Query 025684
Match_columns 249
No_of_seqs 210 out of 624
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 08:24:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025684.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025684hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3026 Splicing factor SPF30 100.0 1.1E-49 2.4E-54 350.3 12.5 220 2-247 37-261 (262)
2 PF06003 SMN: Survival motor n 99.6 4.9E-16 1.1E-20 141.2 6.6 59 49-107 64-124 (264)
3 smart00333 TUDOR Tudor domain. 99.6 5.4E-15 1.2E-19 103.3 6.2 53 53-106 2-55 (57)
4 cd04508 TUDOR Tudor domains ar 99.6 5.2E-15 1.1E-19 100.2 5.4 47 57-103 1-48 (48)
5 smart00743 Agenet Tudor-like d 99.2 6.2E-11 1.3E-15 84.3 6.5 54 53-106 2-58 (61)
6 PF00567 TUDOR: Tudor domain; 98.9 2.1E-09 4.6E-14 82.9 6.0 55 52-106 50-105 (121)
7 KOG4327 mRNA splicing protein 98.9 9.2E-10 2E-14 95.8 3.9 56 49-104 63-120 (218)
8 KOG2039 Transcriptional coacti 98.8 4.8E-09 1E-13 109.1 5.6 56 52-107 694-750 (875)
9 PF09465 LBR_tudor: Lamin-B re 98.6 1.9E-07 4.2E-12 66.0 7.2 50 52-102 4-55 (55)
10 PF11717 Tudor-knot: RNA bindi 98.4 5.8E-07 1.3E-11 63.3 5.7 48 54-102 1-54 (55)
11 PF05641 Agenet: Agenet domain 98.0 1.6E-05 3.5E-10 58.1 5.7 53 54-106 1-65 (68)
12 PLN00104 MYST -like histone ac 97.7 9E-05 2E-09 72.2 7.5 56 48-103 48-113 (450)
13 PF15057 DUF4537: Domain of un 97.3 0.00049 1.1E-08 56.2 5.7 48 57-105 1-49 (124)
14 PF15057 DUF4537: Domain of un 97.1 0.00077 1.7E-08 55.0 4.9 56 51-107 53-115 (124)
15 PF09038 53-BP1_Tudor: Tumour 97.1 0.0014 3E-08 53.6 6.1 50 55-105 4-54 (122)
16 PF07039 DUF1325: SGF29 tudor- 95.5 0.02 4.4E-07 47.2 4.3 52 50-101 68-125 (130)
17 cd05834 HDGF_related The PWWP 95.4 0.03 6.4E-07 42.7 4.7 53 53-106 2-59 (83)
18 PF00855 PWWP: PWWP domain; I 95.3 0.047 1E-06 40.5 5.5 52 54-106 1-60 (86)
19 cd05162 PWWP The PWWP domain, 94.9 0.063 1.4E-06 40.5 5.1 53 54-107 1-64 (87)
20 PF12148 DUF3590: Protein of u 94.8 0.056 1.2E-06 41.7 4.6 46 60-105 2-57 (85)
21 smart00293 PWWP domain with co 94.7 0.085 1.8E-06 37.8 5.2 50 54-104 1-62 (63)
22 smart00561 MBT Present in Dros 94.5 0.22 4.7E-06 38.9 7.6 57 49-105 23-84 (96)
23 cd05841 BS69_related The PWWP 94.4 0.082 1.8E-06 40.6 4.8 53 53-106 6-59 (83)
24 cd06080 MUM1_like Mutated mela 93.3 0.52 1.1E-05 35.9 7.3 53 54-107 1-56 (80)
25 cd05836 N_Pac_NP60 The PWWP do 92.1 0.37 8.1E-06 36.8 5.1 53 54-107 1-62 (86)
26 PF08605 Rad9_Rad53_bind: Fung 92.0 0.26 5.6E-06 40.9 4.4 42 62-105 15-59 (131)
27 KOG1150 Predicted molecular ch 91.6 0.26 5.7E-06 44.0 4.3 44 163-211 184-243 (250)
28 KOG2185 Predicted RNA-processi 91.1 0.41 8.9E-06 46.6 5.4 34 54-88 96-133 (486)
29 cd05840 SPBC215_ISWI_like The 91.0 0.46 1E-05 36.9 4.7 51 54-105 1-65 (93)
30 cd05835 Dnmt3b_related The PWW 90.3 0.42 9.1E-06 36.5 3.9 53 54-107 1-61 (87)
31 cd05838 WHSC1_related The PWWP 87.0 1.3 2.9E-05 34.4 4.7 52 54-106 1-64 (95)
32 KOG3038 Histone acetyltransfer 86.2 1.4 3.1E-05 40.4 5.2 42 48-89 193-237 (264)
33 cd05837 MSH6_like The PWWP dom 85.5 1.4 2.9E-05 35.2 4.2 55 53-108 2-71 (110)
34 KOG2185 Predicted RNA-processi 78.7 1.1 2.3E-05 43.8 1.5 52 52-104 179-230 (486)
35 KOG0644 Uncharacterized conser 75.6 4.8 0.0001 42.7 5.2 38 52-89 977-1028(1113)
36 KOG3548 DNA damage checkpoint 74.8 2.8 6.1E-05 44.8 3.3 52 54-107 726-779 (1176)
37 PF02736 Myosin_N: Myosin N-te 72.2 14 0.0003 24.4 5.1 33 66-99 9-41 (42)
38 KOG3026 Splicing factor SPF30 70.6 6.8 0.00015 35.8 4.4 41 65-105 76-119 (262)
39 cd04452 S1_IF2_alpha S1_IF2_al 69.2 10 0.00023 26.8 4.4 36 67-102 3-39 (76)
40 PF02820 MBT: mbt repeat; Int 69.0 8.4 0.00018 28.1 3.9 38 68-105 12-53 (73)
41 KOG1904 Transcription coactiva 67.3 5.5 0.00012 39.9 3.4 57 51-108 10-73 (496)
42 PF00575 S1: S1 RNA binding do 64.2 17 0.00038 25.6 4.8 36 67-103 4-39 (74)
43 KOG2279 Kinase anchor protein 63.7 4 8.6E-05 41.3 1.6 51 52-104 455-508 (608)
44 PF08863 YolD: YolD-like prote 62.2 27 0.00058 25.9 5.7 50 53-102 38-90 (92)
45 KOG3038 Histone acetyltransfer 61.7 21 0.00046 32.9 5.8 56 52-107 126-187 (264)
46 PRK08559 nusG transcription an 61.6 25 0.00055 29.3 5.9 53 52-105 93-149 (153)
47 cd03694 GTPBP_II Domain II of 60.7 19 0.0004 27.0 4.5 48 52-99 25-72 (87)
48 cd05708 S1_Rrp5_repeat_sc12 S1 60.3 15 0.00033 25.8 3.9 35 68-102 3-37 (77)
49 TIGR00046 RNA methyltransferas 59.7 25 0.00055 31.3 5.9 37 52-89 30-66 (240)
50 cd02421 Peptidase_C39_likeD A 58.0 15 0.00032 28.3 3.7 42 57-101 69-111 (124)
51 cd05686 S1_pNO40 S1_pNO40: pNO 55.3 29 0.00063 24.8 4.7 36 67-102 3-38 (73)
52 cd05839 BR140_related The PWWP 54.0 33 0.00071 27.7 5.1 51 54-105 1-79 (111)
53 PF07039 DUF1325: SGF29 tudor- 53.7 39 0.00085 27.7 5.7 52 55-106 1-60 (130)
54 PF14153 Spore_coat_CotO: Spor 52.8 28 0.00062 30.4 4.9 50 54-105 132-181 (185)
55 cd04471 S1_RNase_R S1_RNase_R: 52.7 27 0.00058 25.0 4.1 35 68-102 2-36 (83)
56 cd04465 S1_RPS1_repeat_ec2_hs2 52.7 25 0.00054 24.5 3.9 33 68-102 1-33 (67)
57 cd05684 S1_DHX8_helicase S1_DH 52.0 33 0.00072 24.7 4.6 35 68-102 1-37 (79)
58 cd05698 S1_Rrp5_repeat_hs6_sc5 51.7 25 0.00054 24.5 3.7 33 68-101 1-33 (70)
59 PRK14639 hypothetical protein; 47.2 71 0.0015 26.5 6.3 50 53-103 84-133 (140)
60 PF04452 Methyltrans_RNA: RNA 45.5 53 0.0011 28.8 5.6 37 52-89 15-51 (225)
61 cd05685 S1_Tex S1_Tex: The C-t 45.4 36 0.00078 23.0 3.7 34 68-102 1-34 (68)
62 cd02419 Peptidase_C39C A sub-f 44.1 28 0.0006 26.8 3.3 41 57-101 74-114 (127)
63 cd01734 YlxS_C YxlS is a Bacil 42.2 1E+02 0.0022 23.0 5.9 52 52-103 20-76 (83)
64 cd04472 S1_PNPase S1_PNPase: P 41.7 50 0.0011 22.4 4.0 34 68-102 1-34 (68)
65 PF01356 A_amylase_inhib: Alph 40.7 62 0.0013 24.0 4.3 35 55-93 24-58 (68)
66 cd05697 S1_Rrp5_repeat_hs5 S1_ 40.3 47 0.001 23.2 3.7 34 68-102 1-34 (69)
67 smart00316 S1 Ribosomal protei 39.9 53 0.0011 21.9 3.8 36 67-103 2-37 (72)
68 PF02576 DUF150: Uncharacteris 39.3 1.2E+02 0.0026 24.7 6.5 50 54-103 84-138 (141)
69 cd02417 Peptidase_C39_likeA A 39.0 32 0.00069 26.2 2.9 38 58-98 70-107 (121)
70 PRK14637 hypothetical protein; 37.2 1E+02 0.0023 25.9 5.9 50 53-104 94-143 (151)
71 PRK11713 16S ribosomal RNA met 36.6 98 0.0021 27.4 5.9 37 52-89 28-64 (234)
72 cd02420 Peptidase_C39D A sub-f 36.6 43 0.00093 25.7 3.3 36 58-97 75-110 (125)
73 cd04461 S1_Rrp5_repeat_hs8_sc7 35.6 52 0.0011 23.9 3.4 34 67-101 14-47 (83)
74 cd05707 S1_Rrp5_repeat_sc11 S1 35.4 62 0.0014 22.4 3.7 33 68-101 1-33 (68)
75 cd05687 S1_RPS1_repeat_ec1_hs1 34.9 64 0.0014 22.4 3.7 33 68-101 1-33 (70)
76 PHA01809 hypothetical protein 34.6 20 0.00043 25.5 0.9 30 50-79 12-44 (65)
77 COG1385 Uncharacterized protei 32.7 99 0.0021 28.1 5.4 37 52-89 32-68 (246)
78 cd05690 S1_RPS1_repeat_ec5 S1_ 32.4 68 0.0015 22.0 3.4 34 68-102 1-34 (69)
79 cd05688 S1_RPS1_repeat_ec3 S1_ 31.7 76 0.0016 21.4 3.6 33 68-102 2-34 (68)
80 cd05694 S1_Rrp5_repeat_hs2_sc2 31.4 86 0.0019 22.8 4.0 34 67-101 4-38 (74)
81 PF11623 DUF3252: Protein of u 30.7 1.3E+02 0.0029 21.2 4.5 38 55-94 3-42 (53)
82 cd04453 S1_RNase_E S1_RNase_E: 30.6 91 0.002 23.5 4.1 34 67-101 7-42 (88)
83 PF09038 53-BP1_Tudor: Tumour 30.6 66 0.0014 26.5 3.5 46 53-101 55-104 (122)
84 PRK02001 hypothetical protein; 30.4 1.9E+02 0.0041 24.4 6.3 36 53-89 86-121 (152)
85 TIGR00405 L26e_arch ribosomal 30.0 1.3E+02 0.0028 24.4 5.3 52 53-105 86-141 (145)
86 cd02259 Peptidase_C39_like Pep 29.9 71 0.0015 24.0 3.5 45 54-101 66-110 (122)
87 PF11302 DUF3104: Protein of u 29.4 2.4E+02 0.0052 21.3 6.0 52 53-104 5-70 (75)
88 smart00326 SH3 Src homology 3 29.2 1.4E+02 0.003 18.9 4.4 28 50-77 17-44 (58)
89 cd05706 S1_Rrp5_repeat_sc10 S1 29.1 1.4E+02 0.003 20.9 4.6 35 67-102 3-37 (73)
90 COG0250 NusG Transcription ant 28.9 1.8E+02 0.0038 25.2 6.1 54 48-104 118-177 (178)
91 PF00018 SH3_1: SH3 domain; I 28.8 83 0.0018 20.5 3.2 29 49-77 11-39 (48)
92 smart00783 A_amylase_inhib Alp 28.6 74 0.0016 23.6 3.1 32 58-93 28-59 (69)
93 PRK14633 hypothetical protein; 28.2 1.8E+02 0.0039 24.3 5.9 52 52-104 89-143 (150)
94 PRK00092 ribosome maturation p 28.0 1.7E+02 0.0038 24.3 5.8 50 52-103 93-147 (154)
95 cd05689 S1_RPS1_repeat_ec4 S1_ 28.0 1.2E+02 0.0025 21.2 4.1 34 67-101 3-36 (72)
96 cd02425 Peptidase_C39F A sub-f 27.7 98 0.0021 23.5 3.9 40 56-99 74-113 (126)
97 TIGR01955 RfaH transcriptional 26.8 99 0.0021 25.3 4.0 42 52-96 107-151 (159)
98 cd05692 S1_RPS1_repeat_hs4 S1_ 26.4 1.4E+02 0.003 20.0 4.1 33 68-101 1-33 (69)
99 PF00552 IN_DBD_C: Integrase D 26.0 2.4E+02 0.0052 19.8 5.3 46 59-105 5-54 (55)
100 PRK15095 FKBP-type peptidyl-pr 25.2 1.8E+02 0.0039 24.4 5.3 34 53-87 92-125 (156)
101 PRK07252 hypothetical protein; 25.2 1.3E+02 0.0029 24.1 4.4 34 68-102 4-37 (120)
102 cd05691 S1_RPS1_repeat_ec6 S1_ 24.9 1.3E+02 0.0029 20.6 3.9 33 68-101 1-33 (73)
103 PRK08582 hypothetical protein; 24.9 1.6E+02 0.0036 24.2 5.0 34 68-102 6-39 (139)
104 PRK03987 translation initiatio 24.7 1E+02 0.0022 28.3 4.0 38 64-101 5-43 (262)
105 PRK14640 hypothetical protein; 24.5 2.3E+02 0.0051 23.7 5.9 49 53-103 93-144 (152)
106 PF08481 GBS_Bsp-like: GBS Bsp 23.5 1.2E+02 0.0026 23.3 3.7 20 55-74 25-49 (95)
107 PF02237 BPL_C: Biotin protein 23.3 2.3E+02 0.005 18.8 6.3 41 56-98 2-42 (48)
108 PF11208 DUF2992: Protein of u 22.6 1.4E+02 0.0031 24.7 4.2 28 63-91 3-30 (132)
109 PF08169 RBB1NT: RBB1NT (NUC16 22.3 3.8E+02 0.0082 21.2 6.2 51 56-107 8-68 (96)
110 KOG3409 Exosomal 3'-5' exoribo 21.3 1.8E+02 0.0039 25.7 4.6 36 49-87 118-155 (193)
111 cd05696 S1_Rrp5_repeat_hs4 S1_ 20.9 1.5E+02 0.0032 21.1 3.5 33 68-101 1-35 (71)
112 TIGR03130 malonate_delta malon 20.8 67 0.0014 25.5 1.7 9 216-224 19-27 (98)
113 PF07238 PilZ: PilZ domain; I 20.3 2E+02 0.0044 20.4 4.2 25 65-89 19-43 (102)
No 1
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=100.00 E-value=1.1e-49 Score=350.29 Aligned_cols=220 Identities=35% Similarity=0.449 Sum_probs=182.9
Q ss_pred hhhhhHHHHHHHhhhccccccccCCCCCCC---CchhhhccccccCCCCCCCCCCCCCCCeEEEEecCCCCEEEEEEeeE
Q 025684 2 QVIALTEELLATAKQNAISVSETGTSASAS---PNLLQSKENKTESGSISDNQEKLAVGTKVQAVYSEDGEWYDATIEAI 78 (249)
Q Consensus 2 EvI~LT~dLl~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~kvGd~ClA~ys~Dg~wY~A~I~~i 78 (249)
|||+||+|||+|+.+++.+.+.+..++... +.+.-.+.+- ++.....+...|.||+.|+|+|++||+||.|+|+.|
T Consensus 37 EvIsLTedLlqT~~ee~~sss~a~~ssq~~h~s~~~~~~~~~~-l~~~~~i~a~~w~vg~K~~A~~~ddg~~y~AtIe~i 115 (262)
T KOG3026|consen 37 EVISLTEDLLQTQKEEDKSSSDAFVSSQPTHSSFTPRWVSGDY-LFYPSRITAVGWKVGDKVQAVFSDDGQIYDATIEHI 115 (262)
T ss_pred HHHHHHHHHHHhhhhhhcccccccccCccccCCCchhhhhhhh-ccccccchhcccccCCEEEEeecCCCceEEeehhhc
Confidence 899999999999999988777776665332 2333332222 344444555689999999999999999999999999
Q ss_pred eC--CeeEEEEecCCceEEEcCCCcccCCchhHHHHHHHHHHHHHHHHhhhhhhccccccCCCccCCCCCCChHHHHHHH
Q 025684 79 TP--NGYYVTYDSWGNKEEVDPANVRPVNLLVEAEKVAEATKLAIKRKIEQAAASDFQSKSLPAKLHINPDDPEDVKAAK 156 (249)
Q Consensus 79 ~~--~~~~V~F~~Ygn~E~V~~~~lrpl~~l~~~~~~a~~~~~~~k~ki~~a~~~~~~~~~~P~~l~i~p~d~E~~k~~K 156 (249)
+. ..+.|.|.+|||...+...++|+++....+ .......|..+.+.|+++|....++
T Consensus 116 ta~~~~~ai~f~s~~~a~~t~~a~lr~~e~~~s~---------------------~~~~~n~P~~~k~~~~~pe~~~~~e 174 (262)
T KOG3026|consen 116 TAMEGTVAIIFASYGTAPSTYAARLRSPEEKSSA---------------------AYTANNKPIQNKHVSTLPEISPIKE 174 (262)
T ss_pred cCCCCceeEEEeeccccccccHhhccCcchhhhh---------------------hcccCCCcchhccCCCCcccccccc
Confidence 98 358999999999999999999988643211 1122335667788899999999999
Q ss_pred HHHHHHhhhhhhHHHHHHHHhHHhhhhHHHHhhhcccccccccCCCcccceeeCCCCCCceeeeecCCCCccccccccee
Q 025684 157 RKKIHAFKSKMRFEQLEVTQNKRQNAWQQFQTTKGKTKKVGFFSGRKRESIFKSPDDPYGKVGVTGSGKGLTDFQKREKH 236 (249)
Q Consensus 157 ~KK~ka~Kkk~R~k~le~e~~~kknkWq~F~~kk~k~kK~g~~~g~kk~SIF~sPd~~~GrVGv~gsGk~MT~~~~r~kh 236 (249)
|||++++||+||+++||++++.+||+||+|++++.+++++| |++++|||+|||++.|||||+|||+ ++.++.|++|
T Consensus 175 ~~k~~a~KKqQr~kele~~~e~~kn~WqqFntr~~kk~kvG---g~k~~SIFkSped~~Grvgvg~~G~-ia~~~~~e~~ 250 (262)
T KOG3026|consen 175 RKKKKALKKQQRQKELEAEREASKNSWQQFNTRAVKKGKVG---GIKKSSIFKSPEDVPGRVGVGGCGN-IADSGMREKH 250 (262)
T ss_pred cccchhHHHHHHHHhHHHHHhhhhhHHHHHHHHhhhccccc---ceeeeccccCCCCCCcccCCCCccc-ccccccceeh
Confidence 99999999999999999999999999999999877777776 8999999999999999999999998 8999999999
Q ss_pred eeecCCcccCC
Q 025684 237 LHLKGGGIADT 247 (249)
Q Consensus 237 ~~~~~~~~~~~ 247 (249)
+|++-|+....
T Consensus 251 ~~~k~g~~d~l 261 (262)
T KOG3026|consen 251 IYNKRGDRDSL 261 (262)
T ss_pred hhhhccccccC
Confidence 99999886543
No 2
>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=99.62 E-value=4.9e-16 Score=141.18 Aligned_cols=59 Identities=41% Similarity=0.655 Sum_probs=48.2
Q ss_pred CCCCCCCCCCeEEEEecCCCCEEEEEEeeEeCC--eeEEEEecCCceEEEcCCCcccCCch
Q 025684 49 DNQEKLAVGTKVQAVYSEDGEWYDATIEAITPN--GYYVTYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 49 ~~~~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~--~~~V~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
.+...|+|||.|+|+||+||+||+|+|++|+.+ .|.|+|+||||.|+|.+.+|+|+...
T Consensus 64 ~~~~~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~~~~~~ 124 (264)
T PF06003_consen 64 APNKKWKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSDLKPSEGD 124 (264)
T ss_dssp TTTT---TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGGEEETT--
T ss_pred CcccCCCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhhhcccccc
Confidence 445789999999999999999999999999974 59999999999999999999999643
No 3
>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=99.57 E-value=5.4e-15 Score=103.34 Aligned_cols=53 Identities=42% Similarity=0.723 Sum_probs=50.0
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeC-CeeEEEEecCCceEEEcCCCcccCCc
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITP-NGYYVTYDSWGNKEEVDPANVRPVNL 106 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~-~~~~V~F~~Ygn~E~V~~~~lrpl~~ 106 (249)
.|++|+.|+|+| .||.||||+|.++.+ +.|.|.|+|||+.+.|+.++||+++.
T Consensus 2 ~~~~G~~~~a~~-~d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 2 TFKVGDKVAARW-EDGEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCCCEEEEEe-CCCCEEEEEEEEECCCCEEEEEEECCCccEEEeHHHeecCCC
Confidence 589999999999 899999999999998 56999999999999999999999974
No 4
>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=99.56 E-value=5.2e-15 Score=100.16 Aligned_cols=47 Identities=38% Similarity=0.671 Sum_probs=43.5
Q ss_pred CCeEEEEecCCCCEEEEEEeeEeC-CeeEEEEecCCceEEEcCCCccc
Q 025684 57 GTKVQAVYSEDGEWYDATIEAITP-NGYYVTYDSWGNKEEVDPANVRP 103 (249)
Q Consensus 57 Gd~ClA~ys~Dg~wY~A~I~~i~~-~~~~V~F~~Ygn~E~V~~~~lrp 103 (249)
|+.|+|+|++||.||||+|.++.+ +.|.|.|+||||.+.|+.++|||
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~~l~~ 48 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILSDGKVEVFFVDYGNTEVVPLSDLRP 48 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECCCCcEEEEEEcCCCcEEEeHHHcCC
Confidence 799999999999999999999994 45999999999999999988875
No 5
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=99.18 E-value=6.2e-11 Score=84.34 Aligned_cols=54 Identities=26% Similarity=0.462 Sum_probs=50.6
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeC-CeeEEEEec--CCceEEEcCCCcccCCc
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITP-NGYYVTYDS--WGNKEEVDPANVRPVNL 106 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~-~~~~V~F~~--Ygn~E~V~~~~lrpl~~ 106 (249)
.|++|+.|.|.|+.||.||+|+|+++.+ +.|.|.|.+ +++.++|+..+|||+++
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~ 58 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPP 58 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCC
Confidence 5899999999999999999999999998 569999999 99999999999999974
No 6
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=98.92 E-value=2.1e-09 Score=82.92 Aligned_cols=55 Identities=36% Similarity=0.582 Sum_probs=46.1
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEE-eeEeCCeeEEEEecCCceEEEcCCCcccCCc
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATI-EAITPNGYYVTYDSWGNKEEVDPANVRPVNL 106 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I-~~i~~~~~~V~F~~Ygn~E~V~~~~lrpl~~ 106 (249)
..+.+|..|++.++.||.||||+| ....++.+.|.|+|||+++.|+.++||+++.
T Consensus 50 ~~~~~~~~~~~~~~~~~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~ 105 (121)
T PF00567_consen 50 PESNPGEGCLCVVSEDGRWYRAVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPP 105 (121)
T ss_dssp ST--TTEEEEEEETTTSEEEEEEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--H
T ss_pred cccccCCEEEEEEecCCceeeEEEEEecccceeEEEEEecCceEEEcHHHhhhhCH
Confidence 468899999999999999999999 5555667999999999999999999999973
No 7
>KOG4327 consensus mRNA splicing protein SMN (survival motor neuron) [RNA processing and modification]
Probab=98.91 E-value=9.2e-10 Score=95.76 Aligned_cols=56 Identities=38% Similarity=0.567 Sum_probs=49.9
Q ss_pred CCCCCCCCCCeEEEEecCCCCEEEEEEeeEeC--CeeEEEEecCCceEEEcCCCcccC
Q 025684 49 DNQEKLAVGTKVQAVYSEDGEWYDATIEAITP--NGYYVTYDSWGNKEEVDPANVRPV 104 (249)
Q Consensus 49 ~~~~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~--~~~~V~F~~Ygn~E~V~~~~lrpl 104 (249)
.....|+|||.|+|.|++||.+|+|+|..|+. ++|.|+|++|||.++|.+.+|-+-
T Consensus 63 ~~~~~wKVgdkc~A~Y~e~g~~ypatidsi~~~~~tcvv~ylgygnr~Ev~lsDLl~~ 120 (218)
T KOG4327|consen 63 ASLQQWKVGDKCSAIYSEDGCIYPATIDSIDFKRETCVVVYLGYGNREEVNLSDLLSP 120 (218)
T ss_pred cchhhheecceeeeeeecCcccccceecccccccCceEEEEEeecchhhhhHHHhccc
Confidence 44578999999999999999999999999994 458999999999999988888765
No 8
>KOG2039 consensus Transcriptional coactivator p100 [Transcription]
Probab=98.80 E-value=4.8e-09 Score=109.05 Aligned_cols=56 Identities=29% Similarity=0.412 Sum_probs=52.4
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeC-CeeEEEEecCCceEEEcCCCcccCCch
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITP-NGYYVTYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~-~~~~V~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
...++||.|+|+|+-||+||||.|.+|.. ..+.|.|+||||+|++|+.+|+++|+.
T Consensus 694 ~~p~~gd~c~A~y~~D~qwyRa~i~~V~~~~~~~V~yiDygn~E~lp~~~l~~lp~~ 750 (875)
T KOG2039|consen 694 YTPKRGDLCVAKYSLDGQWYRALIVEVLDPESMEVFYIDYGNIETLPFVRLKPLPPH 750 (875)
T ss_pred CCCCCCCeeeeeeccccceeeeeeeeeccCcceeEEEEecCcccccccccccCCChH
Confidence 47899999999999999999999999987 779999999999999999999999854
No 9
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=98.61 E-value=1.9e-07 Score=66.05 Aligned_cols=50 Identities=20% Similarity=0.490 Sum_probs=40.4
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeC--CeeEEEEecCCceEEEcCCCcc
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITP--NGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~--~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
..|..|+.++++|.+++.||+|+|++++. ..|.|.|.| |+...|+..+|+
T Consensus 4 ~k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~D-Gtel~lke~dik 55 (55)
T PF09465_consen 4 RKFAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYED-GTELELKENDIK 55 (55)
T ss_dssp SSS-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETT-S-EEEEECCCEE
T ss_pred ccccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcC-CCEEEecccccC
Confidence 67999999999999999999999999885 459999999 999999888874
No 10
>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=98.42 E-value=5.8e-07 Score=63.29 Aligned_cols=48 Identities=42% Similarity=0.857 Sum_probs=40.6
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeCC----eeEEEEecCCc--eEEEcCCCcc
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITPN----GYYVTYDSWGN--KEEVDPANVR 102 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~~----~~~V~F~~Ygn--~E~V~~~~lr 102 (249)
+.||+.|+|.| .+|.||+|+|.++... .|.|.|.||+. .|.|+.++|+
T Consensus 1 ~~vG~~v~~~~-~~~~~y~A~I~~~r~~~~~~~YyVHY~g~nkR~DeWV~~~~i~ 54 (55)
T PF11717_consen 1 FEVGEKVLCKY-KDGQWYEAKILDIREKNGEPEYYVHYQGWNKRLDEWVPESRIR 54 (55)
T ss_dssp --TTEEEEEEE-TTTEEEEEEEEEEEECTTCEEEEEEETTSTGCC-EEEETTTEE
T ss_pred CCcCCEEEEEE-CCCcEEEEEEEEEEecCCCEEEEEEcCCCCCCceeeecHHHcc
Confidence 57999999999 6999999999999853 29999999997 4999998886
No 11
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=97.99 E-value=1.6e-05 Score=58.09 Aligned_cols=53 Identities=32% Similarity=0.521 Sum_probs=37.8
Q ss_pred CCCCCeEEEEecC---CCCEEEEEEeeEeCC-eeEEEEecCC--------ceEEEcCCCcccCCc
Q 025684 54 LAVGTKVQAVYSE---DGEWYDATIEAITPN-GYYVTYDSWG--------NKEEVDPANVRPVNL 106 (249)
Q Consensus 54 ~kvGd~ClA~ys~---Dg~wY~A~I~~i~~~-~~~V~F~~Yg--------n~E~V~~~~lrpl~~ 106 (249)
|++|+.+....-+ .|.||+|+|.+..++ .|.|.|.++- ..|.|+..+|||.|+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~~~~V~Y~~~~~~~~~~~~l~e~V~~~~iRP~pP 65 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDDKYLVEYDDLPDEDGESPPLKEWVDARRIRPCPP 65 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-EEEEEETT-SS--------EEEEEGGGEEE---
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCcEEEEEECCcccccccccccEEEechheEECcCc
Confidence 6789999999855 457999999999988 8999996544 268999999999975
No 12
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=97.72 E-value=9e-05 Score=72.18 Aligned_cols=56 Identities=23% Similarity=0.341 Sum_probs=48.2
Q ss_pred CCCCCCCCCCCeEEEEecCCCCEEEEEEeeEeC--------CeeEEEEecCCce--EEEcCCCccc
Q 025684 48 SDNQEKLAVGTKVQAVYSEDGEWYDATIEAITP--------NGYYVTYDSWGNK--EEVDPANVRP 103 (249)
Q Consensus 48 ~~~~~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~--------~~~~V~F~~Ygn~--E~V~~~~lrp 103 (249)
+.....+.||+.|+|.|+.||+||.|+|.++.. ..|.|.|.||+.. |.|+.++|..
T Consensus 48 ~~~~~~~~VGekVla~~~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~rLdl 113 (450)
T PLN00104 48 PGVMLPLEVGTRVMCRWRFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLEQLDL 113 (450)
T ss_pred CCccceeccCCEEEEEECCCCCEEEEEEEEEeccCCCCCCCceEEEEEecCCccHhhccCHhhccc
Confidence 344567999999999999999999999999875 1499999999987 9998888864
No 13
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=97.32 E-value=0.00049 Score=56.21 Aligned_cols=48 Identities=27% Similarity=0.479 Sum_probs=41.1
Q ss_pred CCeEEEEecCCCCEEEEEEeeEeCC-eeEEEEecCCceEEEcCCCcccCC
Q 025684 57 GTKVQAVYSEDGEWYDATIEAITPN-GYYVTYDSWGNKEEVDPANVRPVN 105 (249)
Q Consensus 57 Gd~ClA~ys~Dg~wY~A~I~~i~~~-~~~V~F~~Ygn~E~V~~~~lrpl~ 105 (249)
|+.++|+|..||-||+++|.+.... .|.|.| ..+..++|+..+|-++.
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~~~~~~lV~f-~~~~~~~v~~~~iI~~~ 49 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCVSSGQFLVEF-DDGDTQEVPISDIIALS 49 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEccCCCEEEEEE-CCCCEEEeChHHeEEcc
Confidence 7899999999999999999987644 489999 66888999888887774
No 14
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=97.12 E-value=0.00077 Score=55.03 Aligned_cols=56 Identities=25% Similarity=0.317 Sum_probs=45.4
Q ss_pred CCCCCCCCeEEEEe-cCCCCEEEEEEeeE-----e-CCeeEEEEecCCceEEEcCCCcccCCch
Q 025684 51 QEKLAVGTKVQAVY-SEDGEWYDATIEAI-----T-PNGYYVTYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 51 ~~~~kvGd~ClA~y-s~Dg~wY~A~I~~i-----~-~~~~~V~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
.+.+++||.|+|+| ..+..|+||+|... . +..|+|.|.+ |.+..|+...+..|++.
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~n-g~~~~vp~~~~~~I~~~ 115 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYN-GKTAKVPRGEVIWISPS 115 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEEC-CCCCccchhhEEECCHH
Confidence 47899999999999 44556999999963 3 3358999987 77899999999999753
No 15
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=97.10 E-value=0.0014 Score=53.55 Aligned_cols=50 Identities=26% Similarity=0.418 Sum_probs=35.8
Q ss_pred CCCCeEEEEecCCCCEEEEEEeeEeC-CeeEEEEecCCceEEEcCCCcccCC
Q 025684 55 AVGTKVQAVYSEDGEWYDATIEAITP-NGYYVTYDSWGNKEEVDPANVRPVN 105 (249)
Q Consensus 55 kvGd~ClA~ys~Dg~wY~A~I~~i~~-~~~~V~F~~Ygn~E~V~~~~lrpl~ 105 (249)
-||-.|.|+||.++-||+.+|..=.+ +.|.|.|.| |..-.|...+|-..+
T Consensus 4 ~iG~rV~AkWS~n~yyY~G~I~~~~~~~kykv~FdD-G~~~~v~~~div~~d 54 (122)
T PF09038_consen 4 FIGLRVFAKWSDNGYYYPGKITSDKGKNKYKVLFDD-GYECRVLGKDIVVCD 54 (122)
T ss_dssp STT-EEEEESSTTSEEEEEEEEEEETTTEEEEEETT-S-EEEEECCCEEEES
T ss_pred ccccEEEEEEccCCcccCceEeecCCCCeEEEEecC-CccceeccCcEEEEc
Confidence 37999999999666669999987544 469999998 665556666665443
No 16
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=95.47 E-value=0.02 Score=47.18 Aligned_cols=52 Identities=25% Similarity=0.382 Sum_probs=35.1
Q ss_pred CCCCCCCCCeEEEEecCCCCEEEEEEeeEe---CCeeEEEEecCCce---EEEcCCCc
Q 025684 50 NQEKLAVGTKVQAVYSEDGEWYDATIEAIT---PNGYYVTYDSWGNK---EEVDPANV 101 (249)
Q Consensus 50 ~~~~~kvGd~ClA~ys~Dg~wY~A~I~~i~---~~~~~V~F~~Ygn~---E~V~~~~l 101 (249)
+...|..|+.|||+|.+==.||+|+|.+.. ...|.+.|.|-... ..|+...|
T Consensus 68 ~~~~f~~g~~VLAlYP~TT~FY~A~V~~~p~~~~~~y~l~Fedd~~~~~~~~V~~r~V 125 (130)
T PF07039_consen 68 PLAEFPKGTKVLALYPDTTCFYPATVVSPPKKKSGEYKLKFEDDEDADGYREVPQRYV 125 (130)
T ss_dssp GGGS--TT-EEEEE-TTSSEEEEEEEEEE-SSTTS-EEEEECTTTSTTSBEEE-GGGE
T ss_pred chhhCCCCCEEEEECCCCceEEEEEEEeCCCCCCCcEEEEEeCCCCcCCcEEEccceE
Confidence 456899999999999777789999999983 33599999997765 35544433
No 17
>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=95.41 E-value=0.03 Score=42.65 Aligned_cols=53 Identities=15% Similarity=0.136 Sum_probs=45.1
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeC-----CeeEEEEecCCceEEEcCCCcccCCc
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITP-----NGYYVTYDSWGNKEEVDPANVRPVNL 106 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~-----~~~~V~F~~Ygn~E~V~~~~lrpl~~ 106 (249)
.+++||.+.|+..+ --|.||+|..... +.|.|.|.|-++...|+..+|.|...
T Consensus 2 ~f~~GdlVwaK~kG-yp~WPa~I~~~~~~~~~~~~~~V~FfGt~~~a~v~~~~l~pf~~ 59 (83)
T cd05834 2 QFKAGDLVFAKVKG-YPAWPARVDEPEDWKPPGKKYPVYFFGTHETAFLKPEDLFPYTE 59 (83)
T ss_pred CCCCCCEEEEecCC-CCCCCEEEecccccCCCCCEEEEEEeCCCCEeEECHHHceeccc
Confidence 58999999999853 3577999998873 45999999999999999999999864
No 18
>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=95.31 E-value=0.047 Score=40.54 Aligned_cols=52 Identities=19% Similarity=0.250 Sum_probs=43.0
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeC--------CeeEEEEecCCceEEEcCCCcccCCc
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITP--------NGYYVTYDSWGNKEEVDPANVRPVNL 106 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~--------~~~~V~F~~Ygn~E~V~~~~lrpl~~ 106 (249)
|.+||.|.|+.. .--|.||+|..... ..|.|.|.|=.+...|+.++|.|+..
T Consensus 1 f~~GdlVWaK~~-g~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg~~~~~wv~~~~i~~f~~ 60 (86)
T PF00855_consen 1 FRPGDLVWAKLK-GYPWWPARVCDPDEKSKKKRKDGHVLVRFFGDNDYAWVKPSNIKPFSE 60 (86)
T ss_dssp -STTEEEEEEET-TSEEEEEEEEECCHCTSCSSSSTEEEEEETTTTEEEEEEGGGEEECCH
T ss_pred CCCCCEEEEEeC-CCCCCceEEeecccccccCCCCCEEEEEecCCCCEEEECHHHhhChhh
Confidence 579999999995 44699999998752 34899999977889999999999973
No 19
>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=94.88 E-value=0.063 Score=40.47 Aligned_cols=53 Identities=15% Similarity=0.114 Sum_probs=43.8
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeC-----------CeeEEEEecCCceEEEcCCCcccCCch
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITP-----------NGYYVTYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~-----------~~~~V~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
|++||.|.|++.+- -|+||+|..... +.|.|.|.|=.+...|+.++|.|+...
T Consensus 1 f~~GdlVwaK~~g~-pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg~~~~~wv~~~~l~pf~~~ 64 (87)
T cd05162 1 FRPGDLVWAKMKGY-PWWPALVVDPPKDSKKAKKKAKEGKVLVLFFGDKTFAWVGAERLKPFTEH 64 (87)
T ss_pred CCCCCEEEEeCCCC-CCCCEEEccccccchhhhccCCCCEEEEEEeCCCcEEEeCccceeeccch
Confidence 57899999999643 688999998764 348999999667799999999999643
No 20
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=94.76 E-value=0.056 Score=41.71 Aligned_cols=46 Identities=30% Similarity=0.579 Sum_probs=33.0
Q ss_pred EEEEecCCCCEEEEEEeeEeCC--------eeEEEEecCCce--EEEcCCCcccCC
Q 025684 60 VQAVYSEDGEWYDATIEAITPN--------GYYVTYDSWGNK--EEVDPANVRPVN 105 (249)
Q Consensus 60 ClA~ys~Dg~wY~A~I~~i~~~--------~~~V~F~~Ygn~--E~V~~~~lrpl~ 105 (249)
+=|+-...|.||+|.|..|+.. .|.|.|.+|.+. ..++..+|||..
T Consensus 2 vD~~d~~~gAWfEa~i~~i~~~~~~~~e~viYhIkyddype~gvv~~~~~~iRpRA 57 (85)
T PF12148_consen 2 VDARDRNMGAWFEAQIVTITKKCMSDDEDVIYHIKYDDYPENGVVEMRSKDIRPRA 57 (85)
T ss_dssp EEEE-TTT-EEEEEEEEEEEES-SSSSTTEEEEEEETT-GGG-EEEEEGGGEEE--
T ss_pred cccccCCCcceEEEEEEEeeccCCCCCCCEEEEEEeccCCCcCceeccccccccee
Confidence 3466677899999999999842 289999999964 667888999873
No 21
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=94.68 E-value=0.085 Score=37.78 Aligned_cols=50 Identities=18% Similarity=0.206 Sum_probs=40.9
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeC------------CeeEEEEecCCceEEEcCCCcccC
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITP------------NGYYVTYDSWGNKEEVDPANVRPV 104 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~------------~~~~V~F~~Ygn~E~V~~~~lrpl 104 (249)
+++||.+.|+..+- -|.+|+|..-.. +.|.|.|.|=++...|+.++|.|+
T Consensus 1 f~~GdlVwaK~~G~-p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg~~~~awv~~~~l~p~ 62 (63)
T smart00293 1 FKPGDLVWAKMKGF-PWWPALVVSPKETPDNIRKRKRFENLYPVLFFGDKDTAWISSSKLFPL 62 (63)
T ss_pred CCCCCEEEEECCCC-CCCCeEEcCcccCChhHhhccCCCCEEEEEEeCCCCEEEECccceeeC
Confidence 57899999998533 588999986541 248999999888899999999986
No 22
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=94.55 E-value=0.22 Score=38.95 Aligned_cols=57 Identities=23% Similarity=0.390 Sum_probs=44.2
Q ss_pred CCCCCCCCCCeEEEEecCC-CCEEEEEEeeEeCCeeEEEEecCCce--EEEcC--CCcccCC
Q 025684 49 DNQEKLAVGTKVQAVYSED-GEWYDATIEAITPNGYYVTYDSWGNK--EEVDP--ANVRPVN 105 (249)
Q Consensus 49 ~~~~~~kvGd~ClA~ys~D-g~wY~A~I~~i~~~~~~V~F~~Ygn~--E~V~~--~~lrpl~ 105 (249)
.....|++|++..|+=..+ ..+..|+|.+|.+..+.|.|+||.+. ..+.. .+|+|+-
T Consensus 23 ~~~~~F~vGmkLEavD~~~~~~i~vAtV~~v~g~~l~v~~dg~~~~~D~W~~~~S~~I~PvG 84 (96)
T smart00561 23 SPPNGFKVGMKLEAVDPRNPSLICVATVVEVKGYRLLLHFDGWDDKYDFWCDADSPDIHPVG 84 (96)
T ss_pred CccCcccCCCEEEEECCCCCceEEEEEEEEEECCEEEEEEccCCCcCCEEEECCCCCcccCc
Confidence 3457899999999995333 45789999999988899999999876 55544 4677763
No 23
>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=94.43 E-value=0.082 Score=40.56 Aligned_cols=53 Identities=13% Similarity=0.123 Sum_probs=45.5
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEec-CCceEEEcCCCcccCCc
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS-WGNKEEVDPANVRPVNL 106 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~-Ygn~E~V~~~~lrpl~~ 106 (249)
-.++||.+.|+..+= -|.||+|...+++.|.|.|-| -.+...|+..+|.|+..
T Consensus 6 c~~p~dLVwAK~kGy-p~WPAkV~~~~~~~~~V~FFG~t~~~a~v~~~~i~~~~~ 59 (83)
T cd05841 6 CRPPHELVWAKLKGF-PYWPAKVMRVEDNQVDVRFFGGQHDRAWIPSNNIQPIST 59 (83)
T ss_pred cCCCCCEEEEeCCCC-CCCCEEEeecCCCeEEEEEcCCCCCeEEEehHHeeehhh
Confidence 457899999998644 356999999988889999999 88999999999999853
No 24
>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=93.30 E-value=0.52 Score=35.87 Aligned_cols=53 Identities=17% Similarity=0.109 Sum_probs=42.5
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeC--CeeEEEEecCC-ceEEEcCCCcccCCch
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITP--NGYYVTYDSWG-NKEEVDPANVRPVNLL 107 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~--~~~~V~F~~Yg-n~E~V~~~~lrpl~~l 107 (249)
|.+||.+-|+..+= -|.||+|.++.. ..|.|.|.|=+ +...+..++|.|-...
T Consensus 1 f~~gdlVWaK~~g~-P~WPa~I~~~~~~~~k~~V~FfG~~~~~a~~~~~~l~p~~~~ 56 (80)
T cd06080 1 FEKNDLVWAKIQGY-PWWPAVIKSISRKKQKARVNFIGDNMQSEKKGIRVVKRWLKH 56 (80)
T ss_pred CCCCCEEEEeCCCC-CCCCEEEeeecCCCCEEEEEEeCCCCceeccchhhccccccc
Confidence 57899999998633 477999999974 34999999977 6788888888887543
No 25
>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=92.06 E-value=0.37 Score=36.81 Aligned_cols=53 Identities=17% Similarity=0.169 Sum_probs=42.9
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEe---------CCeeEEEEecCCceEEEcCCCcccCCch
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAIT---------PNGYYVTYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~---------~~~~~V~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
+++||.+.|+..+- -|.||+|..-. .+.|.|.|.|-++...|..++|.|....
T Consensus 1 f~~GDlVwaK~~g~-P~WPa~V~~~~~~~~~~~~~~~~~~V~FFG~~~~~wv~~~~l~pF~~~ 62 (86)
T cd05836 1 LKLGDLVWAKMKGF-PPWPGRIVKPPKDLKKPRGKAKCFFVFFFGSENHAWIKEENIKPYHEH 62 (86)
T ss_pred CCCCCEEEEeCCCC-CCCCEEEechhhhcccccCCCCeEEEEEeCCCCEEEECHHhCeechhh
Confidence 57999999998643 46699998632 1348999999999999999999999654
No 26
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=91.97 E-value=0.26 Score=40.88 Aligned_cols=42 Identities=19% Similarity=0.271 Sum_probs=33.8
Q ss_pred EEe-cCCCCEEEEEEeeEeCCe--eEEEEecCCceEEEcCCCcccCC
Q 025684 62 AVY-SEDGEWYDATIEAITPNG--YYVTYDSWGNKEEVDPANVRPVN 105 (249)
Q Consensus 62 A~y-s~Dg~wY~A~I~~i~~~~--~~V~F~~Ygn~E~V~~~~lrpl~ 105 (249)
|+| .-+-.||||+|.+...+. +.|.|.+.. ..|...+|+.|+
T Consensus 15 avW~~~~~~yYPa~~~~~~~~~~~~~V~Fedg~--~~i~~~dv~~LD 59 (131)
T PF08605_consen 15 AVWAGYNLKYYPATCVGSGVDRDRSLVRFEDGT--YEIKNEDVKYLD 59 (131)
T ss_pred ceeecCCCeEeeEEEEeecCCCCeEEEEEecCc--eEeCcccEeeee
Confidence 455 237789999999987554 999999955 889999999885
No 27
>KOG1150 consensus Predicted molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=91.63 E-value=0.26 Score=44.00 Aligned_cols=44 Identities=27% Similarity=0.580 Sum_probs=26.6
Q ss_pred hhhhhhHHHHHHH----------------HhHHhhhhHHHHhhhcccccccccCCCcccceeeCC
Q 025684 163 FKSKMRFEQLEVT----------------QNKRQNAWQQFQTTKGKTKKVGFFSGRKRESIFKSP 211 (249)
Q Consensus 163 ~Kkk~R~k~le~e----------------~~~kknkWq~F~~kk~k~kK~g~~~g~kk~SIF~sP 211 (249)
.++.+|..+++++ +..+-++|++|+.+.+|.+| +++-.-+|+-|
T Consensus 184 eRkr~re~eIeaeek~Kr~~E~qKnfEEsRd~Rv~sWrnFq~~t~K~kk-----~Kknk~~~~pP 243 (250)
T KOG1150|consen 184 ERKRQREEEIEAEEKRKREREWQKNFEESRDGRVGSWRNFQAKTKKGKK-----EKKNKTFLRPP 243 (250)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHhhhcchh-----hhhcccccCCC
Confidence 5666777777655 33445799999996444333 23334566644
No 28
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=91.07 E-value=0.41 Score=46.58 Aligned_cols=34 Identities=21% Similarity=0.140 Sum_probs=25.5
Q ss_pred CCCCCeEEEEecCCCCE-E--EEEEeeEeCC-eeEEEEe
Q 025684 54 LAVGTKVQAVYSEDGEW-Y--DATIEAITPN-GYYVTYD 88 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~w-Y--~A~I~~i~~~-~~~V~F~ 88 (249)
--+|.+|+|.|. ++-| | .|+|..+.+. ++.|.|.
T Consensus 96 ~L~GsKcsaph~-ss~gl~yHna~I~g~E~sarvRVlfl 133 (486)
T KOG2185|consen 96 DLDGSKCSAPHT-SSRGLYYHNARIIGFEGSARVRVLFL 133 (486)
T ss_pred hccCCccccccc-CCccceecceeEEeeccccceEEEee
Confidence 357999999995 3333 5 8999999864 5777775
No 29
>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=90.97 E-value=0.46 Score=36.88 Aligned_cols=51 Identities=18% Similarity=0.166 Sum_probs=40.9
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEe--------------CCeeEEEEecCCceEEEcCCCcccCC
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAIT--------------PNGYYVTYDSWGNKEEVDPANVRPVN 105 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~--------------~~~~~V~F~~Ygn~E~V~~~~lrpl~ 105 (249)
|++||.+.|+-. ---|.||+|..-. ...|.|.|-|=++.-.|+..+|.|+.
T Consensus 1 f~~GDlVwaK~~-GyPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg~~~~~Wv~~~~l~pl~ 65 (93)
T cd05840 1 FQPGDRVLAKVK-GFPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFPDGDYYWVPNKDLKPLT 65 (93)
T ss_pred CCCCCEEEEeCC-CCCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEeCCCcEEEEChhhcccCC
Confidence 578999999986 3368899997521 12489999987778999999999996
No 30
>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=90.27 E-value=0.42 Score=36.47 Aligned_cols=53 Identities=23% Similarity=0.310 Sum_probs=42.6
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeCC--------eeEEEEecCCceEEEcCCCcccCCch
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITPN--------GYYVTYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~~--------~~~V~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
|.+||.+-|+-.+- -|.||+|.+...+ .+.|.|-|=++...|+.++|.|..+.
T Consensus 1 f~vGDlVWaK~kg~-pwWP~~V~~~~~~~~~~~~~~~~~V~fFGs~~~a~v~~~~l~pf~e~ 61 (87)
T cd05835 1 FNVGDLVWGKIKGF-PWWPGRVVSITVTSKRPPVVGMRWVTWFGSGTFSEVSVDKLSPFSEF 61 (87)
T ss_pred CCCCCEEEEecCCC-CCCCeEEechhhcccccCCCCeEEEEEeCCCCEeEECHHHCcChhHh
Confidence 57899999997544 4779999887432 38999999788899999999998643
No 31
>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=86.97 E-value=1.3 Score=34.36 Aligned_cols=52 Identities=21% Similarity=0.176 Sum_probs=42.4
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEe---C---------CeeEEEEecCCceEEEcCCCcccCCc
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAIT---P---------NGYYVTYDSWGNKEEVDPANVRPVNL 106 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~---~---------~~~~V~F~~Ygn~E~V~~~~lrpl~~ 106 (249)
+.+||.+.|++.+ --|.||+|.+-. . +.+.|.|-|..+...|+..+|.|...
T Consensus 1 ~~~GdlVWaK~~g-~pwWPa~V~~~~~~p~~~~~~~~~~~~~~V~Ffgs~~y~Wv~~~~l~pf~e 64 (95)
T cd05838 1 PLYGDIVWAKLGN-FRWWPAIICDPREVPPNIQVLRHCIGEFCVMFFGTHDYYWVHRGRVFPYQE 64 (95)
T ss_pred CCcCCEEEEECCC-CCCCCeEEcChhhcChhHhhccCCCCeEEEEEeCCCCEEEeccccccchhh
Confidence 3689999999975 568899998632 1 24899999999999999999998853
No 32
>KOG3038 consensus Histone acetyltransferase SAGA associated factor SGF29 [General function prediction only]
Probab=86.24 E-value=1.4 Score=40.40 Aligned_cols=42 Identities=29% Similarity=0.474 Sum_probs=34.6
Q ss_pred CCCCCCCCCCCeEEEEecCCCCEEEEEEeeEeCCe---eEEEEec
Q 025684 48 SDNQEKLAVGTKVQAVYSEDGEWYDATIEAITPNG---YYVTYDS 89 (249)
Q Consensus 48 ~~~~~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~---~~V~F~~ 89 (249)
+++...|.+|..+||+|.+-=.||+|.|.+--.++ |.|.|.|
T Consensus 193 p~p~~~fpp~~~VLA~YP~TTcFY~aiVh~tp~d~s~~y~vlffD 237 (264)
T KOG3038|consen 193 PPPTALFPPGTIVLAVYPGTTCFYKAIVHSTPRDGSCDYYVLFFD 237 (264)
T ss_pred CCCccCCCCCCEEEEEcCCcceeeeeEeecCCCCCCCcceeeeec
Confidence 45778899999999999988899999998865443 7777755
No 33
>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=85.51 E-value=1.4 Score=35.17 Aligned_cols=55 Identities=20% Similarity=0.250 Sum_probs=42.9
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEe--------------CCeeEEEEecC-CceEEEcCCCcccCCchh
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAIT--------------PNGYYVTYDSW-GNKEEVDPANVRPVNLLV 108 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~--------------~~~~~V~F~~Y-gn~E~V~~~~lrpl~~l~ 108 (249)
.|.+||.+-|+..+ --|+||+|..-. ...|.|.|.|- ++...|+..+|.|+....
T Consensus 2 ~~~~GdlVWaK~~g-~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~~~~aWv~~~~l~pf~~~~ 71 (110)
T cd05837 2 KYQVGDLVWAKVSG-YPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDNPERAWISEKSLKPFKGSK 71 (110)
T ss_pred CCCCCCEEEEeCCC-CCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCCCCEEEecHHHccccCCch
Confidence 58899999999864 358999998511 12489999885 478999999999997554
No 34
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=78.72 E-value=1.1 Score=43.78 Aligned_cols=52 Identities=25% Similarity=0.297 Sum_probs=37.7
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcccC
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPV 104 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrpl 104 (249)
..+.+|..|+|+. +|+.|-.|+|+.|+...+.|.|.--|....+..-|..++
T Consensus 179 s~L~~gs~vlak~-~sdiWh~ari~~vd~~~q~vkv~~~g~~~s~kegD~~~~ 230 (486)
T KOG2185|consen 179 SQLMVGSKVLAKS-GSDIWHKARIESVDDELQVVKVVFRGDKSSAKEGDSLAL 230 (486)
T ss_pred HHHhhcCeeeeec-cchhhhhhheeeeccceeEEEEEeccchhhhhcccccCc
Confidence 4578999999994 689999999999997655555555555444444455555
No 35
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=75.60 E-value=4.8 Score=42.73 Aligned_cols=38 Identities=29% Similarity=0.697 Sum_probs=31.5
Q ss_pred CCCCCCCeEEEEe----cCCCCEEEEEEeeEeCC----------eeEEEEec
Q 025684 52 EKLAVGTKVQAVY----SEDGEWYDATIEAITPN----------GYYVTYDS 89 (249)
Q Consensus 52 ~~~kvGd~ClA~y----s~Dg~wY~A~I~~i~~~----------~~~V~F~~ 89 (249)
..|+.+|.|...| -+||.|++.+|+++... .|.|.|..
T Consensus 977 rnW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 977 RNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDN 1028 (1113)
T ss_pred hccccccceeEEEccCCCcCCceeeeeeeeccCCCCCCCCCcceeEEEEecC
Confidence 5799999999999 46889999999998742 37888764
No 36
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=74.80 E-value=2.8 Score=44.83 Aligned_cols=52 Identities=21% Similarity=0.347 Sum_probs=43.8
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeC-Ce-eEEEEecCCceEEEcCCCcccCCch
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITP-NG-YYVTYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~-~~-~~V~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
--.|-.|.|.|. -.+|++.+.+... .| |.+.|.+|.--.-+++.+|+|+..+
T Consensus 726 ~i~gl~v~a~w~--~~fyp~s~ls~rd~~gr~~~fft~~~~~kdi~~~diiplda~ 779 (1176)
T KOG3548|consen 726 HIPGLRVYAVWQ--KMFYPASVLSERDGLGRYKVFFTVDNVIKDIPNSDIIPLDAL 779 (1176)
T ss_pred CCCceEEEEEee--ccCCCcccceeecCCCcEEEEEeccccccccccccceecccc
Confidence 567899999995 4689999988774 34 8999999998899999999999754
No 37
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=72.23 E-value=14 Score=24.38 Aligned_cols=33 Identities=12% Similarity=0.115 Sum_probs=28.1
Q ss_pred CCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCC
Q 025684 66 EDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPA 99 (249)
Q Consensus 66 ~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~ 99 (249)
+...|=.|.|.++.++.++|...+ |..-+|+.+
T Consensus 9 ~~egfv~g~I~~~~g~~vtV~~~~-G~~~tv~~d 41 (42)
T PF02736_consen 9 PKEGFVKGEIIEEEGDKVTVKTED-GKEVTVKKD 41 (42)
T ss_dssp SSSSEEEEEEEEEESSEEEEEETT-TEEEEEEGG
T ss_pred CcccEEEEEEEEEcCCEEEEEECC-CCEEEeCCC
Confidence 355699999999999999999999 988888654
No 38
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=70.62 E-value=6.8 Score=35.78 Aligned_cols=41 Identities=15% Similarity=0.217 Sum_probs=35.7
Q ss_pred cCCCCEEEEEEeeEe---CCeeEEEEecCCceEEEcCCCcccCC
Q 025684 65 SEDGEWYDATIEAIT---PNGYYVTYDSWGNKEEVDPANVRPVN 105 (249)
Q Consensus 65 s~Dg~wY~A~I~~i~---~~~~~V~F~~Ygn~E~V~~~~lrpl~ 105 (249)
++|-.+|+-.|+.+. ++.|.+.|.+||....+.+++|.+++
T Consensus 76 ~~~~l~~~~~i~a~~w~vg~K~~A~~~ddg~~y~AtIe~ita~~ 119 (262)
T KOG3026|consen 76 SGDYLFYPSRITAVGWKVGDKVQAVFSDDGQIYDATIEHITAME 119 (262)
T ss_pred hhhhccccccchhcccccCCEEEEeecCCCceEEeehhhccCCC
Confidence 668889999999874 34699999999999999999999974
No 39
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=69.18 E-value=10 Score=26.83 Aligned_cols=36 Identities=22% Similarity=0.352 Sum_probs=28.6
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCC-ceEEEcCCCcc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWG-NKEEVDPANVR 102 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Yg-n~E~V~~~~lr 102 (249)
-|..|.|+|.+|...++.|.+.+|+ -.-.|+.++|.
T Consensus 3 ~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~ 39 (76)
T cd04452 3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELS 39 (76)
T ss_pred CCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcC
Confidence 4789999999999999999998875 55666555554
No 40
>PF02820 MBT: mbt repeat; InterPro: IPR004092 The function of the malignant brain tumor (MBT) repeat is unknown, but is found in a number of nuclear proteins involved in transcriptional repression. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function. The crystal structure of the two MBT repeats of human SCM-like 2 protein has been reported. Each repeat consists of an extended "arm" and a globular core. The arm of the first repeat packs against the core of the second repeat and vice versa. The structure of the core-interacting part of each arm consists of an N-terminal alpha-helix and a turn of 310 helix connected by a short beta-strand. The core consists of an Src homology 3-like five-stranded beta-barrel followed by a C-terminal alpha-helix and another short beta-strand. Each arm interacts with its partner core in a similar way, with the orientation of the N-terminal helix relative to the barrel varying slightly. There are also extensive interactions between the two barrels [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P0K_A 3F70_B 3CEY_A 2VYT_A 2BIV_A 1OI1_A 3OQ5_A 2RJE_B 2RJD_A 2RI3_A ....
Probab=68.97 E-value=8.4 Score=28.13 Aligned_cols=38 Identities=21% Similarity=0.287 Sum_probs=29.2
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCce--EEEcCC--CcccCC
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNK--EEVDPA--NVRPVN 105 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~--E~V~~~--~lrpl~ 105 (249)
..++.|+|.+|.+..+.|.|+||.+. ..+..+ +|.|+-
T Consensus 12 ~~~~vAtV~~v~g~~l~v~~dg~~~~~d~w~~~~S~~i~PvG 53 (73)
T PF02820_consen 12 SLICVATVVKVCGGRLLVRYDGWDDDYDFWCHIDSPRIFPVG 53 (73)
T ss_dssp CEEEEEEEEEEETTEEEEEETTSTGGGEEEEETTSTTEEETT
T ss_pred CeEEEEEEEEEeCCEEEEEEcCCCCCccEEEECCCCCeeecc
Confidence 45779999999999999999999974 444444 566663
No 41
>KOG1904 consensus Transcription coactivator [Transcription]
Probab=67.26 E-value=5.5 Score=39.89 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=46.3
Q ss_pred CCCCCCCCeEEEEecCCCCEEEEEEeeEeCC-------eeEEEEecCCceEEEcCCCcccCCchh
Q 025684 51 QEKLAVGTKVQAVYSEDGEWYDATIEAITPN-------GYYVTYDSWGNKEEVDPANVRPVNLLV 108 (249)
Q Consensus 51 ~~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~-------~~~V~F~~Ygn~E~V~~~~lrpl~~l~ 108 (249)
.+.+++||.+.|.-.+==.| +|+|...... .|.|.|.|-+.+..|...+|.|.....
T Consensus 10 ~~~~~~GDLV~AKlkgyp~W-ParI~~~~~~~~kp~pkky~V~FfGT~e~Afl~p~dlqpy~~~k 73 (496)
T KOG1904|consen 10 AGNFKCGDLVFAKLKGYPPW-PARIRNGPDGAVKPPPKKYTVFFFGTKETAFLKPKDLQPYMLNK 73 (496)
T ss_pred cCCCCCCceeeecccCCCCC-cccccCcccccccCCCceeEEEEeccCcccccchhhccchhhhh
Confidence 47899999999998644445 9999876543 499999999999999999999986443
No 42
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=64.16 E-value=17 Score=25.56 Aligned_cols=36 Identities=11% Similarity=0.272 Sum_probs=29.7
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCccc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 103 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrp 103 (249)
-|.-|.|+|.+|...++.|.+. ++-...|+.++|-.
T Consensus 4 ~G~iv~g~V~~v~~~g~~V~l~-~~~~g~ip~~~l~~ 39 (74)
T PF00575_consen 4 EGDIVEGKVTSVEDFGVFVDLG-NGIEGFIPISELSD 39 (74)
T ss_dssp TTSEEEEEEEEEETTEEEEEES-TSSEEEEEGGGSSS
T ss_pred CCCEEEEEEEEEECCEEEEEEC-CcEEEEEEeehhcC
Confidence 3678899999999999999998 78888896666553
No 43
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=63.75 E-value=4 Score=41.29 Aligned_cols=51 Identities=14% Similarity=0.167 Sum_probs=41.4
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCe---eEEEEecCCceEEEcCCCcccC
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNG---YYVTYDSWGNKEEVDPANVRPV 104 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~---~~V~F~~Ygn~E~V~~~~lrpl 104 (249)
..+..+-.|-|. .+++-|.+|.+-.-.++. +.|.|++|| .-.+.+++||++
T Consensus 455 ~P~~~t~~sAAp-~g~~awpra~lvd~~det~l~I~~~~VdyG-Y~~~~~ddlrqi 508 (608)
T KOG2279|consen 455 KPLVATISSAAP-TGISAWPRAYLVDTSDETKLDIGLELVDYG-YAIELPDDLRQI 508 (608)
T ss_pred cchhhceeeecc-cCCCCccceEEEeccCcccchhhheeeccc-ccccchhhhhhh
Confidence 345678888888 579999999998766542 789999999 788888888887
No 44
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=62.16 E-value=27 Score=25.86 Aligned_cols=50 Identities=20% Similarity=0.197 Sum_probs=36.8
Q ss_pred CCCCCCeEEEEecCCCC--EEEEEEeeEeCCeeEEEEec-CCceEEEcCCCcc
Q 025684 53 KLAVGTKVQAVYSEDGE--WYDATIEAITPNGYYVTYDS-WGNKEEVDPANVR 102 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~--wY~A~I~~i~~~~~~V~F~~-Ygn~E~V~~~~lr 102 (249)
.+.-+..|...|..+|. -+.++|..|+...-.+.+.+ .++...+++++|.
T Consensus 38 a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~~~~~~~~I~~~~I~ 90 (92)
T PF08863_consen 38 AYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKDEDGETEKIPFDDII 90 (92)
T ss_pred HhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEhhhEE
Confidence 46668899999987884 45577788887654555555 6889999888875
No 45
>KOG3038 consensus Histone acetyltransferase SAGA associated factor SGF29 [General function prediction only]
Probab=61.69 E-value=21 Score=32.91 Aligned_cols=56 Identities=21% Similarity=0.227 Sum_probs=41.7
Q ss_pred CCCCCCCeEEEEe---cCCCCEEEEEEeeEeCCe-eEEEEecCCc--eEEEcCCCcccCCch
Q 025684 52 EKLAVGTKVQAVY---SEDGEWYDATIEAITPNG-YYVTYDSWGN--KEEVDPANVRPVNLL 107 (249)
Q Consensus 52 ~~~kvGd~ClA~y---s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn--~E~V~~~~lrpl~~l 107 (249)
...-+||.+-|++ ++||.|.-|.|..++.++ |.|.=.|=.- .++-...+|-|+|..
T Consensus 126 ~~~~~gd~VAa~v~~~~~dg~WIlaeVv~~~~~~~ye~ev~D~Epk~d~~g~r~~~yklp~~ 187 (264)
T KOG3038|consen 126 YVLLKGDEVAARVKAVSEDGDWILAEVVKVSSETRYEFEVVDPEPKKDEVGNRGQLYKLPRW 187 (264)
T ss_pred ccccCCceeeeeeeeccCCCCEEEEEEEEEecCCceEeEecCCCccccccccccceecccHh
Confidence 5678899999999 789999999999999887 6555444322 455666667777643
No 46
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=61.63 E-value=25 Score=29.33 Aligned_cols=53 Identities=17% Similarity=0.045 Sum_probs=43.6
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCe--eEEEEecCCce--EEEcCCCcccCC
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNG--YYVTYDSWGNK--EEVDPANVRPVN 105 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~--~~V~F~~Ygn~--E~V~~~~lrpl~ 105 (249)
..+.+||.+.-.- +--.=|.|+|.+++... +.|.+.+.... -+|+.++|+++.
T Consensus 93 ~~~~~G~~V~I~~-Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~ 149 (153)
T PRK08559 93 EGIKEGDIVELIA-GPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVK 149 (153)
T ss_pred cCCCCCCEEEEec-cCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEec
Confidence 5699999999883 33345799999998653 79999999987 999999999874
No 47
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=60.74 E-value=19 Score=27.00 Aligned_cols=48 Identities=17% Similarity=0.182 Sum_probs=35.9
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCC
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPA 99 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~ 99 (249)
..+++||.|+..=+.+|.|+.++|.+|.-+...+.+.-=|..-.+.+.
T Consensus 25 G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~l~ 72 (87)
T cd03694 25 GVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLALK 72 (87)
T ss_pred CEEeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEEEc
Confidence 578999999987655688999999999866556666555666666443
No 48
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=60.32 E-value=15 Score=25.82 Aligned_cols=35 Identities=14% Similarity=0.284 Sum_probs=27.8
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|..|.|+|..|...++.|.+.+.+-.-.++..+|.
T Consensus 3 g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~ 37 (77)
T cd05708 3 GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEIS 37 (77)
T ss_pred CCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCC
Confidence 67899999999999999998876666677655554
No 49
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=59.67 E-value=25 Score=31.33 Aligned_cols=37 Identities=22% Similarity=0.221 Sum_probs=30.7
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEec
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS 89 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~ 89 (249)
...++||.+.+.- ++|..|.|+|..++.+.+.+.+..
T Consensus 30 lR~~~Gd~v~v~~-g~g~~~~a~i~~~~~~~~~~~i~~ 66 (240)
T TIGR00046 30 LRLKKGDKLKLLD-GDGFIYHCEIKKISKKFVKCELLE 66 (240)
T ss_pred ccCCCCCEEEEEe-CCCCEEEEEEEEEcCCeEEEEEEe
Confidence 4789999999975 589999999999998876666554
No 50
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=57.96 E-value=15 Score=28.34 Aligned_cols=42 Identities=7% Similarity=0.042 Sum_probs=28.4
Q ss_pred CCeEEEEecCCCCEEEEEEeeEeCCeeEEEEec-CCceEEEcCCCc
Q 025684 57 GTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS-WGNKEEVDPANV 101 (249)
Q Consensus 57 Gd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~-Ygn~E~V~~~~l 101 (249)
=-+|++.|. ||+| ++|..++++.+.|...+ -+..+.++.+++
T Consensus 69 ~lP~i~~~~-~g~~--~Vl~~~~~~~~~i~dp~~~~~~~~~~~~el 111 (124)
T cd02421 69 LLPAILLLK-NGRA--CVLLGVDDGHARILDPESGGGEVEISLEEL 111 (124)
T ss_pred cCCEEEEEc-CCCE--EEEEEecCCeEEEEccCCCCCcEEEcHHHH
Confidence 358999875 7887 57888888776665554 455666744433
No 51
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=55.34 E-value=29 Score=24.81 Aligned_cols=36 Identities=11% Similarity=0.200 Sum_probs=27.6
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
=|.-|.|+|.+|...|+-|...+++-.-.|+.++|.
T Consensus 3 ~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~ 38 (73)
T cd05686 3 LYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMS 38 (73)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhC
Confidence 367899999999998988888776556667555443
No 52
>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=54.01 E-value=33 Score=27.71 Aligned_cols=51 Identities=20% Similarity=0.053 Sum_probs=38.3
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEe------------------------C-C--eeEEEEec-CCceEEEcCCCcccCC
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAIT------------------------P-N--GYYVTYDS-WGNKEEVDPANVRPVN 105 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~------------------------~-~--~~~V~F~~-Ygn~E~V~~~~lrpl~ 105 (249)
+.+||.+-|+.. ---||+|+|..-+ + + .|.|.|-| -.+-..|+..+|+|+.
T Consensus 1 ~~pg~lVwaK~~-g~P~wPa~iidp~~~~~~~~~~~~p~~~l~~~~~~~~~~~~~~~lV~FFd~~~s~~Wv~~~~l~pl~ 79 (111)
T cd05839 1 LEPLTLVWAKCR-GYPSYPALIIDPKMPRDGVFHNGVPPDVLTLGEARAQNADERLYLVLFFDNKRTWQWLPGDKLEPLG 79 (111)
T ss_pred CCCcCEeeeeec-CCCCCCeEeeCCCCCCcccccCCCCchhhhHHHHHhccCCCcEEEEEEecCCCcceecCHHHCcccc
Confidence 357999999985 3359999998643 0 1 27888877 3566889999999985
No 53
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=53.68 E-value=39 Score=27.71 Aligned_cols=52 Identities=21% Similarity=0.328 Sum_probs=39.7
Q ss_pred CCCCeEEEEe---cCCCCEEEEEEeeEeCCe--eEEEEecCC---ceEEEcCCCcccCCc
Q 025684 55 AVGTKVQAVY---SEDGEWYDATIEAITPNG--YYVTYDSWG---NKEEVDPANVRPVNL 106 (249)
Q Consensus 55 kvGd~ClA~y---s~Dg~wY~A~I~~i~~~~--~~V~F~~Yg---n~E~V~~~~lrpl~~ 106 (249)
++|+.|-|+- .+++.|--|+|.++.+++ |.|.=.+-+ +.-.++..+|-|||.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~ 60 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPK 60 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-S
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCC
Confidence 5799999986 367889999999999765 888877765 356678888888875
No 54
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=52.75 E-value=28 Score=30.44 Aligned_cols=50 Identities=10% Similarity=0.058 Sum_probs=37.3
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcccCC
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPVN 105 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrpl~ 105 (249)
.-+--.|+-.- ++.-|+++|.+.+++.+.|.=.+-++..+|++++|..|.
T Consensus 132 ~lp~i~C~i~t--~~~~Y~G~I~~~~~~~v~i~~~~~~~~~~i~~~~I~sI~ 181 (185)
T PF14153_consen 132 HLPPIKCEIET--KDKSYRGIILSYDEGEVSIMPFNQGEEIEIPIDDITSIK 181 (185)
T ss_pred cCCCCceEEEe--CCceEEEEEEeccCCEEEEeccCCCcceEeehhheeeee
Confidence 34556888884 667899999999987554544445678899999888764
No 55
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=52.74 E-value=27 Score=24.98 Aligned_cols=35 Identities=26% Similarity=0.405 Sum_probs=29.1
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|.-|.|+|..|...|+.|....||-.-.|.+++|.
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~ 36 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLG 36 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecC
Confidence 57899999999999999998888877777666664
No 56
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=52.67 E-value=25 Score=24.51 Aligned_cols=33 Identities=18% Similarity=0.301 Sum_probs=26.1
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|.-|.++|..+...|+.|.| + |-.-.+|.++|.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~-g~~gfip~s~~~ 33 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-E-GVRAFLPASQVD 33 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCC
Confidence 56799999999999999999 3 666777655553
No 57
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=51.97 E-value=33 Score=24.69 Aligned_cols=35 Identities=17% Similarity=0.360 Sum_probs=27.0
Q ss_pred CCEEEEEEeeEeCCeeEEEEecC--CceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSW--GNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Y--gn~E~V~~~~lr 102 (249)
|+-|.|+|..|...++.|.+.++ +-.-.++.++|.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~ 37 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLS 37 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhcc
Confidence 56899999999998998988765 555666555554
No 58
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=51.68 E-value=25 Score=24.52 Aligned_cols=33 Identities=24% Similarity=0.331 Sum_probs=25.0
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
|.-|.|+|..|...++.|.|.+ +-.-.++.++|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~-~~~gli~~s~l 33 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSEL 33 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECC-CCEEEEEHHHc
Confidence 5679999999999999999965 45566644443
No 59
>PRK14639 hypothetical protein; Provisional
Probab=47.22 E-value=71 Score=26.48 Aligned_cols=50 Identities=10% Similarity=0.188 Sum_probs=36.7
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCccc
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 103 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrp 103 (249)
.--+|..|..... +++.|.++|.+++++.+.+....=+....+++++|+.
T Consensus 84 ~r~~G~~v~v~l~-~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~k 133 (140)
T PRK14639 84 AKSIGELVKITTN-EKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKK 133 (140)
T ss_pred HHhCCCEEEEEEC-CCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeee
Confidence 3468999998875 7899999999999987776543223446777776654
No 60
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=45.46 E-value=53 Score=28.83 Aligned_cols=37 Identities=22% Similarity=0.260 Sum_probs=28.0
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEec
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS 89 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~ 89 (249)
...++||.+...- ++|..|.|+|+.++...+.+....
T Consensus 15 lR~k~Gd~i~v~d-g~g~~~~a~i~~i~~~~~~~~i~~ 51 (225)
T PF04452_consen 15 LRLKEGDSIEVFD-GDGGEYRAEITEISKKSATLRILE 51 (225)
T ss_dssp ST--TT-EEEEEE-SSSEEEEEEEEEEESSEEEEEEEE
T ss_pred cCCCCCCEEEEEE-CCCCEEEEEEEECcCcEEEEEEee
Confidence 5689999998885 699999999999998876665553
No 61
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=45.36 E-value=36 Score=22.97 Aligned_cols=34 Identities=12% Similarity=0.211 Sum_probs=24.8
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|.-|.|+|.+|...++.|.+.. +-.-.++..+|.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~ 34 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMA 34 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCC
Confidence 5679999999999888888854 455666555443
No 62
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=44.13 E-value=28 Score=26.80 Aligned_cols=41 Identities=5% Similarity=0.123 Sum_probs=28.0
Q ss_pred CCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 57 GTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 57 Gd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
--+|++.|. ||.| ++|..++++.+.|..-+.| .+.++.+++
T Consensus 74 ~lP~i~~~~-~g~~--~Vl~~~~~~~~~i~dp~~~-~~~~~~~el 114 (127)
T cd02419 74 KLPCILHWD-MNHF--VVLKKVSRRRIVIHDPALG-KRKLSLEEA 114 (127)
T ss_pred CCCEEEEEC-CCEE--EEEEEEcCCEEEEECCccC-CEEEcHHHH
Confidence 458999974 7876 5778887777777766665 556644433
No 63
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=42.20 E-value=1e+02 Score=22.96 Aligned_cols=52 Identities=19% Similarity=0.258 Sum_probs=35.6
Q ss_pred CCCCCCCeEEEEecC--CC-CEEEEEEeeEeCCeeEEEEecC--CceEEEcCCCccc
Q 025684 52 EKLAVGTKVQAVYSE--DG-EWYDATIEAITPNGYYVTYDSW--GNKEEVDPANVRP 103 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~--Dg-~wY~A~I~~i~~~~~~V~F~~Y--gn~E~V~~~~lrp 103 (249)
...-+|..|...+.. +| ..|.++|.+++++.+.+....- +....+++++|+-
T Consensus 20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~k 76 (83)
T cd01734 20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAK 76 (83)
T ss_pred HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeE
Confidence 345689999887631 44 5899999999998776664421 4456676666653
No 64
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=41.73 E-value=50 Score=22.42 Aligned_cols=34 Identities=21% Similarity=0.352 Sum_probs=25.4
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|.-|.|+|..|...++.|.+.+ +-.-.++.++|.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~l~ 34 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILP-GKDGLVHISELS 34 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcC
Confidence 5679999999999888888754 355666555554
No 65
>PF01356 A_amylase_inhib: Alpha amylase inhibitor; InterPro: IPR000833 Alpha-amylase inhibitor inhibits mammalian alpha-amylases specifically, by forming a tight stoichiometric 1:1 complex with alpha-amylase. The inhibitor has no action on plant and microbial alpha amylases. A crystal structure has been determined for tendamistat, the 74-amino acid inhibitor produced by Streptomyces tendae that targets a wide range of mammalian alpha-amylases []. The binding of tendamistat to alpha-amylase leads to the steric blockage of the active site of the enzyme. The crystal structure of tendamistat revealed an immunoglobulin-like fold that could potentially adopt multiple conformations. Such molecular flexibility could enable an induced-fit type of binding that would both optimise binding and allow broad target specificity. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0015066 alpha-amylase inhibitor activity; PDB: 2KER_A 3AIT_A 1BVN_T 1HOE_A 4AIT_A 2AIT_A 1OK0_A.
Probab=40.69 E-value=62 Score=23.98 Aligned_cols=35 Identities=23% Similarity=0.372 Sum_probs=23.3
Q ss_pred CCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCce
Q 025684 55 AVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNK 93 (249)
Q Consensus 55 kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~ 93 (249)
...=.+-..|. ||+|=++++.. -+-.++|-|||+.
T Consensus 24 a~tvsVtV~Y~-dG~~~PCrv~~---PG~~~Tf~Gygt~ 58 (68)
T PF01356_consen 24 ADTVSVTVEYT-DGQEVPCRVIP---PGDIATFPGYGTN 58 (68)
T ss_dssp SS-EEEEEEET-TS-CEEEEEE----TTEEEEEE-TTTT
T ss_pred cccEEEEEEEe-CCCcceeEEeC---CCCEEEecccccC
Confidence 34445667786 99999998863 3468899999974
No 66
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=40.35 E-value=47 Score=23.19 Aligned_cols=34 Identities=26% Similarity=0.453 Sum_probs=25.9
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|+-|.|+|..|...++.|.+.+ +-.-.|+..+|.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~-~v~g~i~~~~l~ 34 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLA 34 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCC
Confidence 5789999999999999888863 456777555443
No 67
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=39.95 E-value=53 Score=21.91 Aligned_cols=36 Identities=22% Similarity=0.339 Sum_probs=26.6
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCccc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 103 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrp 103 (249)
-|.-|.|+|..++..++.|.+. .+-.-.++..++.+
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~-~~~~g~l~~~~~~~ 37 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLG-NGVEGLIPISELSD 37 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeC-CCCEEEEEHHHCCc
Confidence 3778999999999988888775 35556676555554
No 68
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=39.33 E-value=1.2e+02 Score=24.71 Aligned_cols=50 Identities=10% Similarity=0.241 Sum_probs=33.9
Q ss_pred CCCCCeEEEEec---CCCCEEEEEEeeEeCCeeEEEEecCC--ceEEEcCCCccc
Q 025684 54 LAVGTKVQAVYS---EDGEWYDATIEAITPNGYYVTYDSWG--NKEEVDPANVRP 103 (249)
Q Consensus 54 ~kvGd~ClA~ys---~Dg~wY~A~I~~i~~~~~~V~F~~Yg--n~E~V~~~~lrp 103 (249)
.-+|..+...+. ...++|.++|.+++++.+++.+.+-+ ....+++++|+.
T Consensus 84 ~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~k 138 (141)
T PF02576_consen 84 RFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKK 138 (141)
T ss_dssp HH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS
T ss_pred HhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCce
Confidence 457999999983 34469999999999998888888765 367787777764
No 69
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=39.04 E-value=32 Score=26.22 Aligned_cols=38 Identities=13% Similarity=0.074 Sum_probs=26.1
Q ss_pred CeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcC
Q 025684 58 TKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDP 98 (249)
Q Consensus 58 d~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~ 98 (249)
-+|++.+. ||.| ++|..++++.+.|..-+.+..+.++.
T Consensus 70 lP~I~~~~-~g~~--~Vl~~~~~~~~~i~dp~~~~~~~~~~ 107 (121)
T cd02417 70 LPALAWDD-DGGH--FILAKLDGQKYLIQDPISQRPEVLSR 107 (121)
T ss_pred CCEEEEcc-CCCE--EEEEEEcCCCEEEECCCcCCCeecCH
Confidence 38999875 7776 57788887767776665665556633
No 70
>PRK14637 hypothetical protein; Provisional
Probab=37.19 E-value=1e+02 Score=25.89 Aligned_cols=50 Identities=18% Similarity=0.254 Sum_probs=37.0
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcccC
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPV 104 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrpl 104 (249)
.--+|..+...+..++.|+.++|.+++++.+.+.- -+....+++++|+..
T Consensus 94 ~r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~--~~~~~~i~~~~I~ka 143 (151)
T PRK14637 94 SIFVGETVKVWFECTGQWQVGTIAEADETCLVLTS--DGVPVTIPYVQITKA 143 (151)
T ss_pred HHhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeeeE
Confidence 34689999998855778889999999988665542 356677777666543
No 71
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=36.58 E-value=98 Score=27.40 Aligned_cols=37 Identities=22% Similarity=0.181 Sum_probs=29.5
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEec
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS 89 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~ 89 (249)
...++||.....- ++|..|.|+|..++.+.+.+....
T Consensus 28 lR~~~Gd~i~v~~-g~g~~~~~~i~~i~~~~~~~~i~~ 64 (234)
T PRK11713 28 LRLKEGDELRLFD-GDGGEYLAEITEIGKKEVELEILE 64 (234)
T ss_pred ccCCCCCEEEEEe-CCCCEEEEEEEEecCcEEEEEEEe
Confidence 4689999998764 588999999999988766665544
No 72
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=36.57 E-value=43 Score=25.70 Aligned_cols=36 Identities=8% Similarity=0.195 Sum_probs=24.6
Q ss_pred CeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEc
Q 025684 58 TKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVD 97 (249)
Q Consensus 58 d~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~ 97 (249)
-+|++.|. ||.| ++|..++++.+.|...+.+ ...++
T Consensus 75 lP~I~~~~-~g~~--~Vl~~~~~~~~~i~dp~~~-~~~~s 110 (125)
T cd02420 75 LPAIVFWN-FNHF--LVVEGFDKRKVFLNDPATG-RRTVS 110 (125)
T ss_pred CCEEEEeC-CCEE--EEEEEEeCCEEEEECCCcC-ceeec
Confidence 58999985 8877 5788888776666555443 34453
No 73
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.64 E-value=52 Score=23.93 Aligned_cols=34 Identities=21% Similarity=0.317 Sum_probs=24.9
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
-|.-|.|+|..|...++.|.+.+ +-.-.|+..+|
T Consensus 14 ~G~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el 47 (83)
T cd04461 14 PGMVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYI 47 (83)
T ss_pred CCCEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHC
Confidence 56789999999999998888864 34555644433
No 74
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.42 E-value=62 Score=22.45 Aligned_cols=33 Identities=24% Similarity=0.424 Sum_probs=24.6
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
|.-|.|+|..|.+.++.|.+.+ +-.-.|+..+|
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~-~~~G~v~~s~l 33 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGR-GVDARVRVSEL 33 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCC-CCEEEEEHHHC
Confidence 5679999999999999898865 35566644443
No 75
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=34.88 E-value=64 Score=22.40 Aligned_cols=33 Identities=9% Similarity=0.219 Sum_probs=24.7
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
|.-|.|+|.+|.+.++.|.. +++..-.++..++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l-~~~~~g~l~~~e~ 33 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDI-GYKSEGIIPISEF 33 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEe-CCCceEEEEHHHh
Confidence 56789999999988888776 5566677755444
No 76
>PHA01809 hypothetical protein
Probab=34.57 E-value=20 Score=25.50 Aligned_cols=30 Identities=20% Similarity=0.417 Sum_probs=19.7
Q ss_pred CCCCCCCCCeEEEEecC---CCCEEEEEEeeEe
Q 025684 50 NQEKLAVGTKVQAVYSE---DGEWYDATIEAIT 79 (249)
Q Consensus 50 ~~~~~kvGd~ClA~ys~---Dg~wY~A~I~~i~ 79 (249)
+...|+-|..|+|+|.. .=.||+.-|++|.
T Consensus 12 hvfrfkngslcialfdrteneisfydvdideie 44 (65)
T PHA01809 12 HVFRFKNGSLCIALFDRTENEISFYDVDIDEIE 44 (65)
T ss_pred EEEEecCCcEEEEEeccccceeeeEecChHHhh
Confidence 44678999999999921 1136665555554
No 77
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.71 E-value=99 Score=28.05 Aligned_cols=37 Identities=16% Similarity=0.142 Sum_probs=29.4
Q ss_pred CCCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEec
Q 025684 52 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS 89 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~ 89 (249)
...++||.+.... ++|.+|.|.|..++...+.+.+..
T Consensus 32 lRl~~gd~l~l~~-g~g~~~~a~i~~~~kk~~~~~i~~ 68 (246)
T COG1385 32 LRLKEGDELRLFD-GSGGEFLAEITKIGKKEALLKIVE 68 (246)
T ss_pred eecCCCCEEEEEe-CCCcEEEEEEeecCCCceEEEEEe
Confidence 4689999999985 588899999999998765555544
No 78
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=32.36 E-value=68 Score=22.03 Aligned_cols=34 Identities=26% Similarity=0.388 Sum_probs=24.9
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|.-|.|+|..|...++.|.+.+ +-.-.|+..+|.
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~l~ 34 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDIS 34 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCC-CCEEEEEHHHCC
Confidence 5679999999999888888864 445556554443
No 79
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=31.68 E-value=76 Score=21.41 Aligned_cols=33 Identities=21% Similarity=0.385 Sum_probs=23.7
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|.-|.|+|..+...++.|.+. +-.-.++..++.
T Consensus 2 g~~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e~~ 34 (68)
T cd05688 2 GDVVEGTVKSITDFGAFVDLG--GVDGLLHISDMS 34 (68)
T ss_pred CCEEEEEEEEEEeeeEEEEEC--CeEEEEEhHHCC
Confidence 568999999999888888863 344556554443
No 80
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=31.43 E-value=86 Score=22.79 Aligned_cols=34 Identities=9% Similarity=0.228 Sum_probs=25.5
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCCc-eEEEcCCCc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWGN-KEEVDPANV 101 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Ygn-~E~V~~~~l 101 (249)
.|.-+.|.|.+|.+.||.|.| |+++ .--++.++|
T Consensus 4 ~G~~v~g~V~si~d~G~~v~~-g~~gv~Gfl~~~~~ 38 (74)
T cd05694 4 EGMVLSGCVSSVEDHGYILDI-GIPGTTGFLPKKDA 38 (74)
T ss_pred CCCEEEEEEEEEeCCEEEEEe-CCCCcEEEEEHHHC
Confidence 466789999999999999998 6644 566644443
No 81
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=30.65 E-value=1.3e+02 Score=21.21 Aligned_cols=38 Identities=16% Similarity=0.378 Sum_probs=25.5
Q ss_pred CCCCeEEEEecCCCCE--EEEEEeeEeCCeeEEEEecCCceE
Q 025684 55 AVGTKVQAVYSEDGEW--YDATIEAITPNGYYVTYDSWGNKE 94 (249)
Q Consensus 55 kvGd~ClA~ys~Dg~w--Y~A~I~~i~~~~~~V~F~~Ygn~E 94 (249)
-+|..+...-. +..| |...|..|+++.+.|.|.| ||=+
T Consensus 3 lPG~~V~V~n~-~~~Y~~y~G~VQRvsdgkaaVLFEG-GnWd 42 (53)
T PF11623_consen 3 LPGSTVRVKNP-NDIYYGYEGFVQRVSDGKAAVLFEG-GNWD 42 (53)
T ss_dssp -TT-EEEE--T-TSTTTT-EEEEEEEETTEEEEEEEE-TTEE
T ss_pred cCCCEEEEeCC-CCccchheEEEEEeeCCeEEEEecC-CCce
Confidence 35666666643 3333 7899999999999999999 7744
No 82
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=30.64 E-value=91 Score=23.49 Aligned_cols=34 Identities=18% Similarity=0.361 Sum_probs=24.8
Q ss_pred CCCEEEEEEeeEeCC--eeEEEEecCCceEEEcCCCc
Q 025684 67 DGEWYDATIEAITPN--GYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~--~~~V~F~~Ygn~E~V~~~~l 101 (249)
-|..|.|+|+.|.+. ++-|.+.+ |..-.|+.++|
T Consensus 7 ~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~sei 42 (88)
T cd04453 7 VGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDI 42 (88)
T ss_pred CCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHc
Confidence 467999999999985 77777654 45666755554
No 83
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=30.59 E-value=66 Score=26.50 Aligned_cols=46 Identities=24% Similarity=0.416 Sum_probs=32.5
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeCC---e-eEEEEecCCceEEEcCCCc
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITPN---G-YYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~---~-~~V~F~~Ygn~E~V~~~~l 101 (249)
...+|..++|.+ +|.-|.+++|..+..+ - |.|. .+ |..-.++..+|
T Consensus 55 plpl~~eV~A~~-eddY~~~GvV~~h~~~~~e~yY~Ve-~d-G~~~~~~r~~v 104 (122)
T PF09038_consen 55 PLPLGTEVTALS-EDDYFSPGVVKGHKTDSGEVYYCVE-TD-GQRKRYQRKDV 104 (122)
T ss_dssp SS-TTEEEEECC-TTCTSEEEEEEEEEEETTEEEEEEE-ET-TEEEEEEGGGE
T ss_pred ceeccceeEEee-cCCcccccEEEEEEccCCcEEEEEE-EC-CCEEEEEeeeE
Confidence 466799999985 6889999999987633 1 5666 55 77777744443
No 84
>PRK02001 hypothetical protein; Validated
Probab=30.36 E-value=1.9e+02 Score=24.44 Aligned_cols=36 Identities=11% Similarity=0.291 Sum_probs=29.5
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEec
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS 89 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~ 89 (249)
.--+|..+...+. +++.|.++|.+++++++.+...+
T Consensus 86 ~r~~G~~v~V~l~-~~~~~~G~L~~~~~~~i~l~~~~ 121 (152)
T PRK02001 86 KKNIGRELEVLTK-NGKKIEGELKSADENDITLEVKA 121 (152)
T ss_pred HHhCCCEEEEEEC-CCCEEEEEEEEEeCCEEEEEEcc
Confidence 3468999999885 78999999999999877766543
No 85
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=29.96 E-value=1.3e+02 Score=24.42 Aligned_cols=52 Identities=12% Similarity=0.030 Sum_probs=41.2
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeCCe--eEEEEecCCce--EEEcCCCcccCC
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITPNG--YYVTYDSWGNK--EEVDPANVRPVN 105 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~--~~V~F~~Ygn~--E~V~~~~lrpl~ 105 (249)
.+++||.+.-.--+= .=+.|+|..+++.. +.|...+++.. -+|+.++|+.+.
T Consensus 86 ~~~~Gd~V~I~~GPf-~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~ 141 (145)
T TIGR00405 86 SIKKGDIVEIISGPF-KGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQ 141 (145)
T ss_pred ccCCCCEEEEeecCC-CCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEec
Confidence 489999999883211 23799999998643 79999999988 899999998764
No 86
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=29.87 E-value=71 Score=24.01 Aligned_cols=45 Identities=2% Similarity=0.035 Sum_probs=28.9
Q ss_pred CCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 54 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 54 ~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
-+.+-+|++.+. ||.| ++|..++++.+.|..-+.+....++.+++
T Consensus 66 ~~~~~P~i~~~~-~~~~--~Vl~~~~~~~~~i~dp~~~~~~~~~~~~l 110 (122)
T cd02259 66 SRLQLPALLLWK-QGHF--VILYGADKGQVLIADPLEEGPVTLSESEL 110 (122)
T ss_pred ccCCCCEEEEcC-CCcE--EEEEEEcCCEEEEECCcccCCEEeCHHHH
Confidence 345678998864 7775 68888886666665554444456644443
No 87
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=29.36 E-value=2.4e+02 Score=21.33 Aligned_cols=52 Identities=15% Similarity=0.211 Sum_probs=41.5
Q ss_pred CCCCCCeEEEEecC------CCCEEEEEEeeEeCC-------e-eEEEEecCCceEEEcCCCcccC
Q 025684 53 KLAVGTKVQAVYSE------DGEWYDATIEAITPN-------G-YYVTYDSWGNKEEVDPANVRPV 104 (249)
Q Consensus 53 ~~kvGd~ClA~ys~------Dg~wY~A~I~~i~~~-------~-~~V~F~~Ygn~E~V~~~~lrpl 104 (249)
..+.||.++..-.. |+.|+=+.|..+.+. . +.|.-+|-|-...|+.+.+..+
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~wVnaD~Vt~I 70 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGVIRWVNADEVTHI 70 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCeEEEEEchheeee
Confidence 57889999887644 678999999988763 2 7899999999888988877654
No 88
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=29.19 E-value=1.4e+02 Score=18.92 Aligned_cols=28 Identities=11% Similarity=0.391 Sum_probs=21.8
Q ss_pred CCCCCCCCCeEEEEecCCCCEEEEEEee
Q 025684 50 NQEKLAVGTKVQAVYSEDGEWYDATIEA 77 (249)
Q Consensus 50 ~~~~~kvGd~ClA~ys~Dg~wY~A~I~~ 77 (249)
....+..||.+...-..++.|+.++...
T Consensus 17 ~~l~~~~Gd~v~v~~~~~~~w~~~~~~~ 44 (58)
T smart00326 17 DELSFKKGDIITVLEKSDDGWWKGRLGR 44 (58)
T ss_pred CCCCCCCCCEEEEEEcCCCCeEEEEeCC
Confidence 3467899999999876577899887654
No 89
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.07 E-value=1.4e+02 Score=20.87 Aligned_cols=35 Identities=6% Similarity=-0.022 Sum_probs=26.5
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
-|.-|.|+|..|.+.++.|.+.. +-.-.|+..+|.
T Consensus 3 ~G~iv~g~V~~v~~~gi~v~l~~-~~~g~v~~s~l~ 37 (73)
T cd05706 3 VGDILPGRVTKVNDRYVLVQLGN-KVTGPSFITDAL 37 (73)
T ss_pred CCCEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhcc
Confidence 36789999999999888888654 566777665554
No 90
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=28.85 E-value=1.8e+02 Score=25.17 Aligned_cols=54 Identities=19% Similarity=0.373 Sum_probs=38.7
Q ss_pred CCCCCCCCCCCeEEEEecCCCCE--EEEEEeeEeCC--eeEEEEecCCc--eEEEcCCCcccC
Q 025684 48 SDNQEKLAVGTKVQAVYSEDGEW--YDATIEAITPN--GYYVTYDSWGN--KEEVDPANVRPV 104 (249)
Q Consensus 48 ~~~~~~~kvGd~ClA~ys~Dg~w--Y~A~I~~i~~~--~~~V~F~~Ygn--~E~V~~~~lrpl 104 (249)
+.+...+.+||.+.-. ||-| +.|+|++|+.+ ...|...-+|. .-++.+++|+.+
T Consensus 118 ~~~~~~~e~Gd~VrI~---~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVek~ 177 (178)
T COG0250 118 KKPKVDFEPGDVVRII---DGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177 (178)
T ss_pred CcccccCCCCCEEEEe---ccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEEEe
Confidence 4555789999999988 4443 78999999987 25555555664 456777777654
No 91
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=28.76 E-value=83 Score=20.52 Aligned_cols=29 Identities=14% Similarity=0.390 Sum_probs=22.6
Q ss_pred CCCCCCCCCCeEEEEecCCCCEEEEEEee
Q 025684 49 DNQEKLAVGTKVQAVYSEDGEWYDATIEA 77 (249)
Q Consensus 49 ~~~~~~kvGd~ClA~ys~Dg~wY~A~I~~ 77 (249)
.....++.||.+..+-..|+.||.++...
T Consensus 11 ~~eLs~~~Gd~i~v~~~~~~~Ww~~~~~~ 39 (48)
T PF00018_consen 11 PDELSFKKGDIIEVLEKSDDGWWKVRNES 39 (48)
T ss_dssp TTBSEB-TTEEEEEEEESSSSEEEEEETT
T ss_pred CCEEeEECCCEEEEEEecCCCEEEEEECC
Confidence 34578999999999997788899888753
No 92
>smart00783 A_amylase_inhib Alpha amylase inhibitor. Alpha amylase inhibitor inhibits mammalian alpha-amylases specifically, by forming a tight stoichiometric 1:1 complex with alpha-amylase. The inhibitor has no action on plant and microbial alpha amylases.
Probab=28.64 E-value=74 Score=23.61 Aligned_cols=32 Identities=31% Similarity=0.622 Sum_probs=23.6
Q ss_pred CeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCce
Q 025684 58 TKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNK 93 (249)
Q Consensus 58 d~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~ 93 (249)
-.+-..|. ||+|=++++..- +-.++|-|||..
T Consensus 28 vsVtV~Y~-dg~~~pCr~~~P---G~~~Tf~GYgt~ 59 (69)
T smart00783 28 VSVTVVYT-DGTWGPCRTAAP---GDITTFGGYGTN 59 (69)
T ss_pred EEEEEEEe-CCCcceeEeeCC---CCEEEecccccC
Confidence 34566775 999999987543 357888899975
No 93
>PRK14633 hypothetical protein; Provisional
Probab=28.18 E-value=1.8e+02 Score=24.31 Aligned_cols=52 Identities=17% Similarity=0.305 Sum_probs=37.3
Q ss_pred CCCCCCCeEEEEe-c--CCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcccC
Q 025684 52 EKLAVGTKVQAVY-S--EDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPV 104 (249)
Q Consensus 52 ~~~kvGd~ClA~y-s--~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrpl 104 (249)
...-+|..+.... . .++..|.+++.+++++.+.+...+ |..-.+++++|+..
T Consensus 89 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~-~~~~~i~~~~I~ka 143 (150)
T PRK14633 89 AQALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLED-GKEISFDFDELKKL 143 (150)
T ss_pred HHHhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHeeeE
Confidence 3456899988865 3 377899999999998877665532 45567777777643
No 94
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=28.03 E-value=1.7e+02 Score=24.27 Aligned_cols=50 Identities=12% Similarity=0.213 Sum_probs=37.3
Q ss_pred CCCCCCCeEEEEe---cCCCCEEEEEEeeEeCCeeEEEEecCCc--eEEEcCCCccc
Q 025684 52 EKLAVGTKVQAVY---SEDGEWYDATIEAITPNGYYVTYDSWGN--KEEVDPANVRP 103 (249)
Q Consensus 52 ~~~kvGd~ClA~y---s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn--~E~V~~~~lrp 103 (249)
...-+|..+...+ -.++..|.++|.+++++.+.+... |. ...+++++|+.
T Consensus 93 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~--~~~~~~~i~~~~I~~ 147 (154)
T PRK00092 93 FRRFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVE--GKEKEVEIPLDNIAK 147 (154)
T ss_pred HHHhCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEEC--CCeEEEEEEHHHcce
Confidence 3457899999986 257889999999999987766654 34 56677766664
No 95
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=28.01 E-value=1.2e+02 Score=21.19 Aligned_cols=34 Identities=18% Similarity=0.341 Sum_probs=25.4
Q ss_pred CCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 67 DGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 67 Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
-|.-|.|+|..|...++-|.+.. +-.-.++..+|
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~l 36 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEM 36 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCC-CCEEEEEEEec
Confidence 46689999999999898888865 44555655544
No 96
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=27.71 E-value=98 Score=23.50 Aligned_cols=40 Identities=10% Similarity=0.183 Sum_probs=25.1
Q ss_pred CCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCC
Q 025684 56 VGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPA 99 (249)
Q Consensus 56 vGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~ 99 (249)
..-+|++.+. ||+| ++|..++++.+.|.--+. ....++.+
T Consensus 74 ~~lP~I~~~~-~~~~--~Vl~~~~~~~~~i~dp~~-~~~~~~~~ 113 (126)
T cd02425 74 LKLPVIIFWN-NNHF--VVLEKIKKNKVTIVDPAI-GRIKISID 113 (126)
T ss_pred CCCCEEEEEc-CCcE--EEEEEEECCEEEEEcCCC-CCEEECHH
Confidence 4558999874 7776 578888877776633333 33455333
No 97
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=26.75 E-value=99 Score=25.27 Aligned_cols=42 Identities=19% Similarity=0.256 Sum_probs=30.3
Q ss_pred CCCCCCCeEEEEecCCCCE--EEEEEeeEeCCe-eEEEEecCCceEEE
Q 025684 52 EKLAVGTKVQAVYSEDGEW--YDATIEAITPNG-YYVTYDSWGNKEEV 96 (249)
Q Consensus 52 ~~~kvGd~ClA~ys~Dg~w--Y~A~I~~i~~~~-~~V~F~~Ygn~E~V 96 (249)
..+.+||.+.-. +|-+ |.+.|..+++.. +.|...-+|..-.|
T Consensus 107 ~~~~~G~~V~V~---~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v 151 (159)
T TIGR01955 107 TLPYKGDKVRIT---DGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKV 151 (159)
T ss_pred cCCCCCCEEEEe---ccCCCCcEEEEEEECCCceEEEEEhhhCCceEE
Confidence 458999999888 4554 999999998554 66666666655333
No 98
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=26.38 E-value=1.4e+02 Score=19.97 Aligned_cols=33 Identities=21% Similarity=0.388 Sum_probs=23.7
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
|.-|.|+|..+...++.|.... +-.-.++.++|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~-~~~g~l~~~~l 33 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQI 33 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHc
Confidence 5679999999999888887653 44555654444
No 99
>PF00552 IN_DBD_C: Integrase DNA binding domain The structure of the C-terminal DNA binding domain.; InterPro: IPR001037 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic core, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (have been studied most carefully with respect to the structural basis of catalysis. Although the active site of avian virus integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV-1 integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0003676 nucleic acid binding; PDB: 1QMC_B 1IHV_A 1IHW_B 1C6V_X 1C0M_B 1C1A_A 1EX4_A.
Probab=26.01 E-value=2.4e+02 Score=19.85 Aligned_cols=46 Identities=22% Similarity=0.201 Sum_probs=31.1
Q ss_pred eEEEEe--cCCCCEE-EEEEeeEeCCeeEEEEecCCc-eEEEcCCCcccCC
Q 025684 59 KVQAVY--SEDGEWY-DATIEAITPNGYYVTYDSWGN-KEEVDPANVRPVN 105 (249)
Q Consensus 59 ~ClA~y--s~Dg~wY-~A~I~~i~~~~~~V~F~~Ygn-~E~V~~~~lrpl~ 105 (249)
.|+-+| ..|+.|. ++.|+ +-+.|+.|.|..-.. .-.||.-.+|.++
T Consensus 5 ~~yyk~k~~~~~~WkGP~~vL-~~G~Gav~v~~~~~~~~~wvP~R~~K~i~ 54 (55)
T PF00552_consen 5 WVYYKWKDGRDGEWKGPDPVL-WWGEGAVVVKDQESDKPIWVPRRKVKIIP 54 (55)
T ss_dssp EEEEE-ECSSTSSEEEEEEEE-EECSSEEEEECSSC--EEEEEGGGEEEEE
T ss_pred ceEEEcCCCCCCCcCChhHhe-eeccccEEEecCCccCEEEeehhHcEecC
Confidence 577774 6789998 66665 557777777766543 7788877777653
No 100
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=25.21 E-value=1.8e+02 Score=24.37 Aligned_cols=34 Identities=18% Similarity=0.262 Sum_probs=27.0
Q ss_pred CCCCCCeEEEEecCCCCEEEEEEeeEeCCeeEEEE
Q 025684 53 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTY 87 (249)
Q Consensus 53 ~~kvGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F 87 (249)
.+.+|..+... ..+|...+++|.+|+++.++|-|
T Consensus 92 ~~~~G~~~~~~-~~~G~~~~~~V~~i~~~~v~vD~ 125 (156)
T PRK15095 92 EPEIGAIMLFT-AMDGSEMPGVIREINGDSITVDF 125 (156)
T ss_pred CCCCCCEEEEE-CCCCCEEEEEEEEEcCCEEEEEC
Confidence 47899997765 56899999999999988665544
No 101
>PRK07252 hypothetical protein; Provisional
Probab=25.20 E-value=1.3e+02 Score=24.12 Aligned_cols=34 Identities=24% Similarity=0.524 Sum_probs=25.6
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|.-|.|+|..|...|+.|.+.+ +-.-.|+.++|.
T Consensus 4 G~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs 37 (120)
T PRK07252 4 GDKLKGTITGIKPYGAFVALEN-GTTGLIHISEIK 37 (120)
T ss_pred CCEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcC
Confidence 6789999999999999888854 445666555553
No 102
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=24.90 E-value=1.3e+02 Score=20.64 Aligned_cols=33 Identities=15% Similarity=0.265 Sum_probs=23.2
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
|.-|.|+|.+|.+.++.|.+.+ +-.-.++..+|
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~-~~~g~i~~~~~ 33 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGD-GVEGFLRAAEL 33 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHC
Confidence 5678999999999888888764 24455544433
No 103
>PRK08582 hypothetical protein; Provisional
Probab=24.89 E-value=1.6e+02 Score=24.18 Aligned_cols=34 Identities=24% Similarity=0.325 Sum_probs=25.2
Q ss_pred CCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCcc
Q 025684 68 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 102 (249)
Q Consensus 68 g~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lr 102 (249)
|..|.|+|..|+..++.|.+.+ +-.-.|+.++|.
T Consensus 6 G~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSels 39 (139)
T PRK08582 6 GSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVA 39 (139)
T ss_pred CCEEEEEEEEEECCeEEEEECC-CCEEEEEeeccC
Confidence 6789999999999888887753 455666555553
No 104
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=24.75 E-value=1e+02 Score=28.27 Aligned_cols=38 Identities=26% Similarity=0.506 Sum_probs=30.2
Q ss_pred ecCCCCEEEEEEeeEeCCeeEEEEecC-CceEEEcCCCc
Q 025684 64 YSEDGEWYDATIEAITPNGYYVTYDSW-GNKEEVDPANV 101 (249)
Q Consensus 64 ys~Dg~wY~A~I~~i~~~~~~V~F~~Y-gn~E~V~~~~l 101 (249)
|..-|..+.|+|.+|.+.++.|.+.+| |-.-.++.++|
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEl 43 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEV 43 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHc
Confidence 445678899999999999999999999 55666755554
No 105
>PRK14640 hypothetical protein; Provisional
Probab=24.47 E-value=2.3e+02 Score=23.67 Aligned_cols=49 Identities=18% Similarity=0.286 Sum_probs=35.2
Q ss_pred CCCCCCeEEEEec---CCCCEEEEEEeeEeCCeeEEEEecCCceEEEcCCCccc
Q 025684 53 KLAVGTKVQAVYS---EDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 103 (249)
Q Consensus 53 ~~kvGd~ClA~ys---~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~~~lrp 103 (249)
..-+|..+...+. .+++.|.++|.+++++++.+... |....+++++|+-
T Consensus 93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~--~~~~~i~~~~I~k 144 (152)
T PRK14640 93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD--GKDEVLAFTNIQK 144 (152)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC--CeEEEEEhHHeee
Confidence 4578999988763 36789999999999887665532 4456676666653
No 106
>PF08481 GBS_Bsp-like: GBS Bsp-like repeat; InterPro: IPR013688 This repeat is found in a number of Streptococcus proteins including some hypothetical proteins and Bsp. Bsp is a protein of group B Streptococcus (GBS) which might control cell morphology [].
Probab=23.51 E-value=1.2e+02 Score=23.30 Aligned_cols=20 Identities=40% Similarity=0.757 Sum_probs=14.6
Q ss_pred CCCCeEEEEecCCC-C----EEEEE
Q 025684 55 AVGTKVQAVYSEDG-E----WYDAT 74 (249)
Q Consensus 55 kvGd~ClA~ys~Dg-~----wY~A~ 74 (249)
.+...-.|+||+.+ | ||.|.
T Consensus 25 ~i~~V~~aVWSe~nGQdDL~WY~a~ 49 (95)
T PF08481_consen 25 GIKSVKFAVWSEENGQDDLKWYTAT 49 (95)
T ss_pred CeeEEEEEEEcCCCCCCccEEEEee
Confidence 34567789997655 4 99994
No 107
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=23.32 E-value=2.3e+02 Score=18.76 Aligned_cols=41 Identities=15% Similarity=0.211 Sum_probs=28.8
Q ss_pred CCCeEEEEecCCCCEEEEEEeeEeCCeeEEEEecCCceEEEcC
Q 025684 56 VGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDP 98 (249)
Q Consensus 56 vGd~ClA~ys~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~E~V~~ 98 (249)
.|..|.... ++..|.+++..|++++..+.=.+-|....+..
T Consensus 2 lG~~V~v~~--~~~~~~G~~~gId~~G~L~v~~~~g~~~~i~s 42 (48)
T PF02237_consen 2 LGQEVRVET--GDGEIEGIAEGIDDDGALLVRTEDGSIRTISS 42 (48)
T ss_dssp TTSEEEEEE--TSCEEEEEEEEEETTSEEEEEETTEEEEEESS
T ss_pred CCCEEEEEE--CCeEEEEEEEEECCCCEEEEEECCCCEEEEEE
Confidence 366777776 45678999999999987655555565555533
No 108
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.57 E-value=1.4e+02 Score=24.67 Aligned_cols=28 Identities=29% Similarity=0.495 Sum_probs=21.9
Q ss_pred EecCCCCEEEEEEeeEeCCeeEEEEecCC
Q 025684 63 VYSEDGEWYDATIEAITPNGYYVTYDSWG 91 (249)
Q Consensus 63 ~ys~Dg~wY~A~I~~i~~~~~~V~F~~Yg 91 (249)
+|- ||.||-++++.++++.|.|.=.-||
T Consensus 3 V~F-dg~FWvGv~E~~~~~~~~v~rv~FG 30 (132)
T PF11208_consen 3 VYF-DGPFWVGVFERHEDGKYKVARVTFG 30 (132)
T ss_pred EEe-cCCcEEEEEEEEECCEEEEEEEeeC
Confidence 454 9999999999999887755555566
No 109
>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=22.33 E-value=3.8e+02 Score=21.17 Aligned_cols=51 Identities=18% Similarity=0.320 Sum_probs=27.5
Q ss_pred CCCeEEEEe-cCCCCEEEEEEeeEeC--------CeeEE-EEecCCceEEEcCCCcccCCch
Q 025684 56 VGTKVQAVY-SEDGEWYDATIEAITP--------NGYYV-TYDSWGNKEEVDPANVRPVNLL 107 (249)
Q Consensus 56 vGd~ClA~y-s~Dg~wY~A~I~~i~~--------~~~~V-~F~~Ygn~E~V~~~~lrpl~~l 107 (249)
+|-.|+..- ...+.||+|.|.+-+- +.|.| .|.| |---.|+..+|+.+...
T Consensus 8 lGkVV~V~~~~~k~~W~PALVVsPsc~ddv~VkKD~~lVRSFkD-~KfysV~rkd~~e~~~~ 68 (96)
T PF08169_consen 8 LGKVVCVESTKKKTSWFPALVVSPSCNDDVTVKKDQCLVRSFKD-GKFYSVARKDVREFDID 68 (96)
T ss_dssp TTSEEEEE-SS-SS-EEEEEEE--SS-SS----TT-EEEEESSS---EEEE-TTTEE---ST
T ss_pred cCcEEEEEcCCCCCceeeEEEEcCCccceeeeccceEEEEEecc-CceEEEEhhhhhhcccc
Confidence 577777755 3345799999987553 23655 4666 66678999999888643
No 110
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=21.31 E-value=1.8e+02 Score=25.66 Aligned_cols=36 Identities=25% Similarity=0.262 Sum_probs=25.3
Q ss_pred CCCCCCCCCCeEEEEe-c-CCCCEEEEEEeeEeCCeeEEEE
Q 025684 49 DNQEKLAVGTKVQAVY-S-EDGEWYDATIEAITPNGYYVTY 87 (249)
Q Consensus 49 ~~~~~~kvGd~ClA~y-s-~Dg~wY~A~I~~i~~~~~~V~F 87 (249)
.....|++||.++|+- | +||.-| ++.+..|..-|.|
T Consensus 118 ~v~ksFrPgDiVlAkVis~~~~~~y---~LTtAeneLGVV~ 155 (193)
T KOG3409|consen 118 KVYKSFRPGDIVLAKVISLGDGSNY---LLTTAENELGVVF 155 (193)
T ss_pred hhhhccCCCcEEEEEEeecCCCCcE---EEEEecccceEEE
Confidence 3457899999999987 5 888888 5555555433333
No 111
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.93 E-value=1.5e+02 Score=21.08 Aligned_cols=33 Identities=15% Similarity=0.167 Sum_probs=23.8
Q ss_pred CCEEE-EEEeeE-eCCeeEEEEecCCceEEEcCCCc
Q 025684 68 GEWYD-ATIEAI-TPNGYYVTYDSWGNKEEVDPANV 101 (249)
Q Consensus 68 g~wY~-A~I~~i-~~~~~~V~F~~Ygn~E~V~~~~l 101 (249)
|..|. |+|.+| .+.|+.|...+ |-.-.|+.++|
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l 35 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHL 35 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHC
Confidence 56789 999998 57788888866 55566644443
No 112
>TIGR03130 malonate_delta malonate decarboxylase acyl carrier protein. Members of this protein family are the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=20.82 E-value=67 Score=25.49 Aligned_cols=9 Identities=67% Similarity=1.007 Sum_probs=8.1
Q ss_pred ceeeeecCC
Q 025684 216 GKVGVTGSG 224 (249)
Q Consensus 216 GrVGv~gsG 224 (249)
..|||+|||
T Consensus 19 ~lvGVVGSG 27 (98)
T TIGR03130 19 ALVGVVGSG 27 (98)
T ss_pred EEEEEEccC
Confidence 569999999
No 113
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=20.28 E-value=2e+02 Score=20.39 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=21.5
Q ss_pred cCCCCEEEEEEeeEeCCeeEEEEec
Q 025684 65 SEDGEWYDATIEAITPNGYYVTYDS 89 (249)
Q Consensus 65 s~Dg~wY~A~I~~i~~~~~~V~F~~ 89 (249)
..++.+|.+.+.+|+..|+.+.+..
T Consensus 19 ~~~~~~~~~~~~diS~~G~~~~~~~ 43 (102)
T PF07238_consen 19 DPGGSSFQGTIVDISEGGCAFRSPK 43 (102)
T ss_dssp EETTEEEEEEEEEETTSEEEEEECT
T ss_pred ecCCcEEEEEEEEECccceEEEECC
Confidence 4488899999999999998888855
Done!