Query psy6375
Match_columns 86
No_of_seqs 114 out of 1018
Neff 5.5
Searched_HMMs 46136
Date Sat Aug 17 00:52:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6375.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6375hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14548 50S ribosomal protein 100.0 2.1E-39 4.5E-44 207.9 10.2 84 3-86 1-84 (84)
2 PTZ00191 60S ribosomal protein 100.0 2.9E-38 6.3E-43 219.5 9.8 86 1-86 60-145 (145)
3 TIGR03636 L23_arch archaeal ri 100.0 5.8E-37 1.2E-41 193.8 10.0 77 10-86 1-77 (77)
4 CHL00030 rpl23 ribosomal prote 100.0 2E-32 4.3E-37 178.3 7.9 77 4-82 1-90 (93)
5 PRK05738 rplW 50S ribosomal pr 100.0 2.7E-32 5.8E-37 176.9 7.7 77 4-81 1-90 (92)
6 PRK12280 rplW 50S ribosomal pr 100.0 2.4E-31 5.2E-36 187.0 7.3 80 1-82 1-93 (158)
7 COG0089 RplW Ribosomal protein 100.0 3.6E-31 7.8E-36 172.8 6.8 78 3-81 1-92 (94)
8 PF00276 Ribosomal_L23: Riboso 100.0 2.4E-30 5.1E-35 167.1 9.1 78 4-82 1-91 (91)
9 KOG1751|consensus 99.9 1.9E-27 4.2E-32 166.9 6.8 86 1-86 71-157 (157)
10 KOG4089|consensus 98.0 6.5E-06 1.4E-10 58.6 4.4 53 23-75 37-109 (165)
11 PF08777 RRM_3: RNA binding mo 90.6 1.1 2.3E-05 29.3 5.5 53 26-83 4-57 (105)
12 PF14259 RRM_6: RNA recognitio 88.8 0.7 1.5E-05 26.5 3.2 54 29-84 5-60 (70)
13 PRK01178 rps24e 30S ribosomal 86.0 1.4 3E-05 29.0 3.7 45 11-56 5-53 (99)
14 PF00076 RRM_1: RNA recognitio 84.2 3.2 6.9E-05 23.1 4.3 54 28-83 4-59 (70)
15 PF14560 Ubiquitin_2: Ubiquiti 80.4 3 6.6E-05 25.6 3.5 52 24-75 14-65 (87)
16 PRK04046 translation initiatio 77.4 5.2 0.00011 29.4 4.4 49 6-55 68-137 (222)
17 cd01796 DDI1_N DNA damage indu 76.6 6.8 0.00015 23.3 4.1 35 23-57 9-43 (71)
18 smart00213 UBQ Ubiquitin homol 76.3 7 0.00015 21.6 3.9 35 24-58 10-44 (64)
19 PF00240 ubiquitin: Ubiquitin 75.9 8.8 0.00019 22.0 4.4 35 24-58 6-40 (69)
20 cd01812 BAG1_N Ubiquitin-like 75.5 6.2 0.00014 22.7 3.7 35 24-58 10-44 (71)
21 PF03780 Asp23: Asp23 family; 74.6 5.5 0.00012 25.0 3.5 23 36-58 82-104 (108)
22 cd01769 UBL Ubiquitin-like dom 74.1 11 0.00023 21.1 4.4 35 23-57 7-41 (69)
23 cd01789 Alp11_N Ubiquitin-like 71.7 7.6 0.00016 24.0 3.6 36 26-61 15-50 (84)
24 cd04929 ACT_TPH ACT domain of 71.5 6.2 0.00013 24.1 3.1 26 23-48 40-65 (74)
25 cd01813 UBP_N UBP ubiquitin pr 71.0 9.6 0.00021 23.0 3.9 35 24-58 10-44 (74)
26 cd01809 Scythe_N Ubiquitin-lik 70.9 12 0.00027 21.4 4.2 36 23-58 10-45 (72)
27 PLN03134 glycine-rich RNA-bind 70.2 16 0.00035 24.7 5.2 58 24-83 36-96 (144)
28 KOG0107|consensus 69.9 23 0.00051 26.0 6.2 56 23-82 11-66 (195)
29 PTZ00044 ubiquitin; Provisiona 69.3 12 0.00027 21.9 4.1 35 23-57 10-44 (76)
30 cd01798 parkin_N amino-termina 68.1 13 0.00028 21.7 3.9 35 23-57 8-42 (70)
31 cd01806 Nedd8 Nebb8-like ubiq 67.4 19 0.0004 20.8 4.5 34 24-57 11-44 (76)
32 cd01805 RAD23_N Ubiquitin-like 67.2 17 0.00037 21.3 4.4 36 23-58 10-47 (77)
33 cd01803 Ubiquitin Ubiquitin. U 66.7 15 0.00032 21.2 4.0 34 24-57 11-44 (76)
34 PF10298 WhiA_N: WhiA N-termin 65.6 12 0.00025 23.1 3.5 61 23-86 22-86 (86)
35 cd01807 GDX_N ubiquitin-like d 65.1 18 0.00039 21.3 4.2 35 23-57 10-44 (74)
36 TIGR01661 ELAV_HUD_SF ELAV/HuD 64.2 25 0.00055 26.0 5.7 58 24-83 271-331 (352)
37 PLN03120 nucleic acid binding 62.6 22 0.00047 27.1 5.1 51 24-76 6-56 (260)
38 cd01800 SF3a120_C Ubiquitin-li 62.1 19 0.00042 21.5 3.9 35 24-58 8-42 (76)
39 PF10057 DUF2294: Uncharacteri 60.6 34 0.00074 22.4 5.2 39 35-73 76-115 (118)
40 cd04931 ACT_PAH ACT domain of 59.5 12 0.00025 23.8 2.7 24 23-46 54-78 (90)
41 cd04904 ACT_AAAH ACT domain of 59.3 16 0.00034 21.8 3.2 26 23-48 40-65 (74)
42 cd01808 hPLIC_N Ubiquitin-like 59.2 22 0.00047 20.8 3.8 33 25-57 11-43 (71)
43 cd01799 Hoil1_N Ubiquitin-like 59.1 21 0.00045 21.7 3.7 34 23-56 12-45 (75)
44 TIGR02830 spore_III_AG stage I 58.4 13 0.00029 26.9 3.2 32 27-58 149-184 (186)
45 cd01793 Fubi Fubi ubiquitin-li 58.1 25 0.00054 20.8 3.9 35 24-58 9-43 (74)
46 TIGR01661 ELAV_HUD_SF ELAV/HuD 55.3 42 0.00091 24.8 5.5 54 24-79 5-61 (352)
47 PF01282 Ribosomal_S24e: Ribos 54.5 14 0.0003 23.3 2.4 42 32-73 11-56 (84)
48 cd01794 DC_UbP_C dendritic cel 53.5 33 0.00071 20.4 3.9 34 24-57 9-42 (70)
49 PF12426 DUF3674: RNA dependen 52.2 9.3 0.0002 21.5 1.2 16 36-51 3-18 (41)
50 TIGR01659 sex-lethal sex-letha 52.1 44 0.00096 25.9 5.4 57 25-83 110-169 (346)
51 PF08731 AFT: Transcription fa 51.0 30 0.00065 23.3 3.7 39 35-75 3-41 (111)
52 cd01802 AN1_N ubiquitin-like d 50.7 38 0.00082 21.8 4.1 35 23-57 37-71 (103)
53 cd04930 ACT_TH ACT domain of t 50.1 23 0.00049 23.4 3.0 26 23-48 81-106 (115)
54 cd00590 RRM RRM (RNA recogniti 50.0 39 0.00084 17.9 4.9 54 27-82 4-59 (74)
55 cd01810 ISG15_repeat2 ISG15 ub 49.7 39 0.00085 19.9 3.8 34 24-57 9-42 (74)
56 cd01804 midnolin_N Ubiquitin-l 49.6 41 0.00089 20.2 4.0 34 24-57 12-45 (78)
57 PF08766 DEK_C: DEK C terminal 49.5 15 0.00032 20.9 1.8 20 33-52 20-39 (54)
58 KOG3424|consensus 49.1 22 0.00047 24.6 2.9 39 18-57 16-58 (132)
59 cd01791 Ubl5 UBL5 ubiquitin-li 48.9 52 0.0011 19.8 4.3 35 24-58 12-46 (73)
60 PF13893 RRM_5: RNA recognitio 47.7 39 0.00084 18.4 3.4 35 46-83 7-41 (56)
61 PLN03121 nucleic acid binding 47.4 88 0.0019 23.7 6.1 56 25-83 8-63 (243)
62 TIGR01628 PABP-1234 polyadenyl 47.0 63 0.0014 25.9 5.7 57 26-84 4-63 (562)
63 PF07788 DUF1626: Protein of u 46.7 69 0.0015 19.8 6.5 52 23-85 12-69 (70)
64 PF09581 Spore_III_AF: Stage I 46.7 70 0.0015 22.0 5.2 42 33-74 86-133 (188)
65 cd06257 DnaJ DnaJ domain or J- 45.7 14 0.00031 20.0 1.4 20 28-47 6-25 (55)
66 PF02075 RuvC: Crossover junct 45.7 18 0.00039 24.6 2.1 20 32-51 113-132 (149)
67 smart00271 DnaJ DnaJ molecular 44.0 16 0.00036 20.2 1.4 20 28-47 7-26 (60)
68 COG0484 DnaJ DnaJ-class molecu 43.9 15 0.00033 29.3 1.7 20 27-46 9-28 (371)
69 PTZ00071 40S ribosomal protein 43.9 42 0.0009 23.2 3.7 40 14-54 13-57 (132)
70 smart00360 RRM RNA recognition 43.9 49 0.0011 17.3 4.5 50 31-82 5-57 (71)
71 TIGR01649 hnRNP-L_PTB hnRNP-L/ 43.5 82 0.0018 25.1 5.8 54 25-82 278-332 (481)
72 TIGR01628 PABP-1234 polyadenyl 41.4 1.1E+02 0.0024 24.6 6.3 58 23-82 179-238 (562)
73 cd01792 ISG15_repeat1 ISG15 ub 40.8 54 0.0012 19.6 3.5 34 24-57 13-46 (80)
74 PRK06418 transcription elongat 39.1 38 0.00083 24.1 3.0 35 39-74 102-138 (166)
75 PF04432 FrhB_FdhB_C: Coenzyme 39.0 1.2E+02 0.0026 20.5 5.4 45 28-74 39-83 (161)
76 TIGR01659 sex-lethal sex-letha 38.9 1.2E+02 0.0026 23.5 5.9 59 23-83 194-255 (346)
77 cd04905 ACT_CM-PDT C-terminal 37.1 50 0.0011 19.5 2.9 26 23-48 41-68 (80)
78 smart00362 RRM_2 RNA recogniti 36.6 67 0.0015 16.8 4.5 55 27-83 4-59 (72)
79 PF10411 DsbC_N: Disulfide bon 36.5 25 0.00055 20.2 1.5 22 39-60 1-23 (57)
80 KOG0132|consensus 36.5 56 0.0012 29.0 4.0 50 29-83 428-477 (894)
81 COG2004 RPS24A Ribosomal prote 35.6 89 0.0019 20.9 4.1 40 18-58 13-56 (107)
82 TIGR01622 SF-CC1 splicing fact 35.4 1.5E+02 0.0032 23.0 5.9 54 24-79 91-147 (457)
83 smart00654 eIF6 translation in 35.3 59 0.0013 23.5 3.5 30 24-54 107-136 (200)
84 COG1710 Uncharacterized protei 35.2 40 0.00088 23.4 2.5 47 35-85 66-121 (139)
85 PF07626 PSD3: Protein of unkn 34.6 49 0.0011 19.9 2.6 20 32-51 1-20 (67)
86 COG1302 Uncharacterized protei 34.3 65 0.0014 22.1 3.4 23 37-59 90-112 (131)
87 PF13867 SAP30_Sin3_bdg: Sin3 32.8 48 0.001 19.0 2.2 23 29-51 16-38 (53)
88 TIGR01952 nusA_arch NusA famil 32.1 74 0.0016 21.9 3.4 26 49-75 86-111 (141)
89 cd00529 RuvC_resolvase Hollida 32.1 47 0.001 22.5 2.4 20 32-51 114-133 (154)
90 COG1976 TIF6 Translation initi 31.7 65 0.0014 24.2 3.3 30 29-60 157-186 (222)
91 cd04882 ACT_Bt0572_2 C-termina 31.7 84 0.0018 17.0 3.1 38 47-84 23-61 (65)
92 TIGR00228 ruvC crossover junct 31.1 49 0.0011 23.3 2.4 18 33-50 113-130 (156)
93 PTZ00100 DnaJ chaperone protei 31.0 32 0.0007 23.1 1.4 21 27-47 70-90 (116)
94 cd04880 ACT_AAAH-PDT-like ACT 30.8 93 0.002 17.9 3.3 26 23-48 39-66 (75)
95 PRK00039 ruvC Holliday junctio 29.8 53 0.0012 22.9 2.5 19 32-50 116-134 (164)
96 PLN02817 glutathione dehydroge 29.6 54 0.0012 24.3 2.6 40 44-83 23-62 (265)
97 PF02824 TGS: TGS domain; Int 29.0 1.1E+02 0.0024 17.6 3.4 22 60-84 6-27 (60)
98 TIGR01642 U2AF_lg U2 snRNP aux 29.0 1.9E+02 0.0041 22.6 5.7 54 25-80 298-354 (509)
99 TIGR00323 eIF-6 translation in 28.7 98 0.0021 22.7 3.8 31 26-58 148-178 (215)
100 cd00527 IF6 Ribosome anti-asso 28.6 91 0.002 22.9 3.6 33 24-58 152-184 (220)
101 KOG0715|consensus 28.0 41 0.00089 25.6 1.7 21 27-47 48-68 (288)
102 TIGR03380 agmatine_aguA agmati 27.9 58 0.0013 25.6 2.6 20 31-50 174-193 (357)
103 COG4379 Mu-like prophage tail 27.7 86 0.0019 25.3 3.5 59 24-83 92-160 (386)
104 TIGR01645 half-pint poly-U bin 27.6 2E+02 0.0043 24.5 5.8 59 23-83 205-266 (612)
105 cd01763 Sumo Small ubiquitin-r 27.6 1.5E+02 0.0033 18.0 4.7 36 23-58 21-56 (87)
106 PF00226 DnaJ: DnaJ domain; I 26.8 32 0.0007 19.3 0.8 20 28-47 6-25 (64)
107 PF01912 eIF-6: eIF-6 family; 26.1 82 0.0018 23.1 3.0 31 27-59 153-183 (199)
108 PF13592 HTH_33: Winged helix- 26.1 73 0.0016 18.2 2.2 22 35-57 6-27 (60)
109 TIGR01649 hnRNP-L_PTB hnRNP-L/ 26.0 2.4E+02 0.0052 22.5 5.8 58 25-83 397-456 (481)
110 PF07040 DUF1326: Protein of u 25.7 1.1E+02 0.0024 21.9 3.5 32 19-51 56-87 (184)
111 PRK14282 chaperone protein Dna 25.6 46 0.00099 25.9 1.7 20 27-46 9-28 (369)
112 PRK14290 chaperone protein Dna 25.4 46 0.00099 25.8 1.6 19 28-46 9-27 (365)
113 PRK14295 chaperone protein Dna 24.9 47 0.001 26.1 1.6 20 27-46 14-33 (389)
114 PRK14299 chaperone protein Dna 24.7 46 0.00099 25.0 1.5 19 28-46 10-28 (291)
115 PF01250 Ribosomal_S6: Ribosom 24.4 1.4E+02 0.0031 18.2 3.5 33 25-57 4-42 (92)
116 PF02963 EcoRI: Restriction en 24.0 62 0.0013 24.6 2.0 57 17-73 28-98 (257)
117 TIGR01648 hnRNP-R-Q heterogene 23.9 2.2E+02 0.0048 24.0 5.4 59 23-83 59-119 (578)
118 PLN02690 Agmatine deiminase 23.6 78 0.0017 25.1 2.6 20 31-50 186-205 (374)
119 COG1035 FrhB Coenzyme F420-red 23.2 2.4E+02 0.0052 22.2 5.2 44 29-74 181-224 (332)
120 cd03420 SirA_RHOD_Pry_redox Si 22.9 1.7E+02 0.0037 17.0 6.3 44 12-56 15-58 (69)
121 PRK14288 chaperone protein Dna 22.8 67 0.0015 25.0 2.1 19 28-46 9-27 (369)
122 PRK13551 agmatine deiminase; P 22.6 83 0.0018 24.8 2.6 20 31-50 177-196 (362)
123 PRK10767 chaperone protein Dna 22.6 55 0.0012 25.4 1.6 19 28-46 10-28 (371)
124 cd01795 USP48_C USP ubiquitin- 22.6 1.5E+02 0.0032 19.9 3.4 43 16-58 7-49 (107)
125 PF08821 CGGC: CGGC domain; I 22.5 1E+02 0.0022 20.1 2.7 20 33-52 84-103 (107)
126 PRK14276 chaperone protein Dna 22.2 54 0.0012 25.6 1.5 20 28-47 10-29 (380)
127 PRK14278 chaperone protein Dna 22.2 69 0.0015 25.0 2.1 20 27-46 8-27 (378)
128 PRK14285 chaperone protein Dna 22.1 70 0.0015 24.9 2.1 20 28-47 9-28 (365)
129 PRK14283 chaperone protein Dna 22.1 56 0.0012 25.5 1.5 19 28-46 11-29 (378)
130 PRK14279 chaperone protein Dna 22.0 55 0.0012 25.8 1.5 20 27-46 14-33 (392)
131 PF04371 PAD_porph: Porphyromo 21.7 83 0.0018 24.2 2.4 20 31-50 163-182 (329)
132 TIGR01622 SF-CC1 splicing fact 21.4 3.4E+02 0.0075 20.9 5.8 56 25-82 189-247 (457)
133 PRK14284 chaperone protein Dna 21.1 59 0.0013 25.5 1.5 19 28-46 7-25 (391)
134 TIGR01645 half-pint poly-U bin 20.9 2.2E+02 0.0048 24.3 4.8 46 36-83 533-585 (612)
135 smart00257 LysM Lysin motif. 20.8 1.1E+02 0.0024 14.2 2.0 18 68-85 2-19 (44)
136 PRK14298 chaperone protein Dna 20.7 60 0.0013 25.4 1.4 19 28-46 11-29 (377)
137 PRK14287 chaperone protein Dna 20.3 65 0.0014 25.1 1.5 19 28-46 10-28 (371)
138 PTZ00037 DnaJ_C chaperone prot 20.2 63 0.0014 25.9 1.5 20 27-46 33-52 (421)
No 1
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=100.00 E-value=2.1e-39 Score=207.91 Aligned_cols=84 Identities=54% Similarity=0.896 Sum_probs=81.8
Q ss_pred ccccccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHh
Q psy6375 3 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANK 82 (86)
Q Consensus 3 ~~~vi~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~ 82 (86)
++++|++|++|||++.++|++|+|+|.|+++|||.|||+|||++|||+|.+|||++.++|||||||+|++|++|+|+|++
T Consensus 1 ~~~iI~~PviTEK~~~~~e~~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~~~KKA~V~L~~g~~A~~va~k 80 (84)
T PRK14548 1 PYSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGEKKAYVKLAEEYDAEEIASR 80 (84)
T ss_pred CccchhccccCHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCcEEEEEEeCCCCcHHHHHHh
Confidence 47899999999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCC
Q psy6375 83 IGII 86 (86)
Q Consensus 83 ~g~~ 86 (86)
||++
T Consensus 81 ig~~ 84 (84)
T PRK14548 81 LGVF 84 (84)
T ss_pred hccC
Confidence 9986
No 2
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=100.00 E-value=2.9e-38 Score=219.48 Aligned_cols=86 Identities=74% Similarity=1.072 Sum_probs=84.5
Q ss_pred CCccccccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHH
Q psy6375 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVA 80 (86)
Q Consensus 1 m~~~~vi~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a 80 (86)
||.|++|++|++||||+.++|++|+|+|.||++|||.|||+|||++|||+|.+|||+++++|||||||+|++|++|+|+|
T Consensus 60 md~~~IIk~Pl~TEKa~~~~E~~N~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~g~KKA~V~L~~~~~aidva 139 (145)
T PTZ00191 60 LDKYSIIKYPLTTEKAMKKIEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDGLKKAYIRLSPDVDALDVA 139 (145)
T ss_pred CchhhhhhcccccHHHHHHHhhCCEEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCCCceEEEEEECCCCcHHHHH
Confidence 78999999999999999999988999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCCC
Q psy6375 81 NKIGII 86 (86)
Q Consensus 81 ~~~g~~ 86 (86)
++||+|
T Consensus 140 ~kiGi~ 145 (145)
T PTZ00191 140 NKIGII 145 (145)
T ss_pred HhhccC
Confidence 999986
No 3
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=100.00 E-value=5.8e-37 Score=193.82 Aligned_cols=77 Identities=53% Similarity=0.850 Sum_probs=75.6
Q ss_pred cccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhhCCC
Q psy6375 10 PLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKIGII 86 (86)
Q Consensus 10 P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~g~~ 86 (86)
|++||||+.++|+.|+|+|.|+++|||+|||+|||.+|||+|.+|||++.++|||||||+|++|++|+|+|++||++
T Consensus 1 P~iTEKs~~~~e~~n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~~~KKA~VtL~~g~~a~~va~k~g~~ 77 (77)
T TIGR03636 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVKLAEEYAAEEIASRLGVF 77 (77)
T ss_pred CcccHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCceEEEEEECCCCcHHHHHHhhccC
Confidence 89999999999988999999999999999999999999999999999999999999999999999999999999986
No 4
>CHL00030 rpl23 ribosomal protein L23
Probab=99.98 E-value=2e-32 Score=178.34 Aligned_cols=77 Identities=25% Similarity=0.420 Sum_probs=71.8
Q ss_pred cccccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCC-------------eeEEEEEc
Q psy6375 4 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG-------------KKKAYVRL 70 (86)
Q Consensus 4 ~~vi~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~-------------~KKA~VtL 70 (86)
+++|++|++||||+.++| +|+|+|.|+++|||+|||+|||.+|||+|.+|||++.+++ ||||||+|
T Consensus 1 ~~iI~~PivTEKs~~l~e-~n~y~F~V~~~anK~eIK~avE~lf~VkV~~VNt~~~~~k~kr~~~~~G~~~~~KKAiVtL 79 (93)
T CHL00030 1 MDGIKYPVFTDKSIRLLE-KNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMGPIMGHKMHYKRMIITL 79 (93)
T ss_pred CceeccceeCHHHHHhhH-CCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEcCCCccccCCcccccCCcEEEEEEc
Confidence 469999999999999997 5999999999999999999999999999999999998863 99999999
Q ss_pred CCCCcHHHHHHh
Q psy6375 71 ARDYDALDVANK 82 (86)
Q Consensus 71 ~~g~~a~d~a~~ 82 (86)
++|++ ||+++.
T Consensus 80 ~~g~~-I~~~~~ 90 (93)
T CHL00030 80 QPGYS-IPLFRE 90 (93)
T ss_pred CCcCE-eccccc
Confidence 99987 998764
No 5
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=99.97 E-value=2.7e-32 Score=176.90 Aligned_cols=77 Identities=39% Similarity=0.503 Sum_probs=73.0
Q ss_pred cccccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCC-------------CCeeEEEEEc
Q psy6375 4 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-------------DGKKKAYVRL 70 (86)
Q Consensus 4 ~~vi~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~-------------~~~KKA~VtL 70 (86)
+++|++|++||||+.++|++|+|+|.|+++|||+|||+|||++|||+|.+|||++.+ .+||||||+|
T Consensus 1 ~~ii~~P~~TEKs~~~~e~~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~VnT~~~~gk~kr~~~~~g~~~~~KKA~VtL 80 (92)
T PRK05738 1 YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKTKRFGRRIGKRSDWKKAIVTL 80 (92)
T ss_pred CccccccccCHHHHHhHHhCCEEEEEECCCCCHHHHHHHHHHHcCCceeEEEEEEeCCceeeecccccccCCcEEEEEEc
Confidence 469999999999999999789999999999999999999999999999999999998 5899999999
Q ss_pred CCCCcHHHHHH
Q psy6375 71 ARDYDALDVAN 81 (86)
Q Consensus 71 ~~g~~a~d~a~ 81 (86)
++|++ +|+++
T Consensus 81 ~~g~~-i~~~~ 90 (92)
T PRK05738 81 AEGQK-IDFFG 90 (92)
T ss_pred CCCCE-Eeccc
Confidence 99988 88875
No 6
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.97 E-value=2.4e-31 Score=187.04 Aligned_cols=80 Identities=35% Similarity=0.493 Sum_probs=75.6
Q ss_pred CCccccccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC-------------CeeEEE
Q psy6375 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-------------GKKKAY 67 (86)
Q Consensus 1 m~~~~vi~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~-------------~~KKA~ 67 (86)
||++++|++|++||||+.++++ |+|+|.|+++|||+|||+|||.+|||+|.+|||+++++ +|||||
T Consensus 1 Md~~~iIk~PviTEKs~~l~e~-N~ytF~V~~~anK~eIK~AVE~iF~VkV~~VNT~~~~~K~KR~g~~~G~~~~~KKAi 79 (158)
T PRK12280 1 MNINEVIKKPILTEKSYSLMSK-NVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLGRFPGFTNSYKKAY 79 (158)
T ss_pred CChHhhhhccccCHHHHhhhhC-CEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEecCCcccccCCcccccCCcEEEE
Confidence 8999999999999999999985 99999999999999999999999999999999999885 799999
Q ss_pred EEcCCCCcHHHHHHh
Q psy6375 68 VRLARDYDALDVANK 82 (86)
Q Consensus 68 VtL~~g~~a~d~a~~ 82 (86)
|+|++|+. |||++.
T Consensus 80 VtL~~g~~-I~~f~~ 93 (158)
T PRK12280 80 VTLAEGYS-INLFPE 93 (158)
T ss_pred EECCCCCE-eeccCC
Confidence 99999987 888753
No 7
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.6e-31 Score=172.84 Aligned_cols=78 Identities=42% Similarity=0.595 Sum_probs=71.8
Q ss_pred ccccccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC--------------CeeEEEE
Q psy6375 3 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD--------------GKKKAYV 68 (86)
Q Consensus 3 ~~~vi~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~--------------~~KKA~V 68 (86)
++++|++|++||||+.++|++|+|+|.|+++|||+|||+|||++|||+|.+|||+++++ +||||||
T Consensus 1 ~~dvI~~PvvTEKa~~l~~~~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNTl~~k~k~KR~~~k~~G~~~~~kka~V 80 (94)
T COG0089 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGVKRIGLRKDYKKAYV 80 (94)
T ss_pred CcchhhcceecHHHHHhHhhCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEeCCcceEEeccccccCcccceeEE
Confidence 57899999999999999987799999999999999999999999999999999999875 5899999
Q ss_pred EcCCCCcHHHHHH
Q psy6375 69 RLARDYDALDVAN 81 (86)
Q Consensus 69 tL~~g~~a~d~a~ 81 (86)
+|++|+. ||++.
T Consensus 81 ~l~~G~~-i~~~~ 92 (94)
T COG0089 81 TLKEGQS-IDFFG 92 (94)
T ss_pred EccCCCE-Eeecc
Confidence 9999987 77664
No 8
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 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 [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=99.97 E-value=2.4e-30 Score=167.09 Aligned_cols=78 Identities=38% Similarity=0.560 Sum_probs=71.0
Q ss_pred cccccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC-------------CeeEEEEEc
Q psy6375 4 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-------------GKKKAYVRL 70 (86)
Q Consensus 4 ~~vi~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~-------------~~KKA~VtL 70 (86)
|++|++|++||||+.++|+.|+|+|.|+++|||+|||+|||++|||+|.+|||+++++ +||||||+|
T Consensus 1 ~~ii~~p~iTeKs~~~~~~~n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR~g~~~g~~~~~KKaiVtL 80 (91)
T PF00276_consen 1 YDIIKKPVITEKSMKLLENPNQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKRKGKFVGKTKDYKKAIVTL 80 (91)
T ss_dssp TTTEEEE--SHHHHHHHHHSSEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEESSSCEEEE-EEEEEEEEE
T ss_pred CCEeecceecHhHHHhhhcCCEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceEeCCccccCCCcEEEEEEe
Confidence 5799999999999999998899999999999999999999999999999999999883 589999999
Q ss_pred CCCCcHHHHHHh
Q psy6375 71 ARDYDALDVANK 82 (86)
Q Consensus 71 ~~g~~a~d~a~~ 82 (86)
++|+. ++++++
T Consensus 81 ~~~~~-i~~~~~ 91 (91)
T PF00276_consen 81 KEGDK-IPLFEE 91 (91)
T ss_dssp STTSC-HHHHHT
T ss_pred CCCCc-cccccC
Confidence 99955 999874
No 9
>KOG1751|consensus
Probab=99.94 E-value=1.9e-27 Score=166.95 Aligned_cols=86 Identities=83% Similarity=1.167 Sum_probs=82.2
Q ss_pred CCcccc-ccccccchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHH
Q psy6375 1 MDAFNI-IKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDV 79 (86)
Q Consensus 1 m~~~~v-i~~P~~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~ 79 (86)
+|.|.+ |+.|+.||++|+-+|++|+++|.||.+|||.|||+||.+||++.|.+|||++.|+|.|||||+|+++++|+|+
T Consensus 71 ld~y~~iik~plTtEsamKk~ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli~p~g~kkayv~la~dydaldv 150 (157)
T KOG1751|consen 71 LDHYAIIIKFPLTTESAMKKIEDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLIRPDGEKKAYVRLAPDYDALDV 150 (157)
T ss_pred chhhhhHhccccchhhhhcchhhCceeEEEEecccchHHHHHHHHHHhccchhhheeeecCCCceeEEEecCCchhHHHH
Confidence 356555 8999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCC
Q psy6375 80 ANKIGII 86 (86)
Q Consensus 80 a~~~g~~ 86 (86)
|+++|+|
T Consensus 151 ankig~i 157 (157)
T KOG1751|consen 151 ANKIGII 157 (157)
T ss_pred hcccccC
Confidence 9999986
No 10
>KOG4089|consensus
Probab=98.05 E-value=6.5e-06 Score=58.61 Aligned_cols=53 Identities=25% Similarity=0.402 Sum_probs=46.4
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC--------------------CeeEEEEEcCCCCc
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD--------------------GKKKAYVRLARDYD 75 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~--------------------~~KKA~VtL~~g~~ 75 (86)
.++..|.|++.+||.|++++++.+||.+|.+|.|.+.++ +++-|||.++.|.+
T Consensus 37 p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~Gk~~~~~k~r~~~~k~i~kdmd~p~~Yv~~pr~~~ 109 (165)
T KOG4089|consen 37 PKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHGKDYKKTKKRLQSPKRIKKDMDEPVAYVEEPRGSK 109 (165)
T ss_pred CceEEEEcchhhccccHHHHHHHhcCCceeeeeeeeeechhhhcceecccccceeecccccceeeecCCCCcc
Confidence 579999999999999999999999999999999998775 46777887776653
No 11
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=90.57 E-value=1.1 Score=29.28 Aligned_cols=53 Identities=26% Similarity=0.360 Sum_probs=30.5
Q ss_pred EEEE-EeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhh
Q psy6375 26 LVFI-VHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 26 ~~F~-V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
+.|. ++...++.+||.+|.. || .|.-| -...|-+.+||++.....|..+..++
T Consensus 4 l~~~g~~~~~~re~iK~~f~~-~g-~V~yV---D~~~G~~~g~VRf~~~~~A~~a~~~~ 57 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQ-FG-EVAYV---DFSRGDTEGYVRFKTPEAAQKALEKL 57 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-S-S---EEEE---E--TT-SEEEEEESS---HHHHHHHH
T ss_pred EEEecCCCCcCHHHHHHHHHh-cC-CcceE---EecCCCCEEEEEECCcchHHHHHHHH
Confidence 4466 7889999999999998 66 45444 44567799999999998777666543
No 12
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=88.79 E-value=0.7 Score=26.48 Aligned_cols=54 Identities=15% Similarity=0.237 Sum_probs=40.3
Q ss_pred EEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC--CeeEEEEEcCCCCcHHHHHHhhC
Q psy6375 29 IVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD--GKKKAYVRLARDYDALDVANKIG 84 (86)
Q Consensus 29 ~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~--~~KKA~VtL~~g~~a~d~a~~~g 84 (86)
.++++++..+|++.++.. | .|..|.....+. ...-|+|+++...+|.......+
T Consensus 5 nlp~~~~~~~l~~~f~~~-g-~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 5 NLPPSTTEEDLRNFFSRF-G-PVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN 60 (70)
T ss_dssp SSTTT--HHHHHHHCTTS-S-BEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred CCCCCCCHHHHHHHHHhc-C-CcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC
Confidence 357789999999999884 5 588888876543 46899999998888877766554
No 13
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=85.99 E-value=1.4 Score=29.00 Aligned_cols=45 Identities=9% Similarity=0.188 Sum_probs=36.3
Q ss_pred ccchhhhhhhhcCCEEEEEEe----CCCCHHHHHHHHHHHhCCceeeEEE
Q psy6375 11 LTTESAMKKIEDNNTLVFIVH----LQANKHHIKAAVKKMYDINVAKVNT 56 (86)
Q Consensus 11 ~~TEKs~~l~e~~n~~~F~V~----~~a~K~eIk~ave~lf~VkV~~VnT 56 (86)
++.++...|+.. .++.|.|. +..+|.||+..+-++|+.++.-|=.
T Consensus 5 I~~~~~N~LL~R-ke~~~~v~h~g~~tpsr~eirekLa~~~~~~~~~vvv 53 (99)
T PRK01178 5 IISDKENPLLGR-REIKFEVYHEGSATPSRKDVRKKLAAMLNADKELVVV 53 (99)
T ss_pred EEEeeecCCcCc-EEEEEEEEeCCCCCCCHHHHHHHHHHHHCcCCCEEEE
Confidence 567788888865 79999885 5679999999999999988766533
No 14
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=84.24 E-value=3.2 Score=23.07 Aligned_cols=54 Identities=9% Similarity=0.153 Sum_probs=38.2
Q ss_pred EEEeCCCCHHHHHHHHHHHhCCceeeEEEeeC--CCCeeEEEEEcCCCCcHHHHHHhh
Q psy6375 28 FIVHLQANKHHIKAAVKKMYDINVAKVNTLIR--PDGKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~--~~~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
=.++++++..+|+++++. ||-- ..+..... .....-|+|++....+|......+
T Consensus 4 ~nlp~~~t~~~l~~~f~~-~g~i-~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l 59 (70)
T PF00076_consen 4 GNLPPDVTEEELRDFFSQ-FGKI-ESIKVMRNSSGKSKGYAFVEFESEEDAEKALEEL 59 (70)
T ss_dssp ESETTTSSHHHHHHHHHT-TSTE-EEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHH
T ss_pred cCCCCcCCHHHHHHHHHH-hhhc-ccccccccccccccceEEEEEcCHHHHHHHHHHc
Confidence 346889999999999999 6543 45544442 234567999999887776665544
No 15
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=80.44 E-value=3 Score=25.65 Aligned_cols=52 Identities=12% Similarity=0.123 Sum_probs=38.0
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCc
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYD 75 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~ 75 (86)
....-+++++.|=.|+|+-++.+||+++...+.......--..+..+..+..
T Consensus 14 ~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~ 65 (87)
T PF14560_consen 14 RSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDA 65 (87)
T ss_dssp SEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSS
T ss_pred eeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCcc
Confidence 3666889999999999999999999999999998873222244455544433
No 16
>PRK04046 translation initiation factor IF-6; Provisional
Probab=77.41 E-value=5.2 Score=29.43 Aligned_cols=49 Identities=12% Similarity=0.241 Sum_probs=39.0
Q ss_pred cccccccchhhhhhhhcC---------------------CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEE
Q psy6375 6 IIKYPLTTESAMKKIEDN---------------------NTLVFIVHLQANKHHIKAAVKKMYDINVAKVN 55 (86)
Q Consensus 6 vi~~P~~TEKs~~l~e~~---------------------n~~~F~V~~~a~K~eIk~ave~lf~VkV~~Vn 55 (86)
++..|.++++..+.+++. |-..+.|+|.+++.+++ .+++.+||+|....
T Consensus 68 ~lvp~~~~~~e~~~l~e~L~v~V~~~~~~~~~vGn~i~~N~~G~lv~p~~~~ee~~-~i~~~L~V~v~~~t 137 (222)
T PRK04046 68 ILVPSIVLDEELELLKEALDLNVEVLPSKLTALGNLILANDKGALVHPELSDEARK-VIEDTLGVEVERGT 137 (222)
T ss_pred EEeCCCCCHHHHHHHHHhcCceEEEEeccccceEeEEEEcCcEEEECCCCCHHHHH-HHHHhhCceEEEEe
Confidence 466778888877666543 67789999999999998 78899999986655
No 17
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=76.55 E-value=6.8 Score=23.28 Aligned_cols=35 Identities=14% Similarity=0.132 Sum_probs=31.2
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
.+++.+.|++++|=.++|+.|+..+|+++..-+..
T Consensus 9 g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li 43 (71)
T cd01796 9 ETTFSLDVDPDLELENFKALCEAESGIPASQQQLI 43 (71)
T ss_pred CCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEE
Confidence 46899999999999999999999999999876554
No 18
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=76.29 E-value=7 Score=21.60 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=30.9
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
..+.|.|+++.|=.++|+.++..+|+.+...+...
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~ 44 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIY 44 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE
Confidence 47889999999999999999999999988776654
No 19
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=75.86 E-value=8.8 Score=22.00 Aligned_cols=35 Identities=11% Similarity=0.126 Sum_probs=32.4
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
..+.|.|+++.|=.++|+.|+..+|+++...+.+.
T Consensus 6 ~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~ 40 (69)
T PF00240_consen 6 KTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIY 40 (69)
T ss_dssp EEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEE
T ss_pred cEEEEEECCCCCHHHhhhhcccccccccccceeee
Confidence 48999999999999999999999999999888765
No 20
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=75.54 E-value=6.2 Score=22.73 Aligned_cols=35 Identities=9% Similarity=0.091 Sum_probs=31.2
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
..+.+.|++++|=.++|+.++..+|+++...+...
T Consensus 10 ~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 44 (71)
T cd01812 10 ESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIF 44 (71)
T ss_pred EEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEee
Confidence 46889999999999999999999999998877664
No 21
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=74.64 E-value=5.5 Score=24.99 Aligned_cols=23 Identities=35% Similarity=0.559 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhCCceeeEEEee
Q psy6375 36 KHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 36 K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
+..|+++++.+-|.+|.+||...
T Consensus 82 q~~V~~~v~~~tg~~v~~V~V~V 104 (108)
T PF03780_consen 82 QEKVKEAVEEMTGIEVSEVNVHV 104 (108)
T ss_pred HHHHHHHHHHHHCCeeEEEEEEE
Confidence 67899999999999999999875
No 22
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=74.06 E-value=11 Score=21.11 Aligned_cols=35 Identities=11% Similarity=0.112 Sum_probs=31.0
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
...+.|.+++++|=.++|+.+++.+|+.+.+....
T Consensus 7 ~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~ 41 (69)
T cd01769 7 GKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLI 41 (69)
T ss_pred CCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEE
Confidence 46788999999999999999999999999887663
No 23
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=71.65 E-value=7.6 Score=24.02 Aligned_cols=36 Identities=3% Similarity=-0.076 Sum_probs=30.6
Q ss_pred EEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC
Q psy6375 26 LVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD 61 (86)
Q Consensus 26 ~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~ 61 (86)
..-++++..|=.++|+-++.+||+.+...+.....+
T Consensus 15 ~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~ 50 (84)
T cd01789 15 FEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDG 50 (84)
T ss_pred eeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcC
Confidence 345589999999999999999999999999865443
No 24
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=71.53 E-value=6.2 Score=24.06 Aligned_cols=26 Identities=8% Similarity=0.239 Sum_probs=22.6
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhC
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYD 48 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~ 48 (86)
...|.|.++.+.++..++++++.+=.
T Consensus 40 ~~~y~F~id~e~~~~~i~~~l~~l~~ 65 (74)
T cd04929 40 SSEFEIFVDCECDQRRLDELVQLLKR 65 (74)
T ss_pred CceEEEEEEEEcCHHHHHHHHHHHHH
Confidence 36899999999999999999998743
No 25
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=70.98 E-value=9.6 Score=23.04 Aligned_cols=35 Identities=9% Similarity=0.033 Sum_probs=32.5
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
..|.+.|++++|=.++|+.+++..||++..-..+.
T Consensus 10 ~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~ 44 (74)
T cd01813 10 QEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLG 44 (74)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEe
Confidence 57899999999999999999999999999888875
No 26
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=70.95 E-value=12 Score=21.37 Aligned_cols=36 Identities=17% Similarity=0.205 Sum_probs=32.0
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
.+++.|.++++.+=.++|+.++..+|+++...+...
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 45 (72)
T cd01809 10 SQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIY 45 (72)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE
Confidence 368999999999999999999999999988777664
No 27
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=70.25 E-value=16 Score=24.74 Aligned_cols=58 Identities=9% Similarity=0.251 Sum_probs=42.2
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC-C--eeEEEEEcCCCCcHHHHHHhh
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-G--KKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~-~--~KKA~VtL~~g~~a~d~a~~~ 83 (86)
.-|+=.++.+++..+|++.|+. || +|.++.....+. + .-=|||++....+|......+
T Consensus 36 ~lfVgnL~~~~te~~L~~~F~~-~G-~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~l 96 (144)
T PLN03134 36 KLFIGGLSWGTDDASLRDAFAH-FG-DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96 (144)
T ss_pred EEEEeCCCCCCCHHHHHHHHhc-CC-CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHc
Confidence 4667778899999999999998 77 777877765431 2 224999999887666555443
No 28
>KOG0107|consensus
Probab=69.85 E-value=23 Score=25.99 Aligned_cols=56 Identities=25% Similarity=0.274 Sum_probs=45.2
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHh
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANK 82 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~ 82 (86)
...|+=....+|+|.|+..+|-. || ++.+|=....|+|+ |+|.+..--+|.|-.--
T Consensus 11 ~kVYVGnL~~~a~k~eLE~~F~~-yG-~lrsvWvArnPPGf--AFVEFed~RDA~DAvr~ 66 (195)
T KOG0107|consen 11 TKVYVGNLGSRATKRELERAFSK-YG-PLRSVWVARNPPGF--AFVEFEDPRDAEDAVRY 66 (195)
T ss_pred ceEEeccCCCCcchHHHHHHHHh-cC-cceeEEEeecCCCc--eEEeccCcccHHHHHhh
Confidence 35778888899999999888766 66 67788777788997 99999998888876543
No 29
>PTZ00044 ubiquitin; Provisional
Probab=69.30 E-value=12 Score=21.88 Aligned_cols=35 Identities=14% Similarity=0.259 Sum_probs=32.1
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
.+++++.|++..|=.++|+.|+...|+++...+..
T Consensus 10 G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~ 44 (76)
T PTZ00044 10 GKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLI 44 (76)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE
Confidence 36899999999999999999999999999888776
No 30
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=68.12 E-value=13 Score=21.66 Aligned_cols=35 Identities=14% Similarity=0.212 Sum_probs=31.0
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
..++++.|+++.|=.++|+.++...|+++......
T Consensus 8 g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li 42 (70)
T cd01798 8 GHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVI 42 (70)
T ss_pred CCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEE
Confidence 36899999999999999999999999999876554
No 31
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=67.37 E-value=19 Score=20.82 Aligned_cols=34 Identities=12% Similarity=0.111 Sum_probs=30.9
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
....+.++++.|=.++|+.++..+|+++...+..
T Consensus 11 ~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~ 44 (76)
T cd01806 11 KEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI 44 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE
Confidence 5678999999999999999999999999987776
No 32
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=67.20 E-value=17 Score=21.26 Aligned_cols=36 Identities=8% Similarity=0.075 Sum_probs=31.2
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCC--ceeeEEEee
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDI--NVAKVNTLI 58 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~V--kV~~VnT~~ 58 (86)
.+.++|.|+++.|=.++|+.++..+|+ .+.......
T Consensus 10 g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~ 47 (77)
T cd01805 10 QQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIY 47 (77)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEE
Confidence 368999999999999999999999999 877766653
No 33
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=66.69 E-value=15 Score=21.24 Aligned_cols=34 Identities=15% Similarity=0.188 Sum_probs=30.9
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
..+.|.|+++.|=.++|+.+++.+|+++...+..
T Consensus 11 ~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~ 44 (76)
T cd01803 11 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 44 (76)
T ss_pred CEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEE
Confidence 5788999999999999999999999999887766
No 34
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=65.58 E-value=12 Score=23.11 Aligned_cols=61 Identities=20% Similarity=0.427 Sum_probs=20.5
Q ss_pred CCEEEEEEeCC--CCHHHHHHHHHHHhCCceeeEEEeeCCCCe-eEEE-EEcCCCCcHHHHHHhhCCC
Q psy6375 23 NNTLVFIVHLQ--ANKHHIKAAVKKMYDINVAKVNTLIRPDGK-KKAY-VRLARDYDALDVANKIGII 86 (86)
Q Consensus 23 ~n~~~F~V~~~--a~K~eIk~ave~lf~VkV~~VnT~~~~~~~-KKA~-VtL~~g~~a~d~a~~~g~~ 86 (86)
++++.+.+.-+ +.=.-+-.-++++||+.+ .+.+.....-. +..| |.+.++ +.++..++|++
T Consensus 22 ~~~~~l~~~ten~~vARri~~llk~~f~i~~-ei~v~~~~~l~k~~~Y~i~i~~~--~~~iL~~lgll 86 (86)
T PF10298_consen 22 NGRISLEISTENAAVARRIYSLLKKLFDIDP-EISVRRSRNLKKNNVYTIRIEDS--AKEILRDLGLL 86 (86)
T ss_dssp TTEEEE--EES-HHHHHHHHHHHHHTT--EE-EEEEEE-SSSBEEE----------------------
T ss_pred CCEEEEEEEeCCHHHHHHHHHHHHHHhCCCe-EEEEecCCCCCCCCccccccccc--cccccccccCC
Confidence 45666555433 333456668899999998 45444432222 2333 444444 79999999985
No 35
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=65.12 E-value=18 Score=21.33 Aligned_cols=35 Identities=11% Similarity=0.117 Sum_probs=31.4
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
.+.+++.|+++.|=.++|+.++..+|+.+..-+..
T Consensus 10 G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~ 44 (74)
T cd01807 10 GRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLL 44 (74)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE
Confidence 36889999999999999999999999999877665
No 36
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=64.16 E-value=25 Score=25.99 Aligned_cols=58 Identities=10% Similarity=0.110 Sum_probs=43.4
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCC-C--CeeEEEEEcCCCCcHHHHHHhh
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-D--GKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~-~--~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
+-|+...+.+.+..++++.|+. || .|.+|+.+.-+ . ..--|+|++..-.+|......+
T Consensus 271 ~lfV~NL~~~~~e~~L~~~F~~-fG-~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~l 331 (352)
T TIGR01661 271 CIFVYNLSPDTDETVLWQLFGP-FG-AVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331 (352)
T ss_pred EEEEeCCCCCCCHHHHHHHHHh-CC-CeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHh
Confidence 4788899999999999999987 77 68888877644 1 1224999999877766554443
No 37
>PLN03120 nucleic acid binding protein; Provisional
Probab=62.65 E-value=22 Score=27.13 Aligned_cols=51 Identities=22% Similarity=0.191 Sum_probs=38.8
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcH
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDA 76 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a 76 (86)
.-|+=.++++++..+|++.|.. || +|.+|....-.....-|||++....+|
T Consensus 6 tVfVgNLs~~tTE~dLrefFS~-~G-~I~~V~I~~d~~~~GfAFVtF~d~eaA 56 (260)
T PLN03120 6 TVKVSNVSLKATERDIKEFFSF-SG-DIEYVEMQSENERSQIAYVTFKDPQGA 56 (260)
T ss_pred EEEEeCCCCCCCHHHHHHHHHh-cC-CeEEEEEeecCCCCCEEEEEeCcHHHH
Confidence 3566678899999999999966 77 888888865443335799999877554
No 38
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=62.10 E-value=19 Score=21.47 Aligned_cols=35 Identities=14% Similarity=0.176 Sum_probs=31.4
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
..+.+.|+++.|=.++|+-|+...|+++..-..+.
T Consensus 8 ~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~ 42 (76)
T cd01800 8 QMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQY 42 (76)
T ss_pred eEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE
Confidence 58899999999999999999999999998876654
No 39
>PF10057 DUF2294: Uncharacterized conserved protein (DUF2294); InterPro: IPR018745 This domain of unknown function is found in a family of hypothetical bacterial proteins with no known function. It is also found at the C terminus of proteins provisionally annotated as response regulators.
Probab=60.61 E-value=34 Score=22.40 Aligned_cols=39 Identities=13% Similarity=0.214 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHHhCCceeeEEEe-eCCCCeeEEEEEcCCC
Q psy6375 35 NKHHIKAAVKKMYDINVAKVNTL-IRPDGKKKAYVRLARD 73 (86)
Q Consensus 35 ~K~eIk~ave~lf~VkV~~VnT~-~~~~~~KKA~VtL~~g 73 (86)
-+++++..++.+.|++|.+.-+= +...|.--.++.|+.+
T Consensus 76 ~~~~l~~~ie~i~g~~V~~l~~D~~~~t~~~v~vfvl~~~ 115 (118)
T PF10057_consen 76 LKPELKEMIEEILGVKVISLFSDISLETGERVIVFVLDKN 115 (118)
T ss_pred HHHHHHHHHHHHhCCeeEEEEEEcccCCCCEEEEEEEcCC
Confidence 48999999999999999998764 4556777788888765
No 40
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=59.47 E-value=12 Score=23.80 Aligned_cols=24 Identities=13% Similarity=0.394 Sum_probs=19.8
Q ss_pred CCEEEEEEeCCCC-HHHHHHHHHHH
Q psy6375 23 NNTLVFIVHLQAN-KHHIKAAVKKM 46 (86)
Q Consensus 23 ~n~~~F~V~~~a~-K~eIk~ave~l 46 (86)
..+|.|.|+.+.. ...++++++.+
T Consensus 54 ~~~Y~FfVDieg~~~~~~~~~l~~L 78 (90)
T cd04931 54 KDEYEFFINLDKKSAPALDPIIKSL 78 (90)
T ss_pred CceEEEEEEEEcCCCHHHHHHHHHH
Confidence 3689999999986 78888888775
No 41
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=59.35 E-value=16 Score=21.78 Aligned_cols=26 Identities=8% Similarity=0.273 Sum_probs=22.2
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhC
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYD 48 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~ 48 (86)
...|.|.||.+....+++++++.+-.
T Consensus 40 ~~~y~Ffvd~~~~~~~~~~~l~~L~~ 65 (74)
T cd04904 40 GSEYEFFVDCEVDRGDLDQLISSLRR 65 (74)
T ss_pred CceEEEEEEEEcChHHHHHHHHHHHH
Confidence 46899999999988899999988754
No 42
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=59.15 E-value=22 Score=20.78 Aligned_cols=33 Identities=18% Similarity=0.187 Sum_probs=28.6
Q ss_pred EEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 25 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 25 ~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
+.++.+++++|=.++|+.|+..+|+.+...+..
T Consensus 11 ~~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li 43 (71)
T cd01808 11 KEEIEIAEDASVKDFKEAVSKKFKANQEQLVLI 43 (71)
T ss_pred CEEEEECCCChHHHHHHHHHHHhCCCHHHEEEE
Confidence 458999999999999999999999888777653
No 43
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=59.11 E-value=21 Score=21.70 Aligned_cols=34 Identities=18% Similarity=0.061 Sum_probs=31.1
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEE
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNT 56 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT 56 (86)
..+.++.|+++.|=.++|+.++..+|+++..-+.
T Consensus 12 ~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL 45 (75)
T cd01799 12 TVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW 45 (75)
T ss_pred CCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE
Confidence 4689999999999999999999999999987766
No 44
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=58.36 E-value=13 Score=26.87 Aligned_cols=32 Identities=34% Similarity=0.416 Sum_probs=24.3
Q ss_pred EEEEeCCCC----HHHHHHHHHHHhCCceeeEEEee
Q psy6375 27 VFIVHLQAN----KHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 27 ~F~V~~~a~----K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
+..|...|. |.+|-+|++.+|||+..+|+.+-
T Consensus 149 VlVVAeGa~~~~Vk~~I~~AV~~ll~v~~hkI~V~~ 184 (186)
T TIGR02830 149 VLVVAEGAENPQIKYRIVEAVSRVLDVPAHKVSVLP 184 (186)
T ss_pred EEEEeeCCCCHHHHHHHHHHHHHHhCCCcceEEEEe
Confidence 344555554 66777899999999999998763
No 45
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=58.11 E-value=25 Score=20.76 Aligned_cols=35 Identities=31% Similarity=0.258 Sum_probs=30.9
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
++.++.|+++.|=.++|+.|+...|+++...+..-
T Consensus 9 ~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~ 43 (74)
T cd01793 9 NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLL 43 (74)
T ss_pred CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEE
Confidence 57899999999999999999999999998876543
No 46
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=55.32 E-value=42 Score=24.82 Aligned_cols=54 Identities=15% Similarity=0.200 Sum_probs=40.7
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC-Ce--eEEEEEcCCCCcHHHH
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-GK--KKAYVRLARDYDALDV 79 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~-~~--KKA~VtL~~g~~a~d~ 79 (86)
+-|+=..+.+++..|+++.|+. || +|.+|..+..+. |. -=|||++....+|..-
T Consensus 5 ~l~V~nLp~~~~e~~l~~~F~~-~G-~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~A 61 (352)
T TIGR01661 5 NLIVNYLPQTMTQEEIRSLFTS-IG-EIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61 (352)
T ss_pred EEEEeCCCCCCCHHHHHHHHHc-cC-CEEEEEEEEcCCCCccceEEEEEECcHHHHHHH
Confidence 4556667889999999999999 88 889999887542 22 2499999877665543
No 47
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 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 [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=54.54 E-value=14 Score=23.27 Aligned_cols=42 Identities=10% Similarity=0.248 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHHHHHhCCceeeE--EEeeCCC--CeeEEEEEcCCC
Q psy6375 32 LQANKHHIKAAVKKMYDINVAKV--NTLIRPD--GKKKAYVRLARD 73 (86)
Q Consensus 32 ~~a~K~eIk~ave~lf~VkV~~V--nT~~~~~--~~KKA~VtL~~g 73 (86)
+..+|.||+..+-++||+++..| +.+.+.- +.-.++...-++
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~ivv~~~~t~fG~~~s~g~a~IYd~ 56 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLIVVFGIKTEFGGGKSTGFAKIYDS 56 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCEEEEEEEESSSSSEEEEEEEEESS
T ss_pred CCCCHHHHHHHHHHHhCCCCCeEEEeccEecCCCceEEEEEEEeCC
Confidence 67899999999999999988766 4454443 344555555433
No 48
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=53.54 E-value=33 Score=20.42 Aligned_cols=34 Identities=6% Similarity=0.056 Sum_probs=30.4
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
++..+.|+++.|=.++|+.++..+|+++..-+..
T Consensus 9 ~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li 42 (70)
T cd01794 9 KDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWF 42 (70)
T ss_pred CEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEE
Confidence 6889999999999999999999999988776554
No 49
>PF12426 DUF3674: RNA dependent RNA polymerase; InterPro: IPR024378 This domain is found in the RNA-directed RNA polymerase. It is located towards the N terminus and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.
Probab=52.20 E-value=9.3 Score=21.55 Aligned_cols=16 Identities=19% Similarity=0.515 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHhCCce
Q psy6375 36 KHHIKAAVKKMYDINV 51 (86)
Q Consensus 36 K~eIk~ave~lf~VkV 51 (86)
|+|=|.|+|.+||.|-
T Consensus 3 k~eER~aLEAMFNLKF 18 (41)
T PF12426_consen 3 KTEERSALEAMFNLKF 18 (41)
T ss_pred chhHHHHHHHHhceee
Confidence 6777899999999875
No 50
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=52.15 E-value=44 Score=25.95 Aligned_cols=57 Identities=11% Similarity=0.163 Sum_probs=40.1
Q ss_pred EEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCC-CCeeE--EEEEcCCCCcHHHHHHhh
Q psy6375 25 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-DGKKK--AYVRLARDYDALDVANKI 83 (86)
Q Consensus 25 ~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~-~~~KK--A~VtL~~g~~a~d~a~~~ 83 (86)
-|+=.++.+++..++++.|+. || +|.+|..+..+ .++.| |||++....+|......|
T Consensus 110 LfVgnLp~~~te~~L~~lF~~-~G-~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~L 169 (346)
T TIGR01659 110 LIVNYLPQDMTDRELYALFRT-IG-PINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169 (346)
T ss_pred EEEeCCCCCCCHHHHHHHHHh-cC-CEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHc
Confidence 444456899999999999998 44 37777776543 33333 999998887776655443
No 51
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=51.04 E-value=30 Score=23.32 Aligned_cols=39 Identities=21% Similarity=0.290 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCc
Q psy6375 35 NKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYD 75 (86)
Q Consensus 35 ~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~ 75 (86)
+|.|||.+++++|- +..+..++-+.+-+|.|++-+.+..
T Consensus 3 ~k~~ikpwlq~~~~--~~Gi~iVIerSd~~ki~FkCk~~~~ 41 (111)
T PF08731_consen 3 DKDEIKPWLQKIFY--PQGIGIVIERSDKKKIVFKCKNGKR 41 (111)
T ss_pred chHHHHHHHHHHhh--hcCceEEEEecCCceEEEEEecCCC
Confidence 78999999999774 4466677777888888888776654
No 52
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=50.66 E-value=38 Score=21.83 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=30.6
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
..++++.|++..|=.++|+.|+..+|+.+..-...
T Consensus 37 G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi 71 (103)
T cd01802 37 GTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLI 71 (103)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEE
Confidence 36899999999999999999999999988765553
No 53
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=50.07 E-value=23 Score=23.45 Aligned_cols=26 Identities=8% Similarity=0.241 Sum_probs=22.3
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhC
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYD 48 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~ 48 (86)
...|.|.|+...+..+++++++.+=.
T Consensus 81 ~~eY~FfIdieg~~~~~~~aL~~L~~ 106 (115)
T cd04930 81 GGDLEVLVRCEVHRSDLLQLISSLRQ 106 (115)
T ss_pred CceEEEEEEEEeCHHHHHHHHHHHHH
Confidence 36899999999999999999988743
No 54
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=50.00 E-value=39 Score=17.90 Aligned_cols=54 Identities=19% Similarity=0.182 Sum_probs=36.9
Q ss_pred EEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC--CeeEEEEEcCCCCcHHHHHHh
Q psy6375 27 VFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD--GKKKAYVRLARDYDALDVANK 82 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~--~~KKA~VtL~~g~~a~d~a~~ 82 (86)
.--+++.++..++++.++.. -.+..+.....+. +..-|||++..-.+|......
T Consensus 4 i~~l~~~~~~~~i~~~~~~~--g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~ 59 (74)
T cd00590 4 VGNLPPDVTEEDLRELFSKF--GKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEA 59 (74)
T ss_pred EeCCCCccCHHHHHHHHHhc--CCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHH
Confidence 34466788999999999995 3556666654432 356899999877665554443
No 55
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=49.70 E-value=39 Score=19.85 Aligned_cols=34 Identities=12% Similarity=0.153 Sum_probs=30.0
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
..+++.|++++|=.++|+.|+...|+++..-...
T Consensus 9 ~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~ 42 (74)
T cd01810 9 RSSIYEVQLTQTVATLKQQVSQRERVQADQFWLS 42 (74)
T ss_pred CEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEE
Confidence 5889999999999999999999999988766554
No 56
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=49.61 E-value=41 Score=20.23 Aligned_cols=34 Identities=9% Similarity=0.141 Sum_probs=30.0
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
....+.|++++|=.++|+.|++.+|+.+..-+..
T Consensus 12 ~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~ 45 (78)
T cd01804 12 TRFDLSVPPDETVEGLKKRISQRLKVPKERLALL 45 (78)
T ss_pred CEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEE
Confidence 5688999999999999999999999988777665
No 57
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=49.47 E-value=15 Score=20.93 Aligned_cols=20 Identities=5% Similarity=0.453 Sum_probs=13.3
Q ss_pred CCCHHHHHHHHHHHhCCcee
Q psy6375 33 QANKHHIKAAVKKMYDINVA 52 (86)
Q Consensus 33 ~a~K~eIk~ave~lf~VkV~ 52 (86)
..|..+|++++|+-||+...
T Consensus 20 ~vT~k~vr~~Le~~~~~dL~ 39 (54)
T PF08766_consen 20 TVTKKQVREQLEERFGVDLS 39 (54)
T ss_dssp G--HHHHHHHHHHH-SS--S
T ss_pred HhhHHHHHHHHHHHHCCCcH
Confidence 46899999999999998753
No 58
>KOG3424|consensus
Probab=49.12 E-value=22 Score=24.60 Aligned_cols=39 Identities=23% Similarity=0.369 Sum_probs=28.9
Q ss_pred hhhhcCCEEEEEE-e---CCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 18 KKIEDNNTLVFIV-H---LQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 18 ~l~e~~n~~~F~V-~---~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
+|+.. .|.+..| + ++.+|.||++-+-++|.+++..|-..
T Consensus 16 rLL~R-KqmvvdvlHPG~a~vsK~EirEKla~mYkt~~d~V~vf 58 (132)
T KOG3424|consen 16 RLLSR-KQMVVDVLHPGKANVSKTEIREKLAKMYKTTPDAVFVF 58 (132)
T ss_pred hhhhh-hheeEEEecCCCCCCCHHHHHHHHHHHhcCCcceEEEE
Confidence 45554 4555444 2 57899999999999999998877654
No 59
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=48.94 E-value=52 Score=19.78 Aligned_cols=35 Identities=6% Similarity=-0.035 Sum_probs=31.7
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
..+.+.|++++|=.++|+.|+..+|+.+...+...
T Consensus 12 k~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~ 46 (73)
T cd01791 12 KKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKK 46 (73)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEe
Confidence 57778999999999999999999999999988864
No 60
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=47.65 E-value=39 Score=18.40 Aligned_cols=35 Identities=20% Similarity=0.305 Sum_probs=21.6
Q ss_pred HhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhh
Q psy6375 46 MYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 46 lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
-|| +|.+|......+ -.|+|++..-.+|....+.+
T Consensus 7 ~fG-~V~~i~~~~~~~--~~a~V~f~~~~~A~~a~~~l 41 (56)
T PF13893_consen 7 KFG-EVKKIKIFKKKR--GFAFVEFASVEDAQKAIEQL 41 (56)
T ss_dssp TTS--EEEEEEETTST--TEEEEEESSHHHHHHHHHHH
T ss_pred Ccc-cEEEEEEEeCCC--CEEEEEECCHHHHHHHHHHh
Confidence 366 677776654432 36899988777766555443
No 61
>PLN03121 nucleic acid binding protein; Provisional
Probab=47.37 E-value=88 Score=23.73 Aligned_cols=56 Identities=16% Similarity=0.191 Sum_probs=40.5
Q ss_pred EEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhh
Q psy6375 25 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 25 ~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
-++-.++++++-.++++.|.. || +|.+|....-.....-|||++.+.+. .+-|-.|
T Consensus 8 V~V~NLS~~tTE~dLrefFS~-~G-~I~~V~I~~D~et~gfAfVtF~d~~a-aetAllL 63 (243)
T PLN03121 8 AEVTNLSPKATEKDVYDFFSH-CG-AIEHVEIIRSGEYACTAYVTFKDAYA-LETAVLL 63 (243)
T ss_pred EEEecCCCCCCHHHHHHHHHh-cC-CeEEEEEecCCCcceEEEEEECCHHH-HHHHHhc
Confidence 345567899999999999987 66 57788766543334589999998765 4655443
No 62
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=47.03 E-value=63 Score=25.94 Aligned_cols=57 Identities=14% Similarity=0.092 Sum_probs=41.8
Q ss_pred EEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC---CeeEEEEEcCCCCcHHHHHHhhC
Q psy6375 26 LVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD---GKKKAYVRLARDYDALDVANKIG 84 (86)
Q Consensus 26 ~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~---~~KKA~VtL~~g~~a~d~a~~~g 84 (86)
|+=..+.++|..++++.|.. || .|.+|+.+.... ...=|||.+....+|......++
T Consensus 4 ~VgnLp~~vte~~L~~~F~~-~G-~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln 63 (562)
T TIGR01628 4 YVGDLDPDVTEAKLYDLFKP-FG-PVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMN 63 (562)
T ss_pred EEeCCCCCCCHHHHHHHHHh-cC-CEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhC
Confidence 44556788999999998877 56 588888876443 22359999999888877666554
No 63
>PF07788 DUF1626: Protein of unknown function (DUF1626); InterPro: IPR012431 This is a family consisting of sequences from hypothetical proteins of unknown function expressed by certain species of archaea. One member (Q9YCN7 from SWISSPROT) is thought to be similar to tropomyosin [].
Probab=46.66 E-value=69 Score=19.78 Aligned_cols=52 Identities=15% Similarity=0.200 Sum_probs=36.5
Q ss_pred CCEEEEEEeCCCCHHHHH------HHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhhCC
Q psy6375 23 NNTLVFIVHLQANKHHIK------AAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKIGI 85 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk------~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~g~ 85 (86)
...|.+.+-..++|.++- +..|+..|+++.+ ..+|+--=+..|.+.|.+||+
T Consensus 12 g~~ilvEikSs~~~~Dv~~f~rk~~lYek~~grk~~r-----------~ivVtp~id~~a~~~A~~LGI 69 (70)
T PF07788_consen 12 GKVILVEIKSSVSRGDVYIFKRKAELYEKVHGRKVDR-----------LIVVTPYIDDRAKEMAEELGI 69 (70)
T ss_pred CeEEEEEEEccCCHHHHHHHHHHHHHHHHHHCCCcce-----------EEEEEeecCHHHHHHHHHhCC
Confidence 346778888899998873 3456666777643 444444445569999999997
No 64
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=46.65 E-value=70 Score=21.98 Aligned_cols=42 Identities=29% Similarity=0.377 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhCCceeeEEEeeCCC------CeeEEEEEcCCCC
Q psy6375 33 QANKHHIKAAVKKMYDINVAKVNTLIRPD------GKKKAYVRLARDY 74 (86)
Q Consensus 33 ~a~K~eIk~ave~lf~VkV~~VnT~~~~~------~~KKA~VtL~~g~ 74 (86)
+.=+.+|++.++..||+.+.+|..-...+ .-++..|+|.++.
T Consensus 86 ~~l~~~i~~~l~~~~g~~~~~V~v~~~~~~~~~~~~I~~I~v~l~~~~ 133 (188)
T PF09581_consen 86 EQLEKQIKALLEDKYGVEVVKVEVEIDEDEESPDFEIKEIKVTLSEEE 133 (188)
T ss_pred HHHHHHHHHHHhhhcCCceEEEEEEEEcCCCccccceeEEEEEEcCCC
Confidence 33467888889989999999998876543 3588999998854
No 65
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=45.70 E-value=14 Score=19.96 Aligned_cols=20 Identities=30% Similarity=0.295 Sum_probs=16.2
Q ss_pred EEEeCCCCHHHHHHHHHHHh
Q psy6375 28 FIVHLQANKHHIKAAVKKMY 47 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~lf 47 (86)
|-++++++..+||++...+.
T Consensus 6 Lgl~~~~~~~~ik~~y~~l~ 25 (55)
T cd06257 6 LGVPPDASDEEIKKAYRKLA 25 (55)
T ss_pred cCCCCCCCHHHHHHHHHHHH
Confidence 45678899999999888764
No 66
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=45.69 E-value=18 Score=24.64 Aligned_cols=20 Identities=20% Similarity=0.338 Sum_probs=14.0
Q ss_pred CCCCHHHHHHHHHHHhCCce
Q psy6375 32 LQANKHHIKAAVKKMYDINV 51 (86)
Q Consensus 32 ~~a~K~eIk~ave~lf~VkV 51 (86)
-+|+|.|+..++++++|.+.
T Consensus 113 G~A~KeqV~~mv~~ll~l~~ 132 (149)
T PF02075_consen 113 GRASKEQVAFMVRKLLGLDE 132 (149)
T ss_dssp TT--HHHHHHHHHHHTT---
T ss_pred CccCHHHHHHHHHHHhCCCC
Confidence 48999999999999999864
No 67
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=44.01 E-value=16 Score=20.17 Aligned_cols=20 Identities=30% Similarity=0.253 Sum_probs=16.2
Q ss_pred EEEeCCCCHHHHHHHHHHHh
Q psy6375 28 FIVHLQANKHHIKAAVKKMY 47 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~lf 47 (86)
|-++++++..+||++...+.
T Consensus 7 Lgl~~~~~~~~ik~ay~~l~ 26 (60)
T smart00271 7 LGVPRDASLDEIKKAYRKLA 26 (60)
T ss_pred cCCCCCCCHHHHHHHHHHHH
Confidence 45677899999999888764
No 68
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=43.94 E-value=15 Score=29.30 Aligned_cols=20 Identities=30% Similarity=0.413 Sum_probs=17.5
Q ss_pred EEEEeCCCCHHHHHHHHHHH
Q psy6375 27 VFIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~l 46 (86)
++-|+++||..|||+|..+|
T Consensus 9 iLGV~k~As~~EIKkAYRkL 28 (371)
T COG0484 9 ILGVSKDASEEEIKKAYRKL 28 (371)
T ss_pred hcCCCCCCCHHHHHHHHHHH
Confidence 36699999999999998876
No 69
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=43.93 E-value=42 Score=23.20 Aligned_cols=40 Identities=18% Similarity=0.179 Sum_probs=29.4
Q ss_pred hhhhhhhhcCCEEEEEEe----CCCCHHHHHHHHHHHhC-CceeeE
Q psy6375 14 ESAMKKIEDNNTLVFIVH----LQANKHHIKAAVKKMYD-INVAKV 54 (86)
Q Consensus 14 EKs~~l~e~~n~~~F~V~----~~a~K~eIk~ave~lf~-VkV~~V 54 (86)
+....|+.. .++.|.|. +..+|.||++.+-++|+ .++.-|
T Consensus 13 ~~~NpLL~R-kE~~~~v~Hpg~~TpSr~eirekLA~~~~v~d~~~V 57 (132)
T PTZ00071 13 FLVNPLLNR-KQFVVEVLHPGKGTVSKKDIKEKLAKQYKVADARTI 57 (132)
T ss_pred eeeccCcCc-EEEEEEEEeCCCCCCCHHHHHHHHHHHhCCCCCCEE
Confidence 334456654 68888874 56799999999999999 465544
No 70
>smart00360 RRM RNA recognition motif.
Probab=43.86 E-value=49 Score=17.26 Aligned_cols=50 Identities=16% Similarity=0.262 Sum_probs=34.0
Q ss_pred eCCCCHHHHHHHHHHHhCCceeeEEEeeCCC---CeeEEEEEcCCCCcHHHHHHh
Q psy6375 31 HLQANKHHIKAAVKKMYDINVAKVNTLIRPD---GKKKAYVRLARDYDALDVANK 82 (86)
Q Consensus 31 ~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~---~~KKA~VtL~~g~~a~d~a~~ 82 (86)
+...+..+|++.++. || .|..+.....+. ...-|+|++....+|......
T Consensus 5 ~~~~~~~~l~~~f~~-~g-~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~ 57 (71)
T smart00360 5 PPDVTEEELRELFSK-FG-KIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEA 57 (71)
T ss_pred CcccCHHHHHHHHHh-hC-CEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHH
Confidence 567899999999986 66 455666655432 234799999877665554433
No 71
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=43.47 E-value=82 Score=25.14 Aligned_cols=54 Identities=20% Similarity=0.228 Sum_probs=38.2
Q ss_pred EEEEEEeC-CCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHh
Q psy6375 25 TLVFIVHL-QANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANK 82 (86)
Q Consensus 25 ~~~F~V~~-~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~ 82 (86)
-|+-..+. ++|..++++.++. || .|.+|..+..++| =|+|++....+|......
T Consensus 278 l~v~nL~~~~vt~~~L~~lF~~-yG-~V~~vki~~~~~g--~afV~f~~~~~A~~Ai~~ 332 (481)
T TIGR01649 278 LMVSGLHQEKVNCDRLFNLFCV-YG-NVERVKFMKNKKE--TALIEMADPYQAQLALTH 332 (481)
T ss_pred EEEeCCCCCCCCHHHHHHHHHh-cC-CeEEEEEEeCCCC--EEEEEECCHHHHHHHHHH
Confidence 34444555 4899999999986 77 6778877765444 499999988776665543
No 72
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=41.41 E-value=1.1e+02 Score=24.57 Aligned_cols=58 Identities=16% Similarity=0.295 Sum_probs=42.1
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCee--EEEEEcCCCCcHHHHHHh
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKK--KAYVRLARDYDALDVANK 82 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~K--KA~VtL~~g~~a~d~a~~ 82 (86)
.|-|+-.++.+.+..++++.++. || +|.++.......|.- -|||.+....+|......
T Consensus 179 ~~l~V~nl~~~~tee~L~~~F~~-fG-~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~ 238 (562)
T TIGR01628 179 TNLYVKNLDPSVNEDKLRELFAK-FG-EITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE 238 (562)
T ss_pred CeEEEeCCCCcCCHHHHHHHHHh-cC-CEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHH
Confidence 35666778889999999999987 66 366777766554432 599999987776655443
No 73
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=40.83 E-value=54 Score=19.64 Aligned_cols=34 Identities=6% Similarity=0.084 Sum_probs=29.7
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEe
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
..+.+.|++++|=.|+|+.|++.+|+.+..-+..
T Consensus 13 ~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~ 46 (80)
T cd01792 13 NEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLA 46 (80)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEE
Confidence 5788899999999999999999999988777663
No 74
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=39.13 E-value=38 Score=24.09 Aligned_cols=35 Identities=34% Similarity=0.505 Sum_probs=22.5
Q ss_pred HHHHHHHHh-CCceeeEEEeeCCCCeeEEE-EEcCCCC
Q psy6375 39 IKAAVKKMY-DINVAKVNTLIRPDGKKKAY-VRLARDY 74 (86)
Q Consensus 39 Ik~ave~lf-~VkV~~VnT~~~~~~~KKA~-VtL~~g~ 74 (86)
+++-++.+| -..|..|++...++| +.|| |.+++.+
T Consensus 102 ~~~fl~Nl~~PA~V~gV~i~~~~dG-~~~~kV~Vd~~D 138 (166)
T PRK06418 102 IKKLAVQLLSPARVLGVNTVWLPDG-TVQYVIRVSRRD 138 (166)
T ss_pred HHHHHHhcCCCcEEEEEEEEEeCCC-cEEEEEEECHHH
Confidence 334444433 455666677777777 8999 9998754
No 75
>PF04432 FrhB_FdhB_C: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; InterPro: IPR007525 Coenzyme F420 hydrogenase (1.12.99.1 from EC) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C-termini of F420 hydrogenase and dehydrogenase beta subunits [, ]. The C terminus of Methanobacterium formicicum formate dehydrogenase beta chain (1.2.1.2 from EC, P06130 from SWISSPROT) is also represented in this entry []. This region is often found in association with the 4Fe-4S binding domain, fer4 (IPR001450 from INTERPRO), and the N terminus IPR007516 from INTERPRO.
Probab=38.96 E-value=1.2e+02 Score=20.45 Aligned_cols=45 Identities=11% Similarity=0.124 Sum_probs=37.4
Q ss_pred EEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCC
Q psy6375 28 FIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDY 74 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~ 74 (86)
+.++-..+-.-.+++++..+|++..+|..+..++|| ..|++..|.
T Consensus 39 l~C~g~~s~~~~~~~l~~~~~~~~~~v~~~~~r~g~--~~i~~~~g~ 83 (161)
T PF04432_consen 39 LFCHGVPSPKKLRKYLEEQLGIKPDDVKKFDFRDGW--FIITTKDGK 83 (161)
T ss_pred EECCCCCCHHHHHHHHHHHhCCChhheeEEEEeCCe--EEEEEeCCC
Confidence 556667788888999999999999999888888887 888887553
No 76
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=38.93 E-value=1.2e+02 Score=23.55 Aligned_cols=59 Identities=19% Similarity=0.311 Sum_probs=41.2
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCC-CC--eeEEEEEcCCCCcHHHHHHhh
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-DG--KKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~-~~--~KKA~VtL~~g~~a~d~a~~~ 83 (86)
.+-|+--++.+++..++++.|++ || .|..+..+... .| .--|+|++..-.+|.+....|
T Consensus 194 ~~lfV~nLp~~vtee~L~~~F~~-fG-~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~l 255 (346)
T TIGR01659 194 TNLYVTNLPRTITDDQLDTIFGK-YG-QIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255 (346)
T ss_pred ceeEEeCCCCcccHHHHHHHHHh-cC-CEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHh
Confidence 45777788899999999998866 55 45566665433 22 125999998877776665544
No 77
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=37.09 E-value=50 Score=19.48 Aligned_cols=26 Identities=12% Similarity=0.308 Sum_probs=20.5
Q ss_pred CCEEEEEEeCCCC--HHHHHHHHHHHhC
Q psy6375 23 NNTLVFIVHLQAN--KHHIKAAVKKMYD 48 (86)
Q Consensus 23 ~n~~~F~V~~~a~--K~eIk~ave~lf~ 48 (86)
...|.|.|+.++. ..+++++++.+=+
T Consensus 41 ~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 41 LWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 4679999988875 8888888877644
No 78
>smart00362 RRM_2 RNA recognition motif.
Probab=36.59 E-value=67 Score=16.79 Aligned_cols=55 Identities=16% Similarity=0.195 Sum_probs=37.7
Q ss_pred EEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC-CeeEEEEEcCCCCcHHHHHHhh
Q psy6375 27 VFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-GKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~-~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
.--++++.+..+|++.++. || ++..+.....++ ...-|+|++....+|......+
T Consensus 4 i~~l~~~~~~~~l~~~~~~-~g-~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~ 59 (72)
T smart00362 4 VGNLPPDVTEEDLKELFSK-FG-PIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEAL 59 (72)
T ss_pred EcCCCCcCCHHHHHHHHHh-cC-CEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHh
Confidence 3345778899999999986 66 456666665431 2346999999877766655543
No 79
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=36.55 E-value=25 Score=20.24 Aligned_cols=22 Identities=36% Similarity=0.517 Sum_probs=15.5
Q ss_pred HHHHHHHHh-CCceeeEEEeeCC
Q psy6375 39 IKAAVKKMY-DINVAKVNTLIRP 60 (86)
Q Consensus 39 Ik~ave~lf-~VkV~~VnT~~~~ 60 (86)
|++++++.| |++|.+|.-.-.+
T Consensus 1 i~~~l~~~~p~~~v~~v~~spi~ 23 (57)
T PF10411_consen 1 IKQALKKAFPGLKVESVSPSPIP 23 (57)
T ss_dssp CHHHHHCT--T-TCEEEEE-SST
T ss_pred ChhHHHhhcCCCceeEEEcCCCC
Confidence 578999999 9999999776543
No 80
>KOG0132|consensus
Probab=36.54 E-value=56 Score=28.98 Aligned_cols=50 Identities=10% Similarity=0.224 Sum_probs=38.9
Q ss_pred EEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhh
Q psy6375 29 IVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 29 ~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
.++++++-.+++..||. || .|.+|+ .-..++-|||++-.-++|.+...+|
T Consensus 428 ~i~k~v~e~dL~~~fee-fG-eiqSi~---li~~R~cAfI~M~~RqdA~kalqkl 477 (894)
T KOG0132|consen 428 GIPKNVTEQDLANLFEE-FG-EIQSII---LIPPRGCAFIKMVRRQDAEKALQKL 477 (894)
T ss_pred cccchhhHHHHHHHHHh-cc-cceeEe---eccCCceeEEEEeehhHHHHHHHHH
Confidence 47889999999999998 55 233444 4445578999999999998887775
No 81
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=35.60 E-value=89 Score=20.89 Aligned_cols=40 Identities=13% Similarity=0.224 Sum_probs=30.9
Q ss_pred hhhhcCCEEEEEEe----CCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 18 KKIEDNNTLVFIVH----LQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 18 ~l~e~~n~~~F~V~----~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
.|+.. ..+.|.|. +..+|.||++.+-+++|+....|-...
T Consensus 13 pLL~R-kEi~~~v~h~g~~TPSr~evrekla~~l~~d~e~VvV~~ 56 (107)
T COG2004 13 PLLKR-KEIVFVVYHEGSPTPSRKEVREKLAAMLGADKELVVVDY 56 (107)
T ss_pred ccccc-eEEEEEEEeCCCCCCCHHHHHHHHHHHHCCCcceEEEEe
Confidence 44443 57777774 678999999999999999987776544
No 82
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=35.42 E-value=1.5e+02 Score=22.95 Aligned_cols=54 Identities=19% Similarity=0.250 Sum_probs=40.6
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC---CeeEEEEEcCCCCcHHHH
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD---GKKKAYVRLARDYDALDV 79 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~---~~KKA~VtL~~g~~a~d~ 79 (86)
.-|+-.++.+++..+|++.|+. || +|..|..+.-+. ..-=|||.+....+|...
T Consensus 91 ~l~V~nlp~~~~~~~l~~~F~~-~G-~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~A 147 (457)
T TIGR01622 91 TVFVLQLALKARERDLYEFFSK-VG-KVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA 147 (457)
T ss_pred EEEEeCCCCCCCHHHHHHHHHh-cC-CeeEEEEeecCCCCCcceEEEEEECCHHHHHHH
Confidence 4677788899999999999988 78 888998875331 123499999877665443
No 83
>smart00654 eIF6 translation initiation factor 6.
Probab=35.29 E-value=59 Score=23.54 Aligned_cols=30 Identities=10% Similarity=0.093 Sum_probs=24.0
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeE
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKV 54 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~V 54 (86)
|-..-.|+|++++.+++ .++..|||+|..-
T Consensus 107 Nd~g~lvhp~~s~ee~~-~i~d~L~V~v~~g 136 (200)
T smart00654 107 NDHGALASPDLSKETEE-IISDVLGVEVFRG 136 (200)
T ss_pred cCceEEECCCCCHHHHH-HHHHHhCCeEEEE
Confidence 33456799999999886 5999999998654
No 84
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.25 E-value=40 Score=23.38 Aligned_cols=47 Identities=28% Similarity=0.515 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEE---------cCCCCcHHHHHHhhCC
Q psy6375 35 NKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVR---------LARDYDALDVANKIGI 85 (86)
Q Consensus 35 ~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~Vt---------L~~g~~a~d~a~~~g~ 85 (86)
+|.-+| |+|.+ |++|.-|.. ...|.++-|=+ |..|..+-+++..+|+
T Consensus 66 skkvlk-aleq~-gI~vIPvk~--KgrGrprkyd~~t~~~i~emlr~gk~preIsk~lGI 121 (139)
T COG1710 66 SKKVLK-ALEQM-GIKVIPVKL--KGRGRPRKYDRNTLLRIREMLRNGKTPREISKDLGI 121 (139)
T ss_pred HHHHHH-HHHhC-CceEeeeee--cCCCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCC
Confidence 344343 77776 777777661 11355555554 6778888889988886
No 85
>PF07626 PSD3: Protein of unknown function (DUF1587); InterPro: IPR013036 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=34.65 E-value=49 Score=19.86 Aligned_cols=20 Identities=10% Similarity=0.361 Sum_probs=18.0
Q ss_pred CCCCHHHHHHHHHHHhCCce
Q psy6375 32 LQANKHHIKAAVKKMYDINV 51 (86)
Q Consensus 32 ~~a~K~eIk~ave~lf~VkV 51 (86)
++.||.|-.+.|..+||+.+
T Consensus 1 RRLtr~EY~nTvrDLlg~~~ 20 (67)
T PF07626_consen 1 RRLTRREYQNTVRDLLGVDV 20 (67)
T ss_pred CCCCHHHHHHHHHHHhCCCC
Confidence 46799999999999999994
No 86
>COG1302 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.26 E-value=65 Score=22.15 Aligned_cols=23 Identities=26% Similarity=0.434 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhCCceeeEEEeeC
Q psy6375 37 HHIKAAVKKMYDINVAKVNTLIR 59 (86)
Q Consensus 37 ~eIk~ave~lf~VkV~~VnT~~~ 59 (86)
.-|+.+++.+-|.+|.+||...+
T Consensus 90 ~~V~~~v~~mtgl~v~~VNV~V~ 112 (131)
T COG1302 90 ERVKEEVENMTGLKVVEVNVHVV 112 (131)
T ss_pred HHHHHHHHHhhCCceEEEEEEEE
Confidence 34889999999999999999764
No 87
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=32.84 E-value=48 Score=18.98 Aligned_cols=23 Identities=17% Similarity=0.277 Sum_probs=14.6
Q ss_pred EEeCCCCHHHHHHHHHHHhCCce
Q psy6375 29 IVHLQANKHHIKAAVKKMYDINV 51 (86)
Q Consensus 29 ~V~~~a~K~eIk~ave~lf~VkV 51 (86)
...++.+|.|+-.+|.+.|.--.
T Consensus 16 ~~~~~~sK~qLa~~V~kHF~s~~ 38 (53)
T PF13867_consen 16 PERPRSSKEQLANAVRKHFNSQP 38 (53)
T ss_dssp ---SS--HHHHHHHHHHHHTT--
T ss_pred CCCCCCCHHHHHHHHHHHHhcCC
Confidence 34459999999999999997543
No 88
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=32.13 E-value=74 Score=21.92 Aligned_cols=26 Identities=31% Similarity=0.312 Sum_probs=17.0
Q ss_pred CceeeEEEeeCCCCeeEEEEEcCCCCc
Q psy6375 49 INVAKVNTLIRPDGKKKAYVRLARDYD 75 (86)
Q Consensus 49 VkV~~VnT~~~~~~~KKA~VtL~~g~~ 75 (86)
.+|.+|++.. ++|.+.|+|..++++.
T Consensus 86 A~V~~V~i~~-~~~~~~a~V~V~~~d~ 111 (141)
T TIGR01952 86 AEVKNVTVSE-FNGKKVAYVEVHPRDK 111 (141)
T ss_pred ceEEEEEEEc-CCCCEEEEEEEChhhh
Confidence 4455554433 4567899999987654
No 89
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=32.11 E-value=47 Score=22.55 Aligned_cols=20 Identities=20% Similarity=0.429 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHHHHHhCCce
Q psy6375 32 LQANKHHIKAAVKKMYDINV 51 (86)
Q Consensus 32 ~~a~K~eIk~ave~lf~VkV 51 (86)
-+|+|.|+.++|+.+++.+-
T Consensus 114 G~A~KeqV~~mv~~~l~~~~ 133 (154)
T cd00529 114 GKADKDQVQHMVKRLLNLSE 133 (154)
T ss_pred CCCCHHHHHHHHHHHhCCCC
Confidence 47999999999999998764
No 90
>COG1976 TIF6 Translation initiation factor 6 (eIF-6) [Translation, ribosomal structure and biogenesis]
Probab=31.72 E-value=65 Score=24.18 Aligned_cols=30 Identities=17% Similarity=0.393 Sum_probs=25.5
Q ss_pred EEeCCCCHHHHHHHHHHHhCCceeeEEEeeCC
Q psy6375 29 IVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60 (86)
Q Consensus 29 ~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~ 60 (86)
-|+|+++=.|.+ .++++|+|+|. +=|.|.-
T Consensus 157 LvhP~~s~~Ele-~Lse~f~V~v~-~GTvN~G 186 (222)
T COG1976 157 LVHPETSDEELE-ELSELFGVPVD-VGTVNFG 186 (222)
T ss_pred eeCCCCCHHHHH-HHHHHhCeeEE-EeeecCC
Confidence 589999988876 59999999996 8888854
No 91
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=31.68 E-value=84 Score=17.04 Aligned_cols=38 Identities=21% Similarity=0.272 Sum_probs=26.0
Q ss_pred hCCceeeEEEeeCC-CCeeEEEEEcCCCCcHHHHHHhhC
Q psy6375 47 YDINVAKVNTLIRP-DGKKKAYVRLARDYDALDVANKIG 84 (86)
Q Consensus 47 f~VkV~~VnT~~~~-~~~KKA~VtL~~g~~a~d~a~~~g 84 (86)
+|+++.++.+.... .|....++.+...+.+.+...+-|
T Consensus 23 ~~~nI~~i~~~~~~~~~~~~v~~~ve~~~~~~~~L~~~G 61 (65)
T cd04882 23 EGINIEYMYAFVEKKGGKALLIFRTEDIEKAIEVLQERG 61 (65)
T ss_pred CCCChhheEEEccCCCCeEEEEEEeCCHHHHHHHHHHCC
Confidence 48888888775543 367778888877666666665555
No 92
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=31.07 E-value=49 Score=23.25 Aligned_cols=18 Identities=17% Similarity=0.460 Sum_probs=16.6
Q ss_pred CCCHHHHHHHHHHHhCCc
Q psy6375 33 QANKHHIKAAVKKMYDIN 50 (86)
Q Consensus 33 ~a~K~eIk~ave~lf~Vk 50 (86)
+|+|.|+..+|+.+++.+
T Consensus 113 ~A~KeQV~~mV~~lL~l~ 130 (156)
T TIGR00228 113 SAEKSQVQHMVRRLLKLP 130 (156)
T ss_pred CCCHHHHHHHHHHHcCCC
Confidence 799999999999999865
No 93
>PTZ00100 DnaJ chaperone protein; Provisional
Probab=31.03 E-value=32 Score=23.15 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=17.9
Q ss_pred EEEEeCCCCHHHHHHHHHHHh
Q psy6375 27 VFIVHLQANKHHIKAAVKKMY 47 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~lf 47 (86)
++-++++++..|||++..++.
T Consensus 70 ILGv~~~As~~eIkkaYRrLa 90 (116)
T PTZ00100 70 ILNISPTASKERIREAHKQLM 90 (116)
T ss_pred HcCCCCCCCHHHHHHHHHHHH
Confidence 456888999999999998875
No 94
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=30.78 E-value=93 Score=17.95 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=20.5
Q ss_pred CCEEEEEEeCCC--CHHHHHHHHHHHhC
Q psy6375 23 NNTLVFIVHLQA--NKHHIKAAVKKMYD 48 (86)
Q Consensus 23 ~n~~~F~V~~~a--~K~eIk~ave~lf~ 48 (86)
...|.|.++.+. ....++++++.+=.
T Consensus 39 ~~~~~f~id~~~~~~~~~~~~~l~~l~~ 66 (75)
T cd04880 39 LWEYEFFVDFEGHIDDPDVKEALEELKR 66 (75)
T ss_pred CceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 468999999887 58888888887643
No 95
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=29.78 E-value=53 Score=22.86 Aligned_cols=19 Identities=21% Similarity=0.454 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHHHHhCCc
Q psy6375 32 LQANKHHIKAAVKKMYDIN 50 (86)
Q Consensus 32 ~~a~K~eIk~ave~lf~Vk 50 (86)
-+|+|.|+..+++.+++..
T Consensus 116 G~A~K~qV~~mv~~~l~l~ 134 (164)
T PRK00039 116 GRADKEQVQHMVKRLLNLP 134 (164)
T ss_pred CCCCHHHHHHHHHHHhCCC
Confidence 3599999999999999875
No 96
>PLN02817 glutathione dehydrogenase (ascorbate)
Probab=29.62 E-value=54 Score=24.35 Aligned_cols=40 Identities=15% Similarity=0.269 Sum_probs=33.3
Q ss_pred HHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhh
Q psy6375 44 KKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 44 e~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
-..|++...++|+...+++.++++++..+..+.++++-|-
T Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (265)
T PLN02817 23 NPRFGTSHGGAKGVKRVGGRRRKYLTAITMSSPLEVCVKA 62 (265)
T ss_pred cccccceeecccccccCCcccceeEEecCCCccHHHHHhc
Confidence 4457778888888888889999999999998888888764
No 97
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=29.04 E-value=1.1e+02 Score=17.55 Aligned_cols=22 Identities=45% Similarity=0.590 Sum_probs=17.3
Q ss_pred CCCeeEEEEEcCCCCcHHHHHHhhC
Q psy6375 60 PDGKKKAYVRLARDYDALDVANKIG 84 (86)
Q Consensus 60 ~~~~KKA~VtL~~g~~a~d~a~~~g 84 (86)
|+|..+- |+.|..+.|+|..|+
T Consensus 6 pdG~~~~---~~~g~T~~d~A~~I~ 27 (60)
T PF02824_consen 6 PDGSIKE---LPEGSTVLDVAYSIH 27 (60)
T ss_dssp TTSCEEE---EETTBBHHHHHHHHS
T ss_pred CCCCeee---CCCCCCHHHHHHHHC
Confidence 6664433 899999999999886
No 98
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=28.96 E-value=1.9e+02 Score=22.60 Aligned_cols=54 Identities=13% Similarity=0.118 Sum_probs=36.5
Q ss_pred EEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCC-CC--eeEEEEEcCCCCcHHHHH
Q psy6375 25 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-DG--KKKAYVRLARDYDALDVA 80 (86)
Q Consensus 25 ~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~-~~--~KKA~VtL~~g~~a~d~a 80 (86)
-|+=.++..++-.+|++.|+. || .+..++.+..+ .| .-=|+|.+.....|....
T Consensus 298 l~v~nlp~~~~~~~l~~~f~~-~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~ 354 (509)
T TIGR01642 298 IYIGNLPLYLGEDQIKELLES-FG-DLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354 (509)
T ss_pred EEEeCCCCCCCHHHHHHHHHh-cC-CeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHH
Confidence 455557788999999999998 66 56777776533 11 123999998765544433
No 99
>TIGR00323 eIF-6 translation initiation factor eIF-6, putative. This model finds translation initiation factor eIF-6 of eukaryotes, which is a ribosome dissociation factor. It also finds a set of apparent archaeal orthologs, slightly shorter proteins not yet shown to act as initiation factors; these probably should be designated as translation initiation factor aIF-6, putative.
Probab=28.69 E-value=98 Score=22.72 Aligned_cols=31 Identities=13% Similarity=0.123 Sum_probs=24.5
Q ss_pred EEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 26 LVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 26 ~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
..-.|+|++++.+++ .++..|||+|..- |++
T Consensus 148 ~G~lvhP~~s~ee~~-~i~d~LgV~v~~g-Tin 178 (215)
T TIGR00323 148 RGGLVHPQTSVQEQE-ELSSLLGVELVAG-TVN 178 (215)
T ss_pred cEEEECCCCCHHHHH-HHHHHhCCcEEEE-Eec
Confidence 445799999998886 5999999998655 554
No 100
>cd00527 IF6 Ribosome anti-association factor IF6 binds the large ribosomal subunit and prevents the two subunits from associating during translation initiation. IF6 comprises a family of translation factors that includes both eukaryotic (eIF6) and archeal (aIF6) members. All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved C-terminal extension which is not required for ribosomal binding, and may have an alternative function.
Probab=28.65 E-value=91 Score=22.92 Aligned_cols=33 Identities=12% Similarity=0.240 Sum_probs=25.1
Q ss_pred CEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 24 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 24 n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
|-..-.|+|++++.+++ .++..|||+|..- |+|
T Consensus 152 Nd~g~LvhP~~s~ee~~-~i~d~L~V~v~~g-TvN 184 (220)
T cd00527 152 TNKGGLVHPKTSDEELE-ELSELFKVPVVAG-TVN 184 (220)
T ss_pred eccEEEECCCCCHHHHH-HHHHHhCCcEEEE-EEc
Confidence 33445789999998886 5999999998554 654
No 101
>KOG0715|consensus
Probab=28.03 E-value=41 Score=25.58 Aligned_cols=21 Identities=33% Similarity=0.333 Sum_probs=18.5
Q ss_pred EEEEeCCCCHHHHHHHHHHHh
Q psy6375 27 VFIVHLQANKHHIKAAVKKMY 47 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~lf 47 (86)
++-|+++|+..|||.|+-++=
T Consensus 48 vLgv~~~At~~EIK~Af~~La 68 (288)
T KOG0715|consen 48 VLGVSRNATLSEIKSAFRKLA 68 (288)
T ss_pred hhCcCCCCCHHHHHHHHHHHH
Confidence 588999999999999988764
No 102
>TIGR03380 agmatine_aguA agmatine deiminase. Members of this family are agmatine deiminase (3.5.3.12), as characterized in Pseudomonas aeruginosa and plants. Related deiminases include the peptidyl-arginine deiminase (3.5.3.15) as found in Porphyromonas gingivalis.
Probab=27.88 E-value=58 Score=25.63 Aligned_cols=20 Identities=15% Similarity=0.308 Sum_probs=18.3
Q ss_pred eCCCCHHHHHHHHHHHhCCc
Q psy6375 31 HLQANKHHIKAAVKKMYDIN 50 (86)
Q Consensus 31 ~~~a~K~eIk~ave~lf~Vk 50 (86)
+|+.||.||.+.++..+|++
T Consensus 174 NP~ls~~eIe~~Lk~~LGv~ 193 (357)
T TIGR03380 174 NPHLTKEQIEEKLKDYLGVE 193 (357)
T ss_pred CCCCCHHHHHHHHHHHHCCC
Confidence 56889999999999999976
No 103
>COG4379 Mu-like prophage tail protein gpP [General function prediction only]
Probab=27.67 E-value=86 Score=25.27 Aligned_cols=59 Identities=14% Similarity=0.028 Sum_probs=39.1
Q ss_pred CEEEEEEeCCC----------CHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCCcHHHHHHhh
Q psy6375 24 NTLVFIVHLQA----------NKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 24 n~~~F~V~~~a----------~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~~a~d~a~~~ 83 (86)
.+-.+.||+.| |=.||.+.+.+-||+.|...=+-. ....+-=-++|.+|..|-|..+++
T Consensus 92 dk~gdLVDCSAihP~~~~k~~Tv~qIAekl~~P~Gitv~~~V~~~-~~~~~~~~~~iEpGETa~daL~~i 160 (386)
T COG4379 92 DKAGDLVDCSAIHPQSNVKNMTVLQIAEKLAAPFGITVKWQVLDA-EANPALPKFTIEPGETAWDALTHI 160 (386)
T ss_pred ccccceeeecccCCcchhccchHHHHHHHHhccccceEEEEEecc-ccCCCCceeEcCCcchHHHHHHHH
Confidence 45556677666 677899999999999886543221 112233457888888887765543
No 104
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=27.59 E-value=2e+02 Score=24.55 Aligned_cols=59 Identities=14% Similarity=0.220 Sum_probs=42.1
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCC-Cee--EEEEEcCCCCcHHHHHHhh
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-GKK--KAYVRLARDYDALDVANKI 83 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~-~~K--KA~VtL~~g~~a~d~a~~~ 83 (86)
.+-|+..++++.+..++++.|+. || .|.++....-+. |.. =+||.+....+|.+--..+
T Consensus 205 ~rLfVgnLp~~vteedLk~lFs~-FG-~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~am 266 (612)
T TIGR01645 205 NRIYVASVHPDLSETDIKSVFEA-FG-EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266 (612)
T ss_pred ceEEeecCCCCCCHHHHHHHHhh-cC-CeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHh
Confidence 35788889999999999999997 76 466777665332 212 3899999877765554443
No 105
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=27.57 E-value=1.5e+02 Score=18.05 Aligned_cols=36 Identities=14% Similarity=0.197 Sum_probs=31.8
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
.....|.|.++.+=..+++++....|+.+..++-+-
T Consensus 21 g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f 56 (87)
T cd01763 21 GNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLF 56 (87)
T ss_pred CCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEE
Confidence 468899999999999999999999999998776654
No 106
>PF00226 DnaJ: DnaJ domain; InterPro: IPR001623 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Such a structure is shown in the following schematic representation: +------------+-+-------+-----+-----------+--------------------------------+ | N-terminal | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+ It is thought that the 'J' domain of DnaJ mediates the interaction with the dnaK protein and consists of four helices, the second of which has a charged surface that includes at least one pair of basic residues that are essential for interaction with the ATPase domain of Hsp70. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins [], either together or separately. In yeast, J-domains have been classified into 3 groups; the class III proteins are functionally distinct and do not appear to act as molecular chaperones []. ; GO: 0031072 heat shock protein binding; PDB: 2GUZ_C 2L6L_A 1HDJ_A 2EJ7_A 1FPO_C 2CUG_A 2QSA_A 2OCH_A 3BVO_B 3APQ_A ....
Probab=26.75 E-value=32 Score=19.34 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=15.6
Q ss_pred EEEeCCCCHHHHHHHHHHHh
Q psy6375 28 FIVHLQANKHHIKAAVKKMY 47 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~lf 47 (86)
|-++++++..+|+++...+-
T Consensus 6 Lgl~~~~~~~eik~~y~~l~ 25 (64)
T PF00226_consen 6 LGLPPDASDEEIKKAYRRLS 25 (64)
T ss_dssp CTSTTTSSHHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHhhh
Confidence 34677999999999887753
No 107
>PF01912 eIF-6: eIF-6 family; InterPro: IPR002769 This family includes eukaryotic translation initiation factor 6 (eIF6) as well as presumed archaeal homologues. The assembly of 80S ribosomes requires joining of the 40S and 60S subunits, which is triggered by the formation of an initiation complex on the 40S subunit. This event is rate-limiting for translation, and depends on external stimuli and the status of the cell. Eukaryotic translation initiation factor 6 (eIF6) binds specifically to the free 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit ribosomes []. Furthermore, eIF6 interacts in the cytoplasm with RACK1, a receptor for activated protein kinase C (PKC). RACK1 is a major component of translating ribosomes, which harbour significant amounts of PKC. Loading 60S subunits with eIF6 caused a dose-dependent translational block and impairment of 80S formation, which are reversed by expression of RACK1 and stimulation of PKC in vivo and in vitro. PKC stimulation leads to eIF6 phosphorylation and its release, promoting 80S subunit formation. RACK1 provides a physical and functional link between PKC signalling and ribosome activation.; GO: 0043022 ribosome binding, 0042256 mature ribosome assembly; PDB: 4A19_J 4A1D_J 4A1B_J 4A18_J 1G61_A 2X7N_B 1G62_A.
Probab=26.10 E-value=82 Score=23.06 Aligned_cols=31 Identities=19% Similarity=0.372 Sum_probs=21.2
Q ss_pred EEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeC
Q psy6375 27 VFIVHLQANKHHIKAAVKKMYDINVAKVNTLIR 59 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~ 59 (86)
-..|+|+++-.|+++ ++.+|+|++ .+=|.|.
T Consensus 153 G~LvhP~~s~eEl~~-l~~~l~v~~-~~GTVN~ 183 (199)
T PF01912_consen 153 GGLVHPDASEEELEE-LEELLGVPV-DIGTVNR 183 (199)
T ss_dssp EEEE-TT--HHHHHH-HHHHHTSSE-EE--BTT
T ss_pred EEEECCCCCHHHHHH-HHHHhCCce-eeeeecC
Confidence 467999999999875 999999995 6677764
No 108
>PF13592 HTH_33: Winged helix-turn helix
Probab=26.08 E-value=73 Score=18.23 Aligned_cols=22 Identities=9% Similarity=0.223 Sum_probs=17.9
Q ss_pred CHHHHHHHHHHHhCCceeeEEEe
Q psy6375 35 NKHHIKAAVKKMYDINVAKVNTL 57 (86)
Q Consensus 35 ~K~eIk~ave~lf~VkV~~VnT~ 57 (86)
|=.+|.++|+..|||.. +..++
T Consensus 6 t~~~i~~~I~~~fgv~y-s~~~v 27 (60)
T PF13592_consen 6 TLKEIAAYIEEEFGVKY-SPSGV 27 (60)
T ss_pred cHHHHHHHHHHHHCCEE-cHHHH
Confidence 56789999999999998 55553
No 109
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=25.99 E-value=2.4e+02 Score=22.49 Aligned_cols=58 Identities=12% Similarity=0.154 Sum_probs=42.2
Q ss_pred EEEEEEeCCCCHHHHHHHHHHHhCC-ceeeEEEeeCCCC-eeEEEEEcCCCCcHHHHHHhh
Q psy6375 25 TLVFIVHLQANKHHIKAAVKKMYDI-NVAKVNTLIRPDG-KKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 25 ~~~F~V~~~a~K~eIk~ave~lf~V-kV~~VnT~~~~~~-~KKA~VtL~~g~~a~d~a~~~ 83 (86)
-++..++.+.+..++++.++. ||. .|.+|......++ .+=|+|.+....+|.+....+
T Consensus 397 L~v~NLp~~~tee~L~~lF~~-~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~l 456 (481)
T TIGR01649 397 LHLSNIPLSVSEEDLKELFAE-NGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIAL 456 (481)
T ss_pred EEEecCCCCCCHHHHHHHHHh-cCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHh
Confidence 457788889999999999988 565 8888876543322 346999999877776655443
No 110
>PF07040 DUF1326: Protein of unknown function (DUF1326); InterPro: IPR009758 This family consists of several hypothetical bacterial proteins, which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N terminus. The function of this family is unknown.
Probab=25.69 E-value=1.1e+02 Score=21.86 Aligned_cols=32 Identities=13% Similarity=0.227 Sum_probs=24.8
Q ss_pred hhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCce
Q psy6375 19 KIEDNNTLVFIVHLQANKHHIKAAVKKMYDINV 51 (86)
Q Consensus 19 l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV 51 (86)
+.|.+.+.+..||-+||-.| ++|++++|.=+.
T Consensus 56 ~~eG~~~~~~~IDerAs~~Q-reAL~~I~~G~~ 87 (184)
T PF07040_consen 56 MHEGNWKVALYIDERASDAQ-REALEAIFTGQA 87 (184)
T ss_pred cccCceEEEEEECCCCCHHH-HHHHHHHhcCcc
Confidence 45666799999999999888 567888775544
No 111
>PRK14282 chaperone protein DnaJ; Provisional
Probab=25.63 E-value=46 Score=25.87 Aligned_cols=20 Identities=30% Similarity=0.403 Sum_probs=16.0
Q ss_pred EEEEeCCCCHHHHHHHHHHH
Q psy6375 27 VFIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~l 46 (86)
++-|+++|+..|||+|..++
T Consensus 9 ~lgv~~~a~~~eik~ayr~l 28 (369)
T PRK14282 9 ILGVSRNATQEEIKRAYKRL 28 (369)
T ss_pred hcCCCCCCCHHHHHHHHHHH
Confidence 36678888888898888776
No 112
>PRK14290 chaperone protein DnaJ; Provisional
Probab=25.38 E-value=46 Score=25.84 Aligned_cols=19 Identities=26% Similarity=0.377 Sum_probs=14.3
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++|+..|||+|..++
T Consensus 9 Lgv~~~a~~~eik~ayr~l 27 (365)
T PRK14290 9 LGVDRNASQEDIKKAFREL 27 (365)
T ss_pred cCCCCCCCHHHHHHHHHHH
Confidence 5577788888888877766
No 113
>PRK14295 chaperone protein DnaJ; Provisional
Probab=24.94 E-value=47 Score=26.13 Aligned_cols=20 Identities=35% Similarity=0.376 Sum_probs=17.3
Q ss_pred EEEEeCCCCHHHHHHHHHHH
Q psy6375 27 VFIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~l 46 (86)
++-|+++|+..|||+|..++
T Consensus 14 ~Lgv~~~a~~~eik~ayr~l 33 (389)
T PRK14295 14 VLGVPKDATEAEIKKAYRKL 33 (389)
T ss_pred hcCCCCCCCHHHHHHHHHHH
Confidence 47789999999999998876
No 114
>PRK14299 chaperone protein DnaJ; Provisional
Probab=24.74 E-value=46 Score=25.02 Aligned_cols=19 Identities=37% Similarity=0.396 Sum_probs=13.2
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++|+..|||+|..++
T Consensus 10 Lgv~~~a~~~eik~ayr~l 28 (291)
T PRK14299 10 LGVPKNASQDEIKKAFKKL 28 (291)
T ss_pred cCCCCCCCHHHHHHHHHHH
Confidence 4567777777777776655
No 115
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 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 [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=24.36 E-value=1.4e+02 Score=18.15 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=24.0
Q ss_pred EEEEEEeCCCCHHHHHHHHHHHh------CCceeeEEEe
Q psy6375 25 TLVFIVHLQANKHHIKAAVKKMY------DINVAKVNTL 57 (86)
Q Consensus 25 ~~~F~V~~~a~K~eIk~ave~lf------~VkV~~VnT~ 57 (86)
..+|.++++++..++++.++.+- |..|.++...
T Consensus 4 E~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~ 42 (92)
T PF01250_consen 4 ELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENW 42 (92)
T ss_dssp EEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEE
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEE
Confidence 35789999999999988776653 6677777654
No 116
>PF02963 EcoRI: Restriction endonuclease EcoRI; InterPro: IPR004221 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents restriction endonucleases EcoRI, which requires magnesium as a cofactor. EcoRI recognises the DNA sequence GAATTC and cleaves after G-1 [].; GO: 0000287 magnesium ion binding, 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1ERI_A 1CL8_A 1QRH_A 1QPS_A 1CKQ_A 1QC9_B 1QRI_A 2OXV_A.
Probab=23.96 E-value=62 Score=24.56 Aligned_cols=57 Identities=25% Similarity=0.259 Sum_probs=35.3
Q ss_pred hhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhC---CceeeEEEeeCCC-----------CeeEEEEEcCCC
Q psy6375 17 MKKIEDNNTLVFIVHLQANKHHIKAAVKKMYD---INVAKVNTLIRPD-----------GKKKAYVRLARD 73 (86)
Q Consensus 17 ~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~---VkV~~VnT~~~~~-----------~~KKA~VtL~~g 73 (86)
.+|.++..+++|.-.++..|.+|-.++.+++. ..----|+.+.|+ .|+-..|+=++-
T Consensus 28 ~kL~~eFp~LtF~~r~si~k~eIn~~Lrkid~~lg~tlfv~nssIkPDGGIlevkdd~~~wrvvLVsEaKh 98 (257)
T PF02963_consen 28 KKLEEEFPQLTFRYRKSIKKEEINEALRKIDPELGQTLFVENSSIKPDGGILEVKDDNGNWRVVLVSEAKH 98 (257)
T ss_dssp HHHHHHSTTSEEEEES-EEHHHHHHHHHHH-TTSS---SSTT-EE--TTEEEEEE-TTS-EEEEEEEEEEE
T ss_pred HHHHHhCCCceEEeecceeHHHHHHHHHhcCcccccccccccccccCCCCEEEEEcCCCCeEEEEEEhhhh
Confidence 45667788999999999999999999999873 2221124555564 266666665443
No 117
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=23.90 E-value=2.2e+02 Score=24.00 Aligned_cols=59 Identities=10% Similarity=0.159 Sum_probs=42.6
Q ss_pred CCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCee--EEEEEcCCCCcHHHHHHhh
Q psy6375 23 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKK--KAYVRLARDYDALDVANKI 83 (86)
Q Consensus 23 ~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~K--KA~VtL~~g~~a~d~a~~~ 83 (86)
.+-++=..+.+++-.++++.|++ || .|.+++.+....|.- =|||++....+|......+
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~~-~G-~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~l 119 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFEK-AG-PIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLL 119 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHHh-hC-CEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHc
Confidence 35666678889999999999998 66 677887766544322 3999999877766554443
No 118
>PLN02690 Agmatine deiminase
Probab=23.57 E-value=78 Score=25.12 Aligned_cols=20 Identities=15% Similarity=0.313 Sum_probs=18.4
Q ss_pred eCCCCHHHHHHHHHHHhCCc
Q psy6375 31 HLQANKHHIKAAVKKMYDIN 50 (86)
Q Consensus 31 ~~~a~K~eIk~ave~lf~Vk 50 (86)
+|..||.||.+.+++.||++
T Consensus 186 NP~lsk~~ie~~Lk~~LGv~ 205 (374)
T PLN02690 186 NPHLTKEEIEEELKEYLGVE 205 (374)
T ss_pred CCCCCHHHHHHHHHHHhCCC
Confidence 57899999999999999986
No 119
>COG1035 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]
Probab=23.19 E-value=2.4e+02 Score=22.19 Aligned_cols=44 Identities=14% Similarity=0.102 Sum_probs=35.5
Q ss_pred EEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCCeeEEEEEcCCCC
Q psy6375 29 IVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDY 74 (86)
Q Consensus 29 ~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~~KKA~VtL~~g~ 74 (86)
-+-.+-+-..+++.++..+|+.+..|.-+...+| |..|+++.|.
T Consensus 181 fC~e~f~y~~l~~~l~e~~gvd~~dV~k~di~kG--k~~v~~~dG~ 224 (332)
T COG1035 181 FCMENFSYEGLKKFLEEDLGVDPEDVEKMDIRKG--KFVVELKDGE 224 (332)
T ss_pred ecCCCcCHHHHHHHHHHHhCCCHHHeEEEEeeCc--eEEEEecCCc
Confidence 3445566777999999999999999988877666 7888888873
No 120
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=22.89 E-value=1.7e+02 Score=17.03 Aligned_cols=44 Identities=14% Similarity=0.120 Sum_probs=35.5
Q ss_pred cchhhhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEE
Q psy6375 12 TTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNT 56 (86)
Q Consensus 12 ~TEKs~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT 56 (86)
-|.|+++.+.....+...++-.+++.+|.++.+. -|-++.++..
T Consensus 15 ~~kkal~~l~~G~~l~V~~d~~~a~~di~~~~~~-~G~~~~~~~~ 58 (69)
T cd03420 15 KLKKEIDKLQDGEQLEVKASDPGFARDAQAWCKS-TGNTLISLET 58 (69)
T ss_pred HHHHHHHcCCCCCEEEEEECCccHHHHHHHHHHH-cCCEEEEEEe
Confidence 3778887776555799999999999999999976 5777776654
No 121
>PRK14288 chaperone protein DnaJ; Provisional
Probab=22.77 E-value=67 Score=25.04 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=16.8
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++||-.|||+|..++
T Consensus 9 Lgv~~~As~~eIkkayrkl 27 (369)
T PRK14288 9 LEVEKHSNQETIKKSYRKL 27 (369)
T ss_pred cCCCCCCCHHHHHHHHHHH
Confidence 4588999999999999887
No 122
>PRK13551 agmatine deiminase; Provisional
Probab=22.64 E-value=83 Score=24.81 Aligned_cols=20 Identities=10% Similarity=0.283 Sum_probs=18.3
Q ss_pred eCCCCHHHHHHHHHHHhCCc
Q psy6375 31 HLQANKHHIKAAVKKMYDIN 50 (86)
Q Consensus 31 ~~~a~K~eIk~ave~lf~Vk 50 (86)
+|..||.||.+.++..||++
T Consensus 177 NP~ls~~~ie~~Lk~~LGv~ 196 (362)
T PRK13551 177 NPHLTKEQIEQLLRDYLGVE 196 (362)
T ss_pred CCCCCHHHHHHHHHHHHCCC
Confidence 57889999999999999976
No 123
>PRK10767 chaperone protein DnaJ; Provisional
Probab=22.61 E-value=55 Score=25.37 Aligned_cols=19 Identities=32% Similarity=0.375 Sum_probs=14.5
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++|+..|||+|..++
T Consensus 10 Lgv~~~as~~eik~ayr~l 28 (371)
T PRK10767 10 LGVSRNASEDEIKKAYRKL 28 (371)
T ss_pred cCCCCCCCHHHHHHHHHHH
Confidence 5577788888888887765
No 124
>cd01795 USP48_C USP ubiquitin-specific protease. The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,
Probab=22.56 E-value=1.5e+02 Score=19.91 Aligned_cols=43 Identities=12% Similarity=0.189 Sum_probs=33.6
Q ss_pred hhhhhhcCCEEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEee
Q psy6375 16 AMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58 (86)
Q Consensus 16 s~~l~e~~n~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~ 58 (86)
|++..-..+-.+..|++++|=-+.|.-|...|+|.+.+=+.+.
T Consensus 7 s~r~r~~~~~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~ 49 (107)
T cd01795 7 SMRHRKVRGEKALLVSANQTLKELKIQIMHAFSVAPFDQNLSI 49 (107)
T ss_pred hhhhccCCCCceEEeCccccHHHHHHHHHHHhcCCcccceeee
Confidence 3444333457788899999999999999999999998655544
No 125
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=22.49 E-value=1e+02 Score=20.14 Aligned_cols=20 Identities=20% Similarity=0.360 Sum_probs=17.4
Q ss_pred CCCHHHHHHHHHHHhCCcee
Q psy6375 33 QANKHHIKAAVKKMYDINVA 52 (86)
Q Consensus 33 ~a~K~eIk~ave~lf~VkV~ 52 (86)
-....++++.|++.||++|.
T Consensus 84 CP~~~~~~~~I~~~~gi~VV 103 (107)
T PF08821_consen 84 CPHIDEIKKIIEEKFGIEVV 103 (107)
T ss_pred CCCHHHHHHHHHHHhCCCEe
Confidence 35689999999999999885
No 126
>PRK14276 chaperone protein DnaJ; Provisional
Probab=22.18 E-value=54 Score=25.61 Aligned_cols=20 Identities=30% Similarity=0.335 Sum_probs=16.6
Q ss_pred EEEeCCCCHHHHHHHHHHHh
Q psy6375 28 FIVHLQANKHHIKAAVKKMY 47 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~lf 47 (86)
+-|+++|+..|||+|..++-
T Consensus 10 Lgv~~~a~~~eik~ayr~la 29 (380)
T PRK14276 10 LGVSKDASQDEIKKAYRKLS 29 (380)
T ss_pred hCCCCCCCHHHHHHHHHHHH
Confidence 56788999999999988773
No 127
>PRK14278 chaperone protein DnaJ; Provisional
Probab=22.17 E-value=69 Score=25.04 Aligned_cols=20 Identities=30% Similarity=0.351 Sum_probs=15.0
Q ss_pred EEEEeCCCCHHHHHHHHHHH
Q psy6375 27 VFIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~l 46 (86)
++-|+++|+..|||+|..++
T Consensus 8 iLgv~~~a~~~eik~ayr~l 27 (378)
T PRK14278 8 LLGVSRNASDAEIKRAYRKL 27 (378)
T ss_pred ecCCCCCCCHHHHHHHHHHH
Confidence 35577788888888877776
No 128
>PRK14285 chaperone protein DnaJ; Provisional
Probab=22.06 E-value=70 Score=24.88 Aligned_cols=20 Identities=30% Similarity=0.295 Sum_probs=17.4
Q ss_pred EEEeCCCCHHHHHHHHHHHh
Q psy6375 28 FIVHLQANKHHIKAAVKKMY 47 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~lf 47 (86)
+-|+++|+..|||+|..++.
T Consensus 9 Lgv~~~a~~~eIk~ayr~la 28 (365)
T PRK14285 9 LGLSKGASKDEIKKAYRKIA 28 (365)
T ss_pred cCCCCCCCHHHHHHHHHHHH
Confidence 55789999999999998874
No 129
>PRK14283 chaperone protein DnaJ; Provisional
Probab=22.05 E-value=56 Score=25.48 Aligned_cols=19 Identities=37% Similarity=0.447 Sum_probs=15.8
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++|+..|||+|..++
T Consensus 11 Lgv~~~a~~~eik~ayr~l 29 (378)
T PRK14283 11 LGVDRNADKKEIKKAYRKL 29 (378)
T ss_pred hCCCCCCCHHHHHHHHHHH
Confidence 5688889999999888776
No 130
>PRK14279 chaperone protein DnaJ; Provisional
Probab=22.05 E-value=55 Score=25.76 Aligned_cols=20 Identities=30% Similarity=0.303 Sum_probs=16.5
Q ss_pred EEEEeCCCCHHHHHHHHHHH
Q psy6375 27 VFIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~l 46 (86)
++-|+++|+..|||+|..++
T Consensus 14 ~Lgv~~~a~~~eik~ayr~l 33 (392)
T PRK14279 14 ELGVSSDASAEEIKKAYRKL 33 (392)
T ss_pred hcCCCCCCCHHHHHHHHHHH
Confidence 35688899999999988877
No 131
>PF04371 PAD_porph: Porphyromonas-type peptidyl-arginine deiminase; InterPro: IPR007466 Peptidyl-arginine deiminase (PAD) enzymes catalyse the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia. PAD from Porphyromonas gingivalis (Bacteroides gingivalis) (PPAD) appears to be evolutionarily unrelated to mammalian PAD (IPR004303 from INTERPRO), which is a metalloenzyme. PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologs) []. The predicted catalytic residues in PPAD (Q9RQJ2 from SWISSPROT) are Asp130, Asp187, His236, Asp238 and Cys351 []. These are absolutely conserved with the exception of Asp187 which is absent in two family members. PPAD is also able to catalyse the deimination of free L-arginine, but has primarily peptidyl-arginine specificity. It may have a FMN cofactor [].; PDB: 2Q3U_A 1VKP_A 3H7C_X 3H7K_A 2EWO_K 1ZBR_B 1XKN_A 2JER_B 3HVM_A 2CMU_A.
Probab=21.71 E-value=83 Score=24.21 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=16.4
Q ss_pred eCCCCHHHHHHHHHHHhCCc
Q psy6375 31 HLQANKHHIKAAVKKMYDIN 50 (86)
Q Consensus 31 ~~~a~K~eIk~ave~lf~Vk 50 (86)
++..||.||.+.+++.||++
T Consensus 163 Np~~s~~eie~~L~~~lG~~ 182 (329)
T PF04371_consen 163 NPGLSKAEIEAELKRYLGVE 182 (329)
T ss_dssp STTS-HHHHHHHHHHHHT-S
T ss_pred CccCCHHHHHHHHHHHhCCC
Confidence 56789999999999999986
No 132
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=21.37 E-value=3.4e+02 Score=20.88 Aligned_cols=56 Identities=11% Similarity=0.248 Sum_probs=37.4
Q ss_pred EEEEEEeCCCCHHHHHHHHHHHhCCceeeEEEeeCCCC---eeEEEEEcCCCCcHHHHHHh
Q psy6375 25 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG---KKKAYVRLARDYDALDVANK 82 (86)
Q Consensus 25 ~~~F~V~~~a~K~eIk~ave~lf~VkV~~VnT~~~~~~---~KKA~VtL~~g~~a~d~a~~ 82 (86)
-|+=.++.+++..+|++.|+. || .|.+|.....+.+ .--|+|++..-.+|......
T Consensus 189 l~v~nl~~~~te~~l~~~f~~-~G-~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~ 247 (457)
T TIGR01622 189 LYVGNLHFNITEQELRQIFEP-FG-DIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247 (457)
T ss_pred EEEcCCCCCCCHHHHHHHHHh-cC-CeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHh
Confidence 344456678899999998876 66 4677777654422 23589999887666554433
No 133
>PRK14284 chaperone protein DnaJ; Provisional
Probab=21.13 E-value=59 Score=25.50 Aligned_cols=19 Identities=32% Similarity=0.333 Sum_probs=13.2
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++|+..|||+|..++
T Consensus 7 Lgv~~~a~~~eikkayr~l 25 (391)
T PRK14284 7 LGVSKTASPEEIKKAYRKL 25 (391)
T ss_pred cCCCCCCCHHHHHHHHHHH
Confidence 3466777777777777655
No 134
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=20.93 E-value=2.2e+02 Score=24.28 Aligned_cols=46 Identities=15% Similarity=0.248 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhCCceeeEEEeeCCCC-------eeEEEEEcCCCCcHHHHHHhh
Q psy6375 36 KHHIKAAVKKMYDINVAKVNTLIRPDG-------KKKAYVRLARDYDALDVANKI 83 (86)
Q Consensus 36 K~eIk~ave~lf~VkV~~VnT~~~~~~-------~KKA~VtL~~g~~a~d~a~~~ 83 (86)
+.||++..++ || .|.+|.....+++ -=++||.+....+|..-...|
T Consensus 533 ~eDV~eEC~K-~G-~V~~v~I~~~~~~~~~~~~~~g~VfV~F~~~~~A~~A~~~L 585 (612)
T TIGR01645 533 EGEIREECGK-FG-VVDRVIINFEKQGEEEDAEIIVKIFVEFSDSMEVDRAKAAL 585 (612)
T ss_pred HHHHHHHhhc-Cc-eeEEEEEecCCCCccccccceEEEEEEECCHHHHHHHHHHh
Confidence 4677777777 88 7888887765544 457999999887776655443
No 135
>smart00257 LysM Lysin motif.
Probab=20.84 E-value=1.1e+02 Score=14.18 Aligned_cols=18 Identities=17% Similarity=0.292 Sum_probs=12.8
Q ss_pred EEcCCCCcHHHHHHhhCC
Q psy6375 68 VRLARDYDALDVANKIGI 85 (86)
Q Consensus 68 VtL~~g~~a~d~a~~~g~ 85 (86)
+++.+|+..-.+|.+.|+
T Consensus 2 ~~v~~gdt~~~ia~~~~~ 19 (44)
T smart00257 2 YTVKKGDTLSSIARRYGI 19 (44)
T ss_pred eEeCCCCCHHHHHHHhCC
Confidence 456778777778777664
No 136
>PRK14298 chaperone protein DnaJ; Provisional
Probab=20.67 E-value=60 Score=25.43 Aligned_cols=19 Identities=26% Similarity=0.301 Sum_probs=15.1
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++|+..|||+|..++
T Consensus 11 Lgv~~~a~~~eik~ayr~l 29 (377)
T PRK14298 11 LGLSKDASVEDIKKAYRKL 29 (377)
T ss_pred hCCCCCCCHHHHHHHHHHH
Confidence 5577888888888888765
No 137
>PRK14287 chaperone protein DnaJ; Provisional
Probab=20.34 E-value=65 Score=25.15 Aligned_cols=19 Identities=26% Similarity=0.319 Sum_probs=15.4
Q ss_pred EEEeCCCCHHHHHHHHHHH
Q psy6375 28 FIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 28 F~V~~~a~K~eIk~ave~l 46 (86)
+-|+++|+..|||+|..++
T Consensus 10 Lgv~~~a~~~eik~ayr~l 28 (371)
T PRK14287 10 LGVDRNASVDEVKKAYRKL 28 (371)
T ss_pred cCCCCCCCHHHHHHHHHHH
Confidence 5678888888888888765
No 138
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=20.24 E-value=63 Score=25.91 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=17.4
Q ss_pred EEEEeCCCCHHHHHHHHHHH
Q psy6375 27 VFIVHLQANKHHIKAAVKKM 46 (86)
Q Consensus 27 ~F~V~~~a~K~eIk~ave~l 46 (86)
++-|+++||..|||+|..++
T Consensus 33 vLGV~~~As~~eIKkAYrkl 52 (421)
T PTZ00037 33 VLNLSKDCTTSEIKKAYRKL 52 (421)
T ss_pred HcCCCCCCCHHHHHHHHHHH
Confidence 36689999999999998876
Done!