Query 032760
Match_columns 134
No_of_seqs 107 out of 321
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 05:36:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032760.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032760hhsearch_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 1.1E-55 2.4E-60 331.9 13.6 127 5-131 5-131 (132)
2 KOG3424 40S ribosomal protein 100.0 2.8E-56 6.1E-61 330.7 9.0 131 1-133 1-131 (132)
3 PRK01178 rps24e 30S ribosomal 100.0 1.4E-42 3E-47 250.1 11.1 94 8-102 3-96 (99)
4 COG2004 RPS24A Ribosomal prote 100.0 6.1E-42 1.3E-46 249.6 10.4 104 6-115 2-105 (107)
5 PF01282 Ribosomal_S24e: Ribos 100.0 2.6E-35 5.6E-40 206.2 10.0 83 24-107 1-84 (84)
6 PF00076 RRM_1: RNA recognitio 70.3 17 0.00037 21.9 5.0 47 34-87 8-55 (70)
7 smart00360 RRM RNA recognition 65.2 25 0.00053 20.4 5.4 48 34-87 6-54 (71)
8 COG2003 RadC DNA repair protei 60.2 13 0.00028 30.6 3.8 35 28-64 173-210 (224)
9 PF12327 FtsZ_C: FtsZ family, 59.1 11 0.00024 26.4 2.8 52 12-64 22-77 (95)
10 TIGR03636 L23_arch archaeal ri 56.7 42 0.0009 23.1 5.3 57 17-82 9-66 (77)
11 PF00276 Ribosomal_L23: Riboso 54.3 28 0.0006 24.3 4.2 57 15-78 13-77 (91)
12 PTZ00191 60S ribosomal protein 49.7 1.1E+02 0.0024 23.6 7.2 56 22-86 83-141 (145)
13 PRK14548 50S ribosomal protein 49.4 62 0.0013 22.6 5.3 62 13-83 12-74 (84)
14 PF04432 FrhB_FdhB_C: Coenzyme 48.9 33 0.00072 25.7 4.2 44 20-64 29-72 (161)
15 CHL00030 rpl23 ribosomal prote 46.6 51 0.0011 23.4 4.6 45 13-64 11-55 (93)
16 PF08496 Peptidase_S49_N: Pept 46.3 45 0.00097 25.8 4.6 54 21-76 96-150 (155)
17 COG0245 IspF 2C-methyl-D-eryth 43.1 52 0.0011 25.9 4.5 40 24-65 96-135 (159)
18 PF12436 USP7_ICP0_bdg: ICP0-b 42.2 28 0.00061 28.3 3.1 56 15-71 170-234 (249)
19 COG0710 AroD 3-dehydroquinate 40.3 45 0.00098 27.4 4.0 34 25-59 119-152 (231)
20 PRK05738 rplW 50S ribosomal pr 39.7 62 0.0014 22.7 4.1 34 14-51 12-46 (92)
21 PLN03134 glycine-rich RNA-bind 39.3 1.1E+02 0.0023 22.8 5.6 47 34-86 44-91 (144)
22 cd08059 MPN_prok_mb Mpr1p, Pad 38.7 66 0.0014 21.9 4.1 31 24-59 59-90 (101)
23 PRK06425 histidinol-phosphate 36.8 42 0.00092 27.4 3.3 26 34-60 38-63 (332)
24 KOG2116 Protein involved in pl 35.7 61 0.0013 31.0 4.5 34 43-78 491-524 (738)
25 PF14560 Ubiquitin_2: Ubiquiti 35.6 1.2E+02 0.0025 20.3 4.9 27 34-61 22-48 (87)
26 PRK10513 sugar phosphate phosp 35.5 54 0.0012 25.7 3.7 33 25-61 187-219 (270)
27 PRK15126 thiamin pyrimidine py 35.0 48 0.001 26.2 3.3 33 25-61 179-211 (272)
28 PRK14864 putative biofilm stre 34.7 1.8E+02 0.0039 21.1 6.2 51 25-79 53-103 (104)
29 PRK00084 ispF 2-C-methyl-D-ery 34.6 62 0.0013 25.3 3.8 39 24-64 98-136 (159)
30 TIGR00608 radc DNA repair prot 34.4 42 0.00091 27.1 2.9 36 24-59 163-204 (218)
31 PRK12280 rplW 50S ribosomal pr 34.2 43 0.00094 26.2 2.8 36 12-51 13-48 (158)
32 PRK10976 putative hydrolase; P 34.2 54 0.0012 25.7 3.4 33 25-61 181-213 (266)
33 PRK00024 hypothetical protein; 34.2 66 0.0014 25.9 4.0 36 24-59 169-210 (224)
34 KOG3969 Uncharacterized conser 33.8 47 0.001 28.7 3.2 58 38-96 218-290 (310)
35 TIGR01482 SPP-subfamily Sucros 33.5 70 0.0015 24.1 3.9 33 25-61 140-172 (225)
36 TIGR01485 SPP_plant-cyano sucr 33.3 90 0.0019 24.5 4.6 32 26-61 159-190 (249)
37 PF07338 DUF1471: Protein of u 33.0 1.3E+02 0.0029 19.1 4.9 49 25-78 7-55 (56)
38 cd00590 RRM RRM (RNA recogniti 33.0 1E+02 0.0022 17.8 5.2 47 34-87 9-56 (74)
39 PTZ00397 macrophage migration 31.5 1E+02 0.0022 21.7 4.2 35 25-60 60-99 (116)
40 PRK01688 histidinol-phosphate 31.4 43 0.00092 27.7 2.6 27 34-61 55-81 (351)
41 smart00362 RRM_2 RNA recogniti 31.0 1.1E+02 0.0024 17.5 5.0 46 34-87 9-55 (72)
42 PF01996 F420_ligase: F420-0:G 30.6 36 0.00078 27.6 1.9 53 27-81 125-177 (228)
43 TIGR01661 ELAV_HUD_SF ELAV/HuD 30.2 1.5E+02 0.0033 24.0 5.6 53 26-85 272-325 (352)
44 COG3561 Phage anti-repressor p 29.8 1E+02 0.0022 22.9 4.0 58 32-89 23-80 (110)
45 PHA01976 helix-turn-helix prot 29.5 26 0.00056 21.9 0.8 24 32-57 38-61 (67)
46 COG2006 Uncharacterized conser 29.1 59 0.0013 27.9 3.0 43 29-73 171-213 (293)
47 PRK06959 putative threonine-ph 29.0 61 0.0013 26.8 3.1 25 36-61 54-78 (339)
48 cd00554 MECDP_synthase MECDP_s 28.7 98 0.0021 24.0 4.0 36 24-61 95-130 (153)
49 TIGR00151 ispF 2C-methyl-D-ery 28.7 92 0.002 24.2 3.8 36 24-61 95-130 (155)
50 PRK13817 ribosome-binding fact 28.6 2E+02 0.0044 20.9 5.5 44 39-82 10-57 (119)
51 KOG3439 Protein conjugation fa 28.5 2.6E+02 0.0055 21.0 6.2 34 33-67 83-116 (116)
52 cd02777 MopB_CT_DMSOR-like The 28.2 1.5E+02 0.0032 20.9 4.6 38 39-81 36-73 (127)
53 PF02542 YgbB: YgbB family; I 28.2 55 0.0012 25.5 2.5 31 28-60 100-130 (157)
54 PRK13815 ribosome-binding fact 28.0 2.4E+02 0.0053 20.6 6.0 44 39-82 10-57 (122)
55 PRK01158 phosphoglycolate phos 27.8 81 0.0018 23.9 3.4 33 25-61 148-180 (230)
56 PF08766 DEK_C: DEK C terminal 27.1 53 0.0011 20.5 1.9 21 32-53 17-37 (54)
57 PF09581 Spore_III_AF: Stage I 26.7 41 0.00088 25.5 1.6 23 37-60 165-187 (188)
58 cd08071 MPN_DUF2466 Mov34/MPN/ 26.7 1.3E+02 0.0029 21.5 4.2 38 22-59 61-104 (113)
59 PRK05387 histidinol-phosphate 26.6 57 0.0012 26.4 2.5 25 36-61 60-84 (353)
60 PLN03026 histidinol-phosphate 26.5 72 0.0016 26.8 3.1 25 35-60 85-109 (380)
61 PRK04781 histidinol-phosphate 26.4 61 0.0013 27.0 2.7 26 35-61 58-83 (364)
62 TIGR03576 pyridox_MJ0158 pyrid 26.2 60 0.0013 27.3 2.6 28 33-61 51-78 (346)
63 PF02594 DUF167: Uncharacteris 25.1 1E+02 0.0022 21.0 3.1 43 22-64 26-68 (77)
64 PRK07392 threonine-phosphate d 25.0 74 0.0016 26.2 2.9 25 36-61 57-81 (360)
65 cd01804 midnolin_N Ubiquitin-l 24.8 2.1E+02 0.0046 18.8 4.9 24 34-58 20-43 (78)
66 cd00508 MopB_CT_Fdh-Nap-like T 24.7 1.5E+02 0.0033 20.1 4.1 36 41-81 39-74 (120)
67 PF03090 Replicase: Replicase 24.6 1.3E+02 0.0029 22.6 4.0 39 14-59 18-56 (137)
68 TIGR01484 HAD-SF-IIB HAD-super 24.6 1.2E+02 0.0027 22.6 3.8 33 25-61 154-186 (204)
69 PRK10259 hypothetical protein; 24.4 2.1E+02 0.0046 20.1 4.7 40 37-79 47-86 (86)
70 PF14535 AMP-binding_C_2: AMP- 24.3 2.2E+02 0.0048 19.3 4.8 39 21-60 33-78 (96)
71 PRK14807 histidinol-phosphate 24.2 95 0.0021 25.5 3.4 26 35-61 58-83 (351)
72 PRK02220 4-oxalocrotonate taut 24.1 88 0.0019 19.2 2.5 19 40-59 23-41 (61)
73 TIGR01642 U2AF_lg U2 snRNP aux 23.6 1.4E+02 0.0031 25.7 4.5 46 34-85 305-351 (509)
74 cd06397 PB1_UP1 Uncharacterize 23.6 1.5E+02 0.0033 20.9 3.8 30 34-64 18-47 (82)
75 PRK14809 histidinol-phosphate 23.5 97 0.0021 25.4 3.3 25 36-61 65-89 (357)
76 PF10264 Stork_head: Winged he 23.5 85 0.0018 21.9 2.5 23 29-51 42-64 (80)
77 COG0561 Cof Predicted hydrolas 23.5 1E+02 0.0022 24.2 3.3 31 26-60 181-211 (264)
78 COG0299 PurN Folate-dependent 23.3 1.3E+02 0.0027 24.6 3.8 31 33-63 59-89 (200)
79 COG1888 Uncharacterized protei 23.1 1.9E+02 0.004 21.1 4.2 48 22-71 6-53 (97)
80 PF10503 Esterase_phd: Esteras 22.9 9.7 0.00021 30.7 -2.6 34 37-73 80-113 (220)
81 PRK01964 4-oxalocrotonate taut 22.9 96 0.0021 19.4 2.5 20 40-60 23-42 (64)
82 PF04110 APG12: Ubiquitin-like 22.7 28 0.00062 24.6 0.0 33 34-67 55-87 (87)
83 TIGR00013 taut 4-oxalocrotonat 22.7 1.2E+02 0.0025 18.7 2.9 19 40-59 23-41 (63)
84 TIGR00099 Cof-subfamily Cof su 22.7 1.1E+02 0.0024 23.8 3.3 33 25-61 179-211 (256)
85 PRK04635 histidinol-phosphate 22.5 79 0.0017 26.0 2.6 25 36-61 60-84 (354)
86 cd01796 DDI1_N DNA damage indu 22.4 99 0.0021 20.0 2.6 26 34-60 18-44 (71)
87 cd02794 MopB_CT_DmsA-EC The Mo 22.3 2.3E+02 0.005 19.7 4.7 38 40-82 33-70 (121)
88 TIGR01141 hisC histidinol-phos 22.3 87 0.0019 25.3 2.8 27 34-61 52-78 (346)
89 PRK06358 threonine-phosphate d 22.2 94 0.002 25.7 3.0 25 36-61 54-78 (354)
90 PRK01261 aroD 3-dehydroquinate 22.1 1.2E+02 0.0027 24.5 3.6 21 35-56 128-148 (229)
91 PRK08056 threonine-phosphate d 21.9 84 0.0018 25.9 2.7 25 36-61 55-79 (356)
92 KOG0113 U1 small nuclear ribon 21.7 2.1E+02 0.0045 25.0 5.0 52 24-85 105-157 (335)
93 cd01806 Nedd8 Nebb8-like ubiq 21.7 1.4E+02 0.0031 18.7 3.2 22 34-56 19-40 (76)
94 PRK08153 histidinol-phosphate 21.6 70 0.0015 26.6 2.1 25 36-61 67-91 (369)
95 PF00388 PI-PLC-X: Phosphatidy 21.2 2.4E+02 0.0051 20.4 4.7 54 6-68 43-98 (146)
96 cd01791 Ubl5 UBL5 ubiquitin-li 21.0 1.3E+02 0.0028 19.9 3.0 25 34-59 20-44 (73)
97 PRK01533 histidinol-phosphate 20.9 1.2E+02 0.0026 25.4 3.4 25 36-61 64-88 (366)
98 PF01394 Clathrin_propel: Clat 20.8 1E+02 0.0023 17.9 2.2 22 53-79 14-35 (37)
99 PLN02862 2-C-methyl-D-erythrit 20.8 1.4E+02 0.0031 24.5 3.7 35 25-61 156-190 (216)
100 PRK09105 putative aminotransfe 20.7 95 0.0021 26.0 2.8 24 37-61 79-102 (370)
101 cd00491 4Oxalocrotonate_Tautom 20.4 1.3E+02 0.0029 18.0 2.8 19 40-59 22-40 (58)
102 cd01789 Alp11_N Ubiquitin-like 20.2 2.8E+02 0.0061 18.6 5.3 34 23-59 12-45 (84)
103 TIGR01140 L_thr_O3P_dcar L-thr 20.2 1.1E+02 0.0023 25.0 2.9 27 34-61 45-71 (330)
104 PHA01632 hypothetical protein 20.1 47 0.001 22.2 0.7 36 14-51 8-43 (64)
No 1
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=100.00 E-value=1.1e-55 Score=331.86 Aligned_cols=127 Identities=60% Similarity=0.955 Sum_probs=122.3
Q ss_pred ceEEEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHHHH
Q 032760 5 AVTIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVDSA 84 (134)
Q Consensus 5 ~v~i~~~k~~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e~~ 84 (134)
+|||+|++|++||||+|+||+|+|+|||.||||+.||+++||+||+++|+|+|||++|+|+||+|+|+|||+||||+|+|
T Consensus 5 ~~~ir~rk~~~NpLL~RkE~~~~v~Hpg~~TpSr~eirekLA~~~~v~d~~~Vvv~~~~T~fG~g~StG~a~IYds~e~~ 84 (132)
T PTZ00071 5 EFTVRTRKFLVNPLLNRKQFVVEVLHPGKGTVSKKDIKEKLAKQYKVADARTIVLFGFKTKFGGGKTTGFGLIYDNLAAL 84 (132)
T ss_pred cEEEEEeeeeeccCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHhCCCCCCEEEEEccEecCCCceEEEEEEEECCHHHH
Confidence 69999999999999999999999999999999999999999999994499999999999999999999999999999999
Q ss_pred HhcCCchhhhhcCCccccccchhhHHHHhhhccccccccccccchhh
Q 032760 85 KKFEPKYRLIRNGLDTKVEKSRKQMKERKNRAKKIRGVKKTKASDAA 131 (134)
Q Consensus 85 kk~Epk~~l~Rn~~~e~~k~~rk~~ke~kn~~kk~~Gt~k~~~~~~~ 131 (134)
++|||+|+|+||++.+..+.+|+|+||.||++||+|||+++++..++
T Consensus 85 kk~Epk~~l~Rngl~~~~~~~rk~rke~knr~kk~rg~~k~k~~~~~ 131 (132)
T PTZ00071 85 KKFEPKYRLIRLGLIKKKKAGRKARKELKNRRKKVRGKEKTKVSGKK 131 (132)
T ss_pred HhhCchheeeecCccccCccchHHHHHHHhhhhhhccchhhhhhhcc
Confidence 99999999999999998888999999999999999999999986544
No 2
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-56 Score=330.72 Aligned_cols=131 Identities=74% Similarity=1.109 Sum_probs=128.1
Q ss_pred CCCcceEEEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCC
Q 032760 1 MADKAVTIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDS 80 (134)
Q Consensus 1 m~~~~v~i~~~k~~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds 80 (134)
|+| +|||+|++||+|+||+|+||++||+|||.|+||++||+|+||+||.+ ++|+||||+|+|+||+|+|+|||+||||
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 777 89999999999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred HHHHHhcCCchhhhhcCCccccccchhhHHHHhhhccccccccccccchhhhc
Q 032760 81 VDSAKKFEPKYRLIRNGLDTKVEKSRKQMKERKNRAKKIRGVKKTKASDAAKK 133 (134)
Q Consensus 81 ~e~~kk~Epk~~l~Rn~~~e~~k~~rk~~ke~kn~~kk~~Gt~k~~~~~~~k~ 133 (134)
+|+|++|||+|+|+|+|+.|..+++|+||||++|+++|+|||.|++++.++++
T Consensus 79 ve~akkfEpkyrl~r~gl~e~~kt~RkqrKerknr~kKi~Gt~K~~~~~~~k~ 131 (132)
T KOG3424|consen 79 VEYAKKFEPKYRLVRLGLAEKIKTSRKQRKERKNRMKKIFGTGKRKAKKAKKK 131 (132)
T ss_pred HHHHHhcCcceeeeecccccccccHHHHHHHHhhccchheeHHHHHhhhhhcc
Confidence 99999999999999999999998899999999999999999999999988875
No 3
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=100.00 E-value=1.4e-42 Score=250.12 Aligned_cols=94 Identities=36% Similarity=0.610 Sum_probs=91.4
Q ss_pred EEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHHHHHhc
Q 032760 8 IRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVDSAKKF 87 (134)
Q Consensus 8 i~~~k~~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e~~kk~ 87 (134)
|.|.++.+||||+|+||+|+|+|||.|||||.||+++||+||++ |+|+|||++|+|+||+|+|+|||+||||.|+|++|
T Consensus 3 i~I~~~~~N~LL~Rke~~~~v~h~g~~tpsr~eirekLa~~~~~-~~~~vvv~~~~t~fG~g~s~G~a~IYds~e~~kk~ 81 (99)
T PRK01178 3 IKIISDKENPLLGRREIKFEVYHEGSATPSRKDVRKKLAAMLNA-DKELVVVRKIKTEYGMGKSKGYAKVYDDKERARKI 81 (99)
T ss_pred EEEEEeeecCCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHHCc-CCCEEEEEccCccCCCceEEEEEEEECCHHHHHhh
Confidence 67889999999999999999999999999999999999999998 99999999999999999999999999999999999
Q ss_pred CCchhhhhcCCcccc
Q 032760 88 EPKYRLIRNGLDTKV 102 (134)
Q Consensus 88 Epk~~l~Rn~~~e~~ 102 (134)
||+|+|.||++.+++
T Consensus 82 Epk~~l~Rn~~~~~~ 96 (99)
T PRK01178 82 EPKYILERNKIEEEE 96 (99)
T ss_pred CchheeeecCccccc
Confidence 999999999998764
No 4
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.1e-42 Score=249.55 Aligned_cols=104 Identities=42% Similarity=0.633 Sum_probs=99.6
Q ss_pred eEEEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHHHHH
Q 032760 6 VTIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVDSAK 85 (134)
Q Consensus 6 v~i~~~k~~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e~~k 85 (134)
++|.|.++++||||+|+||+|+|+|||++||||.||+++||++|++ |+++|||++|+|+||+|+|+|||+||||.+.|+
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 MEIKILEKRDNPLLKRKEIVFVVYHEGSPTPSRKEVREKLAAMLGA-DKELVVVDYIKTEFGKGRSKGYAKIYDSVERAK 80 (107)
T ss_pred ceEEeehcccCccccceEEEEEEEeCCCCCCCHHHHHHHHHHHHCC-CcceEEEEehhhhcCCcceeEEEEEECCHHHHH
Confidence 6899999999999999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred hcCCchhhhhcCCccccccchhhHHHHhhh
Q 032760 86 KFEPKYRLIRNGLDTKVEKSRKQMKERKNR 115 (134)
Q Consensus 86 k~Epk~~l~Rn~~~e~~k~~rk~~ke~kn~ 115 (134)
+|||+|+|.||++ ..+.+.+|++++
T Consensus 81 ~iEp~yiL~Rn~~-----~~~~~~eE~e~r 105 (107)
T COG2004 81 KIEPEYILERNGG-----AERQEAEEAENR 105 (107)
T ss_pred hcCcceEEEeccc-----hhhhhhHhhhcc
Confidence 9999999999998 456777787777
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=2.6e-35 Score=206.23 Aligned_cols=83 Identities=60% Similarity=1.016 Sum_probs=74.6
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHHHHHhcCCchhhhhcCCccccc
Q 032760 24 FVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVDSAKKFEPKYRLIRNGLDTKVE 103 (134)
Q Consensus 24 i~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e~~kk~Epk~~l~Rn~~~e~~k 103 (134)
|+|+|+|||.|||||+||+++||+|||+ |+|+|||++|+|+||++.|+|||+||||+|+|++|||+|+|.||++.++..
T Consensus 1 ~~~~v~h~g~~Tpsr~ei~~klA~~~~~-~~~~ivv~~~~t~fG~~~s~g~a~IYd~~e~~kk~Ep~~~l~R~~~~e~~~ 79 (84)
T PF01282_consen 1 MVFEVLHPGKPTPSRKEIREKLAAMLNV-DPDLIVVFGIKTEFGGGKSTGFAKIYDSAEALKKFEPKYRLKRNGLEEKKE 79 (84)
T ss_dssp EEEEEE-SSSSS--HHHHHHHHHHHHTS-TGCCEEEEEEEESSSSSEEEEEEEEESSHHHHHHHSTHHHHHHTTSSSS-S
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHhCC-CCCeEEEeccEecCCCceEEEEEEEeCCHHHHHHhCcHHHhHhcCcccccc
Confidence 6899999999999999999999999999 999999999999999999999999999999999999999999999988754
Q ss_pred -cchh
Q 032760 104 -KSRK 107 (134)
Q Consensus 104 -~~rk 107 (134)
.+|+
T Consensus 80 ~~~r~ 84 (84)
T PF01282_consen 80 KEGRK 84 (84)
T ss_dssp -S-HH
T ss_pred ccccC
Confidence 4553
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=70.30 E-value=17 Score=21.95 Aligned_cols=47 Identities=23% Similarity=0.496 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHHhc
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAKKF 87 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~kk~ 87 (134)
+..+..||++.+.. +|. -... .+.+. +.+.+.|||.| |+|.+.+++.
T Consensus 8 ~~~t~~~l~~~f~~-~g~-i~~~----~~~~~-~~~~~~~~a~V~F~~~~~a~~a 55 (70)
T PF00076_consen 8 PDVTEEELRDFFSQ-FGK-IESI----KVMRN-SSGKSKGYAFVEFESEEDAEKA 55 (70)
T ss_dssp TTSSHHHHHHHHHT-TST-EEEE----EEEEE-TTSSEEEEEEEEESSHHHHHHH
T ss_pred CcCCHHHHHHHHHH-hhh-cccc----ccccc-ccccccceEEEEEcCHHHHHHH
Confidence 45778999999866 666 2122 22232 77778888876 7787777653
No 7
>smart00360 RRM RNA recognition motif.
Probab=65.16 E-value=25 Score=20.36 Aligned_cols=48 Identities=25% Similarity=0.466 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHHhc
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAKKF 87 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~kk~ 87 (134)
...+..+|++.+. .+|. -.++ .+......+.+.|||.| |++.+.+...
T Consensus 6 ~~~~~~~l~~~f~-~~g~-v~~~----~i~~~~~~~~~~~~a~v~f~~~~~a~~a 54 (71)
T smart00360 6 PDVTEEELRELFS-KFGK-IESV----RLVRDKDTGKSKGFAFVEFESEEDAEKA 54 (71)
T ss_pred cccCHHHHHHHHH-hhCC-EeEE----EEEeCCCCCCCCceEEEEeCCHHHHHHH
Confidence 3467889998885 5563 1222 22334446778888888 7888877654
No 8
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=60.21 E-value=13 Score=30.65 Aligned_cols=35 Identities=20% Similarity=0.254 Sum_probs=27.3
Q ss_pred EEcC-CCCCCCHHHH--HHHHHhHcCCCCCCeEEEeceEe
Q 032760 28 VLHP-GRANVSKAEL--KEKLARMYDVKDPNSIFVFKFRT 64 (134)
Q Consensus 28 v~H~-g~~Tpsr~eI--~~kLA~~~~~~~~~~ivV~~~~T 64 (134)
=.|| |.+|||++|+ -++|++..+. -+..+++.|-.
T Consensus 173 HNHPSGd~~PS~aD~~iT~rl~~a~~l--l~I~vLDHiIi 210 (224)
T COG2003 173 HNHPSGDPTPSRADILITERLKEAGKL--LGIRLLDHIII 210 (224)
T ss_pred ccCCCCCCCcCHHHHHHHHHHHHHHHh--cCceeeeeEEe
Confidence 3578 6899999965 6788888776 57778887777
No 9
>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=59.09 E-value=11 Score=26.38 Aligned_cols=52 Identities=17% Similarity=0.282 Sum_probs=30.8
Q ss_pred eeeeccCccceEE----EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEe
Q 032760 12 KFMTNRLLSRKQF----VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRT 64 (134)
Q Consensus 12 k~~~NpLL~RkEi----~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T 64 (134)
+-+.||||+ ..+ .+-|.-.|++.++-.|+.+.+-......+++.-+++|...
T Consensus 22 ~Al~spLl~-~~i~~A~~vLvni~~~~d~~l~ev~~~~~~i~~~~~~~a~ii~G~~i 77 (95)
T PF12327_consen 22 QALNSPLLD-VDIKGAKGVLVNITGGPDLSLSEVNEAMEIIREKADPDANIIWGASI 77 (95)
T ss_dssp HHHTSTTST-S-GGG-SEEEEEEEE-TTS-HHHHHHHHHHHHHHSSTTSEEEEEEEE
T ss_pred HHHhCcccc-CChHHhceEEEEEEcCCCCCHHHHHHHHHHHHHHhhcCceEEEEEEE
Confidence 346799998 444 2333334568899998888776554433566666666543
No 10
>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=56.72 E-value=42 Score=23.06 Aligned_cols=57 Identities=16% Similarity=0.293 Sum_probs=38.3
Q ss_pred cCccc-eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHH
Q 032760 17 RLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVD 82 (134)
Q Consensus 17 pLL~R-kEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e 82 (134)
.|+.. .++.|.|.-. .++.||++.+-.+|++ .+.=|..+... ++.=.+|....+..+
T Consensus 9 ~~~e~~n~y~F~V~~~----anK~eIK~avE~lf~V---kV~~Vnt~~~~--~~~KKA~VtL~~g~~ 66 (77)
T TIGR03636 9 NLIEKENKLTFIVDRK----ATKGDIKRAVEKLFDV---KVEKVNTLITP--RGEKKAYVKLAEEYA 66 (77)
T ss_pred HHHHhCCEEEEEECCC----CCHHHHHHHHHHHhCC---ceEEEEeEEcC--CCceEEEEEECCCCc
Confidence 35554 6888888654 7799999999999999 44445555443 344556666555443
No 11
>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=54.27 E-value=28 Score=24.26 Aligned_cols=57 Identities=25% Similarity=0.398 Sum_probs=36.1
Q ss_pred eccCccc-eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEec-----CCC--CEEEEEEEEe
Q 032760 15 TNRLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTH-----FGG--GKSTGFGLIY 78 (134)
Q Consensus 15 ~NpLL~R-kEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~-----fG~--g~s~g~a~IY 78 (134)
...|+.. .++.|.|. +..++.||++.|-+.||+ . ++-|..+... +|. |...+|=+.|
T Consensus 13 s~~~~~~~n~~tF~V~----~~atK~~Ik~aie~iy~V-~--V~~Vnt~~~~gk~kR~g~~~g~~~~~KKai 77 (91)
T PF00276_consen 13 SMKLLENPNQYTFEVD----PRATKTEIKEAIEKIYGV-K--VKKVNTMNYPGKKKRKGKFVGKTKDYKKAI 77 (91)
T ss_dssp HHHHHHHSSEEEEEET----TTSTHHHHHHHHHHHHTS-E--EEEEEEEEETSEEEESSSCEEEE-EEEEEE
T ss_pred HHHhhhcCCEEEEEEe----CCCCHHHHHHHHHhhcCC-C--eeEEEEeEeCCCceEeCCccccCCCcEEEE
Confidence 3345555 77888763 347899999999999999 3 4444444444 665 4444443333
No 12
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=49.74 E-value=1.1e+02 Score=23.63 Aligned_cols=56 Identities=25% Similarity=0.353 Sum_probs=40.0
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE---eCCHHHHHh
Q 032760 22 KQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI---YDSVDSAKK 86 (134)
Q Consensus 22 kEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I---Yds~e~~kk 86 (134)
.+++|.|.-. .++.||++.+-.+|++ +++=|..+.+.- |.=.+|+.. ||.+|.+.+
T Consensus 83 N~yvF~Vd~k----AnK~qIK~AVEklf~V---kV~kVNTli~p~--g~KKA~V~L~~~~~aidva~k 141 (145)
T PTZ00191 83 NTLVFIVDQR----ANKTQIKKAVEKLYDV---KVVKVNTLITPD--GLKKAYIRLSPDVDALDVANK 141 (145)
T ss_pred CEEEEEEcCC----CCHHHHHHHHHHHhCC---eeEEEEeEEcCC--CceEEEEEECCCCcHHHHHHh
Confidence 6788887654 7799999999999999 566666666543 555667777 444555543
No 13
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=49.41 E-value=62 Score=22.59 Aligned_cols=62 Identities=16% Similarity=0.250 Sum_probs=42.9
Q ss_pred eeeccCccc-eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHHH
Q 032760 13 FMTNRLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVDS 83 (134)
Q Consensus 13 ~~~NpLL~R-kEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e~ 83 (134)
++.+.|+.. .++.|.|. +..++.||++.+-.+|++ .+.-|..+.+. .+.-.+|....+..++
T Consensus 12 EK~~~~~e~~n~y~F~V~----~~anK~eIK~AvE~lf~V---kV~~VnT~~~~--~~~KKA~V~L~~g~~A 74 (84)
T PRK14548 12 EKAMNLIEKENKLTFIVD----RRATKPDIKRAVEELFDV---KVEKVNTLITP--KGEKKAYVKLAEEYDA 74 (84)
T ss_pred HHHHHHHHhCCEEEEEEC----CCCCHHHHHHHHHHHhCC---ceEEEEeEEcC--CCcEEEEEEeCCCCcH
Confidence 444556664 68888874 448899999999999999 55566666664 4555666666655443
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=48.89 E-value=33 Score=25.65 Aligned_cols=44 Identities=20% Similarity=0.323 Sum_probs=33.5
Q ss_pred cceEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEe
Q 032760 20 SRKQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRT 64 (134)
Q Consensus 20 ~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T 64 (134)
++.++.+.|--.-.++||..-+++-|+..+++ +++.|.=+.|+.
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 34335555555667899999999999999999 877777777776
No 15
>CHL00030 rpl23 ribosomal protein L23
Probab=46.60 E-value=51 Score=23.43 Aligned_cols=45 Identities=29% Similarity=0.365 Sum_probs=32.2
Q ss_pred eeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEe
Q 032760 13 FMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRT 64 (134)
Q Consensus 13 ~~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T 64 (134)
++..-|+...++.|.|.- ..++.||++++-.+|++ .++=|..+.+
T Consensus 11 EKs~~l~e~n~y~F~V~~----~anK~eIK~avE~lf~V---kV~~VNt~~~ 55 (93)
T CHL00030 11 DKSIRLLEKNQYTFDVDS----GSTKTEIKHWIELFFGV---KVIAVNSHRL 55 (93)
T ss_pred HHHHHhhHCCEEEEEECC----CCCHHHHHHHHHHHhCC---eEEEEEEEEc
Confidence 344556667788888754 47899999999999999 4444444444
No 16
>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=46.34 E-value=45 Score=25.75 Aligned_cols=54 Identities=22% Similarity=0.450 Sum_probs=39.6
Q ss_pred ceEEEEEEEcCCCCCCCH-HHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEE
Q 032760 21 RKQFVIDVLHPGRANVSK-AELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGL 76 (134)
Q Consensus 21 RkEi~~~v~H~g~~Tpsr-~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~ 76 (134)
.+.-.|.+.|.|.---|- +.+|+.+.+.+.+++|+==||-.+.+ |||...||++
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 455677888887543333 47899999999987776666666666 9999999975
No 17
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=43.12 E-value=52 Score=25.89 Aligned_cols=40 Identities=15% Similarity=0.229 Sum_probs=31.5
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEec
Q 032760 24 FVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTH 65 (134)
Q Consensus 24 i~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~ 65 (134)
+.+...-| +-.|-+.++++.||++|++ +++.|-|.-=.|+
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 44455556 6789999999999999999 9999988654443
No 18
>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=42.23 E-value=28 Score=28.26 Aligned_cols=56 Identities=23% Similarity=0.284 Sum_probs=32.9
Q ss_pred eccCccceEEEEEEEcCCC---------CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEE
Q 032760 15 TNRLLSRKQFVIDVLHPGR---------ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKS 71 (134)
Q Consensus 15 ~NpLL~RkEi~~~v~H~g~---------~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s 71 (134)
.+-|++|.+|.|.-.+... ..-+=.||.+++|+.+++ ||+.|=++......|...+
T Consensus 170 y~~l~nrv~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~~-dP~~lr~~~~~~~~~~P~~ 234 (249)
T PF12436_consen 170 YDFLYNRVEVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLNV-DPEHLRFFTVNPYSGKPKS 234 (249)
T ss_dssp HHHHHHEEEEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHTS--GGGEEEE---TTS-S---
T ss_pred HHHHhCeEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHCC-ChHHEEEEEeccCCCCCCC
Confidence 3446666666655433211 234678999999999999 9999999988876666553
No 19
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=40.31 E-value=45 Score=27.39 Aligned_cols=34 Identities=21% Similarity=0.249 Sum_probs=28.7
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV 59 (134)
++.=+|.=..|||.+++.+.|.+|... ++|.+=|
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 556688889999999999999999999 7776543
No 20
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=39.66 E-value=62 Score=22.67 Aligned_cols=34 Identities=21% Similarity=0.553 Sum_probs=25.9
Q ss_pred eeccCcc-ceEEEEEEEcCCCCCCCHHHHHHHHHhHcCC
Q 032760 14 MTNRLLS-RKQFVIDVLHPGRANVSKAELKEKLARMYDV 51 (134)
Q Consensus 14 ~~NpLL~-RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~ 51 (134)
+.+.|+. -.++.|.|. +..++.||++.|-++|++
T Consensus 12 Ks~~~~e~~n~~~F~V~----~~a~K~eIK~aie~lf~V 46 (92)
T PRK05738 12 KSTLLMEKQNKYVFEVA----PDATKPEIKAAVEKLFGV 46 (92)
T ss_pred HHHHhHHhCCEEEEEEC----CCCCHHHHHHHHHHHcCC
Confidence 3444555 467777764 458899999999999999
No 21
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=39.29 E-value=1.1e+02 Score=22.80 Aligned_cols=47 Identities=21% Similarity=0.444 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHHh
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAKK 86 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~kk 86 (134)
.+.+-++|++.+.. |+. =.++.++.+-.| +.+.|||.| |.|.++|..
T Consensus 44 ~~~te~~L~~~F~~-~G~-I~~v~i~~d~~t----g~~kGfaFV~F~~~e~A~~ 91 (144)
T PLN03134 44 WGTDDASLRDAFAH-FGD-VVDAKVIVDRET----GRSRGFGFVNFNDEGAATA 91 (144)
T ss_pred CCCCHHHHHHHHhc-CCC-eEEEEEEecCCC----CCcceEEEEEECCHHHHHH
Confidence 45678899998855 665 355555555554 556666664 555555543
No 22
>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=38.72 E-value=66 Score=21.89 Aligned_cols=31 Identities=26% Similarity=0.398 Sum_probs=20.2
Q ss_pred EEEEEEcC-CCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 032760 24 FVIDVLHP-GRANVSKAELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 24 i~~~v~H~-g~~Tpsr~eI~~kLA~~~~~~~~~~ivV 59 (134)
+.+.=.|| |.+.||.+|+. ++..++. +.++|
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 34444577 67899999985 3344444 66666
No 23
>PRK06425 histidinol-phosphate aminotransferase; Validated
Probab=36.79 E-value=42 Score=27.41 Aligned_cols=26 Identities=4% Similarity=0.093 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~ 60 (134)
|.|.-.++++.||+.+++ +++.|+|.
T Consensus 38 p~~~~~~lr~~ia~~~~~-~~~~I~it 63 (332)
T PRK06425 38 PEISYTDIEDQIKIYTQG-LKIKVLIG 63 (332)
T ss_pred cCcCHHHHHHHHHHHhCC-CcceEEEC
Confidence 457789999999999999 88888764
No 24
>KOG2116 consensus Protein involved in plasmid maintenance/nuclear protein involved in lipid metabolism [Cell motility; Lipid transport and metabolism]
Probab=35.69 E-value=61 Score=31.02 Aligned_cols=34 Identities=32% Similarity=0.541 Sum_probs=27.2
Q ss_pred HHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEe
Q 032760 43 EKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIY 78 (134)
Q Consensus 43 ~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IY 78 (134)
+.| +.||.++-.+-|+|+|.|.|+| .+.+-|+||
T Consensus 491 EQL-~sLnLk~G~N~v~FsisT~~~G-t~~c~~~IY 524 (738)
T KOG2116|consen 491 EQL-KSLNLKDGKNDVVFSISTQYQG-TAQCEGNIY 524 (738)
T ss_pred HHH-hhcCCccCCceeEEEEEecccc-eEEEeeEEE
Confidence 344 6789889999999999999986 456677777
No 25
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=35.61 E-value=1.2e+02 Score=20.29 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.+-+-.|++.+|...+|+ +++..-+.-
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 456789999999999999 777766644
No 26
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=35.47 E-value=54 Score=25.69 Aligned_cols=33 Identities=18% Similarity=0.377 Sum_probs=26.9
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.++|.++| .|+..--+.|++.||. +++.++++|
T Consensus 187 ~~eI~~~g---vsKg~al~~l~~~~gi-~~~~v~afG 219 (270)
T PRK10513 187 FLEILDKR---VNKGTGVKSLAEHLGI-KPEEVMAIG 219 (270)
T ss_pred eEEEeCCC---CChHHHHHHHHHHhCC-CHHHEEEEC
Confidence 46777776 8999999999999999 777777664
No 27
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=34.96 E-value=48 Score=26.21 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=26.4
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.++|.++| .|+..--+.|++.||+ +++-++++|
T Consensus 179 ~~eI~~~g---~sKg~al~~l~~~~gi-~~~~v~afG 211 (272)
T PRK15126 179 CLEVLPVG---CNKGAALAVLSQHLGL-SLADCMAFG 211 (272)
T ss_pred EEEeecCC---CChHHHHHHHHHHhCC-CHHHeEEec
Confidence 45677765 7899999999999999 877777654
No 28
>PRK14864 putative biofilm stress and motility protein A; Provisional
Probab=34.74 E-value=1.8e+02 Score=21.14 Aligned_cols=51 Identities=8% Similarity=0.146 Sum_probs=39.7
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeC
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYD 79 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYd 79 (134)
+|.|.|. + |-.|+.+.||+.=+........|-.....=|.+.-.|.|-||.
T Consensus 53 tVSvs~~--g--sp~d~~~~La~KAda~GA~yYrIi~~~e~~~~~~~~atA~iYk 103 (104)
T PRK14864 53 TVSALVR--G--SPDDAEREIQAKANAAGADYYVIVMVDETVVPGQWYSQAILYR 103 (104)
T ss_pred EEEEecC--C--CHHHHHHHHHHHHHHcCCCEEEEEEccccCCCCeEEEEEEEec
Confidence 6667764 3 4568888888877766678888888877677899999999995
No 29
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=34.60 E-value=62 Score=25.30 Aligned_cols=39 Identities=15% Similarity=0.179 Sum_probs=29.8
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEe
Q 032760 24 FVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRT 64 (134)
Q Consensus 24 i~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T 64 (134)
+.+....| +=.|-+.++++.||+.+++ +++.|-|.-=.|
T Consensus 98 ~tii~e~P-Ki~p~~~~m~~~la~~L~i-~~~~V~iKatT~ 136 (159)
T PRK00084 98 ITIIAQRP-KMAPHIEEMRANIAEDLGI-PLDDVNVKATTT 136 (159)
T ss_pred EEEEcCCC-cchHHHHHHHHHHHHHhCC-CcceEEEEEecC
Confidence 34444555 5688999999999999999 888888765433
No 30
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.36 E-value=42 Score=27.08 Aligned_cols=36 Identities=17% Similarity=0.460 Sum_probs=20.8
Q ss_pred EEEEEEcC-CCCCCCHHHHH--HHHH---hHcCCCCCCeEEE
Q 032760 24 FVIDVLHP-GRANVSKAELK--EKLA---RMYDVKDPNSIFV 59 (134)
Q Consensus 24 i~~~v~H~-g~~Tpsr~eI~--~kLA---~~~~~~~~~~ivV 59 (134)
|.+.=.|| |.++||.+|+. ..|. +.+++.=-|-|||
T Consensus 163 vIlaHNHPSG~~~PS~~Di~~T~~l~~a~~~lgI~llDHiIv 204 (218)
T TIGR00608 163 LILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLII 204 (218)
T ss_pred EEEEeecCCCCCCCCHHHHHHHHHHHHHHHhCCCEEeeEEEE
Confidence 34444688 67999999875 3444 4555422334444
No 31
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=34.21 E-value=43 Score=26.18 Aligned_cols=36 Identities=19% Similarity=0.328 Sum_probs=28.7
Q ss_pred eeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCC
Q 032760 12 KFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDV 51 (134)
Q Consensus 12 k~~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~ 51 (134)
.+..+-|+...++.|.|... .++.||+..+-.+|++
T Consensus 13 TEKs~~l~e~N~ytF~V~~~----anK~eIK~AVE~iF~V 48 (158)
T PRK12280 13 TEKSYSLMSKNVYTFKVDRR----ANKIEIKKAVEFIFKV 48 (158)
T ss_pred CHHHHhhhhCCEEEEEECCC----CCHHHHHHHHHHHhCC
Confidence 34456667777888888653 7899999999999999
No 32
>PRK10976 putative hydrolase; Provisional
Probab=34.21 E-value=54 Score=25.72 Aligned_cols=33 Identities=24% Similarity=0.359 Sum_probs=25.4
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.++|.++| .|+..--+.|++.||. +++.++++|
T Consensus 181 ~~eI~~~g---vsKg~al~~l~~~lgi-~~~~viafG 213 (266)
T PRK10976 181 CLEVMAGG---VSKGHALEAVAKKLGY-SLKDCIAFG 213 (266)
T ss_pred eEEEEcCC---CChHHHHHHHHHHcCC-CHHHeEEEc
Confidence 35666655 7899999999999999 777777654
No 33
>PRK00024 hypothetical protein; Reviewed
Probab=34.21 E-value=66 Score=25.90 Aligned_cols=36 Identities=17% Similarity=0.441 Sum_probs=21.2
Q ss_pred EEEEEEcC-CCCCCCHHHHH--HH---HHhHcCCCCCCeEEE
Q 032760 24 FVIDVLHP-GRANVSKAELK--EK---LARMYDVKDPNSIFV 59 (134)
Q Consensus 24 i~~~v~H~-g~~Tpsr~eI~--~k---LA~~~~~~~~~~ivV 59 (134)
|.+.=.|| |.++||.+|+. .. .++++++.=-|-|||
T Consensus 169 iIl~HNHPSG~~~PS~~D~~~T~~l~~a~~~l~I~llDHiIv 210 (224)
T PRK00024 169 LILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIII 210 (224)
T ss_pred eEEEecCCCCCCCCCHHHHHHHHHHHHHHHhCCCEEeeEEEE
Confidence 33444588 57999999875 33 445555533344444
No 34
>KOG3969 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.83 E-value=47 Score=28.66 Aligned_cols=58 Identities=19% Similarity=0.413 Sum_probs=45.9
Q ss_pred HHHHHHHHHhHcCCCCCCeEEEe---------------ceEecCCCCEEEEEEEEeCCHHHHHhcCCchhhhhc
Q 032760 38 KAELKEKLARMYDVKDPNSIFVF---------------KFRTHFGGGKSTGFGLIYDSVDSAKKFEPKYRLIRN 96 (134)
Q Consensus 38 r~eI~~kLA~~~~~~~~~~ivV~---------------~~~T~fG~g~s~g~a~IYds~e~~kk~Epk~~l~Rn 96 (134)
|..+++.+...|++ ++|.+.+| +++-.-|.|.+.|.|+.-|++=..-.+-|+|--.+.
T Consensus 218 r~k~~~~i~~~y~v-~~dqlrmf~HYqPSyYHlHVHi~nik~~~~~~~~~~rAilLddVI~nL~~~P~~Y~k~t 290 (310)
T KOG3969|consen 218 RNKSREAIPQRYGV-DPDQLRMFFHYQPSYYHLHVHIVNIKHDHAPGSGCGRAILLDDVIENLELDPEGYKKST 290 (310)
T ss_pred HHHHHHHHHHHhCC-CchhEEEEEEecCceEEEEEEEEeccCCCCCCccccceeeHHHHHHHhccChHhhhhee
Confidence 55678899999999 99988765 334445999999999999998777777888765553
No 35
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=33.54 E-value=70 Score=24.12 Aligned_cols=33 Identities=27% Similarity=0.394 Sum_probs=24.3
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.++|.++| .++..--..|++.++. +++.++.+|
T Consensus 140 ~~ei~~~~---~~K~~~i~~l~~~~~i-~~~~~i~~G 172 (225)
T TIGR01482 140 DIHILPQG---VNKGVAVKKLKEKLGI-KPGETLVCG 172 (225)
T ss_pred EEEEeeCC---CCHHHHHHHHHHHhCC-CHHHEEEEC
Confidence 45666654 7888888999999999 766665543
No 36
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=33.28 E-value=90 Score=24.47 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=23.2
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 26 IDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 26 ~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
++|.++| .|+..--+.|++.|+. +++.++++|
T Consensus 159 ldi~~~~---~~K~~al~~l~~~~~i-~~~~~i~~G 190 (249)
T TIGR01485 159 LDILPQG---SGKGQALQYLLQKLAM-EPSQTLVCG 190 (249)
T ss_pred EEEEeCC---CChHHHHHHHHHHcCC-CccCEEEEE
Confidence 4566654 6777778999999999 666666654
No 37
>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=33.04 E-value=1.3e+02 Score=19.10 Aligned_cols=49 Identities=20% Similarity=0.153 Sum_probs=33.5
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEe
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIY 78 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IY 78 (134)
.|.|.+.. + |-.|+.++||+.=.....+...|-.+.+ .++.-.+-|-||
T Consensus 7 ~Isvs~~~-~--s~~d~~~~la~kAd~~GA~~y~I~~~~~--~~~~~~~tA~lY 55 (56)
T PF07338_consen 7 TISVSGNF-G--SPDDAEEALAKKADEKGAKYYRITSASE--DGNNWHATAELY 55 (56)
T ss_dssp EEEEEEEC-S--SHHHHHHHHHHHHHHTT-SEEEEEEEEE--CSSEEEEEEEEE
T ss_pred EEEEcccc-C--CHHHHHHHHHHHHHHcCCCEEEEEEEEc--CCCeEEEEEEEE
Confidence 34555542 3 3456777776654444557888888888 899999999999
No 38
>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=33.00 E-value=1e+02 Score=17.80 Aligned_cols=47 Identities=23% Similarity=0.418 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHHhc
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAKKF 87 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~kk~ 87 (134)
+..+..+|++.++...++ .+..+.. ...+ ...|+|.| |.|.+.+...
T Consensus 9 ~~~~~~~i~~~~~~~g~i--~~~~~~~---~~~~--~~~~~~~v~f~s~~~a~~a 56 (74)
T cd00590 9 PDVTEEDLRELFSKFGKV--ESVRIVR---DKDT--KSKGFAFVEFEDEEDAEKA 56 (74)
T ss_pred CccCHHHHHHHHHhcCCE--EEEEEee---CCCC--CcceEEEEEECCHHHHHHH
Confidence 346788999999775323 2222222 2222 56777777 6888877544
No 39
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=31.48 E-value=1e+02 Score=21.72 Aligned_cols=35 Identities=20% Similarity=0.298 Sum_probs=23.3
Q ss_pred EEEEEcCCCCCCCH-----HHHHHHHHhHcCCCCCCeEEEe
Q 032760 25 VIDVLHPGRANVSK-----AELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr-----~eI~~kLA~~~~~~~~~~ivV~ 60 (134)
.+.|.-.|..++.. .+|-+.|++.+|+ +++.|+|.
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 45555555555542 2677888899999 77777663
No 40
>PRK01688 histidinol-phosphate aminotransferase; Provisional
Probab=31.40 E-value=43 Score=27.68 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
|-|.-.++++.+|+.+|+ +++.|++.+
T Consensus 55 p~~~~~~l~~~~a~~~g~-~~~~I~~~~ 81 (351)
T PRK01688 55 PECQPKAVIENYAAYAGV-KPEQVLVSR 81 (351)
T ss_pred CCCChHHHHHHHHHHhCC-CHHHEEEcC
Confidence 445668999999999999 999988855
No 41
>smart00362 RRM_2 RNA recognition motif.
Probab=31.02 E-value=1.1e+02 Score=17.55 Aligned_cols=46 Identities=26% Similarity=0.489 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHHhc
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAKKF 87 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~kk~ 87 (134)
...+..||++.+. .||. -.+..+. ... +.+.|+|.| |++.+.+...
T Consensus 9 ~~~~~~~l~~~~~-~~g~-v~~~~~~---~~~---~~~~~~~~v~f~~~~~a~~a 55 (72)
T smart00362 9 PDVTEEDLKELFS-KFGP-IESVKIP---KDT---GKSKGFAFVEFESEEDAEKA 55 (72)
T ss_pred CcCCHHHHHHHHH-hcCC-EEEEEEe---cCC---CCCCceEEEEeCCHHHHHHH
Confidence 3456789998885 4554 2232222 222 445555555 5666666543
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=30.57 E-value=36 Score=27.56 Aligned_cols=53 Identities=21% Similarity=0.222 Sum_probs=37.9
Q ss_pred EEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCH
Q 032760 27 DVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSV 81 (134)
Q Consensus 27 ~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~ 81 (134)
.++.|..|.-|-.+|+++|.+.+|. +..+||++.+-+-|=.| ++|+|.=+.-+
T Consensus 125 v~LlP~dPd~sA~~i~~~l~~~~g~-~v~ViI~Dt~gr~~r~G-~~~vaig~~Gi 177 (228)
T PF01996_consen 125 VVLLPEDPDASARRIREELKERTGK-DVGVIITDTNGRPWRLG-QTGVAIGVAGI 177 (228)
T ss_dssp EE---S-HHHHHHHHHHHHHHHHS----EEEEEEEEEETTEEC-EEEEEEEEESB
T ss_pred EEECCCCHHHHHHHHHHHHHHHHCC-ceEEEEECCCCcEEecC-CccchhhccCC
Confidence 4677777777888999999999999 99999999988777666 88888766553
No 43
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=30.25 E-value=1.5e+02 Score=24.04 Aligned_cols=53 Identities=15% Similarity=0.264 Sum_probs=33.7
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHH
Q 032760 26 IDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAK 85 (134)
Q Consensus 26 ~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~k 85 (134)
+-|.+- ...-+-++|++.++ .||. =.++-|+.+-. .|.+.|||.| |+|.+.|.
T Consensus 272 lfV~NL-~~~~~e~~L~~~F~-~fG~-v~~v~i~~d~~----t~~skG~aFV~F~~~~~A~ 325 (352)
T TIGR01661 272 IFVYNL-SPDTDETVLWQLFG-PFGA-VQNVKIIRDLT----TNQCKGYGFVSMTNYDEAA 325 (352)
T ss_pred EEEeCC-CCCCCHHHHHHHHH-hCCC-eEEEEEeEcCC----CCCccceEEEEECCHHHHH
Confidence 345554 34557888888885 4554 34555554433 4678888887 77777654
No 44
>COG3561 Phage anti-repressor protein [Transcription]
Probab=29.80 E-value=1e+02 Score=22.86 Aligned_cols=58 Identities=14% Similarity=0.147 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHHHHHhcCC
Q 032760 32 GRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVDSAKKFEP 89 (134)
Q Consensus 32 g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e~~kk~Ep 89 (134)
|-+||+-..+++...+.-=+.+.|.|+|..+...|-+....+|+.--|-...+--+||
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 5689999999988866655668899999999988888777888888776655555544
No 45
>PHA01976 helix-turn-helix protein
Probab=29.53 E-value=26 Score=21.94 Aligned_cols=24 Identities=17% Similarity=0.112 Sum_probs=17.2
Q ss_pred CCCCCCHHHHHHHHHhHcCCCCCCeE
Q 032760 32 GRANVSKAELKEKLARMYDVKDPNSI 57 (134)
Q Consensus 32 g~~Tpsr~eI~~kLA~~~~~~~~~~i 57 (134)
|...|+...+ .+||..|++ +++.+
T Consensus 38 g~~~p~~~~l-~~ia~~l~v-~~~~l 61 (67)
T PHA01976 38 DKRLPNLKTL-LRLADALGV-TLDWL 61 (67)
T ss_pred CCCCCCHHHH-HHHHHHHCc-CHHHH
Confidence 4456665544 799999999 77654
No 46
>COG2006 Uncharacterized conserved protein [Function unknown]
Probab=29.13 E-value=59 Score=27.92 Aligned_cols=43 Identities=23% Similarity=0.308 Sum_probs=36.0
Q ss_pred EcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEE
Q 032760 29 LHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTG 73 (134)
Q Consensus 29 ~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g 73 (134)
+|.+.+ .+....+.||..|.+=.|++.+++++.-.=|.|-+.|
T Consensus 171 ~h~~~~--~~~~Fg~mlvei~~~~~P~ltI~Dgi~G~egNGP~~G 213 (293)
T COG2006 171 WHMEEG--DRDRFGEMLVEIYLVVKPDLTIMDGIIGMEGNGPSGG 213 (293)
T ss_pred cchhcC--chHHHHHHHHHHHhhcCCcEEEEeeeEecccCCCCCC
Confidence 455444 6778999999999987999999999999888887766
No 47
>PRK06959 putative threonine-phosphate decarboxylase; Provisional
Probab=28.97 E-value=61 Score=26.78 Aligned_cols=25 Identities=20% Similarity=0.240 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
|. .++++.||+.+++.+++.|+|.+
T Consensus 54 ~~-~~L~~~ia~~~~~~~~~~I~i~~ 78 (339)
T PRK06959 54 DD-DGLAACAARYYGAPDAAHVLPVA 78 (339)
T ss_pred ch-HHHHHHHHHHhCCCCcccEEECc
Confidence 55 89999999999994457777643
No 48
>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=28.73 E-value=98 Score=24.00 Aligned_cols=36 Identities=14% Similarity=0.322 Sum_probs=28.3
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 24 FVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 24 i~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.+....| +=.|=+.++++.||+.++. +.+.|-|.-
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 44445555 5678999999999999999 888887753
No 49
>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=28.70 E-value=92 Score=24.24 Aligned_cols=36 Identities=17% Similarity=0.235 Sum_probs=28.0
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 24 FVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 24 i~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.+....| +=.|=+.++++.||+.++. +++.|-|.-
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 34444555 5678899999999999999 888887754
No 50
>PRK13817 ribosome-binding factor A; Provisional
Probab=28.60 E-value=2e+02 Score=20.94 Aligned_cols=44 Identities=14% Similarity=0.192 Sum_probs=34.1
Q ss_pred HHHHHHHHhHc--CCCCCC--eEEEeceEecCCCCEEEEEEEEeCCHH
Q 032760 39 AELKEKLARMY--DVKDPN--SIFVFKFRTHFGGGKSTGFGLIYDSVD 82 (134)
Q Consensus 39 ~eI~~kLA~~~--~~~~~~--~ivV~~~~T~fG~g~s~g~a~IYds~e 82 (134)
.+|++.||..+ .+.||. .|-|.++...-+...++.|.-+|++.+
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 35667777666 354554 689999999999999999999997643
No 51
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=28.51 E-value=2.6e+02 Score=21.00 Aligned_cols=34 Identities=12% Similarity=0.229 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCC
Q 032760 33 RANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFG 67 (134)
Q Consensus 33 ~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG 67 (134)
.-.||-.++-+.|-..|++ |..+++=+.+...||
T Consensus 83 sFAPsPDq~v~~Ly~cf~~-d~~Lvl~Yc~s~A~G 116 (116)
T KOG3439|consen 83 SFAPSPDQIVGNLYECFGT-DGKLVLNYCISVAWG 116 (116)
T ss_pred ccCCCchhHHHHHHHhcCC-CCEEEEEEeeecccC
Confidence 4678889999999999999 877777777766666
No 52
>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=28.23 E-value=1.5e+02 Score=20.87 Aligned_cols=38 Identities=18% Similarity=0.164 Sum_probs=30.0
Q ss_pred HHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCH
Q 032760 39 AELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSV 81 (134)
Q Consensus 39 ~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~ 81 (134)
-+|-...|+.+|+.+-|.|.|.+ +.|...+.|.|-+++
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 55666789999998899998874 456788888887764
No 53
>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=28.17 E-value=55 Score=25.54 Aligned_cols=31 Identities=16% Similarity=0.445 Sum_probs=24.9
Q ss_pred EEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 032760 28 VLHPGRANVSKAELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 28 v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~ 60 (134)
...| +=.|=+.++++.||+.++. +++.|-|.
T Consensus 100 ~e~P-Ki~p~~~~m~~~la~~L~~-~~~~V~iK 130 (157)
T PF02542_consen 100 AERP-KISPYRPAMRENLAKLLGI-PPDRVNIK 130 (157)
T ss_dssp SSSS-TTGGGHHHHHHHHHHHHTS--GGGEEEE
T ss_pred cCCC-ccHHHHHHHHHHHHHHhCC-CcceEEEE
Confidence 3344 5688999999999999999 98988775
No 54
>PRK13815 ribosome-binding factor A; Provisional
Probab=27.99 E-value=2.4e+02 Score=20.62 Aligned_cols=44 Identities=11% Similarity=0.130 Sum_probs=34.5
Q ss_pred HHHHHHHHhHc--CCCCCC--eEEEeceEecCCCCEEEEEEEEeCCHH
Q 032760 39 AELKEKLARMY--DVKDPN--SIFVFKFRTHFGGGKSTGFGLIYDSVD 82 (134)
Q Consensus 39 ~eI~~kLA~~~--~~~~~~--~ivV~~~~T~fG~g~s~g~a~IYds~e 82 (134)
++|++.||.++ +++||. .|-|.++...=....++.|.-++.+.+
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 46777787776 455666 488999999999999999999987544
No 55
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=27.85 E-value=81 Score=23.91 Aligned_cols=33 Identities=30% Similarity=0.527 Sum_probs=24.8
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.+++.++| +|+..--..|++.|+. +++.++++|
T Consensus 148 ~~ei~~~~---~~Kg~al~~l~~~~~i-~~~~~i~~G 180 (230)
T PRK01158 148 AIHIKSPG---VNKGTGLKKLAELMGI-DPEEVAAIG 180 (230)
T ss_pred EEEEeeCC---CChHHHHHHHHHHhCC-CHHHEEEEC
Confidence 35666654 7888888899999999 776666654
No 56
>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=27.15 E-value=53 Score=20.48 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=14.6
Q ss_pred CCCCCCHHHHHHHHHhHcCCCC
Q 032760 32 GRANVSKAELKEKLARMYDVKD 53 (134)
Q Consensus 32 g~~Tpsr~eI~~kLA~~~~~~~ 53 (134)
+-.|.|..+|++.|.+.||+ |
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 45688999999999999998 5
No 57
>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=26.70 E-value=41 Score=25.55 Aligned_cols=23 Identities=35% Similarity=0.691 Sum_probs=19.7
Q ss_pred CHHHHHHHHHhHcCCCCCCeEEEe
Q 032760 37 SKAELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 37 sr~eI~~kLA~~~~~~~~~~ivV~ 60 (134)
...+|+..||..||+ +++.|-|.
T Consensus 165 ~~~~i~~~la~~~~i-~~~~I~V~ 187 (188)
T PF09581_consen 165 EEEEIKQYLADFYGI-SPEQIKVY 187 (188)
T ss_pred HHHHHHHHHHHHhCC-CHHHeEEe
Confidence 346899999999999 99998774
No 58
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains 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. However, to date, the name RadC has been misleading and no function has been determined.
Probab=26.70 E-value=1.3e+02 Score=21.45 Aligned_cols=38 Identities=16% Similarity=0.421 Sum_probs=22.6
Q ss_pred eEEEEEEEcC-CCCCCCHHHHH--HH---HHhHcCCCCCCeEEE
Q 032760 22 KQFVIDVLHP-GRANVSKAELK--EK---LARMYDVKDPNSIFV 59 (134)
Q Consensus 22 kEi~~~v~H~-g~~Tpsr~eI~--~k---LA~~~~~~~~~~ivV 59 (134)
..+.+.=.|| |.+.||.+|+. ++ .++++|+.=-|-++|
T Consensus 61 ~~vil~HNHPsG~~~PS~~D~~~T~~l~~~~~~l~i~llDHiIi 104 (113)
T cd08071 61 AAIILAHNHPSGDPTPSREDIELTKRLKEAGELLGIRLLDHIIV 104 (113)
T ss_pred heEEEEeeCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEeeEEEE
Confidence 3456666788 56899998765 33 445555522344444
No 59
>PRK05387 histidinol-phosphate aminotransferase; Provisional
Probab=26.61 E-value=57 Score=26.44 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
|.-.++++.||+.|++ +++.|+|..
T Consensus 60 ~~~~~lr~aia~~~~~-~~~~I~it~ 84 (353)
T PRK05387 60 PNADALRQAIAAYYGL-DPEQVFVGN 84 (353)
T ss_pred CcHHHHHHHHHHHhCC-CHHHEEEcC
Confidence 3457999999999999 888888765
No 60
>PLN03026 histidinol-phosphate aminotransferase; Provisional
Probab=26.50 E-value=72 Score=26.76 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHHhHcCCCCCCeEEEe
Q 032760 35 NVSKAELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 35 Tpsr~eI~~kLA~~~~~~~~~~ivV~ 60 (134)
.|.-.++++.||+.+++ +++.|++.
T Consensus 85 ~~~~~~lr~~ia~~~~~-~~~~I~~t 109 (380)
T PLN03026 85 DPESRRLRAALAEDSGL-ESENILVG 109 (380)
T ss_pred CCCHHHHHHHHHHHhCc-ChhhEEEc
Confidence 35567999999999999 88888764
No 61
>PRK04781 histidinol-phosphate aminotransferase; Provisional
Probab=26.38 E-value=61 Score=26.96 Aligned_cols=26 Identities=19% Similarity=0.466 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 35 NVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 35 Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.|.-.++++.||+.+++ +++.|++..
T Consensus 58 ~~~~~~lr~~ia~~~~~-~~~~I~~t~ 83 (364)
T PRK04781 58 DPQPPGLRSALAALYGC-APEQLLIGR 83 (364)
T ss_pred CCCHHHHHHHHHHHhCc-ChHHEEEeC
Confidence 45568999999999999 888887744
No 62
>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=26.16 E-value=60 Score=27.28 Aligned_cols=28 Identities=14% Similarity=0.173 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 33 RANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 33 ~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.++--.++.+.||+.+|+ +++.++|+.
T Consensus 51 g~~~~~~~Le~~lA~~~g~-~~e~ilv~~ 78 (346)
T TIGR03576 51 GPAIFEEKVQELGREHLGG-PEEKILVFN 78 (346)
T ss_pred CCHHHHHHHHHHHHHHcCC-CcceEEEEC
Confidence 5667788999999999999 778887765
No 63
>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=25.09 E-value=1e+02 Score=20.99 Aligned_cols=43 Identities=19% Similarity=0.145 Sum_probs=26.2
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEe
Q 032760 22 KQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRT 64 (134)
Q Consensus 22 kEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T 64 (134)
.++.+.|..|-.--=.-++|.+-||+.|+++..++-++.|-.+
T Consensus 26 ~~l~i~v~app~~GkAN~ali~~La~~l~v~ks~i~i~~G~~S 68 (77)
T PF02594_consen 26 GALKIRVTAPPVDGKANKALIRFLAKALGVPKSDIEIVSGHTS 68 (77)
T ss_dssp T-EEEEBSTTCCCCCHHHHHHHHHHHHCT--TTCEEECC-CCC
T ss_pred eEEEEEEecCCCcChhHHHHHHHHHHHhCCCcccEEEEecCCC
Confidence 3566666665222233569999999999996667777766543
No 64
>PRK07392 threonine-phosphate decarboxylase; Validated
Probab=25.00 E-value=74 Score=26.16 Aligned_cols=25 Identities=24% Similarity=0.195 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
|.-.++++.||+.|++ +++.|+|..
T Consensus 57 ~~~~~Lr~aia~~~~v-~~~~I~it~ 81 (360)
T PRK07392 57 PDYRELRLALAQHHQL-PPEWILPGN 81 (360)
T ss_pred cCHHHHHHHHHHHhCc-ChhhEEECC
Confidence 3456899999999999 899888764
No 65
>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=24.79 E-value=2.1e+02 Score=18.79 Aligned_cols=24 Identities=13% Similarity=0.254 Sum_probs=18.6
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEE
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIF 58 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~iv 58 (134)
++-+-.||++.+|+..++ +++..-
T Consensus 20 ~~~TV~~LK~~I~~~~~~-~~~~qr 43 (78)
T cd01804 20 PDETVEGLKKRISQRLKV-PKERLA 43 (78)
T ss_pred CcCHHHHHHHHHHHHhCC-ChHHEE
Confidence 456788999999999998 555443
No 66
>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=24.67 E-value=1.5e+02 Score=20.05 Aligned_cols=36 Identities=19% Similarity=0.141 Sum_probs=27.3
Q ss_pred HHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCH
Q 032760 41 LKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSV 81 (134)
Q Consensus 41 I~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~ 81 (134)
|-..-|+.+|+++-|.|.|++ +.|...+.|.|-+++
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 334579999998999999885 445777888777664
No 67
>PF03090 Replicase: Replicase family; InterPro: IPR004322 This is a family of bacterial plasmid DNA replication initiator proteins. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or may be mediated by Hsp70 chaperones. A similar RepA family of proteins found mainly in Escherichia coli is involved in plasmid replication (see IPR000525 from INTERPRO).
Probab=24.62 E-value=1.3e+02 Score=22.60 Aligned_cols=39 Identities=26% Similarity=0.197 Sum_probs=25.3
Q ss_pred eeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 032760 14 MTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 14 ~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV 59 (134)
.-||..-+.-|+|||.|++. ... -.-...+.+.|..|++
T Consensus 18 q~N~~~~~~~lV~DiD~~~~-----~~~--~~w~~~~lp~Pn~i~~ 56 (137)
T PF03090_consen 18 QLNPPQYVNWLVFDIDHPGA-----ALA--LAWEDEGLPPPNWIVI 56 (137)
T ss_pred eeCChhhEEEEEEECCCCCc-----hhh--HHHHhcCCCCCeEEEE
Confidence 35887778889999999974 111 1223345645777766
No 68
>TIGR01484 HAD-SF-IIB HAD-superfamily hydrolase, subfamily IIB. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing sequences whose relationship to the other groups is unclear.
Probab=24.56 E-value=1.2e+02 Score=22.57 Aligned_cols=33 Identities=24% Similarity=0.385 Sum_probs=24.2
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.++|.++| .++.+.-+.|++.++. +++.++++|
T Consensus 154 ~~ev~p~~---~~K~~~~~~~~~~~~~-~~~~~~~~G 186 (204)
T TIGR01484 154 DLEVLPAG---VDKGSALQALLKELNG-KRDEILAFG 186 (204)
T ss_pred EEEEecCC---CChHHHHHHHHHHhCC-CHHHEEEEc
Confidence 44666543 7888899999999998 777666554
No 69
>PRK10259 hypothetical protein; Provisional
Probab=24.37 E-value=2.1e+02 Score=20.07 Aligned_cols=40 Identities=20% Similarity=0.232 Sum_probs=30.1
Q ss_pred CHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeC
Q 032760 37 SKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYD 79 (134)
Q Consensus 37 sr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYd 79 (134)
+-.|+.++||+.=.....+...|-.. .|.+.-.|-|-||.
T Consensus 47 s~~d~~~~La~KAd~~GA~~YrIi~a---~~~n~~~~tA~iYk 86 (86)
T PRK10259 47 TLDALEAKLAEKAAAAGASGYSITSA---TNNNKLSGTAVIYK 86 (86)
T ss_pred CHHHHHHHHHHHHHHcCCCEEEEEEe---cCCCcEEEEEEEeC
Confidence 44899999988776655666666655 56688999999994
No 70
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=24.34 E-value=2.2e+02 Score=19.33 Aligned_cols=39 Identities=15% Similarity=0.146 Sum_probs=25.7
Q ss_pred ceEEEEEEEcCCCCCCC-------HHHHHHHHHhHcCCCCCCeEEEe
Q 032760 21 RKQFVIDVLHPGRANVS-------KAELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 21 RkEi~~~v~H~g~~Tps-------r~eI~~kLA~~~~~~~~~~ivV~ 60 (134)
+-+|.+.|-.....+.+ ..+|.+.|.+.+++ .+++.+|-
T Consensus 33 ~D~l~v~vE~~~~~~~~~~~~~~l~~~i~~~lk~~lgv-~~~V~lv~ 78 (96)
T PF14535_consen 33 LDELTVRVELRPGFSDDAEDLEALAERIAERLKERLGV-RPEVELVP 78 (96)
T ss_dssp EEEEEEEEEESTTCCTTHHHHHHHHHHHHHHHHHHHSS--EEEEEE-
T ss_pred CcEEEEEEEECCccCcchHHHHHHHHHHHHHHHhhcCc-eEEEEEEC
Confidence 66676666665444432 56788888899999 88776664
No 71
>PRK14807 histidinol-phosphate aminotransferase; Provisional
Probab=24.21 E-value=95 Score=25.50 Aligned_cols=26 Identities=38% Similarity=0.572 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 35 NVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 35 Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.|.-.++++.||+.+++ +++.|+|.+
T Consensus 58 ~~~~~~lr~~ia~~~~~-~~~~i~it~ 83 (351)
T PRK14807 58 DPTAEKLREELARYCSV-VPTNIFVGN 83 (351)
T ss_pred CccHHHHHHHHHHHhCC-CcccEEEec
Confidence 35568999999999999 888777654
No 72
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=24.10 E-value=88 Score=19.19 Aligned_cols=19 Identities=11% Similarity=0.239 Sum_probs=13.3
Q ss_pred HHHHHHHhHcCCCCCCeEEE
Q 032760 40 ELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 40 eI~~kLA~~~~~~~~~~ivV 59 (134)
+|-+.|+..+++ +++.|+|
T Consensus 23 ~it~~l~~~~~~-p~~~v~V 41 (61)
T PRK02220 23 DVTAAVSKNTGA-PAEHIHV 41 (61)
T ss_pred HHHHHHHHHhCc-ChhhEEE
Confidence 466678889999 5665554
No 73
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=23.62 E-value=1.4e+02 Score=25.72 Aligned_cols=46 Identities=15% Similarity=0.259 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHH
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAK 85 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~k 85 (134)
.+.+-++|++.+.. ||. =..+.++... ..|.+.|||.| |.+.+.+.
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 45677888888754 554 2344444433 34677788887 77766653
No 74
>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=23.57 E-value=1.5e+02 Score=20.91 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEe
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRT 64 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T 64 (134)
..|+-..++++|...|+. +++-+.|.-+..
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 379999999999999999 766676665554
No 75
>PRK14809 histidinol-phosphate aminotransferase; Provisional
Probab=23.51 E-value=97 Score=25.39 Aligned_cols=25 Identities=32% Similarity=0.594 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.-.++++.||+.+++ +++.|+|..
T Consensus 65 ~~~~~lr~~ia~~~~~-~~~~I~it~ 89 (357)
T PRK14809 65 ASHADLTAALADRWDV-SPEQVWLAN 89 (357)
T ss_pred CCHHHHHHHHHHHhCC-CcceEEECC
Confidence 4567999999999999 888887643
No 76
>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=23.51 E-value=85 Score=21.95 Aligned_cols=23 Identities=26% Similarity=0.222 Sum_probs=20.6
Q ss_pred EcCCCCCCCHHHHHHHHHhHcCC
Q 032760 29 LHPGRANVSKAELKEKLARMYDV 51 (134)
Q Consensus 29 ~H~g~~Tpsr~eI~~kLA~~~~~ 51 (134)
.|||-++||.+.|...|+..+..
T Consensus 42 ~yp~i~~Ps~e~l~~~L~~Li~e 64 (80)
T PF10264_consen 42 HYPGIAIPSQEVLYNTLGTLIKE 64 (80)
T ss_pred hCCCCCCCCHHHHHHHHHHHHHc
Confidence 47899999999999999998776
No 77
>COG0561 Cof Predicted hydrolases of the HAD superfamily [General function prediction only]
Probab=23.50 E-value=1e+02 Score=24.17 Aligned_cols=31 Identities=26% Similarity=0.512 Sum_probs=24.7
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEe
Q 032760 26 IDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 26 ~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~ 60 (134)
++|.++| .|+..--..|++.|+. +++.|+.|
T Consensus 181 lei~~~g---~~K~~al~~l~~~lgi-~~~~v~af 211 (264)
T COG0561 181 LDITPKG---VSKGYALQRLAKLLGI-KLEEVIAF 211 (264)
T ss_pred EEEecCC---CchHHHHHHHHHHhCC-CHHHeEEe
Confidence 5666665 7899999999999999 66766655
No 78
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=23.31 E-value=1.3e+02 Score=24.55 Aligned_cols=31 Identities=13% Similarity=0.244 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHHHhHcCCCCCCeEEEeceE
Q 032760 33 RANVSKAELKEKLARMYDVKDPNSIFVFKFR 63 (134)
Q Consensus 33 ~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~ 63 (134)
+.-|||.+.-..|++.+....+|+|++-|+-
T Consensus 59 k~~~~r~~~d~~l~~~l~~~~~dlvvLAGyM 89 (200)
T COG0299 59 KEFPSREAFDRALVEALDEYGPDLVVLAGYM 89 (200)
T ss_pred ccCCCHHHHHHHHHHHHHhcCCCEEEEcchH
Confidence 5789999999999999998899999998753
No 79
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.10 E-value=1.9e+02 Score=21.08 Aligned_cols=48 Identities=25% Similarity=0.330 Sum_probs=37.7
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEE
Q 032760 22 KQFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKS 71 (134)
Q Consensus 22 kEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s 71 (134)
|-+++||+-| ---|+-.|+-..|++.-|+ +.=+|.|..+.-.-=+-..
T Consensus 6 RRlVLDvlKP-~~~p~ive~A~~lskl~gV-egVNItv~eiD~et~~~~i 53 (97)
T COG1888 6 RRLVLDVLKP-HRGPTIVELALELSKLEGV-EGVNITVTEIDVETENLKI 53 (97)
T ss_pred eeeeeeecCC-cCCCcHHHHHHHHhhcCCc-ceEEEEEEEeeehhcceEE
Confidence 3488999988 3459999999999999999 8888888887665444333
No 80
>PF10503 Esterase_phd: Esterase PHB depolymerase
Probab=22.93 E-value=9.7 Score=30.68 Aligned_cols=34 Identities=26% Similarity=0.448 Sum_probs=26.8
Q ss_pred CHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEE
Q 032760 37 SKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTG 73 (134)
Q Consensus 37 sr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g 73 (134)
.-.+|-+.|+..|++ |++.|+|-||.. |+..+..
T Consensus 80 ~i~~lv~~v~~~~~i-D~~RVyv~G~S~--Gg~ma~~ 113 (220)
T PF10503_consen 80 FIAALVDYVAARYNI-DPSRVYVTGLSN--GGMMANV 113 (220)
T ss_pred hHHHHHHhHhhhccc-CCCceeeEEECH--HHHHHHH
Confidence 455778889999999 999999999986 5554433
No 81
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=22.87 E-value=96 Score=19.42 Aligned_cols=20 Identities=25% Similarity=0.388 Sum_probs=14.2
Q ss_pred HHHHHHHhHcCCCCCCeEEEe
Q 032760 40 ELKEKLARMYDVKDPNSIFVF 60 (134)
Q Consensus 40 eI~~kLA~~~~~~~~~~ivV~ 60 (134)
.|-+.|+..+++ +++.|+|.
T Consensus 23 ~it~~l~~~lg~-p~~~v~V~ 42 (64)
T PRK01964 23 EVTEAISATLDV-PKERVRVI 42 (64)
T ss_pred HHHHHHHHHhCc-ChhhEEEE
Confidence 456677888999 66666653
No 82
>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=22.70 E-value=28 Score=24.56 Aligned_cols=33 Identities=18% Similarity=0.221 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCC
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFG 67 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG 67 (134)
-.||-.|.-+-|...|++ +.++|+=+..-.-||
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 456666777777777776 666665554444443
No 83
>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=22.70 E-value=1.2e+02 Score=18.68 Aligned_cols=19 Identities=26% Similarity=0.352 Sum_probs=12.8
Q ss_pred HHHHHHHhHcCCCCCCeEEE
Q 032760 40 ELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 40 eI~~kLA~~~~~~~~~~ivV 59 (134)
+|-+.|+..+|+ +++.++|
T Consensus 23 ~it~~l~~~lg~-~~~~v~V 41 (63)
T TIGR00013 23 GVTEAMAETLGA-NLESIVV 41 (63)
T ss_pred HHHHHHHHHhCC-CcccEEE
Confidence 466677788999 5555544
No 84
>TIGR00099 Cof-subfamily Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences.
Probab=22.67 E-value=1.1e+02 Score=23.84 Aligned_cols=33 Identities=24% Similarity=0.402 Sum_probs=24.9
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.++|.++| .|+..--+.|++.++. +++.++++|
T Consensus 179 ~leI~~~~---~~K~~~i~~~~~~~~~-~~~~~~~~G 211 (256)
T TIGR00099 179 SIEITAKG---VSKGSALQSLAEALGI-SLEDVIAFG 211 (256)
T ss_pred eEEecCCC---CChHHHHHHHHHHcCC-CHHHEEEeC
Confidence 34566654 7799999999999999 777776654
No 85
>PRK04635 histidinol-phosphate aminotransferase; Provisional
Probab=22.48 E-value=79 Score=26.00 Aligned_cols=25 Identities=20% Similarity=0.292 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
|.-.++++.||+.+++ +++.|++..
T Consensus 60 ~~~~~Lr~aia~~~~~-~~~~I~it~ 84 (354)
T PRK04635 60 CQPPELINAYSAYAGV-APEQILTSR 84 (354)
T ss_pred CCHHHHHHHHHHHhCc-CHHHEEEeC
Confidence 3457999999999999 999888754
No 86
>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=22.41 E-value=99 Score=19.98 Aligned_cols=26 Identities=4% Similarity=0.163 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHHhHcCCCCCC-eEEEe
Q 032760 34 ANVSKAELKEKLARMYDVKDPN-SIFVF 60 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~-~ivV~ 60 (134)
++-+-.+|++.|++..|+ +++ ..+++
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 557788999999999999 555 44443
No 87
>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=22.30 E-value=2.3e+02 Score=19.68 Aligned_cols=38 Identities=18% Similarity=0.184 Sum_probs=29.5
Q ss_pred HHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEEeCCHH
Q 032760 40 ELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLIYDSVD 82 (134)
Q Consensus 40 eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~IYds~e 82 (134)
+|-...|+.+|+.+-|.|.|.+ +.|...+.|.|.+++.
T Consensus 33 ~i~p~~A~~~gi~~Gd~V~v~s-----~~g~i~~~a~~~~~v~ 70 (121)
T cd02794 33 WINPLDAAARGIKDGDRVLVFN-----DRGKVIRPVKVTERIM 70 (121)
T ss_pred EECHHHHHHcCCCCCCEEEEEc-----CCceEEEEEEECCCcc
Confidence 5556789999998999998764 3357788888888754
No 88
>TIGR01141 hisC histidinol-phosphate aminotransferase. Histidinol-phosphate aminotransferase is a pyridoxal-phosphate dependent enzyme.
Probab=22.26 E-value=87 Score=25.29 Aligned_cols=27 Identities=41% Similarity=0.607 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.|.-.++++.||+.+++ +++.|++..
T Consensus 52 ~~~~~~~lr~~ia~~~~~-~~~~i~~~~ 78 (346)
T TIGR01141 52 PDPDPAELKQALADYYGV-DPEQILLGN 78 (346)
T ss_pred CCCCHHHHHHHHHHHhCc-ChHHEEEcC
Confidence 345568999999999998 777776643
No 89
>PRK06358 threonine-phosphate decarboxylase; Provisional
Probab=22.17 E-value=94 Score=25.67 Aligned_cols=25 Identities=16% Similarity=0.294 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
|.-.++++.+|+.+++ +++.|++..
T Consensus 54 ~~~~~lr~~ia~~~~~-~~~~i~it~ 78 (354)
T PRK06358 54 PDYLELRKRIASFEQL-DLENVILGN 78 (354)
T ss_pred ccHHHHHHHHHHHhCC-ChhhEEECC
Confidence 4557999999999999 888887754
No 90
>PRK01261 aroD 3-dehydroquinate dehydratase; Provisional
Probab=22.06 E-value=1.2e+02 Score=24.51 Aligned_cols=21 Identities=14% Similarity=0.245 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHhHcCCCCCCe
Q 032760 35 NVSKAELKEKLARMYDVKDPNS 56 (134)
Q Consensus 35 Tpsr~eI~~kLA~~~~~~~~~~ 56 (134)
||+.+|+.+.|.+|... .+|.
T Consensus 128 tp~~eeL~~~l~~m~~~-gaDI 148 (229)
T PRK01261 128 TNNSDNMPAILDIMNEK-NPDY 148 (229)
T ss_pred CCCHHHHHHHHHHHHHh-CCCE
Confidence 89999999999999987 6663
No 91
>PRK08056 threonine-phosphate decarboxylase; Provisional
Probab=21.93 E-value=84 Score=25.87 Aligned_cols=25 Identities=28% Similarity=0.242 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.-.++++.||+.|++ +++.|++..
T Consensus 55 ~~~~~lr~~ia~~~~~-~~~~i~it~ 79 (356)
T PRK08056 55 VEYRHLHQALARHHQV-PASWILAGN 79 (356)
T ss_pred ccHHHHHHHHHHHhCc-ChhhEEECC
Confidence 4568999999999999 888887643
No 92
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=21.74 E-value=2.1e+02 Score=25.03 Aligned_cols=52 Identities=27% Similarity=0.381 Sum_probs=36.7
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEeceEecCCCCEEEEEEEE-eCCHHHHH
Q 032760 24 FVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFKFRTHFGGGKSTGFGLI-YDSVDSAK 85 (134)
Q Consensus 24 i~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~g~s~g~a~I-Yds~e~~k 85 (134)
|+..+.|. -|-.+|+..+ ..||- =..+.+|.+..| |+|.|||.| |...-.|+
T Consensus 105 Fv~RLnyd----T~EskLrreF-~~YG~-IkrirlV~d~vT----gkskGYAFIeye~erdm~ 157 (335)
T KOG0113|consen 105 FVARLNYD----TSESKLRREF-EKYGP-IKRIRLVRDKVT----GKSKGYAFIEYEHERDMK 157 (335)
T ss_pred eeeecccc----ccHHHHHHHH-HhcCc-ceeEEEeeeccc----CCccceEEEEeccHHHHH
Confidence 45555665 3466788888 45665 588999999988 678899987 66655553
No 93
>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=21.71 E-value=1.4e+02 Score=18.66 Aligned_cols=22 Identities=14% Similarity=0.276 Sum_probs=18.3
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCe
Q 032760 34 ANVSKAELKEKLARMYDVKDPNS 56 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ 56 (134)
++-+-.+|+++|+...++ +++.
T Consensus 19 ~~~tv~~lK~~i~~~~g~-~~~~ 40 (76)
T cd01806 19 PTDKVERIKERVEEKEGI-PPQQ 40 (76)
T ss_pred CCCCHHHHHHHHhHhhCC-Chhh
Confidence 556789999999999999 6554
No 94
>PRK08153 histidinol-phosphate aminotransferase; Provisional
Probab=21.55 E-value=70 Score=26.60 Aligned_cols=25 Identities=28% Similarity=0.371 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
|.-.++++.||+.+++ +++.|++..
T Consensus 67 ~~~~~Lr~~ia~~~~~-~~~~I~it~ 91 (369)
T PRK08153 67 PENHDLRHALAAHHGV-APENIMVGE 91 (369)
T ss_pred CccHHHHHHHHHHhCC-CHHHEEEcC
Confidence 3467999999999999 888887754
No 95
>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=21.18 E-value=2.4e+02 Score=20.44 Aligned_cols=54 Identities=7% Similarity=0.166 Sum_probs=38.8
Q ss_pred eEEEeeeeeeccCccceEEEEEEEcCCCCC--CCHHHHHHHHHhHcCCCCCCeEEEeceEecCCC
Q 032760 6 VTIRTRKFMTNRLLSRKQFVIDVLHPGRAN--VSKAELKEKLARMYDVKDPNSIFVFKFRTHFGG 68 (134)
Q Consensus 6 v~i~~~k~~~NpLL~RkEi~~~v~H~g~~T--psr~eI~~kLA~~~~~~~~~~ivV~~~~T~fG~ 68 (134)
|.|++...-.+ .+.|.|-.-.+ .+-.+|-+.+..-+.. .|+-+||-.|+.+++.
T Consensus 43 lDlrv~~~~~~--------~~~v~Hg~~~~~~~~~~dvL~~i~~fl~~-~p~E~VIl~~~~~~~~ 98 (146)
T PF00388_consen 43 LDLRVWDGNDG--------ELVVYHGITSTSGITFEDVLNDIRDFLFE-HPSEPVILSLKHEYSP 98 (146)
T ss_dssp EEEEEEEETTS--------SEEEEETTSEE-EEEHHHHHHHHHHHTTH-STTS-EEEEEEEESTH
T ss_pred EEEEEEcCCCC--------ceEEEeCCEeeeeEeHHHHHHHHHHHHhc-CCCeEEEEEeecccch
Confidence 56676633322 26789943333 6788999999999998 9999999999988754
No 96
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=20.97 E-value=1.3e+02 Score=19.86 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEE
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV 59 (134)
++.+-.|++++||+..+. +++..-+
T Consensus 20 ~~~TV~~LK~~I~~~~~~-~~~~qrL 44 (73)
T cd01791 20 PDDTIGDLKKLIAAQTGT-RPEKIVL 44 (73)
T ss_pred CCCcHHHHHHHHHHHhCC-ChHHEEE
Confidence 667889999999999999 6665544
No 97
>PRK01533 histidinol-phosphate aminotransferase; Validated
Probab=20.92 E-value=1.2e+02 Score=25.42 Aligned_cols=25 Identities=12% Similarity=0.173 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 36 VSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 36 psr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.-.++++.||+.+++ +++.|+|..
T Consensus 64 ~g~~~Lr~aia~~~~~-~~~~I~vt~ 88 (366)
T PRK01533 64 GGATTLRQTIANKLHV-KMEQVLCGS 88 (366)
T ss_pred CCHHHHHHHHHHHhCC-CcceEEECC
Confidence 3456899999999999 888888754
No 98
>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=20.83 E-value=1e+02 Score=17.94 Aligned_cols=22 Identities=18% Similarity=0.326 Sum_probs=17.3
Q ss_pred CCCeEEEeceEecCCCCEEEEEEEEeC
Q 032760 53 DPNSIFVFKFRTHFGGGKSTGFGLIYD 79 (134)
Q Consensus 53 ~~~~ivV~~~~T~fG~g~s~g~a~IYd 79 (134)
++...++.++. +...|+.++||
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 56677888887 67789999986
No 99
>PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Probab=20.77 E-value=1.4e+02 Score=24.53 Aligned_cols=35 Identities=14% Similarity=0.369 Sum_probs=27.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 25 VIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 25 ~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.+....| +=.|=+.++++.||+.+++ +++.|-|.-
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 3444455 5678999999999999999 888887754
No 100
>PRK09105 putative aminotransferase; Provisional
Probab=20.73 E-value=95 Score=25.97 Aligned_cols=24 Identities=8% Similarity=0.267 Sum_probs=20.4
Q ss_pred CHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 37 SKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 37 sr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
.-.++++.||+.+++ +++.|+|..
T Consensus 79 ~~~~Lr~aia~~~~v-~~e~I~it~ 102 (370)
T PRK09105 79 LEDDLRTLFAAQEGL-PADHVMAYA 102 (370)
T ss_pred hHHHHHHHHHHHhCc-ChhhEEEcC
Confidence 477999999999999 888888753
No 101
>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=20.44 E-value=1.3e+02 Score=17.99 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=12.1
Q ss_pred HHHHHHHhHcCCCCCCeEEE
Q 032760 40 ELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 40 eI~~kLA~~~~~~~~~~ivV 59 (134)
+|-+.|+..+++ +++.++|
T Consensus 22 ~i~~~l~~~~g~-~~~~v~V 40 (58)
T cd00491 22 RVTEAVSEILGA-PEATIVV 40 (58)
T ss_pred HHHHHHHHHhCc-CcccEEE
Confidence 456667778888 5554443
No 102
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=20.24 E-value=2.8e+02 Score=18.57 Aligned_cols=34 Identities=24% Similarity=0.287 Sum_probs=25.0
Q ss_pred EEEEEEEcCCCCCCCHHHHHHHHHhHcCCCCCCeEEE
Q 032760 23 QFVIDVLHPGRANVSKAELKEKLARMYDVKDPNSIFV 59 (134)
Q Consensus 23 Ei~~~v~H~g~~Tpsr~eI~~kLA~~~~~~~~~~ivV 59 (134)
...++...| +..+-.+++++|....|+ +++.--+
T Consensus 12 ~~~~ekr~~--~~~Tv~~lK~kl~~~~G~-~~~~mrL 45 (84)
T cd01789 12 SFSFEKKYS--RGLTIAELKKKLELVVGT-PASSMRL 45 (84)
T ss_pred ceeeeEecC--CCCcHHHHHHHHHHHHCC-CccceEE
Confidence 344566666 678889999999999999 6555433
No 103
>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=20.21 E-value=1.1e+02 Score=25.04 Aligned_cols=27 Identities=19% Similarity=0.300 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHhHcCCCCCCeEEEec
Q 032760 34 ANVSKAELKEKLARMYDVKDPNSIFVFK 61 (134)
Q Consensus 34 ~Tpsr~eI~~kLA~~~~~~~~~~ivV~~ 61 (134)
+.|.-.++++.||+.|++ +++.|++..
T Consensus 45 ~~~~~~~lr~~la~~~~~-~~~~i~~t~ 71 (330)
T TIGR01140 45 PDPEYDELRAAAAAYYGL-PAASVLPVN 71 (330)
T ss_pred CCccHHHHHHHHHHHhCC-ChhhEEECC
Confidence 555668999999999999 877777643
No 104
>PHA01632 hypothetical protein
Probab=20.10 E-value=47 Score=22.19 Aligned_cols=36 Identities=19% Similarity=0.233 Sum_probs=24.2
Q ss_pred eeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHcCC
Q 032760 14 MTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDV 51 (134)
Q Consensus 14 ~~NpLL~RkEi~~~v~H~g~~Tpsr~eI~~kLA~~~~~ 51 (134)
-.|.+|.=+ +.+-|.|. ---|+-+|++..|.+++..
T Consensus 8 eknk~lhik-iyilieqv-p~kpteeelrkvlpkilkd 43 (64)
T PHA01632 8 EKNKTLHIK-IYILIEQV-PQKPTEEELRKVLPKILKD 43 (64)
T ss_pred CCCcEEEEE-EEEehhhc-CCCCCHHHHHHHHHHHHHH
Confidence 356666543 34444443 3569999999999998864
Done!