLVVLENLDPSYTSTVVEDLVWHAFKEN--CSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 590 (680)
Q Consensus 513 e~G~lvllqNLdps~ts~eVedlv~~a~ke~--c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gR 590 (680)
.|+.-|++-|||+-.|- .|+|.-|-|. +--=-||+--+..-|-|=+||=|.|.|-||-||.=|+--=| .||
T Consensus 7 nqd~tiyvgnld~kvs~----~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkL---Ygr 79 (203)
T KOG0131|consen 7 NQDATLYVGNLDEKVSE----ELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKL---YGR 79 (203)
T ss_pred CCCceEEEecCCHHHHH----HHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHh---cCc
Confidence 46677899999998764 5666665543 11225899999999999999999999999999999993333 999
Q ss_pred eeeeecCC
Q 005739 591 PLLGSIGT 598 (680)
Q Consensus 591 pl~~s~~~ 598 (680)
||--++..
T Consensus 80 pIrv~kas 87 (203)
T KOG0131|consen 80 PIRVNKAS 87 (203)
T ss_pred eeEEEecc
Confidence 99877766
No 52
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=86.13 E-value=2.8 Score=49.56 Aligned_cols=118 Identities=20% Similarity=0.218 Sum_probs=92.2
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceec-----cCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMI-----PRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI-----~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
++++||.=+=|-..++++..+ .=+-+|| ....---|-.|=+||=|.+.+.|..|++.|+--- -+|++|
T Consensus 518 lfvkNlnf~Tt~e~l~~~F~k----~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtv---ldGH~l 590 (725)
T KOG0110|consen 518 LFVKNLNFDTTLEDLEDLFSK----QGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTV---LDGHKL 590 (725)
T ss_pred hhhhcCCcccchhHHHHHHHh----cCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCce---ecCceE
Confidence 899999999898899988776 3344444 3333233457999999999999999999999433 499999
Q ss_pred eeecCC--------CccCCCCCceeeeeeehhHHHHHH-HHHHhhhccc----CCCCCCcchhhh
Q 005739 593 LGSIGT--------PCFTGKQSKFVGHLALDKLKFQMQ-REMREAVSTS----HCSQPNSLEYDM 644 (680)
Q Consensus 593 ~~s~~~--------~~~p~k~~~f~GH~~i~k~~~~~q-remr~avsTS----HcSQPN~iEydm 644 (680)
..++.. +..|-++. .+-|-|-++.+|.+ ||.|+-.++. -|.=|+-+-|.|
T Consensus 591 ~lk~S~~k~~~~~gK~~~~kk~--~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a 653 (725)
T KOG0110|consen 591 ELKISENKPASTVGKKKSKKKK--GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGA 653 (725)
T ss_pred EEEeccCccccccccccccccc--cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchh
Confidence 998876 33333333 56788889999877 9999999888 589999999999
No 53
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=84.46 E-value=0.77 Score=47.54 Aligned_cols=61 Identities=25% Similarity=0.408 Sum_probs=44.8
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCC-CCCCceeEEEEeehhHHHHHHHhhc
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFA-SPYFGQSFVIFKTREVAELVVTKLE 580 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~s-sp~~G~A~vIFkt~eaae~ai~kl~ 580 (680)
.||.||.-----.|+-...+.-|.+-= +.+.-.++. =+..|||||||+.-++|-.|++.|+
T Consensus 12 lYInnLnekI~~~elkrsL~~LFsqfG--~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~ 73 (221)
T KOG4206|consen 12 LYINNLNEKIKKDELKRSLYLLFSQFG--KILDISAFKTPKMRGQAFVVFKETEAASAALRALQ 73 (221)
T ss_pred EeehhccccccHHHHHHHHHHHHHhhC--CeEEEEecCCCCccCceEEEecChhHHHHHHHHhc
Confidence 467888777777777776666665532 334444553 3578999999999999999999885
No 54
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=83.16 E-value=2.2 Score=46.77 Aligned_cols=72 Identities=28% Similarity=0.311 Sum_probs=57.9
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeeecC
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIG 597 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~~ 597 (680)
|.|-||||+.|..++.|+. ..|-+-..+|.--..-- --|- ||=|-+-++|..||.+||..-| +|.+++...-
T Consensus 79 ~~i~nl~~~~~~~~~~d~f-~~~g~ilS~kv~~~~~g---~kg~-FV~f~~e~~a~~ai~~~ng~ll---~~kki~vg~~ 150 (369)
T KOG0123|consen 79 VFIKNLDESIDNKSLYDTF-SEFGNILSCKVATDENG---SKGY-FVQFESEESAKKAIEKLNGMLL---NGKKIYVGLF 150 (369)
T ss_pred eeecCCCcccCcHHHHHHH-HhhcCeeEEEEEEcCCC---ceee-EEEeCCHHHHHHHHHHhcCccc---CCCeeEEeec
Confidence 9999999999999998876 46777666665444333 4456 9999999999999999999855 8999887544
No 55
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=82.50 E-value=1.5 Score=48.02 Aligned_cols=88 Identities=23% Similarity=0.333 Sum_probs=70.6
Q ss_pred HHHHHhh-hccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccce
Q 005739 505 EERIRVA-HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGC 583 (680)
Q Consensus 505 ee~~~~a-~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egc 583 (680)
.++++.- --++.-|+++|||...+..++.+++ ..|.+-|.+|++.-. +.++.|-+||.|-+-+.|..|+..+++.-
T Consensus 259 ~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f-~~~GeI~s~kv~~~~--~g~skG~gfV~fs~~eeA~~A~~~~n~~~ 335 (369)
T KOG0123|consen 259 QEFAKRSVSLQGANLYVKNLDETLSDEKLRKIF-SSFGEITSAKVMVDE--NGKSKGFGFVEFSSPEEAKKAMTEMNGRL 335 (369)
T ss_pred hhhhhccccccccccccccCccccchhHHHHHH-hcccceeeEEEEecc--CCCccceEEEEcCCHHHHHHHHHhhChhh
Confidence 3444444 4578889999999999999998876 568999998888654 46778899999999999999988888774
Q ss_pred eeecCCceeeeecCC
Q 005739 584 LLLSNGRPLLGSIGT 598 (680)
Q Consensus 584 l~ls~gRpl~~s~~~ 598 (680)
-.|+||+-+.+-
T Consensus 336 ---i~~k~l~vav~q 347 (369)
T KOG0123|consen 336 ---IGGKPLYVAVAQ 347 (369)
T ss_pred ---hcCCchhhhHHh
Confidence 489998776664
No 56
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=80.10 E-value=0.28 Score=52.83 Aligned_cols=92 Identities=12% Similarity=-0.030 Sum_probs=73.9
Q ss_pred EEEEEECCEEEEeCceEEEeeCCC-CCCeEEEEEEEEeeCCCceEEEEEeecChhcccccCCCccCCCCceEEecCCCCc
Q 005739 30 YQSFTYDGVEYTLYDCVYLYKEGD-AEPHVGKLIKIWENADKAKKVKLLWFFRPSDISNFLGNVQTLENELILACGEGVG 108 (680)
Q Consensus 30 YeSft~dG~tYrLGDCVyVkseg~-~ePYIGRIvemWE~~DGek~VkVqWFyRPEEI~~~lg~~~~~pNELFLSsgeg~g 108 (680)
-.++.+.+....+|+++.+.+... ..|.++.+...|.+.+...+.-+.|||+|++.. ++....++.+++....
T Consensus 267 ~~~~~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~----- 340 (371)
T COG5076 267 RESVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETF-VRDAKLFFDNCVMYNG----- 340 (371)
T ss_pred chhhcccccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCcccc-ccccchhhhcccccch-----
Confidence 355667777999999999998765 689999999999998888888999999999542 2333467778887753
Q ss_pred ccccCccceeecceEEEec
Q 005739 109 LTNINPLEAIAGKCNVVCT 127 (680)
Q Consensus 109 ~~DdNPLe~I~GKC~VVsi 127 (680)
..+.+++..+.+.|.|...
T Consensus 341 ~~~~~~~~~~~~~~~~~~~ 359 (371)
T COG5076 341 EVTDYYKNANVLEDFVIKK 359 (371)
T ss_pred hhhhhhhhccchhhhHhhh
Confidence 4788999999999999753
No 57
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=78.14 E-value=0.88 Score=39.35 Aligned_cols=75 Identities=32% Similarity=0.358 Sum_probs=49.9
Q ss_pred EEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeeec
Q 005739 517 LVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 596 (680)
Q Consensus 517 lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~ 596 (680)
.|+|-| |+--|=..|-+.+.++| .|+-..=..-+...=..|+|.|...+++.|+....+|...= =..|.||.+++
T Consensus 8 ~vvL~N-De~ht~~~Vi~~L~~~~--~~s~~~A~~~a~~v~~~G~avv~~~~~e~ae~~~~~l~~~g--~~~~~PL~~ti 82 (82)
T PF02617_consen 8 RVVLWN-DEVHTFEQVIDVLRRVF--GCSEEQARQIAMEVHREGRAVVGTGSREEAEEYAEKLQRAG--RDSGHPLRATI 82 (82)
T ss_dssp EEEEE---SSSBHHHHHHHHHHHC-----HHHHHHHHHHHHHHSEEEEEEEEHHHHHHHHHHHHHHH--HHTT---EEEE
T ss_pred EEEEEc-CCCCCHHHHHHHHHHHH--CCCHHHHHHHHHHHhHcCCEeeeeCCHHHHHHHHHHHHHHh--hccCCCeEEeC
Confidence 355556 77778888999999998 56544333334444567999999999999999999998763 23788998764
No 58
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=75.81 E-value=3.2 Score=34.36 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=28.2
Q ss_pred EEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEeecChhc
Q 005739 40 YTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLWFFRPSD 84 (680)
Q Consensus 40 YrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqWFyRPEE 84 (680)
|++||-|.+++.| +..-|..|-.- ......++.++||---.+
T Consensus 1 f~~GDvV~LKSGG-p~MTV~~v~~~--~~~~~~~v~C~WFd~~~~ 42 (53)
T PF09926_consen 1 FKIGDVVQLKSGG-PRMTVTEVGPN--AGASGGWVECQWFDGHGE 42 (53)
T ss_pred CCCCCEEEEccCC-CCeEEEEcccc--ccCCCCeEEEEeCCCCCc
Confidence 5789999999866 45555544332 233457899999975443
No 59
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=72.89 E-value=17 Score=39.38 Aligned_cols=90 Identities=23% Similarity=0.323 Sum_probs=71.2
Q ss_pred CCChHHHHHhhhccccEEEEecCCCCCchhHHHHHHHHHHhcc---ccceeccCCCCCCCCCceeEEEEeehhHHHHHHH
Q 005739 501 ELPWEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKEN---CSAKMIPRVAFASPYFGQSFVIFKTREVAELVVT 577 (680)
Q Consensus 501 ~~Pwee~~~~a~e~G~lvllqNLdps~ts~eVedlv~~a~ke~---c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~ 577 (680)
++-+||-.--+--..|-||.-|+-+-+| |||++++|-.- -+.|.. +--|-|||=|-|||||..||-
T Consensus 150 ~ltfdeV~NQssp~NtsVY~G~I~~~lt----e~~mr~~Fs~fG~I~EVRvF-------k~qGYaFVrF~tkEaAahAIv 218 (321)
T KOG0148|consen 150 PLTFDEVYNQSSPDNTSVYVGNIASGLT----EDLMRQTFSPFGPIQEVRVF-------KDQGYAFVRFETKEAAAHAIV 218 (321)
T ss_pred CccHHHHhccCCCCCceEEeCCcCcccc----HHHHHHhcccCCcceEEEEe-------cccceEEEEecchhhHHHHHH
Confidence 3789999999999999999999988666 67888887432 222222 456889999999999999999
Q ss_pred hhccceeeecCCceeeeecCCCccCCC
Q 005739 578 KLEEGCLLLSNGRPLLGSIGTPCFTGK 604 (680)
Q Consensus 578 kl~egcl~ls~gRpl~~s~~~~~~p~k 604 (680)
..+.-=+ +|.++=||-|+-..-++
T Consensus 219 ~mNntei---~G~~VkCsWGKe~~~~~ 242 (321)
T KOG0148|consen 219 QMNNTEI---GGQLVRCSWGKEGDDGI 242 (321)
T ss_pred HhcCcee---CceEEEEeccccCCCCC
Confidence 9998765 89999999986554444
No 60
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=70.45 E-value=6.1 Score=41.36 Aligned_cols=79 Identities=23% Similarity=0.381 Sum_probs=58.9
Q ss_pred EEEEecCCCCCchhHHHHHHHHHHhc--cccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCcee--
Q 005739 517 LVVLENLDPSYTSTVVEDLVWHAFKE--NCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL-- 592 (680)
Q Consensus 517 lvllqNLdps~ts~eVedlv~~a~ke--~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl-- 592 (680)
-+.+.||-=.-|..++--+ |+. .+--=.||+-.|+=---|=|||-|.-|.-||-|+..||-.-| +||-|
T Consensus 15 SLkVdNLTyRTspd~Lrrv----FekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~l---dgRelrV 87 (256)
T KOG4207|consen 15 SLKVDNLTYRTSPDDLRRV----FEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVL---DGRELRV 87 (256)
T ss_pred eEEecceeccCCHHHHHHH----HHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceee---ccceeee
Confidence 3556777655555444332 321 223346999999988899999999999999999999998755 89999
Q ss_pred -eeecCCCccC
Q 005739 593 -LGSIGTPCFT 602 (680)
Q Consensus 593 -~~s~~~~~~p 602 (680)
+|-.|-|..+
T Consensus 88 q~arygr~~d~ 98 (256)
T KOG4207|consen 88 QMARYGRPSDL 98 (256)
T ss_pred hhhhcCCCccc
Confidence 8888888554
No 61
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=68.86 E-value=11 Score=41.79 Aligned_cols=74 Identities=26% Similarity=0.257 Sum_probs=50.6
Q ss_pred cEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeee
Q 005739 516 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 595 (680)
Q Consensus 516 ~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s 595 (680)
+.++|-+|-++-+-.++ ++-|-+-=+-+ +-...|+-|=|||-|.||+|||.|.-++-. -|+-+|+-|-=-
T Consensus 229 ~tLyIg~l~d~v~e~dI----rdhFyqyGeir----si~~~~~~~CAFv~ftTR~aAE~Aae~~~n--~lvI~G~Rl~i~ 298 (377)
T KOG0153|consen 229 KTLYIGGLNDEVLEQDI----RDHFYQYGEIR----SIRILPRKGCAFVTFTTREAAEKAAEKSFN--KLVINGFRLKIK 298 (377)
T ss_pred eEEEecccccchhHHHH----HHHHhhcCCee----eEEeecccccceeeehhhHHHHHHHHhhcc--eeeecceEEEEE
Confidence 56889999886554443 44443333333 335678889999999999999999999888 344577554433
Q ss_pred cCCC
Q 005739 596 IGTP 599 (680)
Q Consensus 596 ~~~~ 599 (680)
.|.|
T Consensus 299 Wg~~ 302 (377)
T KOG0153|consen 299 WGRP 302 (377)
T ss_pred eCCC
Confidence 4444
No 62
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=68.13 E-value=16 Score=33.66 Aligned_cols=71 Identities=20% Similarity=0.330 Sum_probs=41.2
Q ss_pred cEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeee
Q 005739 516 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 595 (680)
Q Consensus 516 ~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s 595 (680)
+++++-||--.-...-|-.=+. -|-++|-.|++.-+ .|-|.+=|.+-|+|+.|-.+++.-= +-|+-+.-|
T Consensus 3 s~L~V~NLP~~~d~~~I~~RL~-qLsdNCGGkVl~v~------~~tAilrF~~~~~A~RA~KRmegEd---VfG~kI~v~ 72 (90)
T PF11608_consen 3 SLLYVSNLPTNKDPSSIKNRLR-QLSDNCGGKVLSVS------GGTAILRFPNQEFAERAQKRMEGED---VFGNKISVS 72 (90)
T ss_dssp EEEEEES--TTS-HHHHHHHHH-HHHHTTT--EEE--------TT-EEEEESSHHHHHHHHHHHTT-----SSSS--EEE
T ss_pred cEEEEecCCCCCCHHHHHHHHH-HHhhccCCEEEEEe------CCEEEEEeCCHHHHHHHHHhhcccc---cccceEEEE
Confidence 6889999944344333332222 24479999999875 4899999999999999999997431 345544444
Q ss_pred c
Q 005739 596 I 596 (680)
Q Consensus 596 ~ 596 (680)
+
T Consensus 73 ~ 73 (90)
T PF11608_consen 73 F 73 (90)
T ss_dssp S
T ss_pred E
Confidence 3
No 63
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=66.40 E-value=19 Score=34.40 Aligned_cols=76 Identities=20% Similarity=0.177 Sum_probs=56.2
Q ss_pred hccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCce
Q 005739 512 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 591 (680)
Q Consensus 512 ~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRp 591 (680)
.|-.+|+++-||-=.-||.|+=||+ -+--+-+-|- ---.--.-|-|||+|-.=.-|..|+..|.--- +.+|+
T Consensus 15 pevnriLyirNLp~~ITseemydlF----Gkyg~IrQIR-iG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n---~~~ry 86 (124)
T KOG0114|consen 15 PEVNRILYIRNLPFKITSEEMYDLF----GKYGTIRQIR-IGNTKETRGTAFVVYEDIFDAKKACDHLSGYN---VDNRY 86 (124)
T ss_pred hhhheeEEEecCCccccHHHHHHHh----hcccceEEEE-ecCccCcCceEEEEehHhhhHHHHHHHhcccc---cCCce
Confidence 4567899999999999999998885 3333333331 11122346999999999999999999997553 48999
Q ss_pred eeee
Q 005739 592 LLGS 595 (680)
Q Consensus 592 l~~s 595 (680)
|+.=
T Consensus 87 l~vl 90 (124)
T KOG0114|consen 87 LVVL 90 (124)
T ss_pred EEEE
Confidence 9853
No 64
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=65.99 E-value=7.9 Score=35.72 Aligned_cols=69 Identities=25% Similarity=0.247 Sum_probs=51.6
Q ss_pred EEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeeec
Q 005739 517 LVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 596 (680)
Q Consensus 517 lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~ 596 (680)
-|+|-| |+==|=.-|-+++.+.| .++..--..-+.-.=+.|+|.|...++|.||.-+.+| .|.||.+++
T Consensus 29 ~ViL~N-Dd~ntmd~Vv~vL~~vf--~~s~~~A~~iml~vH~~G~avv~~~~~e~AE~~~~~l--------~~~~L~~~i 97 (100)
T PRK00033 29 KVLLHN-DDYTPMEFVVYVLQKFF--GYDRERATQIMLEVHNEGKAVVGVCTREVAETKVEQV--------HQHGLLCTM 97 (100)
T ss_pred EEEEEc-CCCCCHHHHHHHHHHHH--CCCHHHHHHHHHHHhcCCcEEEEEEcHHHHHHHHHHH--------HcCCCeEEE
Confidence 366666 44445556777888888 5555444444555678999999999999999999999 788888775
No 65
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=59.64 E-value=13 Score=38.01 Aligned_cols=73 Identities=29% Similarity=0.275 Sum_probs=55.1
Q ss_pred cccEEEEecCCCCCchhHHHHHHHH--HHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccce-------e
Q 005739 514 HGTLVVLENLDPSYTSTVVEDLVWH--AFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGC-------L 584 (680)
Q Consensus 514 ~G~lvllqNLdps~ts~eVedlv~~--a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egc-------l 584 (680)
-.|=||+-||.+.-|..|+|.++.- -|.---.|+++| |=|||=|.-.--||-||+-||-.= +
T Consensus 9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPP---------GfAFVEFed~RDA~DAvr~LDG~~~cG~r~rV 79 (195)
T KOG0107|consen 9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPP---------GFAFVEFEDPRDAEDAVRYLDGKDICGSRIRV 79 (195)
T ss_pred CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCC---------CceEEeccCcccHHHHHhhcCCccccCceEEE
Confidence 3688999999999999999987643 233334455443 889999999999999999998642 3
Q ss_pred eecCCceeeee
Q 005739 585 LLSNGRPLLGS 595 (680)
Q Consensus 585 ~ls~gRpl~~s 595 (680)
=||.|+|-=+-
T Consensus 80 E~S~G~~r~~r 90 (195)
T KOG0107|consen 80 ELSTGRPRGSR 90 (195)
T ss_pred EeecCCccccc
Confidence 46788876433
No 66
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=58.95 E-value=17 Score=38.81 Aligned_cols=62 Identities=19% Similarity=0.181 Sum_probs=45.8
Q ss_pred EEEEecCCCCCchhHHHHHHHH-HHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhcc
Q 005739 517 LVVLENLDPSYTSTVVEDLVWH-AFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEE 581 (680)
Q Consensus 517 lvllqNLdps~ts~eVedlv~~-a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~e 581 (680)
-|-|-||--+-+..++++|+.- +.-.+|---+=.- +.---|=|||-|.+||-|..||..||.
T Consensus 191 tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~---TG~~kGFAFVtF~sRddA~rAI~~LnG 253 (270)
T KOG0122|consen 191 TVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKE---TGLSKGFAFVTFESRDDAARAIADLNG 253 (270)
T ss_pred eeEEecCccccChhHHHHHhhccCccceeEEEEccc---cCcccceEEEEEecHHHHHHHHHHccC
Confidence 3789999999999999999874 2223332222222 233458899999999999999999985
No 67
>PLN03213 repressor of silencing 3; Provisional
Probab=56.66 E-value=33 Score=39.99 Aligned_cols=94 Identities=14% Similarity=0.149 Sum_probs=71.4
Q ss_pred ccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeeh--hHHHHHHHhhccceeeecCCc
Q 005739 513 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTR--EVAELVVTKLEEGCLLLSNGR 590 (680)
Q Consensus 513 e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~--eaae~ai~kl~egcl~ls~gR 590 (680)
..|.=+++-||..+-|..+++.++ ..|-+--.+.+| |.+. -|=|||=|.+- ..++.||..||..=+ .||
T Consensus 8 ~~gMRIYVGNLSydVTEDDLravF-SeFGsVkdVEIp-RETG----RGFAFVEMssdddaEeeKAISaLNGAEW---KGR 78 (759)
T PLN03213 8 GGGVRLHVGGLGESVGRDDLLKIF-SPMGTVDAVEFV-RTKG----RSFAYIDFSPSSTNSLTKLFSTYNGCVW---KGG 78 (759)
T ss_pred CcceEEEEeCCCCCCCHHHHHHHH-HhcCCeeEEEEe-cccC----CceEEEEecCCcHHHHHHHHHHhcCCee---cCc
Confidence 345678999999999999999874 456666667777 5544 78999999997 679999999985433 699
Q ss_pred eeeeecCCCccCCCCCceeeeeeehhHHHHHHHHHHhhhcc
Q 005739 591 PLLGSIGTPCFTGKQSKFVGHLALDKLKFQMQREMREAVST 631 (680)
Q Consensus 591 pl~~s~~~~~~p~k~~~f~GH~~i~k~~~~~qremr~avsT 631 (680)
.|---.+.|.| +++ ++||-.+|+|+
T Consensus 79 ~LKVNKAKP~Y------------LeR----LkrEReea~s~ 103 (759)
T PLN03213 79 RLRLEKAKEHY------------LAR----LKREWEAASST 103 (759)
T ss_pred eeEEeeccHHH------------HHH----HHHHHHHhhcc
Confidence 99888888765 333 45666677665
No 68
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=55.26 E-value=14 Score=33.81 Aligned_cols=60 Identities=22% Similarity=0.269 Sum_probs=35.4
Q ss_pred ccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccc
Q 005739 515 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 582 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~eg 582 (680)
|.||-+.++++.-+ -+-|..+|++.+..+.|.-+. -.-.|||=|++-++|..|+.++.+.
T Consensus 1 G~il~~~g~~~~~~----re~iK~~f~~~g~V~yVD~~~----G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 1 GCILKFSGLGEPTS----REDIKEAFSQFGEVAYVDFSR----GDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp --EEEEEE--SS------HHHHHHHT-SS--EEEEE--T----T-SEEEEEESS---HHHHHHHHHHT
T ss_pred CeEEEEecCCCCcC----HHHHHHHHHhcCCcceEEecC----CCCEEEEEECCcchHHHHHHHHHhc
Confidence 78999999888866 233567788877665554322 2338999999999999999999987
No 69
>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.
Probab=54.09 E-value=7.5 Score=38.51 Aligned_cols=71 Identities=17% Similarity=0.256 Sum_probs=44.2
Q ss_pred hccccEEEEecCCCCCchhHHHHHHHHHHhccccce----eccCCCCCCCCCceeEEEEeehhHHHHHHHhhccc
Q 005739 512 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAK----MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 582 (680)
Q Consensus 512 ~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~Ak----mI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~eg 582 (680)
+..|+=|+|-+|-|++|-.|..+.|-.+|.+.-+=. -.....|-.|.+.+||+.|++.+....-+..++.-
T Consensus 4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~ 78 (176)
T PF03467_consen 4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGH 78 (176)
T ss_dssp -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTE
T ss_pred cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCc
Confidence 456778999999999999888776554555541111 24566777888899999999999988888877653
No 70
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=53.78 E-value=42 Score=39.50 Aligned_cols=89 Identities=26% Similarity=0.298 Sum_probs=62.1
Q ss_pred HHhhhccccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhh----ccce
Q 005739 508 IRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKL----EEGC 583 (680)
Q Consensus 508 ~~~a~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl----~egc 583 (680)
++.-+-.|..|.|-||-=.-|-.||-..+. -|-+---|++.-+...- ---|.|||=|+|-.||..+|.-- +.|-
T Consensus 285 ~~en~~~~~tVFvRNL~fD~tEEel~~~fs-kFG~v~ya~iV~~k~T~-~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~ 362 (678)
T KOG0127|consen 285 TRENITEGKTVFVRNLPFDTTEEELKEHFS-KFGEVKYAIIVKDKDTG-HSKGTAFVKFKTQIAAQNCIEAASPASEDGS 362 (678)
T ss_pred ccccccccceEEEecCCccccHHHHHHHHH-hhccceeEEEEeccCCC-CcccceEEEeccHHHHHHHHHhcCccCCCce
Confidence 455667899999999965555555544443 35555566665554322 23489999999999999999988 6776
Q ss_pred eeecCCceeeeecCCC
Q 005739 584 LLLSNGRPLLGSIGTP 599 (680)
Q Consensus 584 l~ls~gRpl~~s~~~~ 599 (680)
++| +||-|=...+++
T Consensus 363 ~ll-~GR~Lkv~~Av~ 377 (678)
T KOG0127|consen 363 VLL-DGRLLKVTLAVT 377 (678)
T ss_pred EEE-eccEEeeeeccc
Confidence 767 899876555543
No 71
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=50.24 E-value=41 Score=38.72 Aligned_cols=73 Identities=25% Similarity=0.238 Sum_probs=52.4
Q ss_pred EEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeee
Q 005739 517 LVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 594 (680)
Q Consensus 517 lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~ 594 (680)
-|+|.|+--.|-=.++.|||+.-.-|---..+.-- -+----|-|.|=||+.|-++-|+.+|+.--+ +||||+.
T Consensus 46 ~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D--~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~---~GR~l~v 118 (608)
T KOG4212|consen 46 SVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD--ESGKARGCAVVEFKDPENVQKALEKLNKYEV---NGRELVV 118 (608)
T ss_pred eEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc--cCCCcCCceEEEeeCHHHHHHHHHHhhhccc---cCceEEE
Confidence 38888887777777888888876554322222111 0112347799999999999999999999876 9999974
No 72
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=48.62 E-value=20 Score=39.87 Aligned_cols=76 Identities=26% Similarity=0.441 Sum_probs=57.4
Q ss_pred ccEEEEecCCCCCchhHHH---HHH---HHHHhccccce-eccC-CCCCCCCCceeEEEEeehhHHHHHHHhhccceeee
Q 005739 515 GTLVVLENLDPSYTSTVVE---DLV---WHAFKENCSAK-MIPR-VAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLL 586 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVe---dlv---~~a~ke~c~Ak-mI~~-~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~l 586 (680)
-+.|.|-|+ ||..+.+ +|| ..-|.|.|.-= ++-+ .-|.-+.-|-|.|-|++.++|+.+|.-++-+-+
T Consensus 265 ~~tVi~kn~---Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~f-- 339 (382)
T KOG1548|consen 265 DRTVILKNM---FTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWF-- 339 (382)
T ss_pred CcEEEeeec---CCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeee--
Confidence 467888887 6666655 334 34477777531 2222 346668889999999999999999999999966
Q ss_pred cCCceeeeec
Q 005739 587 SNGRPLLGSI 596 (680)
Q Consensus 587 s~gRpl~~s~ 596 (680)
+||-|.||+
T Consensus 340 -dgRql~A~i 348 (382)
T KOG1548|consen 340 -DGRQLTASI 348 (382)
T ss_pred -cceEEEEEE
Confidence 999999997
No 73
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=45.86 E-value=46 Score=38.25 Aligned_cols=79 Identities=22% Similarity=0.210 Sum_probs=58.2
Q ss_pred hccccEEEEecCCCCCchhHHHHHHHHHHhcc-ccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCc
Q 005739 512 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKEN-CSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 590 (680)
Q Consensus 512 ~e~G~lvllqNLdps~ts~eVedlv~~a~ke~-c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gR 590 (680)
..+=.++++-||--+-|-. ++-..|++- |--|.--- --=|||=|-.|+.|-.||..+|.-|| +|-
T Consensus 256 ms~VKvLYVRNL~~~tTeE----~lk~~F~~~G~veRVkk~-------rDYaFVHf~eR~davkAm~~~ngkel---dG~ 321 (506)
T KOG0117|consen 256 MSKVKVLYVRNLMESTTEE----TLKKLFNEFGKVERVKKP-------RDYAFVHFAEREDAVKAMKETNGKEL---DGS 321 (506)
T ss_pred hhheeeeeeeccchhhhHH----HHHHHHHhccceEEeecc-------cceeEEeecchHHHHHHHHHhcCcee---cCc
Confidence 3456789999998877754 444555543 22222111 11599999999999999999999999 999
Q ss_pred eeeeecCCCccCCC
Q 005739 591 PLLGSIGTPCFTGK 604 (680)
Q Consensus 591 pl~~s~~~~~~p~k 604 (680)
||=++.++|..-.+
T Consensus 322 ~iEvtLAKP~~k~k 335 (506)
T KOG0117|consen 322 PIEVTLAKPVDKKK 335 (506)
T ss_pred eEEEEecCChhhhc
Confidence 99999999875443
No 74
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=45.47 E-value=19 Score=44.66 Aligned_cols=57 Identities=21% Similarity=0.483 Sum_probs=45.0
Q ss_pred eeEEEEEECCEEEEeCceEEEeeCCCCCC--------------------e---EEEEEEEEeeCCC-ceEEEEEeecChh
Q 005739 28 QFYQSFTYDGVEYTLYDCVYLYKEGDAEP--------------------H---VGKLIKIWENADK-AKKVKLLWFFRPS 83 (680)
Q Consensus 28 ~fYeSft~dG~tYrLGDCVyVkseg~~eP--------------------Y---IGRIvemWE~~DG-ek~VkVqWFyRPE 83 (680)
..|+++.+|++.|.+||.|++.-++.... | =|+|-.|+.+.+. ...+.|+.||--.
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 57999999999999999999987654322 2 4889999986544 4577899998877
Q ss_pred c
Q 005739 84 D 84 (680)
Q Consensus 84 E 84 (680)
|
T Consensus 521 d 521 (1164)
T PTZ00112 521 D 521 (1164)
T ss_pred c
Confidence 6
No 75
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=45.28 E-value=29 Score=38.71 Aligned_cols=82 Identities=18% Similarity=0.331 Sum_probs=54.6
Q ss_pred cccEEEEecCCCCCchhHHHHHH-HHH-Hhccccce--eccCCC-CCCCCCcee--EEEEeehhHHHHHHHhhccceeee
Q 005739 514 HGTLVVLENLDPSYTSTVVEDLV-WHA-FKENCSAK--MIPRVA-FASPYFGQS--FVIFKTREVAELVVTKLEEGCLLL 586 (680)
Q Consensus 514 ~G~lvllqNLdps~ts~eVedlv-~~a-~ke~c~Ak--mI~~~~-~ssp~~G~A--~vIFkt~eaae~ai~kl~egcl~l 586 (680)
|..|||+-.|-|-|.-.||-..+ +|- |-|-=--+ .|++-+ -...-+|-| |+-|.|+|-|.++|..+|+..
T Consensus 113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~--- 189 (480)
T COG5175 113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL--- 189 (480)
T ss_pred ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc---
Confidence 44689999999999999976433 222 22221111 122222 111122234 999999999999999999884
Q ss_pred cCCceeeeecCC
Q 005739 587 SNGRPLLGSIGT 598 (680)
Q Consensus 587 s~gRpl~~s~~~ 598 (680)
.+||-|-|+.|+
T Consensus 190 ~DGr~lkatYGT 201 (480)
T COG5175 190 LDGRVLKATYGT 201 (480)
T ss_pred ccCceEeeecCc
Confidence 599999999886
No 76
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=44.44 E-value=33 Score=38.99 Aligned_cols=71 Identities=18% Similarity=0.147 Sum_probs=55.7
Q ss_pred cEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCC----ceeEEEEeehhHHHHHHHhhccceeeecCCce
Q 005739 516 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYF----GQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 591 (680)
Q Consensus 516 ~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~----G~A~vIFkt~eaae~ai~kl~egcl~ls~gRp 591 (680)
..|++-|+..+.|.++|.+|+-.+.. .+..-...++-+ |=||+=|+.=+-|++||+.|+..=+ +||+
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~g~------v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~---~gr~ 89 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGVGP------VLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEF---NGRK 89 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhccCc------cceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCccc---CCce
Confidence 78999999999999999998875532 334444444544 4699999999999999999998755 8888
Q ss_pred eeee
Q 005739 592 LLGS 595 (680)
Q Consensus 592 l~~s 595 (680)
|-..
T Consensus 90 l~v~ 93 (435)
T KOG0108|consen 90 LRVN 93 (435)
T ss_pred EEee
Confidence 7543
No 77
>PF08075 NOPS: NOPS (NUC059) domain; InterPro: IPR012975 This domain is found C-terminal to 1 or 2 IPR000504 from INTERPRO domains [] in NONA and PSP1 proteins.; PDB: 3SDE_B.
Probab=44.40 E-value=11 Score=31.54 Aligned_cols=19 Identities=26% Similarity=0.774 Sum_probs=14.4
Q ss_pred cccCCCCCCcchhhhhhhh
Q 005739 630 STSHCSQPNSLEYDMAIEW 648 (680)
Q Consensus 630 sTSHcSQPN~iEydma~eW 648 (680)
.--|-.||||.||+.|+-|
T Consensus 33 ~~PRFA~pgsfE~eyg~RW 51 (52)
T PF08075_consen 33 QGPRFAQPGSFEFEYGMRW 51 (52)
T ss_dssp S-SEE--TTSHHHHHHHHH
T ss_pred cCCCcCCCCCcchhhcccc
Confidence 4567889999999999999
No 78
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=41.54 E-value=14 Score=45.50 Aligned_cols=128 Identities=21% Similarity=0.145 Sum_probs=86.1
Q ss_pred ECCEEEEeCceEEEeeCCCCCCeEEEEEEEEeeCC-CceEEEEEeecChhcccccC-----------------CCccCCC
Q 005739 35 YDGVEYTLYDCVYLYKEGDAEPHVGKLIKIWENAD-KAKKVKLLWFFRPSDISNFL-----------------GNVQTLE 96 (680)
Q Consensus 35 ~dG~tYrLGDCVyVkseg~~ePYIGRIvemWE~~D-Gek~VkVqWFyRPEEI~~~l-----------------g~~~~~p 96 (680)
.++..|.++|.+.+..+...+.-|+.|+.+=++.. ...+++.-.++|+++|.+.+ ..-....
T Consensus 141 ~~e~~y~~~~~l~~~v~~~~p~lia~~~~~~~~Kr~~~~~~k~s~~~r~~d~Pet~y~~~m~pe~Ar~e~~P~~~pq~~s 220 (1229)
T KOG2133|consen 141 HDETLYDLRDSLFVEVSQPEPYLIAAICGFKYTKRDDRQVVKLSFYFRADDIPETGYLNLMKPERARLEINPHLCPQPLS 220 (1229)
T ss_pred ccchhhhhhhhhhhhhccCCccccccccCccccccccccccccccccccccCcccccccccCchhhhhccCCccCCCcch
Confidence 45567899999999887654445787777766653 34566777888998876321 0011345
Q ss_pred CceEEecCCCCcccccCccceeecceEEEecCCCcCCCCCCC--ccCCCCcEEEEeeeeCcceEEEehhhhhh
Q 005739 97 NELILACGEGVGLTNINPLEAIAGKCNVVCTSKDARNPQPSD--EELQISDFIFCRTFDVGLRKVLDKIDEKI 167 (680)
Q Consensus 97 NELFLSsgeg~g~~DdNPLe~I~GKC~VVsiskD~rn~rPS~--~ei~~aDFYf~R~YDv~t~RivD~f~dkI 167 (680)
.++|.+... -=+-|..|--|||.+. .++|++.-+-+. -.++...||++-+|.+.+....++..=.|
T Consensus 221 q~l~~s~l~----~i~qppscp~gk~~~~-~skd~~h~~~~n~p~~ld~~i~fk~agglpps~k~a~P~~~~~ 288 (1229)
T KOG2133|consen 221 QELFNSELQ----GITQPPSCPRGKGIAE-YSKDVRHGGNTNAPFSLDNDIFFKCAGGLPPSTKPASPTHYAI 288 (1229)
T ss_pred hhhhccccc----CCCCCCcCCCCCceEE-eecccccCCccCCCCcccceeeeecccCCCCCCCCCCCccccc
Confidence 778887641 1357899999999987 568886422111 12356678999999999998888654443
No 79
>PRK10708 hypothetical protein; Provisional
Probab=40.45 E-value=53 Score=28.32 Aligned_cols=43 Identities=19% Similarity=0.363 Sum_probs=31.3
Q ss_pred EeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEE-------EEEeecChhc
Q 005739 41 TLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKV-------KLLWFFRPSD 84 (680)
Q Consensus 41 rLGDCVyVkseg~~ePYIGRIvemWE~~DGek~V-------kVqWFyRPEE 84 (680)
++.|-|+|+.+|. +-..|.|..+-+=..|.||. ..-|||...+
T Consensus 2 kvnD~VtVKTDG~-~rR~G~iLavE~F~EG~MyLvaL~dYP~GiWFFNE~~ 51 (62)
T PRK10708 2 KVNDRVTVKTDGG-PRRPGVVLAVEEFSEGTMYLVSLEDYPLGIWFFNEAG 51 (62)
T ss_pred ccccEEEEecCCC-ccccceEEEEeeccCcEEEEEEcCcCCCceEEEeccC
Confidence 5789999999764 45778887776666787765 4568886654
No 80
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=37.26 E-value=67 Score=33.32 Aligned_cols=75 Identities=21% Similarity=0.342 Sum_probs=50.2
Q ss_pred EEEecCCCCCchhHHHHHHHHHHhccccceeccCCC-CCCCC----CceeEEEEeehhHHHHHHHhhccceeeecCCcee
Q 005739 518 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVA-FASPY----FGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 592 (680)
Q Consensus 518 vllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~-~ssp~----~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl 592 (680)
..++||||.- + |.+.|+-|.-. ..+|..+- +-.|+ -|=+|+-|.+.||++.||.-++.--| +-||.
T Consensus 99 lfvgNLd~~v--D--e~~L~dtFsaf--G~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l---~nr~i 169 (203)
T KOG0131|consen 99 LFVGNLDPEV--D--EKLLYDTFSAF--GVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYL---CNRPI 169 (203)
T ss_pred ccccccCcch--h--HHHHHHHHHhc--cccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchh---cCCce
Confidence 4589999932 2 45777766432 23333221 23333 23689999999999999999987755 77898
Q ss_pred eeecCCCcc
Q 005739 593 LGSIGTPCF 601 (680)
Q Consensus 593 ~~s~~~~~~ 601 (680)
+-|.+.-..
T Consensus 170 tv~ya~k~~ 178 (203)
T KOG0131|consen 170 TVSYAFKKD 178 (203)
T ss_pred EEEEEEecC
Confidence 888775443
No 81
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=37.14 E-value=51 Score=34.34 Aligned_cols=81 Identities=22% Similarity=0.277 Sum_probs=65.4
Q ss_pred ccEEEEecCCCCCchhHHHHHHHHHHhccccce---eccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCce
Q 005739 515 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAK---MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 591 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVedlv~~a~ke~c~Ak---mI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRp 591 (680)
=+.|.+-|+|..=|-.++|..+ +.|-.- +|+.--+.-+.=|-||+-|...++++.++. ||.+-| -||+
T Consensus 101 ~~sv~v~nvd~~~t~~~~e~hf-----~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i---~~~~ 171 (231)
T KOG4209|consen 101 APSVWVGNVDFLVTLTKIELHF-----ESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEI---PGPA 171 (231)
T ss_pred CceEEEeccccccccchhhhee-----eccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccc---cccc
Confidence 4789999999999998877665 688887 788888887788999999999999999999 999976 7888
Q ss_pred eeeecCCCccCCC
Q 005739 592 LLGSIGTPCFTGK 604 (680)
Q Consensus 592 l~~s~~~~~~p~k 604 (680)
+.-+.-.--.||.
T Consensus 172 i~vt~~r~~~pg~ 184 (231)
T KOG4209|consen 172 IEVTLKRTNVPGM 184 (231)
T ss_pred ceeeeeeeecCCc
Confidence 7665443224443
No 82
>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=36.57 E-value=67 Score=27.71 Aligned_cols=44 Identities=18% Similarity=0.346 Sum_probs=31.4
Q ss_pred EeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEE-------EEEeecChhcc
Q 005739 41 TLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKV-------KLLWFFRPSDI 85 (680)
Q Consensus 41 rLGDCVyVkseg~~ePYIGRIvemWE~~DGek~V-------kVqWFyRPEEI 85 (680)
++.|-|+|+.+|. +-.-|.|..+-+=..|.||. ..-|||...+-
T Consensus 2 kvnD~VtVKTDG~-~rR~G~ilavE~F~EG~MYLvaL~dYP~GiWFFNE~~~ 52 (62)
T PF10781_consen 2 KVNDRVTVKTDGG-PRREGVILAVEPFNEGTMYLVALEDYPAGIWFFNEKDS 52 (62)
T ss_pred ccccEEEEecCCc-ccccceEEEEeeccCcEEEEEEcCcCCcceEEEecCCC
Confidence 5789999999764 45677777776656677665 45688876543
No 83
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=36.24 E-value=20 Score=41.60 Aligned_cols=59 Identities=19% Similarity=0.182 Sum_probs=45.2
Q ss_pred HHHHHhccccceeccCCCCCCCCC-ceeEEEEeehhHHHHHHHhhccceeeecCCceeeeecC
Q 005739 536 VWHAFKENCSAKMIPRVAFASPYF-GQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIG 597 (680)
Q Consensus 536 v~~a~ke~c~AkmI~~~~~ssp~~-G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~~ 597 (680)
|.+-.+|.|...==-.--|-+++| |.-||=|-+-+||..|++-|.-.-+ .||-+.+++=
T Consensus 466 I~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF---~gr~Ita~~~ 525 (549)
T KOG0147|consen 466 IREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWF---AGRMITAKYL 525 (549)
T ss_pred HHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhh---ccceeEEEEe
Confidence 445566777544323334667888 9999999999999999999998876 8888877763
No 84
>COG5475 Uncharacterized small protein [Function unknown]
Probab=35.87 E-value=75 Score=27.37 Aligned_cols=37 Identities=16% Similarity=0.225 Sum_probs=25.3
Q ss_pred EEEEeCceEEEeeCCCCCCeEEEEEEEEeeC-CCceEEEEEeecChh
Q 005739 38 VEYTLYDCVYLYKEGDAEPHVGKLIKIWENA-DKAKKVKLLWFFRPS 83 (680)
Q Consensus 38 ~tYrLGDCVyVkseg~~ePYIGRIvemWE~~-DGek~VkVqWFyRPE 83 (680)
..++.||-|.|++.|+ +|--+. ....++.++||-+..
T Consensus 3 ~~FstgdvV~lKsGGP---------~Mtvs~~ss~Gmy~C~Wf~g~g 40 (60)
T COG5475 3 MSFSTGDVVTLKSGGP---------RMTVSGYSSDGMYECRWFDGYG 40 (60)
T ss_pred ceeecCcEEEeecCCc---------eEEEeccccCCeEEEEEecCCC
Confidence 5689999999988653 233222 122589999997765
No 85
>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=35.76 E-value=88 Score=25.42 Aligned_cols=37 Identities=14% Similarity=0.137 Sum_probs=25.8
Q ss_pred EEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEe
Q 005739 40 YTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLW 78 (680)
Q Consensus 40 YrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqW 78 (680)
+.+|+-|++.- ..+.+|-|+|+++-+ ..+...+-|++
T Consensus 1 ~~vG~~v~~~~-~~~~~y~A~I~~~r~-~~~~~~YyVHY 37 (55)
T PF11717_consen 1 FEVGEKVLCKY-KDGQWYEAKILDIRE-KNGEPEYYVHY 37 (55)
T ss_dssp --TTEEEEEEE-TTTEEEEEEEEEEEE-CTTCEEEEEEE
T ss_pred CCcCCEEEEEE-CCCcEEEEEEEEEEe-cCCCEEEEEEc
Confidence 46899999988 345789999999999 44444444443
No 86
>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=32.40 E-value=60 Score=28.68 Aligned_cols=45 Identities=13% Similarity=0.116 Sum_probs=34.9
Q ss_pred EEEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEeecChhc
Q 005739 39 EYTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLWFFRPSD 84 (680)
Q Consensus 39 tYrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqWFyRPEE 84 (680)
.|.+||-|.-+-.| -++|=|+|+..=+.......+.|+||-.++-
T Consensus 2 ~f~~GdlVwaK~kG-yp~WPa~I~~~~~~~~~~~~~~V~FfGt~~~ 46 (83)
T cd05834 2 QFKAGDLVFAKVKG-YPAWPARVDEPEDWKPPGKKYPVYFFGTHET 46 (83)
T ss_pred CCCCCCEEEEecCC-CCCCCEEEecccccCCCCCEEEEEEeCCCCE
Confidence 46899999998855 4789999999866434457899999987543
No 87
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=32.02 E-value=1.9e+02 Score=28.89 Aligned_cols=96 Identities=24% Similarity=0.287 Sum_probs=67.2
Q ss_pred CccccccccCCChHHHHHhhhccccEEEEecCCCCCchhHHHHHHHHHHhccccceecc--CCCCCCCCCceeEEEEeeh
Q 005739 492 SLDRSKWFKELPWEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIP--RVAFASPYFGQSFVIFKTR 569 (680)
Q Consensus 492 ~~d~skwfk~~Pwee~~~~a~e~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~--~~~~ssp~~G~A~vIFkt~ 569 (680)
.+-|-+-|++. .|+--.|..+-.-|++-||-- ||. |+-||.-|-..=+.|-|- .--|.-.-.|=.||+|-++
T Consensus 15 s~Yr~~~f~gt--~~e~~~a~r~S~tvyVgNlSf-ytt---EEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~ 88 (153)
T KOG0121|consen 15 SAYRDRRFRGT--DEEQLEALRKSCTVYVGNLSF-YTT---EEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSR 88 (153)
T ss_pred hHHHHHHhcCc--hHHHHHHHhhcceEEEeeeee-eec---HHHHHHHHHhccchheeEeccccCCcCccceEEEEEecc
Confidence 34455556652 333445677778899999954 443 457888776655555442 3345556789999999999
Q ss_pred hHHHHHHHhhccceeeecCCceeeeec
Q 005739 570 EVAELVVTKLEEGCLLLSNGRPLLGSI 596 (680)
Q Consensus 570 eaae~ai~kl~egcl~ls~gRpl~~s~ 596 (680)
+-|+.|++-|+.-=| +.||+-.-.
T Consensus 89 ~dA~~AlryisgtrL---ddr~ir~D~ 112 (153)
T KOG0121|consen 89 DDAEDALRYISGTRL---DDRPIRIDW 112 (153)
T ss_pred hhHHHHHHHhccCcc---cccceeeec
Confidence 999999999987766 788876544
No 88
>PF12083 DUF3560: Domain of unknown function (DUF3560); InterPro: IPR021944 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif.
Probab=30.84 E-value=1e+02 Score=29.81 Aligned_cols=59 Identities=22% Similarity=0.260 Sum_probs=37.5
Q ss_pred cCCCCCceeeeeeehhHHH---HHHHHHHhhh------------------cccCCCCCCcchhhhhhhhhHhHHHHHHHH
Q 005739 601 FTGKQSKFVGHLALDKLKF---QMQREMREAV------------------STSHCSQPNSLEYDMAIEWSLLQERLDCAW 659 (680)
Q Consensus 601 ~p~k~~~f~GH~~i~k~~~---~~qremr~av------------------sTSHcSQPN~iEydma~eW~l~qe~~~~~~ 659 (680)
+|-.||.++||+|=-..|- .+-+=|.+|| .|.+-.-|.+|++ |+++|-+-|..+.+
T Consensus 39 ip~GQPIlVGHHSE~R~Rr~~eR~~~~m~kav~~~~kA~y~~~rA~aa~~~~i~~~~Pda~~r---i~~~la~~r~~q~~ 115 (126)
T PF12083_consen 39 IPFGQPILVGHHSEKRHRRYRERIHNRMGKAVEAMDKAEYYEQRAAAAGRTAISSDDPDALRR---IKKKLAELRASQRR 115 (126)
T ss_pred cCCCCCeeccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhccChHHHHH---HHHHHHHHHHHHHH
Confidence 4457889999999776554 3335666666 3556666777655 66666666655554
Q ss_pred HHH
Q 005739 660 KKL 662 (680)
Q Consensus 660 ~~l 662 (680)
-+-
T Consensus 116 mk~ 118 (126)
T PF12083_consen 116 MKA 118 (126)
T ss_pred HHH
Confidence 443
No 89
>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2. It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).
Probab=30.66 E-value=1.6e+02 Score=27.19 Aligned_cols=68 Identities=19% Similarity=0.218 Sum_probs=49.1
Q ss_pred cEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccce
Q 005739 516 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGC 583 (680)
Q Consensus 516 ~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egc 583 (680)
|-|.|-|+-..||..++.++|...++-.=+==-.|----..-+-|=|||=|.+-++|..-....+...
T Consensus 2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~ 69 (97)
T PF04059_consen 2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKK 69 (97)
T ss_pred eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCc
Confidence 56889999999999999999987653221111122223345578999999999999998888776433
No 90
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=27.80 E-value=86 Score=37.09 Aligned_cols=78 Identities=21% Similarity=0.281 Sum_probs=57.4
Q ss_pred EEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeeecCC
Q 005739 519 VLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIGT 598 (680)
Q Consensus 519 llqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~~~ 598 (680)
.|-||-=+--..+++.++ .+|---.++ .|| +-+.--..|=|||-|+-+.+|+.|+..+|.-=+ +|||+-.=.++
T Consensus 121 IIRNLPf~~k~~dLk~vF-s~~G~V~Ei-~IP-~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i---~gR~VAVDWAV 194 (678)
T KOG0127|consen 121 IIRNLPFKCKKPDLKNVF-SNFGKVVEI-VIP-RKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKI---DGRPVAVDWAV 194 (678)
T ss_pred EeecCCcccCcHHHHHHH-hhcceEEEE-Ecc-cCCCCCccceEEEEEeeHHHHHHHHHhccCcee---cCceeEEeeec
Confidence 567776565555555443 445444444 467 555666679999999999999999999998744 99999999988
Q ss_pred CccC
Q 005739 599 PCFT 602 (680)
Q Consensus 599 ~~~p 602 (680)
+...
T Consensus 195 ~Kd~ 198 (678)
T KOG0127|consen 195 DKDT 198 (678)
T ss_pred cccc
Confidence 7654
No 91
>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=27.16 E-value=66 Score=28.48 Aligned_cols=42 Identities=17% Similarity=0.184 Sum_probs=32.0
Q ss_pred EEeCceEEEeeCCCCCCeEEEEEEEEeeCC---CceEEEEEeecCh
Q 005739 40 YTLYDCVYLYKEGDAEPHVGKLIKIWENAD---KAKKVKLLWFFRP 82 (680)
Q Consensus 40 YrLGDCVyVkseg~~ePYIGRIvemWE~~D---Gek~VkVqWFyRP 82 (680)
|.+||-|..+-.| -++|=|+|+....+.. ....+.|+||-.+
T Consensus 1 f~vGDlVWaK~kg-~pwWP~~V~~~~~~~~~~~~~~~~~V~fFGs~ 45 (87)
T cd05835 1 FNVGDLVWGKIKG-FPWWPGRVVSITVTSKRPPVVGMRWVTWFGSG 45 (87)
T ss_pred CCCCCEEEEecCC-CCCCCeEEechhhcccccCCCCeEEEEEeCCC
Confidence 4689999998765 4689999999987542 2357999999644
No 92
>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=26.23 E-value=2.7e+02 Score=26.87 Aligned_cols=41 Identities=15% Similarity=0.013 Sum_probs=31.0
Q ss_pred eeEEEEEECCEEEEeCceEEEeeCC-----------CCCCeEEEEEEEEeeC
Q 005739 28 QFYQSFTYDGVEYTLYDCVYLYKEG-----------DAEPHVGKLIKIWENA 68 (680)
Q Consensus 28 ~fYeSft~dG~tYrLGDCVyVkseg-----------~~ePYIGRIvemWE~~ 68 (680)
.||..+-++-+.+.+||+|-|++.. ....-|=.|.+|....
T Consensus 1 i~y~GiflGAE~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~ 52 (139)
T PF10383_consen 1 IYYRGIFLGAEMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRL 52 (139)
T ss_pred CeECeEEEeeEEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEec
Confidence 4899999999999999999995431 1234666777777654
No 93
>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=25.86 E-value=88 Score=27.98 Aligned_cols=39 Identities=15% Similarity=0.111 Sum_probs=31.1
Q ss_pred EEeCceEEEeeCCCCCCeEEEEEEEEeeCCCceEEEEEeecCh
Q 005739 40 YTLYDCVYLYKEGDAEPHVGKLIKIWENADKAKKVKLLWFFRP 82 (680)
Q Consensus 40 YrLGDCVyVkseg~~ePYIGRIvemWE~~DGek~VkVqWFyRP 82 (680)
|.+||.|.-+-.+ -|+|-|+|.++-. +...+.|.||=..
T Consensus 1 f~~gdlVWaK~~g-~P~WPa~I~~~~~---~~~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQG-YPWWPAVIKSISR---KKQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCCC-CCCCCEEEeeecC---CCCEEEEEEeCCC
Confidence 4689999998765 4789999998854 3678999999777
No 94
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=25.24 E-value=1.6e+02 Score=24.78 Aligned_cols=41 Identities=20% Similarity=0.259 Sum_probs=26.8
Q ss_pred eeEEEEEECCEEEEeCceEEEeeCCC-CCCeEEEEEEEEeeC
Q 005739 28 QFYQSFTYDGVEYTLYDCVYLYKEGD-AEPHVGKLIKIWENA 68 (680)
Q Consensus 28 ~fYeSft~dG~tYrLGDCVyVkseg~-~ePYIGRIvemWE~~ 68 (680)
.+..........++.||-|++...+. ...+|.||+.+|--.
T Consensus 20 v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~~~~~g 61 (85)
T cd06530 20 VLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIGYFVLG 61 (85)
T ss_pred EEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEEEEEee
Confidence 44443333334577899999887764 467899998866533
No 95
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=24.30 E-value=1.1e+02 Score=35.72 Aligned_cols=65 Identities=22% Similarity=0.345 Sum_probs=51.6
Q ss_pred chhHHHHHHHHHHhcccc------ceeccCC---CCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeeec
Q 005739 528 TSTVVEDLVWHAFKENCS------AKMIPRV---AFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 596 (680)
Q Consensus 528 ts~eVedlv~~a~ke~c~------AkmI~~~---~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~ 596 (680)
.-.|+|+|+ ..+++.|. -=+|||. .+.-|-.|+-||=|.+-++++.|+..|.-. . =+||-+|+|.
T Consensus 415 dd~EyeeIl-Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~Gr-K--F~nRtVvtsY 488 (500)
T KOG0120|consen 415 DDEEYEEIL-EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGR-K--FANRTVVASY 488 (500)
T ss_pred chHHHHHHH-HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCc-e--eCCcEEEEEe
Confidence 455777765 67898884 3488998 456667789999999999999999999754 4 3899999885
No 96
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=22.52 E-value=79 Score=38.11 Aligned_cols=76 Identities=26% Similarity=0.246 Sum_probs=59.6
Q ss_pred cccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceee
Q 005739 514 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 593 (680)
Q Consensus 514 ~G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~ 593 (680)
+||=+|++||-=.-|.-||+.|. .+|-+--+.++-.+ .=-.-|.|-+||=|-|..-|..|+..|-.--| .||-||
T Consensus 612 ~~tKIlVRNipFeAt~rEVr~LF-~aFGqlksvRlPKK-~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHl---yGRrLV 686 (725)
T KOG0110|consen 612 KGTKILVRNIPFEATKREVRKLF-TAFGQLKSVRLPKK-IGKGAHRGFGFVDFLTPREAKNAFDALGSTHL---YGRRLV 686 (725)
T ss_pred ccceeeeeccchHHHHHHHHHHH-hcccceeeeccchh-hcchhhccceeeeccCcHHHHHHHHhhcccce---echhhh
Confidence 38999999998888999999886 57766556665545 33456889999999999999999999985555 577666
Q ss_pred e
Q 005739 594 G 594 (680)
Q Consensus 594 ~ 594 (680)
=
T Consensus 687 L 687 (725)
T KOG0110|consen 687 L 687 (725)
T ss_pred e
Confidence 3
No 97
>PRK03187 tgl transglutaminase; Provisional
Probab=22.20 E-value=44 Score=36.05 Aligned_cols=19 Identities=32% Similarity=0.555 Sum_probs=15.6
Q ss_pred EECCEEEEeCceEEEeeCC
Q 005739 34 TYDGVEYTLYDCVYLYKEG 52 (680)
Q Consensus 34 t~dG~tYrLGDCVyVkseg 52 (680)
+.-|..|.+||||||++++
T Consensus 160 t~~g~~~~PGD~vYFkNPd 178 (272)
T PRK03187 160 TKTGGDFLPGDCVYFKNPD 178 (272)
T ss_pred EecCCCCCCCcEEEecCCC
Confidence 3456788999999999976
No 98
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=21.31 E-value=60 Score=34.86 Aligned_cols=48 Identities=23% Similarity=0.390 Sum_probs=38.8
Q ss_pred cCCCCCCCCCceeEEEEeehhHHHHHHHhhccceeeecCCceeeeecCCCc
Q 005739 550 PRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIGTPC 600 (680)
Q Consensus 550 ~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~egcl~ls~gRpl~~s~~~~~ 600 (680)
.+.-...---|-+||-|+.=|.|+.|+.-|+..=+ +|||++|=+.-.+
T Consensus 101 Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~---~G~pi~ae~~pvT 148 (260)
T KOG2202|consen 101 VCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWY---NGRPIHAELSPVT 148 (260)
T ss_pred hhcccchhhhhhhhhhcccHHHHHHHHHHHcCccc---cCCcceeeecCcC
Confidence 33444445579999999999999999999999976 9999998776443
No 99
>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=21.08 E-value=1.2e+02 Score=26.29 Aligned_cols=40 Identities=20% Similarity=0.178 Sum_probs=30.6
Q ss_pred EEeCceEEEeeCCCCCCeEEEEEEEEeeCC------CceEEEEEeec
Q 005739 40 YTLYDCVYLYKEGDAEPHVGKLIKIWENAD------KAKKVKLLWFF 80 (680)
Q Consensus 40 YrLGDCVyVkseg~~ePYIGRIvemWE~~D------Gek~VkVqWFy 80 (680)
|++||.|..+-.+ -+.|=|+|+...+... ....+.|+||-
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 4689999998865 3689999999987532 24578888886
No 100
>PF13041 PPR_2: PPR repeat family
Probab=20.91 E-value=1.1e+02 Score=23.45 Aligned_cols=30 Identities=20% Similarity=0.264 Sum_probs=26.9
Q ss_pred CCcchhhhhhhhhHhHHHHHHHHHHHHHHH
Q 005739 637 PNSLEYDMAIEWSLLQERLDCAWKKLYEQQ 666 (680)
Q Consensus 637 PN~iEydma~eW~l~qe~~~~~~~~l~~~~ 666 (680)
||.+-|.-.|.++..+.+.+.+|+.+-+-+
T Consensus 1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~ 30 (50)
T PF13041_consen 1 PDVVTYNTLISGYCKAGKFEEALKLFKEMK 30 (50)
T ss_pred CchHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 899999999999999999999998775544
No 101
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=20.59 E-value=1.7e+02 Score=32.07 Aligned_cols=65 Identities=17% Similarity=0.227 Sum_probs=49.9
Q ss_pred ccEEEEecCCCCCchhHHHHHHHHHHhccccceeccCCCCCCCCCceeEEEEeehhHHHHHHHhhcc
Q 005739 515 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEE 581 (680)
Q Consensus 515 G~lvllqNLdps~ts~eVedlv~~a~ke~c~AkmI~~~~~ssp~~G~A~vIFkt~eaae~ai~kl~e 581 (680)
|.=+|+..|--+.|--|+|+|+.. |-.--|.|...-- ..--.-|-+|+=|-.|+-||.||.-||.
T Consensus 127 ~aNLYvSGlPktMtqkelE~iFs~-fGrIItSRiL~dq-vtg~srGVgFiRFDKr~EAe~AIk~lNG 191 (360)
T KOG0145|consen 127 DANLYVSGLPKTMTQKELEQIFSP-FGRIITSRILVDQ-VTGLSRGVGFIRFDKRIEAEEAIKGLNG 191 (360)
T ss_pred ccceEEecCCccchHHHHHHHHHH-hhhhhhhhhhhhc-ccceecceeEEEecchhHHHHHHHhccC
Confidence 445789999999999999998865 5555555544322 2244567899999999999999999873
Done!