Query 000633
Match_columns 1380
No_of_seqs 201 out of 511
Neff 3.2
Searched_HMMs 46136
Date Mon Apr 1 21:08:38 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000633hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1904 Transcription coactiva 99.9 3.8E-23 8.3E-28 239.0 15.5 234 20-416 11-244 (496)
2 cd05834 HDGF_related The PWWP 99.9 1.2E-22 2.6E-27 187.7 8.3 81 21-106 2-82 (83)
3 cd05836 N_Pac_NP60 The PWWP do 99.9 2.9E-22 6.4E-27 186.1 8.3 84 22-108 1-86 (86)
4 PF12243 CTK3: CTD kinase subu 99.9 5.1E-22 1.1E-26 199.2 10.6 124 859-985 5-136 (139)
5 cd05840 SPBC215_ISWI_like The 99.9 7.7E-22 1.7E-26 185.9 8.3 85 22-106 1-92 (93)
6 cd05835 Dnmt3b_related The PWW 99.8 2E-21 4.3E-26 180.5 8.1 85 22-107 1-86 (87)
7 cd05838 WHSC1_related The PWWP 99.8 5.5E-21 1.2E-25 180.3 8.5 89 22-110 1-94 (95)
8 cd05162 PWWP The PWWP domain, 99.8 9.4E-21 2E-25 173.6 9.3 82 22-106 1-86 (87)
9 PF00855 PWWP: PWWP domain; I 99.8 7.1E-21 1.5E-25 171.7 5.1 85 22-107 1-86 (86)
10 cd05841 BS69_related The PWWP 99.8 2.6E-20 5.6E-25 173.2 7.1 77 20-106 5-82 (83)
11 cd05837 MSH6_like The PWWP dom 99.7 1.1E-17 2.4E-22 161.6 9.2 89 21-109 2-104 (110)
12 smart00293 PWWP domain with co 99.7 7.5E-18 1.6E-22 148.0 6.7 58 22-79 1-63 (63)
13 cd06080 MUM1_like Mutated mela 99.6 5.2E-16 1.1E-20 143.8 7.9 77 22-106 1-78 (80)
14 smart00582 RPR domain present 99.6 2.2E-15 4.7E-20 144.3 9.4 109 863-980 1-119 (121)
15 cd05839 BR140_related The PWWP 99.6 2.2E-15 4.8E-20 147.0 7.1 85 22-106 1-110 (111)
16 cd03562 CID CID (CTD-Interacti 98.9 1.8E-09 4E-14 103.3 6.9 106 864-974 7-114 (114)
17 KOG1924 RhoA GTPase effector D 98.9 2.6E-09 5.7E-14 128.2 9.4 26 859-884 332-357 (1102)
18 KOG1924 RhoA GTPase effector D 98.8 1.3E-08 2.8E-13 122.4 10.6 12 896-907 386-397 (1102)
19 KOG0132 RNA polymerase II C-te 98.6 1.6E-07 3.5E-12 113.6 9.2 117 857-985 7-136 (894)
20 PF04818 CTD_bind: RNA polymer 98.3 3.9E-07 8.5E-12 80.2 2.8 58 914-973 1-64 (64)
21 KOG2669 Regulator of nuclear m 97.8 6.7E-05 1.5E-09 85.5 9.0 118 861-985 6-130 (325)
22 KOG0151 Predicted splicing reg 97.8 6.6E-05 1.4E-09 91.1 8.9 122 859-982 431-567 (877)
23 KOG1830 Wiskott Aldrich syndro 97.1 0.022 4.8E-07 67.1 18.6 35 951-985 139-180 (518)
24 KOG1081 Transcription factor N 97.0 0.00036 7.9E-09 82.9 2.7 93 20-117 134-226 (463)
25 PHA03247 large tegument protei 96.4 0.065 1.4E-06 73.4 17.0 26 965-990 2411-2440(3151)
26 PHA03247 large tegument protei 96.1 0.22 4.8E-06 68.7 19.1 32 900-931 2374-2411(3151)
27 KOG3671 Actin regulatory prote 95.6 0.12 2.7E-06 62.2 13.0 15 918-932 66-80 (569)
28 KOG0132 RNA polymerase II C-te 95.5 0.82 1.8E-05 57.8 19.7 20 954-973 465-484 (894)
29 KOG3671 Actin regulatory prote 94.0 0.69 1.5E-05 56.2 13.5 16 897-912 81-96 (569)
30 KOG4368 Predicted RNA binding 93.8 0.19 4.1E-06 61.4 8.3 108 874-981 118-231 (757)
31 KOG4849 mRNA cleavage factor I 92.5 1.9 4.1E-05 50.7 13.5 28 937-964 55-87 (498)
32 KOG1923 Rac1 GTPase effector F 90.2 0.95 2.1E-05 57.2 8.7 53 967-1023 165-220 (830)
33 smart00333 TUDOR Tudor domain. 89.9 0.42 9E-06 40.9 3.9 53 21-79 2-54 (57)
34 KOG1830 Wiskott Aldrich syndro 89.5 4.1 8.8E-05 49.1 12.6 11 1021-1031 224-234 (518)
35 COG5178 PRP8 U5 snRNP spliceos 88.2 0.32 7E-06 62.8 2.9 18 1126-1143 10-27 (2365)
36 smart00743 Agenet Tudor-like d 87.6 0.72 1.6E-05 40.5 3.9 51 21-77 2-55 (61)
37 KOG0119 Splicing factor 1/bran 87.1 8 0.00017 47.5 13.2 13 1231-1243 497-509 (554)
38 KOG1923 Rac1 GTPase effector F 86.7 2.5 5.3E-05 53.8 9.0 14 1079-1094 238-251 (830)
39 COG5178 PRP8 U5 snRNP spliceos 85.3 0.6 1.3E-05 60.6 3.1 28 1124-1151 4-32 (2365)
40 KOG4849 mRNA cleavage factor I 85.3 9.7 0.00021 45.2 12.3 8 905-912 115-122 (498)
41 KOG4672 Uncharacterized conser 84.6 13 0.00029 44.8 13.2 24 1007-1030 171-207 (487)
42 PRK15319 AIDA autotransporter- 84.3 1.3 2.9E-05 60.3 5.6 67 281-350 441-515 (2039)
43 KOG2071 mRNA cleavage and poly 84.1 1.3 2.7E-05 55.0 4.9 99 860-967 5-110 (579)
44 KOG4672 Uncharacterized conser 82.3 34 0.00074 41.6 15.2 28 846-877 8-35 (487)
45 cd04508 TUDOR Tudor domains ar 78.5 2.2 4.9E-05 35.3 3.1 47 25-77 1-48 (48)
46 cd03561 VHS VHS domain family; 75.6 6.2 0.00013 40.0 5.9 85 885-970 24-114 (133)
47 PRK09752 adhesin; Provisional 74.3 2.7 5.8E-05 55.7 3.7 10 1344-1353 1122-1131(1250)
48 PF15057 DUF4537: Domain of un 72.5 6.5 0.00014 40.1 5.2 60 19-80 53-114 (124)
49 cd00197 VHS_ENTH_ANTH VHS, ENT 69.4 14 0.00031 36.1 6.6 75 892-967 33-114 (115)
50 KOG0307 Vesicle coat complex C 67.0 3.1E+02 0.0068 37.3 19.2 21 404-424 220-240 (1049)
51 PF04858 TH1: TH1 protein; In 66.2 45 0.00097 42.2 11.4 130 855-984 376-532 (584)
52 PF11717 Tudor-knot: RNA bindi 65.1 5.4 0.00012 35.2 2.5 52 22-76 1-54 (55)
53 PRK09752 adhesin; Provisional 64.9 5.4 0.00012 53.1 3.5 11 1033-1043 825-835 (1250)
54 KOG2675 Adenylate cyclase-asso 63.1 4.8 0.0001 48.7 2.4 9 861-869 50-58 (480)
55 PRK15319 AIDA autotransporter- 62.3 5.8 0.00013 54.7 3.2 8 1035-1042 1582-1589(2039)
56 KOG1925 Rac1 GTPase effector F 60.6 7.8 0.00017 47.7 3.5 6 1086-1091 166-171 (817)
57 KOG4264 Nucleo-cytoplasmic pro 54.5 59 0.0013 40.8 9.3 20 1336-1355 657-676 (694)
58 KOG0307 Vesicle coat complex C 53.7 4.1E+02 0.0088 36.3 16.9 26 960-985 618-645 (1049)
59 PF08169 RBB1NT: RBB1NT (NUC16 52.6 17 0.00038 36.4 3.9 80 24-110 8-90 (96)
60 KOG1080 Histone H3 (Lys4) meth 51.6 6.6 0.00014 51.8 1.1 95 19-113 189-297 (1005)
61 KOG2893 Zn finger protein [Gen 50.7 2.6E+02 0.0057 32.5 12.9 17 1268-1285 226-242 (341)
62 PRK15313 autotransport protein 49.5 39 0.00085 44.7 7.3 11 1033-1043 473-483 (955)
63 PF00790 VHS: VHS domain; Int 48.1 35 0.00076 34.9 5.4 84 886-970 30-120 (140)
64 TIGR01628 PABP-1234 polyadenyl 45.6 76 0.0017 38.9 8.6 8 1034-1041 313-320 (562)
65 KOG1070 rRNA processing protei 40.1 94 0.002 43.1 8.6 105 851-968 1574-1679(1710)
66 PLN00104 MYST -like histone ac 35.7 34 0.00073 42.1 3.6 58 20-77 52-113 (450)
67 PF01213 CAP_N: Adenylate cycl 35.2 13 0.00027 43.6 0.0 13 857-869 42-54 (312)
68 PF12348 CLASP_N: CLASP N term 34.6 1.7E+02 0.0036 31.3 8.1 101 860-963 92-204 (228)
69 smart00288 VHS Domain present 34.4 83 0.0018 32.3 5.6 82 886-969 25-112 (133)
70 PF12868 DUF3824: Domain of un 34.3 65 0.0014 34.1 4.9 20 1240-1259 101-120 (137)
71 KOG2675 Adenylate cyclase-asso 31.8 33 0.00072 42.0 2.7 6 1073-1078 202-207 (480)
72 cd06224 REM Guanine nucleotide 30.8 1.5E+02 0.0033 28.6 6.6 19 954-972 65-83 (122)
73 KOG0260 RNA polymerase II, lar 30.7 7.9E+02 0.017 34.5 14.3 38 866-906 1053-1093(1605)
74 PF01213 CAP_N: Adenylate cycl 28.2 19 0.00042 42.1 0.0 11 959-969 114-124 (312)
75 cd03565 VHS_Tom1 VHS domain fa 26.5 99 0.0022 32.3 4.7 74 893-969 35-116 (141)
76 COG5475 Uncharacterized small 26.1 1.3E+02 0.0028 28.2 4.7 52 20-80 3-56 (60)
77 PF06003 SMN: Survival motor n 25.6 60 0.0013 37.2 3.2 59 18-81 65-124 (264)
78 PRK02853 hypothetical protein; 25.1 91 0.002 33.9 4.2 47 863-909 87-140 (161)
79 KOG2391 Vacuolar sorting prote 24.1 1.2E+02 0.0025 36.6 5.2 16 1014-1031 56-71 (365)
80 KOG0260 RNA polymerase II, lar 24.0 1.4E+03 0.03 32.4 14.7 17 895-911 1052-1068(1605)
81 PF06793 UPF0262: Uncharacteri 24.0 66 0.0014 34.9 2.9 48 862-909 83-137 (158)
82 cd03567 VHS_GGA VHS domain fam 23.7 1.3E+02 0.0029 31.5 5.0 74 894-969 36-117 (139)
83 cd04370 BAH BAH, or Bromo Adja 23.2 87 0.0019 29.9 3.4 42 20-63 2-47 (123)
84 KOG4264 Nucleo-cytoplasmic pro 22.1 5.1E+02 0.011 33.2 9.9 6 997-1002 300-305 (694)
85 cd03569 VHS_Hrs_Vps27p VHS dom 21.5 1.5E+02 0.0032 31.1 4.8 74 892-968 37-114 (142)
86 cd03568 VHS_STAM VHS domain fa 21.5 1.4E+02 0.0031 31.3 4.8 87 893-985 34-129 (144)
87 PF15195 TMEM210: TMEM210 fami 21.5 58 0.0012 33.1 1.8 11 1013-1023 50-60 (116)
88 KOG1922 Rho GTPase effector BN 21.5 1.2E+02 0.0027 39.3 5.2 46 1118-1163 315-371 (833)
89 PF10447 EXOSC1: Exosome compo 21.1 56 0.0012 31.8 1.6 14 19-32 66-79 (82)
90 COG1107 Archaea-specific RecJ- 21.0 1.6E+02 0.0034 37.9 5.6 79 910-1018 308-401 (715)
91 PF03154 Atrophin-1: Atrophin- 20.6 2.4E+03 0.051 29.4 19.4 9 1045-1053 124-132 (982)
No 1
>KOG1904 consensus Transcription coactivator [Transcription]
Probab=99.89 E-value=3.8e-23 Score=239.00 Aligned_cols=234 Identities=34% Similarity=0.467 Sum_probs=166.3
Q ss_pred CCCCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHHHH
Q 000633 20 RQWKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVR 99 (1380)
Q Consensus 20 ~~Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~Fre 99 (1380)
..|++||||||||||||.|||+|.++..+..++..++|.||||||+++|||.+++|++|..++.. +..-.+...+.|++
T Consensus 11 ~~~~~GDLV~AKlkgyp~WParI~~~~~~~~kp~pkky~V~FfGT~e~Afl~p~dlqpy~~~k~~-~g~~~k~~~k~F~~ 89 (496)
T KOG1904|consen 11 GNFKCGDLVFAKLKGYPPWPARIRNGPDGAVKPPPKKYTVFFFGTKETAFLKPKDLQPYMLNKEK-LGKPNKRVWKGFIE 89 (496)
T ss_pred CCCCCCceeeecccCCCCCcccccCcccccccCCCceeEEEEeccCcccccchhhccchhhhhhh-cccchhhhhHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999988763 33212113499999
Q ss_pred HHHHHHHHHHHHhhhcccCcCCCcccccccCCCCCCccccccccccchhhcccccCCCCCCCCCCCCCCCCCCCcccccc
Q 000633 100 AVQEIIDSYEKLKKQDQVDSNSGDELTVANGGNSVNSISHLKDRTEASEATLDSQMKPSNSTAGDGLNLPTEDSPAGRQL 179 (1380)
Q Consensus 100 ALeEAee~~e~LK~qeq~~~~~aee~~~a~~~~~~~s~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~a~~~~ 179 (1380)
|+++|.+++ +... .++...+. +. +..+.-+..
T Consensus 90 av~eI~~a~-----~np~-~~~~~~~~---------~~------------------------~~~~~~~~~--------- 121 (496)
T KOG1904|consen 90 AVEEIREAF-----NNPK-SESDGIFF---------SA------------------------TATGRLLGP--------- 121 (496)
T ss_pred HHHHHHHHh-----cCCC-ccccCccc---------cc------------------------ccccccccc---------
Confidence 999999988 1000 11100000 00 000000000
Q ss_pred cCCCCCCCCCCCCCcCcccccCCCccccccccccCCCccccccccCCccccccCcccchhhhhccccccccccCCCCCCC
Q 000633 180 DALPAKEPLPEQPSENLVAKATPVLTTYSSRKRSGGSRLQSTQRMAPSTRRSRSSTMVESCRLQNLMMPYNNEGKNAEGI 259 (1380)
Q Consensus 180 ~~~~~~~~~~~~p~en~~~~~~~~~~t~S~~kr~~~~~~~~~~~r~~s~rrsrSs~~~~s~r~q~~~~p~~d~gk~~g~~ 259 (1380)
+++ . +.+. ..+|.|++-
T Consensus 122 ----------------------~~~--------------------~-----------~~~~-------~~~~~~~~~--- 138 (496)
T KOG1904|consen 122 ----------------------ENL--------------------F-----------VASS-------VLNDTGNSE--- 138 (496)
T ss_pred ----------------------ccc--------------------c-----------cccc-------ccccccccc---
Confidence 010 0 0000 011233111
Q ss_pred cccccccCceeccccccCCCCCCCCCccCccccccCCccCCCCCceeeeecCccccCCCCccCCCCCccccchhhhcccc
Q 000633 260 SAKSILDGSLIRNKRTRKSPDGSECNDLDSSALMSNGSIEDNSSEIVTVESDAFSLNEGSTVDSGCKVEDSETVLECLDG 339 (1380)
Q Consensus 260 s~~~~~d~~~~~~k~~~~S~~~s~~ddv~Ss~~~~ngs~edn~sei~t~~sd~~slNegs~vds~~~~E~Se~~~e~~e~ 339 (1380)
...|..+.+.++|.+.++++. -+++..+|+..+.|.+...=+...|
T Consensus 139 ---------------------------------~~~~~~~~~~s~~as~e~~~~-~~~~~~~~~~~~~d~~~~~d~~~~~ 184 (496)
T KOG1904|consen 139 ---------------------------------GEPGADENNASEIATPESDNN-RPEGNGEDSSSKVDYSDSTDHFELG 184 (496)
T ss_pred ---------------------------------ccccccccccccccccccccc-CCccCcccccccccccccccccccc
Confidence 223334444555666655554 6788899999999987776677888
Q ss_pred ccccccccccceeeeeeccccCCCCcccccCCCCCccccCccccccccccccccCCcccCCCCCCCCCccCCCCCcc
Q 000633 340 DEMLSKRLDFQIKAVVVKKKRKPNRKRVCNDAVDPPARINTATEVDVSTRNTCHSSENTGGNLDERDFKEDGDEHLP 416 (1380)
Q Consensus 340 ~~~l~~~~d~~~k~vv~kkKRKpnrkr~tnd~~~p~~~~~~~~~l~~~~~~~~~~s~N~~~ns~e~~~k~DGDEHLP 416 (1380)
..+|++++.++|.+.+.++|||..|||.|.+ +... ++.++|-..-+.++.++++|++|+|
T Consensus 185 ~~el~~~~~~~~~~~~~r~~~kg~rkr~ts~-------------~~~~----~~~~~a~~~k~t~~~~~~~~s~krP 244 (496)
T KOG1904|consen 185 GDELNKGKRKPIDTMVKRKKRKGTRKRKTSD-------------AEPK----VQRSQASHEKLTERPCESNGSEKRP 244 (496)
T ss_pred chhhccccccccccccccccCcccccccccc-------------cccc----ccccccchhhccCCCcccccccccc
Confidence 9999999999999999999999999999888 1223 4477777888999999999999999
No 2
>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=99.87 E-value=1.2e-22 Score=187.73 Aligned_cols=81 Identities=51% Similarity=0.835 Sum_probs=71.4
Q ss_pred CCCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHHHHH
Q 000633 21 QWKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVRA 100 (1380)
Q Consensus 21 ~Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~FreA 100 (1380)
+|++||||||||+|||||||+|+++... +...++|+|+|||+++|+||..++|+||++++. .+..+ .|.+.|++|
T Consensus 2 ~f~~GdlVwaK~kGyp~WPa~I~~~~~~--~~~~~~~~V~FfGt~~~a~v~~~~l~pf~~~~~-~~~~~--~k~k~F~~A 76 (83)
T cd05834 2 QFKAGDLVFAKVKGYPAWPARVDEPEDW--KPPGKKYPVYFFGTHETAFLKPEDLFPYTENKK-KFGKP--KKRKGFNEA 76 (83)
T ss_pred CCCCCCEEEEecCCCCCCCEEEeccccc--CCCCCEEEEEEeCCCCEeEECHHHceecccchh-hhccc--cchHHHHHH
Confidence 6999999999999999999999998764 455689999999999999999999999999865 35533 478999999
Q ss_pred HHHHHH
Q 000633 101 VQEIID 106 (1380)
Q Consensus 101 LeEAee 106 (1380)
|+||++
T Consensus 77 v~eie~ 82 (83)
T cd05834 77 VWEIEK 82 (83)
T ss_pred HHHHhh
Confidence 999986
No 3
>cd05836 N_Pac_NP60 The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the nucleus. In addition to the PWWP domain, NP60 also contains an AT-hook and a C-terminal NAD-binding domain. 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=99.86 E-value=2.9e-22 Score=186.08 Aligned_cols=84 Identities=36% Similarity=0.674 Sum_probs=70.8
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCCC--CCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHHHH
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGYS--ADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVR 99 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K--~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~Fre 99 (1380)
|++||||||||+|||||||+|+++.....+ ...+.|+|+|||+++|+||..++|+||++++. .|. +..|.+.|++
T Consensus 1 f~~GDlVwaK~~g~P~WPa~V~~~~~~~~~~~~~~~~~~V~FFG~~~~~wv~~~~l~pF~~~~~-~~~--~~~k~~~F~~ 77 (86)
T cd05836 1 LKLGDLVWAKMKGFPPWPGRIVKPPKDLKKPRGKAKCFFVFFFGSENHAWIKEENIKPYHEHKE-EMI--KLNKGARFQQ 77 (86)
T ss_pred CCCCCEEEEeCCCCCCCCEEEechhhhcccccCCCCeEEEEEeCCCCEEEECHHhCeechhhHH-HHh--cccchHHHHH
Confidence 789999999999999999999996543222 22478999999999999999999999999876 354 2457899999
Q ss_pred HHHHHHHHH
Q 000633 100 AVQEIIDSY 108 (1380)
Q Consensus 100 ALeEAee~~ 108 (1380)
||+||++++
T Consensus 78 Av~~ie~~~ 86 (86)
T cd05836 78 AVDAIEEYI 86 (86)
T ss_pred HHHHHHHhC
Confidence 999999863
No 4
>PF12243 CTK3: CTD kinase subunit gamma CTK3
Probab=99.86 E-value=5.1e-22 Score=199.17 Aligned_cols=124 Identities=27% Similarity=0.464 Sum_probs=118.3
Q ss_pred HHHHHHHHHhhhhchhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh------
Q 000633 859 AALSSFEAVLGSLTRTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK------ 932 (1380)
Q Consensus 859 ~a~~~Fe~~L~tLtRtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k------ 932 (1380)
-||..|.++|.+|+++++||.+||++||+| ++..++++++|+++||++ ++.+|++||||||+|+++|+..+
T Consensus 5 E~r~~F~~~L~~L~aS~qSi~kaa~fAlk~--~~~~edL~~cIle~le~~-~lN~R~nI~~fID~l~e~~~~~~~~~~~Y 81 (139)
T PF12243_consen 5 EVRMQFTQLLRRLNASQQSIQKAAQFALKN--RDMEEDLWSCILEQLEKE-NLNTRINIFYFIDSLCESSQKSKKYNYPY 81 (139)
T ss_pred HHHHHHHHHHHHcchhHHHHHHHHHHHHHc--cccHHHHHHHHHHHHhcc-chhhHHHHHHHHHHHHHHHHhcccccchh
Confidence 367889999999999999999999999999 779999999999999997 99999999999999999998664
Q ss_pred --HHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHHhccCCchHHHHHHHhhhc
Q 000633 933 --AILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWLERRILPESIIRHHMRELD 985 (1380)
Q Consensus 933 --~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWleR~ilpe~~lr~~~~ei~ 985 (1380)
.|+..|||||.+.+|+|+.++.|+++|.|||+.|.+|++|.+.++++.+..|+
T Consensus 82 v~~l~~dL~~Iv~~V~P~~~~g~~N~~~~~kvL~~~~~k~~l~~~~~~~~~~~l~ 136 (139)
T PF12243_consen 82 VSMLQRDLPRIVDAVAPPDNSGAANLKSVRKVLKNWSKKKILDPEEYEEIEASLK 136 (139)
T ss_pred HHHHHHHHHHHHHHhCCCCCccchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHh
Confidence 89999999999999999999999999999999999999999999999999886
No 5
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=99.85 E-value=7.7e-22 Score=185.88 Aligned_cols=85 Identities=34% Similarity=0.543 Sum_probs=76.1
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCC-------CCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCCh
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGY-------SADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRG 94 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~-------K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~ 94 (1380)
|++||||||||+|||||||+|++++..+. +.....|+|+|||+++|+||..++|++|+++.+.+|+.+.++|.
T Consensus 1 f~~GDlVwaK~~GyPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg~~~~~Wv~~~~l~pl~~~~~~~~l~~~~~k~ 80 (93)
T cd05840 1 FQPGDRVLAKVKGFPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFPDGDYYWVPNKDLKPLTEEKIAKFLKKPKRKD 80 (93)
T ss_pred CCCCCEEEEeCCCCCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEeCCCcEEEEChhhcccCCHHHHHHHhhcCCCCC
Confidence 78999999999999999999999765532 23467899999999999999999999999999988998888899
Q ss_pred HHHHHHHHHHHH
Q 000633 95 ADFVRAVQEIID 106 (1380)
Q Consensus 95 K~FreALeEAee 106 (1380)
+.|.+||+.|.+
T Consensus 81 k~l~~ay~~A~~ 92 (93)
T cd05840 81 KELIKAYKAAKD 92 (93)
T ss_pred HHHHHHHHHhcC
Confidence 999999999975
No 6
>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=99.84 E-value=2e-21 Score=180.47 Aligned_cols=85 Identities=25% Similarity=0.388 Sum_probs=72.1
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCC-CCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHHHHH
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGY-SADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVRA 100 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~-K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~FreA 100 (1380)
|.+||||||||+|||||||+|+++..... ....++++|+|||+++|+||.+++|+||.++.+. |....+.|++.|++|
T Consensus 1 f~vGDlVWaK~kg~pwWP~~V~~~~~~~~~~~~~~~~~V~fFGs~~~a~v~~~~l~pf~e~~~~-f~~~~~~k~~~f~~A 79 (87)
T cd05835 1 FNVGDLVWGKIKGFPWWPGRVVSITVTSKRPPVVGMRWVTWFGSGTFSEVSVDKLSPFSEFFKA-FSRYNRKKKGLYKKA 79 (87)
T ss_pred CCCCCEEEEecCCCCCCCeEEechhhcccccCCCCeEEEEEeCCCCEeEECHHHCcChhHhHHH-HhhhhhhhhHHHHHH
Confidence 78999999999999999999999765432 3456789999999999999999999999998763 443444578999999
Q ss_pred HHHHHHH
Q 000633 101 VQEIIDS 107 (1380)
Q Consensus 101 LeEAee~ 107 (1380)
|+||++.
T Consensus 80 i~eA~e~ 86 (87)
T cd05835 80 IYEALEV 86 (87)
T ss_pred HHHHHHc
Confidence 9999874
No 7
>cd05838 WHSC1_related The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP domain. 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=99.83 E-value=5.5e-21 Score=180.34 Aligned_cols=89 Identities=24% Similarity=0.337 Sum_probs=72.2
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCC-----CCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHH
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGY-----SADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGAD 96 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~-----K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~ 96 (1380)
+.+||||||||+|||||||+|+++...+. +...+.|+|+|||+++|+||..++|+||+++....+...++.+.+.
T Consensus 1 ~~~GdlVWaK~~g~pwWPa~V~~~~~~p~~~~~~~~~~~~~~V~Ffgs~~y~Wv~~~~l~pf~e~~~~~~~~~~~~~~~~ 80 (95)
T cd05838 1 PLYGDIVWAKLGNFRWWPAIICDPREVPPNIQVLRHCIGEFCVMFFGTHDYYWVHRGRVFPYQEGDKGFKEQTKSYLAKR 80 (95)
T ss_pred CCcCCEEEEECCCCCCCCeEEcChhhcChhHhhccCCCCeEEEEEeCCCCEEEeccccccchhhhhhhhhhhhhhhhHHH
Confidence 46899999999999999999999765432 2345789999999999999999999999988663222112246789
Q ss_pred HHHHHHHHHHHHHH
Q 000633 97 FVRAVQEIIDSYEK 110 (1380)
Q Consensus 97 FreALeEAee~~e~ 110 (1380)
|++||+||.++++.
T Consensus 81 f~~AleEA~~~~~~ 94 (95)
T cd05838 81 FRKALEEASLAFKG 94 (95)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999998764
No 8
>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=99.83 E-value=9.4e-21 Score=173.63 Aligned_cols=82 Identities=39% Similarity=0.679 Sum_probs=71.2
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCC----CCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHH
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGY----SADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADF 97 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~----K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~F 97 (1380)
|++||||||||+|||||||+|+++..... +...+.|+|+|||+++|+||..++|+||.++.+. . .++.|.+.|
T Consensus 1 f~~GdlVwaK~~g~pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg~~~~~wv~~~~l~pf~~~~~~-~--~~~~k~~~f 77 (87)
T cd05162 1 FRPGDLVWAKMKGYPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFGDKTFAWVGAERLKPFTEHKES-E--AKQSKRKGF 77 (87)
T ss_pred CCCCCEEEEeCCCCCCCCEEEccccccchhhhccCCCCEEEEEEeCCCcEEEeCccceeeccchHHh-h--ccCCccHHH
Confidence 78999999999999999999999776542 3445789999999999999999999999998875 2 345678999
Q ss_pred HHHHHHHHH
Q 000633 98 VRAVQEIID 106 (1380)
Q Consensus 98 reALeEAee 106 (1380)
++||+||++
T Consensus 78 ~~A~~eA~~ 86 (87)
T cd05162 78 KKAYDEALE 86 (87)
T ss_pred HHHHHHHHh
Confidence 999999986
No 9
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=99.82 E-value=7.1e-21 Score=171.73 Aligned_cols=85 Identities=35% Similarity=0.677 Sum_probs=70.4
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCC-CCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHHHHH
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGY-SADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVRA 100 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~-K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~FreA 100 (1380)
|++||||||||+|||||||+|+.+..... +.....|+|+|||+++|+||..++|++|.+... .+..+.+.|.+.|++|
T Consensus 1 f~~GdlVWaK~~g~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg~~~~~wv~~~~i~~f~~~~~-~~~~~~~~k~~~~~~A 79 (86)
T PF00855_consen 1 FRPGDLVWAKLKGYPWWPARVCDPDEKSKKKRKDGHVLVRFFGDNDYAWVKPSNIKPFSEFKE-KLKKKKKKKRKSFRKA 79 (86)
T ss_dssp -STTEEEEEEETTSEEEEEEEEECCHCTSCSSSSTEEEEEETTTTEEEEEEGGGEEECCHHHH-HHHHHHHHHSHHHHHH
T ss_pred CCCCCEEEEEeCCCCCCceEEeecccccccCCCCCEEEEEecCCCCEEEECHHHhhChhhhHH-HHHHhhccchHHHHHH
Confidence 78999999999999999999999865433 345678999999999999999999999996554 4554433467899999
Q ss_pred HHHHHHH
Q 000633 101 VQEIIDS 107 (1380)
Q Consensus 101 LeEAee~ 107 (1380)
|+||+++
T Consensus 80 i~eA~~~ 86 (86)
T PF00855_consen 80 IEEAEEA 86 (86)
T ss_dssp HHHHHHH
T ss_pred HHHHHhC
Confidence 9999874
No 10
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. 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=99.81 E-value=2.6e-20 Score=173.22 Aligned_cols=77 Identities=35% Similarity=0.496 Sum_probs=67.2
Q ss_pred CCCCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeC-CCCeeeecCCCccccchHHHHhhhhhcCCChHHHH
Q 000633 20 RQWKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFG-TQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFV 98 (1380)
Q Consensus 20 ~~Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFG-T~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~Fr 98 (1380)
..+++||||||||+|||||||+|+... .++|+|+||| ++++|||+.++|++|+++... +..+ .|++.|+
T Consensus 5 pc~~p~dLVwAK~kGyp~WPAkV~~~~-------~~~~~V~FFG~t~~~a~v~~~~i~~~~~~~~~-~~~~--~k~~~f~ 74 (83)
T cd05841 5 PCRPPHELVWAKLKGFPYWPAKVMRVE-------DNQVDVRFFGGQHDRAWIPSNNIQPISTEIPQ-QLVK--KRSRGFN 74 (83)
T ss_pred ccCCCCCEEEEeCCCCCCCCEEEeecC-------CCeEEEEEcCCCCCeEEEehHHeeehhhhhhh-hccc--cccHHHH
Confidence 368999999999999999999999864 3799999999 999999999999999988653 4433 3678999
Q ss_pred HHHHHHHH
Q 000633 99 RAVQEIID 106 (1380)
Q Consensus 99 eALeEAee 106 (1380)
+||+||+.
T Consensus 75 ~A~~Eie~ 82 (83)
T cd05841 75 KAMDELEL 82 (83)
T ss_pred HHHHHHHh
Confidence 99999985
No 11
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. 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 pro
Probab=99.72 E-value=1.1e-17 Score=161.62 Aligned_cols=89 Identities=28% Similarity=0.427 Sum_probs=65.4
Q ss_pred CCCcCCEEEEecCCCCCCCeeeeCCCCCC-------CCCCCCeEEEEEeCC-CCeeeecCCCccccchHHHHh--hhhh-
Q 000633 21 QWKVGDLVLAKVKGFPAWPATVSEPEKWG-------YSADWKKVLVFFFGT-QQIAFCNPADVEAFTEEKKQS--LLTK- 89 (1380)
Q Consensus 21 ~Fk~GDLVWAKVKGYPwWPArI~~Pe~~~-------~K~~~nkylV~FFGT-~EyAWV~pkdLkPFsE~kkes--flnK- 89 (1380)
.|++||||||||+|||||||+|++....+ .+...+.|+|+|||+ ++|+||..++|.||++.+.+. ...+
T Consensus 2 ~~~~GdlVWaK~~g~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~~~~aWv~~~~l~pf~~~~~~~~~~~~~~ 81 (110)
T cd05837 2 KYQVGDLVWAKVSGYPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDNPERAWISEKSLKPFKGSKQFESEKGEKF 81 (110)
T ss_pred CCCCCCEEEEeCCCCCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCCCCEEEecHHHccccCCchhhhhhhhhhh
Confidence 69999999999999999999999754432 123467899999997 599999999999999887642 1111
Q ss_pred --cCC-ChHHHHHHHHHHHHHHH
Q 000633 90 --RQG-RGADFVRAVQEIIDSYE 109 (1380)
Q Consensus 90 --rkg-K~K~FreALeEAee~~e 109 (1380)
.+. .++.+..|+.+|+...+
T Consensus 82 ~~~K~~~~~~~~~a~~~~~~~~~ 104 (110)
T cd05837 82 KVRKPNIKKARQKADIAIMQAEK 104 (110)
T ss_pred hccCCcchhHHHHHHHHHHHHHH
Confidence 111 24566666666666333
No 12
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=99.72 E-value=7.5e-18 Score=147.97 Aligned_cols=58 Identities=38% Similarity=0.592 Sum_probs=51.7
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCC-----CCCCCeEEEEEeCCCCeeeecCCCccccc
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGY-----SADWKKVLVFFFGTQQIAFCNPADVEAFT 79 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~-----K~~~nkylV~FFGT~EyAWV~pkdLkPFs 79 (1380)
|++||||||||+|||||||+|+++...+. +...+.|+|+|||+++||||..++|+||+
T Consensus 1 f~~GdlVwaK~~G~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg~~~~awv~~~~l~p~~ 63 (63)
T smart00293 1 FKPGDLVWAKMKGFPWWPALVVSPKETPDNIRKRKRFENLYPVLFFGDKDTAWISSSKLFPLT 63 (63)
T ss_pred CCCCCEEEEECCCCCCCCeEEcCcccCChhHhhccCCCCEEEEEEeCCCCEEEECccceeeCC
Confidence 78999999999999999999999776542 34467899999999999999999999985
No 13
>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=99.63 E-value=5.2e-16 Score=143.84 Aligned_cols=77 Identities=25% Similarity=0.348 Sum_probs=62.1
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeCCC-CeeeecCCCccccchHHHHhhhhhcCCChHHHHHH
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFGTQ-QIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVRA 100 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFGT~-EyAWV~pkdLkPFsE~kkesflnKrkgK~K~FreA 100 (1380)
|.+||||||||+|||||||+|.++.. ..++|+|+|||++ +++|+..++|+||.++..... | ..+.+..+++
T Consensus 1 f~~gdlVWaK~~g~P~WPa~I~~~~~-----~~~k~~V~FfG~~~~~a~~~~~~l~p~~~~~~~~e--k-~~~~~k~ke~ 72 (80)
T cd06080 1 FEKNDLVWAKIQGYPWWPAVIKSISR-----KKQKARVNFIGDNMQSEKKGIRVVKRWLKHFDCTE--K-QKLTNKAKES 72 (80)
T ss_pred CCCCCEEEEeCCCCCCCCEEEeeecC-----CCCEEEEEEeCCCCceeccchhhcccccccHHHHH--H-HHHHHHHHHH
Confidence 78999999999999999999998753 2679999999999 999999999999998876421 1 1134456677
Q ss_pred HHHHHH
Q 000633 101 VQEIID 106 (1380)
Q Consensus 101 LeEAee 106 (1380)
|.+|.+
T Consensus 73 ~~~ai~ 78 (80)
T cd06080 73 YEQAIQ 78 (80)
T ss_pred HHHHhc
Confidence 776653
No 14
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=99.60 E-value=2.2e-15 Score=144.26 Aligned_cols=109 Identities=32% Similarity=0.530 Sum_probs=93.6
Q ss_pred HHHHHhhhhchhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh----------
Q 000633 863 SFEAVLGSLTRTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK---------- 932 (1380)
Q Consensus 863 ~Fe~~L~tLtRtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k---------- 932 (1380)
+|+++|++|+.||++|..+|.+||+++++ +.++|++|.+++.+.+. .+||.+|||+|+|+|.|+.+.
T Consensus 1 ~f~~~L~~L~~s~~~I~~lt~~~~~~~~~--a~~Iv~~i~~~~~~~~~-~~kL~~LYlindIl~n~~~~~~~~f~~~~~~ 77 (121)
T smart00582 1 AFEQKLESLNNSQESIQTLTKWAIEHASH--AKEIVELWEKYIKKAPP-PRKLPLLYLLDSIVQNSKRKYGSEFGDELGP 77 (121)
T ss_pred ChHHHHHhccccHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHhCCc-cceehhHHhHHHHHHHHhhccHHHHHHHHHH
Confidence 49999999999999999999999999995 46899999999988554 799999999999999998762
Q ss_pred HHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHHhccCCchHHHHHH
Q 000633 933 AILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWLERRILPESIIRHH 980 (1380)
Q Consensus 933 ~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWleR~ilpe~~lr~~ 980 (1380)
.+..+|+.++..+ ..+.|+++.|||++|.+|+|||+.+|++.
T Consensus 78 ~~~~~~~~~~~~~------~~~~~~ki~kll~iW~~~~iF~~~~i~~L 119 (121)
T smart00582 78 VFQDALRDVLGAA------NDETKKKIRRLLNIWEERGIFPPSVLRPL 119 (121)
T ss_pred HHHHHHHHHHHhC------CHHHHHHHHHHHHHHhcCCCCCHHHHHHh
Confidence 4445555555432 26899999999999999999999999864
No 15
>cd05839 BR140_related The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, BR140 is disrupted by chromosomal translocations, similar to translocations of WHSC1 in lymphoid multiple myeloma. 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=99.58 E-value=2.2e-15 Score=146.99 Aligned_cols=85 Identities=21% Similarity=0.354 Sum_probs=63.9
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCC--------------------CCCCCeEEEEEeCC-CCeeeecCCCccccch
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGY--------------------SADWKKVLVFFFGT-QQIAFCNPADVEAFTE 80 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~--------------------K~~~nkylV~FFGT-~EyAWV~pkdLkPFsE 80 (1380)
+.+||||||||+|||||||+|+++..-.. ....+.|+|.||++ ..|+||+.++|+||.+
T Consensus 1 ~~pg~lVwaK~~g~P~wPa~iidp~~~~~~~~~~~~p~~~l~~~~~~~~~~~~~~~lV~FFd~~~s~~Wv~~~~l~pl~~ 80 (111)
T cd05839 1 LEPLTLVWAKCRGYPSYPALIIDPKMPRDGVFHNGVPPDVLTLGEARAQNADERLYLVLFFDNKRTWQWLPGDKLEPLGV 80 (111)
T ss_pred CCCcCEeeeeecCCCCCCeEeeCCCCCCcccccCCCCchhhhHHHHHhccCCCcEEEEEEecCCCcceecCHHHCccccc
Confidence 57899999999999999999999753110 12345799999997 7999999999999998
Q ss_pred HHHH---hhh-hhcCCChHHHHHHHHHHHH
Q 000633 81 EKKQ---SLL-TKRQGRGADFVRAVQEIID 106 (1380)
Q Consensus 81 ~kke---sfl-nKrkgK~K~FreALeEAee 106 (1380)
.... ++. .++..+++.++.||+.|++
T Consensus 81 ~~~~D~~kl~~~rk~~~rk~~~~Ay~~Al~ 110 (111)
T cd05839 81 DETLDKLKLKEGRKPSIRKAVQKAYDDALS 110 (111)
T ss_pred chhhhhhhhhhccCHHHHHHHHHHHHHHhc
Confidence 6552 111 1223346678888888765
No 16
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=98.92 E-value=1.8e-09 Score=103.31 Aligned_cols=106 Identities=24% Similarity=0.372 Sum_probs=83.0
Q ss_pred HHHHhhhhchhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh--HHHHHhhhh
Q 000633 864 FEAVLGSLTRTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK--AILTVLPRL 941 (1380)
Q Consensus 864 Fe~~L~tLtRtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k--~iqa~lPRl 941 (1380)
+...|.+|.-++++|...|..|++..+ -+.++|++|.++|.+ ....+||-+|||+|||+|.|+..- .....++.+
T Consensus 7 ~l~~L~~~~~S~~~I~~lt~~a~~~~~--~a~~iv~~i~~~i~~-~~~~~KL~~LYL~dsIvkn~~~~~~~~~~~~~~~~ 83 (114)
T cd03562 7 LLEKLTFNKNSQPSIQTLTKLAIENRK--HAKEIVEIIEKHIKK-CPPEQKLPLLYLLDSIVKNVGRKYKEFFSEFLVPL 83 (114)
T ss_pred HHHHHHcCcccHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHHHcccchHHHHHHHHHHH
Confidence 344444444489999999999999987 678999999999977 555999999999999999998663 555554555
Q ss_pred hhccCCCCChhhhhhHHHHHHHHHHHhccCCch
Q 000633 942 LSAAAPPGNVAQENRRQCLKVLRLWLERRILPE 974 (1380)
Q Consensus 942 L~aaappg~~a~enRrqclKVL~LWleR~ilpe 974 (1380)
+..+.- .....-|.+..|||.+|.+|++|+.
T Consensus 84 f~~~~~--~~~~~~r~kl~rl~~iW~~~~~f~~ 114 (114)
T cd03562 84 FLDAYE--KVDEKTRKKLERLLNIWEERFVFGS 114 (114)
T ss_pred HHHHHH--hCCHHHHHHHHHHHHHccCCCCCCC
Confidence 533332 4467778899999999999999974
No 17
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=98.92 E-value=2.6e-09 Score=128.23 Aligned_cols=26 Identities=15% Similarity=0.042 Sum_probs=13.2
Q ss_pred HHHHHHHHHhhhhchhhhhHHHHHHH
Q 000633 859 AALSSFEAVLGSLTRTKESIGRATRI 884 (1380)
Q Consensus 859 ~a~~~Fe~~L~tLtRtKeSI~raTr~ 884 (1380)
++|+-...+|+.||..+.-|-....-
T Consensus 332 ~mr~gL~~~l~~l~~i~n~~ldvqlk 357 (1102)
T KOG1924|consen 332 FMRDGLHKYLPDLTEINNDILDVQLK 357 (1102)
T ss_pred HHHHhHHHHHHHhhhhccHHHHHHHH
Confidence 35555566666665554444433333
No 18
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=98.82 E-value=1.3e-08 Score=122.45 Aligned_cols=12 Identities=25% Similarity=0.523 Sum_probs=5.6
Q ss_pred HHHHHHHHHhhh
Q 000633 896 KVVEIVARHLES 907 (1380)
Q Consensus 896 ~vv~~l~~~le~ 907 (1380)
+|+++|....+.
T Consensus 386 ~~f~lL~n~vkd 397 (1102)
T KOG1924|consen 386 EVFELLANTVKD 397 (1102)
T ss_pred HHHHHHHHhhhh
Confidence 455555444443
No 19
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=98.55 E-value=1.6e-07 Score=113.56 Aligned_cols=117 Identities=22% Similarity=0.318 Sum_probs=94.0
Q ss_pred hHHHHHHHHHHhhhhchhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh----
Q 000633 857 AHAALSSFEAVLGSLTRTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK---- 932 (1380)
Q Consensus 857 a~~a~~~Fe~~L~tLtRtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k---- 932 (1380)
+...++.|+.+=..++++| |...|..||++.|.+ +.|.-+++|+.+.---..||--||+||||+..+++|.
T Consensus 7 Fn~eL~SL~DsK~~IS~sK--i~~ITkaAikaIk~y---khVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~k 81 (894)
T KOG0132|consen 7 FNGELDSLEDSKPGISGSK--ILKITKAAIKAIKLY---KHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEK 81 (894)
T ss_pred HHHHHHHhhccCCcccHHH--HHHHHHHHHHHHHHH---HHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhcccc
Confidence 3344445555544567777 999999999999977 7888999999999999999999999999999999883
Q ss_pred ---------HHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHHhccCCchHHHHHHHhhhc
Q 000633 933 ---------AILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWLERRILPESIIRHHMRELD 985 (1380)
Q Consensus 933 ---------~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWleR~ilpe~~lr~~~~ei~ 985 (1380)
.+.+.+=-|+-| +.|..-..+.||+||.+.+||.+++|+...+-.+
T Consensus 82 d~F~prf~~n~~~tf~~L~~c-------~~edks~iIrvlNlwqkn~VfK~e~IqpLlDm~~ 136 (894)
T KOG0132|consen 82 DVFGPRFSKNFTGTFQNLYEC-------PQEDKSDIIRVLNLWQKNNVFKSEIIQPLLDMAD 136 (894)
T ss_pred cccCCccchhHHHHHHHHHhc-------CHHHHHHHHHhhhhhhcccchhHHHHHHHHHHHh
Confidence 333443344444 6788888899999999999999999999887655
No 20
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=98.29 E-value=3.9e-07 Score=80.22 Aligned_cols=58 Identities=29% Similarity=0.529 Sum_probs=49.2
Q ss_pred ccceeehhhhHHHhhcchh------HHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHHhccCCc
Q 000633 914 RVDLFFLVDSIMQCSRGMK------AILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWLERRILP 973 (1380)
Q Consensus 914 RvdLffLvDSI~Q~sr~~k------~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWleR~ilp 973 (1380)
||-||||+|+|+|.|+.+. +...+||.++..+...+ ..+.|+++.+||++|.+|+||+
T Consensus 1 KL~~lYl~ndI~q~sk~k~~~~f~~~F~~~l~~~~~~~~~~~--~~~~~~kv~rll~iW~~r~if~ 64 (64)
T PF04818_consen 1 KLALLYLANDILQNSKRKNPDEFAPAFSPVLPDAFAHAYKNV--DPEVRKKVQRLLNIWEERNIFS 64 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHTTHCHHHHHHCCHHHHHHHHCCCS---HHHHHHHHHHHHHHHHCTSS-
T ss_pred CcceeehHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHhhCCCCCC
Confidence 6889999999999998542 77888888887777666 8899999999999999999985
No 21
>KOG2669 consensus Regulator of nuclear mRNA [RNA processing and modification]
Probab=97.79 E-value=6.7e-05 Score=85.45 Aligned_cols=118 Identities=23% Similarity=0.337 Sum_probs=91.3
Q ss_pred HHHHHHHhhhhchhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh---HHHHH
Q 000633 861 LSSFEAVLGSLTRTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK---AILTV 937 (1380)
Q Consensus 861 ~~~Fe~~L~tLtRtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k---~iqa~ 937 (1380)
.++|+..|.+|.-|.|||.-....-|---|+ +..||++-.+-|.+.+.-+|++ ||||.--|+|.| ..| -++++
T Consensus 6 ee~l~~kL~~L~~TQeSIqtlS~Wli~hkk~--a~~IV~~Wl~~~~~~~~~~Kl~-llYLaNDVvQns-krk~~ef~~ef 81 (325)
T KOG2669|consen 6 EEALEKKLAELSNTQESIQTLSLWLIHHKKH--ARLIVDVWLKELKKSSVNHKLT-LLYLANDVVQNS-KRKGPEFVDEF 81 (325)
T ss_pred HHHHHHHHHhccchHHHHHHHHHHHHHHhhh--hhHHHHHHHHHHhccCCCceee-ehhhhHHHHHHh-hhcCchhHHHH
Confidence 4689999999999999999888777776664 4789999999999977777766 999999999999 333 55566
Q ss_pred hhhhhhccCCCCChhhhhhHHH----HHHHHHHHhccCCchHHHHHHHhhhc
Q 000633 938 LPRLLSAAAPPGNVAQENRRQC----LKVLRLWLERRILPESIIRHHMRELD 985 (1380)
Q Consensus 938 lPRlL~aaappg~~a~enRrqc----lKVL~LWleR~ilpe~~lr~~~~ei~ 985 (1380)
-|-++.|.+-- .++-+..| .+|++||.+|+||.+..|..-..-+.
T Consensus 82 ~~v~~~a~~~i---~~~~~~~~k~~l~Rl~nIw~eR~Vf~~~~~~~l~~~l~ 130 (325)
T KOG2669|consen 82 WPVVLKAFAHI---VEETDVKCKKKLGRLINIWEERNVFSPESLVDLEESLG 130 (325)
T ss_pred HHHHHHHHHHH---HHhcchhhhHHHHHHHHHHHHhccCCHHHHHHHHHHhc
Confidence 66666543221 23333444 47999999999999999988777666
No 22
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=97.77 E-value=6.6e-05 Score=91.14 Aligned_cols=122 Identities=24% Similarity=0.423 Sum_probs=99.1
Q ss_pred HHHHHHHHHhhhhchhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhcc-ccccccceeehhhhHHHhhcch------
Q 000633 859 AALSSFEAVLGSLTRTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESES-SLYRRVDLFFLVDSIMQCSRGM------ 931 (1380)
Q Consensus 859 ~a~~~Fe~~L~tLtRtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~es-s~~rRvdLffLvDSI~Q~sr~~------ 931 (1380)
.-|+.||.||..||=-|-+||.|--+||+.|+ .|.+|+|.|.+-|-.+. .++++|-+||||--|.-.|-..
T Consensus 431 ~qRdklE~liR~LTpEk~sIg~aM~FalenA~--aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~ 508 (877)
T KOG0151|consen 431 LQRDKLEDLIRGLTPEKSSIGDAMVFALENAD--AAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASA 508 (877)
T ss_pred HHHHHHHHHHHhcCcccchHHHHHHHHHhhhh--hHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHH
Confidence 35778999999999999999999999999999 67899999999998766 9999999999999998777533
Q ss_pred --hHHHHHhhhhhhc-----cCCCCC-hhhhhhHHHHHHHHHHHhccCCchHHHHHHHh
Q 000633 932 --KAILTVLPRLLSA-----AAPPGN-VAQENRRQCLKVLRLWLERRILPESIIRHHMR 982 (1380)
Q Consensus 932 --k~iqa~lPRlL~a-----aappg~-~a~enRrqclKVL~LWleR~ilpe~~lr~~~~ 982 (1380)
+...+-|++|+-+ -+..|- .+..=.+.++|||+.|.+=-|||+.-|-+.-.
T Consensus 509 YR~~FEa~L~~Ifd~l~~~yr~I~gRIkaE~fkqRV~kVirvWedW~ifpe~~l~~l~~ 567 (877)
T KOG0151|consen 509 YRKSFEATLEDIFDDLNDLYRSIGGRIKAEAFKQRVMKVIRVWEDWAIFPEDFLIGLQN 567 (877)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHH
Confidence 2788888888722 234443 22223566889999999999999988766443
No 23
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=97.15 E-value=0.022 Score=67.11 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=19.2
Q ss_pred hhhhhhHHHHH-------HHHHHHhccCCchHHHHHHHhhhc
Q 000633 951 VAQENRRQCLK-------VLRLWLERRILPESIIRHHMRELD 985 (1380)
Q Consensus 951 ~a~enRrqclK-------VL~LWleR~ilpe~~lr~~~~ei~ 985 (1380)
--|+.-+-.|| .+-||-|.-+---..++|.-|.-.
T Consensus 139 pYRDdgk~gLkfYTdPsyFFDLWKekmLqdted~~kekrk~k 180 (518)
T KOG1830|consen 139 PYRDDGKDGLKFYTDPSYFFDLWKEKMLQDTEDKMKEKRKQK 180 (518)
T ss_pred ccccCCcccceeecCcHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 34555555565 688997754444444444444433
No 24
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=97.00 E-value=0.00036 Score=82.93 Aligned_cols=93 Identities=27% Similarity=0.425 Sum_probs=66.9
Q ss_pred CCCCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHHHH
Q 000633 20 RQWKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVR 99 (1380)
Q Consensus 20 ~~Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~Fre 99 (1380)
..+..||+||-|+..|+||||+|+....+.. ..+..+|+|||. ++|+....++.| +.....++..-.++...+.+
T Consensus 134 ~~~~~~~~vw~~vg~~~~~~c~vc~~~~~~~--~~~~~~~~f~~~--~~~~~~~~~~~~-~g~~~~~l~~~~~~~s~~~~ 208 (463)
T KOG1081|consen 134 KKREVGDLVWSKVGEYPWWPCMVCHDPLLPK--GMKHDHVNFFGC--YAWTHEKRVFPY-EGQSSKLIPHSKKPASTMSE 208 (463)
T ss_pred ccccceeEEeEEcCcccccccceecCcccch--hhccccceeccc--hhhHHHhhhhhc-cchHHHhhhhccccchhhhh
Confidence 4899999999999999999999999776641 111128999999 999999999999 33333444333334567777
Q ss_pred HHHHHHHHHHHHhhhccc
Q 000633 100 AVQEIIDSYEKLKKQDQV 117 (1380)
Q Consensus 100 ALeEAee~~e~LK~qeq~ 117 (1380)
++...+.....++.|.+.
T Consensus 209 ~~~~~~~r~~~~~~q~~~ 226 (463)
T KOG1081|consen 209 KIKEAKARFGKLKAQWEA 226 (463)
T ss_pred hhhcccchhhhcccchhh
Confidence 777777666655555433
No 25
>PHA03247 large tegument protein UL36; Provisional
Probab=96.42 E-value=0.065 Score=73.37 Aligned_cols=26 Identities=23% Similarity=0.308 Sum_probs=12.6
Q ss_pred HHHhccCCchHHHH----HHHhhhccccCC
Q 000633 965 LWLERRILPESIIR----HHMRELDTVTCS 990 (1380)
Q Consensus 965 LWleR~ilpe~~lr----~~~~ei~~~~~~ 990 (1380)
||.+-.-=+..+|| ..|.||=+++.+
T Consensus 2411 LWe~~~~p~~p~irl~~~d~i~eLPyi~~~ 2440 (3151)
T PHA03247 2411 LWEQPDPPGPPDVRFVGSEEIEELPFVSPG 2440 (3151)
T ss_pred eccCCCCCCCCeeEecCcchhhhCCcccCC
Confidence 56654433333333 336666655444
No 26
>PHA03247 large tegument protein UL36; Provisional
Probab=96.08 E-value=0.22 Score=68.68 Aligned_cols=32 Identities=28% Similarity=0.171 Sum_probs=17.9
Q ss_pred HHHHHhhhcc------ccccccceeehhhhHHHhhcch
Q 000633 900 IVARHLESES------SLYRRVDLFFLVDSIMQCSRGM 931 (1380)
Q Consensus 900 ~l~~~le~es------s~~rRvdLffLvDSI~Q~sr~~ 931 (1380)
.|+-+||..| -|..---.|+|||.=.+-.+.+
T Consensus 2374 CL~~QLe~LSaLiAsKPLa~aPPCLvlvD~~m~p~~VL 2411 (3151)
T PHA03247 2374 CLAAQLPALSALIAARPLARSPPCLVLVDISMAPLFVL 2411 (3151)
T ss_pred HHHHHHHHHHHHHhcCcccCCCCeEEEEcCCCceeEEe
Confidence 3555555544 2334446788888765555543
No 27
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=95.65 E-value=0.12 Score=62.19 Aligned_cols=15 Identities=27% Similarity=0.164 Sum_probs=9.2
Q ss_pred eehhhhHHHhhcchh
Q 000633 918 FFLVDSIMQCSRGMK 932 (1380)
Q Consensus 918 ffLvDSI~Q~sr~~k 932 (1380)
+-||+--+|.|.=.+
T Consensus 66 l~lVkD~~~rsyFlr 80 (569)
T KOG3671|consen 66 LCLVKDNAQRSYFLR 80 (569)
T ss_pred EEEeeccccceeeeE
Confidence 356666677666544
No 28
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=95.54 E-value=0.82 Score=57.80 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=10.6
Q ss_pred hhhHHHHHHHHHHHhccCCc
Q 000633 954 ENRRQCLKVLRLWLERRILP 973 (1380)
Q Consensus 954 enRrqclKVL~LWleR~ilp 973 (1380)
++|+..-|||.---+-+|..
T Consensus 465 ~~RqdA~kalqkl~n~kv~~ 484 (894)
T KOG0132|consen 465 VRRQDAEKALQKLSNVKVAD 484 (894)
T ss_pred eehhHHHHHHHHHhcccccc
Confidence 45555666665544444443
No 29
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=94.05 E-value=0.69 Score=56.17 Aligned_cols=16 Identities=38% Similarity=0.600 Sum_probs=7.5
Q ss_pred HHHHHHHHhhhccccc
Q 000633 897 VVEIVARHLESESSLY 912 (1380)
Q Consensus 897 vv~~l~~~le~ess~~ 912 (1380)
+|||+-+||.=|..||
T Consensus 81 l~di~~~rliWdqELY 96 (569)
T KOG3671|consen 81 LVDIVNNRLIWDQELY 96 (569)
T ss_pred EeeecCceeeehHHhh
Confidence 4455555554444443
No 30
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=93.76 E-value=0.19 Score=61.44 Aligned_cols=108 Identities=17% Similarity=0.338 Sum_probs=64.8
Q ss_pred hhhhHHHHHHHHHHhhccCchHH-HHHHHHHHhhhcc-ccccccceeehhhhHHHhhcchh--HHHHHhhhhh-hccCCC
Q 000633 874 TKESIGRATRIAIDCAKFGVSSK-VVEIVARHLESES-SLYRRVDLFFLVDSIMQCSRGMK--AILTVLPRLL-SAAAPP 948 (1380)
Q Consensus 874 tKeSI~raTr~Aidcak~gia~~-vv~~l~~~le~es-s~~rRvdLffLvDSI~Q~sr~~k--~iqa~lPRlL-~aaapp 948 (1380)
||+.|..+-.--+..+|-----+ +...|+.|+..|. .|.-||-|+|||.-++-.|.-.+ -.-+||-|+. ++-...
T Consensus 118 ~kd~is~~k~w~f~~~~s~~~~e~~~~~l~n~~~~~~~~~~lrlh~~ylind~~~hcqrk~~~~~~~~l~~~v~~~yc~~ 197 (757)
T KOG4368|consen 118 TKDAISAGKNWMFSNAKSPPHCELMAGHLRNRITADGAHFELRLHLIYLINDVLHHCQRKQARELLAALQKVVVPIYCTS 197 (757)
T ss_pred hHHHHHHhhhhhhhcCCCchHHHHHHHHHHhhhcccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhh
Confidence 55555555555555554321112 2245666777666 78899999999988877665443 3334444433 111111
Q ss_pred CChhhhhhHH-HHHHHHHHHhccCCchHHHHHHH
Q 000633 949 GNVAQENRRQ-CLKVLRLWLERRILPESIIRHHM 981 (1380)
Q Consensus 949 g~~a~enRrq-clKVL~LWleR~ilpe~~lr~~~ 981 (1380)
-..-.|...| -.|+|.||++|..|-.+||+..-
T Consensus 198 ~~~~~e~~~~~~~~ll~~we~~~yf~ds~~~ql~ 231 (757)
T KOG4368|consen 198 FLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQ 231 (757)
T ss_pred hhhhHhHHHHHHHHHHHHHhhcCchhHHHHHHhh
Confidence 2223344433 34999999999999999998754
No 31
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=92.53 E-value=1.9 Score=50.74 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=17.7
Q ss_pred HhhhhhhccCCCCC-----hhhhhhHHHHHHHH
Q 000633 937 VLPRLLSAAAPPGN-----VAQENRRQCLKVLR 964 (1380)
Q Consensus 937 ~lPRlL~aaappg~-----~a~enRrqclKVL~ 964 (1380)
++|-+.++.||-|. ...|.||-|+-|=+
T Consensus 55 ~~P~~~~~~~~~~~~~~~~~s~~Grk~~~YvGN 87 (498)
T KOG4849|consen 55 VSPTITTVTAPTAIGAKPATSSEGRKYCCYVGN 87 (498)
T ss_pred cCCCcccccccccccCCccccccCceEEEEecc
Confidence 66777766666653 44577777765543
No 32
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=90.17 E-value=0.95 Score=57.22 Aligned_cols=53 Identities=28% Similarity=0.231 Sum_probs=28.3
Q ss_pred HhccCCchHHHHHHHhhhccccCCC--cccccccCCcc-ccccCCCcccccCCccccccC
Q 000633 967 LERRILPESIIRHHMRELDTVTCSS--SAVAYSRRSSR-TERALDDPVRDMEGMLVDEYG 1023 (1380)
Q Consensus 967 leR~ilpe~~lr~~~~ei~~~~~~~--~~~~~~rRpsr-~ERa~dDPiRemegMlVDEYG 1023 (1380)
|+|..=++..|.| ++..++-..-. .+..-.+-.++ .|| +|++.|++-++||-+
T Consensus 165 le~v~~~~~~ish-er~~~v~~~~~s~~A~l~~~s~sl~~er---~~~~~~~~~~~dels 220 (830)
T KOG1923|consen 165 LEFVETPADQISH-ERLQAVEMAQASAPAPLPGASSSLNKER---EPQSYQRKALLDELS 220 (830)
T ss_pred HHhhcchhhhhhH-HHHHHHHHHHhcCcccCchhhhhhhhhh---hHHHHHHHHhcchhH
Confidence 4566666777766 55554332221 11211111111 233 688888888888876
No 33
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=89.90 E-value=0.42 Score=40.89 Aligned_cols=53 Identities=23% Similarity=0.290 Sum_probs=45.6
Q ss_pred CCCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeCCCCeeeecCCCccccc
Q 000633 21 QWKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFGTQQIAFCNPADVEAFT 79 (1380)
Q Consensus 21 ~Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFGT~EyAWV~pkdLkPFs 79 (1380)
.|++|++|.|+...=-|..|+|..... .+.|.|+|...+...||+..+|+++.
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~------~~~~~V~f~D~G~~~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDG------EQLYEVFFIDYGNEEVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECC------CCEEEEEEECCCccEEEeHHHeecCC
Confidence 589999999999666788999998642 27899999999999999999998865
No 34
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=89.53 E-value=4.1 Score=49.14 Aligned_cols=11 Identities=36% Similarity=0.450 Sum_probs=7.1
Q ss_pred ccCCCCccccC
Q 000633 1021 EYGSNSSFQLP 1031 (1380)
Q Consensus 1021 EYGSNa~fqlp 1031 (1380)
-||-|.-|+++
T Consensus 224 ~~g~~~v~~~~ 234 (518)
T KOG1830|consen 224 GNGPNSVFSTR 234 (518)
T ss_pred ccCCcccccCC
Confidence 36667777664
No 35
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=88.21 E-value=0.32 Score=62.85 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCCCCCCCC
Q 000633 1126 QDVPPSSPPLPSSPPPVL 1143 (1380)
Q Consensus 1126 ~~~PP~ppp~p~~PPPPP 1143 (1380)
|||||||+..|++-||||
T Consensus 10 pppppppg~epps~pppP 27 (2365)
T COG5178 10 PPPPPPPGFEPPSQPPPP 27 (2365)
T ss_pred cccccCCCCCCCCCCCCc
Confidence 444555666666654444
No 36
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=87.55 E-value=0.72 Score=40.45 Aligned_cols=51 Identities=22% Similarity=0.172 Sum_probs=38.2
Q ss_pred CCCcCCEEEEec-CCCCCCCeeeeCCCCCCCCCCCCeEEEEEeC--CCCeeeecCCCccc
Q 000633 21 QWKVGDLVLAKV-KGFPAWPATVSEPEKWGYSADWKKVLVFFFG--TQQIAFCNPADVEA 77 (1380)
Q Consensus 21 ~Fk~GDLVWAKV-KGYPwWPArI~~Pe~~~~K~~~nkylV~FFG--T~EyAWV~pkdLkP 77 (1380)
.|+.||+|-|+. ..--||+|+|..... .++|.|+|.+ ..+.-=+...+|.|
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~------~~~~~V~~~~~~~~~~e~v~~~~LRp 55 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG------DGKYLVRYLTESEPLKETVDWSDLRP 55 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC------CCEEEEEECCCCcccEEEEeHHHccc
Confidence 699999999998 346899999997532 4689999998 55555555555554
No 37
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=87.15 E-value=8 Score=47.54 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCCC
Q 000633 1231 TDGPRFHNKPYPP 1243 (1380)
Q Consensus 1231 ~~~~~~~n~gy~~ 1243 (1380)
++|.++|..+|..
T Consensus 497 ~Pg~p~~~~~~~~ 509 (554)
T KOG0119|consen 497 PPGAPFHGGNYNA 509 (554)
T ss_pred CCCCCCCCCCCCC
Confidence 4555666666554
No 38
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=86.66 E-value=2.5 Score=53.80 Aligned_cols=14 Identities=36% Similarity=0.449 Sum_probs=7.4
Q ss_pred cccccccCceecccCC
Q 000633 1079 HILEEVDGELEMEDVA 1094 (1380)
Q Consensus 1079 ~iledVdGelEMEDVs 1094 (1380)
..||---| ||+-.+
T Consensus 238 ~~l~~ki~--emq~~s 251 (830)
T KOG1923|consen 238 RLLETKIG--EMQLAS 251 (830)
T ss_pred HhccCCcc--cccccc
Confidence 35566556 455443
No 39
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=85.34 E-value=0.6 Score=60.61 Aligned_cols=28 Identities=46% Similarity=0.944 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCCCCCCCCC-CCCCCCCCC
Q 000633 1124 LPQDVPPSSPPLPSSPPPV-LPPPPSIPH 1151 (1380)
Q Consensus 1124 ~P~~~PP~ppp~p~~PPPP-PppPP~p~~ 1151 (1380)
+||.-||||||+|+.-||. |||||+|+-
T Consensus 4 lppg~ppppppppg~epps~pppPppPg~ 32 (2365)
T COG5178 4 LPPGNPPPPPPPPGFEPPSQPPPPPPPGV 32 (2365)
T ss_pred CCCCCCcccccCCCCCCCCCCCCccCCCc
Confidence 3456677777777777664 555555543
No 40
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=85.31 E-value=9.7 Score=45.21 Aligned_cols=8 Identities=13% Similarity=0.135 Sum_probs=3.4
Q ss_pred hhhccccc
Q 000633 905 LESESSLY 912 (1380)
Q Consensus 905 le~ess~~ 912 (1380)
+|+-.+..
T Consensus 115 FENR~NGQ 122 (498)
T KOG4849|consen 115 FENRTNGQ 122 (498)
T ss_pred hhcccCCc
Confidence 44444433
No 41
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=84.63 E-value=13 Score=44.84 Aligned_cols=24 Identities=25% Similarity=0.249 Sum_probs=18.4
Q ss_pred CCCcccccCC-------------ccccccCCCCcccc
Q 000633 1007 LDDPVRDMEG-------------MLVDEYGSNSSFQL 1030 (1380)
Q Consensus 1007 ~dDPiRemeg-------------MlVDEYGSNa~fql 1030 (1380)
+++|.|-|.| -||--||---.|-|
T Consensus 171 ~~~pPplp~g~~p~~s~~gPP~~qv~~~~g~k~~~~l 207 (487)
T KOG4672|consen 171 EADPPPLPMGNAPPVSLPGPPNPQLLAPAGIKRKVEL 207 (487)
T ss_pred ccCCCCCCCCCCCCCCCCCCCcccccccccccccccC
Confidence 4789998888 46778888777665
No 42
>PRK15319 AIDA autotransporter-like protein ShdA; Provisional
Probab=84.34 E-value=1.3 Score=60.31 Aligned_cols=67 Identities=25% Similarity=0.483 Sum_probs=42.0
Q ss_pred CCCCCccCcc---ccccCCccC-CCC--Cc--eeeeecCccccCCCCccCCCCCccccchhhhccccccccccccccc
Q 000633 281 GSECNDLDSS---ALMSNGSIE-DNS--SE--IVTVESDAFSLNEGSTVDSGCKVEDSETVLECLDGDEMLSKRLDFQ 350 (1380)
Q Consensus 281 ~s~~ddv~Ss---~~~~ngs~e-dn~--se--i~t~~sd~~slNegs~vds~~~~E~Se~~~e~~e~~~~l~~~~d~~ 350 (1380)
.+.|.=++=| .|..+|.++ ++. +. ..|++ |++.+-.|+.++-+...-.|...|-+ +++-|-++|++.
T Consensus 441 ~s~WtltgdS~vt~Lt~~G~~~~~~~~~~~~~~~~~~-~~l~~qd~s~~~~~~~~~~~~p~i~~--~~~~l~g~l~~~ 515 (2039)
T PRK15319 441 TSQWNMTDPSTVGNLTNDGDITLGNASGSTGTLLTVD-NTLTLQDGSQINATLDTANSSPIIKA--ANVTLDGTLNLS 515 (2039)
T ss_pred CCeEEEeCCceeehhccCCcEEEecCCCCcceEEecc-ceeeecCCCEEEEeecccCCCCeEEe--ccccccceeeec
Confidence 3555433322 456777776 222 22 55666 89999999988888776667665443 357777776654
No 43
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=84.06 E-value=1.3 Score=54.96 Aligned_cols=99 Identities=18% Similarity=0.320 Sum_probs=71.1
Q ss_pred HHHHHHHHhhhhc-hhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcch-h-----
Q 000633 860 ALSSFEAVLGSLT-RTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGM-K----- 932 (1380)
Q Consensus 860 a~~~Fe~~L~tLt-RtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~-k----- 932 (1380)
|...|+..|+.|| +.|.-|---|-+|=+... .|..+|+.|-++|++ -.-..+|+.|||.|||+-..-.. +
T Consensus 5 ~~~dy~s~ledltfnskp~i~~lt~la~En~~--~a~~iv~~iE~hi~k-cpp~~kL~~~y~~dsi~knvg~py~~~fs~ 81 (579)
T KOG2071|consen 5 ACRDYQSSLEDLTFNSKPIINTLTILAEENLP--FAKSIVSAIEAHIAK-CPPSQKLPVMYLLDSIVKNVGSPYTTAFSR 81 (579)
T ss_pred hHHHHHHHHHHHhcCCcchhHHhhHhhhhccc--ccHHHHHHHHHHHhh-CCcccccchhhhhHHHHhhcCCcchhhhhh
Confidence 4456899999997 789999999999999777 667899999999999 45567899999999998754322 1
Q ss_pred HHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHH
Q 000633 933 AILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWL 967 (1380)
Q Consensus 933 ~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWl 967 (1380)
-+=+++-+.... .+.--|.+-.+.+..|.
T Consensus 82 ~l~a~f~~~~~~------vd~r~r~~l~~~~~tw~ 110 (579)
T KOG2071|consen 82 NLVATFICAFTK------VDERTRTSLFKLRATWD 110 (579)
T ss_pred hHHHHHHHHHhh------ccccccchhHhhHHhhc
Confidence 111111111111 13334667779999998
No 44
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=82.31 E-value=34 Score=41.62 Aligned_cols=28 Identities=25% Similarity=0.260 Sum_probs=16.6
Q ss_pred CCcCCCCcchhhHHHHHHHHHHhhhhchhhhh
Q 000633 846 KSVGKWSSCSEAHAALSSFEAVLGSLTRTKES 877 (1380)
Q Consensus 846 ~~~g~lsg~~ea~~a~~~Fe~~L~tLtRtKeS 877 (1380)
..+|+.-..|+++- =++-...|.|.|.-
T Consensus 8 tk~gk~mnPTDqaR----Ke~RKkElKrNKK~ 35 (487)
T KOG4672|consen 8 TKGGKYMNPTDQAR----KEARKKELKRNKKD 35 (487)
T ss_pred ccCCcccCccHHHH----HHHHHHHhhhhHHH
Confidence 34566655565432 35557778888844
No 45
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=78.52 E-value=2.2 Score=35.34 Aligned_cols=47 Identities=28% Similarity=0.266 Sum_probs=39.0
Q ss_pred CCEEEEecCC-CCCCCeeeeCCCCCCCCCCCCeEEEEEeCCCCeeeecCCCccc
Q 000633 25 GDLVLAKVKG-FPAWPATVSEPEKWGYSADWKKVLVFFFGTQQIAFCNPADVEA 77 (1380)
Q Consensus 25 GDLVWAKVKG-YPwWPArI~~Pe~~~~K~~~nkylV~FFGT~EyAWV~pkdLkP 77 (1380)
|++|.|+... --|.+|+|..... .+.+.|+|..-++...|+.++|.+
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~------~~~~~V~f~DyG~~~~v~~~~l~~ 48 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILS------DGKVEVFFVDYGNTEVVPLSDLRP 48 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECC------CCcEEEEEEcCCCcEEEeHHHcCC
Confidence 7899999987 7788999998642 478999999989988888877753
No 46
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=75.59 E-value=6.2 Score=40.01 Aligned_cols=85 Identities=12% Similarity=0.124 Sum_probs=61.8
Q ss_pred HHHhhccC--chHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh----HHHHHhhhhhhccCCCCChhhhhhHH
Q 000633 885 AIDCAKFG--VSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK----AILTVLPRLLSAAAPPGNVAQENRRQ 958 (1380)
Q Consensus 885 Aidcak~g--ia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k----~iqa~lPRlL~aaappg~~a~enRrq 958 (1380)
-.|.++.+ -+.+++..|.+||.. .+.+..+=-|.|+|+++..|-... +-...|-.++.-.........+-|++
T Consensus 24 icd~I~~~~~~~k~a~raL~krl~~-~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~k 102 (133)
T cd03561 24 LCDLINLKPNGPKEAARAIRKKIKY-GNPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREK 102 (133)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHH
Confidence 34555554 678899999999998 577788888999999999996543 22334444444333334567889999
Q ss_pred HHHHHHHHHhcc
Q 000633 959 CLKVLRLWLERR 970 (1380)
Q Consensus 959 clKVL~LWleR~ 970 (1380)
|+.+|.-|-..-
T Consensus 103 il~ll~~W~~~f 114 (133)
T cd03561 103 ALELILAWSESF 114 (133)
T ss_pred HHHHHHHHHHHh
Confidence 999999998743
No 47
>PRK09752 adhesin; Provisional
Probab=74.26 E-value=2.7 Score=55.71 Aligned_cols=10 Identities=30% Similarity=0.581 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q 000633 1344 NRGWAYPPRP 1353 (1380)
Q Consensus 1344 ~~~w~~ppr~ 1353 (1380)
+++|.--|+.
T Consensus 1122 g~gw~LEPQA 1131 (1250)
T PRK09752 1122 GRGVVIEPQA 1131 (1250)
T ss_pred CCCEEEeeeE
Confidence 4566666654
No 48
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=72.52 E-value=6.5 Score=40.08 Aligned_cols=60 Identities=25% Similarity=0.232 Sum_probs=44.7
Q ss_pred cCCCCcCCEEEEecC--CCCCCCeeeeCCCCCCCCCCCCeEEEEEeCCCCeeeecCCCccccch
Q 000633 19 RRQWKVGDLVLAKVK--GFPAWPATVSEPEKWGYSADWKKVLVFFFGTQQIAFCNPADVEAFTE 80 (1380)
Q Consensus 19 ~~~Fk~GDLVWAKVK--GYPwWPArI~~Pe~~~~K~~~nkylV~FFGT~EyAWV~pkdLkPFsE 80 (1380)
...+++||-|+|+-. ++.|=||+|..-.+.. ....+.|.|.||... .++|+...+.....
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~-~~~~~~~~V~f~ng~-~~~vp~~~~~~I~~ 114 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRYGPGTVIAGPERR-ASEDKEYTVRFYNGK-TAKVPRGEVIWISP 114 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEEeCEEEEECcccc-ccCCceEEEEEECCC-CCccchhhEEECCH
Confidence 568999999999964 7778899999722211 345688999999654 77777777777654
No 49
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=69.42 E-value=14 Score=36.09 Aligned_cols=75 Identities=13% Similarity=0.210 Sum_probs=50.6
Q ss_pred CchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh----HHHHHhhhhhhc--cCCCC-ChhhhhhHHHHHHHH
Q 000633 892 GVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK----AILTVLPRLLSA--AAPPG-NVAQENRRQCLKVLR 964 (1380)
Q Consensus 892 gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k----~iqa~lPRlL~a--aappg-~~a~enRrqclKVL~ 964 (1380)
..+.++|+.|.+||.+ .+-+..+=-|+|+|++++.|.... +-..++-.++-- .-..| .....-|.+++.++.
T Consensus 33 ~~~~~~~~~l~kRl~~-~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~~~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~ 111 (115)
T cd00197 33 VGPKEAVDAIKKRINN-KNPHVVLKALTLLEYCVKNCGERFHQEVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQ 111 (115)
T ss_pred ccHHHHHHHHHHHhcC-CcHHHHHHHHHHHHHHHHHccHHHHHHHHHhHHHHHHHHhhccccccCCCChHHHHHHHHHHH
Confidence 3567899999999987 577777788899999999997553 111222222211 11123 245667999999999
Q ss_pred HHH
Q 000633 965 LWL 967 (1380)
Q Consensus 965 LWl 967 (1380)
+|.
T Consensus 112 ~w~ 114 (115)
T cd00197 112 LWA 114 (115)
T ss_pred HHh
Confidence 995
No 50
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.99 E-value=3.1e+02 Score=37.28 Aligned_cols=21 Identities=19% Similarity=0.401 Sum_probs=17.0
Q ss_pred CCCCccCCCCCccccchhhhc
Q 000633 404 ERDFKEDGDEHLPLVKRARVR 424 (1380)
Q Consensus 404 e~~~k~DGDEHLPLVKRARVR 424 (1380)
+++--.-||.|+|-++-+-.|
T Consensus 220 Tql~~As~dd~~PviqlWDlR 240 (1049)
T KOG0307|consen 220 TQLLVASGDDSAPVIQLWDLR 240 (1049)
T ss_pred eeeeeecCCCCCceeEeeccc
Confidence 455556789999999999888
No 51
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=66.16 E-value=45 Score=42.25 Aligned_cols=130 Identities=20% Similarity=0.266 Sum_probs=84.9
Q ss_pred hhhHHHHHHHHHH---hhhhchhhhhHHHHHHHHHHhhcc-CchHHHHHHHHHHhhhccccccccc----eeehhhhHHH
Q 000633 855 SEAHAALSSFEAV---LGSLTRTKESIGRATRIAIDCAKF-GVSSKVVEIVARHLESESSLYRRVD----LFFLVDSIMQ 926 (1380)
Q Consensus 855 ~ea~~a~~~Fe~~---L~tLtRtKeSI~raTr~Aidcak~-gia~~vv~~l~~~le~ess~~rRvd----LffLvDSI~Q 926 (1380)
+|...++.+.|.. +..-++....-.+.-+..+.|+++ =|+--|+-.|...|-+++-+....+ +|-|+|-|+.
T Consensus 376 del~~t~~ale~a~~ic~~~~~g~~~~~~el~~L~~~i~~PvVa~GVL~wi~~~l~~~~~~~~~~~~~p~~L~LLdeIa~ 455 (584)
T PF04858_consen 376 DELKSTKQALEKAHAICCNAARGSSELQAELPKLYSCIRYPVVAMGVLRWIESFLTDPSYFSSITELTPVHLALLDEIAT 455 (584)
T ss_pred HHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhCCChhhHHHHHHHHHHhcCcchhhhccccCchHHHHhhHHHh
Confidence 4555544444443 343333222334555677888888 4555578888888887754433223 3559999999
Q ss_pred hhcchh-HHHHHhhhhhhccCCCCC--hhhhhhHHHH----------------HHHHHHHhccCCchHHHHHHHhhh
Q 000633 927 CSRGMK-AILTVLPRLLSAAAPPGN--VAQENRRQCL----------------KVLRLWLERRILPESIIRHHMREL 984 (1380)
Q Consensus 927 ~sr~~k-~iqa~lPRlL~aaappg~--~a~enRrqcl----------------KVL~LWleR~ilpe~~lr~~~~ei 984 (1380)
+.-.+. .|=.+|-++|.+...... ..-|-||.++ +.++-|..+.-+-.++||+|+-++
T Consensus 456 ~Hp~lr~~vl~lL~~~le~~~~~l~~l~~le~kr~ilD~~V~L~s~G~VlPVl~~i~~~~~~~~iD~SLiRyFv~eV 532 (584)
T PF04858_consen 456 RHPLLRPSVLDLLVRLLESEGDELDILVQLELKRTILDRMVHLLSRGYVLPVLEYIRKCWARGDIDPSLIRYFVTEV 532 (584)
T ss_pred cCHhhHHHHHHHHHHHHHccCCcccHHHHHHHHHHHHHHHHHHHhCCeeehHHHHHHHHHhccCCcHHHHHHHHHHH
Confidence 988776 888888899986555443 3467777766 233445566678899999999885
No 52
>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=65.06 E-value=5.4 Score=35.21 Aligned_cols=52 Identities=17% Similarity=0.242 Sum_probs=39.0
Q ss_pred CCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeCCCC--eeeecCCCcc
Q 000633 22 WKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFGTQQ--IAFCNPADVE 76 (1380)
Q Consensus 22 Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFGT~E--yAWV~pkdLk 76 (1380)
|++|+.|+++.+.--|-+|+|+.... +.....|.|.|.|-+. =-||+.++|.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~---~~~~~~YyVHY~g~nkR~DeWV~~~~i~ 54 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIRE---KNGEPEYYVHYQGWNKRLDEWVPESRIR 54 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEE---CTTCEEEEEEETTSTGCC-EEEETTTEE
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEe---cCCCEEEEEEcCCCCCCceeeecHHHcc
Confidence 68999999999667778999998543 2334689999999764 4799888774
No 53
>PRK09752 adhesin; Provisional
Probab=64.87 E-value=5.4 Score=53.11 Aligned_cols=11 Identities=27% Similarity=0.447 Sum_probs=6.3
Q ss_pred ccccCcccCCC
Q 000633 1033 FCMPRMLKDDD 1043 (1380)
Q Consensus 1033 ~~~~~~~ede~ 1043 (1380)
|.+-.+|.||+
T Consensus 825 l~lnT~Lg~D~ 835 (1250)
T PRK09752 825 LLLDSELNGDD 835 (1250)
T ss_pred EEEEeeecCCC
Confidence 44556676654
No 54
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=63.10 E-value=4.8 Score=48.74 Aligned_cols=9 Identities=0% Similarity=0.600 Sum_probs=5.2
Q ss_pred HHHHHHHhh
Q 000633 861 LSSFEAVLG 869 (1380)
Q Consensus 861 ~~~Fe~~L~ 869 (1380)
..+|+.+|.
T Consensus 50 i~Ayd~~i~ 58 (480)
T KOG2675|consen 50 IRAYDDLIS 58 (480)
T ss_pred HHHHHHHHH
Confidence 346766654
No 55
>PRK15319 AIDA autotransporter-like protein ShdA; Provisional
Probab=62.31 E-value=5.8 Score=54.68 Aligned_cols=8 Identities=38% Similarity=0.650 Sum_probs=3.8
Q ss_pred ccCcccCC
Q 000633 1035 MPRMLKDD 1042 (1380)
Q Consensus 1035 ~~~~~ede 1042 (1380)
+--+|.||
T Consensus 1582 lnT~LgdD 1589 (2039)
T PRK15319 1582 LNTVLGDD 1589 (2039)
T ss_pred EEEEECCC
Confidence 34455544
No 56
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=60.57 E-value=7.8 Score=47.66 Aligned_cols=6 Identities=33% Similarity=0.329 Sum_probs=2.6
Q ss_pred Cceecc
Q 000633 1086 GELEME 1091 (1380)
Q Consensus 1086 GelEME 1091 (1380)
.+.|||
T Consensus 166 ~~AE~~ 171 (817)
T KOG1925|consen 166 AAAETE 171 (817)
T ss_pred HHHHHH
Confidence 344444
No 57
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=54.55 E-value=59 Score=40.76 Aligned_cols=20 Identities=20% Similarity=0.404 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 000633 1336 LREPPRYSNRGWAYPPRPMN 1355 (1380)
Q Consensus 1336 p~e~~r~~~~~w~~ppr~~n 1355 (1380)
...|.-.+.++-.-|||..-
T Consensus 657 y~~P~qqQ~t~~p~Ppr~tk 676 (694)
T KOG4264|consen 657 YFDPQQQQGTRQPLPPRSTK 676 (694)
T ss_pred eeChHHhcccCCCCCCCCCc
Confidence 44455566666666666543
No 58
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.65 E-value=4.1e+02 Score=36.30 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=17.2
Q ss_pred HHHHHHHHhccCCc--hHHHHHHHhhhc
Q 000633 960 LKVLRLWLERRILP--ESIIRHHMRELD 985 (1380)
Q Consensus 960 lKVL~LWleR~ilp--e~~lr~~~~ei~ 985 (1380)
+|+..+|++-.=+. ..++..|+.++-
T Consensus 618 ~k~v~~w~~~~~~~~~~~~y~~~~e~l~ 645 (1049)
T KOG0307|consen 618 DKLVEIWLKALDLELAPTSYQDLAEDLM 645 (1049)
T ss_pred hhhHHHHHHhcccccchHHHHHHHHHHH
Confidence 38888999876664 555566655544
No 59
>PF08169 RBB1NT: RBB1NT (NUC162) domain; InterPro: IPR012603 This domain is found N-terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family [].; PDB: 2YRV_A.
Probab=52.57 E-value=17 Score=36.38 Aligned_cols=80 Identities=19% Similarity=0.195 Sum_probs=44.6
Q ss_pred cCCEEEEec--CCCCCCCeeeeCCCCCC-CCCCCCeEEEEEeCCCCeeeecCCCccccchHHHHhhhhhcCCChHHHHHH
Q 000633 24 VGDLVLAKV--KGFPAWPATVSEPEKWG-YSADWKKVLVFFFGTQQIAFCNPADVEAFTEEKKQSLLTKRQGRGADFVRA 100 (1380)
Q Consensus 24 ~GDLVWAKV--KGYPwWPArI~~Pe~~~-~K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~kkesflnKrkgK~K~FreA 100 (1380)
+|-+|.... +.-.|.||.|+.|.-.. ....+.+|+|+=|-+..|+-|..+++..|...... | ....++.|
T Consensus 8 lGkVV~V~~~~~k~~W~PALVVsPsc~ddv~VkKD~~lVRSFkD~KfysV~rkd~~e~~~~~~~----k---~e~s~k~a 80 (96)
T PF08169_consen 8 LGKVVCVESTKKKTSWFPALVVSPSCNDDVTVKKDQCLVRSFKDGKFYSVARKDVREFDIDSLP----K---SESSLKPA 80 (96)
T ss_dssp TTSEEEEE-SS-SS-EEEEEEE--SS-SS----TT-EEEEESSS--EEEE-TTTEE---STTS-----H---HHHHH-HH
T ss_pred cCcEEEEEcCCCCCceeeEEEEcCCccceeeeccceEEEEEeccCceEEEEhhhhhhcccccCC----c---ccchhhHH
Confidence 677777655 33468899999975321 12335689999999999999999999998744211 0 12346788
Q ss_pred HHHHHHHHHH
Q 000633 101 VQEIIDSYEK 110 (1380)
Q Consensus 101 LeEAee~~e~ 110 (1380)
++.|..+++.
T Consensus 81 l~~A~~Fl~~ 90 (96)
T PF08169_consen 81 LDKASTFLKT 90 (96)
T ss_dssp HHHHHHHHHS
T ss_pred HHHHHHHHhc
Confidence 8888877653
No 60
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=51.62 E-value=6.6 Score=51.85 Aligned_cols=95 Identities=25% Similarity=0.356 Sum_probs=63.7
Q ss_pred cCCCCcCCEEEEec-CCCCCCCeeeeCCCCCCCC---C--CCCeEEEEEeCC------CCeeeecCCCccccchHHHH--
Q 000633 19 RRQWKVGDLVLAKV-KGFPAWPATVSEPEKWGYS---A--DWKKVLVFFFGT------QQIAFCNPADVEAFTEEKKQ-- 84 (1380)
Q Consensus 19 ~~~Fk~GDLVWAKV-KGYPwWPArI~~Pe~~~~K---~--~~nkylV~FFGT------~EyAWV~pkdLkPFsE~kke-- 84 (1380)
...|+.|++||+|. ++.+.|+|.+..+...+.. . .....+|.||+. ..++|+....+.+|......
T Consensus 189 ~~~~~~e~~~~~~~~~~~~~~~a~~~d~~~~~~~~v~as~~~~~~~~~~~~~s~~~~~~~~~~~r~~m~~~~~~~~~~~~ 268 (1005)
T KOG1080|consen 189 PEEFTVGDLVWAKSGRNEPPWPAIVIDPIRQAPRGVLASCLPVAACVMFFGNSGVPTERDYAWVRRGMERPFSRPVRPFQ 268 (1005)
T ss_pred CcccccchhhhcccccCCcccccceeehhhcchhhhhccCcchhhhheeeeccCCccccchhhhhhccccccchhhhhcc
Confidence 45899999999998 7999999999997654321 1 123456777772 35999999999998865431
Q ss_pred hhhhhcCCChHHHHHHHHHHHHHHHHHhh
Q 000633 85 SLLTKRQGRGADFVRAVQEIIDSYEKLKK 113 (1380)
Q Consensus 85 sflnKrkgK~K~FreALeEAee~~e~LK~ 113 (1380)
.+..-...+...|.++++++.+...-.++
T Consensus 269 ~~~~~~~~~~~~~e~~~~~~~~~e~~~~~ 297 (1005)
T KOG1080|consen 269 DQTELKREKARSFEQALEEAGLAEQGNWK 297 (1005)
T ss_pred ccccccccCccchhHHHHHhhcccccccc
Confidence 11111122456888888888765444443
No 61
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=50.70 E-value=2.6e+02 Score=32.51 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=7.8
Q ss_pred CCCCCCCCCCCCCCCCCC
Q 000633 1268 EAPHPSNSHRFHPHPNFD 1285 (1380)
Q Consensus 1268 ~~p~psyp~R~h~~~n~~ 1285 (1380)
++--|+|-+ -||.+.+.
T Consensus 226 vp~~pp~~~-~~~~~~~q 242 (341)
T KOG2893|consen 226 VPRTPPYEN-EHEHQDYQ 242 (341)
T ss_pred CCCCCCcCC-cccccccc
Confidence 333355544 45544443
No 62
>PRK15313 autotransport protein MisL; Provisional
Probab=49.45 E-value=39 Score=44.69 Aligned_cols=11 Identities=36% Similarity=0.697 Sum_probs=5.8
Q ss_pred ccccCcccCCC
Q 000633 1033 FCMPRMLKDDD 1043 (1380)
Q Consensus 1033 ~~~~~~~ede~ 1043 (1380)
|.+-.+|.||+
T Consensus 473 l~lnT~LgdD~ 483 (955)
T PRK15313 473 LVFNTVLNDDD 483 (955)
T ss_pred EEEEeEeCCCC
Confidence 34455666553
No 63
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=48.08 E-value=35 Score=34.92 Aligned_cols=84 Identities=12% Similarity=0.126 Sum_probs=53.7
Q ss_pred HHhhccC--chHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchhHH----HHHhhhhhhccCCCCCh-hhhhhHH
Q 000633 886 IDCAKFG--VSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMKAI----LTVLPRLLSAAAPPGNV-AQENRRQ 958 (1380)
Q Consensus 886 idcak~g--ia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k~i----qa~lPRlL~aaappg~~-a~enRrq 958 (1380)
.|+++.+ -+.+++..|.+||.. .+.+.-+=-+.|+|++++.|-..... ..+|-.|.......... ...-|++
T Consensus 30 cD~i~~~~~~~kea~~~l~krl~~-~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~~~~~~~Vk~k 108 (140)
T PF00790_consen 30 CDLINSSPDGAKEAARALRKRLKH-GNPNVQLLALTLLDALVKNCGPRFHREVASKEFLDELVKLIKSKKTDPETPVKEK 108 (140)
T ss_dssp HHHHHTSTTHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTTTHHHSHHHHH
T ss_pred HHHHHcCCccHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccCCCCchhHHHHH
Confidence 4566654 567899999999999 66666666689999999999544311 12332222211111111 1126999
Q ss_pred HHHHHHHHHhcc
Q 000633 959 CLKVLRLWLERR 970 (1380)
Q Consensus 959 clKVL~LWleR~ 970 (1380)
++++|..|-+.-
T Consensus 109 ~l~ll~~W~~~f 120 (140)
T PF00790_consen 109 ILELLQEWAEAF 120 (140)
T ss_dssp HHHHHHHHHHHT
T ss_pred HHHHHHHHHHHH
Confidence 999999998754
No 64
>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=45.56 E-value=76 Score=38.86 Aligned_cols=8 Identities=13% Similarity=0.339 Sum_probs=4.0
Q ss_pred cccCcccC
Q 000633 1034 CMPRMLKD 1041 (1380)
Q Consensus 1034 ~~~~~~ed 1041 (1380)
...+++.|
T Consensus 313 ~~~~i~~d 320 (562)
T TIGR01628 313 TSAKVMLD 320 (562)
T ss_pred EEEEEEEC
Confidence 34455555
No 65
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=40.09 E-value=94 Score=43.05 Aligned_cols=105 Identities=21% Similarity=0.252 Sum_probs=75.3
Q ss_pred CCcchhhHHHHHHHHHHhhhhchhhhhHHHHHHHHHHhhccCchHHHHHHHHHHhhhccccccccceeeh-hhhHHHhhc
Q 000633 851 WSSCSEAHAALSSFEAVLGSLTRTKESIGRATRIAIDCAKFGVSSKVVEIVARHLESESSLYRRVDLFFL-VDSIMQCSR 929 (1380)
Q Consensus 851 lsg~~ea~~a~~~Fe~~L~tLtRtKeSI~raTr~Aidcak~gia~~vv~~l~~~le~ess~~rRvdLffL-vDSI~Q~sr 929 (1380)
|---+||.+||.-...+|..|-+ +|-|+=..++|+=.-|+|-|++--.++...| ++.+||.|||-+ ||- .--.-
T Consensus 1574 Ll~~ne~~aa~~lL~rAL~~lPk-~eHv~~IskfAqLEFk~GDaeRGRtlfEgll---~ayPKRtDlW~VYid~-eik~~ 1648 (1710)
T KOG1070|consen 1574 LLRQNEAEAARELLKRALKSLPK-QEHVEFISKFAQLEFKYGDAERGRTLFEGLL---SAYPKRTDLWSVYIDM-EIKHG 1648 (1710)
T ss_pred HhcccHHHHHHHHHHHHHhhcch-hhhHHHHHHHHHHHhhcCCchhhHHHHHHHH---hhCccchhHHHHHHHH-HHccC
Confidence 33468999999999999999988 7888888999999999999999544444444 578999999975 332 22222
Q ss_pred chhHHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHHh
Q 000633 930 GMKAILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWLE 968 (1380)
Q Consensus 930 ~~k~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWle 968 (1380)
.++.|.-++-|++.--.+++. ---.++-||+
T Consensus 1649 ~~~~vR~lfeRvi~l~l~~kk--------mKfffKkwLe 1679 (1710)
T KOG1070|consen 1649 DIKYVRDLFERVIELKLSIKK--------MKFFFKKWLE 1679 (1710)
T ss_pred CHHHHHHHHHHHHhcCCChhH--------hHHHHHHHHH
Confidence 445777788888755444432 3345677876
No 66
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=35.72 E-value=34 Score=42.10 Aligned_cols=58 Identities=14% Similarity=0.155 Sum_probs=45.8
Q ss_pred CCCCcCCEEEEecCCCCCC-CeeeeCCCCCC-CCCCCCeEEEEEeCCCCe--eeecCCCccc
Q 000633 20 RQWKVGDLVLAKVKGFPAW-PATVSEPEKWG-YSADWKKVLVFFFGTQQI--AFCNPADVEA 77 (1380)
Q Consensus 20 ~~Fk~GDLVWAKVKGYPwW-PArI~~Pe~~~-~K~~~nkylV~FFGT~Ey--AWV~pkdLkP 77 (1380)
..|.+|+.|+|+..+-+-| .|.|+...... .......|.|.|-|.+.+ -||..++|..
T Consensus 52 ~~~~VGekVla~~~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~rLdl 113 (450)
T PLN00104 52 LPLEVGTRVMCRWRFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLEQLDL 113 (450)
T ss_pred ceeccCCEEEEEECCCCCEEEEEEEEEeccCCCCCCCceEEEEEecCCccHhhccCHhhccc
Confidence 4699999999999988888 99999854321 122335799999999988 9999999853
No 67
>PF01213 CAP_N: Adenylate cyclase associated (CAP) N terminal; InterPro: IPR013992 Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [, , , ]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [, ]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed. This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [].; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1TJF_B 1S0P_A.
Probab=35.24 E-value=13 Score=43.60 Aligned_cols=13 Identities=8% Similarity=0.468 Sum_probs=7.3
Q ss_pred hHHHHHHHHHHhh
Q 000633 857 AHAALSSFEAVLG 869 (1380)
Q Consensus 857 a~~a~~~Fe~~L~ 869 (1380)
...++.+|+.+|.
T Consensus 42 ~p~sV~afD~~i~ 54 (312)
T PF01213_consen 42 VPPSVEAFDELIN 54 (312)
T ss_dssp -HHHHHHHHHHHH
T ss_pred CCchHHHHHHHHH
Confidence 3445667776653
No 68
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=34.57 E-value=1.7e+02 Score=31.34 Aligned_cols=101 Identities=27% Similarity=0.300 Sum_probs=59.8
Q ss_pred HHHHHHHHhhhhchhhhhHHHHHHHHHHhhccCch--HHH-HHHHHHHhhhccccccccceeehhhhHHHhh---cch--
Q 000633 860 ALSSFEAVLGSLTRTKESIGRATRIAIDCAKFGVS--SKV-VEIVARHLESESSLYRRVDLFFLVDSIMQCS---RGM-- 931 (1380)
Q Consensus 860 a~~~Fe~~L~tLtRtKeSI~raTr~Aidcak~gia--~~v-v~~l~~~le~ess~~rRvdLffLvDSI~Q~s---r~~-- 931 (1380)
+...+...|+.+..+|..|..++..||+..=..+. .++ +.+|..-+...+..-|..-+-||.--|..+. ...
T Consensus 92 ~~~~l~~Ll~~~~~~~~~i~~~a~~~L~~i~~~~~~~~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~ 171 (228)
T PF12348_consen 92 ADILLPPLLKKLGDSKKFIREAANNALDAIIESCSYSPKILLEILSQGLKSKNPQVREECAEWLAIILEKWGSDSSVLQK 171 (228)
T ss_dssp HHHHHHHHHHGGG---HHHHHHHHHHHHHHHTTS-H--HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHTT-----GGG--
T ss_pred HHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHCCcHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHccchHhhhcc
Confidence 44456667888999999999999999886655444 677 7777777777666666666666666666666 111
Q ss_pred ----hHHHHHhhhhhhccCCCCChhhhhhHHHHHHH
Q 000633 932 ----KAILTVLPRLLSAAAPPGNVAQENRRQCLKVL 963 (1380)
Q Consensus 932 ----k~iqa~lPRlL~aaappg~~a~enRrqclKVL 963 (1380)
+.+-.++-++|..+ -...|+.-|+|+..|
T Consensus 172 ~~~~~~l~~~l~~~l~D~---~~~VR~~Ar~~~~~l 204 (228)
T PF12348_consen 172 SAFLKQLVKALVKLLSDA---DPEVREAARECLWAL 204 (228)
T ss_dssp HHHHHHHHHHHHHHHTSS----HHHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHHCCCC---CHHHHHHHHHHHHHH
Confidence 13444445555442 335677777776554
No 69
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=34.43 E-value=83 Score=32.27 Aligned_cols=82 Identities=13% Similarity=0.181 Sum_probs=53.9
Q ss_pred HHhhccC--chHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh----HHHHHhhhhhhccCCCCChhhhhhHHH
Q 000633 886 IDCAKFG--VSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK----AILTVLPRLLSAAAPPGNVAQENRRQC 959 (1380)
Q Consensus 886 idcak~g--ia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k----~iqa~lPRlL~aaappg~~a~enRrqc 959 (1380)
.|.++.+ .+.+++..|.+||.. .+-+.-+=.|-|+|++++.|-... +-..+|-+|.....+..... +-|.++
T Consensus 25 cD~i~~~~~~~k~a~r~l~krl~~-~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~-~Vk~ki 102 (133)
T smart00288 25 CDLINSTPDGPKDAVRLLKKRLNN-KNPHVALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLP-LVKKRI 102 (133)
T ss_pred HHHHhCCCccHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcH-HHHHHH
Confidence 4555443 367788999999996 555555555779999999995443 33334444443333343333 389999
Q ss_pred HHHHHHHHhc
Q 000633 960 LKVLRLWLER 969 (1380)
Q Consensus 960 lKVL~LWleR 969 (1380)
+.+|.-|-..
T Consensus 103 l~li~~W~~~ 112 (133)
T smart00288 103 LELIQEWADA 112 (133)
T ss_pred HHHHHHHHHH
Confidence 9999999873
No 70
>PF12868 DUF3824: Domain of unknwon function (DUF3824); InterPro: IPR024436 This repeating domain is proline-rich but its function is unknown.
Probab=34.26 E-value=65 Score=34.12 Aligned_cols=20 Identities=30% Similarity=0.762 Sum_probs=11.4
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 000633 1240 PYPPRPPHAPQSNHFSYVQA 1259 (1380)
Q Consensus 1240 gy~~pPPpppP~nqf~y~~~ 1259 (1380)
.|+++|...+|+.++.|.++
T Consensus 101 dYPppP~~~~p~~~~~yp~~ 120 (137)
T PF12868_consen 101 DYPPPPGAVPPPQPYPYPPP 120 (137)
T ss_pred cCCCCCCCCCCCCCCCCCCC
Confidence 44444444456677777554
No 71
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=31.84 E-value=33 Score=42.01 Aligned_cols=6 Identities=33% Similarity=0.595 Sum_probs=2.9
Q ss_pred Cccccc
Q 000633 1073 SMKKHR 1078 (1380)
Q Consensus 1073 ~~~~h~ 1078 (1380)
.++.|+
T Consensus 202 YVk~hh 207 (480)
T KOG2675|consen 202 YVKEHH 207 (480)
T ss_pred HHHHhc
Confidence 355554
No 72
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=30.84 E-value=1.5e+02 Score=28.56 Aligned_cols=19 Identities=37% Similarity=0.559 Sum_probs=14.8
Q ss_pred hhhHHHHHHHHHHHhccCC
Q 000633 954 ENRRQCLKVLRLWLERRIL 972 (1380)
Q Consensus 954 enRrqclKVL~LWleR~il 972 (1380)
..|.++++||+.|++.--.
T Consensus 65 ~~~~~v~~~l~~Wv~~~~~ 83 (122)
T cd06224 65 PIRLRVLNVLRTWVENYPY 83 (122)
T ss_pred HHHHHHHHHHHHHHHhCCC
Confidence 3477799999999997543
No 73
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=30.71 E-value=7.9e+02 Score=34.47 Aligned_cols=38 Identities=34% Similarity=0.564 Sum_probs=19.5
Q ss_pred HHhhhhchhhhhHHH-HHHHHHHhhcc--CchHHHHHHHHHHhh
Q 000633 866 AVLGSLTRTKESIGR-ATRIAIDCAKF--GVSSKVVEIVARHLE 906 (1380)
Q Consensus 866 ~~L~tLtRtKeSI~r-aTr~Aidcak~--gia~~vv~~l~~~le 906 (1380)
+||++| |-+|||+ ||+.-+. .+| ||+.+-|-+=+.||.
T Consensus 1053 emvg~l--AaqsvgePatqmTln-tfh~aGVssknVt~gvprlk 1093 (1605)
T KOG0260|consen 1053 EMVGAL--AAQSVGEPATQMTLN-TFHYAGVSSKNVTLGVPRLK 1093 (1605)
T ss_pred chHhHH--HHHHhCCchhhcccc-hhcccceeeeeeeccCcchh
Confidence 466666 6666765 4444443 333 666654443334433
No 74
>PF01213 CAP_N: Adenylate cyclase associated (CAP) N terminal; InterPro: IPR013992 Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [, , , ]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [, ]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed. This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [].; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1TJF_B 1S0P_A.
Probab=28.17 E-value=19 Score=42.10 Aligned_cols=11 Identities=9% Similarity=-0.009 Sum_probs=5.1
Q ss_pred HHHHHHHHHhc
Q 000633 959 CLKVLRLWLER 969 (1380)
Q Consensus 959 clKVL~LWleR 969 (1380)
..+|-.+..++
T Consensus 114 i~~i~~~ke~n 124 (312)
T PF01213_consen 114 IQKIQEFKEKN 124 (312)
T ss_dssp HHHHHHHHHTT
T ss_pred HHHHHHHHhcc
Confidence 33444555543
No 75
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=26.49 E-value=99 Score=32.28 Aligned_cols=74 Identities=14% Similarity=0.233 Sum_probs=48.0
Q ss_pred chHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh--------HHHHHhhhhhhccCCCCChhhhhhHHHHHHHH
Q 000633 893 VSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK--------AILTVLPRLLSAAAPPGNVAQENRRQCLKVLR 964 (1380)
Q Consensus 893 ia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k--------~iqa~lPRlL~aaappg~~a~enRrqclKVL~ 964 (1380)
-+.++|..|.+||..-.+.+--+=-|-|+|++++.|-... -++.+|=+++. +.+....+=+.+|+.++.
T Consensus 35 ~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~fh~eiask~Fl~e~L~~~i~---~~~~~~~~Vk~kil~li~ 111 (141)
T cd03565 35 GPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFHVLVAKKDFIKDVLVKLIN---PKNNPPTIVQEKVLALIQ 111 (141)
T ss_pred cHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHhhhHHHHHHHc---ccCCCcHHHHHHHHHHHH
Confidence 3567889999999632333333334779999999995432 34443444543 333344567899999999
Q ss_pred HHHhc
Q 000633 965 LWLER 969 (1380)
Q Consensus 965 LWleR 969 (1380)
-|-+-
T Consensus 112 ~W~~~ 116 (141)
T cd03565 112 AWADA 116 (141)
T ss_pred HHHHH
Confidence 99853
No 76
>COG5475 Uncharacterized small protein [Function unknown]
Probab=26.14 E-value=1.3e+02 Score=28.16 Aligned_cols=52 Identities=13% Similarity=0.086 Sum_probs=41.5
Q ss_pred CCCCcCCEEEEecCCCCCCCeeeeCCCCCCCCCCCCeEEEEEeC--CCCeeeecCCCccccch
Q 000633 20 RQWKVGDLVLAKVKGFPAWPATVSEPEKWGYSADWKKVLVFFFG--TQQIAFCNPADVEAFTE 80 (1380)
Q Consensus 20 ~~Fk~GDLVWAKVKGYPwWPArI~~Pe~~~~K~~~nkylV~FFG--T~EyAWV~pkdLkPFsE 80 (1380)
..|..||.|--|-.| |+|++..-. ..+.|..+||. ..+++=..++.|.|+..
T Consensus 3 ~~FstgdvV~lKsGG----P~Mtvs~~s-----s~Gmy~C~Wf~g~g~~~~~F~ed~Lvp~~a 56 (60)
T COG5475 3 MSFSTGDVVTLKSGG----PRMTVSGYS-----SDGMYECRWFDGYGVKREAFHEDELVPGEA 56 (60)
T ss_pred ceeecCcEEEeecCC----ceEEEeccc-----cCCeEEEEEecCCCcccccccccceecccc
Confidence 479999999999887 888887432 23789999997 46788888899988764
No 77
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=25.65 E-value=60 Score=37.20 Aligned_cols=59 Identities=24% Similarity=0.369 Sum_probs=40.8
Q ss_pred hcCCCCcCCEEEEecCCC-CCCCeeeeCCCCCCCCCCCCeEEEEEeCCCCeeeecCCCccccchH
Q 000633 18 ARRQWKVGDLVLAKVKGF-PAWPATVSEPEKWGYSADWKKVLVFFFGTQQIAFCNPADVEAFTEE 81 (1380)
Q Consensus 18 a~~~Fk~GDLVWAKVKGY-PwWPArI~~Pe~~~~K~~~nkylV~FFGT~EyAWV~pkdLkPFsE~ 81 (1380)
....|++||.+.|+..+= -|-||+|..... ..+.+.|.|.|-++.-.|...+|++....
T Consensus 65 ~~~~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~-----~~~~~~V~f~gYgn~e~v~l~dL~~~~~~ 124 (264)
T PF06003_consen 65 PNKKWKVGDKCMAVYSEDGQYYPATIESIDE-----EDGTCVVVFTGYGNEEEVNLSDLKPSEGD 124 (264)
T ss_dssp TTT---TT-EEEEE-TTTSSEEEEEEEEEET-----TTTEEEEEETTTTEEEEEEGGGEEETT--
T ss_pred cccCCCCCCEEEEEECCCCCEEEEEEEEEcC-----CCCEEEEEEcccCCeEeeehhhhcccccc
Confidence 356999999999985322 245999998542 24578899999999999999999998765
No 78
>PRK02853 hypothetical protein; Provisional
Probab=25.12 E-value=91 Score=33.94 Aligned_cols=47 Identities=28% Similarity=0.310 Sum_probs=36.3
Q ss_pred HHHHHhhhhchhhhhHHHHHH-------HHHHhhccCchHHHHHHHHHHhhhcc
Q 000633 863 SFEAVLGSLTRTKESIGRATR-------IAIDCAKFGVSSKVVEIVARHLESES 909 (1380)
Q Consensus 863 ~Fe~~L~tLtRtKeSI~raTr-------~Aidcak~gia~~vv~~l~~~le~es 909 (1380)
.|...++.--.-=||-+.|.| .|||++++||-++--++|.+||+-.-
T Consensus 87 PfRrvvKDYf~ICeSYy~Air~a~p~qIEaIDMgRRGiHNEgs~lL~eRL~GKi 140 (161)
T PRK02853 87 PFRRVVKDYFMICESYYQAIRTATPSQIEAIDMGRRGLHNEGSELLQERLEGKI 140 (161)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHhHhhhhhhhccccchHHHHHHHHHHcCCe
Confidence 455555555556666666655 68999999999999999999998743
No 79
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.14 E-value=1.2e+02 Score=36.61 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=10.7
Q ss_pred cCCccccccCCCCccccC
Q 000633 1014 MEGMLVDEYGSNSSFQLP 1031 (1380)
Q Consensus 1014 megMlVDEYGSNa~fqlp 1031 (1380)
-.+.-|=+|| .+..+|
T Consensus 56 ~GTIp~~~~G--~tYnIP 71 (365)
T KOG2391|consen 56 DGTIPVPYQG--VTYNIP 71 (365)
T ss_pred cCcccccccC--Ccccce
Confidence 3466677788 566666
No 80
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=24.02 E-value=1.4e+03 Score=32.40 Aligned_cols=17 Identities=18% Similarity=0.198 Sum_probs=10.6
Q ss_pred HHHHHHHHHHhhhcccc
Q 000633 895 SKVVEIVARHLESESSL 911 (1380)
Q Consensus 895 ~~vv~~l~~~le~ess~ 911 (1380)
.++|.+|+-|+--|...
T Consensus 1052 gemvg~lAaqsvgePat 1068 (1605)
T KOG0260|consen 1052 GEMVGALAAQSVGEPAT 1068 (1605)
T ss_pred cchHhHHHHHHhCCchh
Confidence 35667777766666543
No 81
>PF06793 UPF0262: Uncharacterised protein family (UPF0262); InterPro: IPR008321 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.95 E-value=66 Score=34.90 Aligned_cols=48 Identities=27% Similarity=0.321 Sum_probs=37.4
Q ss_pred HHHHHHhhhhchhhhhHHHHHH-------HHHHhhccCchHHHHHHHHHHhhhcc
Q 000633 862 SSFEAVLGSLTRTKESIGRATR-------IAIDCAKFGVSSKVVEIVARHLESES 909 (1380)
Q Consensus 862 ~~Fe~~L~tLtRtKeSI~raTr-------~Aidcak~gia~~vv~~l~~~le~es 909 (1380)
..|...++.--+-=||-+.|.| .|||++++||-++--++|.+||+-.-
T Consensus 83 ~PfRrvikDYf~ICeSYy~Air~a~p~qIEaIDMgRRGlHNEGa~lL~eRL~GKi 137 (158)
T PF06793_consen 83 TPFRRVIKDYFMICESYYEAIRTATPSQIEAIDMGRRGLHNEGAELLQERLEGKI 137 (158)
T ss_pred ccHHHHHHHHHHHHHHHHHHHhhCCHhhhhhhhhhhhccchHHHHHHHHHhcCCc
Confidence 3466666666666677776665 68999999999999999999998743
No 82
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=23.66 E-value=1.3e+02 Score=31.54 Aligned_cols=74 Identities=11% Similarity=0.185 Sum_probs=46.9
Q ss_pred hHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh--------HHHHHhhhhhhccCCCCChhhhhhHHHHHHHHH
Q 000633 894 SSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK--------AILTVLPRLLSAAAPPGNVAQENRRQCLKVLRL 965 (1380)
Q Consensus 894 a~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k--------~iqa~lPRlL~aaappg~~a~enRrqclKVL~L 965 (1380)
+.+++..|.+||.. .+.+.-+=.|.|+|++++.|-... -++.+ =+++..-........+-|.+++.+|..
T Consensus 36 ~k~a~rai~krl~~-~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~el-~kl~~~k~~~~~~~~~Vk~kil~li~~ 113 (139)
T cd03567 36 PQLAVRLLAHKIQS-PQEKEALQALTVLEACMKNCGERFHSEVGKFRFLNEL-IKLVSPKYLGSRTSEKVKTKIIELLYS 113 (139)
T ss_pred HHHHHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHHHH-HHHhccccCCCCCCHHHHHHHHHHHHH
Confidence 45678889999875 343333344558999999996442 23332 233321111124568889999999999
Q ss_pred HHhc
Q 000633 966 WLER 969 (1380)
Q Consensus 966 WleR 969 (1380)
|-+-
T Consensus 114 W~~~ 117 (139)
T cd03567 114 WTLE 117 (139)
T ss_pred HHHH
Confidence 9863
No 83
>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=23.19 E-value=87 Score=29.87 Aligned_cols=42 Identities=26% Similarity=0.265 Sum_probs=31.2
Q ss_pred CCCCcCCEEEEecCC----CCCCCeeeeCCCCCCCCCCCCeEEEEEeC
Q 000633 20 RQWKVGDLVLAKVKG----FPAWPATVSEPEKWGYSADWKKVLVFFFG 63 (1380)
Q Consensus 20 ~~Fk~GDLVWAKVKG----YPwWPArI~~Pe~~~~K~~~nkylV~FFG 63 (1380)
..|++||.|+.+-.. -+.|-|+|...-.. +.....+.|+||-
T Consensus 2 ~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~--~~~~~~~~v~wf~ 47 (123)
T cd04370 2 ITYEVGDSVYVEPDDSIKSDPPYIARIEELWED--TNGSKQVKVRWFY 47 (123)
T ss_pred CEEecCCEEEEecCCcCCCCCCEEEEEeeeeEC--CCCCEEEEEEEEE
Confidence 368999999999877 58999999884321 1234577888876
No 84
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=22.07 E-value=5.1e+02 Score=33.23 Aligned_cols=6 Identities=50% Similarity=0.606 Sum_probs=2.5
Q ss_pred ccCCcc
Q 000633 997 SRRSSR 1002 (1380)
Q Consensus 997 ~rRpsr 1002 (1380)
+|+|+|
T Consensus 300 srnp~r 305 (694)
T KOG4264|consen 300 SRNPMR 305 (694)
T ss_pred CCCccc
Confidence 344444
No 85
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=21.50 E-value=1.5e+02 Score=31.13 Aligned_cols=74 Identities=14% Similarity=0.161 Sum_probs=50.3
Q ss_pred CchHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh----HHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHH
Q 000633 892 GVSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK----AILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWL 967 (1380)
Q Consensus 892 gia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k----~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWl 967 (1380)
.-+.+++..|.+||.. .+.+.-+=.|-|+|++++.|-... +-..+|-+|..-+.+ ....+-|.+|+.++.-|-
T Consensus 37 ~~~k~a~ral~krl~~-~n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~--~~~~~Vk~kil~li~~W~ 113 (142)
T cd03569 37 VQPKYAMRALKKRLLS-KNPNVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIKT--TKNEEVRQKILELIQAWA 113 (142)
T ss_pred CCHHHHHHHHHHHHcC-CChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcc--cCCHHHHHHHHHHHHHHH
Confidence 4477899999999977 555444455679999999984332 333333333332222 556788899999999998
Q ss_pred h
Q 000633 968 E 968 (1380)
Q Consensus 968 e 968 (1380)
.
T Consensus 114 ~ 114 (142)
T cd03569 114 L 114 (142)
T ss_pred H
Confidence 5
No 86
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=21.49 E-value=1.4e+02 Score=31.33 Aligned_cols=87 Identities=13% Similarity=0.193 Sum_probs=55.1
Q ss_pred chHHHHHHHHHHhhhccccccccceeehhhhHHHhhcchh----HHHHH---hhhhhhccCCCCChhhhhhHHHHHHHHH
Q 000633 893 VSSKVVEIVARHLESESSLYRRVDLFFLVDSIMQCSRGMK----AILTV---LPRLLSAAAPPGNVAQENRRQCLKVLRL 965 (1380)
Q Consensus 893 ia~~vv~~l~~~le~ess~~rRvdLffLvDSI~Q~sr~~k----~iqa~---lPRlL~aaappg~~a~enRrqclKVL~L 965 (1380)
-+.++|..|.+||.. .+.+.-+=-|-|+|.+++.|-... +=..+ |-+++.. . ...+-|.+++.+|.-
T Consensus 34 ~~k~a~ral~KRl~~-~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~---~--~~~~Vk~kil~li~~ 107 (144)
T cd03568 34 GAKDCLKAIMKRLNH-KDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLIND---R--VHPTVKEKLREVVKQ 107 (144)
T ss_pred cHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcc---c--CCHHHHHHHHHHHHH
Confidence 355788999999986 455555556779999999996442 11222 3333322 2 466889999999999
Q ss_pred HHhccC--CchHHHHHHHhhhc
Q 000633 966 WLERRI--LPESIIRHHMRELD 985 (1380)
Q Consensus 966 WleR~i--lpe~~lr~~~~ei~ 985 (1380)
|-+.-= -.-..+......|.
T Consensus 108 W~~~f~~~~~l~~i~~~y~~L~ 129 (144)
T cd03568 108 WADEFKNDPSLSLMSDLYKKLK 129 (144)
T ss_pred HHHHhCCCcccHHHHHHHHHHH
Confidence 975432 11224555555554
No 87
>PF15195 TMEM210: TMEM210 family
Probab=21.48 E-value=58 Score=33.08 Aligned_cols=11 Identities=36% Similarity=0.779 Sum_probs=5.3
Q ss_pred ccCCccccccC
Q 000633 1013 DMEGMLVDEYG 1023 (1380)
Q Consensus 1013 emegMlVDEYG 1023 (1380)
-|++-||.-||
T Consensus 50 h~~~Rlv~~~G 60 (116)
T PF15195_consen 50 HMDNRLVGHFG 60 (116)
T ss_pred ccccchhhccc
Confidence 34444555554
No 88
>KOG1922 consensus Rho GTPase effector BNI1 and related formins [Signal transduction mechanisms; Cytoskeleton]
Probab=21.47 E-value=1.2e+02 Score=39.26 Aligned_cols=46 Identities=28% Similarity=0.414 Sum_probs=0.0
Q ss_pred CCCCCCCCCC--------CCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 000633 1118 LSFVPPLPQD--------VPPSSPPL---PSSPPPVLPPPPSIPHSCAFSDSYSNGA 1163 (1380)
Q Consensus 1118 ~~~~Pp~P~~--------~PP~ppp~---p~~PPPPPppPP~p~~~~~~~Dp~~~~~ 1163 (1380)
.++.|+++.+ ++|++++. .+.|+||||||+.+.+....+-+..+..
T Consensus 315 ~~~~p~~~~~~l~~~~~~s~~~~~~~~~~~~~p~pppppp~~~~~~~~~~~~~~~~~ 371 (833)
T KOG1922|consen 315 SPPPPPILTPKLPALISPTPPPPPPPPNNSGGPPPPPPPPGLALPSPPPPLPPLPAL 371 (833)
T ss_pred cCCCCCCCCcccccccCCCCCCCCCCCccCCCCCCCCCCCCccccCCCCCCCCCccc
No 89
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=21.09 E-value=56 Score=31.81 Aligned_cols=14 Identities=36% Similarity=0.567 Sum_probs=10.5
Q ss_pred cCCCCcCCEEEEec
Q 000633 19 RRQWKVGDLVLAKV 32 (1380)
Q Consensus 19 ~~~Fk~GDLVWAKV 32 (1380)
...|++||+|.||+
T Consensus 66 ~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 66 YDCFRPGDIVRARV 79 (82)
T ss_dssp GGT--SSSEEEEEE
T ss_pred HhccCCCCEEEEEE
Confidence 46899999999997
No 90
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=21.03 E-value=1.6e+02 Score=37.92 Aligned_cols=79 Identities=27% Similarity=0.376 Sum_probs=53.4
Q ss_pred ccccccceeehhhhHHHhhcchhHHHHHhhhhhhccCCCCChhhhhhHHHHHHHHHHHhccCC---------------ch
Q 000633 910 SLYRRVDLFFLVDSIMQCSRGMKAILTVLPRLLSAAAPPGNVAQENRRQCLKVLRLWLERRIL---------------PE 974 (1380)
Q Consensus 910 s~~rRvdLffLvDSI~Q~sr~~k~iqa~lPRlL~aaappg~~a~enRrqclKVL~LWleR~il---------------pe 974 (1380)
..+-.++ |||||= ++.+..|+++-+ |.+=||+.+ ..|-|+ =|
T Consensus 308 AeP~~~~--~lvdse--------~lE~L~p~m~~v-------Ak~irrAV~------egRPIiiRHHaDaDG~~agvAlE 364 (715)
T COG1107 308 AEPADVG--FLVDSE--------VLEALKPDMVDV-------AKEIRRAVL------EGRPIIIRHHADADGYCAGVALE 364 (715)
T ss_pred cCCcccc--cccCHH--------HHHHhhHHHHHH-------HHHHHHHHh------cCCceEEecccCcccccchhhHH
Confidence 3444555 999985 788999999988 888888876 222221 24
Q ss_pred HHHHHHHhhhccccCCCcccccccCCccccccCCCcccccCCcc
Q 000633 975 SIIRHHMRELDTVTCSSSAVAYSRRSSRTERALDDPVRDMEGML 1018 (1380)
Q Consensus 975 ~~lr~~~~ei~~~~~~~~~~~~~rRpsr~ERa~dDPiRemegMl 1018 (1380)
..|.+.|+++. ...|.---|+-||||++ |+-|||+..
T Consensus 365 ~AilplI~~~~-~d~DAeyh~~KRrPskA------PfYeleDvt 401 (715)
T COG1107 365 KAILPLIEDVH-PDEDAEYHLFKRRPSKA------PFYELEDVT 401 (715)
T ss_pred HHHHHHHHHhC-CChhhhhHHhhcCcccC------CceeHHhhh
Confidence 55667788877 44444456789999874 666666543
No 91
>PF03154 Atrophin-1: Atrophin-1 family; InterPro: IPR002951 Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA (OMIM:125370) is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins [, ]. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity [].. This entry includes Atrophin-1 and related proteins.
Probab=20.59 E-value=2.4e+03 Score=29.45 Aligned_cols=9 Identities=56% Similarity=0.818 Sum_probs=4.6
Q ss_pred CCCCCCCCc
Q 000633 1045 GSDSDGGSF 1053 (1380)
Q Consensus 1045 ~~~~~~~~~ 1053 (1380)
++++|++++
T Consensus 124 ~es~d~rs~ 132 (982)
T PF03154_consen 124 GESSDGRSV 132 (982)
T ss_pred ccccccccc
Confidence 345555554
Done!