Query 034307
Match_columns 98
No_of_seqs 108 out of 314
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 12:03:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034307hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00071 40S ribosomal protein 100.0 4.1E-45 8.8E-50 257.8 13.0 94 4-97 4-97 (132)
2 PRK01178 rps24e 30S ribosomal 100.0 3.6E-44 7.9E-49 242.6 11.3 90 7-97 2-91 (99)
3 KOG3424 40S ribosomal protein 100.0 9.7E-44 2.1E-48 247.7 8.5 96 1-98 1-96 (132)
4 COG2004 RPS24A Ribosomal prote 100.0 2.8E-42 6E-47 236.0 10.6 92 6-98 2-93 (107)
5 PF01282 Ribosomal_S24e: Ribos 100.0 1.2E-34 2.5E-39 190.7 7.8 73 24-97 1-73 (84)
6 PF00076 RRM_1: RNA recognitio 73.6 14 0.00031 20.9 5.0 47 34-87 8-55 (70)
7 COG2003 RadC DNA repair protei 69.5 7.1 0.00015 30.1 3.7 34 29-64 174-210 (224)
8 smart00360 RRM RNA recognition 67.6 18 0.00039 19.6 4.3 48 34-87 6-54 (71)
9 PRK14548 50S ribosomal protein 66.4 28 0.0006 22.8 5.5 63 12-83 11-74 (84)
10 PF00276 Ribosomal_L23: Riboso 64.5 20 0.00043 23.4 4.6 46 13-65 11-57 (91)
11 TIGR03636 L23_arch archaeal ri 61.1 35 0.00075 21.9 5.2 59 15-82 7-66 (77)
12 CHL00030 rpl23 ribosomal prote 60.4 29 0.00064 23.0 4.9 46 12-64 10-55 (93)
13 PF12436 USP7_ICP0_bdg: ICP0-b 52.8 18 0.00038 27.5 3.2 55 16-71 171-234 (249)
14 PF04432 FrhB_FdhB_C: Coenzyme 51.0 28 0.00061 24.3 3.8 44 20-64 29-72 (161)
15 PRK05738 rplW 50S ribosomal pr 50.7 35 0.00076 22.4 4.0 45 12-63 10-55 (92)
16 COG2006 Uncharacterized conser 48.9 19 0.00042 28.8 3.0 44 29-74 171-214 (293)
17 COG0245 IspF 2C-methyl-D-eryth 48.7 42 0.00091 24.7 4.5 40 24-65 96-135 (159)
18 PRK06425 histidinol-phosphate 46.7 26 0.00056 26.8 3.3 26 34-60 38-63 (332)
19 PRK00084 ispF 2-C-methyl-D-ery 45.6 37 0.0008 24.8 3.8 37 25-63 99-135 (159)
20 PF08496 Peptidase_S49_N: Pept 44.9 29 0.00063 25.0 3.2 54 21-76 96-150 (155)
21 COG0710 AroD 3-dehydroquinate 43.7 41 0.00088 25.9 3.9 34 25-59 119-152 (231)
22 PF08766 DEK_C: DEK C terminal 43.3 22 0.00047 20.8 1.9 21 32-53 17-37 (54)
23 KOG3439 Protein conjugation fa 43.2 1.1E+02 0.0025 21.3 6.4 62 5-67 30-116 (116)
24 cd00554 MECDP_synthase MECDP_s 39.5 58 0.0013 23.6 4.0 36 24-61 95-130 (153)
25 PRK01688 histidinol-phosphate 38.4 28 0.00061 26.9 2.4 27 34-61 55-81 (351)
26 PF12327 FtsZ_C: FtsZ family, 37.7 33 0.00072 22.4 2.3 50 13-63 23-76 (95)
27 cd02777 MopB_CT_DMSOR-like The 37.5 1.1E+02 0.0024 20.1 4.9 38 39-81 36-73 (127)
28 PRK06959 putative threonine-ph 37.4 38 0.00083 26.2 3.0 25 36-61 54-78 (339)
29 TIGR00151 ispF 2C-methyl-D-ery 37.2 62 0.0013 23.6 3.8 36 24-61 95-130 (155)
30 PF02542 YgbB: YgbB family; I 36.2 38 0.00082 24.7 2.6 27 33-60 104-130 (157)
31 TIGR00608 radc DNA repair prot 36.1 41 0.00089 25.4 2.9 27 24-50 163-192 (218)
32 cd00590 RRM RRM (RNA recogniti 35.6 77 0.0017 17.2 4.2 47 34-87 9-56 (74)
33 KOG3969 Uncharacterized conser 34.2 49 0.0011 26.7 3.1 55 38-93 218-287 (310)
34 PHA01976 helix-turn-helix prot 33.6 19 0.00042 21.1 0.6 24 32-57 38-61 (67)
35 PF09581 Spore_III_AF: Stage I 33.5 27 0.00058 24.8 1.5 24 36-60 164-187 (188)
36 PLN03026 histidinol-phosphate 32.0 52 0.0011 25.8 3.0 26 34-60 84-109 (380)
37 TIGR03576 pyridox_MJ0158 pyrid 31.9 45 0.00098 26.2 2.6 29 32-61 50-78 (346)
38 PRK05387 histidinol-phosphate 31.9 41 0.00089 25.5 2.4 26 35-61 59-84 (353)
39 cd00508 MopB_CT_Fdh-Nap-like T 31.8 1.3E+02 0.0028 19.1 4.4 36 41-81 39-74 (120)
40 COG0299 PurN Folate-dependent 31.6 78 0.0017 24.1 3.7 30 33-62 59-88 (200)
41 PF14560 Ubiquitin_2: Ubiquiti 31.2 1.3E+02 0.0029 18.7 4.7 27 34-61 22-48 (87)
42 PF01996 F420_ligase: F420-0:G 31.1 39 0.00085 25.5 2.1 52 27-80 125-176 (228)
43 PRK04781 histidinol-phosphate 30.9 46 0.001 25.9 2.5 27 34-61 57-83 (364)
44 PRK13815 ribosome-binding fact 30.5 1.8E+02 0.0039 19.9 6.0 44 39-82 10-57 (122)
45 PRK12280 rplW 50S ribosomal pr 30.3 55 0.0012 23.9 2.7 37 11-51 12-48 (158)
46 PTZ00397 macrophage migration 30.2 65 0.0014 21.2 2.9 35 25-60 60-99 (116)
47 COG1888 Uncharacterized protei 30.1 1.4E+02 0.003 20.3 4.4 43 22-66 6-48 (97)
48 PRK14807 histidinol-phosphate 29.8 70 0.0015 24.6 3.4 26 35-61 58-83 (351)
49 cd02794 MopB_CT_DmsA-EC The Mo 29.4 1.6E+02 0.0036 19.1 4.8 39 39-82 32-70 (121)
50 cd01796 DDI1_N DNA damage indu 29.3 67 0.0014 19.4 2.6 26 34-60 18-44 (71)
51 PRK14864 putative biofilm stre 28.9 1.8E+02 0.0039 19.7 4.9 51 25-79 53-103 (104)
52 PF02594 DUF167: Uncharacteris 28.8 93 0.002 19.7 3.3 42 22-63 26-67 (77)
53 PLN02862 2-C-methyl-D-erythrit 28.7 1E+02 0.0022 23.7 3.9 35 25-61 156-190 (216)
54 PRK07392 threonine-phosphate d 28.7 59 0.0013 25.0 2.8 25 36-61 57-81 (360)
55 cd01806 Nedd8 Nebb8-like ubiq 28.3 1E+02 0.0022 18.1 3.2 22 34-56 19-40 (76)
56 PF07338 DUF1471: Protein of u 27.8 1.4E+02 0.003 17.7 4.9 41 37-79 16-56 (56)
57 KOG0113 U1 small nuclear ribon 27.7 1.1E+02 0.0024 24.9 4.2 42 38-85 115-157 (335)
58 cd06397 PB1_UP1 Uncharacterize 27.5 87 0.0019 20.7 3.0 30 34-64 18-47 (82)
59 KOG2116 Protein involved in pl 27.5 97 0.0021 27.8 4.1 31 47-78 494-524 (738)
60 PTZ00191 60S ribosomal protein 27.5 2.4E+02 0.0052 20.3 7.3 62 16-86 76-141 (145)
61 PRK14809 histidinol-phosphate 27.5 79 0.0017 24.2 3.3 24 36-60 65-88 (357)
62 PF04110 APG12: Ubiquitin-like 27.1 22 0.00048 23.4 0.1 33 34-67 55-87 (87)
63 PRK04635 histidinol-phosphate 27.1 58 0.0013 25.0 2.5 25 36-61 60-84 (354)
64 PF02671 PAH: Paired amphipath 27.0 28 0.00061 19.5 0.6 24 33-57 16-39 (47)
65 PRK13817 ribosome-binding fact 26.6 2.1E+02 0.0046 19.4 5.3 44 39-82 10-57 (119)
66 cd02783 MopB_CT_2 The MopB_CT_ 26.6 1.8E+02 0.0039 20.2 4.7 38 39-81 34-71 (156)
67 PRK00024 hypothetical protein; 26.6 67 0.0014 24.2 2.7 27 25-51 170-202 (224)
68 PRK06358 threonine-phosphate d 26.5 71 0.0015 24.7 2.9 25 36-61 54-78 (354)
69 COG4099 Predicted peptidase [G 26.4 57 0.0012 27.0 2.4 25 39-64 254-278 (387)
70 cd02785 MopB_CT_4 The MopB_CT_ 25.7 2E+02 0.0043 18.8 4.9 38 39-81 34-71 (124)
71 PRK08056 threonine-phosphate d 25.6 65 0.0014 24.8 2.5 24 36-60 55-78 (356)
72 PRK08153 histidinol-phosphate 25.5 52 0.0011 25.6 2.0 25 36-61 67-91 (369)
73 PRK10534 L-threonine aldolase; 25.2 52 0.0011 24.8 1.9 27 34-61 32-58 (333)
74 TIGR01141 hisC histidinol-phos 25.2 71 0.0015 24.1 2.6 26 34-60 52-77 (346)
75 cd03033 ArsC_15kD Arsenate Red 25.2 37 0.0008 22.8 0.9 32 18-50 19-50 (113)
76 PRK09105 putative aminotransfe 25.0 71 0.0015 25.0 2.6 24 37-61 79-102 (370)
77 COG1942 Uncharacterized protei 25.0 95 0.0021 19.4 2.8 27 32-59 11-42 (69)
78 PF00046 Homeobox: Homeobox do 25.0 18 0.00039 20.6 -0.6 22 33-56 22-43 (57)
79 PRK02220 4-oxalocrotonate taut 24.7 88 0.0019 17.9 2.5 20 40-60 23-42 (61)
80 cd08059 MPN_prok_mb Mpr1p, Pad 24.7 88 0.0019 19.8 2.7 31 24-59 59-90 (101)
81 PRK06696 uridine kinase; Valid 24.5 42 0.00091 24.4 1.2 19 32-50 29-47 (223)
82 TIGR00013 taut 4-oxalocrotonat 24.2 1E+02 0.0023 17.6 2.7 19 40-59 23-41 (63)
83 PRK01533 histidinol-phosphate 24.1 99 0.0021 24.2 3.3 25 36-61 64-88 (366)
84 COG3561 Phage anti-repressor p 23.9 1.8E+02 0.0039 20.1 4.2 58 32-89 23-80 (110)
85 PRK03967 histidinol-phosphate 23.9 1E+02 0.0022 23.6 3.3 25 36-61 55-79 (337)
86 cd03035 ArsC_Yffb Arsenate Red 23.8 53 0.0012 21.6 1.5 32 18-50 18-49 (105)
87 PF11241 DUF3043: Protein of u 23.8 56 0.0012 24.1 1.7 12 32-43 3-14 (170)
88 PF14464 Prok-JAB: Prokaryotic 23.7 57 0.0012 20.5 1.6 15 29-43 67-82 (104)
89 TIGR01642 U2AF_lg U2 snRNP aux 23.7 1.6E+02 0.0036 23.7 4.6 46 34-85 305-351 (509)
90 PLN02382 probable sucrose-phos 23.6 2.2E+02 0.0047 23.3 5.3 45 19-64 313-360 (413)
91 PRK01964 4-oxalocrotonate taut 23.5 96 0.0021 18.1 2.5 20 40-60 23-42 (64)
92 cd02778 MopB_CT_Thiosulfate-R- 23.5 2E+02 0.0043 18.5 4.2 38 39-81 32-69 (123)
93 TIGR01140 L_thr_O3P_dcar L-thr 23.4 86 0.0019 23.9 2.8 27 33-60 44-70 (330)
94 cd01794 DC_UbP_C dendritic cel 23.3 92 0.002 19.0 2.4 32 22-58 9-40 (70)
95 PF04015 DUF362: Domain of unk 23.0 59 0.0013 23.3 1.7 40 36-75 144-183 (206)
96 PRK10513 sugar phosphate phosp 23.0 1.3E+02 0.0028 22.0 3.6 32 26-61 188-219 (270)
97 cd01793 Fubi Fubi ubiquitin-li 22.9 1.1E+02 0.0023 18.5 2.6 24 33-57 16-39 (74)
98 PRK01310 hypothetical protein; 22.8 2.5E+02 0.0054 18.9 4.6 44 21-64 37-80 (104)
99 PF02680 DUF211: Uncharacteriz 22.7 1.2E+02 0.0027 20.4 3.1 39 22-63 5-43 (95)
100 PF00388 PI-PLC-X: Phosphatidy 22.7 2.4E+02 0.0053 19.0 4.7 54 6-68 43-98 (146)
101 PF01394 Clathrin_propel: Clat 22.7 1E+02 0.0022 16.8 2.3 22 53-79 14-35 (37)
102 cd01813 UBP_N UBP ubiquitin pr 22.6 1.5E+02 0.0032 18.2 3.3 34 21-59 9-42 (74)
103 PF10264 Stork_head: Winged he 22.5 86 0.0019 20.5 2.3 22 29-50 42-63 (80)
104 PF14453 ThiS-like: ThiS-like 22.3 1E+02 0.0022 18.8 2.4 22 43-65 19-40 (57)
105 cd02789 MopB_CT_FmdC-FwdD The 22.3 2.3E+02 0.005 18.3 4.7 38 39-81 33-70 (106)
106 PRK03321 putative aminotransfe 22.2 79 0.0017 24.1 2.4 26 35-61 56-81 (352)
107 cd00491 4Oxalocrotonate_Tautom 22.1 1.2E+02 0.0027 16.9 2.7 19 40-59 22-40 (58)
108 cd01809 Scythe_N Ubiquitin-lik 22.0 1.2E+02 0.0026 17.6 2.7 22 34-56 19-40 (72)
109 smart00760 Bac_DnaA_C Bacteria 21.8 43 0.00094 19.7 0.7 18 38-56 2-19 (60)
110 TIGR01617 arsC_related transcr 21.6 48 0.001 21.9 1.0 32 18-49 18-49 (117)
111 PRK09382 ispDF bifunctional 2- 21.5 1.6E+02 0.0036 23.8 4.2 37 24-62 313-349 (378)
112 cd01804 midnolin_N Ubiquitin-l 21.1 2.1E+02 0.0046 17.5 4.8 24 34-58 20-43 (78)
113 cd00502 DHQase_I Type I 3-dehy 21.0 1.9E+02 0.0042 21.1 4.2 35 21-57 113-147 (225)
114 PF01863 DUF45: Protein of unk 21.0 1.1E+02 0.0024 21.6 2.8 29 44-73 120-148 (205)
115 COG1035 FrhB Coenzyme F420-red 21.0 1.5E+02 0.0033 24.0 3.9 40 23-63 173-212 (332)
116 PF04371 PAD_porph: Porphyromo 20.9 44 0.00095 26.5 0.7 40 34-75 164-205 (329)
117 smart00455 RBD Raf-like Ras-bi 20.8 1.3E+02 0.0027 18.6 2.7 29 33-62 17-45 (70)
118 PF05402 PqqD: Coenzyme PQQ sy 20.7 59 0.0013 19.1 1.1 21 34-55 28-48 (68)
119 cd08619 PI-PLCXDc_plant Cataly 20.6 3.5E+02 0.0076 21.5 5.7 46 26-72 81-126 (285)
120 PRK01261 aroD 3-dehydroquinate 20.5 1.5E+02 0.0033 22.4 3.6 21 35-56 128-148 (229)
121 PRK00950 histidinol-phosphate 20.5 93 0.002 23.6 2.5 26 34-60 67-92 (361)
122 COG0070 GltB Glutamate synthas 20.3 82 0.0018 25.3 2.2 38 53-90 187-226 (301)
123 PRK02731 histidinol-phosphate 20.2 95 0.0021 23.7 2.4 23 38-61 69-91 (367)
124 PHA01632 hypothetical protein 20.2 26 0.00057 21.9 -0.5 53 14-82 8-60 (64)
125 PRK14808 histidinol-phosphate 20.0 1.4E+02 0.003 23.0 3.3 25 35-60 55-82 (335)
126 cd01798 parkin_N amino-termina 20.0 1.2E+02 0.0026 17.9 2.4 25 34-59 17-41 (70)
No 1
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=100.00 E-value=4.1e-45 Score=257.79 Aligned_cols=94 Identities=63% Similarity=1.078 Sum_probs=91.6
Q ss_pred ccEEEEEeeeeeccCcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHH
Q 034307 4 KAITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVES 83 (98)
Q Consensus 4 ~~~~i~i~k~~~N~LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e~ 83 (98)
++|+|+|+++++||||+|+||+|+|+|||.|||||+||+++||++|+|+|+++|||++|+|+||+|+|+|||+||||.|+
T Consensus 4 ~~~~ir~rk~~~NpLL~RkE~~~~v~Hpg~~TpSr~eirekLA~~~~v~d~~~Vvv~~~~T~fG~g~StG~a~IYds~e~ 83 (132)
T PTZ00071 4 AEFTVRTRKFLVNPLLNRKQFVVEVLHPGKGTVSKKDIKEKLAKQYKVADARTIVLFGFKTKFGGGKTTGFGLIYDNLAA 83 (132)
T ss_pred ccEEEEEeeeeeccCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHhCCCCCCEEEEEccEecCCCceEEEEEEEECCHHH
Confidence 36999999999999999999999999999999999999999999999669999999999999999999999999999999
Q ss_pred HHhcCcceeeeccC
Q 034307 84 AKKFEPKYRLIRVI 97 (98)
Q Consensus 84 ~kk~Epk~~l~Rn~ 97 (98)
|++|||+|+|.||+
T Consensus 84 ~kk~Epk~~l~Rng 97 (132)
T PTZ00071 84 LKKFEPKYRLIRLG 97 (132)
T ss_pred HHhhCchheeeecC
Confidence 99999999999996
No 2
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=100.00 E-value=3.6e-44 Score=242.58 Aligned_cols=90 Identities=38% Similarity=0.599 Sum_probs=88.2
Q ss_pred EEEEeeeeeccCcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHHHHh
Q 034307 7 TIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVESAKK 86 (98)
Q Consensus 7 ~i~i~k~~~N~LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e~~kk 86 (98)
.|.|.++++||||+|||++|+|.|||+|||||+||+++||++|+ +|+++|||++|+|+||+|+|+|||+||||.|+|++
T Consensus 2 ei~I~~~~~N~LL~Rke~~~~v~h~g~~tpsr~eirekLa~~~~-~~~~~vvv~~~~t~fG~g~s~G~a~IYds~e~~kk 80 (99)
T PRK01178 2 EIKIISDKENPLLGRREIKFEVYHEGSATPSRKDVRKKLAAMLN-ADKELVVVRKIKTEYGMGKSKGYAKVYDDKERARK 80 (99)
T ss_pred cEEEEEeeecCCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHHC-cCCCEEEEEccCccCCCceEEEEEEEECCHHHHHh
Confidence 68899999999999999999999999999999999999999999 69999999999999999999999999999999999
Q ss_pred cCcceeeeccC
Q 034307 87 FEPKYRLIRVI 97 (98)
Q Consensus 87 ~Epk~~l~Rn~ 97 (98)
|||+|+|.||+
T Consensus 81 ~Epk~~l~Rn~ 91 (99)
T PRK01178 81 IEPKYILERNK 91 (99)
T ss_pred hCchheeeecC
Confidence 99999999996
No 3
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.7e-44 Score=247.69 Aligned_cols=96 Identities=77% Similarity=1.202 Sum_probs=92.7
Q ss_pred CCCccEEEEEeeeeeccCcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCC
Q 034307 1 MADKAITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDS 80 (98)
Q Consensus 1 m~~~~~~i~i~k~~~N~LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds 80 (98)
|+| +|||+|+++++|+||+|+|++++|+|||.|+||++||+||||+||++ ++|.|+||+|+|+||+|+|+|||+||||
T Consensus 1 ~~~-~vtirtrk~~tNrLL~RKqmvvdvlHPG~a~vsK~EirEKla~mYkt-~~d~V~vfgfrt~~GggkstgfalIYds 78 (132)
T KOG3424|consen 1 MSD-AVTIRTRKFMTNRLLSRKQMVVDVLHPGKANVSKTEIREKLAKMYKT-TPDAVFVFGFRTHFGGGKSTGFALIYDS 78 (132)
T ss_pred CCc-cEEEehhhhhhhhhhhhhheeEEEecCCCCCCCHHHHHHHHHHHhcC-CcceEEEEEeeeccCCcccceeeeeeeh
Confidence 555 89999999999999999999999999999999999999999999994 9999999999999999999999999999
Q ss_pred HHHHHhcCcceeeeccCC
Q 034307 81 VESAKKFEPKYRLIRVIN 98 (98)
Q Consensus 81 ~e~~kk~Epk~~l~Rn~~ 98 (98)
.|.+++|||+|+|+|++.
T Consensus 79 ve~akkfEpkyrl~r~gl 96 (132)
T KOG3424|consen 79 VEYAKKFEPKYRLVRLGL 96 (132)
T ss_pred HHHHHhcCcceeeeeccc
Confidence 999999999999999863
No 4
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-42 Score=235.97 Aligned_cols=92 Identities=42% Similarity=0.604 Sum_probs=89.9
Q ss_pred EEEEEeeeeeccCcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHHHH
Q 034307 6 ITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVESAK 85 (98)
Q Consensus 6 ~~i~i~k~~~N~LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e~~k 85 (98)
++|+|.++++||||+|||+.|+|+|+|++||||+||+++||++|| +|+++|+|++|+|+||+|+|+|||+||||.+.|+
T Consensus 2 ~ei~I~~~r~NpLL~RkEi~~~v~h~g~~TPSr~evrekla~~l~-~d~e~VvV~~ikt~fG~~~s~g~akIY~s~e~~~ 80 (107)
T COG2004 2 MEIKILEKRDNPLLKRKEIVFVVYHEGSPTPSRKEVREKLAAMLG-ADKELVVVDYIKTEFGKGRSKGYAKIYDSVERAK 80 (107)
T ss_pred ceEEeehcccCccccceEEEEEEEeCCCCCCCHHHHHHHHHHHHC-CCcceEEEEehhhhcCCcceeEEEEEECCHHHHH
Confidence 689999999999999999999999999999999999999999999 5999999999999999999999999999999999
Q ss_pred hcCcceeeeccCC
Q 034307 86 KFEPKYRLIRVIN 98 (98)
Q Consensus 86 k~Epk~~l~Rn~~ 98 (98)
+|||+|+|.||++
T Consensus 81 ~iEp~yiL~Rn~~ 93 (107)
T COG2004 81 KIEPEYILERNGG 93 (107)
T ss_pred hcCcceEEEeccc
Confidence 9999999999963
No 5
>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=100.00 E-value=1.2e-34 Score=190.70 Aligned_cols=73 Identities=59% Similarity=0.955 Sum_probs=68.2
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHHHHhcCcceeeeccC
Q 034307 24 FVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVESAKKFEPKYRLIRVI 97 (98)
Q Consensus 24 i~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e~~kk~Epk~~l~Rn~ 97 (98)
|+|+|.|+|+|||||+||+++||++||+ |+++|||++|+|+||+++|+|||+||||.|+|+++||+|+|.||+
T Consensus 1 ~~~~v~h~g~~Tpsr~ei~~klA~~~~~-~~~~ivv~~~~t~fG~~~s~g~a~IYd~~e~~kk~Ep~~~l~R~~ 73 (84)
T PF01282_consen 1 MVFEVLHPGKPTPSRKEIREKLAAMLNV-DPDLIVVFGIKTEFGGGKSTGFAKIYDSAEALKKFEPKYRLKRNG 73 (84)
T ss_dssp EEEEEE-SSSSS--HHHHHHHHHHHHTS-TGCCEEEEEEEESSSSSEEEEEEEEESSHHHHHHHSTHHHHHHTT
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHhCC-CCCeEEEeccEecCCCceEEEEEEEeCCHHHHHHhCcHHHhHhcC
Confidence 6899999999999999999999999996 999999999999999999999999999999999999999999994
No 6
>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=73.60 E-value=14 Score=20.90 Aligned_cols=47 Identities=26% Similarity=0.495 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHHhc
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLI-YDSVESAKKF 87 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~I-Yds~e~~kk~ 87 (98)
...+..||++.+.. +|. - ..+ .+.+. +.+.+.|+|.| |+|.+.+++.
T Consensus 8 ~~~t~~~l~~~f~~-~g~-i---~~~-~~~~~-~~~~~~~~a~V~F~~~~~a~~a 55 (70)
T PF00076_consen 8 PDVTEEELRDFFSQ-FGK-I---ESI-KVMRN-SSGKSKGYAFVEFESEEDAEKA 55 (70)
T ss_dssp TTSSHHHHHHHHHT-TST-E---EEE-EEEEE-TTSSEEEEEEEEESSHHHHHHH
T ss_pred CcCCHHHHHHHHHH-hhh-c---ccc-ccccc-ccccccceEEEEEcCHHHHHHH
Confidence 45677899988887 662 2 222 22222 67777777766 7777777653
No 7
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=69.53 E-value=7.1 Score=30.08 Aligned_cols=34 Identities=21% Similarity=0.301 Sum_probs=27.5
Q ss_pred EcC-CCCCCCHHHH--HHHHHhHcCCCCCCeEEEeceee
Q 034307 29 LHP-GRANVSKAEL--KEKLARMYDVRDANAIFVFKFRT 64 (98)
Q Consensus 29 ~h~-~~~TPsr~ei--~~klA~~~~v~~~~~ivV~~~~t 64 (98)
.|| |.+|||++|+ .++|++..+. -+..+++.+-.
T Consensus 174 NHPSGd~~PS~aD~~iT~rl~~a~~l--l~I~vLDHiIi 210 (224)
T COG2003 174 NHPSGDPTPSRADILITERLKEAGKL--LGIRLLDHIII 210 (224)
T ss_pred cCCCCCCCcCHHHHHHHHHHHHHHHh--cCceeeeeEEe
Confidence 688 5689999986 6888888884 67888888877
No 8
>smart00360 RRM RNA recognition motif.
Probab=67.61 E-value=18 Score=19.65 Aligned_cols=48 Identities=27% Similarity=0.547 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHHhc
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLI-YDSVESAKKF 87 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~I-Yds~e~~kk~ 87 (98)
...+..+|++.+. .+| +...+ .+......+.+.|+|.| |.+.+.++..
T Consensus 6 ~~~~~~~l~~~f~-~~g--~v~~~---~i~~~~~~~~~~~~a~v~f~~~~~a~~a 54 (71)
T smart00360 6 PDVTEEELRELFS-KFG--KIESV---RLVRDKDTGKSKGFAFVEFESEEDAEKA 54 (71)
T ss_pred cccCHHHHHHHHH-hhC--CEeEE---EEEeCCCCCCCCceEEEEeCCHHHHHHH
Confidence 3457788888775 566 12222 22233446677888887 6777777653
No 9
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=66.37 E-value=28 Score=22.77 Aligned_cols=63 Identities=14% Similarity=0.261 Sum_probs=44.0
Q ss_pred eeeeccCcce-eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHH
Q 034307 12 KFMTNRLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVES 83 (98)
Q Consensus 12 k~~~N~LL~R-kEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e~ 83 (98)
.++...|+.+ .++.|.| .+..++.||++.+-++||| ...-|..+.+. .+.-.+|....+..++
T Consensus 11 TEK~~~~~e~~n~y~F~V----~~~anK~eIK~AvE~lf~V---kV~~VnT~~~~--~~~KKA~V~L~~g~~A 74 (84)
T PRK14548 11 TEKAMNLIEKENKLTFIV----DRRATKPDIKRAVEELFDV---KVEKVNTLITP--KGEKKAYVKLAEEYDA 74 (84)
T ss_pred CHHHHHHHHhCCEEEEEE----CCCCCHHHHHHHHHHHhCC---ceEEEEeEEcC--CCcEEEEEEeCCCCcH
Confidence 4455566664 7888885 3567899999999999997 56666666665 4455566666555443
No 10
>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=64.48 E-value=20 Score=23.37 Aligned_cols=46 Identities=24% Similarity=0.362 Sum_probs=32.1
Q ss_pred eeeccCcce-eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeec
Q 034307 13 FMTNRLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTH 65 (98)
Q Consensus 13 ~~~N~LL~R-kEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~ 65 (98)
++...++.. .++.|.|. ...++.||++.|-+.||| ...-|..+...
T Consensus 11 eKs~~~~~~~n~~tF~V~----~~atK~~Ik~aie~iy~V---~V~~Vnt~~~~ 57 (91)
T PF00276_consen 11 EKSMKLLENPNQYTFEVD----PRATKTEIKEAIEKIYGV---KVKKVNTMNYP 57 (91)
T ss_dssp HHHHHHHHHSSEEEEEET----TTSTHHHHHHHHHHHHTS---EEEEEEEEEET
T ss_pred HhHHHhhhcCCEEEEEEe----CCCCHHHHHHHHHhhcCC---CeeEEEEeEeC
Confidence 334445555 78888852 457799999999999997 45555555554
No 11
>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=61.11 E-value=35 Score=21.91 Aligned_cols=59 Identities=15% Similarity=0.290 Sum_probs=39.1
Q ss_pred eccCcce-eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHH
Q 034307 15 TNRLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVE 82 (98)
Q Consensus 15 ~N~LL~R-kEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e 82 (98)
...|+.+ .++.|.|.. ..+|.||++.+-++||| ...-|..+... ++.-.+|....+..+
T Consensus 7 s~~~~e~~n~y~F~V~~----~anK~eIK~avE~lf~V---kV~~Vnt~~~~--~~~KKA~VtL~~g~~ 66 (77)
T TIGR03636 7 AMNLIEKENKLTFIVDR----KATKGDIKRAVEKLFDV---KVEKVNTLITP--RGEKKAYVKLAEEYA 66 (77)
T ss_pred HHHHHHhCCEEEEEECC----CCCHHHHHHHHHHHhCC---ceEEEEeEEcC--CCceEEEEEECCCCc
Confidence 3445554 688888644 46799999999999997 45555555554 344555665555433
No 12
>CHL00030 rpl23 ribosomal protein L23
Probab=60.45 E-value=29 Score=23.04 Aligned_cols=46 Identities=28% Similarity=0.375 Sum_probs=33.7
Q ss_pred eeeeccCcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceee
Q 034307 12 KFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRT 64 (98)
Q Consensus 12 k~~~N~LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t 64 (98)
.++...|+...++.|.|. ...++.||++.+-++|+| ...-|..+.+
T Consensus 10 TEKs~~l~e~n~y~F~V~----~~anK~eIK~avE~lf~V---kV~~VNt~~~ 55 (93)
T CHL00030 10 TDKSIRLLEKNQYTFDVD----SGSTKTEIKHWIELFFGV---KVIAVNSHRL 55 (93)
T ss_pred CHHHHHhhHCCEEEEEEC----CCCCHHHHHHHHHHHhCC---eEEEEEEEEc
Confidence 445556667788998864 456799999999999997 4555555544
No 13
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=52.82 E-value=18 Score=27.52 Aligned_cols=55 Identities=22% Similarity=0.250 Sum_probs=32.3
Q ss_pred ccCcceeEEEEEEEcCC---------CCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEE
Q 034307 16 NRLLSRKQFVIDVLHPG---------RANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKS 71 (98)
Q Consensus 16 N~LL~RkEi~~~v~h~~---------~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s 71 (98)
+-|++|.+|.|.=.+.. ...-+=.|+.+++|+.+|+ ||+.+=++......|...+
T Consensus 171 ~~l~nrv~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~~-dP~~lr~~~~~~~~~~P~~ 234 (249)
T PF12436_consen 171 DFLYNRVEVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLNV-DPEHLRFFTVNPYSGKPKS 234 (249)
T ss_dssp HHHHHEEEEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHTS--GGGEEEE---TTS-S---
T ss_pred HHHhCeEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHCC-ChHHEEEEEeccCCCCCCC
Confidence 34566776666533221 1234568999999999997 9999999998886666653
No 14
>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=50.97 E-value=28 Score=24.35 Aligned_cols=44 Identities=18% Similarity=0.262 Sum_probs=33.8
Q ss_pred ceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceee
Q 034307 20 SRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRT 64 (98)
Q Consensus 20 ~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t 64 (98)
.+.++.+.|--+-.++||..-+++.|+..+++ +++.|.=..++.
T Consensus 29 ~~~~~~~~igl~C~g~~s~~~~~~~l~~~~~~-~~~~v~~~~~r~ 72 (161)
T PF04432_consen 29 NRDEIVYTIGLFCHGVPSPKKLRKYLEEQLGI-KPDDVKKFDFRD 72 (161)
T ss_pred cCcceEEEEeEECCCCCCHHHHHHHHHHHhCC-ChhheeEEEEeC
Confidence 33335566666678999999999999999996 877776667766
No 15
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=50.68 E-value=35 Score=22.38 Aligned_cols=45 Identities=18% Similarity=0.378 Sum_probs=31.0
Q ss_pred eeeeccCcc-eeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEecee
Q 034307 12 KFMTNRLLS-RKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFR 63 (98)
Q Consensus 12 k~~~N~LL~-RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~ 63 (98)
.++.+.|+. ..++.|.| .+..++.||++.+-++|+| + .+=|..+.
T Consensus 10 TEKs~~~~e~~n~~~F~V----~~~a~K~eIK~aie~lf~V-k--V~~VnT~~ 55 (92)
T PRK05738 10 TEKSTLLMEKQNKYVFEV----APDATKPEIKAAVEKLFGV-K--VESVNTLN 55 (92)
T ss_pred CHHHHHhHHhCCEEEEEE----CCCCCHHHHHHHHHHHcCC-c--eeEEEEEE
Confidence 344455666 56888875 3567899999999999998 4 34444443
No 16
>COG2006 Uncharacterized conserved protein [Function unknown]
Probab=48.88 E-value=19 Score=28.79 Aligned_cols=44 Identities=20% Similarity=0.234 Sum_probs=36.7
Q ss_pred EcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEE
Q 034307 29 LHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGF 74 (98)
Q Consensus 29 ~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~ 74 (98)
.|.+.+ .+..-.+.||..+.+-.|++.+++++.-.=|.|-+.|-
T Consensus 171 ~h~~~~--~~~~Fg~mlvei~~~~~P~ltI~Dgi~G~egNGP~~G~ 214 (293)
T COG2006 171 WHMEEG--DRDRFGEMLVEIYLVVKPDLTIMDGIIGMEGNGPSGGT 214 (293)
T ss_pred cchhcC--chHHHHHHHHHHHhhcCCcEEEEeeeEecccCCCCCCc
Confidence 454444 67788999999999999999999999998888887763
No 17
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=48.65 E-value=42 Score=24.66 Aligned_cols=40 Identities=15% Similarity=0.242 Sum_probs=30.9
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeec
Q 034307 24 FVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTH 65 (98)
Q Consensus 24 i~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~ 65 (98)
+.+...-| +=.|-+.++++.||+.+++ +++.|-|.-=.|+
T Consensus 96 ~tii~~~P-K~~P~~~amr~~ia~~L~i-~~~~invKatT~E 135 (159)
T COG0245 96 ITIIAQRP-KLGPYREAMRANIAELLGI-PVDRINVKATTTE 135 (159)
T ss_pred EEEEEecC-cccchHHHHHHHHHHHhCC-CchheEEEEeccC
Confidence 34444454 7789999999999999995 9999988754443
No 18
>PRK06425 histidinol-phosphate aminotransferase; Validated
Probab=46.73 E-value=26 Score=26.80 Aligned_cols=26 Identities=4% Similarity=0.089 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
|-|...+++++||+.+++ +++.|++.
T Consensus 38 p~~~~~~lr~~ia~~~~~-~~~~I~it 63 (332)
T PRK06425 38 PEISYTDIEDQIKIYTQG-LKIKVLIG 63 (332)
T ss_pred cCcCHHHHHHHHHHHhCC-CcceEEEC
Confidence 567789999999999997 88888764
No 19
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=45.57 E-value=37 Score=24.82 Aligned_cols=37 Identities=14% Similarity=0.160 Sum_probs=28.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEecee
Q 034307 25 VIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFR 63 (98)
Q Consensus 25 ~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~ 63 (98)
.+....| +=.|-+.++++.||+.+++ +++.|-|.-=.
T Consensus 99 tii~e~P-Ki~p~~~~m~~~la~~L~i-~~~~V~iKatT 135 (159)
T PRK00084 99 TIIAQRP-KMAPHIEEMRANIAEDLGI-PLDDVNVKATT 135 (159)
T ss_pred EEEcCCC-cchHHHHHHHHHHHHHhCC-CcceEEEEEec
Confidence 3444444 6689999999999999996 88888876533
No 20
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=44.94 E-value=29 Score=25.02 Aligned_cols=54 Identities=20% Similarity=0.381 Sum_probs=37.0
Q ss_pred eeEEEEEEEcCCCCCCC-HHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEE
Q 034307 21 RKQFVIDVLHPGRANVS-KAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGL 76 (98)
Q Consensus 21 RkEi~~~v~h~~~~TPs-r~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~ 76 (98)
.+.-.|.+.+.|.---| -+.+|+++.+.+.+++|+==||-.+.+ |||.-.||+.
T Consensus 96 ~~~r~~VldF~Gdi~A~~v~~LReeisail~~a~~~DeV~~rLES--~GG~Vh~YGL 150 (155)
T PF08496_consen 96 PKPRLFVLDFKGDIKASEVESLREEISAILSVATPEDEVLVRLES--PGGMVHGYGL 150 (155)
T ss_pred CCCeEEEEecCCCccHHHHHHHHHHHHHHHHhCCCCCeEEEEEec--CCceeeccch
Confidence 45556667776543222 356788888888877776666656666 9999999875
No 21
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=43.66 E-value=41 Score=25.87 Aligned_cols=34 Identities=24% Similarity=0.279 Sum_probs=27.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 034307 25 VIDVLHPGRANVSKAELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 25 ~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV 59 (98)
.+.=+|.-..|||.+++.+.+.+|... ++|.+=|
T Consensus 119 vI~SyH~F~~TP~~~~i~~~l~km~~~-~aDivKi 152 (231)
T COG0710 119 VIVSYHDFEKTPPLEEIIERLDKMESL-GADIVKI 152 (231)
T ss_pred EEEEeccCCCCCcHHHHHHHHHHHHhh-CCCeEEE
Confidence 344489889999999999999999994 7776544
No 22
>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=43.31 E-value=22 Score=20.82 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=14.4
Q ss_pred CCCCCCHHHHHHHHHhHcCCCC
Q 034307 32 GRANVSKAELKEKLARMYDVRD 53 (98)
Q Consensus 32 ~~~TPsr~ei~~klA~~~~v~~ 53 (98)
+-.|.|.++|++.|.+.||+ |
T Consensus 17 dl~~vT~k~vr~~Le~~~~~-d 37 (54)
T PF08766_consen 17 DLDTVTKKQVREQLEERFGV-D 37 (54)
T ss_dssp -GGG--HHHHHHHHHHH-SS--
T ss_pred CHhHhhHHHHHHHHHHHHCC-C
Confidence 45688999999999999996 5
No 23
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=43.20 E-value=1.1e+02 Score=21.34 Aligned_cols=62 Identities=16% Similarity=0.318 Sum_probs=42.6
Q ss_pred cEEEEEeeeeeccCcceeEEEEE-------------------------EEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 034307 5 AITIRTRKFMTNRLLSRKQFVID-------------------------VLHPGRANVSKAELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 5 ~~~i~i~k~~~N~LL~RkEi~~~-------------------------v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV 59 (98)
.|+|+.+..-.=|+|..+-+.+. ++--..-.||-.++-+.|-..|++ |..+|+=
T Consensus 30 kV~i~l~aiG~~PilK~~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sFAPsPDq~v~~Ly~cf~~-d~~Lvl~ 108 (116)
T KOG3439|consen 30 KVQIRLRAIGDAPILKKSKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFGT-DGKLVLN 108 (116)
T ss_pred eEEEEEeccCCCcceecceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCccCCCchhHHHHHHHhcCC-CCEEEEE
Confidence 56666666666666655544433 222235689999999999999995 8888887
Q ss_pred eceeecCC
Q 034307 60 FKFRTHFG 67 (98)
Q Consensus 60 ~~~~t~fG 67 (98)
+.+...||
T Consensus 109 Yc~s~A~G 116 (116)
T KOG3439|consen 109 YCISVAWG 116 (116)
T ss_pred EeeecccC
Confidence 77777666
No 24
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=39.53 E-value=58 Score=23.63 Aligned_cols=36 Identities=11% Similarity=0.251 Sum_probs=27.9
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 24 FVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 24 i~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
+.+....| +=.|=|.++++.||+.+++ +.+.|-|.-
T Consensus 95 ~tii~e~P-Ki~p~~~~m~~~ls~~L~~-~~~~V~iKa 130 (153)
T cd00554 95 ITIIAERP-KISPYREAMRANLAELLGI-PPSRVNIKA 130 (153)
T ss_pred EEEEecCC-cchHHHHHHHHHHHHHhCC-CCceEEEEE
Confidence 34444454 6788999999999999996 888887753
No 25
>PRK01688 histidinol-phosphate aminotransferase; Provisional
Probab=38.41 E-value=28 Score=26.87 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
+-|.-.++++++|+.+|+ +++.|++.+
T Consensus 55 p~~~~~~l~~~~a~~~g~-~~~~I~~~~ 81 (351)
T PRK01688 55 PECQPKAVIENYAAYAGV-KPEQVLVSR 81 (351)
T ss_pred CCCChHHHHHHHHHHhCC-CHHHEEEcC
Confidence 455668999999999997 999988754
No 26
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=37.73 E-value=33 Score=22.35 Aligned_cols=50 Identities=18% Similarity=0.246 Sum_probs=27.1
Q ss_pred eeeccCcceeEE----EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEecee
Q 034307 13 FMTNRLLSRKQF----VIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFR 63 (98)
Q Consensus 13 ~~~N~LL~RkEi----~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~ 63 (98)
-..||||+ ..+ .+-|.-.+++.++-.|+.+.+-......+++.-+++|..
T Consensus 23 Al~spLl~-~~i~~A~~vLvni~~~~d~~l~ev~~~~~~i~~~~~~~a~ii~G~~ 76 (95)
T PF12327_consen 23 ALNSPLLD-VDIKGAKGVLVNITGGPDLSLSEVNEAMEIIREKADPDANIIWGAS 76 (95)
T ss_dssp HHTSTTST-S-GGG-SEEEEEEEE-TTS-HHHHHHHHHHHHHHSSTTSEEEEEEE
T ss_pred HHhCcccc-CChHHhceEEEEEEcCCCCCHHHHHHHHHHHHHHhhcCceEEEEEE
Confidence 35789988 443 222333357889998888766554322345555555543
No 27
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=37.52 E-value=1.1e+02 Score=20.14 Aligned_cols=38 Identities=16% Similarity=0.187 Sum_probs=29.4
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCH
Q 034307 39 AELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSV 81 (98)
Q Consensus 39 ~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~ 81 (98)
-+|-.+.|+.+|+.+.|.|.|.+ +.|...+.|+|-++.
T Consensus 36 v~i~p~dA~~lgi~~Gd~V~v~s-----~~g~i~~~v~i~~~v 73 (127)
T cd02777 36 VWINPLDAAARGIKDGDIVRVFN-----DRGAVLAGARVTDRI 73 (127)
T ss_pred EEECHHHHHHcCCCCCCEEEEEc-----CCeEEEEEEEECCCc
Confidence 55666889999998899998774 456788888886663
No 28
>PRK06959 putative threonine-phosphate decarboxylase; Provisional
Probab=37.44 E-value=38 Score=26.17 Aligned_cols=25 Identities=24% Similarity=0.256 Sum_probs=19.4
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
|. .+++++||+.+++.+++.|++.+
T Consensus 54 ~~-~~L~~~ia~~~~~~~~~~I~i~~ 78 (339)
T PRK06959 54 DD-DGLAACAARYYGAPDAAHVLPVA 78 (339)
T ss_pred ch-HHHHHHHHHHhCCCCcccEEECc
Confidence 45 89999999999984457777643
No 29
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=37.19 E-value=62 Score=23.56 Aligned_cols=36 Identities=14% Similarity=0.235 Sum_probs=27.5
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 24 FVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 24 i~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
+.+....| +=.|=|.++++.||+.+++ +++.|-|.-
T Consensus 95 ~tii~e~P-Ki~p~~~~m~~~la~~L~~-~~~~V~iKa 130 (155)
T TIGR00151 95 ITIIAQRP-KLLPHIPAMRENIAELLGI-PLDSVNVKA 130 (155)
T ss_pred EEEEcCCC-cchHHHHHHHHHHHHHhCC-CcceEEEEE
Confidence 34444444 6688999999999999996 888887754
No 30
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=36.21 E-value=38 Score=24.69 Aligned_cols=27 Identities=11% Similarity=0.348 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 33 RANVSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 33 ~~TPsr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
+=.|=+.++++.||+.+++ +++.|-|.
T Consensus 104 Ki~p~~~~m~~~la~~L~~-~~~~V~iK 130 (157)
T PF02542_consen 104 KISPYRPAMRENLAKLLGI-PPDRVNIK 130 (157)
T ss_dssp TTGGGHHHHHHHHHHHHTS--GGGEEEE
T ss_pred ccHHHHHHHHHHHHHHhCC-CcceEEEE
Confidence 6689999999999999996 98888775
No 31
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.06 E-value=41 Score=25.37 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=17.1
Q ss_pred EEEEEEcC-CCCCCCHHHHH--HHHHhHcC
Q 034307 24 FVIDVLHP-GRANVSKAELK--EKLARMYD 50 (98)
Q Consensus 24 i~~~v~h~-~~~TPsr~ei~--~klA~~~~ 50 (98)
+.+.=.|| |.++||++|+. ++|.+..+
T Consensus 163 vIlaHNHPSG~~~PS~~Di~~T~~l~~a~~ 192 (218)
T TIGR00608 163 LILAHNHPSGEPSPSQEDILITERLRKAAE 192 (218)
T ss_pred EEEEeecCCCCCCCCHHHHHHHHHHHHHHH
Confidence 33444688 46899999975 34444433
No 32
>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=35.62 E-value=77 Score=17.16 Aligned_cols=47 Identities=26% Similarity=0.506 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHHhc
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLI-YDSVESAKKF 87 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~I-Yds~e~~kk~ 87 (98)
...+..+|++.++...++ ..+.+. ....+ ...|+|.| |.|.+.++..
T Consensus 9 ~~~~~~~i~~~~~~~g~i---~~~~~~--~~~~~--~~~~~~~v~f~s~~~a~~a 56 (74)
T cd00590 9 PDVTEEDLRELFSKFGKV---ESVRIV--RDKDT--KSKGFAFVEFEDEEDAEKA 56 (74)
T ss_pred CccCHHHHHHHHHhcCCE---EEEEEe--eCCCC--CcceEEEEEECCHHHHHHH
Confidence 346788999998886332 222222 22222 55777777 6888776543
No 33
>KOG3969 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.16 E-value=49 Score=26.71 Aligned_cols=55 Identities=18% Similarity=0.406 Sum_probs=42.8
Q ss_pred HHHHHHHHHhHcCCCCCCeEEEe---------------ceeecCCCCEEEEEEEEeCCHHHHHhcCcceee
Q 034307 38 KAELKEKLARMYDVRDANAIFVF---------------KFRTHFGGGKSTGFGLIYDSVESAKKFEPKYRL 93 (98)
Q Consensus 38 r~ei~~klA~~~~v~~~~~ivV~---------------~~~t~fG~~~s~g~a~IYds~e~~kk~Epk~~l 93 (98)
|..+++.+...|++ ++|.+.++ +++-.-|.|.+.|.|+.-|+.=..-.+-|+|--
T Consensus 218 r~k~~~~i~~~y~v-~~dqlrmf~HYqPSyYHlHVHi~nik~~~~~~~~~~rAilLddVI~nL~~~P~~Y~ 287 (310)
T KOG3969|consen 218 RNKSREAIPQRYGV-DPDQLRMFFHYQPSYYHLHVHIVNIKHDHAPGSGCGRAILLDDVIENLELDPEGYK 287 (310)
T ss_pred HHHHHHHHHHHhCC-CchhEEEEEEecCceEEEEEEEEeccCCCCCCccccceeeHHHHHHHhccChHhhh
Confidence 56778999999998 99987654 445555999999999998887666667777643
No 34
>PHA01976 helix-turn-helix protein
Probab=33.55 E-value=19 Score=21.08 Aligned_cols=24 Identities=13% Similarity=0.039 Sum_probs=16.8
Q ss_pred CCCCCCHHHHHHHHHhHcCCCCCCeE
Q 034307 32 GRANVSKAELKEKLARMYDVRDANAI 57 (98)
Q Consensus 32 ~~~TPsr~ei~~klA~~~~v~~~~~i 57 (98)
|...|+... ..+||+.||+ +++.+
T Consensus 38 g~~~p~~~~-l~~ia~~l~v-~~~~l 61 (67)
T PHA01976 38 DKRLPNLKT-LLRLADALGV-TLDWL 61 (67)
T ss_pred CCCCCCHHH-HHHHHHHHCc-CHHHH
Confidence 455676544 4799999997 76644
No 35
>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=33.53 E-value=27 Score=24.83 Aligned_cols=24 Identities=29% Similarity=0.530 Sum_probs=20.1
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
....+|+..||+.||+ +++.|-|.
T Consensus 164 ~~~~~i~~~la~~~~i-~~~~I~V~ 187 (188)
T PF09581_consen 164 EEEEEIKQYLADFYGI-SPEQIKVY 187 (188)
T ss_pred HHHHHHHHHHHHHhCC-CHHHeEEe
Confidence 4467899999999998 99988774
No 36
>PLN03026 histidinol-phosphate aminotransferase; Provisional
Probab=32.00 E-value=52 Score=25.81 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
+.|.-.+++++||+.+++ +++.|++.
T Consensus 84 p~~~~~~lr~~ia~~~~~-~~~~I~~t 109 (380)
T PLN03026 84 PDPESRRLRAALAEDSGL-ESENILVG 109 (380)
T ss_pred CCCCHHHHHHHHHHHhCc-ChhhEEEc
Confidence 345578999999999996 88887763
No 37
>TIGR03576 pyridox_MJ0158 pyridoxal phosphate enzyme, MJ0158 family. Members of this archaeal protein family are pyridoxal phosphate enzymes of unknown function. Sequence similarity to SelA, a bacterial enzyme of selenocysteine biosynthesis, has led to some members being misannotated as functionally equivalent, but selenocysteine is made on tRNA in Archaea by a two-step process that does not involve a SelA homolog.
Probab=31.89 E-value=45 Score=26.19 Aligned_cols=29 Identities=14% Similarity=0.130 Sum_probs=23.2
Q ss_pred CCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 32 GRANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 32 ~~~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
++.++--.++.++||+.+|+ +++.++|++
T Consensus 50 ~g~~~~~~~Le~~lA~~~g~-~~e~ilv~~ 78 (346)
T TIGR03576 50 VGPAIFEEKVQELGREHLGG-PEEKILVFN 78 (346)
T ss_pred cCCHHHHHHHHHHHHHHcCC-CcceEEEEC
Confidence 46677789999999999995 777777764
No 38
>PRK05387 histidinol-phosphate aminotransferase; Provisional
Probab=31.87 E-value=41 Score=25.51 Aligned_cols=26 Identities=23% Similarity=0.482 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 35 NVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 35 TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
.|.-.++++.||+.+++ +++.|++..
T Consensus 59 ~~~~~~lr~aia~~~~~-~~~~I~it~ 84 (353)
T PRK05387 59 DPNADALRQAIAAYYGL-DPEQVFVGN 84 (353)
T ss_pred CCcHHHHHHHHHHHhCC-CHHHEEEcC
Confidence 34457999999999996 888887754
No 39
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.84 E-value=1.3e+02 Score=19.12 Aligned_cols=36 Identities=17% Similarity=0.164 Sum_probs=27.0
Q ss_pred HHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCH
Q 034307 41 LKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSV 81 (98)
Q Consensus 41 i~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~ 81 (98)
|-.+-|+.+|+.+-|.|.|.+ +.|+..+.|+|-++.
T Consensus 39 inp~dA~~lgi~~Gd~V~v~~-----~~G~~~~~v~~~~~i 74 (120)
T cd00508 39 IHPEDAARLGIKDGDLVRVSS-----RRGSVVVRARVTDRV 74 (120)
T ss_pred ECHHHHHHcCCCCCCEEEEEe-----CCEEEEEEEEECCCc
Confidence 444689999998999998885 445777777776653
No 40
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=31.63 E-value=78 Score=24.07 Aligned_cols=30 Identities=10% Similarity=0.203 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeEEEece
Q 034307 33 RANVSKAELKEKLARMYDVRDANAIFVFKF 62 (98)
Q Consensus 33 ~~TPsr~ei~~klA~~~~v~~~~~ivV~~~ 62 (98)
+.-|||.+.-..|++.+....+|+|++-|+
T Consensus 59 k~~~~r~~~d~~l~~~l~~~~~dlvvLAGy 88 (200)
T COG0299 59 KEFPSREAFDRALVEALDEYGPDLVVLAGY 88 (200)
T ss_pred ccCCCHHHHHHHHHHHHHhcCCCEEEEcch
Confidence 788999999999999988789999999765
No 41
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=31.22 E-value=1.3e+02 Score=18.65 Aligned_cols=27 Identities=19% Similarity=0.342 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
.+-+-.|+|++|...+|+ +++..-+.-
T Consensus 22 ~~~Tv~eLK~kl~~~~Gi-~~~~m~L~l 48 (87)
T PF14560_consen 22 KSITVSELKQKLEKLTGI-PPSDMRLQL 48 (87)
T ss_dssp TTSBHHHHHHHHHHHHTS--TTTEEEEE
T ss_pred CCCCHHHHHHHHHHHhCC-CcccEEEEE
Confidence 345688999999999997 777766644
No 42
>PF01996 F420_ligase: F420-0:Gamma-glutamyl ligase; InterPro: IPR002847 This entry contains F420-0:gamma-glutamyl ligase and related proteins. F420-0:gamma-glutamyl ligase catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives [, , , ].; PDB: 2G9I_A 2PHN_A.
Probab=31.08 E-value=39 Score=25.53 Aligned_cols=52 Identities=21% Similarity=0.226 Sum_probs=36.0
Q ss_pred EEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCC
Q 034307 27 DVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDS 80 (98)
Q Consensus 27 ~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds 80 (98)
.++.|..|.-|-++|+++|.+.+|. +...++.+..-+-|=.| ++|+|.=+.-
T Consensus 125 v~LlP~dPd~sA~~i~~~l~~~~g~-~v~ViI~Dt~gr~~r~G-~~~vaig~~G 176 (228)
T PF01996_consen 125 VVLLPEDPDASARRIREELKERTGK-DVGVIITDTNGRPWRLG-QTGVAIGVAG 176 (228)
T ss_dssp EE---S-HHHHHHHHHHHHHHHHS----EEEEEEEEEETTEEC-EEEEEEEEES
T ss_pred EEECCCCHHHHHHHHHHHHHHHHCC-ceEEEEECCCCcEEecC-CccchhhccC
Confidence 3566777778889999999999995 99999999888776666 7777764443
No 43
>PRK04781 histidinol-phosphate aminotransferase; Provisional
Probab=30.91 E-value=46 Score=25.87 Aligned_cols=27 Identities=15% Similarity=0.358 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
+.|...++++.||+.+++ +++.|++..
T Consensus 57 ~~~~~~~lr~~ia~~~~~-~~~~I~~t~ 83 (364)
T PRK04781 57 PDPQPPGLRSALAALYGC-APEQLLIGR 83 (364)
T ss_pred CCCCHHHHHHHHHHHhCc-ChHHEEEeC
Confidence 345578999999999996 888877643
No 44
>PRK13815 ribosome-binding factor A; Provisional
Probab=30.51 E-value=1.8e+02 Score=19.90 Aligned_cols=44 Identities=9% Similarity=0.082 Sum_probs=33.7
Q ss_pred HHHHHHHHhHc--CCCCCC--eEEEeceeecCCCCEEEEEEEEeCCHH
Q 034307 39 AELKEKLARMY--DVRDAN--AIFVFKFRTHFGGGKSTGFGLIYDSVE 82 (98)
Q Consensus 39 ~ei~~klA~~~--~v~~~~--~ivV~~~~t~fG~~~s~g~a~IYds~e 82 (98)
++|++.||..+ ++.||. .|.|.+.+..=....++.|.-++.+.+
T Consensus 10 ~~Ir~eis~il~~~i~dprl~~vtVt~V~vS~Dl~~AkVyvs~~~~~~ 57 (122)
T PRK13815 10 EAIHELISGLLVKGLKDPRIGFVTITGVKVTDDLHLATIYFTVIGDDE 57 (122)
T ss_pred HHHHHHHHHHHHHhCcCCCCCceEEeEEEECCCCCEEEEEEEECCCch
Confidence 46677777664 344565 589999999999999999999997654
No 45
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=30.31 E-value=55 Score=23.91 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=29.2
Q ss_pred eeeeeccCcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCC
Q 034307 11 RKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDV 51 (98)
Q Consensus 11 ~k~~~N~LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v 51 (98)
..++.+.|+...++.|.|. +..++.||++.+-.+|||
T Consensus 12 iTEKs~~l~e~N~ytF~V~----~~anK~eIK~AVE~iF~V 48 (158)
T PRK12280 12 LTEKSYSLMSKNVYTFKVD----RRANKIEIKKAVEFIFKV 48 (158)
T ss_pred cCHHHHhhhhCCEEEEEEC----CCCCHHHHHHHHHHHhCC
Confidence 3455566777788888864 456799999999999997
No 46
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=30.21 E-value=65 Score=21.22 Aligned_cols=35 Identities=20% Similarity=0.301 Sum_probs=22.9
Q ss_pred EEEEEcCCCCCCCH-----HHHHHHHHhHcCCCCCCeEEEe
Q 034307 25 VIDVLHPGRANVSK-----AELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 25 ~~~v~h~~~~TPsr-----~ei~~klA~~~~v~~~~~ivV~ 60 (98)
.+.|.-.|+.++.. ++|-+.|++.+|+ +++.|+|.
T Consensus 60 ~v~i~~~g~~~~e~k~~l~~~i~~~l~~~lgi-~~~rv~I~ 99 (116)
T PTZ00397 60 FVRVTSIGGISRSNNSSIAAAITKILASHLKV-KSERVYIE 99 (116)
T ss_pred EEEEEEecCCCHHHHHHHHHHHHHHHHHHhCc-CcccEEEE
Confidence 44455445566552 3577778888997 77777763
No 47
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.09 E-value=1.4e+02 Score=20.26 Aligned_cols=43 Identities=26% Similarity=0.401 Sum_probs=34.7
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecC
Q 034307 22 KQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHF 66 (98)
Q Consensus 22 kEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~f 66 (98)
|-++++++-| -.-|+--|+..+|++.-|+ +.=+|.|..+.-.-
T Consensus 6 RRlVLDvlKP-~~~p~ive~A~~lskl~gV-egVNItv~eiD~et 48 (97)
T COG1888 6 RRLVLDVLKP-HRGPTIVELALELSKLEGV-EGVNITVTEIDVET 48 (97)
T ss_pred eeeeeeecCC-cCCCcHHHHHHHHhhcCCc-ceEEEEEEEeeehh
Confidence 4578888776 4569999999999999998 88888888776543
No 48
>PRK14807 histidinol-phosphate aminotransferase; Provisional
Probab=29.78 E-value=70 Score=24.55 Aligned_cols=26 Identities=35% Similarity=0.464 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 35 NVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 35 TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
.|.-.+++++||+.+++ +++.|++.+
T Consensus 58 ~~~~~~lr~~ia~~~~~-~~~~i~it~ 83 (351)
T PRK14807 58 DPTAEKLREELARYCSV-VPTNIFVGN 83 (351)
T ss_pred CccHHHHHHHHHHHhCC-CcccEEEec
Confidence 45668999999999996 887777654
No 49
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=29.42 E-value=1.6e+02 Score=19.09 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=29.1
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHH
Q 034307 39 AELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVE 82 (98)
Q Consensus 39 ~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e 82 (98)
-+|-...|+.+|+.+.|.|.|.+ +.|+..+.|.|.++..
T Consensus 32 v~i~p~~A~~~gi~~Gd~V~v~s-----~~g~i~~~a~~~~~v~ 70 (121)
T cd02794 32 VWINPLDAAARGIKDGDRVLVFN-----DRGKVIRPVKVTERIM 70 (121)
T ss_pred EEECHHHHHHcCCCCCCEEEEEc-----CCceEEEEEEECCCcc
Confidence 35566889999998999998764 3357778888877643
No 50
>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=29.33 E-value=67 Score=19.44 Aligned_cols=26 Identities=8% Similarity=0.185 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHHHhHcCCCCCC-eEEEe
Q 034307 34 ANVSKAELKEKLARMYDVRDAN-AIFVF 60 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~-~ivV~ 60 (98)
++-+-.+++++|++..|+ +++ ..+++
T Consensus 18 ~~~TV~~lK~~I~~~~gi-p~~~q~Li~ 44 (71)
T cd01796 18 PDLELENFKALCEAESGI-PASQQQLIY 44 (71)
T ss_pred CcCCHHHHHHHHHHHhCC-CHHHeEEEE
Confidence 566788999999999998 555 44443
No 51
>PRK14864 putative biofilm stress and motility protein A; Provisional
Probab=28.94 E-value=1.8e+02 Score=19.71 Aligned_cols=51 Identities=12% Similarity=0.193 Sum_probs=37.0
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeC
Q 034307 25 VIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYD 79 (98)
Q Consensus 25 ~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYd 79 (98)
.+.|.+ .+ |-.|++++||++=+-.......|-.....-|.+.-.|.|-||.
T Consensus 53 tVSvs~--~g--sp~d~~~~La~KAda~GA~yYrIi~~~e~~~~~~~~atA~iYk 103 (104)
T PRK14864 53 TVSALV--RG--SPDDAEREIQAKANAAGADYYVIVMVDETVVPGQWYSQAILYR 103 (104)
T ss_pred EEEEec--CC--CHHHHHHHHHHHHHHcCCCEEEEEEccccCCCCeEEEEEEEec
Confidence 556665 33 4568888888875444556777777776677899999999995
No 52
>PF02594 DUF167: Uncharacterised ACR, YggU family COG1872; InterPro: IPR003746 This entry describes proteins of unknown function. Structures for two of these proteins, YggU from Escherichia coli and MTH637 from the archaea Methanobacterium thermoautotrophicum, have been determined; they have a core 2-layer alpha/beta structure consisting of beta(2)-loop-alpha-beta(2)-alpha [, ].; PDB: 1YH5_A 1N91_A 1JRM_A.
Probab=28.79 E-value=93 Score=19.74 Aligned_cols=42 Identities=19% Similarity=0.148 Sum_probs=25.4
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEecee
Q 034307 22 KQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFR 63 (98)
Q Consensus 22 kEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~ 63 (98)
.++.+.|..|-.--=.-+++.+-||+.|++...+.-++.|-.
T Consensus 26 ~~l~i~v~app~~GkAN~ali~~La~~l~v~ks~i~i~~G~~ 67 (77)
T PF02594_consen 26 GALKIRVTAPPVDGKANKALIRFLAKALGVPKSDIEIVSGHT 67 (77)
T ss_dssp T-EEEEBSTTCCCCCHHHHHHHHHHHHCT--TTCEEECC-CC
T ss_pred eEEEEEEecCCCcChhHHHHHHHHHHHhCCCcccEEEEecCC
Confidence 355666655533333468999999999999555555655544
No 53
>PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Probab=28.66 E-value=1e+02 Score=23.75 Aligned_cols=35 Identities=11% Similarity=0.310 Sum_probs=27.2
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 25 VIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 25 ~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
.+....| +=.|=+.++++.||+.+++ +++.|-|.-
T Consensus 156 tII~q~P-Ki~p~~~~m~~~La~lL~i-~~~~VnIKA 190 (216)
T PLN02862 156 TLILQRP-KLSPHKEAIRSNLSKLLGA-DPSVVNLKA 190 (216)
T ss_pred EEEcCCC-cchHHHHHHHHHHHHHhCC-CcceEEEEE
Confidence 3334444 6689999999999999996 888887754
No 54
>PRK07392 threonine-phosphate decarboxylase; Validated
Probab=28.65 E-value=59 Score=25.01 Aligned_cols=25 Identities=20% Similarity=0.094 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
|.-.++++.||+.+++ +++.|+|..
T Consensus 57 ~~~~~Lr~aia~~~~v-~~~~I~it~ 81 (360)
T PRK07392 57 PDYRELRLALAQHHQL-PPEWILPGN 81 (360)
T ss_pred cCHHHHHHHHHHHhCc-ChhhEEECC
Confidence 4456899999999996 888887754
No 55
>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=28.26 E-value=1e+02 Score=18.13 Aligned_cols=22 Identities=9% Similarity=0.160 Sum_probs=18.3
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCe
Q 034307 34 ANVSKAELKEKLARMYDVRDANA 56 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ 56 (98)
++-+-.+++++|++..++ +++.
T Consensus 19 ~~~tv~~lK~~i~~~~g~-~~~~ 40 (76)
T cd01806 19 PTDKVERIKERVEEKEGI-PPQQ 40 (76)
T ss_pred CCCCHHHHHHHHhHhhCC-Chhh
Confidence 566789999999999997 6664
No 56
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=27.85 E-value=1.4e+02 Score=17.72 Aligned_cols=41 Identities=20% Similarity=0.207 Sum_probs=28.4
Q ss_pred CHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeC
Q 034307 37 SKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYD 79 (98)
Q Consensus 37 sr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYd 79 (98)
|-.|+.++||++=.-...+...|-.+.+ .++.-.+-|-||.
T Consensus 16 s~~d~~~~la~kAd~~GA~~y~I~~~~~--~~~~~~~tA~lYk 56 (56)
T PF07338_consen 16 SPDDAEEALAKKADEKGAKYYRITSASE--DGNNWHATAELYK 56 (56)
T ss_dssp SHHHHHHHHHHHHHHTT-SEEEEEEEEE--CSSEEEEEEEEEE
T ss_pred CHHHHHHHHHHHHHHcCCCEEEEEEEEc--CCCeEEEEEEEEC
Confidence 4467777776653222346777777777 8999999999993
No 57
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=27.67 E-value=1.1e+02 Score=24.92 Aligned_cols=42 Identities=26% Similarity=0.432 Sum_probs=29.9
Q ss_pred HHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHH
Q 034307 38 KAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLI-YDSVESAK 85 (98)
Q Consensus 38 r~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~I-Yds~e~~k 85 (98)
-.+|+.... .|| .=+.+.+|.+..| |+|.|||.| |..+-.|+
T Consensus 115 EskLrreF~-~YG-~IkrirlV~d~vT----gkskGYAFIeye~erdm~ 157 (335)
T KOG0113|consen 115 ESKLRREFE-KYG-PIKRIRLVRDKVT----GKSKGYAFIEYEHERDMK 157 (335)
T ss_pred HHHHHHHHH-hcC-cceeEEEeeeccc----CCccceEEEEeccHHHHH
Confidence 345555554 466 4688899999988 678899987 77666654
No 58
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=27.52 E-value=87 Score=20.67 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceee
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFKFRT 64 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t 64 (98)
..|+-..+++||...|+. +++-+.|.-+..
T Consensus 18 ~~pt~~~L~~kl~~Lf~l-p~~~~~vtYiDe 47 (82)
T cd06397 18 DIPTWEALASKLENLYNL-PEIKVGVTYIDN 47 (82)
T ss_pred CCccHHHHHHHHHHHhCC-ChhHeEEEEEcC
Confidence 389999999999999997 766677665554
No 59
>KOG2116 consensus Protein involved in plasmid maintenance/nuclear protein involved in lipid metabolism [Cell motility; Lipid transport and metabolism]
Probab=27.49 E-value=97 Score=27.83 Aligned_cols=31 Identities=26% Similarity=0.500 Sum_probs=24.5
Q ss_pred hHcCCCCCCeEEEeceeecCCCCEEEEEEEEe
Q 034307 47 RMYDVRDANAIFVFKFRTHFGGGKSTGFGLIY 78 (98)
Q Consensus 47 ~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IY 78 (98)
+.||..+..+=|+|+|.|+|++ ...+-|+||
T Consensus 494 ~sLnLk~G~N~v~FsisT~~~G-t~~c~~~IY 524 (738)
T KOG2116|consen 494 KSLNLKDGKNDVVFSISTQYQG-TAQCEGNIY 524 (738)
T ss_pred hhcCCccCCceeEEEEEecccc-eEEEeeEEE
Confidence 4566678899999999999986 456677777
No 60
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=27.49 E-value=2.4e+02 Score=20.34 Aligned_cols=62 Identities=21% Similarity=0.330 Sum_probs=42.2
Q ss_pred ccCcc-eeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEE---eCCHHHHHh
Q 034307 16 NRLLS-RKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLI---YDSVESAKK 86 (98)
Q Consensus 16 N~LL~-RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~I---Yds~e~~kk 86 (98)
..++. ..+++|.|.. ..++.||++.+-++|+| +..=|..+.+.- |.=.+|+.. ||..|.+.+
T Consensus 76 ~~~~E~~N~yvF~Vd~----kAnK~qIK~AVEklf~V---kV~kVNTli~p~--g~KKA~V~L~~~~~aidva~k 141 (145)
T PTZ00191 76 MKKIEDNNTLVFIVDQ----RANKTQIKKAVEKLYDV---KVVKVNTLITPD--GLKKAYIRLSPDVDALDVANK 141 (145)
T ss_pred HHHHhhCCEEEEEEcC----CCCHHHHHHHHHHHhCC---eeEEEEeEEcCC--CceEEEEEECCCCcHHHHHHh
Confidence 34444 3688888654 46799999999999997 666677766644 445567777 444555544
No 61
>PRK14809 histidinol-phosphate aminotransferase; Provisional
Probab=27.47 E-value=79 Score=24.22 Aligned_cols=24 Identities=29% Similarity=0.501 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
+.-.++++.||+.+++ +++.|++.
T Consensus 65 ~~~~~lr~~ia~~~~~-~~~~I~it 88 (357)
T PRK14809 65 ASHADLTAALADRWDV-SPEQVWLA 88 (357)
T ss_pred CCHHHHHHHHHHHhCC-CcceEEEC
Confidence 4577999999999996 88877764
No 62
>PF04110 APG12: Ubiquitin-like autophagy protein Apg12 ; InterPro: IPR007242 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents Apg12, which is covalently bound to Apg5 [].; GO: 0000045 autophagic vacuole assembly, 0005737 cytoplasm; PDB: 1WZ3_B.
Probab=27.14 E-value=22 Score=23.45 Aligned_cols=33 Identities=18% Similarity=0.251 Sum_probs=15.7
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCC
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFKFRTHFG 67 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG 67 (98)
-.||-.|.-+-|.+.|++ +.++|+=+..-.-||
T Consensus 55 FaPspDe~vg~L~~~f~~-~~~Liv~Ys~t~A~G 87 (87)
T PF04110_consen 55 FAPSPDETVGDLYRCFGT-NGELIVSYSKTPAWG 87 (87)
T ss_dssp E---TTSBHHHHHHHH-B-TTBEEEEEESSS---
T ss_pred cCCCchhHHHHHHHHhCC-CCEEEEEEecccccC
Confidence 456666667777777773 666665444444443
No 63
>PRK04635 histidinol-phosphate aminotransferase; Provisional
Probab=27.06 E-value=58 Score=25.03 Aligned_cols=25 Identities=16% Similarity=0.190 Sum_probs=20.6
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
|.-.++++.+|+.+++ +++.|++..
T Consensus 60 ~~~~~Lr~aia~~~~~-~~~~I~it~ 84 (354)
T PRK04635 60 CQPPELINAYSAYAGV-APEQILTSR 84 (354)
T ss_pred CCHHHHHHHHHHHhCc-CHHHEEEeC
Confidence 3468999999999996 888888743
No 64
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=26.97 E-value=28 Score=19.49 Aligned_cols=24 Identities=13% Similarity=0.418 Sum_probs=19.3
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeE
Q 034307 33 RANVSKAELKEKLARMYDVRDANAI 57 (98)
Q Consensus 33 ~~TPsr~ei~~klA~~~~v~~~~~i 57 (98)
....|+.++.++++..++ ..||++
T Consensus 16 ~~~~~~~~v~~~v~~Ll~-~hpdLl 39 (47)
T PF02671_consen 16 KGRISRSEVIEEVSELLR-GHPDLL 39 (47)
T ss_dssp CTCSCHHHHHHHHHHHTT-T-HHHH
T ss_pred hcCCCHHHHHHHHHHHHc-cCHHHH
Confidence 467899999999999999 577764
No 65
>PRK13817 ribosome-binding factor A; Provisional
Probab=26.64 E-value=2.1e+02 Score=19.44 Aligned_cols=44 Identities=16% Similarity=0.199 Sum_probs=33.1
Q ss_pred HHHHHHHHhHc--CCCCCC--eEEEeceeecCCCCEEEEEEEEeCCHH
Q 034307 39 AELKEKLARMY--DVRDAN--AIFVFKFRTHFGGGKSTGFGLIYDSVE 82 (98)
Q Consensus 39 ~ei~~klA~~~--~v~~~~--~ivV~~~~t~fG~~~s~g~a~IYds~e 82 (98)
.+|++.||..+ .+.||. .|.|.+.+..-+...++.|.-+|++.+
T Consensus 10 ~~I~reis~il~~ei~dp~l~~vtVt~V~vS~Dl~~AkVyvs~~~~~~ 57 (119)
T PRK13817 10 DLIHQQLAELLKKEVRDSRLSKISLTAVSISPDLKQAKVFYSLLENQN 57 (119)
T ss_pred HHHHHHHHHHHHHhccCCCCCceEEeEEEECCCCCEEEEEEEECCCcc
Confidence 35666666655 333554 699999999999999999999997653
No 66
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.63 E-value=1.8e+02 Score=20.24 Aligned_cols=38 Identities=18% Similarity=0.285 Sum_probs=28.8
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCH
Q 034307 39 AELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSV 81 (98)
Q Consensus 39 ~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~ 81 (98)
-+|-.+-|+.+|+.+-|.|.|.+ .. |+..+.|+|-+..
T Consensus 34 v~inp~dA~~~GI~dGd~V~v~s---~~--G~~~~~a~v~~~i 71 (156)
T cd02783 34 LYMHPKTAKELGIKDGDWVWVES---VN--GRVKGQARFTETV 71 (156)
T ss_pred EEECHHHHHHcCCCCCCEEEEEc---CC--eeEEEEEEECCCc
Confidence 45566899999999999999986 22 5677778776543
No 67
>PRK00024 hypothetical protein; Reviewed
Probab=26.55 E-value=67 Score=24.18 Aligned_cols=27 Identities=19% Similarity=0.459 Sum_probs=17.3
Q ss_pred EEEEEcCC-CCCCCHHHHH--HHHH---hHcCC
Q 034307 25 VIDVLHPG-RANVSKAELK--EKLA---RMYDV 51 (98)
Q Consensus 25 ~~~v~h~~-~~TPsr~ei~--~klA---~~~~v 51 (98)
.+.=.||+ .++||.+|+. ++|+ +.+++
T Consensus 170 Il~HNHPSG~~~PS~~D~~~T~~l~~a~~~l~I 202 (224)
T PRK00024 170 ILAHNHPSGDPEPSQADILITKRLKEAGELLGI 202 (224)
T ss_pred EEEecCCCCCCCCCHHHHHHHHHHHHHHHhCCC
Confidence 33346884 6899999975 3444 45554
No 68
>PRK06358 threonine-phosphate decarboxylase; Provisional
Probab=26.46 E-value=71 Score=24.66 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
|.-.++|+++|+.+++ +++.|++..
T Consensus 54 ~~~~~lr~~ia~~~~~-~~~~i~it~ 78 (354)
T PRK06358 54 PDYLELRKRIASFEQL-DLENVILGN 78 (354)
T ss_pred ccHHHHHHHHHHHhCC-ChhhEEECC
Confidence 4557999999999996 888887653
No 69
>COG4099 Predicted peptidase [General function prediction only]
Probab=26.44 E-value=57 Score=26.95 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=21.4
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceee
Q 034307 39 AELKEKLARMYDVRDANAIFVFKFRT 64 (98)
Q Consensus 39 ~ei~~klA~~~~v~~~~~ivV~~~~t 64 (98)
+-|.++||..||+ |...|+|-|+.-
T Consensus 254 dli~~vlas~ynI-D~sRIYviGlSr 278 (387)
T COG4099 254 DLILEVLASTYNI-DRSRIYVIGLSR 278 (387)
T ss_pred HHHHHHHhhccCc-ccceEEEEeecC
Confidence 4467799999997 999999999864
No 70
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=25.70 E-value=2e+02 Score=18.79 Aligned_cols=38 Identities=11% Similarity=0.151 Sum_probs=27.7
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCH
Q 034307 39 AELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSV 81 (98)
Q Consensus 39 ~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~ 81 (98)
-+|-...|+.+|+.+-|.|.|.+ +.|+..+.|+|-++.
T Consensus 34 v~i~p~dA~~~gi~~Gd~V~v~s-----~~G~i~~~a~~~~~v 71 (124)
T cd02785 34 VKINPIDAAARGIAHGDLVEVYN-----DRGSVVCKAKVDDGI 71 (124)
T ss_pred EEECHHHHHHcCCCCCCEEEEEe-----CCCEEEEEEEECCCc
Confidence 34556789999998899987764 346777777776543
No 71
>PRK08056 threonine-phosphate decarboxylase; Provisional
Probab=25.63 E-value=65 Score=24.81 Aligned_cols=24 Identities=33% Similarity=0.265 Sum_probs=19.9
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
+.-.++|+.||+.+++ +++.|++.
T Consensus 55 ~~~~~lr~~ia~~~~~-~~~~i~it 78 (356)
T PRK08056 55 VEYRHLHQALARHHQV-PASWILAG 78 (356)
T ss_pred ccHHHHHHHHHHHhCc-ChhhEEEC
Confidence 4578999999999996 88888764
No 72
>PRK08153 histidinol-phosphate aminotransferase; Provisional
Probab=25.47 E-value=52 Score=25.56 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
|.-.+++++||+.+++ +++.|++..
T Consensus 67 ~~~~~Lr~~ia~~~~~-~~~~I~it~ 91 (369)
T PRK08153 67 PENHDLRHALAAHHGV-APENIMVGE 91 (369)
T ss_pred CccHHHHHHHHHHhCC-CHHHEEEcC
Confidence 3467999999999996 887777654
No 73
>PRK10534 L-threonine aldolase; Provisional
Probab=25.21 E-value=52 Score=24.80 Aligned_cols=27 Identities=11% Similarity=0.102 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
+.|...+++++||+.+|+ ++.+++.-+
T Consensus 32 ~~~~~~~L~~~la~~~g~-~~~~v~~~g 58 (333)
T PRK10534 32 DDPTVNALQDYAAELSGK-EAALFLPTG 58 (333)
T ss_pred CCHHHHHHHHHHHHHhCC-CeEEEeCch
Confidence 678889999999999996 666555443
No 74
>TIGR01141 hisC histidinol-phosphate aminotransferase. Histidinol-phosphate aminotransferase is a pyridoxal-phosphate dependent enzyme.
Probab=25.16 E-value=71 Score=24.14 Aligned_cols=26 Identities=38% Similarity=0.521 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
+.|.-.++++.+|+.+++ +++.|++.
T Consensus 52 ~~~~~~~lr~~ia~~~~~-~~~~i~~~ 77 (346)
T TIGR01141 52 PDPDPAELKQALADYYGV-DPEQILLG 77 (346)
T ss_pred CCCCHHHHHHHHHHHhCc-ChHHEEEc
Confidence 445568999999999995 77776653
No 75
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=25.15 E-value=37 Score=22.83 Aligned_cols=32 Identities=13% Similarity=0.071 Sum_probs=25.8
Q ss_pred CcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcC
Q 034307 18 LLSRKQFVIDVLHPGRANVSKAELKEKLARMYD 50 (98)
Q Consensus 18 LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~ 50 (98)
+|....+.+++.+.-+-.||++|+++-+++ +|
T Consensus 19 ~L~~~gi~~~~~d~~~~p~s~~eL~~~l~~-~g 50 (113)
T cd03033 19 LLEAAGHEVEVRDLLTEPWTAETLRPFFGD-LP 50 (113)
T ss_pred HHHHcCCCcEEeehhcCCCCHHHHHHHHHH-cC
Confidence 456667888888888889999999999983 45
No 76
>PRK09105 putative aminotransferase; Provisional
Probab=25.03 E-value=71 Score=24.99 Aligned_cols=24 Identities=13% Similarity=0.288 Sum_probs=20.0
Q ss_pred CHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 37 SKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 37 sr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
...++++.||+.+++ +++.|++..
T Consensus 79 ~~~~Lr~aia~~~~v-~~e~I~it~ 102 (370)
T PRK09105 79 LEDDLRTLFAAQEGL-PADHVMAYA 102 (370)
T ss_pred hHHHHHHHHHHHhCc-ChhhEEEcC
Confidence 478999999999997 888887743
No 77
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=24.98 E-value=95 Score=19.44 Aligned_cols=27 Identities=37% Similarity=0.502 Sum_probs=17.7
Q ss_pred CCCCCC-HH----HHHHHHHhHcCCCCCCeEEE
Q 034307 32 GRANVS-KA----ELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 32 ~~~TPs-r~----ei~~klA~~~~v~~~~~ivV 59 (98)
|+.+.. +. +|.+.+++.+| ++++.|.|
T Consensus 11 g~~~~~~K~~la~~vT~~~~~~lg-~~~~~i~V 42 (69)
T COG1942 11 GRLDEEQKAELAAEVTEVTVETLG-KDPSAIHV 42 (69)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhC-CCcccEEE
Confidence 445554 33 55667788899 58887655
No 78
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=24.97 E-value=18 Score=20.60 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=16.0
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCe
Q 034307 33 RANVSKAELKEKLARMYDVRDANA 56 (98)
Q Consensus 33 ~~TPsr~ei~~klA~~~~v~~~~~ 56 (98)
.+.|+..+ .+.||+.+|+ ++..
T Consensus 22 ~~~p~~~~-~~~la~~l~l-~~~~ 43 (57)
T PF00046_consen 22 NPYPSKEE-REELAKELGL-TERQ 43 (57)
T ss_dssp SSSCHHHH-HHHHHHHHTS-SHHH
T ss_pred hccccccc-cccccccccc-cccc
Confidence 56777766 6789999997 5543
No 79
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=24.72 E-value=88 Score=17.90 Aligned_cols=20 Identities=15% Similarity=0.268 Sum_probs=13.6
Q ss_pred HHHHHHHhHcCCCCCCeEEEe
Q 034307 40 ELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 40 ei~~klA~~~~v~~~~~ivV~ 60 (98)
+|.+.+++.+++ +++.|+|.
T Consensus 23 ~it~~l~~~~~~-p~~~v~V~ 42 (61)
T PRK02220 23 DVTAAVSKNTGA-PAEHIHVI 42 (61)
T ss_pred HHHHHHHHHhCc-ChhhEEEE
Confidence 456677888996 66666553
No 80
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=24.69 E-value=88 Score=19.84 Aligned_cols=31 Identities=26% Similarity=0.392 Sum_probs=20.0
Q ss_pred EEEEEEcC-CCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 034307 24 FVIDVLHP-GRANVSKAELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 24 i~~~v~h~-~~~TPsr~ei~~klA~~~~v~~~~~ivV 59 (98)
+.+-=.|| |.+.||.+|+. +++..++ +.++|
T Consensus 59 v~i~HsHP~g~~~PS~~D~~--~~~~~~~---~~iIv 90 (101)
T cd08059 59 VGLVHSHPSGSCRPSEADLS--LFTRFGL---YHVIV 90 (101)
T ss_pred EEEEecCcCCCCCCCHHHHH--HHHhcCC---eEEEE
Confidence 33444677 57899999985 4444453 56666
No 81
>PRK06696 uridine kinase; Validated
Probab=24.54 E-value=42 Score=24.43 Aligned_cols=19 Identities=21% Similarity=0.312 Sum_probs=12.6
Q ss_pred CCCCCCHHHHHHHHHhHcC
Q 034307 32 GRANVSKAELKEKLARMYD 50 (98)
Q Consensus 32 ~~~TPsr~ei~~klA~~~~ 50 (98)
|.+---|+-+-++||+.++
T Consensus 29 G~sgsGKSTlA~~L~~~l~ 47 (223)
T PRK06696 29 GITASGKTTFADELAEEIK 47 (223)
T ss_pred CCCCCCHHHHHHHHHHHHH
Confidence 4444457777777777775
No 82
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=24.20 E-value=1e+02 Score=17.64 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=13.1
Q ss_pred HHHHHHHhHcCCCCCCeEEE
Q 034307 40 ELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 40 ei~~klA~~~~v~~~~~ivV 59 (98)
+|.+.++..+|+ +++.+.|
T Consensus 23 ~it~~l~~~lg~-~~~~v~V 41 (63)
T TIGR00013 23 GVTEAMAETLGA-NLESIVV 41 (63)
T ss_pred HHHHHHHHHhCC-CcccEEE
Confidence 466777888995 6666554
No 83
>PRK01533 histidinol-phosphate aminotransferase; Validated
Probab=24.05 E-value=99 Score=24.20 Aligned_cols=25 Identities=12% Similarity=0.190 Sum_probs=20.1
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
+.-.++++.||+.+++ +++.|++..
T Consensus 64 ~g~~~Lr~aia~~~~~-~~~~I~vt~ 88 (366)
T PRK01533 64 GGATTLRQTIANKLHV-KMEQVLCGS 88 (366)
T ss_pred CCHHHHHHHHHHHhCC-CcceEEECC
Confidence 3456899999999996 888887753
No 84
>COG3561 Phage anti-repressor protein [Transcription]
Probab=23.94 E-value=1.8e+02 Score=20.13 Aligned_cols=58 Identities=14% Similarity=0.155 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHHHHhcCc
Q 034307 32 GRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVESAKKFEP 89 (98)
Q Consensus 32 ~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e~~kk~Ep 89 (98)
+-+||+.+.+++.+.+.-=+-+.|.+.+......|-+....+|+.-=|-....-.+||
T Consensus 23 ~~~tr~s~wf~er~~~ygfien~d~i~~~~~~~~~~~~~~~d~~l~id~aKei~M~er 80 (110)
T COG3561 23 DVKTRYSAWFRERISEYGFIENIDYIGCSDYGEEFSGVIGMDYALTIDMAKEIAMVER 80 (110)
T ss_pred hccchHHHHHHHHHHhhcceeccceEEEEecccccccccccceeeeechhhhhheecc
Confidence 5689999999999888754468899999999888877777788877776655555554
No 85
>PRK03967 histidinol-phosphate aminotransferase; Provisional
Probab=23.92 E-value=1e+02 Score=23.59 Aligned_cols=25 Identities=32% Similarity=0.522 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
+.-.++++.||+.+++ +++.|++..
T Consensus 55 ~g~~~lr~~ia~~~~~-~~~~I~~t~ 79 (337)
T PRK03967 55 ITSDPLREAIAEFYGL-DAENIAVGN 79 (337)
T ss_pred CCHHHHHHHHHHHhCc-CcceEEEcC
Confidence 4568999999999996 888887643
No 86
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=23.83 E-value=53 Score=21.62 Aligned_cols=32 Identities=16% Similarity=0.167 Sum_probs=24.7
Q ss_pred CcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcC
Q 034307 18 LLSRKQFVIDVLHPGRANVSKAELKEKLARMYD 50 (98)
Q Consensus 18 LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~ 50 (98)
+|....+.+.+.+.-+-.||++|+++-+++ +|
T Consensus 18 ~L~~~~i~~~~~di~~~p~s~~eL~~~l~~-~g 49 (105)
T cd03035 18 WLEARGVAYTFHDYRKDGLDAATLERWLAK-VG 49 (105)
T ss_pred HHHHcCCCeEEEecccCCCCHHHHHHHHHH-hC
Confidence 456667788888887888999999998874 34
No 87
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=23.78 E-value=56 Score=24.14 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=10.3
Q ss_pred CCCCCCHHHHHH
Q 034307 32 GRANVSKAELKE 43 (98)
Q Consensus 32 ~~~TPsr~ei~~ 43 (98)
|.|||+|+|-..
T Consensus 3 GrPTPkRkeaea 14 (170)
T PF11241_consen 3 GRPTPKRKEAEA 14 (170)
T ss_pred CCCCCChHHHHH
Confidence 789999999765
No 88
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=23.74 E-value=57 Score=20.50 Aligned_cols=15 Identities=27% Similarity=0.439 Sum_probs=9.7
Q ss_pred EcCCC-CCCCHHHHHH
Q 034307 29 LHPGR-ANVSKAELKE 43 (98)
Q Consensus 29 ~h~~~-~TPsr~ei~~ 43 (98)
.||+. |.||..|++.
T Consensus 67 SHP~~~a~pS~~D~~~ 82 (104)
T PF14464_consen 67 SHPSGPAFPSSTDIRS 82 (104)
T ss_dssp EESSSSSS--HHHHHT
T ss_pred cCCCCCCCCCHHHHHh
Confidence 57865 5999999865
No 89
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=23.65 E-value=1.6e+02 Score=23.68 Aligned_cols=46 Identities=15% Similarity=0.262 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHH
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLI-YDSVESAK 85 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~I-Yds~e~~k 85 (98)
.+.+-.+|++.+.. ||. =....++... ..|.+.|||.| |.+.+.+.
T Consensus 305 ~~~~~~~l~~~f~~-~G~-i~~~~~~~~~----~~g~~~g~afv~f~~~~~a~ 351 (509)
T TIGR01642 305 LYLGEDQIKELLES-FGD-LKAFNLIKDI----ATGLSKGYAFCEYKDPSVTD 351 (509)
T ss_pred CCCCHHHHHHHHHh-cCC-eeEEEEEecC----CCCCcCeEEEEEECCHHHHH
Confidence 35567788766654 562 2333444333 34667788886 77766654
No 90
>PLN02382 probable sucrose-phosphatase
Probab=23.59 E-value=2.2e+02 Score=23.25 Aligned_cols=45 Identities=16% Similarity=0.127 Sum_probs=35.4
Q ss_pred cceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCC---eEEEeceee
Q 034307 19 LSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDAN---AIFVFKFRT 64 (98)
Q Consensus 19 L~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~---~ivV~~~~t 64 (98)
+.+--=.|...||.+.--++.+..+.+++.+| +.|. .|-|+.+..
T Consensus 313 ~~~~~p~~~~v~p~G~~~~~~~~~~~~~~~~G-~~~g~~~~i~vd~~~~ 360 (413)
T PLN02382 313 KSSCAPNGVFVHPSGVEKSLHDSIDELRSCYG-DKKGKKFRVWVDRVLS 360 (413)
T ss_pred HHhcCCCeeEECCCcccCCHHHHHHHHHHhhC-CCCCCEEEEEEeeEEE
Confidence 33334467889999999999999999999999 5887 566666654
No 91
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=23.55 E-value=96 Score=18.12 Aligned_cols=20 Identities=25% Similarity=0.385 Sum_probs=13.9
Q ss_pred HHHHHHHhHcCCCCCCeEEEe
Q 034307 40 ELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 40 ei~~klA~~~~v~~~~~ivV~ 60 (98)
+|.+.+++.+++ +++.++|.
T Consensus 23 ~it~~l~~~lg~-p~~~v~V~ 42 (64)
T PRK01964 23 EVTEAISATLDV-PKERVRVI 42 (64)
T ss_pred HHHHHHHHHhCc-ChhhEEEE
Confidence 455667788996 77776653
No 92
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.47 E-value=2e+02 Score=18.51 Aligned_cols=38 Identities=18% Similarity=0.262 Sum_probs=26.9
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCH
Q 034307 39 AELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSV 81 (98)
Q Consensus 39 ~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~ 81 (98)
-+|-..-|+.+|+++-|.|.|.+ +.|+..+.|.|.++.
T Consensus 32 v~i~p~dA~~~gi~~Gd~V~v~s-----~~G~i~~~v~v~~~v 69 (123)
T cd02778 32 LWINPETAARLGIKDGDRVEVSS-----ARGKVTGKARLTEGI 69 (123)
T ss_pred EEECHHHHHHcCCCCCCEEEEEe-----CCCcEEEEEEEcCCc
Confidence 44555789999998889987764 345666777776644
No 93
>TIGR01140 L_thr_O3P_dcar L-threonine-O-3-phosphate decarboxylase. This family contains pyridoxal phosphate-binding class II aminotransferases (see PFAM:PF00222) closely related to, yet distinct from, histidinol-phosphate aminotransferase (HisC). It is found in cobalamin biosynthesis operons in Salmonella typhimurium and Bacillus halodurans (each of which also has HisC) and has been shown to have L-threonine-O-3-phosphate decarboxylase activity in Salmonella. Although the gene symbol cobD was assigned in Salmonella, cobD in other contexts refers to a different cobalamin biosynthesis enzyme, modeled by pfam03186 and called cbiB in Salmonella.
Probab=23.39 E-value=86 Score=23.89 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 33 RANVSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 33 ~~TPsr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
-+.|.-.++++.||+.+++ +++.|++.
T Consensus 44 y~~~~~~~lr~~la~~~~~-~~~~i~~t 70 (330)
T TIGR01140 44 YPDPEYDELRAAAAAYYGL-PAASVLPV 70 (330)
T ss_pred CCCccHHHHHHHHHHHhCC-ChhhEEEC
Confidence 3556679999999999996 77777654
No 94
>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=23.26 E-value=92 Score=18.97 Aligned_cols=32 Identities=22% Similarity=0.229 Sum_probs=22.5
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEE
Q 034307 22 KQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIF 58 (98)
Q Consensus 22 kEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~iv 58 (98)
+.+.++| .++=+-.++|++|++..|+ +++..-
T Consensus 9 ~~~~l~v----~~~~TV~~lK~~I~~~~gi-~~~~q~ 40 (70)
T cd01794 9 KDVKLSV----SSKDTVGQLKKQLQAAEGV-DPCCQR 40 (70)
T ss_pred CEEEEEE----CCcChHHHHHHHHHHHhCC-CHHHeE
Confidence 4555554 3455788999999999997 665433
No 95
>PF04015 DUF362: Domain of unknown function (DUF362) ; InterPro: IPR007160 This domain is found in some iron-sulphur proteins.
Probab=23.01 E-value=59 Score=23.29 Aligned_cols=40 Identities=15% Similarity=0.187 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEE
Q 034307 36 VSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFG 75 (98)
Q Consensus 36 Psr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a 75 (98)
++..++.+.||..+....+++.|++++..-.|.|-..|..
T Consensus 144 ~~~~~~~~~i~d~~~~~k~~l~I~Dg~~~~~~~GP~~g~~ 183 (206)
T PF04015_consen 144 PGQDDFHEAIADLNSALKPDLNIVDGIIAMEGNGPCSGTP 183 (206)
T ss_pred cccccHHHHHHHHHHhhCCcEEEEEEEEECCCCCCCCCCc
Confidence 5677888889988777789999999999977766655554
No 96
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=22.99 E-value=1.3e+02 Score=21.98 Aligned_cols=32 Identities=16% Similarity=0.323 Sum_probs=24.4
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 26 IDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 26 ~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
++|.++ -.||..--+.|++.+|+ +++.++.+|
T Consensus 188 ~eI~~~---gvsKg~al~~l~~~~gi-~~~~v~afG 219 (270)
T PRK10513 188 LEILDK---RVNKGTGVKSLAEHLGI-KPEEVMAIG 219 (270)
T ss_pred EEEeCC---CCChHHHHHHHHHHhCC-CHHHEEEEC
Confidence 455554 37899999999999997 777777654
No 97
>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=22.85 E-value=1.1e+02 Score=18.50 Aligned_cols=24 Identities=13% Similarity=0.270 Sum_probs=18.6
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeE
Q 034307 33 RANVSKAELKEKLARMYDVRDANAI 57 (98)
Q Consensus 33 ~~TPsr~ei~~klA~~~~v~~~~~i 57 (98)
.++=+-.+++++|++..|+ +++..
T Consensus 16 ~~~~tV~~lK~~i~~~~gi-p~~~q 39 (74)
T cd01793 16 TGQETVSDIKAHVAGLEGI-DVEDQ 39 (74)
T ss_pred CCcCcHHHHHHHHHhhhCC-CHHHE
Confidence 3556788999999999997 55543
No 98
>PRK01310 hypothetical protein; Validated
Probab=22.77 E-value=2.5e+02 Score=18.93 Aligned_cols=44 Identities=16% Similarity=0.132 Sum_probs=29.7
Q ss_pred eeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceee
Q 034307 21 RKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRT 64 (98)
Q Consensus 21 RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t 64 (98)
|..+.+.|.-|-.--=.-+++..-||+.|++...+.-++.|-.+
T Consensus 37 ~~~lkv~v~apPv~GkAN~ali~~LA~~l~v~ks~I~iv~G~ts 80 (104)
T PRK01310 37 RAVLKVRVRAVPEGGEANRALIELLAKALGVPKSSVRLLSGATS 80 (104)
T ss_pred ccEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCC
Confidence 45677777665333334689999999999985555556565443
No 99
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=22.73 E-value=1.2e+02 Score=20.43 Aligned_cols=39 Identities=33% Similarity=0.491 Sum_probs=30.6
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEecee
Q 034307 22 KQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFR 63 (98)
Q Consensus 22 kEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~ 63 (98)
|-++++|+-| --||--|+..+||+.-|+ +.=+|.|..+.
T Consensus 5 rRlVLDVlKP--~~p~i~e~A~~l~~~~gV-~gVnitv~EvD 43 (95)
T PF02680_consen 5 RRLVLDVLKP--HEPSIVELAKALSELEGV-DGVNITVVEVD 43 (95)
T ss_dssp EEEEEEEEEE--SSS-HHHHHHHHHTSTTE-EEEEEEEEEE-
T ss_pred eEEEEEeecC--CCCCHHHHHHHHHhCCCc-ceEEEEEEEee
Confidence 5689999998 789999999999999997 66666665543
No 100
>PF00388 PI-PLC-X: Phosphatidylinositol-specific phospholipase C, X domain This entry is for the whole phospholipase C protein; InterPro: IPR000909 Phosphatidylinositol-specific phospholipase C (3.1.4.11 from EC), a eukaryotic intracellular enzyme, plays an important role in signal transduction processes []. It catalyzes the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messenger molecules diacylglycerol and inositol-1,4,5-triphosphate. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [, , ]. In mammals, there are at least 6 different isoforms of PI-PLC, they differ in their domain structure, their regulation, and their tissue distribution. Lower eukaryotes also possess multiple isoforms of PI-PLC. All eukaryotic PI-PLCs contain two regions of homology, sometimes referred to as the 'X-box' and 'Y-box'. The order of these two regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distance between these two regions is only 50-100 residues but in the gamma isoforms one PH domain, two SH2 domains, and one SH3 domain are inserted between the two PLC-specific domains. The two conserved regions have been shown to be important for the catalytic activity. By profile analysis, we could show that sequences with significant similarity to the X-box domain occur also in prokaryotic and trypanosome PI-specific phospholipases C. Apart from this region, the prokaryotic enzymes show no similarity to their eukaryotic counterparts.; GO: 0004629 phospholipase C activity, 0006629 lipid metabolic process, 0035556 intracellular signal transduction; PDB: 2FJU_B 2ZKM_X 3V18_A 3V1H_A 3V16_A 3QR1_D 3EA3_A 3EA1_A 2OR2_A 1T6M_B ....
Probab=22.71 E-value=2.4e+02 Score=19.01 Aligned_cols=54 Identities=6% Similarity=0.140 Sum_probs=38.7
Q ss_pred EEEEEeeeeeccCcceeEEEEEEEcCCCC--CCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCC
Q 034307 6 ITIRTRKFMTNRLLSRKQFVIDVLHPGRA--NVSKAELKEKLARMYDVRDANAIFVFKFRTHFGG 68 (98)
Q Consensus 6 ~~i~i~k~~~N~LL~RkEi~~~v~h~~~~--TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~ 68 (98)
+.|++.....+ .+.+.|-.-. .-+-.++-+.+..-+. ..|+.+||-.|+.+++.
T Consensus 43 lDlrv~~~~~~--------~~~v~Hg~~~~~~~~~~dvL~~i~~fl~-~~p~E~VIl~~~~~~~~ 98 (146)
T PF00388_consen 43 LDLRVWDGNDG--------ELVVYHGITSTSGITFEDVLNDIRDFLF-EHPSEPVILSLKHEYSP 98 (146)
T ss_dssp EEEEEEEETTS--------SEEEEETTSEE-EEEHHHHHHHHHHHTT-HSTTS-EEEEEEEESTH
T ss_pred EEEEEEcCCCC--------ceEEEeCCEeeeeEeHHHHHHHHHHHHh-cCCCeEEEEEeecccch
Confidence 66777643333 2678893323 3678999999999999 58999999999988753
No 101
>PF01394 Clathrin_propel: Clathrin propeller repeat; InterPro: IPR022365 This entry represents the propeller repeat found in clathrin heavy chains. The N terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller []. Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1UTC_B 3GD1_I 3GC3_B 1BPO_C 1C9I_B 1C9L_A 2XZG_A 2XZH_A.
Probab=22.68 E-value=1e+02 Score=16.80 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=16.8
Q ss_pred CCCeEEEeceeecCCCCEEEEEEEEeC
Q 034307 53 DANAIFVFKFRTHFGGGKSTGFGLIYD 79 (98)
Q Consensus 53 ~~~~ivV~~~~t~fG~~~s~g~a~IYd 79 (98)
++...++.++. +...|+.++|+
T Consensus 14 ~es~~~iigi~-----~~~~G~v~l~s 35 (37)
T PF01394_consen 14 MESWKFIIGIS-----GRVKGQVQLYS 35 (37)
T ss_dssp CCEEEEEEEEE-----TCTEEEEEEEE
T ss_pred CcCeEEEEEEE-----eeeeeEEEEEE
Confidence 55677777777 66788999986
No 102
>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=22.61 E-value=1.5e+02 Score=18.25 Aligned_cols=34 Identities=12% Similarity=0.190 Sum_probs=22.9
Q ss_pred eeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 034307 21 RKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 21 RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV 59 (98)
-+.+.++|. ++-+-.+++++|++..++ +++.-=+
T Consensus 9 g~~~~v~v~----~~~Tv~~lK~~i~~~tgv-p~~~QKL 42 (74)
T cd01813 9 GQEYSVTTL----SEDTVLDLKQFIKTLTGV-LPERQKL 42 (74)
T ss_pred CEEEEEEEC----CCCCHHHHHHHHHHHHCC-CHHHEEE
Confidence 344554432 456677999999999998 6664333
No 103
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=22.54 E-value=86 Score=20.47 Aligned_cols=22 Identities=27% Similarity=0.261 Sum_probs=19.9
Q ss_pred EcCCCCCCCHHHHHHHHHhHcC
Q 034307 29 LHPGRANVSKAELKEKLARMYD 50 (98)
Q Consensus 29 ~h~~~~TPsr~ei~~klA~~~~ 50 (98)
.+||-++||.+-|...|+.+..
T Consensus 42 ~yp~i~~Ps~e~l~~~L~~Li~ 63 (80)
T PF10264_consen 42 HYPGIAIPSQEVLYNTLGTLIK 63 (80)
T ss_pred hCCCCCCCCHHHHHHHHHHHHH
Confidence 4688899999999999999987
No 104
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=22.33 E-value=1e+02 Score=18.84 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=17.4
Q ss_pred HHHHhHcCCCCCCeEEEeceeec
Q 034307 43 EKLARMYDVRDANAIFVFKFRTH 65 (98)
Q Consensus 43 ~klA~~~~v~~~~~ivV~~~~t~ 65 (98)
..|.+.++ .+.|.+++.||-|.
T Consensus 19 ~~lr~~~k-~~~DI~I~NGF~~~ 40 (57)
T PF14453_consen 19 FELRKESK-PDADIVILNGFPTK 40 (57)
T ss_pred HHHHHhhC-CCCCEEEEcCcccC
Confidence 45667788 69999999998774
No 105
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.33 E-value=2.3e+02 Score=18.34 Aligned_cols=38 Identities=16% Similarity=0.277 Sum_probs=27.4
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCH
Q 034307 39 AELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSV 81 (98)
Q Consensus 39 ~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~ 81 (98)
-+|-...|+.+|+.+.|.|.|. +.. |+..+.|.+.++.
T Consensus 33 v~i~p~dA~~lgi~~Gd~V~v~---~~~--G~v~~~v~~~~~v 70 (106)
T cd02789 33 CEINPEDYKLLGKPEGDKVKVT---SEF--GEVVVFAKENEGV 70 (106)
T ss_pred EEECHHHHHHcCCCCCCEEEEE---cCC--EEEEEEEEECCCC
Confidence 4455578999999888988776 444 4667777777643
No 106
>PRK03321 putative aminotransferase; Provisional
Probab=22.24 E-value=79 Score=24.06 Aligned_cols=26 Identities=23% Similarity=0.241 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHHhHcCCCCCCeEEEec
Q 034307 35 NVSKAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 35 TPsr~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
.+.-.++++.+|+.+++ +++.|++.+
T Consensus 56 ~~g~~~lr~~ia~~~~~-~~~~I~~~~ 81 (352)
T PRK03321 56 DMGAVELRAALAEHLGV-PPEHVAVGC 81 (352)
T ss_pred CCcHHHHHHHHHHHhCc-CHHHEEECC
Confidence 45678999999999995 887777653
No 107
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=22.13 E-value=1.2e+02 Score=16.92 Aligned_cols=19 Identities=16% Similarity=0.328 Sum_probs=12.2
Q ss_pred HHHHHHHhHcCCCCCCeEEE
Q 034307 40 ELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 40 ei~~klA~~~~v~~~~~ivV 59 (98)
+|.+.+++.+++ +++.++|
T Consensus 22 ~i~~~l~~~~g~-~~~~v~V 40 (58)
T cd00491 22 RVTEAVSEILGA-PEATIVV 40 (58)
T ss_pred HHHHHHHHHhCc-CcccEEE
Confidence 456667777885 6665554
No 108
>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=22.04 E-value=1.2e+02 Score=17.59 Aligned_cols=22 Identities=23% Similarity=0.382 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCe
Q 034307 34 ANVSKAELKEKLARMYDVRDANA 56 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ 56 (98)
++.+-.+++++|++..|+ +++.
T Consensus 19 ~~~tv~~lK~~i~~~~gi-~~~~ 40 (72)
T cd01809 19 EEITVLDLKEKIAEEVGI-PVEQ 40 (72)
T ss_pred CCCcHHHHHHHHHHHHCc-CHHH
Confidence 567899999999999997 5553
No 109
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=21.80 E-value=43 Score=19.70 Aligned_cols=18 Identities=22% Similarity=0.368 Sum_probs=14.7
Q ss_pred HHHHHHHHHhHcCCCCCCe
Q 034307 38 KAELKEKLARMYDVRDANA 56 (98)
Q Consensus 38 r~ei~~klA~~~~v~~~~~ 56 (98)
-++|.+.+|+.||+ +++-
T Consensus 2 ~~~I~~~Va~~~~i-~~~~ 19 (60)
T smart00760 2 IEEIIEAVAEYFGV-KPED 19 (60)
T ss_pred HHHHHHHHHHHhCC-CHHH
Confidence 57899999999997 5544
No 110
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=21.64 E-value=48 Score=21.90 Aligned_cols=32 Identities=16% Similarity=0.224 Sum_probs=23.6
Q ss_pred CcceeEEEEEEEcCCCCCCCHHHHHHHHHhHc
Q 034307 18 LLSRKQFVIDVLHPGRANVSKAELKEKLARMY 49 (98)
Q Consensus 18 LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~ 49 (98)
+|+.+.+.+++.+..+..|+++|+.+-++..-
T Consensus 18 ~L~~~~i~~~~idi~~~~~~~~el~~l~~~~~ 49 (117)
T TIGR01617 18 WLEANGIEYQFIDIGEDGPTREELLDILSLLE 49 (117)
T ss_pred HHHHcCCceEEEecCCChhhHHHHHHHHHHcC
Confidence 45667788888888777888888877666543
No 111
>PRK09382 ispDF bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional
Probab=21.50 E-value=1.6e+02 Score=23.81 Aligned_cols=37 Identities=19% Similarity=0.258 Sum_probs=28.7
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEece
Q 034307 24 FVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKF 62 (98)
Q Consensus 24 i~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~ 62 (98)
+.+....| +=.|-|.++++.||+.+++ +++.|-|.-=
T Consensus 313 ~~i~~~~p-k~~~~~~~~~~~~~~~l~~-~~~~v~~ka~ 349 (378)
T PRK09382 313 VTIIAEAP-KIGPHKQAMRENLAEILGI-PKDRVSVKAT 349 (378)
T ss_pred EEEEecCC-cchHHHHHHHHHHHHHhCC-CcceEEEEEe
Confidence 34444454 6789999999999999997 8888887643
No 112
>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=21.15 E-value=2.1e+02 Score=17.50 Aligned_cols=24 Identities=13% Similarity=0.252 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEE
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIF 58 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~iv 58 (98)
++-+-.|++++||+..++ +++..-
T Consensus 20 ~~~TV~~LK~~I~~~~~~-~~~~qr 43 (78)
T cd01804 20 PDETVEGLKKRISQRLKV-PKERLA 43 (78)
T ss_pred CcCHHHHHHHHHHHHhCC-ChHHEE
Confidence 455688999999999986 555443
No 113
>cd00502 DHQase_I Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is involved in the biosynthesis of aromatic amino acids. Type I DHQase exists as a homodimer. Type II 3-dehydroquinase also catalyzes the same overall reaction, but is unrelated in terms of sequence and structure, and utilizes a completely different reaction mechanism.
Probab=21.04 E-value=1.9e+02 Score=21.09 Aligned_cols=35 Identities=20% Similarity=0.286 Sum_probs=26.0
Q ss_pred eeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeE
Q 034307 21 RKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAI 57 (98)
Q Consensus 21 RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~i 57 (98)
+..+.+. +|.-.+||+..++.+.+.++... ..|.+
T Consensus 113 ~~kiI~S-~H~f~~tp~~~~l~~~~~~~~~~-gadiv 147 (225)
T cd00502 113 NTKIIGS-YHDFSGTPSDEELVSRLEKMAAL-GADIV 147 (225)
T ss_pred CCEEEEE-eccCCCCcCHHHHHHHHHHHHHh-CCCEE
Confidence 3455555 67678999999999999999773 55544
No 114
>PF01863 DUF45: Protein of unknown function DUF45; InterPro: IPR002725 Members of this family are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.
Probab=20.98 E-value=1.1e+02 Score=21.58 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=23.8
Q ss_pred HHHhHcCCCCCCeEEEeceeecCCCCEEEE
Q 034307 44 KLARMYDVRDANAIFVFKFRTHFGGGKSTG 73 (98)
Q Consensus 44 klA~~~~v~~~~~ivV~~~~t~fG~~~s~g 73 (98)
..++.+++ .+..|.|..++|..|.-.++|
T Consensus 120 ~~~~~~~~-~~~~i~ir~~ksrWGsc~~~~ 148 (205)
T PF01863_consen 120 KYAKKLGL-PPPKIKIRDMKSRWGSCSSKG 148 (205)
T ss_pred HHHHHcCC-CcceEEEeehhhccccCCCCC
Confidence 34788997 899999999999999874444
No 115
>COG1035 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]
Probab=20.97 E-value=1.5e+02 Score=23.98 Aligned_cols=40 Identities=23% Similarity=0.133 Sum_probs=32.1
Q ss_pred EEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEecee
Q 034307 23 QFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFR 63 (98)
Q Consensus 23 Ei~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~ 63 (98)
++.+.|--.-..|.+...+++.|-.++++ |+..|.=..+.
T Consensus 173 ~i~~~iGlfC~e~f~y~~l~~~l~e~~gv-d~~dV~k~di~ 212 (332)
T COG1035 173 KIVYVIGLFCMENFSYEGLKKFLEEDLGV-DPEDVEKMDIR 212 (332)
T ss_pred ceEEEEeeecCCCcCHHHHHHHHHHHhCC-CHHHeEEEEee
Confidence 46666666678999999999999999997 88777666654
No 116
>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=20.91 E-value=44 Score=26.51 Aligned_cols=40 Identities=25% Similarity=0.361 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEe-ceeecC-CCCEEEEEE
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVF-KFRTHF-GGGKSTGFG 75 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~-~~~t~f-G~~~s~g~a 75 (98)
+.-|+.||.++|.+.||+ .+.|.+- ++.... ..|.+.|+|
T Consensus 164 p~~s~~eie~~L~~~lG~--~kviwL~~g~~~~d~t~GHiD~~a 205 (329)
T PF04371_consen 164 PGLSKAEIEAELKRYLGV--EKVIWLPHGLLGDDDTDGHIDGIA 205 (329)
T ss_dssp TTS-HHHHHHHHHHHHT---SEEEEESS-STTTTTTSS-GGGTE
T ss_pred ccCCHHHHHHHHHHHhCC--CEEEEecCCcCCCCCcCCccceeE
Confidence 456899999999999997 5777777 444333 445544443
No 117
>smart00455 RBD Raf-like Ras-binding domain.
Probab=20.81 E-value=1.3e+02 Score=18.63 Aligned_cols=29 Identities=10% Similarity=0.029 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeEEEece
Q 034307 33 RANVSKAELKEKLARMYDVRDANAIFVFKF 62 (98)
Q Consensus 33 ~~TPsr~ei~~klA~~~~v~~~~~ivV~~~ 62 (98)
+|+-+-.|+-+++.+++|. +++.+.|+-.
T Consensus 17 rpg~tl~e~L~~~~~kr~l-~~~~~~v~~~ 45 (70)
T smart00455 17 RPGKTVRDALAKALKKRGL-NPECCVVRLR 45 (70)
T ss_pred CCCCCHHHHHHHHHHHcCC-CHHHEEEEEc
Confidence 5677899999999999997 9999999864
No 118
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=20.69 E-value=59 Score=19.06 Aligned_cols=21 Identities=33% Similarity=0.493 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHHHhHcCCCCCC
Q 034307 34 ANVSKAELKEKLARMYDVRDAN 55 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~ 55 (98)
+.-|..||.+.|++.|++ +++
T Consensus 28 g~~t~~ei~~~l~~~y~~-~~~ 48 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDV-DPE 48 (68)
T ss_dssp SSS-HHHHHHHHHHHTT---HH
T ss_pred CCCCHHHHHHHHHHHcCC-CHH
Confidence 357899999999999996 665
No 119
>cd08619 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains u
Probab=20.59 E-value=3.5e+02 Score=21.50 Aligned_cols=46 Identities=13% Similarity=0.238 Sum_probs=36.2
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEE
Q 034307 26 IDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKST 72 (98)
Q Consensus 26 ~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~ 72 (98)
+.+.|---..-+-.++-+.+..-+. ..|.-+||-.|+..||.....
T Consensus 81 ~~~~HG~~~~~~~~dvL~~i~~FL~-~hp~EvVIL~~k~ey~~~~~~ 126 (285)
T cd08619 81 RRVCHGCLKTYPVDVVLNDIKRFLS-ETKSEFVILEIRTEYGHEDPP 126 (285)
T ss_pred eEEECCCcCCCcHHHHHHHHHHHHH-HCCCeEEEEEEeecccCCCch
Confidence 4567822244578899999999998 589889999999999998663
No 120
>PRK01261 aroD 3-dehydroquinate dehydratase; Provisional
Probab=20.48 E-value=1.5e+02 Score=22.44 Aligned_cols=21 Identities=10% Similarity=0.124 Sum_probs=17.7
Q ss_pred CCCHHHHHHHHHhHcCCCCCCe
Q 034307 35 NVSKAELKEKLARMYDVRDANA 56 (98)
Q Consensus 35 TPsr~ei~~klA~~~~v~~~~~ 56 (98)
||+.+|+.+.+++|... ..|.
T Consensus 128 tp~~eeL~~~l~~m~~~-gaDI 148 (229)
T PRK01261 128 TNNSDNMPAILDIMNEK-NPDY 148 (229)
T ss_pred CCCHHHHHHHHHHHHHh-CCCE
Confidence 99999999999999873 5553
No 121
>PRK00950 histidinol-phosphate aminotransferase; Validated
Probab=20.47 E-value=93 Score=23.63 Aligned_cols=26 Identities=27% Similarity=0.331 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFVF 60 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV~ 60 (98)
+.|.-.++++.||+.+++ +++.|++.
T Consensus 67 ~~~~~~~lr~~ia~~~~~-~~~~i~~~ 92 (361)
T PRK00950 67 PEPDAPELREALSKYTGV-PVENIIVG 92 (361)
T ss_pred CCCCHHHHHHHHHHHhCC-CHHHEEEe
Confidence 334558999999999996 88888873
No 122
>COG0070 GltB Glutamate synthase domain 3 [Amino acid transport and metabolism]
Probab=20.30 E-value=82 Score=25.26 Aligned_cols=38 Identities=18% Similarity=0.288 Sum_probs=26.4
Q ss_pred CCCeEEEeceeecCCCCEEEEEEEEeCCHHH--HHhcCcc
Q 034307 53 DANAIFVFKFRTHFGGGKSTGFGLIYDSVES--AKKFEPK 90 (98)
Q Consensus 53 ~~~~ivV~~~~t~fG~~~s~g~a~IYds~e~--~kk~Epk 90 (98)
.-.+||+-..--.||.|.|-|.|.|||+.+. .++..++
T Consensus 187 GG~VvVLG~~G~nfgaGMsGG~aYV~~~~~~~f~~~~n~~ 226 (301)
T COG0070 187 GGRVVVLGDTGRNFGAGMSGGVAYVRGEVGSDFPLGVNAE 226 (301)
T ss_pred CCEEEEeCCcchhhcCcccceEEEEecCccchhhcCccce
Confidence 4455555555544999999999999999863 3444443
No 123
>PRK02731 histidinol-phosphate aminotransferase; Validated
Probab=20.23 E-value=95 Score=23.72 Aligned_cols=23 Identities=35% Similarity=0.417 Sum_probs=18.4
Q ss_pred HHHHHHHHHhHcCCCCCCeEEEec
Q 034307 38 KAELKEKLARMYDVRDANAIFVFK 61 (98)
Q Consensus 38 r~ei~~klA~~~~v~~~~~ivV~~ 61 (98)
-.++++.+|+.+++ +++.|++.+
T Consensus 69 ~~~lr~~ia~~~~~-~~~~i~~t~ 91 (367)
T PRK02731 69 GFELKAALAEKFGV-DPERIILGN 91 (367)
T ss_pred HHHHHHHHHHHhCc-CHHHEEEcC
Confidence 46899999999996 887776543
No 124
>PHA01632 hypothetical protein
Probab=20.16 E-value=26 Score=21.85 Aligned_cols=53 Identities=25% Similarity=0.294 Sum_probs=32.8
Q ss_pred eeccCcceeEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceeecCCCCEEEEEEEEeCCHH
Q 034307 14 MTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFGLIYDSVE 82 (98)
Q Consensus 14 ~~N~LL~RkEi~~~v~h~~~~TPsr~ei~~klA~~~~v~~~~~ivV~~~~t~fG~~~s~g~a~IYds~e 82 (98)
..|++|.=+-. +-|.+. ---|+.+|++..|.++++ | |+...-.|..+|-||.+
T Consensus 8 eknk~lhikiy-ilieqv-p~kpteeelrkvlpkilk--d------------yanmie~gk~ki~ds~e 60 (64)
T PHA01632 8 EKNKTLHIKIY-ILIEQV-PQKPTEEELRKVLPKILK--D------------YANMIENGKIKILDSKE 60 (64)
T ss_pred CCCcEEEEEEE-Eehhhc-CCCCCHHHHHHHHHHHHH--H------------HHHHHhcCceEEecccc
Confidence 34666654322 223332 457899999999999987 2 44555556666666643
No 125
>PRK14808 histidinol-phosphate aminotransferase; Provisional
Probab=20.01 E-value=1.4e+02 Score=22.99 Aligned_cols=25 Identities=28% Similarity=0.324 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHhHcC---CCCCCeEEEe
Q 034307 35 NVSKAELKEKLARMYD---VRDANAIFVF 60 (98)
Q Consensus 35 TPsr~ei~~klA~~~~---v~~~~~ivV~ 60 (98)
.|.-.++++++|+.++ + +++.|++.
T Consensus 55 ~~~~~~Lr~aia~~~~~~~~-~~~~i~it 82 (335)
T PRK14808 55 DSPDEELIEKILSYLDTDFL-SKNNVSVG 82 (335)
T ss_pred CCChHHHHHHHHHHhCCCCC-CcceEEEc
Confidence 3467899999999998 6 67777664
No 126
>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=20.00 E-value=1.2e+02 Score=17.95 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEE
Q 034307 34 ANVSKAELKEKLARMYDVRDANAIFV 59 (98)
Q Consensus 34 ~TPsr~ei~~klA~~~~v~~~~~ivV 59 (98)
++=+-.++++.||+..|+ +++...+
T Consensus 17 ~~~tV~~lK~~i~~~~gi-~~~~q~L 41 (70)
T cd01798 17 PDTDIKQLKEVVAKRQGV-PPDQLRV 41 (70)
T ss_pred CCChHHHHHHHHHHHHCC-CHHHeEE
Confidence 455788999999999997 6655444
Done!