Query psy15694
Match_columns 81
No_of_seqs 34 out of 36
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 19:05:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15694.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15694hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04858 TH1: TH1 protein; In 99.9 4.2E-24 9.1E-29 176.4 7.7 79 1-81 1-83 (584)
2 cd06561 AlkD_like A new struct 79.9 4.7 0.0001 27.4 4.5 48 30-79 137-184 (197)
3 PF13556 HTH_30: PucR C-termin 74.7 4.2 9.2E-05 24.0 2.8 23 55-77 2-24 (59)
4 TIGR00742 yjbN tRNA dihydrouri 73.8 6.7 0.00014 30.5 4.4 34 45-79 216-261 (318)
5 PF08532 Glyco_hydro_42M: Beta 71.5 2.5 5.4E-05 30.1 1.5 20 48-67 67-86 (207)
6 PF12169 DNA_pol3_gamma3: DNA 71.2 8.3 0.00018 25.3 3.8 45 33-80 15-59 (143)
7 KOG1684|consensus 70.6 10 0.00022 31.8 4.9 46 29-75 237-285 (401)
8 PF11517 Nab2: Nuclear abundan 69.3 8.1 0.00018 27.2 3.6 23 57-79 36-58 (107)
9 PF12926 MOZART2: Mitotic-spin 66.8 11 0.00025 25.5 3.8 33 45-77 36-68 (88)
10 TIGR02366 DHAK_reg probable di 66.6 11 0.00023 25.1 3.7 29 50-78 141-171 (176)
11 PF11387 DUF2795: Protein of u 65.9 8.9 0.00019 22.1 2.8 22 56-77 11-32 (44)
12 PRK10415 tRNA-dihydrouridine s 63.0 17 0.00037 28.0 4.6 37 44-80 216-264 (321)
13 COG5140 UFD1 Ubiquitin fusion- 61.9 5.3 0.00012 32.4 1.7 19 28-46 136-154 (331)
14 PRK13916 plasmid segregation p 60.5 8.6 0.00019 26.6 2.3 22 45-66 27-48 (97)
15 PF00627 UBA: UBA/TS-N domain; 59.8 17 0.00038 19.5 3.1 20 56-75 18-37 (37)
16 COG3905 Predicted transcriptio 57.5 19 0.00041 24.2 3.5 49 32-80 13-77 (83)
17 TIGR01669 phage_XkdX phage unc 56.1 14 0.00031 21.7 2.5 21 55-75 6-27 (45)
18 PF05201 GlutR_N: Glutamyl-tRN 55.2 31 0.00067 24.0 4.5 42 31-72 87-134 (152)
19 cd03143 A4_beta-galactosidase_ 53.9 12 0.00027 24.8 2.2 19 48-66 63-81 (154)
20 PF08713 DNA_alkylation: DNA a 52.4 20 0.00044 24.6 3.2 48 30-79 151-198 (213)
21 cd07064 AlkD_like_1 A new stru 52.3 31 0.00068 24.9 4.3 48 31-80 147-194 (208)
22 PF11740 KfrA_N: Plasmid repli 50.4 47 0.001 21.3 4.5 42 31-77 2-43 (120)
23 TIGR00737 nifR3_yhdG putative 50.2 42 0.00091 25.4 4.8 42 36-78 207-260 (319)
24 PF02845 CUE: CUE domain; Int 49.5 36 0.00079 18.7 3.4 20 59-78 22-41 (42)
25 PF09693 Phage_XkdX: Phage unc 48.2 22 0.00047 20.2 2.4 22 55-76 1-23 (40)
26 smart00546 CUE Domain that may 46.5 35 0.00077 18.7 3.0 16 62-77 26-41 (43)
27 PF13625 Helicase_C_3: Helicas 46.2 27 0.00059 23.1 3.0 41 34-78 23-67 (129)
28 PRK05451 dihydroorotase; Provi 46.0 33 0.00071 26.4 3.7 20 59-78 277-296 (345)
29 PF00482 T2SF: Type II secreti 45.1 47 0.001 19.8 3.6 29 52-80 60-88 (124)
30 PF12637 TSCPD: TSCPD domain; 44.1 36 0.00079 22.1 3.2 21 57-77 46-66 (95)
31 cd07347 harmonin_N_like N-term 43.4 38 0.00082 22.1 3.2 22 53-75 23-44 (78)
32 CHL00173 cpeA phycoerythrin al 42.8 23 0.0005 25.8 2.3 28 52-79 21-48 (164)
33 PRK10122 GalU regulator GalF; 42.8 20 0.00042 27.2 2.1 32 47-79 214-249 (297)
34 PF10540 Membr_traf_MHD: Munc1 41.7 20 0.00043 24.7 1.8 14 54-67 90-103 (137)
35 PF08569 Mo25: Mo25-like; Int 41.3 6.3 0.00014 31.2 -0.8 49 31-79 142-207 (335)
36 PF10281 Ish1: Putative stress 41.3 53 0.0011 17.9 3.2 24 56-79 7-38 (38)
37 KOG1816|consensus 38.9 20 0.00044 29.1 1.7 25 28-52 128-155 (308)
38 PF06337 DUSP: DUSP domain; I 38.8 30 0.00065 21.4 2.2 23 45-69 69-92 (99)
39 PF05402 PqqD: Coenzyme PQQ sy 38.3 57 0.0012 18.8 3.2 32 48-80 13-44 (68)
40 PF06755 DUF1219: Protein of u 37.4 48 0.0011 23.5 3.2 24 56-79 47-70 (114)
41 PF12127 YdfA_immunity: SigmaW 37.1 39 0.00085 27.6 3.0 27 55-81 69-95 (316)
42 PRK13389 UTP--glucose-1-phosph 36.5 27 0.00059 26.5 2.0 32 48-79 218-252 (302)
43 PF08158 NUC130_3NT: NUC130/3N 36.4 26 0.00056 21.2 1.5 14 67-80 16-29 (52)
44 PF02681 DUF212: Divergent PAP 36.4 17 0.00037 26.0 0.8 13 58-70 34-46 (141)
45 PF08101 DUF1708: Domain of un 36.3 70 0.0015 26.5 4.4 49 29-78 255-305 (420)
46 PHA02589 rnlA RNA ligase A; Pr 36.1 28 0.0006 28.6 2.1 39 41-79 319-366 (378)
47 COG1433 Uncharacterized conser 35.8 37 0.0008 23.6 2.4 34 45-78 65-107 (121)
48 PRK08560 tyrosyl-tRNA syntheta 35.4 87 0.0019 24.3 4.6 50 28-77 226-307 (329)
49 PF00772 DnaB: DnaB-like helic 34.4 1.1E+02 0.0024 18.6 4.5 44 35-78 22-69 (103)
50 PF00502 Phycobilisome: Phycob 34.0 33 0.00072 24.0 2.0 29 51-79 15-43 (157)
51 PF02194 PXA: PXA domain; Int 33.7 19 0.00042 24.5 0.7 18 34-51 159-176 (185)
52 PF01402 RHH_1: Ribbon-helix-h 33.3 78 0.0017 16.6 3.1 30 50-79 6-36 (39)
53 PF08311 Mad3_BUB1_I: Mad3/BUB 33.2 1E+02 0.0022 20.7 4.2 48 31-78 44-92 (126)
54 PF13043 DUF3903: Domain of un 33.1 32 0.0007 20.4 1.5 14 32-45 10-23 (40)
55 smart00165 UBA Ubiquitin assoc 33.0 76 0.0016 16.5 2.9 19 57-75 18-36 (37)
56 TIGR03687 pupylate_cterm ubiqu 32.6 28 0.0006 20.0 1.1 19 48-66 14-32 (33)
57 PRK07764 DNA polymerase III su 32.6 1E+02 0.0022 27.5 5.0 47 31-80 246-292 (824)
58 CHL00170 cpcA phycocyanin alph 32.4 49 0.0011 24.2 2.7 28 52-79 21-48 (162)
59 PF08383 Maf_N: Maf N-terminal 32.4 32 0.00069 19.9 1.4 14 65-78 22-35 (35)
60 TIGR02960 SigX5 RNA polymerase 31.1 93 0.002 22.9 4.0 27 52-78 204-232 (324)
61 PF08712 Nfu_N: Scaffold prote 30.9 21 0.00045 23.0 0.5 15 51-65 73-87 (87)
62 cd04763 HTH_MlrA-like Helix-Tu 30.9 73 0.0016 18.5 2.9 23 54-76 46-68 (68)
63 TIGR01099 galU UTP-glucose-1-p 30.6 47 0.001 23.5 2.3 32 48-79 203-237 (260)
64 PF14164 YqzH: YqzH-like prote 30.6 1.2E+02 0.0025 19.5 3.9 32 33-64 7-40 (64)
65 TIGR01128 holA DNA polymerase 30.2 78 0.0017 22.7 3.4 28 53-80 197-224 (302)
66 PF13709 DUF4159: Domain of un 29.8 56 0.0012 23.9 2.6 20 47-66 64-83 (207)
67 CHL00172 cpeB phycoerythrin be 29.8 60 0.0013 24.2 2.8 29 51-79 20-48 (177)
68 COG1094 Predicted RNA-binding 29.8 52 0.0011 25.0 2.5 29 52-80 61-92 (194)
69 PF04867 DUF643: Protein of un 29.6 40 0.00086 23.9 1.7 19 31-49 94-112 (114)
70 PRK11477 carbohydrate diacid t 29.6 1.1E+02 0.0023 23.5 4.3 34 41-76 312-345 (385)
71 PF15606 Toxin_55: Putative to 29.5 1E+02 0.0022 20.6 3.5 26 54-79 24-52 (77)
72 cd02538 G1P_TT_short G1P_TT_sh 29.4 33 0.00072 24.0 1.3 31 48-78 174-207 (240)
73 cd00043 CYCLIN Cyclin box fold 29.2 86 0.0019 17.4 2.9 23 51-73 2-24 (88)
74 cd05401 NT_GlnE_GlnD_like Nucl 29.1 1E+02 0.0022 20.9 3.7 26 53-78 6-31 (172)
75 PHA02099 hypothetical protein 29.0 31 0.00068 23.2 1.1 26 37-62 35-65 (84)
76 PF00296 Bac_luciferase: Lucif 28.9 23 0.0005 25.5 0.5 14 66-80 288-301 (307)
77 PF04405 ScdA_N: Domain of Unk 28.9 85 0.0018 18.9 2.9 12 67-78 44-55 (56)
78 cd08767 Cdt1_c The C-terminal 28.8 1.1E+02 0.0024 20.8 3.8 29 52-80 44-76 (126)
79 smart00777 Mad3_BUB1_I Mad3/BU 28.8 1.8E+02 0.004 20.1 5.0 49 30-78 43-92 (125)
80 cd00781 ketosteroid_isomerase 28.8 71 0.0015 19.7 2.6 25 55-79 6-32 (122)
81 cd03345 eu_TyrOH Eukaryotic ty 28.7 65 0.0014 25.9 3.0 40 40-79 150-206 (298)
82 PF05184 SapB_1: Saposin-like 28.6 97 0.0021 16.1 3.1 25 53-77 9-33 (39)
83 PRK11815 tRNA-dihydrouridine s 28.4 1.2E+02 0.0025 23.6 4.3 33 45-78 226-270 (333)
84 PF14258 DUF4350: Domain of un 28.3 61 0.0013 19.0 2.2 23 45-67 42-65 (70)
85 TIGR01339 phycocy_beta phycocy 27.8 59 0.0013 23.9 2.5 29 51-79 18-46 (170)
86 PF07515 DUF1528: Protein of u 27.8 32 0.00069 23.1 1.0 13 48-63 18-30 (106)
87 TIGR03557 F420_G6P_family F420 27.7 42 0.00092 25.5 1.8 19 58-76 262-280 (316)
88 PLN02599 dihydroorotase 27.6 92 0.002 24.8 3.7 25 54-78 291-315 (364)
89 PRK13665 hypothetical protein; 27.5 66 0.0014 26.3 2.9 47 31-81 54-100 (316)
90 PF12816 Vps8: Golgi CORVET co 27.4 1E+02 0.0022 22.4 3.6 42 34-75 2-45 (196)
91 smart00076 IFabd Interferon al 27.2 71 0.0015 21.8 2.6 30 35-64 61-91 (117)
92 CHL00086 apcA allophycocyanin 27.0 64 0.0014 23.2 2.5 29 51-79 19-47 (161)
93 PF05924 SAMP: SAMP Motif; In 26.6 50 0.0011 17.0 1.4 9 33-41 3-11 (20)
94 TIGR01338 phycocy_alpha phycoc 26.4 69 0.0015 23.3 2.6 28 52-79 20-47 (161)
95 PF12162 STAT1_TAZ2bind: STAT1 26.3 66 0.0014 17.1 1.8 13 50-62 10-22 (23)
96 cd03347 eu_PheOH Eukaryotic ph 26.3 75 0.0016 25.6 3.0 40 40-79 151-207 (306)
97 PF05305 DUF732: Protein of un 26.2 1.4E+02 0.003 18.5 3.7 28 52-79 46-73 (100)
98 cd04658 Piwi_piwi-like_Euk Piw 26.1 51 0.0011 26.2 2.0 42 32-73 138-187 (448)
99 cd01782 AF6_RA_repeat1 Ubiquit 26.1 28 0.00061 24.6 0.5 24 57-80 23-60 (112)
100 PRK05574 holA DNA polymerase I 26.1 98 0.0021 22.7 3.4 28 53-80 232-259 (340)
101 PRK04358 hypothetical protein; 26.0 1.2E+02 0.0027 23.4 4.0 46 30-75 25-76 (217)
102 smart00544 MA3 Domain in DAP-5 25.7 1.3E+02 0.0028 18.8 3.5 24 53-77 4-27 (113)
103 PF02637 GatB_Yqey: GatB domai 25.6 97 0.0021 20.9 3.1 39 36-75 45-83 (148)
104 PF02701 zf-Dof: Dof domain, z 25.5 35 0.00075 22.0 0.8 11 58-68 36-46 (63)
105 PRK04149 sat sulfate adenylylt 25.2 62 0.0013 26.4 2.4 39 31-69 350-388 (391)
106 COG4687 Uncharacterized protei 25.0 1.3E+02 0.0027 21.7 3.6 34 31-64 85-118 (122)
107 smart00229 RasGEFN Guanine nuc 25.0 1.5E+02 0.0033 18.8 3.8 46 31-80 9-54 (127)
108 smart00845 GatB_Yqey GatB doma 24.9 1.1E+02 0.0023 20.9 3.2 41 34-75 42-82 (147)
109 TIGR03875 RNA_lig_partner RNA 24.7 88 0.0019 24.1 3.0 28 48-75 45-72 (206)
110 PF12668 DUF3791: Protein of u 24.4 35 0.00077 20.4 0.7 24 38-61 6-29 (62)
111 TIGR03612 RutA pyrimidine util 24.3 48 0.001 25.7 1.5 16 64-79 304-319 (355)
112 cd01096 Alkanal_monooxygenase 24.2 46 0.001 24.9 1.4 14 64-77 272-285 (315)
113 COG1210 GalU UDP-glucose pyrop 24.2 38 0.00082 27.3 1.0 17 48-65 208-224 (291)
114 smart00185 ARM Armadillo/beta- 24.2 93 0.002 15.5 2.2 19 58-76 4-22 (41)
115 PF06496 DUF1097: Protein of u 23.9 73 0.0016 21.8 2.2 26 54-79 25-50 (144)
116 cd01269 PLX Pollux (PLX) Phosp 23.4 49 0.0011 23.9 1.3 15 31-45 19-33 (129)
117 cd01308 Isoaspartyl-dipeptidas 22.9 1.4E+02 0.0029 22.6 3.7 25 54-78 309-334 (387)
118 cd08819 CARD_MDA5_2 Caspase ac 22.9 2.4E+02 0.0052 19.0 4.5 40 32-76 21-60 (88)
119 PF03770 IPK: Inositol polypho 22.6 1.1E+02 0.0023 21.9 2.9 23 51-73 80-102 (197)
120 PF03445 DUF294: Putative nucl 22.3 1.5E+02 0.0033 20.0 3.6 26 54-79 3-28 (138)
121 cd06454 KBL_like KBL_like; thi 22.3 1.8E+02 0.004 20.8 4.1 25 42-66 5-32 (349)
122 PF13428 TPR_14: Tetratricopep 22.3 1.4E+02 0.003 15.9 3.5 26 52-77 1-26 (44)
123 cd00194 UBA Ubiquitin Associat 22.2 1.3E+02 0.0029 15.6 3.0 20 57-76 18-37 (38)
124 PRK01215 competence damage-ind 22.2 1.5E+02 0.0033 22.5 3.9 37 31-67 75-111 (264)
125 PF14454 Prok_Ub: Prokaryotic 22.2 66 0.0014 20.4 1.6 23 57-79 5-37 (65)
126 COG0042 tRNA-dihydrouridine sy 22.0 1.8E+02 0.0038 22.8 4.2 41 37-79 214-265 (323)
127 PF08412 Ion_trans_N: Ion tran 21.9 77 0.0017 20.5 1.9 32 31-64 20-51 (77)
128 cd02826 Piwi-like Piwi-like: P 21.8 53 0.0011 25.7 1.3 42 32-73 82-130 (393)
129 PF08491 SE: Squalene epoxidas 21.7 69 0.0015 25.2 2.0 32 41-76 203-238 (276)
130 PF14676 FANCI_S2: FANCI solen 21.6 1.4E+02 0.0029 21.3 3.3 41 33-77 39-81 (158)
131 PF13758 Prefoldin_3: Prefoldi 21.5 65 0.0014 22.1 1.6 11 67-77 65-75 (99)
132 PRK00440 rfc replication facto 21.4 2.4E+02 0.0053 20.2 4.6 28 47-76 178-205 (319)
133 CHL00090 apcD allophycocyanin 21.4 79 0.0017 22.7 2.1 29 51-79 19-47 (161)
134 TIGR03646 YtoQ_fam YtoQ family 21.3 64 0.0014 23.8 1.6 10 67-76 131-140 (144)
135 PF13348 Y_phosphatase3C: Tyro 21.2 78 0.0017 18.5 1.7 26 54-79 41-67 (68)
136 PF07217 Het-C: Heterokaryon i 21.2 3E+02 0.0066 24.4 5.8 47 31-77 506-558 (606)
137 TIGR02096 conserved hypothetic 21.0 98 0.0021 19.1 2.2 22 57-78 3-26 (129)
138 COG2971 Predicted N-acetylgluc 21.0 1.9E+02 0.0041 23.3 4.3 41 32-77 158-199 (301)
139 PF08941 USP8_interact: USP8 i 20.9 40 0.00086 25.5 0.5 33 43-79 82-114 (179)
140 TIGR01267 Phe4hydrox_mono phen 20.9 81 0.0018 24.7 2.2 40 40-79 97-154 (248)
141 TIGR02898 spore_YhcN_YlaJ spor 20.9 3.2E+02 0.007 19.7 5.1 49 31-79 95-153 (158)
142 PF02847 MA3: MA3 domain; Int 20.9 1.8E+02 0.0039 18.0 3.5 24 53-77 4-27 (113)
143 TIGR02257 cobalto_cobN cobalto 20.8 1.6E+02 0.0035 27.4 4.3 23 52-75 132-154 (1122)
144 CHL00088 apcB allophycocyanin 20.8 74 0.0016 22.9 1.8 29 51-79 20-48 (161)
145 TIGR01446 DnaD_dom DnaD and ph 20.8 1.5E+02 0.0033 17.4 3.0 25 51-75 14-38 (73)
146 TIGR00635 ruvB Holliday juncti 20.7 2E+02 0.0044 20.8 4.1 30 46-77 175-204 (305)
147 cd04181 NTP_transferase NTP_tr 20.5 96 0.0021 20.7 2.2 30 48-78 170-201 (217)
148 cd01318 DHOase_IIb Dihydroorot 20.4 1.5E+02 0.0033 22.9 3.6 23 56-78 276-299 (361)
149 PF05524 PEP-utilisers_N: PEP- 20.3 1.3E+02 0.0029 19.4 2.8 29 51-79 79-107 (123)
150 COG1955 FlaJ Archaeal flagella 20.3 61 0.0013 28.1 1.5 22 59-80 377-398 (527)
151 TIGR00640 acid_CoA_mut_C methy 20.2 1.5E+02 0.0033 20.2 3.2 22 56-77 20-51 (132)
152 PF12029 DUF3516: Domain of un 20.0 1.8E+02 0.0039 25.0 4.1 53 9-81 229-281 (461)
No 1
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=99.90 E-value=4.2e-24 Score=176.38 Aligned_cols=79 Identities=44% Similarity=0.897 Sum_probs=66.7
Q ss_pred CCCcccccccCCCcc---cCcC-CCCCCCCCCCCChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHH
Q psy15694 1 MNDDYDDEQTHRWDQ---DMVD-VDSDGGDDPMENPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 1 Me~dyd~~~~~~W~~---~~~~-~~~~~~~~~~e~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLS 76 (81)
|++||+..+ +|+. +.+. +++++..+..+++++++++|+++|++|||||||+||.+||+||++||+|++||++||
T Consensus 1 ~~~~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~Imep~i~~~i~~y~~~gG~p~~vv~~Ls 78 (584)
T PF04858_consen 1 MEEDYEGDR--GWESSDGEGDDQEDDEEESEADEEPEEVLEECLRRLSQPDAIMEPSIFDTIKRYFRAGGDPEEVVELLS 78 (584)
T ss_pred CCchhhhcc--ccccccCCCCcccCccccccCCCChHHHHHHHHHhcCCCCeeeCchHHHHHHHHHHCCCCHHHHHHHHH
Confidence 899999544 6953 3222 344445555779999999999999999999999999999999999999999999999
Q ss_pred hhccC
Q psy15694 77 IDNMA 81 (81)
Q Consensus 77 eny~~ 81 (81)
+||++
T Consensus 79 ~~Y~g 83 (584)
T PF04858_consen 79 ENYRG 83 (584)
T ss_pred Hhccc
Confidence 99985
No 2
>cd06561 AlkD_like A new structural DNA glycosylase. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity.
Probab=79.86 E-value=4.7 Score=27.38 Aligned_cols=48 Identities=17% Similarity=0.286 Sum_probs=44.3
Q ss_pred CChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 30 ENPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 30 e~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++..+++-|.+....++|-..=+|.-.|+.|.+- .|+.|++.|..|.
T Consensus 137 ~~~~~~l~~~~~~~~d~~~~Vqkav~w~L~~~~~~--~~~~v~~~l~~~~ 184 (197)
T cd06561 137 TDFDLLLEIIERLLHDEEYFVQKAVGWALREYGKK--DPERVIAFLEKNG 184 (197)
T ss_pred ccHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhh--CHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999 9999999998775
No 3
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=74.68 E-value=4.2 Score=23.99 Aligned_cols=23 Identities=22% Similarity=0.471 Sum_probs=17.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 55 FSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 55 f~~lkrYfqaGG~PE~VI~lLSe 77 (81)
..+|+.|+.+||+..++-+.|--
T Consensus 2 ~~TL~~yl~~~~n~~~tA~~L~i 24 (59)
T PF13556_consen 2 LETLRAYLENNGNISKTARALHI 24 (59)
T ss_dssp --HHHHHHHTTT-HHHHHHHHTS
T ss_pred hhHHHHHHHcCCCHHHHHHHHCC
Confidence 46899999999999999887743
No 4
>TIGR00742 yjbN tRNA dihydrouridine synthase A. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase.
Probab=73.84 E-value=6.7 Score=30.50 Aligned_cols=34 Identities=18% Similarity=0.286 Sum_probs=26.9
Q ss_pred CCCccc-------chhHHHHHHHHHHcCC-----CHHHHHHHHHhhc
Q psy15694 45 TPDYIM-------EPGIFSQLKRYFQAGG-----NPEQVIELMIIDN 79 (81)
Q Consensus 45 ~~DyIM-------EP~If~~lkrYfqaGG-----~PE~VI~lLSeny 79 (81)
..|-|| .|.||..++.|+. || ++++.++.+.+++
T Consensus 216 g~dgVMigRgal~nP~if~~~~~~l~-~~~~~~~~~~e~~~~~~~~~ 261 (318)
T TIGR00742 216 HVDGVMVGREAYENPYLLANVDREIF-NETDEILTRKEIVEQMLPYI 261 (318)
T ss_pred CCCEEEECHHHHhCCHHHHHHHHHhc-CCCCCCCCHHHHHHHHHHHH
Confidence 588888 9999999999998 65 4567777766554
No 5
>PF08532 Glyco_hydro_42M: Beta-galactosidase trimerisation domain; InterPro: IPR013738 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is non catalytic domain B of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. This domain is related to glutamine amidotransferase enzymes, but the catalytic residues are replaced by non functional amino acids. This domain is involved in trimerisation. ; GO: 0004565 beta-galactosidase activity, 0005975 carbohydrate metabolic process; PDB: 1KWK_A 1KWG_A.
Probab=71.50 E-value=2.5 Score=30.07 Aligned_cols=20 Identities=35% Similarity=0.851 Sum_probs=12.3
Q ss_pred cccchhHHHHHHHHHHcCCC
Q psy15694 48 YIMEPGIFSQLKRYFQAGGN 67 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaGG~ 67 (81)
++|.|.....|++|.++||.
T Consensus 67 ~~l~~~~~~~L~~yV~~GG~ 86 (207)
T PF08532_consen 67 YILSPEFAERLRAYVENGGT 86 (207)
T ss_dssp SC--HHH---HHHHHT-SS-
T ss_pred EEEChHHHHHHHHHHHCCCE
Confidence 78899999999999999994
No 6
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=71.19 E-value=8.3 Score=25.25 Aligned_cols=45 Identities=20% Similarity=0.276 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 33 QEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 33 ~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
.+.+-+.+......|. +.++..+++.+..|-+|.++++-|.+.+|
T Consensus 15 ~~~i~~l~~ai~~~d~---~~~l~~~~~l~~~G~d~~~~l~~L~~~~R 59 (143)
T PF12169_consen 15 EEQIFELLDAILEGDA---AEALELLNELLEQGKDPKQFLDDLIEYLR 59 (143)
T ss_dssp THHHHHHHHHHHTT-H---HHHHHHHHHHHHCT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCH---HHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3445556666666775 79999999999999999999999998887
No 7
>KOG1684|consensus
Probab=70.63 E-value=10 Score=31.77 Aligned_cols=46 Identities=30% Similarity=0.537 Sum_probs=35.7
Q ss_pred CCChHHHHHHHHHhcCCCC---cccchhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 29 MENPQEVLNECLEKFSTPD---YIMEPGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 29 ~e~~~~vl~eCl~~fs~~D---yIMEP~If~~lkrYfqaGG~PE~VI~lL 75 (81)
-++|++++++|+++|+++= .-.-+-..+++..+|.+- +.|++|+-|
T Consensus 237 ~~dp~~~I~~~l~~y~~~~~~~~~~~~~~~~~i~~~Fs~~-tVeeIie~l 285 (401)
T KOG1684|consen 237 NDDPQSVINETLEKYASPAKDESFSLSLKLDVINKCFSAN-TVEEIIEAL 285 (401)
T ss_pred CCCcHHHHHHHHHHhcccCCCccccchhhHHHHHHhhccc-cHHHHHHHH
Confidence 3478899999999999872 222333778899999777 999999966
No 8
>PF11517 Nab2: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); InterPro: IPR021083 Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 []. The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA []. An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 [].; PDB: 3LCN_B 2V75_A 2JPS_A.
Probab=69.25 E-value=8.1 Score=27.17 Aligned_cols=23 Identities=13% Similarity=0.167 Sum_probs=15.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 57 QLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 57 ~lkrYfqaGG~PE~VI~lLSeny 79 (81)
++-=-+.+||+|+.|++-||.=+
T Consensus 36 yIvlLisNggs~esivqELssLF 58 (107)
T PF11517_consen 36 YIVLLISNGGSVESIVQELSSLF 58 (107)
T ss_dssp HHHHHHHTT--HHHHHHHHHHH-
T ss_pred HhheeeeCCCCHHHHHHHHHHHH
Confidence 34445789999999999999643
No 9
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=66.80 E-value=11 Score=25.47 Aligned_cols=33 Identities=12% Similarity=0.360 Sum_probs=30.5
Q ss_pred CCCcccchhHHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 45 TPDYIMEPGIFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 45 ~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
...-.|-|++|..|=...+.+=+|+-|.++|++
T Consensus 36 ~AGv~~dp~VFriildLL~~nVsP~AI~qmLK~ 68 (88)
T PF12926_consen 36 LAGVPMDPEVFRIILDLLRLNVSPDAIFQMLKS 68 (88)
T ss_pred HhCCCcChHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 467889999999999999999999999999975
No 10
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=66.60 E-value=11 Score=25.09 Aligned_cols=29 Identities=14% Similarity=0.256 Sum_probs=24.6
Q ss_pred cchhHHHHHHHHHHcCC--CHHHHHHHHHhh
Q psy15694 50 MEPGIFSQLKRYFQAGG--NPEQVIELMIID 78 (81)
Q Consensus 50 MEP~If~~lkrYfqaGG--~PE~VI~lLSen 78 (81)
+--++++.+.++++.|+ +|++|++.++.-
T Consensus 141 ~~~~~~g~i~~Wl~~~~~~~~~~~a~~~~~~ 171 (176)
T TIGR02366 141 YSAGAVGSITKWIVANCPEDPEVLSQHIKNL 171 (176)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 46678889999999999 899999888753
No 11
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=65.95 E-value=8.9 Score=22.13 Aligned_cols=22 Identities=23% Similarity=0.439 Sum_probs=19.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHh
Q psy15694 56 SQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 56 ~~lkrYfqaGG~PE~VI~lLSe 77 (81)
..|-++-+..|.|.+||+.|..
T Consensus 11 ~~Lv~~A~~~gA~~~vl~~L~~ 32 (44)
T PF11387_consen 11 DELVRHARRNGAPDDVLDALER 32 (44)
T ss_pred HHHHHHHHHcCCCHHHHHHHHH
Confidence 5688889999999999999963
No 12
>PRK10415 tRNA-dihydrouridine synthase B; Provisional
Probab=63.01 E-value=17 Score=28.02 Aligned_cols=37 Identities=24% Similarity=0.455 Sum_probs=28.8
Q ss_pred CCCCccc-------chhHHHHHHHHHHcCC-----CHHHHHHHHHhhcc
Q psy15694 44 STPDYIM-------EPGIFSQLKRYFQAGG-----NPEQVIELMIIDNM 80 (81)
Q Consensus 44 s~~DyIM-------EP~If~~lkrYfqaGG-----~PE~VI~lLSeny~ 80 (81)
.-.|.|| .|.||..+++|+.-|- ++++++.++.++++
T Consensus 216 ~gadgVmiGR~~l~nP~if~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 264 (321)
T PRK10415 216 TGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVR 264 (321)
T ss_pred cCCCEEEEChHhhcCChHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHH
Confidence 4588877 9999999999998664 34688888777653
No 13
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=61.88 E-value=5.3 Score=32.39 Aligned_cols=19 Identities=47% Similarity=0.912 Sum_probs=16.4
Q ss_pred CCCChHHHHHHHHHhcCCC
Q psy15694 28 PMENPQEVLNECLEKFSTP 46 (81)
Q Consensus 28 ~~e~~~~vl~eCl~~fs~~ 46 (81)
+-++|.+||+.|||.||+-
T Consensus 136 dI~dpkavLEn~LRNfstL 154 (331)
T COG5140 136 DIEDPKAVLENCLRNFSTL 154 (331)
T ss_pred eccChHHHHHHHHhhcccc
Confidence 3468999999999999974
No 14
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=60.52 E-value=8.6 Score=26.57 Aligned_cols=22 Identities=27% Similarity=0.378 Sum_probs=19.3
Q ss_pred CCCcccchhHHHHHHHHHHcCC
Q psy15694 45 TPDYIMEPGIFSQLKRYFQAGG 66 (81)
Q Consensus 45 ~~DyIMEP~If~~lkrYfqaGG 66 (81)
.||=-|-.-|-..|+||+|.||
T Consensus 27 ~P~GT~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 27 VPRGTKTAHIREALRRYIEEIG 48 (97)
T ss_pred CCCCCccHHHHHHHHHHHHhcC
Confidence 4777788888899999999999
No 15
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=59.78 E-value=17 Score=19.51 Aligned_cols=20 Identities=15% Similarity=0.295 Sum_probs=16.6
Q ss_pred HHHHHHHHcCCCHHHHHHHH
Q psy15694 56 SQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 56 ~~lkrYfqaGG~PE~VI~lL 75 (81)
...+....+||+.+..|+.|
T Consensus 18 ~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 18 QAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHhC
Confidence 45677888999999999887
No 16
>COG3905 Predicted transcriptional regulator [Transcription]
Probab=57.50 E-value=19 Score=24.23 Aligned_cols=49 Identities=27% Similarity=0.294 Sum_probs=33.8
Q ss_pred hHHHHHHHHHhc-CCCCcccchhHHHHHHHH-H-----Hc------CC---CHHHHHHHHHhhcc
Q psy15694 32 PQEVLNECLEKF-STPDYIMEPGIFSQLKRY-F-----QA------GG---NPEQVIELMIIDNM 80 (81)
Q Consensus 32 ~~~vl~eCl~~f-s~~DyIMEP~If~~lkrY-f-----qa------GG---~PE~VI~lLSeny~ 80 (81)
-..-|++..++. +++-|||++.|++.++|= + ++ -| ++|+|++-|+.-|.
T Consensus 13 l~~rLd~lAe~~~rsrs~i~~~Aia~~v~re~~q~a~i~aGla~a~aGr~v~heEv~a~i~~~~t 77 (83)
T COG3905 13 LKRRLDELAEATDRSRSYIAEQAIADFVDREEWQLAAIKAGLADAEAGRFVTHEEVIAWIDSWGT 77 (83)
T ss_pred HHHHHHHHHHHhccChhhhHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCcCCHHHHHHHHHhhcC
Confidence 344555554444 567799999999988875 2 22 23 88999988877654
No 17
>TIGR01669 phage_XkdX phage uncharacterized protein, XkdX family. This model represents a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=56.06 E-value=14 Score=21.68 Aligned_cols=21 Identities=29% Similarity=0.536 Sum_probs=16.9
Q ss_pred HHHHHHHHHcCC-CHHHHHHHH
Q psy15694 55 FSQLKRYFQAGG-NPEQVIELM 75 (81)
Q Consensus 55 f~~lkrYfqaGG-~PE~VI~lL 75 (81)
|..+|+|+..|. ++++|-...
T Consensus 6 ~e~iK~~Y~~g~~t~e~v~~~V 27 (45)
T TIGR01669 6 FEKVKTYYLWGYYSNEDVNKFV 27 (45)
T ss_pred HHHHHHHHHcCCCCHHHHHHHh
Confidence 788999999998 888876543
No 18
>PF05201 GlutR_N: Glutamyl-tRNAGlu reductase, N-terminal domain; InterPro: IPR015895 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents the N-terminal domain of glutamyl-tRNA reductase (1.2.1.70 from EC), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway [, ]. The enzyme requires NADPH as a cofactor.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process, 0055114 oxidation-reduction process; PDB: 1GPJ_A.
Probab=55.21 E-value=31 Score=24.02 Aligned_cols=42 Identities=21% Similarity=0.260 Sum_probs=30.2
Q ss_pred ChHHHHHHHHHhcCCCCccc--chhHHHHHHHHHHc----CCCHHHHH
Q psy15694 31 NPQEVLNECLEKFSTPDYIM--EPGIFSQLKRYFQA----GGNPEQVI 72 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIM--EP~If~~lkrYfqa----GG~PE~VI 72 (81)
...+.+.+.++--+--|+.+ |++|++|+|+=++. |.....+=
T Consensus 87 ~g~~a~~HLf~VasGLdS~V~GE~qIlgQvk~A~~~A~~~g~~g~~L~ 134 (152)
T PF05201_consen 87 TGDEAVRHLFRVASGLDSMVVGEDQILGQVKRAYEFAREAGTTGPILN 134 (152)
T ss_dssp EHHHHHHHHHHHHTTTTSSSTT-HHHHHHHHHHHHHHHHHT---HHHH
T ss_pred cChHHHHHHHHHHhcchhhhcChHHHHHHHHHHHHHHHHcCChhHHHH
Confidence 45788899999999999877 99999999997764 55444433
No 19
>cd03143 A4_beta-galactosidase_middle_domain A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain. A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to beta-galactosidase from Thermus thermophilus. Beta-Galactosidase hydrolyzes the beta-1,4-D-galactosidic linkage of lactose, as well as those of related chromogens, o-nitrophenyl-beta-D-galactopyranoside (ONP-Gal) and 5-bromo-4-chloro-3-indolyl-beta-D-galactoside (X-gal). This A4 beta-galactosidase middle domain lacks the catalytic triad of typical GATase1 domains. The reactive Cys residue found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow in typical GATase1 domains is not conserved in this group.
Probab=53.88 E-value=12 Score=24.81 Aligned_cols=19 Identities=26% Similarity=0.702 Sum_probs=14.7
Q ss_pred cccchhHHHHHHHHHHcCC
Q psy15694 48 YIMEPGIFSQLKRYFQAGG 66 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaGG 66 (81)
++|.+.....|++|+.+||
T Consensus 63 ~~~~~~~~~~l~~~v~~GG 81 (154)
T cd03143 63 YLLSDATAAALRAYVENGG 81 (154)
T ss_pred hcCCHHHHHHHHHHHHCCC
Confidence 3445555689999999999
No 20
>PF08713 DNA_alkylation: DNA alkylation repair enzyme; InterPro: IPR014825 These proteins are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein shows it to adopt a super coiled alpha helical structure. ; PDB: 3JY1_A 3JXY_A 3JX7_A 3JXZ_A 3BVS_A 2B6C_B 1T06_B 3L9T_A.
Probab=52.42 E-value=20 Score=24.58 Aligned_cols=48 Identities=19% Similarity=0.311 Sum_probs=41.0
Q ss_pred CChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 30 ENPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 30 e~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.+...++.-|......++|-..=+|--.|+.+.+- .|+.|.+.|..|+
T Consensus 151 ~~~~~~l~~~~~~~~d~~~~vq~ai~w~L~~~~~~--~~~~v~~~l~~~~ 198 (213)
T PF08713_consen 151 EDFDELLEIIEALLKDEEYYVQKAIGWALREIGKK--DPDEVLEFLQKNS 198 (213)
T ss_dssp CHHHHHHHHHHHCTTGS-HHHHHHHHHHHHHHCTT---HHHHHHHHHHS-
T ss_pred cCHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHh--CHHHHHHHHHHCc
Confidence 46789999999999999999999999999999876 8999999999986
No 21
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=52.29 E-value=31 Score=24.92 Aligned_cols=48 Identities=15% Similarity=0.360 Sum_probs=42.1
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
++..+++=|......++|.+.=.|-=.||.|-+- +|..|+..|.+|+.
T Consensus 147 ~~~~l~~~~~~~~~d~e~fI~KAiGW~LRe~~k~--d~~~V~~fl~~~~~ 194 (208)
T cd07064 147 DTDLLFEIILANLGSKEFFIRKAIGWALREYSKT--NPDWVRDFVAAHKL 194 (208)
T ss_pred CHHHHHHHHHHhCCChHHHHHHHHHHHHHHHhcc--CHHHHHHHHHHhhh
Confidence 3566777788899999999999999999999988 99999999999873
No 22
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=50.40 E-value=47 Score=21.26 Aligned_cols=42 Identities=12% Similarity=0.262 Sum_probs=29.1
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
+.+.|.+-|.+.++.-- .|++.. |+.-+. ||++.+|...|-+
T Consensus 2 T~e~V~~Aa~~L~~~G~---~pT~~~-Vr~~lG-~GS~~ti~~~l~~ 43 (120)
T PF11740_consen 2 TYEDVIEAADELLAAGK---KPTVRA-VRERLG-GGSMSTISKHLKE 43 (120)
T ss_pred cHHHHHHHHHHHHHcCC---CCCHHH-HHHHHC-CCCHHHHHHHHHH
Confidence 35678888888887776 455553 333333 7999999988864
No 23
>TIGR00737 nifR3_yhdG putative TIM-barrel protein, nifR3 family. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase.
Probab=50.18 E-value=42 Score=25.38 Aligned_cols=42 Identities=21% Similarity=0.414 Sum_probs=29.5
Q ss_pred HHHHHHhcCCCCccc-------chhHHHHHHHHHHcCC-----CHHHHHHHHHhh
Q psy15694 36 LNECLEKFSTPDYIM-------EPGIFSQLKRYFQAGG-----NPEQVIELMIID 78 (81)
Q Consensus 36 l~eCl~~fs~~DyIM-------EP~If~~lkrYfqaGG-----~PE~VI~lLSen 78 (81)
.++|++ ..-.|.|| .|.+|..+++++..|. +++++++++.++
T Consensus 207 a~~~l~-~~gad~VmigR~~l~~P~l~~~~~~~~~~~~~~~~~~~~e~~~~~~~~ 260 (319)
T TIGR00737 207 AKAMLE-TTGCDGVMIGRGALGNPWLFRQIEQYLTTGKYKPPPTFAEKLDAILRH 260 (319)
T ss_pred HHHHHH-hhCCCEEEEChhhhhCChHHHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 344552 24578777 9999999999999887 344666666554
No 24
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=49.54 E-value=36 Score=18.70 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=16.2
Q ss_pred HHHHHcCCCHHHHHHHHHhh
Q psy15694 59 KRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 59 krYfqaGG~PE~VI~lLSen 78 (81)
+...+++|+.+.+|+.|.++
T Consensus 22 ~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 22 AVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHHcC
Confidence 34458999999999998764
No 25
>PF09693 Phage_XkdX: Phage uncharacterised protein (Phage_XkdX); InterPro: IPR010022 This entry is represented by Bacteriophage 69, Orf86. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=48.23 E-value=22 Score=20.16 Aligned_cols=22 Identities=32% Similarity=0.587 Sum_probs=15.4
Q ss_pred HHHHHHHHHcCC-CHHHHHHHHH
Q psy15694 55 FSQLKRYFQAGG-NPEQVIELMI 76 (81)
Q Consensus 55 f~~lkrYfqaGG-~PE~VI~lLS 76 (81)
|..+|+|+..|- ++++|-....
T Consensus 1 f~~iK~~Y~~g~~t~~~v~~~V~ 23 (40)
T PF09693_consen 1 FEDIKRYYDWGLYTKEDVKNFVE 23 (40)
T ss_pred ChHHHHHHHcCCCCHHHHHHHhh
Confidence 567888888887 6666655443
No 26
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=46.47 E-value=35 Score=18.72 Aligned_cols=16 Identities=25% Similarity=0.268 Sum_probs=12.9
Q ss_pred HHcCCCHHHHHHHHHh
Q psy15694 62 FQAGGNPEQVIELMII 77 (81)
Q Consensus 62 fqaGG~PE~VI~lLSe 77 (81)
-+++|+.+.+|+.|-+
T Consensus 26 ~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 26 EANNGNVEATINNLLE 41 (43)
T ss_pred HHcCCCHHHHHHHHHc
Confidence 3489999999987754
No 27
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=46.19 E-value=27 Score=23.13 Aligned_cols=41 Identities=29% Similarity=0.360 Sum_probs=29.3
Q ss_pred HHHHHHHHhcCCCCcc----cchhHHHHHHHHHHcCCCHHHHHHHHHhh
Q psy15694 34 EVLNECLEKFSTPDYI----MEPGIFSQLKRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 34 ~vl~eCl~~fs~~DyI----MEP~If~~lkrYfqaGG~PE~VI~lLSen 78 (81)
..|..|.+. .++|++ +.|. -|.+.+.+|-++++++++|...
T Consensus 23 ~~L~~fae~-~s~~~~~~yrlT~~---Sl~~A~~~G~~~e~i~~~L~~~ 67 (129)
T PF13625_consen 23 WFLARFAEL-KSPDTMHVYRLTPA---SLWRAASAGLTAEEIIEFLERY 67 (129)
T ss_pred HHHHHHhcc-cccCceEEEEECHH---HHHHHHHcCCCHHHHHHHHHHH
Confidence 445556666 777744 3443 3678899999999999999764
No 28
>PRK05451 dihydroorotase; Provisional
Probab=45.97 E-value=33 Score=26.41 Aligned_cols=20 Identities=10% Similarity=0.333 Sum_probs=16.1
Q ss_pred HHHHHcCCCHHHHHHHHHhh
Q psy15694 59 KRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 59 krYfqaGG~PE~VI~lLSen 78 (81)
-..+..+|+++++|+++|.|
T Consensus 277 ~~~~~~~~~l~~~v~~~s~n 296 (345)
T PRK05451 277 AEVFEEAGALDKLEAFASLN 296 (345)
T ss_pred HHHHHcCCCHHHHHHHHhHH
Confidence 33455677999999999998
No 29
>PF00482 T2SF: Type II secretion system (T2SS), protein F; InterPro: IPR018076 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) [], have been found to be evolutionary related. These are proteins of about 400 amino acids that are highly hydrophobic and which are thought to be integral protein of the inner membrane. Proteins with this domain form a platform for the type II secretion machinery, as well as the type IV pili and the archaeal flagellae [].; PDB: 2VMA_A 3C1Q_A 2VMB_B 2WHN_B.
Probab=45.13 E-value=47 Score=19.76 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=22.5
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 52 PGIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 52 P~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
|..+..+-.-...||+..++++.+++.++
T Consensus 60 ~~~~~~~~~~~~~g~~~~~~l~~~a~~~~ 88 (124)
T PF00482_consen 60 PDFVASLIQAGESGGDLSEVLEQLADQLR 88 (124)
T ss_dssp -HHHHHHHHHHHHHT-HHHHHHHHHHHHH
T ss_pred chHHHHHHHHHhhCCcHHHHHHHHHHHHH
Confidence 77777777888899999999999888764
No 30
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=44.07 E-value=36 Score=22.10 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=16.4
Q ss_pred HHHHHHHcCCCHHHHHHHHHh
Q psy15694 57 QLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 57 ~lkrYfqaGG~PE~VI~lLSe 77 (81)
.+--.+|.|.+|+.||+.|+-
T Consensus 46 liS~~Lr~G~~~~~ii~~L~g 66 (95)
T PF12637_consen 46 LISLALRSGVPPEEIIDQLRG 66 (95)
T ss_pred HHHHHHHcCCCHHHHHHHhcC
Confidence 344455899999999999974
No 31
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=43.35 E-value=38 Score=22.10 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 53 GIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 53 ~If~~lkrYfqaGG~PE~VI~lL 75 (81)
.++..|++|++.+ +-+..|.-|
T Consensus 23 ~~~~~L~~Y~~~~-~Vd~LV~~L 44 (78)
T cd07347 23 QVTRALERYHQER-NVDDLVRDL 44 (78)
T ss_pred HHHHHHHHHHhcC-CHHHHHHHH
Confidence 4678899999988 666666544
No 32
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=42.84 E-value=23 Score=25.82 Aligned_cols=28 Identities=7% Similarity=0.080 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 52 PGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 52 P~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
++=.+.||.||+.|..--++++.|++|.
T Consensus 21 ~~eL~~l~~~~~~a~~rl~aa~~L~~na 48 (164)
T CHL00173 21 SSDLESVQGNIQRAAARLEAAEKLASNH 48 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999999999985
No 33
>PRK10122 GalU regulator GalF; Provisional
Probab=42.78 E-value=20 Score=27.17 Aligned_cols=32 Identities=19% Similarity=0.395 Sum_probs=22.8
Q ss_pred CcccchhHHHHHHHHHHcCCC----HHHHHHHHHhhc
Q psy15694 47 DYIMEPGIFSQLKRYFQAGGN----PEQVIELMIIDN 79 (81)
Q Consensus 47 DyIMEP~If~~lkrYfqaGG~----PE~VI~lLSeny 79 (81)
=||+.|.||..|++ .+.++. ...+|+.|.++.
T Consensus 214 iYi~~~~i~~~l~~-~~~~~~~e~~ltd~i~~l~~~~ 249 (297)
T PRK10122 214 RYVLSADIWPELER-TEPGAWGRIQLTDAIAELAKKQ 249 (297)
T ss_pred EEEECHHHHHHHHh-CCCCCCCeeeHHHHHHHHHhCC
Confidence 39999999999988 444432 237888877653
No 34
>PF10540 Membr_traf_MHD: Munc13 (mammalian uncoordinated) homology domain; InterPro: IPR019558 Mammalian uncoordinated homology 13 (Munc13) proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana (Mouse-ear cress), C. elegans, Drosophila melanogaster (Fruit fly), Mus musculus (Mouse), Rattus norvegicus (Rat) and Homo sapiens (Human), some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical. ; PDB: 3SWH_A.
Probab=41.71 E-value=20 Score=24.70 Aligned_cols=14 Identities=43% Similarity=0.783 Sum_probs=11.5
Q ss_pred HHHHHHHHHHcCCC
Q psy15694 54 IFSQLKRYFQAGGN 67 (81)
Q Consensus 54 If~~lkrYfqaGG~ 67 (81)
..+.|+.||-|||.
T Consensus 90 ~L~~L~~FFhA~G~ 103 (137)
T PF10540_consen 90 WLDTLKDFFHAEGN 103 (137)
T ss_dssp HHHHHHHHHHCCCT
T ss_pred HHHHHHHHHhCCCC
Confidence 34678999999994
No 35
>PF08569 Mo25: Mo25-like; InterPro: IPR013878 Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localised alternately to the spindle pole body and to the site of cell division in a cell cycle dependent manner [, ]. ; PDB: 2WTK_A 1UPK_A 3GNI_A 1UPL_A.
Probab=41.33 E-value=6.3 Score=31.20 Aligned_cols=49 Identities=22% Similarity=0.341 Sum_probs=32.1
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCC-----------------CHHHHHHHHHhhc
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGG-----------------NPEQVIELMIIDN 79 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG-----------------~PE~VI~lLSeny 79 (81)
+-..|+.+|++.=+..-+|.++.+|..+=+|++.+. .+.-|.+.|+.||
T Consensus 142 ~~g~mlRec~k~e~l~~~iL~~~~f~~ff~~~~~~~Fdiasdaf~t~~~llt~hk~~~a~fl~~n~ 207 (335)
T PF08569_consen 142 NCGDMLRECIKHESLAKIILYSECFWKFFKYVQLPNFDIASDAFSTFKELLTRHKKLVAEFLSNNY 207 (335)
T ss_dssp HHHHHHHHHTTSHHHHHHHHTSGGGGGHHHHTTSSSHHHHHHHHHHHHHHHHSSHHHHHHHHHHTH
T ss_pred hHHHHHHHHHhhHHHHHHHhCcHHHHHHHHHhcCCccHhHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence 346788888876555556666665555555555443 5777788888887
No 36
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=41.31 E-value=53 Score=17.94 Aligned_cols=24 Identities=21% Similarity=0.469 Sum_probs=18.1
Q ss_pred HHHHHHHHcCC--------CHHHHHHHHHhhc
Q psy15694 56 SQLKRYFQAGG--------NPEQVIELMIIDN 79 (81)
Q Consensus 56 ~~lkrYfqaGG--------~PE~VI~lLSeny 79 (81)
++||.|...-| +-+++|+++.+||
T Consensus 7 ~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~~y 38 (38)
T PF10281_consen 7 SDLKSWLKSHGIPVPKSAKTRDELLKLAKKNY 38 (38)
T ss_pred HHHHHHHHHcCCCCCCCCCCHHHHHHHHHHhC
Confidence 45777766555 5789999999987
No 37
>KOG1816|consensus
Probab=38.87 E-value=20 Score=29.05 Aligned_cols=25 Identities=28% Similarity=0.539 Sum_probs=19.6
Q ss_pred CCCChHHHHHHHHHhcCC---CCcccch
Q psy15694 28 PMENPQEVLNECLEKFST---PDYIMEP 52 (81)
Q Consensus 28 ~~e~~~~vl~eCl~~fs~---~DyIMEP 52 (81)
+-.||.+||+-|||.||+ .|-||-+
T Consensus 128 DItNpKAvLE~~LRn~acLT~gDvi~i~ 155 (308)
T KOG1816|consen 128 DITNPKAVLENALRNYACLTTGDVILIN 155 (308)
T ss_pred ccCChHHHHHHHHhhccccccCCEEEEe
Confidence 345999999999999975 5677643
No 38
>PF06337 DUSP: DUSP domain; InterPro: IPR006615 Deubiquitinating enzymes (DUB) form a large family of cysteine protease that can deconjugate ubiquitin or ubiquitin-like proteins (see PDOC00271 from PROSITEDOC) from ubiquitin-conjugated proteins. All DUBs contain a catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. The ~120-residue DUSP (domain present in ubiquitin-specific proteases) domain is one of these specific subdomains. Single or tandem DUSP domains are located both N- and C-terminal to the ubiquitin carboxyl-terminal hydrolase catalytic core domain (see PDOC00750 from PROSITEDOC) []. The DUSP domain displays a tripod-like AB3 fold with a three-helix bundle and a three-stranded anti-parallel beta-sheet resembling the legs and seat of the tripod. Conserved residues are predominantly involved in hydrophobic packing interactions within the three alpha-helices. The most conserved DUSP residues, forming the PGPI motif, are flanked by two long loops that vary both in length and sequence. The PGPI motif packs against the three-helix bundle and is highly ordered []. The function of the DUSP domain is unknown but it may play a role in protein/protein interaction or substrate recognition. This domain is associated with ubiquitin carboxyl-terminal hydrolase family 2 (IPR001394 from INTERPRO, MEROPS peptidase family C19). They are a family 100 to 200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast; others include: Mammalian ubiquitin carboxyl-terminal hydrolase 4 (USP4), Mammalian ubiquitin carboxyl-terminal hydrolase 11 (USP11), Mammalian ubiquitin carboxyl-terminal hydrolase 15 (USP15), Mammalian ubiquitin carboxyl-terminal hydrolase 20 (USP20), Mammalian ubiquitin carboxyl-terminal hydrolase 32 (USP32), Vertebrate ubiquitin carboxyl-terminal hydrolase 33 (USP33), Vertebrate ubiquitin carboxyl-terminal hydrolase 48 (USP48). ; GO: 0004221 ubiquitin thiolesterase activity; PDB: 4A3O_B 3PPA_A 3LMN_A 1W6V_A 3T9L_A 4A3P_A 3PV1_A 3JYU_B.
Probab=38.81 E-value=30 Score=21.37 Aligned_cols=23 Identities=26% Similarity=0.641 Sum_probs=15.3
Q ss_pred CCCccc-chhHHHHHHHHHHcCCCHH
Q psy15694 45 TPDYIM-EPGIFSQLKRYFQAGGNPE 69 (81)
Q Consensus 45 ~~DyIM-EP~If~~lkrYfqaGG~PE 69 (81)
..||++ ...+...|.+.+. |.|+
T Consensus 69 ~~Dy~~v~~~~W~~l~~~Yg--ggp~ 92 (99)
T PF06337_consen 69 GVDYELVPEEVWDYLHSWYG--GGPE 92 (99)
T ss_dssp TTTEEEEEHHHHHHHHHHH---T---
T ss_pred CCCEEEECHHHHHHHHHHcC--CCCc
Confidence 478887 5678999999984 6664
No 39
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=38.34 E-value=57 Score=18.82 Aligned_cols=32 Identities=3% Similarity=0.057 Sum_probs=16.8
Q ss_pred cccchhHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 48 YIMEPGIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
|.+.+.....++.. .-+.+.+++++.|.+.|-
T Consensus 13 ~~Ln~~a~~Iw~~~-~g~~t~~ei~~~l~~~y~ 44 (68)
T PF05402_consen 13 FTLNETAAFIWELL-DGPRTVEEIVDALAEEYD 44 (68)
T ss_dssp ----THHHHHHHH---SSS-HHHHHHHHHHHTT
T ss_pred ccccHHHHHHHHHc-cCCCCHHHHHHHHHHHcC
Confidence 44544444444444 555688888888888874
No 40
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=37.44 E-value=48 Score=23.51 Aligned_cols=24 Identities=13% Similarity=0.372 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 56 SQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 56 ~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++++++.+|=+|-++||.|-+-|
T Consensus 47 ~vI~~hidaGIs~~~AVN~LVeKY 70 (114)
T PF06755_consen 47 TVIQEHIDAGISPADAVNFLVEKY 70 (114)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHH
Confidence 458899999999999999999887
No 41
>PF12127 YdfA_immunity: SigmaW regulon antibacterial; InterPro: IPR022853 This entry represents the uncharacterised protein family UPF0365. Its function is not known. The proteins in this family are found in bacteria. They are about 330 amino acids in length and encoded by a gene located in an operon which confers immunity for the host species to a broad range of antibacterial compounds, unlike the specific immunity proteins that are linked to and co-regulated with their antibiotic-synthesis proteins.
Probab=37.14 E-value=39 Score=27.59 Aligned_cols=27 Identities=33% Similarity=0.546 Sum_probs=22.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhhccC
Q psy15694 55 FSQLKRYFQAGGNPEQVIELMIIDNMA 81 (81)
Q Consensus 55 f~~lkrYfqaGG~PE~VI~lLSeny~~ 81 (81)
.++|...+-|||++..||+-|-.-.||
T Consensus 69 ~~~LEaHyLAGGnV~~VV~ALIaA~rA 95 (316)
T PF12127_consen 69 TNQLEAHYLAGGNVDRVVDALIAAQRA 95 (316)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHhc
Confidence 467889999999999999999776554
No 42
>PRK13389 UTP--glucose-1-phosphate uridylyltransferase subunit GalU; Provisional
Probab=36.54 E-value=27 Score=26.52 Aligned_cols=32 Identities=16% Similarity=0.382 Sum_probs=22.9
Q ss_pred cccchhHHHHHHHHHHcC-C--CHHHHHHHHHhhc
Q psy15694 48 YIMEPGIFSQLKRYFQAG-G--NPEQVIELMIIDN 79 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaG-G--~PE~VI~lLSeny 79 (81)
|||.|.||..|++..... | ....+|+.|.++.
T Consensus 218 Yi~~~~il~~l~~~~~~~~~e~~l~d~i~~l~~~~ 252 (302)
T PRK13389 218 YVLSADIWPLLAKTPPGAGDEIQLTDAIDMLIEKE 252 (302)
T ss_pred EEECHHHHHHHHhCCCCCCCeeeHHHHHHHHHHcC
Confidence 999999998887754322 2 4667888887654
No 43
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=36.43 E-value=26 Score=21.16 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=12.2
Q ss_pred CHHHHHHHHHhhcc
Q psy15694 67 NPEQVIELMIIDNM 80 (81)
Q Consensus 67 ~PE~VI~lLSeny~ 80 (81)
=|+++++||++|+.
T Consensus 16 Fp~~L~~lL~~~~~ 29 (52)
T PF08158_consen 16 FPQELIDLLRNHHT 29 (52)
T ss_pred HHHHHHHHHHhccc
Confidence 49999999999874
No 44
>PF02681 DUF212: Divergent PAP2 family; InterPro: IPR003832 This family is related to the acid phosphatase/vanadium-dependent haloperoxidases; members of this group are uncharacterised.
Probab=36.36 E-value=17 Score=26.05 Aligned_cols=13 Identities=38% Similarity=1.002 Sum_probs=11.2
Q ss_pred HHHHHHcCCCHHH
Q psy15694 58 LKRYFQAGGNPEQ 70 (81)
Q Consensus 58 lkrYfqaGG~PE~ 70 (81)
+++.|+.||.|+-
T Consensus 34 ~~~~~~sGGMPSS 46 (141)
T PF02681_consen 34 WRRFFSSGGMPSS 46 (141)
T ss_pred HHHHhhcCCCCch
Confidence 5899999999973
No 45
>PF08101 DUF1708: Domain of unknown function (DUF1708); InterPro: IPR012965 This is a fungal domain of unknown function, though the yeast protein MSB1(P21339 from SWISSPROT) which contains this domain is thought to play a role in bud formation [].
Probab=36.30 E-value=70 Score=26.51 Aligned_cols=49 Identities=20% Similarity=0.302 Sum_probs=39.2
Q ss_pred CCChHHHHHHHHH--hcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhh
Q psy15694 29 MENPQEVLNECLE--KFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 29 ~e~~~~vl~eCl~--~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSen 78 (81)
.-+|-++|+.|-. .|+.+|.---=.-|..||..|+.-++++ |.+.||+.
T Consensus 255 s~~p~~LL~ra~~~l~~~~~~~f~~re~~~~L~~~f~~e~~~~-i~~~lt~e 305 (420)
T PF08101_consen 255 SPTPFELLRRAAKLLDFDKSDAFESRESYSILKNLFKFEDPVE-ISQALTEE 305 (420)
T ss_pred CCCHHHHHHHHHhhcCcccccchhhhhhHHHHHHHHhccCchh-HHHhhCHH
Confidence 4579999999988 4555555555566888999999999999 99998864
No 46
>PHA02589 rnlA RNA ligase A; Provisional
Probab=36.10 E-value=28 Score=28.63 Aligned_cols=39 Identities=21% Similarity=0.262 Sum_probs=31.3
Q ss_pred HhcCCCCcccc---------hhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 41 EKFSTPDYIME---------PGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 41 ~~fs~~DyIME---------P~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
+.++.+||-++ |.||+.+-++|+-+.++++|+.-+-++|
T Consensus 319 ~~~~rk~~a~~~~~~~~~~~~~~f~~~m~~~~~~~~~~~~~~~~~~~~ 366 (378)
T PHA02589 319 KGKDRKDYAIEAQADLKGDGRYLFGILMQAYQGDTDYEKVMDAIESVF 366 (378)
T ss_pred cCCchhhHhhhccccccCCCceehHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 34566666554 8999999999999999999988776654
No 47
>COG1433 Uncharacterized conserved protein [Function unknown]
Probab=35.80 E-value=37 Score=23.60 Aligned_cols=34 Identities=24% Similarity=0.454 Sum_probs=25.3
Q ss_pred CCCccc----chhHHHHHHHH-----HHcCCCHHHHHHHHHhh
Q psy15694 45 TPDYIM----EPGIFSQLKRY-----FQAGGNPEQVIELMIID 78 (81)
Q Consensus 45 ~~DyIM----EP~If~~lkrY-----fqaGG~PE~VI~lLSen 78 (81)
-.|.|. =|..|..||.+ .-.||++++||+++++.
T Consensus 65 gvdvvi~~~iG~~a~~~l~~~GIkv~~~~~~~V~e~i~~~~~g 107 (121)
T COG1433 65 GVDVVIASNIGPNAYNALKAAGIKVYVAPGGTVEEAIKAFLEG 107 (121)
T ss_pred CCCEEEECccCHHHHHHHHHcCcEEEecCCCCHHHHHHHHhcC
Confidence 356555 46677787776 55789999999999863
No 48
>PRK08560 tyrosyl-tRNA synthetase; Validated
Probab=35.43 E-value=87 Score=24.32 Aligned_cols=50 Identities=18% Similarity=0.436 Sum_probs=33.8
Q ss_pred CCCChHHHHHHHHHhcCCCC------------cccch-------------------hHHHHHHHHHHcCC-CHHHHHHHH
Q psy15694 28 PMENPQEVLNECLEKFSTPD------------YIMEP-------------------GIFSQLKRYFQAGG-NPEQVIELM 75 (81)
Q Consensus 28 ~~e~~~~vl~eCl~~fs~~D------------yIMEP-------------------~If~~lkrYfqaGG-~PE~VI~lL 75 (81)
..|+|++|.+++.+.|..+. |+..| .-+..|+..|..|. .|-++=+.|
T Consensus 226 L~D~~~~I~~KI~kA~t~~~~~~~n~v~~~~~~~~~~~~~~~~~~r~~~~g~~~~~~~~eel~~~y~~g~l~~~~lK~~l 305 (329)
T PRK08560 226 VHDSPEEIRRKIKKAYCPPGEVEGNPVLEIAKYHIFPRYDPFVIERPEKYGGDLEYESYEELERDYAEGKLHPMDLKNAV 305 (329)
T ss_pred ccCCHHHHHHHHHhccCCCCCcCCCcHHHHHHHHhhccccceEEechhhcCCCCCcCCHHHHHHHHHcCCCCHHHHHHHH
Confidence 36789999999999888763 33333 34567777777776 566555555
Q ss_pred Hh
Q psy15694 76 II 77 (81)
Q Consensus 76 Se 77 (81)
++
T Consensus 306 a~ 307 (329)
T PRK08560 306 AE 307 (329)
T ss_pred HH
Confidence 43
No 49
>PF00772 DnaB: DnaB-like helicase N terminal domain; InterPro: IPR007693 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1B79_D 1JWE_A 3GXV_C 3BGW_C 2R6D_B 2R6C_D 2R6E_B 2R6A_A 2VYE_A 2VYF_B ....
Probab=34.44 E-value=1.1e+02 Score=18.60 Aligned_cols=44 Identities=23% Similarity=0.455 Sum_probs=31.5
Q ss_pred HHHHHHHhcCCCCcccch--hHHHHHHHHHHcCC--CHHHHHHHHHhh
Q psy15694 35 VLNECLEKFSTPDYIMEP--GIFSQLKRYFQAGG--NPEQVIELMIID 78 (81)
Q Consensus 35 vl~eCl~~fs~~DyIMEP--~If~~lkrYfqaGG--~PE~VI~lLSen 78 (81)
.+.++...++..||.-.. .||..+++..+.|. +|-.|.+.|+..
T Consensus 22 ~~~~i~~~L~~e~F~~~~h~~If~~i~~l~~~~~~id~~~v~~~l~~~ 69 (103)
T PF00772_consen 22 AIDEIIDKLSPEDFYDPAHRRIFEAILELYREGEPIDPITVAEELSDE 69 (103)
T ss_dssp HHHHHHTT-SGGGSSSHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHT
T ss_pred HHHHHhccCCHHHhCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHC
Confidence 456666666666666533 69999999999998 677777777654
No 50
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=34.03 E-value=33 Score=23.96 Aligned_cols=29 Identities=24% Similarity=0.324 Sum_probs=25.0
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++=.+.||.||+.|...-.+++.|.+|-
T Consensus 15 s~~EL~~l~~~~~~~~~Rl~aa~~L~~~a 43 (157)
T PF00502_consen 15 SDGELQALKGYFQSANARLEAAEKLRDNA 43 (157)
T ss_dssp EHHHHHHHHHHHHTHHHHHHHHHHHHHTH
T ss_pred CHHHHHHHHHHHHhHHHHHHHHHHHHHhH
Confidence 45667889999999999999999998873
No 51
>PF02194 PXA: PXA domain; InterPro: IPR003114 This domain is found associated with PX domains. The PX (phox) domain [] occurs in a variety of eukaryotic proteins associated with intracellular signalling pathways.
Probab=33.66 E-value=19 Score=24.50 Aligned_cols=18 Identities=39% Similarity=0.702 Sum_probs=14.5
Q ss_pred HHHHHHHHhcCCCCcccc
Q psy15694 34 EVLNECLEKFSTPDYIME 51 (81)
Q Consensus 34 ~vl~eCl~~fs~~DyIME 51 (81)
.|+...+.++|.||||-.
T Consensus 159 ~VL~p~i~~lsdPd~iN~ 176 (185)
T PF02194_consen 159 QVLLPLIDKLSDPDFINQ 176 (185)
T ss_pred HHHHHHHHHhCCHHHHHH
Confidence 477888899999999853
No 52
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=33.28 E-value=78 Score=16.57 Aligned_cols=30 Identities=13% Similarity=0.271 Sum_probs=24.2
Q ss_pred cchhHHHHHHHHHHcCC-CHHHHHHHHHhhc
Q psy15694 50 MEPGIFSQLKRYFQAGG-NPEQVIELMIIDN 79 (81)
Q Consensus 50 MEP~If~~lkrYfqaGG-~PE~VI~lLSeny 79 (81)
|.+..+..|+++-+.-| +.+++|..+-.+|
T Consensus 6 l~~~~~~~l~~~a~~~g~s~s~~ir~ai~~~ 36 (39)
T PF01402_consen 6 LPDELYERLDELAKELGRSRSELIREAIREY 36 (39)
T ss_dssp EEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred eCHHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56788888999887766 8889998887776
No 53
>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.
Probab=33.17 E-value=1e+02 Score=20.68 Aligned_cols=48 Identities=17% Similarity=0.448 Sum_probs=32.9
Q ss_pred ChHHHHHHHHHhcCCCC-cccchhHHHHHHHHHHcCCCHHHHHHHHHhh
Q psy15694 31 NPQEVLNECLEKFSTPD-YIMEPGIFSQLKRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~D-yIMEP~If~~lkrYfqaGG~PE~VI~lLSen 78 (81)
.-..+++.|+++|.... |==-|--...--+|...=-+|.+|.+.|.++
T Consensus 44 ~L~~lLer~~~~f~~~~~Y~nD~RylkiWi~ya~~~~~~~~if~~l~~~ 92 (126)
T PF08311_consen 44 GLLELLERCIRKFKDDERYKNDERYLKIWIKYADLSSDPREIFKFLYSK 92 (126)
T ss_dssp HHHHHHHHHHHHHTTSGGGTT-HHHHHHHHHHHTTBSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhhHhhcCCHHHHHHHHHHHHHccCHHHHHHHHHHc
Confidence 45679999999998754 3334555555556666666888888887664
No 54
>PF13043 DUF3903: Domain of unknown function (DUF3903)
Probab=33.07 E-value=32 Score=20.41 Aligned_cols=14 Identities=36% Similarity=0.615 Sum_probs=11.3
Q ss_pred hHHHHHHHHHhcCC
Q psy15694 32 PQEVLNECLEKFST 45 (81)
Q Consensus 32 ~~~vl~eCl~~fs~ 45 (81)
-+.|..||.|+|.-
T Consensus 10 i~kvr~eckrrfgk 23 (40)
T PF13043_consen 10 IQKVRAECKRRFGK 23 (40)
T ss_pred HHHHHHHHHHHhch
Confidence 36788999999963
No 55
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=33.03 E-value=76 Score=16.50 Aligned_cols=19 Identities=37% Similarity=0.443 Sum_probs=14.5
Q ss_pred HHHHHHHcCCCHHHHHHHH
Q psy15694 57 QLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 57 ~lkrYfqaGG~PE~VI~lL 75 (81)
.++...++||+.+.+++.|
T Consensus 18 a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 18 ALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 4566677888888888876
No 56
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=32.58 E-value=28 Score=19.98 Aligned_cols=19 Identities=21% Similarity=0.412 Sum_probs=14.3
Q ss_pred cccchhHHHHHHHHHHcCC
Q psy15694 48 YIMEPGIFSQLKRYFQAGG 66 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaGG 66 (81)
-+.|...-..+|.|+|-||
T Consensus 14 ~vLe~NAe~FV~~fVQKGG 32 (33)
T TIGR03687 14 GVLESNAEEFVRGFVQKGG 32 (33)
T ss_pred HHHHHhHHHHHHHHHHccC
Confidence 3455556666999999998
No 57
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=32.56 E-value=1e+02 Score=27.52 Aligned_cols=47 Identities=17% Similarity=0.381 Sum_probs=37.3
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
+....+.+.+..+...|. -.+|..|++.++.|-.|..++.+|...||
T Consensus 246 ~~~~~I~~lidAL~~~D~---a~al~~l~~Li~~G~dp~~~L~~LL~~fR 292 (824)
T PRK07764 246 TDSALIDEAVDALAAGDG---AALFGTVDRVIEAGHDPRRFAEDLLERLR 292 (824)
T ss_pred CCHHHHHHHHHHHHcCCH---HHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 345556677777777774 36888999999999999999999998876
No 58
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=32.37 E-value=49 Score=24.18 Aligned_cols=28 Identities=11% Similarity=0.127 Sum_probs=25.1
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 52 PGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 52 P~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.+=.+.||.||+-|=..=++++.|++|-
T Consensus 21 ~~eL~~l~~~~~~g~~RL~aa~~Lt~nA 48 (162)
T CHL00170 21 NGELQACNGRFQRAAASLEAARSLTSNA 48 (162)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHhhH
Confidence 5667899999999999999999999883
No 59
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=32.37 E-value=32 Score=19.93 Aligned_cols=14 Identities=36% Similarity=0.593 Sum_probs=11.2
Q ss_pred CCCHHHHHHHHHhh
Q psy15694 65 GGNPEQVIELMIID 78 (81)
Q Consensus 65 GG~PE~VI~lLSen 78 (81)
|=+||++|+.|..|
T Consensus 22 ~LtpEDAvEaLi~~ 35 (35)
T PF08383_consen 22 GLTPEDAVEALIGN 35 (35)
T ss_pred CCCHHHHHHHHhcC
Confidence 34899999999754
No 60
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=31.09 E-value=93 Score=22.87 Aligned_cols=27 Identities=26% Similarity=0.346 Sum_probs=21.4
Q ss_pred hhHHHHHHHHHHc--CCCHHHHHHHHHhh
Q psy15694 52 PGIFSQLKRYFQA--GGNPEQVIELMIID 78 (81)
Q Consensus 52 P~If~~lkrYfqa--GG~PE~VI~lLSen 78 (81)
+..-..|.+|+.| .|+++.+..||+++
T Consensus 204 ~~~~~~v~~~~~a~~~gD~~~l~~Lla~D 232 (324)
T TIGR02960 204 PEEQDLLERYIAAFESYDLDALTALLHED 232 (324)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHhcCC
Confidence 4566778888874 78999999999875
No 61
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=30.91 E-value=21 Score=23.02 Aligned_cols=15 Identities=20% Similarity=0.574 Sum_probs=8.5
Q ss_pred chhHHHHHHHHHHcC
Q psy15694 51 EPGIFSQLKRYFQAG 65 (81)
Q Consensus 51 EP~If~~lkrYfqaG 65 (81)
.|.|+..|+.|++.|
T Consensus 73 ~~~I~~~I~~~l~sG 87 (87)
T PF08712_consen 73 KPEIREVIMEFLESG 87 (87)
T ss_dssp HHHHHHHTH------
T ss_pred HHHHHHHHhhhccCC
Confidence 799999999999987
No 62
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=30.86 E-value=73 Score=18.55 Aligned_cols=23 Identities=22% Similarity=0.378 Sum_probs=19.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHH
Q psy15694 54 IFSQLKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 54 If~~lkrYfqaGG~PE~VI~lLS 76 (81)
.+..++.+.+.|=+.+++.++||
T Consensus 46 ~l~~i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 46 RILEIKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhC
Confidence 45678888888989999998886
No 63
>TIGR01099 galU UTP-glucose-1-phosphate uridylyltransferase. Built to distinquish between the highly similar genes galU and galF
Probab=30.64 E-value=47 Score=23.49 Aligned_cols=32 Identities=22% Similarity=0.514 Sum_probs=22.1
Q ss_pred cccchhHHHHHHHHHHc-CC--CHHHHHHHHHhhc
Q psy15694 48 YIMEPGIFSQLKRYFQA-GG--NPEQVIELMIIDN 79 (81)
Q Consensus 48 yIMEP~If~~lkrYfqa-GG--~PE~VI~lLSeny 79 (81)
|||.|.+|..|.+.-.. +| ....+|+.|.+++
T Consensus 203 yi~~~~~~~~l~~~~~~~~~~~~l~d~i~~l~~~~ 237 (260)
T TIGR01099 203 YVLTPDIFDLLEETPPGAGGEIQLTDALRKLLEKE 237 (260)
T ss_pred EECCHHHHHHHHhCCCCCCCceeHHHHHHHHHhcC
Confidence 99999999998664322 22 3457888877654
No 64
>PF14164 YqzH: YqzH-like protein
Probab=30.61 E-value=1.2e+02 Score=19.49 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=22.5
Q ss_pred HHHHHHHHHhcCCCCccc--chhHHHHHHHHHHc
Q psy15694 33 QEVLNECLEKFSTPDYIM--EPGIFSQLKRYFQA 64 (81)
Q Consensus 33 ~~vl~eCl~~fs~~DyIM--EP~If~~lkrYfqa 64 (81)
+..+..||+.++-.+-.| .|.=+..|+++++.
T Consensus 7 ~Kmi~~~l~QYg~d~~~~pls~~E~~~L~~~i~~ 40 (64)
T PF14164_consen 7 EKMIINCLRQYGYDVECMPLSDEEWEELCKHIQE 40 (64)
T ss_pred HHHHHHHHHHhCCcccCCCCCHHHHHHHHHHHHH
Confidence 345678999997776666 45566778887764
No 65
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=30.17 E-value=78 Score=22.68 Aligned_cols=28 Identities=18% Similarity=0.218 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 53 GIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 53 ~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
..+..+++.++.|-+|-.++.+|+..+|
T Consensus 197 ~a~~~l~~l~~~~~~~~~il~~l~~~~~ 224 (302)
T TIGR01128 197 RALRILKGLLGEGEEPLILLALLQRQLR 224 (302)
T ss_pred HHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 4667888888899999999999988775
No 66
>PF13709 DUF4159: Domain of unknown function (DUF4159)
Probab=29.83 E-value=56 Score=23.89 Aligned_cols=20 Identities=30% Similarity=0.743 Sum_probs=17.6
Q ss_pred CcccchhHHHHHHHHHHcCC
Q psy15694 47 DYIMEPGIFSQLKRYFQAGG 66 (81)
Q Consensus 47 DyIMEP~If~~lkrYfqaGG 66 (81)
+....|.-..-||+|.+.||
T Consensus 64 ~~~~s~~e~~~Lr~Yl~~GG 83 (207)
T PF13709_consen 64 DFPLSDEEIANLRRYLENGG 83 (207)
T ss_pred CCCCCHHHHHHHHHHHHcCC
Confidence 45668899999999999999
No 67
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=29.82 E-value=60 Score=24.16 Aligned_cols=29 Identities=10% Similarity=0.278 Sum_probs=25.4
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++=.+.||.||+-|=..=++++.|++|-
T Consensus 20 s~~eL~~L~~~~~~g~~RL~aa~~L~~NA 48 (177)
T CHL00172 20 GGSDLQALKKFISEGNKRLDSVNSIVSNA 48 (177)
T ss_pred CHHHHHHHHHHHHhhHHHHHHHHHHHHhH
Confidence 45667889999999999999999999883
No 68
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=29.79 E-value=52 Score=24.96 Aligned_cols=29 Identities=24% Similarity=0.338 Sum_probs=22.5
Q ss_pred hhHHHHHHHHHHcCC---CHHHHHHHHHhhcc
Q psy15694 52 PGIFSQLKRYFQAGG---NPEQVIELMIIDNM 80 (81)
Q Consensus 52 P~If~~lkrYfqaGG---~PE~VI~lLSeny~ 80 (81)
|..+..-+.++||=| +|++.+.||.++|.
T Consensus 61 p~~~~ka~d~VkAIgrGF~pe~A~~LL~d~~~ 92 (194)
T COG1094 61 PLALLKARDVVKAIGRGFPPEKALKLLEDDYY 92 (194)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHhcCCcE
Confidence 666666677777744 99999999998763
No 69
>PF04867 DUF643: Protein of unknown function (DUF643); InterPro: IPR006951 These are proteins of unknown function found in Borrelia burgdorferi (Lyme disease spirochete)
Probab=29.63 E-value=40 Score=23.94 Aligned_cols=19 Identities=32% Similarity=0.581 Sum_probs=15.3
Q ss_pred ChHHHHHHHHHhcCCCCcc
Q psy15694 31 NPQEVLNECLEKFSTPDYI 49 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyI 49 (81)
-.+.+|++||.++.....|
T Consensus 94 yKegmLekCL~klGE~~S~ 112 (114)
T PF04867_consen 94 YKEGMLEKCLEKLGEDKSI 112 (114)
T ss_pred HhHhHHHHHHHHhcccccc
Confidence 4688999999999876554
No 70
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=29.60 E-value=1.1e+02 Score=23.53 Aligned_cols=34 Identities=12% Similarity=0.196 Sum_probs=25.1
Q ss_pred HhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHH
Q psy15694 41 EKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 41 ~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLS 76 (81)
.++...|. +.....+|+.||.++|+-.+.-+.|-
T Consensus 312 ~~l~~~d~--~~~L~~TL~~y~~~~~ni~~tA~~L~ 345 (385)
T PRK11477 312 ARLKAMDN--NGLLRRTLAAWFRHNVQPLATSKALF 345 (385)
T ss_pred HHHHhccC--cchHHHHHHHHHHcCCCHHHHHHHhC
Confidence 34444442 45677899999999999988887774
No 71
>PF15606 Toxin_55: Putative toxin 55
Probab=29.49 E-value=1e+02 Score=20.62 Aligned_cols=26 Identities=23% Similarity=0.452 Sum_probs=16.8
Q ss_pred HHHHHHHHHHcCCCH---HHHHHHHHhhc
Q psy15694 54 IFSQLKRYFQAGGNP---EQVIELMIIDN 79 (81)
Q Consensus 54 If~~lkrYfqaGG~P---E~VI~lLSeny 79 (81)
+...+..||++||.- =.|.++|.+-+
T Consensus 24 v~~~~~~~~~~~GK~~drCd~Lqelid~g 52 (77)
T PF15606_consen 24 VYEIISDAFQSGGKAPDRCDVLQELIDCG 52 (77)
T ss_pred HHHHHHHHHhhcCCCCcHHHHHHHHHHcc
Confidence 445567899999963 35666665443
No 72
>cd02538 G1P_TT_short G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase. This family is the short form of glucose-1-phosphate thymidylyltransferase. Glucose-1-phosphate thymidylyltransferase catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate. It is the first enzyme in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.There are two forms of Glucose-1-phosphate thymidylyltransferase in bacteria and archeae; short form and long form. The homotetrameric, feedback inhibited short form is found in numerous bacterial species that produce dTDP-L-rhamnose. The long form, which has an extra 50 amino acids c-terminal, is found in many species for which it serves as a sugar-activating enzyme for antibiotic biosynthesis and or other, unknown pathways, and in which dTDP-L-rhamnose is not necessarily produced.
Probab=29.37 E-value=33 Score=24.03 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=20.7
Q ss_pred cccchhHHHHHHHHHHcC-CCH--HHHHHHHHhh
Q psy15694 48 YIMEPGIFSQLKRYFQAG-GNP--EQVIELMIID 78 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaG-G~P--E~VI~lLSen 78 (81)
|||+|.+|..|+.+...+ |.- ..+++.|..+
T Consensus 174 yi~~~~~l~~l~~~~~~~~~~~~l~d~~~~l~~~ 207 (240)
T cd02538 174 YFYDNDVFEIAKQLKPSARGELEITDVNNEYLEK 207 (240)
T ss_pred EEECHHHHHHHHhcCCCCCCeEEhHHHHHHHHHh
Confidence 999999998887655332 322 2677777654
No 73
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=29.18 E-value=86 Score=17.36 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=14.2
Q ss_pred chhHHHHHHHHHHcCCCHHHHHH
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIE 73 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~ 73 (81)
-|.++..|.+|...-+.|.+++.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~ 24 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLT 24 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHH
Confidence 35566666677666666666543
No 74
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family conta
Probab=29.11 E-value=1e+02 Score=20.90 Aligned_cols=26 Identities=12% Similarity=0.070 Sum_probs=22.2
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHhh
Q psy15694 53 GIFSQLKRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 53 ~If~~lkrYfqaGG~PE~VI~lLSen 78 (81)
.+...+.++|..|.++.++...||.-
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~ls~l 31 (172)
T cd05401 6 QLRRILRRDLLGGASIRAISRALSDL 31 (172)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 35677899999999999999999864
No 75
>PHA02099 hypothetical protein
Probab=29.03 E-value=31 Score=23.18 Aligned_cols=26 Identities=27% Similarity=0.570 Sum_probs=22.6
Q ss_pred HHHHHhcCCCCccc-----chhHHHHHHHHH
Q psy15694 37 NECLEKFSTPDYIM-----EPGIFSQLKRYF 62 (81)
Q Consensus 37 ~eCl~~fs~~DyIM-----EP~If~~lkrYf 62 (81)
.+.||.|+-.|.|. .|+++.-||||.
T Consensus 35 mhilr~~~g~diifha~gy~p~ly~e~~r~~ 65 (84)
T PHA02099 35 MHILRNFEGVDIVFHAEGYNPDLYAELKRHV 65 (84)
T ss_pred EEEEeecCCccEEEEcCCCCHHHHHHHHHhh
Confidence 35688999999887 899999999996
No 76
>PF00296 Bac_luciferase: Luciferase-like monooxygenase; InterPro: IPR011251 Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor []. Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a single TIM (beta/alpha)8-barrel domain. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulphonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds [, , ]. More information about these proteins can be found at Protein of the Month: Luciferase [].; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0055114 oxidation-reduction process; PDB: 2I7G_B 1NFP_A 1TVL_A 1YW1_A 1M41_B 1NQK_A 2B81_A 3RAO_A 1LUC_B 3FGC_B ....
Probab=28.89 E-value=23 Score=25.54 Aligned_cols=14 Identities=36% Similarity=0.439 Sum_probs=12.0
Q ss_pred CCHHHHHHHHHhhcc
Q psy15694 66 GNPEQVIELMIIDNM 80 (81)
Q Consensus 66 G~PE~VI~lLSeny~ 80 (81)
|+|++|++.|-+ |+
T Consensus 288 Gtpe~v~~~l~~-~~ 301 (307)
T PF00296_consen 288 GTPEQVADRLRE-YE 301 (307)
T ss_dssp ESHHHHHHHHHH-HH
T ss_pred eCHHHHHHHHHH-HH
Confidence 599999999987 54
No 77
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=28.88 E-value=85 Score=18.95 Aligned_cols=12 Identities=33% Similarity=0.481 Sum_probs=9.1
Q ss_pred CHHHHHHHHHhh
Q psy15694 67 NPEQVIELMIID 78 (81)
Q Consensus 67 ~PE~VI~lLSen 78 (81)
+|+.|++.|.+-
T Consensus 44 d~~~vl~~L~~l 55 (56)
T PF04405_consen 44 DPEEVLEELNAL 55 (56)
T ss_pred CHHHHHHHHHHc
Confidence 788888888653
No 78
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=28.82 E-value=1.1e+02 Score=20.83 Aligned_cols=29 Identities=14% Similarity=0.177 Sum_probs=23.5
Q ss_pred hhHHHHHHHHHHcCC----CHHHHHHHHHhhcc
Q psy15694 52 PGIFSQLKRYFQAGG----NPEQVIELMIIDNM 80 (81)
Q Consensus 52 P~If~~lkrYfqaGG----~PE~VI~lLSeny~ 80 (81)
|++|..|+..|++-= +-+.|+.-|..+|+
T Consensus 44 P~la~~v~~if~s~~k~~l~~e~l~~kl~~S~~ 76 (126)
T cd08767 44 PELARILRNIFVSEKKTVLPLEELVYKLQASYP 76 (126)
T ss_pred HHHHHHHHHHHHhcccccccHHHHHHHHHHhCC
Confidence 999999999999844 34667888888876
No 79
>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.
Probab=28.81 E-value=1.8e+02 Score=20.06 Aligned_cols=49 Identities=10% Similarity=0.295 Sum_probs=33.8
Q ss_pred CChHHHHHHHHHhcCCCCcccchhHH-HHHHHHHHcCCCHHHHHHHHHhh
Q psy15694 30 ENPQEVLNECLEKFSTPDYIMEPGIF-SQLKRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 30 e~~~~vl~eCl~~fs~~DyIMEP~If-~~lkrYfqaGG~PE~VI~lLSen 78 (81)
..-..+|+.|+++|....-.-.=.-| ..==.|...=+.|.++.+.|..|
T Consensus 43 s~L~~lLerc~~~f~~~~~YknD~RyLkiWi~ya~~~~dp~~if~~L~~~ 92 (125)
T smart00777 43 SGLLTLLERCIRYFEDDERYKNDPRYLKIWLKYADNCDEPRELFQFLYSK 92 (125)
T ss_pred hhHHHHHHHHHHHhhhhhhhcCCHHHHHHHHHHHHhcCCHHHHHHHHHHC
Confidence 35678999999999887644433222 22235666668899999888765
No 80
>cd00781 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria.
Probab=28.79 E-value=71 Score=19.66 Aligned_cols=25 Identities=28% Similarity=0.614 Sum_probs=16.3
Q ss_pred HHHHHHHHH--cCCCHHHHHHHHHhhc
Q psy15694 55 FSQLKRYFQ--AGGNPEQVIELMIIDN 79 (81)
Q Consensus 55 f~~lkrYfq--aGG~PE~VI~lLSeny 79 (81)
-..+++|++ +.|+++.+..||+++.
T Consensus 6 ~~~v~~~~~a~~~~D~~~~~~l~aed~ 32 (122)
T cd00781 6 KAAVQRYVEAVNAGDPEGIVALFADDA 32 (122)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHcCCCe
Confidence 344666665 3667777777777764
No 81
>cd03345 eu_TyrOH Eukaryotic tyrosine hydroxylase (TyrOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tryptophan hydroxylase (TrpOH). TyrOH catalyzes the conversion of tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of the catecholamines dopamine, noradrenaline, and adrenaline.
Probab=28.69 E-value=65 Score=25.89 Aligned_cols=40 Identities=20% Similarity=0.155 Sum_probs=25.5
Q ss_pred HHhcCCCCcccchhHHHH----------------HHHHHHcC-CCHHHHHHHHHhhc
Q psy15694 40 LEKFSTPDYIMEPGIFSQ----------------LKRYFQAG-GNPEQVIELMIIDN 79 (81)
Q Consensus 40 l~~fs~~DyIMEP~If~~----------------lkrYfqaG-G~PE~VI~lLSeny 79 (81)
+|+-+.+||.=||+||-. ++.|=++| |++++.|+.|+.=|
T Consensus 150 IR~~~~~~YtpEPDi~HEl~GHvPlLadp~FA~f~q~~G~~~l~a~~~~i~~LarlY 206 (298)
T cd03345 150 IRHASSPMHSPEPDCCHELLGHVPMLADPTFAQFSQDIGLASLGASDEEIEKLSTLY 206 (298)
T ss_pred ecCCcccCCCCCCchHHHHhccchhhCCHHHHHHHHHHHHHhcCCCHHHHHHHhHhh
Confidence 467788899999999832 33433332 34567777777543
No 82
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=28.56 E-value=97 Score=16.15 Aligned_cols=25 Identities=4% Similarity=0.179 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 53 GIFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 53 ~If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
.++..++.+.+..=+-++|++.|..
T Consensus 9 ~~v~~i~~~l~~~~t~~~I~~~l~~ 33 (39)
T PF05184_consen 9 FVVKEIEKLLKNNKTEEEIKKALEK 33 (39)
T ss_dssp HHHHHHHHHHHSTCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCccHHHHHHHHHH
Confidence 4678899999988888888888864
No 83
>PRK11815 tRNA-dihydrouridine synthase A; Provisional
Probab=28.43 E-value=1.2e+02 Score=23.60 Aligned_cols=33 Identities=24% Similarity=0.403 Sum_probs=24.2
Q ss_pred CCCccc-------chhHHHHHHHHHHcCC-----CHHHHHHHHHhh
Q psy15694 45 TPDYIM-------EPGIFSQLKRYFQAGG-----NPEQVIELMIID 78 (81)
Q Consensus 45 ~~DyIM-------EP~If~~lkrYfqaGG-----~PE~VI~lLSen 78 (81)
..|.|| .|.+|..+++++. |- ++.+++..+..+
T Consensus 226 ~aDgVmIGRa~l~nP~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 270 (333)
T PRK11815 226 HVDGVMIGRAAYHNPYLLAEVDRELF-GEPAPPLSRSEVLEAMLPY 270 (333)
T ss_pred cCCEEEEcHHHHhCCHHHHHHHHHhc-CCCCCCCCHHHHHHHHHHH
Confidence 389888 9999999999988 53 345666655544
No 84
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=28.30 E-value=61 Score=19.01 Aligned_cols=23 Identities=30% Similarity=0.498 Sum_probs=17.3
Q ss_pred CCC-cccchhHHHHHHHHHHcCCC
Q psy15694 45 TPD-YIMEPGIFSQLKRYFQAGGN 67 (81)
Q Consensus 45 ~~D-yIMEP~If~~lkrYfqaGG~ 67 (81)
.++ .+.+|.-+..|.++...||.
T Consensus 42 ~~~~~~~~~~~~~~l~~~v~~G~~ 65 (70)
T PF14258_consen 42 GPDLRLSEPEEAEALLEWVEAGNT 65 (70)
T ss_pred eCCCCCCchHHHHHHHHHHHcCCE
Confidence 344 33347888999999999985
No 85
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=27.79 E-value=59 Score=23.91 Aligned_cols=29 Identities=7% Similarity=0.197 Sum_probs=25.3
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++=.+.||.||+.|=..-++++.|+.|.
T Consensus 18 ~~~eL~~l~~~~~~~~~Rl~aa~~L~~na 46 (170)
T TIGR01339 18 SSSQIDALSKLVADGNKRSDAVSRITNNA 46 (170)
T ss_pred CHHHHHHHHHHHHhhHHHHHHHHHHHHhH
Confidence 45667889999999999999999999884
No 86
>PF07515 DUF1528: Protein of unknown function (DUF1528); InterPro: IPR011093 This entry contains proteins some of which are from pathogenic strains of Gammaproteobacteria. Though the function of these proteins is unknown, they could be involved in pathogenesis. This domain is found at the C terminus of proteins that contain a N-terminal metal-dependent phosphohydrolase (HD) region and are considered to be helicases/relaxases. ; PDB: 2IPQ_X 3KQ5_A.
Probab=27.76 E-value=32 Score=23.08 Aligned_cols=13 Identities=54% Similarity=1.262 Sum_probs=11.1
Q ss_pred cccchhHHHHHHHHHH
Q psy15694 48 YIMEPGIFSQLKRYFQ 63 (81)
Q Consensus 48 yIMEP~If~~lkrYfq 63 (81)
|+..|+|| +||.+
T Consensus 18 fLvsP~IF---~~y~~ 30 (106)
T PF07515_consen 18 FLVSPGIF---QRYAQ 30 (106)
T ss_dssp EEETTCHH---HHHHH
T ss_pred EEECHHHH---HHHHH
Confidence 67799999 78887
No 87
>TIGR03557 F420_G6P_family F420-dependent oxidoreductase, G6PDH family. Members of this protein family include F420-dependent glucose-6-phosphate dehydrogenases (TIGR03554) and related proteins. All members of this family come from species that synthesize coenzyme F420.
Probab=27.73 E-value=42 Score=25.46 Aligned_cols=19 Identities=16% Similarity=0.385 Sum_probs=14.9
Q ss_pred HHHHHHcCCCHHHHHHHHH
Q psy15694 58 LKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 58 lkrYfqaGG~PE~VI~lLS 76 (81)
+.+.+-+||+|++|++.|.
T Consensus 262 ~~~~~i~ggtpe~~~~~l~ 280 (316)
T TIGR03557 262 VAASIPCGPDPDRHVEAVR 280 (316)
T ss_pred HhhcCccCCCHHHHHHHHH
Confidence 4455568889999999886
No 88
>PLN02599 dihydroorotase
Probab=27.59 E-value=92 Score=24.76 Aligned_cols=25 Identities=12% Similarity=0.284 Sum_probs=19.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhh
Q psy15694 54 IFSQLKRYFQAGGNPEQVIELMIID 78 (81)
Q Consensus 54 If~~lkrYfqaGG~PE~VI~lLSen 78 (81)
.+..|-..|..+|+.+++++++|.|
T Consensus 291 ~l~~l~~~~~~~g~l~~l~~~~S~n 315 (364)
T PLN02599 291 ALSLYAKAFEEAGALDKLEAFTSFN 315 (364)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHhHH
Confidence 3444656666667999999999987
No 89
>PRK13665 hypothetical protein; Provisional
Probab=27.54 E-value=66 Score=26.30 Aligned_cols=47 Identities=23% Similarity=0.400 Sum_probs=30.5
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhccC
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDNMA 81 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny~~ 81 (81)
+|..|...+....+.-=-| -.++|...+-|||+...||+-|-.-.||
T Consensus 54 ~p~~iV~~~I~a~kAGl~i----~~~~LEaHyLAGGnV~~VV~AlIAA~rA 100 (316)
T PRK13665 54 PPSRIVNPLIKAHKAGLDL----TTNQLEAHYLAGGNVDRVVDALIAAQRA 100 (316)
T ss_pred CHHHHHHHHHHHHHcCCCC----chhHHHHHHhcCCCHHHHHHHHHHHHhc
Confidence 3555555555443221001 1367888999999999999999776554
No 90
>PF12816 Vps8: Golgi CORVET complex core vacuolar protein 8
Probab=27.36 E-value=1e+02 Score=22.37 Aligned_cols=42 Identities=31% Similarity=0.535 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCCccc--chhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 34 EVLNECLEKFSTPDYIM--EPGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 34 ~vl~eCl~~fs~~DyIM--EP~If~~lkrYfqaGG~PE~VI~lL 75 (81)
.|.=+||+.|-..+.|- -|.|++.|=.|++..|..+.|=+++
T Consensus 2 ~vFle~Lep~Il~~~i~~lpp~v~k~lv~~y~~~~~~~~lE~lI 45 (196)
T PF12816_consen 2 GVFLECLEPFILSGKIKSLPPEVFKALVEHYASKGRLERLEQLI 45 (196)
T ss_pred chHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 35567888888888665 8999999999999999887765544
No 91
>smart00076 IFabd Interferon alpha, beta and delta. Interferons produce antiviral and antiproliferative responses in cells. They are classified into five groups, all of them related but gamma-interferon.
Probab=27.18 E-value=71 Score=21.82 Aligned_cols=30 Identities=27% Similarity=0.451 Sum_probs=15.3
Q ss_pred HHHHHHHhcC-CCCcccchhHHHHHHHHHHc
Q psy15694 35 VLNECLEKFS-TPDYIMEPGIFSQLKRYFQA 64 (81)
Q Consensus 35 vl~eCl~~fs-~~DyIMEP~If~~lkrYfqa 64 (81)
-|+.|+..=. ..+.-+.....-.||+||+.
T Consensus 61 ~Le~Cl~~~~~~~~~~~~~~~~l~lk~YF~r 91 (117)
T smart00076 61 HLEACLKQEMEEEDTPLPRNTHLALRKYFQR 91 (117)
T ss_pred HHHHHHHHhcccccCCccccchHHHHHHHHH
Confidence 3677775321 11222222345569999973
No 92
>CHL00086 apcA allophycocyanin alpha subunit
Probab=26.96 E-value=64 Score=23.24 Aligned_cols=29 Identities=14% Similarity=0.433 Sum_probs=24.6
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++=.+.||.||+.|-..=++++.|+.|-
T Consensus 19 s~~eL~~l~~~~~~~~~Rl~aa~~l~~na 47 (161)
T CHL00086 19 SPGELDRIKSFVLSGQRRLRIAQILTDNR 47 (161)
T ss_pred CHHHHHHHHHHHHhhHHHHHHHHHHHHhH
Confidence 45556889999999999999999998874
No 93
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=26.60 E-value=50 Score=17.01 Aligned_cols=9 Identities=44% Similarity=1.088 Sum_probs=7.4
Q ss_pred HHHHHHHHH
Q psy15694 33 QEVLNECLE 41 (81)
Q Consensus 33 ~~vl~eCl~ 41 (81)
+++|++|+.
T Consensus 3 deiL~~CI~ 11 (20)
T PF05924_consen 3 DEILQECIG 11 (20)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 389999984
No 94
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=26.36 E-value=69 Score=23.31 Aligned_cols=28 Identities=11% Similarity=0.125 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 52 PGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 52 P~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.+=.+.||.||+-|=..=++++.|++|-
T Consensus 20 ~~eL~~l~~~~~~g~~RL~aa~~Lt~na 47 (161)
T TIGR01338 20 NGELQSIFGRFQRATASLEAAKSLTSNA 47 (161)
T ss_pred HHHHHHHHHHHHchHHHHHHHHHHHhhH
Confidence 4667889999999999999999999873
No 95
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=26.30 E-value=66 Score=17.11 Aligned_cols=13 Identities=31% Similarity=0.654 Sum_probs=10.7
Q ss_pred cchhHHHHHHHHH
Q psy15694 50 MEPGIFSQLKRYF 62 (81)
Q Consensus 50 MEP~If~~lkrYf 62 (81)
|.|+-|.-|.|++
T Consensus 10 MSPddy~~l~~~V 22 (23)
T PF12162_consen 10 MSPDDYDELERMV 22 (23)
T ss_dssp S-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHhh
Confidence 6999999999985
No 96
>cd03347 eu_PheOH Eukaryotic phenylalanine-4-hydroxylase (eu_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic phenylalanine-4-hydroxylase (pro_PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH catalyzes the first and rate-limiting step in the metabolism of the amino acid L-phenylalanine (L-Phe), the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor. The catalytic activity of the tetrameric enzyme is tightly regulated by the binding of L-Phe and BH4 as well as by phosphorylation. Mutations in the human enzyme are linked to a severe variant of phenylketonuria.
Probab=26.28 E-value=75 Score=25.64 Aligned_cols=40 Identities=28% Similarity=0.321 Sum_probs=25.3
Q ss_pred HHhcCCCCcccchhHHH----------------HHHHHHHcC-CCHHHHHHHHHhhc
Q psy15694 40 LEKFSTPDYIMEPGIFS----------------QLKRYFQAG-GNPEQVIELMIIDN 79 (81)
Q Consensus 40 l~~fs~~DyIMEP~If~----------------~lkrYfqaG-G~PE~VI~lLSeny 79 (81)
+|+-+.+||.=||+||- .+++|=++| |.++..|+.|+.=|
T Consensus 151 IR~~~~~~YtpEPDifHEl~GHvPlLadp~FA~f~q~~G~~~l~a~~~~i~~LarlY 207 (306)
T cd03347 151 IRHPSKPMYTPEPDICHELLGHVPLFADPSFAQFSQEIGLASLGAPDEYIEKLATVY 207 (306)
T ss_pred ecCccccCCCCCCchHHHHhccchhhcCHHHHHHHHHHHHHhcCCCHHHHHHHhhhe
Confidence 46677888998999883 233443332 45567777777543
No 97
>PF05305 DUF732: Protein of unknown function (DUF732); InterPro: IPR007969 This entry represents several uncharacterised Mycobacterium tuberculosis proteins of unknown function.
Probab=26.19 E-value=1.4e+02 Score=18.54 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=23.1
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 52 PGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 52 P~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
..+-..++..+..|-++.+|++.|..+.
T Consensus 46 i~~g~~vC~~l~~G~~~~~v~~~v~~~~ 73 (100)
T PF05305_consen 46 IALGHAVCDQLDSGTSPEQVVDAVQANN 73 (100)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHhC
Confidence 3556678899999999999999998764
No 98
>cd04658 Piwi_piwi-like_Euk Piwi_piwi-like_Euk: PIWI domain, Piwi-like subfamily found in eukaryotes. This domain is found in Piwi and closely related proteins, where it is believed to perform a crucial role in germline cells, via RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The mechanism in Piwi is believed to be similar to that in Argonaute, the central component of the RNA-induced silencing complex (RISC). The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
Probab=26.14 E-value=51 Score=26.18 Aligned_cols=42 Identities=19% Similarity=0.396 Sum_probs=31.4
Q ss_pred hHHHHHHHHHhc-CCCCccc--c----hhHHHHHHHHHHc-CCCHHHHHH
Q psy15694 32 PQEVLNECLEKF-STPDYIM--E----PGIFSQLKRYFQA-GGNPEQVIE 73 (81)
Q Consensus 32 ~~~vl~eCl~~f-s~~DyIM--E----P~If~~lkrYfqa-GG~PE~VI~ 73 (81)
.+.+++.|.+.+ ..+++|+ - ..++..||+++-. -|-|.|+|.
T Consensus 138 ~~~~~~~l~~~~~~~~~lvvvilp~~~~~~Y~~iK~~~~~~~gI~tQ~i~ 187 (448)
T cd04658 138 IETYIRALKDAFRSDPQLVVIILPGNKKDLYDAIKKFCCVECPVPSQVIT 187 (448)
T ss_pred HHHHHHHHHHhhcCCCcEEEEEECCCCchhHHHHHHHhhcccCcCCEEEe
Confidence 556777777766 4677666 2 4699999999988 888888775
No 99
>cd01782 AF6_RA_repeat1 Ubiquitin domain of AT-6, first repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=26.10 E-value=28 Score=24.61 Aligned_cols=24 Identities=29% Similarity=0.500 Sum_probs=17.4
Q ss_pred HHHHHHHcCC--------------CHHHHHHHHHhhcc
Q psy15694 57 QLKRYFQAGG--------------NPEQVIELMIIDNM 80 (81)
Q Consensus 57 ~lkrYfqaGG--------------~PE~VI~lLSeny~ 80 (81)
.++=|||-+| +-.+||++|.+-||
T Consensus 23 vmrf~~qd~~~k~atK~VrVsS~~tt~eVI~~LLeKFk 60 (112)
T cd01782 23 VMRFYFQDGGEKVATKCIRVSSTATTRDVIDTLSEKFR 60 (112)
T ss_pred EEEEEEEcCCCcEEEEEEEEecCCCHHHHHHHHHHHhc
Confidence 3455677666 56889999988776
No 100
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=26.10 E-value=98 Score=22.65 Aligned_cols=28 Identities=11% Similarity=0.118 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 53 GIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 53 ~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
.++..+++.++.|-+|-.++.+|+..+|
T Consensus 232 ~a~~~l~~l~~~~~~~~~il~~l~~~~~ 259 (340)
T PRK05574 232 RALRILDGLRLEGEEPIKLLAALQREFR 259 (340)
T ss_pred HHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 4556788888888889999999988765
No 101
>PRK04358 hypothetical protein; Provisional
Probab=26.02 E-value=1.2e+02 Score=23.40 Aligned_cols=46 Identities=20% Similarity=0.471 Sum_probs=32.8
Q ss_pred CChHHHHHHHHHhcC------CCCcccchhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 30 ENPQEVLNECLEKFS------TPDYIMEPGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 30 e~~~~vl~eCl~~fs------~~DyIMEP~If~~lkrYfqaGG~PE~VI~lL 75 (81)
+++.+..+.-+..-+ .--+-|-|+|+.-|+.|....|-+++||.-|
T Consensus 25 e~l~ea~~~~l~Lia~arl~l~is~YmPpSVy~El~~f~~~~~~~~e~~~kl 76 (217)
T PRK04358 25 EDLEEAVEKFLDLIARARLKLGISCYMPPSVYKELRGFLERNGCSPEVIAKL 76 (217)
T ss_pred CCHHHHHHHHHHHHHHhhhccCceEEcCHHHHHHHHHHHHhcCCCHHHHhhh
Confidence 355555555544433 3345677999999999999999988887654
No 102
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=25.75 E-value=1.3e+02 Score=18.83 Aligned_cols=24 Identities=17% Similarity=0.552 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 53 GIFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 53 ~If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
.|+..|+.||..| ...++++-|.+
T Consensus 4 ~i~~~l~ey~~~~-D~~ea~~~l~~ 27 (113)
T smart00544 4 KIFLIIEEYLSSG-DTDEAVHCLLE 27 (113)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHHHH
Confidence 5788899999875 66666666654
No 103
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=25.56 E-value=97 Score=20.90 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=26.2
Q ss_pred HHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 36 LNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 36 l~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lL 75 (81)
+.+.+..+. ..-|--..+-..|+.++..|++|+++|+-+
T Consensus 45 l~~li~l~~-~~~Is~~~ak~ll~~~~~~~~~~~~ii~~~ 83 (148)
T PF02637_consen 45 LAELINLLE-DGKISKKSAKELLRELLENGKSPEEIIEEN 83 (148)
T ss_dssp HHHHHHHHH-TTSSGHHHHHHHHHHHHHHTS-HHHHHHHT
T ss_pred HHHHHHHHH-cCCCCHHHHHHHHHHHHHcCCCHHHHHHHc
Confidence 334443333 346777777888888998899999998754
No 104
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=25.54 E-value=35 Score=22.00 Aligned_cols=11 Identities=36% Similarity=0.845 Sum_probs=9.3
Q ss_pred HHHHHHcCCCH
Q psy15694 58 LKRYFQAGGNP 68 (81)
Q Consensus 58 lkrYfqaGG~P 68 (81)
-|||+++||+-
T Consensus 36 C~rywT~GG~l 46 (63)
T PF02701_consen 36 CRRYWTHGGTL 46 (63)
T ss_pred HHHHHHhccee
Confidence 58999999963
No 105
>PRK04149 sat sulfate adenylyltransferase; Reviewed
Probab=25.25 E-value=62 Score=26.40 Aligned_cols=39 Identities=18% Similarity=0.164 Sum_probs=32.5
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHH
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPE 69 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE 69 (81)
..+.|.+-...-..-|+.+|.|.|...|.+|++.-|.|.
T Consensus 350 Sgt~iR~~L~~G~~pP~~f~rpeV~~iL~~~~~~~~~~~ 388 (391)
T PRK04149 350 SGTKVREMLREGEKPPPEFSRPEVAEVLIKGLKKYGYPS 388 (391)
T ss_pred CHHHHHHHHHCcCCCCCccCcHHHHHHHHHHhhhcCCCc
Confidence 566676666677888999999999999999999877664
No 106
>COG4687 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.96 E-value=1.3e+02 Score=21.68 Aligned_cols=34 Identities=18% Similarity=0.418 Sum_probs=27.2
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHc
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQA 64 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqa 64 (81)
++..||+..-+..-..-.|--|+.++++||.|+.
T Consensus 85 dsg~iLk~ir~yvg~~~vV~spsl~d~~kr~fk~ 118 (122)
T COG4687 85 DSGKILKKIREYVGNEKVVKSPSLLDTFKRAFKS 118 (122)
T ss_pred CchhHHHHHHHHhCccceecchHHHHHHHHHHHH
Confidence 4677888777777666678899999999999963
No 107
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=24.96 E-value=1.5e+02 Score=18.84 Aligned_cols=46 Identities=15% Similarity=0.286 Sum_probs=22.0
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhcc
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny~ 80 (81)
+..++++.|......+|.-.. .+|=.-=|.|. +|++++.+|.+-|.
T Consensus 9 tl~~Li~~L~~~~~~~d~~f~-~~Flltyr~F~---tp~~ll~~L~~rf~ 54 (127)
T smart00229 9 TLEKLIEHLTEAFDKADPFFV-ETFLLTYRSFI---TTQELLQLLLYRYN 54 (127)
T ss_pred cHHHHHHHHcCCCcCCCHHHH-HHHHHHhhhhC---CHHHHHHHHHHHhC
Confidence 456666666665554442211 12211222222 57777777765553
No 108
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=24.89 E-value=1.1e+02 Score=20.92 Aligned_cols=41 Identities=24% Similarity=0.293 Sum_probs=28.0
Q ss_pred HHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 34 EVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 34 ~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lL 75 (81)
+-+.+.+.... ..-|--..+-..|+.++..|++|+++|+-+
T Consensus 42 ~~l~~li~lv~-~g~It~~~ak~vl~~~~~~~~~~~~ii~~~ 82 (147)
T smart00845 42 EHLAELLKLIE-DGTISGKIAKEVLEELLESGKSPEEIVEEK 82 (147)
T ss_pred HHHHHHHHHHH-cCCCcHHHHHHHHHHHHHcCCCHHHHHHHc
Confidence 33444443332 445667777788888898899999998753
No 109
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=24.75 E-value=88 Score=24.07 Aligned_cols=28 Identities=18% Similarity=0.589 Sum_probs=23.5
Q ss_pred cccchhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 48 YIMEPGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaGG~PE~VI~lL 75 (81)
+-|-|+|+.-|+.|....|-|++||-.|
T Consensus 45 cYmPpsVy~El~~fl~~~~~~~e~~~kl 72 (206)
T TIGR03875 45 CYMPPSVYKELRRFLERNGCDPETLAKL 72 (206)
T ss_pred eecCHHHHHHHHHHHHhcCCCHHHHHhh
Confidence 4566999999999999999888777654
No 110
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=24.41 E-value=35 Score=20.39 Aligned_cols=24 Identities=25% Similarity=0.409 Sum_probs=16.8
Q ss_pred HHHHhcCCCCcccchhHHHHHHHH
Q psy15694 38 ECLEKFSTPDYIMEPGIFSQLKRY 61 (81)
Q Consensus 38 eCl~~fs~~DyIMEP~If~~lkrY 61 (81)
-|++.|+.+==|--+.+++.++||
T Consensus 6 ~~Ie~~A~~~~~s~~ea~~~~~~~ 29 (62)
T PF12668_consen 6 FCIEEFAKKLNISGEEAYNYFKRS 29 (62)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHc
Confidence 377777766667777777777765
No 111
>TIGR03612 RutA pyrimidine utilization protein A. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the luciferase family defined by pfam00296 and is likely a FMN-dependent monoxygenase.
Probab=24.31 E-value=48 Score=25.67 Aligned_cols=16 Identities=19% Similarity=0.052 Sum_probs=12.9
Q ss_pred cCCCHHHHHHHHHhhc
Q psy15694 64 AGGNPEQVIELMIIDN 79 (81)
Q Consensus 64 aGG~PE~VI~lLSeny 79 (81)
.-|+|++|++.|.+-+
T Consensus 304 lvGtPe~Vae~l~~~~ 319 (355)
T TIGR03612 304 LVGSYETVARMLDEVA 319 (355)
T ss_pred EEECHHHHHHHHHHHH
Confidence 3489999999997654
No 112
>cd01096 Alkanal_monooxygenase Alkanal monooxygenase are flavin monoxygenases. Molecular oxygen is activated by reaction with reduced flavin mononucleotide (FMNH2) and reacts with an aldehyde to yield the carboxylic acid, oxidized flavin (FMN) and a blue-green light. Bacterial luciferases are heterodimers made of alpha and beta subunits which are homologous. The single activer center is on the alpha subunit. The alpha subunit has a stretch of 30 amino acid residues that is not present in the beta subunit. The beta subunit does not contain the active site and is required for the formation of the fully active heterodimer. The beta subunit does not contribute anything directly to the active site. Its role is probably to stabilize the high quantum yield conformation of the alpha subunit through interactionbs across the subunit interface.
Probab=24.23 E-value=46 Score=24.93 Aligned_cols=14 Identities=43% Similarity=0.783 Sum_probs=11.7
Q ss_pred cCCCHHHHHHHHHh
Q psy15694 64 AGGNPEQVIELMII 77 (81)
Q Consensus 64 aGG~PE~VI~lLSe 77 (81)
.-|+|++|++.|.+
T Consensus 272 ~vGtpe~v~~~l~~ 285 (315)
T cd01096 272 AVGTPEECIEIIQL 285 (315)
T ss_pred CCCCHHHHHHHHHH
Confidence 45999999999864
No 113
>COG1210 GalU UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]
Probab=24.20 E-value=38 Score=27.29 Aligned_cols=17 Identities=35% Similarity=0.819 Sum_probs=14.5
Q ss_pred cccchhHHHHHHHHHHcC
Q psy15694 48 YIMEPGIFSQLKRYFQAG 65 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaG 65 (81)
||..|.||+.|++ ...|
T Consensus 208 Yil~p~IFd~L~~-~~~G 224 (291)
T COG1210 208 YVLTPEIFDILEE-TKPG 224 (291)
T ss_pred eecCHHHHHHHhh-CCCC
Confidence 9999999999999 4444
No 114
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=24.15 E-value=93 Score=15.49 Aligned_cols=19 Identities=21% Similarity=0.298 Sum_probs=9.9
Q ss_pred HHHHHHcCCCHHHHHHHHH
Q psy15694 58 LKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 58 lkrYfqaGG~PE~VI~lLS 76 (81)
.|+++..-|..+-+++||+
T Consensus 4 ~~~~i~~~g~i~~L~~ll~ 22 (41)
T smart00185 4 QKQAVVDAGGLPALVELLK 22 (41)
T ss_pred HHHHHHHCCCHHHHHHHHc
Confidence 3445544444555666665
No 115
>PF06496 DUF1097: Protein of unknown function (DUF1097); InterPro: IPR009476 This family consists of several bacterial putative membrane proteins.
Probab=23.87 E-value=73 Score=21.82 Aligned_cols=26 Identities=23% Similarity=0.345 Sum_probs=20.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 54 IFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 54 If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.|-.---||.+|++++.+++.+-.|.
T Consensus 25 ~Figwa~yfa~G~~~~~~~~~~~~~~ 50 (144)
T PF06496_consen 25 GFIGWASYFAAGGGKKGLKKSLASNL 50 (144)
T ss_pred HHHHHHHHHHcCCChhHHHHHHHHHH
Confidence 35556689999999999999887664
No 116
>cd01269 PLX Pollux (PLX) Phosphotyrosine-binding (PTB) domain. Pollux (PLX) Phosphotyrosine-binding (PTB) domain. PLX is calmodulin-binding protein containing a TBC domain, which is conserved from yeast to man, but it only has an N-terminal PTB domain in mammals. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=23.42 E-value=49 Score=23.89 Aligned_cols=15 Identities=40% Similarity=1.026 Sum_probs=13.3
Q ss_pred ChHHHHHHHHHhcCC
Q psy15694 31 NPQEVLNECLEKFST 45 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~ 45 (81)
.|-+|+.||.+||.-
T Consensus 19 ~~~~li~e~I~K~~~ 33 (129)
T cd01269 19 APSSLIDDCIEKFSL 33 (129)
T ss_pred CChHHHHHHHHHhhh
Confidence 588999999999974
No 117
>cd01308 Isoaspartyl-dipeptidase Isoaspartyl dipeptidase hydrolyzes the beta-L-isoaspartyl linkages in dipeptides, as part of the degradative pathway to eliminate proteins with beta-L-isoaspartyl peptide bonds, bonds whereby the beta-group of an aspartate forms the peptide link with the amino group of the following amino acid. Formation of this bond is a spontaneous nonenzymatic reaction in nature and can profoundly effect the function of the protein. Isoaspartyl dipeptidase is an octameric enzyme that contains a binuclear zinc center in the active site of each subunit and shows a strong preference of hydrolyzing Asp-Leu dipeptides.
Probab=22.91 E-value=1.4e+02 Score=22.61 Aligned_cols=25 Identities=8% Similarity=0.323 Sum_probs=19.5
Q ss_pred HHHHHHHHHHcCC-CHHHHHHHHHhh
Q psy15694 54 IFSQLKRYFQAGG-NPEQVIELMIID 78 (81)
Q Consensus 54 If~~lkrYfqaGG-~PE~VI~lLSen 78 (81)
++..++...+.|| ++++++++++.|
T Consensus 309 ~~~~~~~~v~~~~i~~~~al~~~T~n 334 (387)
T cd01308 309 LLREVREAVKCGDIPLEVALRVITSN 334 (387)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 4466777777776 889999999987
No 118
>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei
Probab=22.91 E-value=2.4e+02 Score=18.98 Aligned_cols=40 Identities=20% Similarity=0.354 Sum_probs=28.4
Q ss_pred hHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHH
Q psy15694 32 PQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 32 ~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLS 76 (81)
+..|...|++ ++ |..+.-...+++=-..||+-.++.+||.
T Consensus 21 ~~~v~d~ll~----~~-ilT~~d~e~I~aa~~~~g~~~~ar~LL~ 60 (88)
T cd08819 21 TRDVCDKCLE----QG-LLTEEDRNRIEAATENHGNESGARELLK 60 (88)
T ss_pred HHHHHHHHHh----cC-CCCHHHHHHHHHhccccCcHHHHHHHHH
Confidence 5667777774 34 6666666666665556899999999985
No 119
>PF03770 IPK: Inositol polyphosphate kinase ; InterPro: IPR005522 ArgRIII has been demonstrated to be an inositol polyphosphate kinase [] which catalyses the reaction ATP + 1D-myo-inositol 1,4,5-trisphosphate = ADP + 1D-myo-inositol 1,3,4,5-tetrakisphosphate .; GO: 0008440 inositol trisphosphate 3-kinase activity; PDB: 2IF8_B 2IEW_B 1W2C_A 1W2F_A 1W2D_A 2A98_A 2AQX_A 1TZD_A.
Probab=22.55 E-value=1.1e+02 Score=21.94 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=15.6
Q ss_pred chhHHHHHHHHHHcCCCHHHHHH
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIE 73 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~ 73 (81)
.-++...|++||.+|+.+.....
T Consensus 80 ~~~~~~~l~~Ff~~~~~~~~~~~ 102 (197)
T PF03770_consen 80 PEEVRDALKKFFNNGSSPRRRRE 102 (197)
T ss_dssp HHHHHHHHHHHHT-TT-HHTHHH
T ss_pred HHHHHHHHHHHhcCCCccHHHHH
Confidence 34788899999999987664333
No 120
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=22.29 E-value=1.5e+02 Score=20.03 Aligned_cols=26 Identities=19% Similarity=0.271 Sum_probs=22.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 54 IFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 54 If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
|-..+.++|..|.++.++..++|.-|
T Consensus 3 ~~~l~~~l~~~g~~~~~i~~~~s~~~ 28 (138)
T PF03445_consen 3 IRELVAALFRRGASVRQIARILSELN 28 (138)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 44678999999999999999999765
No 121
>cd06454 KBL_like KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life.
Probab=22.28 E-value=1.8e+02 Score=20.82 Aligned_cols=25 Identities=24% Similarity=0.493 Sum_probs=16.6
Q ss_pred hcCCCCccc---chhHHHHHHHHHHcCC
Q psy15694 42 KFSTPDYIM---EPGIFSQLKRYFQAGG 66 (81)
Q Consensus 42 ~fs~~DyIM---EP~If~~lkrYfqaGG 66 (81)
.|++.||.= -|.|...|+.+++.+|
T Consensus 5 ~~~~~~~~~~~~~~~v~~a~~~~~~~~~ 32 (349)
T cd06454 5 NFCSNDYLGLANHPEVIEAAKEALDKYG 32 (349)
T ss_pred ecccCCccccCCCHHHHHHHHHHHHHhC
Confidence 366777753 4677777877777543
No 122
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=22.27 E-value=1.4e+02 Score=15.85 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=21.1
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 52 PGIFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 52 P~If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
|.++..|-+....-|.|++.+++|..
T Consensus 1 p~~~~~la~~~~~~G~~~~A~~~~~~ 26 (44)
T PF13428_consen 1 PAAWLALARAYRRLGQPDEAERLLRR 26 (44)
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 66777888888888999999888754
No 123
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=22.23 E-value=1.3e+02 Score=15.56 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=15.5
Q ss_pred HHHHHHHcCCCHHHHHHHHH
Q psy15694 57 QLKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 57 ~lkrYfqaGG~PE~VI~lLS 76 (81)
.++....++|+.+..++.|-
T Consensus 18 ~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 18 ARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHhCCCHHHHHHHHh
Confidence 35666788899999988874
No 124
>PRK01215 competence damage-inducible protein A; Provisional
Probab=22.22 E-value=1.5e+02 Score=22.52 Aligned_cols=37 Identities=11% Similarity=0.117 Sum_probs=30.0
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCC
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGN 67 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~ 67 (81)
++.-+..+++.++-....+.-|.++..|++||+..|.
T Consensus 75 t~dD~t~eaia~~~g~~l~~~~e~~~~l~~~~~~~~~ 111 (264)
T PRK01215 75 TYDDKTNEGFAKALGVELELNEDALRMILEKYEKRGI 111 (264)
T ss_pred ChhhhHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC
Confidence 4556777777777777888999999999999987763
No 125
>PF14454 Prok_Ub: Prokaryotic Ubiquitin
Probab=22.18 E-value=66 Score=20.42 Aligned_cols=23 Identities=30% Similarity=0.554 Sum_probs=17.2
Q ss_pred HHHHHHHcCC----------CHHHHHHHHHhhc
Q psy15694 57 QLKRYFQAGG----------NPEQVIELMIIDN 79 (81)
Q Consensus 57 ~lkrYfqaGG----------~PE~VI~lLSeny 79 (81)
.|+|=|.-+| +|++|-++.|-+|
T Consensus 5 ~L~R~F~~~g~~L~DP~p~~spe~V~~~ya~~Y 37 (65)
T PF14454_consen 5 TLTRVFRYNGITLPDPNPSLSPEEVRDFYAAQY 37 (65)
T ss_pred EEEEEEEECCEECCCCCCCCCHHHHHHHHhhhC
Confidence 3455555555 7999999999888
No 126
>COG0042 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=21.97 E-value=1.8e+02 Score=22.76 Aligned_cols=41 Identities=27% Similarity=0.485 Sum_probs=29.6
Q ss_pred HHHHHhcCCCCccc-------chhHHHHHHHHHHcCC----CHHHHHHHHHhhc
Q psy15694 37 NECLEKFSTPDYIM-------EPGIFSQLKRYFQAGG----NPEQVIELMIIDN 79 (81)
Q Consensus 37 ~eCl~~fs~~DyIM-------EP~If~~lkrYfqaGG----~PE~VI~lLSeny 79 (81)
++|++... .|=|| .|.||.++ +|+..|- +..++.+.+-.++
T Consensus 214 ~~~l~~tg-~DgVMigRga~~nP~l~~~i-~~~~~g~~~~~~~~e~~~~~~~~~ 265 (323)
T COG0042 214 KEMLEYTG-ADGVMIGRGALGNPWLFRQI-DYLETGELLPPTLAEVLDILREHL 265 (323)
T ss_pred HHHHHhhC-CCEEEEcHHHccCCcHHHHH-HHhhcCCCCCCCHHHHHHHHHHHH
Confidence 45665544 68888 89999999 8888887 3467777666554
No 127
>PF08412 Ion_trans_N: Ion transport protein N-terminal; InterPro: IPR013621 This domain is found to the N terminus of IPR005821 from INTERPRO in voltage- and cyclic nucleotide-gated K/Na ion channels.
Probab=21.89 E-value=77 Score=20.47 Aligned_cols=32 Identities=19% Similarity=0.321 Sum_probs=25.4
Q ss_pred ChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHc
Q psy15694 31 NPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQA 64 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqa 64 (81)
...+|..|+.|..+.+-+|+-|. +..|.|...
T Consensus 20 S~~ai~~E~~R~~~~~~~IIHP~--S~fR~~WD~ 51 (77)
T PF08412_consen 20 SKKAIEKEKERQRSSGPWIIHPF--SKFRFYWDL 51 (77)
T ss_pred cHHHHHHHHHHHhcCCCeEEcCC--ccHHHHHHH
Confidence 36789999999999999999994 446766543
No 128
>cd02826 Piwi-like Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism.
Probab=21.77 E-value=53 Score=25.73 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=30.4
Q ss_pred hHHHHHHHHHhcC-CCCccc------chhHHHHHHHHHHcCCCHHHHHH
Q psy15694 32 PQEVLNECLEKFS-TPDYIM------EPGIFSQLKRYFQAGGNPEQVIE 73 (81)
Q Consensus 32 ~~~vl~eCl~~fs-~~DyIM------EP~If~~lkrYfqaGG~PE~VI~ 73 (81)
.+.+.+.+.+.+. .+++|| .+.+++.||++.-.-|-|.|+|.
T Consensus 82 ~~~~~~~~~~~~~~~~~lv~~ilp~~~~~~Y~~iK~~~~~~gI~tQ~i~ 130 (393)
T cd02826 82 FKDLKSVFKNAIKAGVQLVIFILKEKKPPLHDEIKRLEAKSDIPSQVIQ 130 (393)
T ss_pred HHHHHHHHHHHhhcCCCEEEEEEcCCCccHHHHHHHHHhccCCceEEEe
Confidence 4455555555543 688776 24899999999988799998874
No 129
>PF08491 SE: Squalene epoxidase; InterPro: IPR013698 This domain is found in squalene epoxidase (SE) and related proteins which are found in taxonomically diverse groups of eukaryotes and also in bacteria. SE was first cloned from Saccharomyces cerevisiae (Baker's yeast) where it was named ERG1. It contains a putative FAD binding site and is a key enzyme in the sterol biosynthetic pathway []. Putative transmembrane regions are found to the protein's C terminus. ; GO: 0004506 squalene monooxygenase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=21.75 E-value=69 Score=25.19 Aligned_cols=32 Identities=31% Similarity=0.620 Sum_probs=21.9
Q ss_pred HhcCCCCc---ccchhHHHHHHHHHHcCCC-HHHHHHHHH
Q psy15694 41 EKFSTPDY---IMEPGIFSQLKRYFQAGGN-PEQVIELMI 76 (81)
Q Consensus 41 ~~fs~~Dy---IMEP~If~~lkrYfqaGG~-PE~VI~lLS 76 (81)
.-|+..|- +|.=++| +|||.||. -..-|.|||
T Consensus 203 ~lF~a~~~~l~~Lr~gcf----~Yf~~GG~~~~gpv~LLs 238 (276)
T PF08491_consen 203 SLFAADDDYLKALRQGCF----KYFQLGGECVSGPVALLS 238 (276)
T ss_pred HHHhCCCHHHHHHHHHHH----HHHHcCCCCCcchHHHhc
Confidence 34666663 3455555 79999995 777788887
No 130
>PF14676 FANCI_S2: FANCI solenoid 2; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=21.65 E-value=1.4e+02 Score=21.33 Aligned_cols=41 Identities=20% Similarity=0.253 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCH--HHHHHHHHh
Q psy15694 33 QEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNP--EQVIELMII 77 (81)
Q Consensus 33 ~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~P--E~VI~lLSe 77 (81)
-.||.++-+ .-.++.++|+++++..+....+. .+.|++|+.
T Consensus 39 ~~IL~~~fk----~h~~~r~~Ile~l~~rI~~~s~~~~~~~idlL~~ 81 (158)
T PF14676_consen 39 IQILLELFK----VHEMIRSEILEQLLNRIVTKSSSPSSQYIDLLSE 81 (158)
T ss_dssp HHHHHHHHH----H-GGGHHHHHHHHHHHHHH--SS--HHHHHHHHH
T ss_pred HHHHHHHHH----HhHHHHHHHHHHHHHHHHhcCccchhHHHHHHHH
Confidence 345555443 44577899999999888888776 899999975
No 131
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=21.48 E-value=65 Score=22.12 Aligned_cols=11 Identities=27% Similarity=0.471 Sum_probs=9.8
Q ss_pred CHHHHHHHHHh
Q psy15694 67 NPEQVIELMII 77 (81)
Q Consensus 67 ~PE~VI~lLSe 77 (81)
+|+|||++||-
T Consensus 65 t~~Qvv~~l~R 75 (99)
T PF13758_consen 65 TREQVVDVLSR 75 (99)
T ss_pred CHHHHHHHHHH
Confidence 79999999984
No 132
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=21.40 E-value=2.4e+02 Score=20.18 Aligned_cols=28 Identities=7% Similarity=0.131 Sum_probs=17.7
Q ss_pred CcccchhHHHHHHHHHHcCCCHHHHHHHHH
Q psy15694 47 DYIMEPGIFSQLKRYFQAGGNPEQVIELMI 76 (81)
Q Consensus 47 DyIMEP~If~~lkrYfqaGG~PE~VI~lLS 76 (81)
..-+.|.....|-+. +||++-.++++|-
T Consensus 178 ~~~i~~~al~~l~~~--~~gd~r~~~~~l~ 205 (319)
T PRK00440 178 GIEITDDALEAIYYV--SEGDMRKAINALQ 205 (319)
T ss_pred CCCCCHHHHHHHHHH--cCCCHHHHHHHHH
Confidence 444566666666543 5777777777763
No 133
>CHL00090 apcD allophycocyanin gamma subunit
Probab=21.40 E-value=79 Score=22.73 Aligned_cols=29 Identities=10% Similarity=0.331 Sum_probs=24.2
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++=.+.||.||+.|-..=++++.|+.|-
T Consensus 19 s~~EL~~l~~~~~~~~~Rl~aa~~l~~na 47 (161)
T CHL00090 19 TIGELESIQDYLKTGEKRIRIATILRDNE 47 (161)
T ss_pred CHHHHHHHHHHHHhHHHHhHHHHHHHHHH
Confidence 34556789999999999999999998873
No 134
>TIGR03646 YtoQ_fam YtoQ family protein. Members of this family are uncharacterized proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=21.25 E-value=64 Score=23.76 Aligned_cols=10 Identities=50% Similarity=0.717 Sum_probs=8.7
Q ss_pred CHHHHHHHHH
Q psy15694 67 NPEQVIELMI 76 (81)
Q Consensus 67 ~PE~VI~lLS 76 (81)
+|+|||+.|+
T Consensus 131 tp~Qvv~iL~ 140 (144)
T TIGR03646 131 TPEQAIETLK 140 (144)
T ss_pred CHHHHHHHHH
Confidence 7999999886
No 135
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=21.21 E-value=78 Score=18.55 Aligned_cols=26 Identities=19% Similarity=0.300 Sum_probs=17.7
Q ss_pred HHHHHHHHHHcC-CCHHHHHHHHHhhc
Q psy15694 54 IFSQLKRYFQAG-GNPEQVIELMIIDN 79 (81)
Q Consensus 54 If~~lkrYfqaG-G~PE~VI~lLSeny 79 (81)
-|+-+..|++.+ |-.++-|+.|-++|
T Consensus 41 ~yGs~e~Yl~~~lgl~~~~i~~Lr~~l 67 (68)
T PF13348_consen 41 RYGSVENYLREELGLSEEDIERLRERL 67 (68)
T ss_dssp HHSSHHHHHHHT-T--HHHHHHHHHHH
T ss_pred HcCCHHHHHHHcCCCCHHHHHHHHHHc
Confidence 355567899777 87778888887776
No 136
>PF07217 Het-C: Heterokaryon incompatibility protein Het-C; InterPro: IPR010816 In filamentous fungi, het loci (for heterokaryon incompatibility) are believed to regulate self/nonself-recognition during vegetative growth. As filamentous fungi grow, hyphal fusion occurs within an individual colony to form a network. Hyphal fusion can occur also between different individuals to form a heterokaryon, in which genetically distinct nuclei occupy a common cytoplasm. However, heterokaryotic cells are viable only if the individuals involved have identical alleles at all het loci [].
Probab=21.16 E-value=3e+02 Score=24.40 Aligned_cols=47 Identities=17% Similarity=0.409 Sum_probs=37.3
Q ss_pred ChHHHHHHHHHhcCCCCcc-----cchhHHHHHHHHHHcCCCHHH-HHHHHHh
Q psy15694 31 NPQEVLNECLEKFSTPDYI-----MEPGIFSQLKRYFQAGGNPEQ-VIELMII 77 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~DyI-----MEP~If~~lkrYfqaGG~PE~-VI~lLSe 77 (81)
++..|+..|++.|--|.+- +.=..|..++++++.=+.-++ +.+.||.
T Consensus 506 dv~~vl~~il~vfHHPa~rd~~~eiqr~Mf~~V~~W~~~~~~~~~~l~~~LS~ 558 (606)
T PF07217_consen 506 DVDRVLNDILRVFHHPAFRDMNSEIQREMFETVEEWWNEMSDRERDLRRRLSK 558 (606)
T ss_pred CHHHHHHHHHHHcCCcccCCchhHHHHHHHHHHHHHHHhCChhhHHHHHHhhH
Confidence 5899999999999888765 344678999999987766544 8888885
No 137
>TIGR02096 conserved hypothetical protein, steroid delta-isomerase-related. This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes.
Probab=21.01 E-value=98 Score=19.06 Aligned_cols=22 Identities=23% Similarity=0.465 Sum_probs=15.5
Q ss_pred HHHHHHHc--CCCHHHHHHHHHhh
Q psy15694 57 QLKRYFQA--GGNPEQVIELMIID 78 (81)
Q Consensus 57 ~lkrYfqa--GG~PE~VI~lLSen 78 (81)
.+++||++ -|.++.+..+++++
T Consensus 3 iv~~~~~a~~~~d~~~~~~~~~~d 26 (129)
T TIGR02096 3 LAQHWIEAFNRGDMDAVLALLAED 26 (129)
T ss_pred HHHHHHHHHHCCCHHHHHHhcCCC
Confidence 45667664 56788888888776
No 138
>COG2971 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]
Probab=20.99 E-value=1.9e+02 Score=23.26 Aligned_cols=41 Identities=24% Similarity=0.393 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhcCCCCcccchh-HHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 32 PQEVLNECLEKFSTPDYIMEPG-IFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 32 ~~~vl~eCl~~fs~~DyIMEP~-If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
-.++|++||+.| |-|-+-. +-..+.++|.. +|+++|+....
T Consensus 158 g~~~L~~~lra~---DG~~~~t~L~d~v~~~f~~--d~edlv~~~y~ 199 (301)
T COG2971 158 GREALQEALRAF---DGRREATPLTDAVMAEFNL--DPEDLVAFIYK 199 (301)
T ss_pred HHHHHHHHHHHh---cCCccCChHHHHHHHHhCC--CHHHHHHHHHh
Confidence 467889999876 6666655 67778888866 89999987653
No 139
>PF08941 USP8_interact: USP8 interacting; InterPro: IPR015036 This protein interacts with the UBP deubiquitinating enzyme USP8. ; GO: 0016881 acid-amino acid ligase activity, 0031386 protein tag, 0016567 protein ubiquitination; PDB: 2FZP_A 2GWF_B 2OGB_A.
Probab=20.88 E-value=40 Score=25.51 Aligned_cols=33 Identities=21% Similarity=0.539 Sum_probs=22.3
Q ss_pred cCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 43 FSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 43 fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
-||||.+|- ..+||=..+-|-|..+|+.|-+|-
T Consensus 82 ISTPD~~Lq----~~ir~~L~~sgCP~hi~~~l~e~~ 114 (179)
T PF08941_consen 82 ISTPDSVLQ----AMIRRSLSESGCPMHILNELMENC 114 (179)
T ss_dssp ESS--HHHH----HHHHHHHHHTT--CCCHHHHHHTT
T ss_pred ccCccHHHH----HHHHHHHHhcCCCHHHHHHHHHHh
Confidence 466666653 357888889999999999998873
No 140
>TIGR01267 Phe4hydrox_mono phenylalanine-4-hydroxylase, monomeric form. This family is of biopterin and metal-dependent hydroxylases is related to a family of longer, multimeric aromatic amino acid hydroxylases that have additional N-terminal regulatory sequences. These include tyrosine 3-monooxygenase, phenylalanine-4-hydroxylase, and tryptophan 5-monoxygenase.
Probab=20.87 E-value=81 Score=24.65 Aligned_cols=40 Identities=23% Similarity=0.275 Sum_probs=25.5
Q ss_pred HHhcCCCCcccchhHHH----------------HHHHHHHc--CCCHHHHHHHHHhhc
Q psy15694 40 LEKFSTPDYIMEPGIFS----------------QLKRYFQA--GGNPEQVIELMIIDN 79 (81)
Q Consensus 40 l~~fs~~DyIMEP~If~----------------~lkrYfqa--GG~PE~VI~lLSeny 79 (81)
+|+-+.+||+=||+||- .+++|=++ |.+.++.++.|+.=|
T Consensus 97 iR~~~~~~YtpEPDifHe~fGH~P~L~~P~FA~f~q~~G~~~l~a~~~~~~~~Larly 154 (248)
T TIGR01267 97 LRTPEELDYLQEPDIFHDIFGHVPLLTNPVFADFTHTYGKLGLKASALGRVEMLARLY 154 (248)
T ss_pred ecCccccCCCCCchHHHHHhccccccCChHHHHHHHHHHHHHhCCCchHHHHHHhhhh
Confidence 46778899999999982 33333333 335666677776543
No 141
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=20.86 E-value=3.2e+02 Score=19.66 Aligned_cols=49 Identities=18% Similarity=0.385 Sum_probs=38.2
Q ss_pred ChHHHHHHHHHhcCCCC------ccc-chhHHHHHHHH---HHcCCCHHHHHHHHHhhc
Q psy15694 31 NPQEVLNECLEKFSTPD------YIM-EPGIFSQLKRY---FQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 31 ~~~~vl~eCl~~fs~~D------yIM-EP~If~~lkrY---fqaGG~PE~VI~lLSeny 79 (81)
-..+|.++-.++.++.| ||. -|++|+.|++| ++.|+.-+++.+-|.+-.
T Consensus 95 ~~~~iK~~Va~~Vk~~dp~~~~VyVsaDpd~~~Ri~~~~~~i~~G~pv~~~~~e~~~iv 153 (158)
T TIGR02898 95 VTDELKEKVAETVKSTDNRIANVYVSADPDTVERIRRYGKGIKEGRPVEGFLDELAEIV 153 (158)
T ss_pred hHHHHHHHHHHHHHhhCCCcceEEEEcCHHHHHHHHHHHHHhHcCCChHHHHHHHHHHH
Confidence 45677777777777744 444 79999999998 789999999988887643
No 142
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=20.86 E-value=1.8e+02 Score=18.04 Aligned_cols=24 Identities=33% Similarity=0.611 Sum_probs=17.1
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 53 GIFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 53 ~If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
.|+..|+.||..| ...+++.-|.+
T Consensus 4 ~i~~~l~ey~~~~-d~~ea~~~l~e 27 (113)
T PF02847_consen 4 KIFSILMEYFSSG-DVDEAVECLKE 27 (113)
T ss_dssp HHHHHHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHhcCC-CHHHHHHHHHH
Confidence 5788899999884 66777666654
No 143
>TIGR02257 cobalto_cobN cobaltochelatase, CobN subunit.
Probab=20.85 E-value=1.6e+02 Score=27.43 Aligned_cols=23 Identities=26% Similarity=0.605 Sum_probs=19.0
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 52 PGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 52 P~If~~lkrYfqaGG~PE~VI~lL 75 (81)
+.....|.+|++.|| ++.+-+||
T Consensus 132 ~~~~~~l~~Y~~~GG-~~N~~~~l 154 (1122)
T TIGR02257 132 LDLSDRLWKYLREGG-PENMGRFL 154 (1122)
T ss_pred HHHHHHHHHHHHcCC-HHHHHHHH
Confidence 788999999999999 66666665
No 144
>CHL00088 apcB allophycocyanin beta subunit
Probab=20.84 E-value=74 Score=22.89 Aligned_cols=29 Identities=17% Similarity=0.338 Sum_probs=24.7
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
.++=.+.||.||+.|-..=++++.|++|-
T Consensus 20 s~~eL~~l~~~~~~~~~Rl~aa~~L~~na 48 (161)
T CHL00088 20 DDNSVEKLRSYFQTGELRVRAAATIAANA 48 (161)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 34556889999999999999999999874
No 145
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=20.77 E-value=1.5e+02 Score=17.38 Aligned_cols=25 Identities=24% Similarity=0.339 Sum_probs=16.3
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHH
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELM 75 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lL 75 (81)
.|.....|+.++.-=|.|..||..+
T Consensus 14 s~~e~~~i~~~~~~~~~~~evI~~a 38 (73)
T TIGR01446 14 SPFEMEDLKYWLDEFGNSPELIKEA 38 (73)
T ss_pred CHHHHHHHHHHHHHhCCCHHHHHHH
Confidence 4667777777777666555555544
No 146
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=20.66 E-value=2e+02 Score=20.83 Aligned_cols=30 Identities=20% Similarity=0.266 Sum_probs=22.1
Q ss_pred CCcccchhHHHHHHHHHHcCCCHHHHHHHHHh
Q psy15694 46 PDYIMEPGIFSQLKRYFQAGGNPEQVIELMII 77 (81)
Q Consensus 46 ~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSe 77 (81)
.....+|++...|-+. ++|.|-.++++|..
T Consensus 175 ~~~~~~~~al~~ia~~--~~G~pR~~~~ll~~ 204 (305)
T TIGR00635 175 LNVEIEPEAALEIARR--SRGTPRIANRLLRR 204 (305)
T ss_pred hCCCcCHHHHHHHHHH--hCCCcchHHHHHHH
Confidence 3456788888777664 88999888877753
No 147
>cd04181 NTP_transferase NTP_transferases catalyze the transfer of nucleotides onto phosphosugars. Nucleotidyltransferases transfer nucleotides onto phosphosugars. The enzyme family includes Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase. The products are activated sugars that are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides.
Probab=20.50 E-value=96 Score=20.70 Aligned_cols=30 Identities=30% Similarity=0.575 Sum_probs=21.1
Q ss_pred cccchhHHHHHHHHHHcCC--CHHHHHHHHHhh
Q psy15694 48 YIMEPGIFSQLKRYFQAGG--NPEQVIELMIID 78 (81)
Q Consensus 48 yIMEP~If~~lkrYfqaGG--~PE~VI~lLSen 78 (81)
||+.|.+|..|+..++ ++ ....+++.|..+
T Consensus 170 y~~~~~~~~~l~~~~~-~~~~~~~~~~~~l~~~ 201 (217)
T cd04181 170 YIFEPEILDYIPEILP-RGEDELTDAIPLLIEE 201 (217)
T ss_pred EEECHHHHHhhhhcCC-cccccHHHHHHHHHhc
Confidence 8999999988877665 22 234677777654
No 148
>cd01318 DHOase_IIb Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family.
Probab=20.35 E-value=1.5e+02 Score=22.91 Aligned_cols=23 Identities=13% Similarity=0.156 Sum_probs=17.9
Q ss_pred HHHHHHHHcCC-CHHHHHHHHHhh
Q psy15694 56 SQLKRYFQAGG-NPEQVIELMIID 78 (81)
Q Consensus 56 ~~lkrYfqaGG-~PE~VI~lLSen 78 (81)
..+..+++.|| +++++|+++|.|
T Consensus 276 ~~~~~~v~~~~l~l~~a~~~~t~n 299 (361)
T cd01318 276 PLMLTLVNKGILSLSRVVRLTSHN 299 (361)
T ss_pred HHHHHHHHcCCCCHHHHHHHHhHH
Confidence 34556777766 999999999986
No 149
>PF05524 PEP-utilisers_N: PEP-utilising enzyme, N-terminal; InterPro: IPR008731 This sequence identifies proteins which are a component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), a major carbohydrate active transport system. The PTS system is found throughout the bacterial kingdom, and is responsible for the coupled phosphorylation and translocation of numerous sugars across the cytoplasmic membrane []. This entry represents the N-terminal domain of enzyme I (EIN) which transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) which in turn phosphorylates a group of membrane-associated proteins, known as enzyme II. The N-terminal domain of EI (EIN) extends from residues 1 to 259 and can be phosphorylated in a fully reversible manner by phosphorylated HPr. EIN, however, cannot be autophosphorylated by PEP [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0008965 phosphoenolpyruvate-protein phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2WQD_A 2XDF_B 2HWG_A 3EZB_A 2L5H_A 3EZA_A 1EZB_A 2EZA_A 1EZA_A 1EZC_A ....
Probab=20.33 E-value=1.3e+02 Score=19.39 Aligned_cols=29 Identities=17% Similarity=0.452 Sum_probs=22.0
Q ss_pred chhHHHHHHHHHHcCCCHHHHHHHHHhhc
Q psy15694 51 EPGIFSQLKRYFQAGGNPEQVIELMIIDN 79 (81)
Q Consensus 51 EP~If~~lkrYfqaGG~PE~VI~lLSeny 79 (81)
-|.++..+++.+..|.+.+.+|..-.++|
T Consensus 79 D~~l~~~v~~~I~~~~~Ae~Av~~~~~~~ 107 (123)
T PF05524_consen 79 DPELIDEVEELIREGKNAEYAVQEVIEEY 107 (123)
T ss_dssp -HHHHHHHHHHHHHH--HHHHHHHHHHHH
T ss_pred CHhHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence 68899999999999999998887666554
No 150
>COG1955 FlaJ Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.25 E-value=61 Score=28.07 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=19.1
Q ss_pred HHHHHcCCCHHHHHHHHHhhcc
Q psy15694 59 KRYFQAGGNPEQVIELMIIDNM 80 (81)
Q Consensus 59 krYfqaGG~PE~VI~lLSeny~ 80 (81)
-+=++.||+|..|=+++|+|..
T Consensus 377 ~d~i~lGGdp~~~GeiIS~n~~ 398 (527)
T COG1955 377 TDAIDLGGDPDVVGEIISENFL 398 (527)
T ss_pred HHHHHcCCCHHHHHHHHHHhHH
Confidence 4557899999999999999974
No 151
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=20.24 E-value=1.5e+02 Score=20.18 Aligned_cols=22 Identities=14% Similarity=0.299 Sum_probs=17.4
Q ss_pred HHHHHHHHcCC----------CHHHHHHHHHh
Q psy15694 56 SQLKRYFQAGG----------NPEQVIELMII 77 (81)
Q Consensus 56 ~~lkrYfqaGG----------~PE~VI~lLSe 77 (81)
+.++++|+++| +||++|+-..+
T Consensus 20 ~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e 51 (132)
T TIGR00640 20 KVIATAYADLGFDVDVGPLFQTPEEIARQAVE 51 (132)
T ss_pred HHHHHHHHhCCcEEEECCCCCCHHHHHHHHHH
Confidence 45789999998 78998886554
No 152
>PF12029 DUF3516: Domain of unknown function (DUF3516); InterPro: IPR021904 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with PF00270 from PFAM, PF00271 from PFAM.
Probab=20.01 E-value=1.8e+02 Score=24.97 Aligned_cols=53 Identities=19% Similarity=0.297 Sum_probs=34.7
Q ss_pred ccCCCcccCcCCCCCCCCCCCCChHHHHHHHHHhcCCCCcccchhHHHHHHHHHHcCCCHHHHHHHHHhhccC
Q psy15694 9 QTHRWDQDMVDVDSDGGDDPMENPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMIIDNMA 81 (81)
Q Consensus 9 ~~~~W~~~~~~~~~~~~~~~~e~~~~vl~eCl~~fs~~DyIMEP~If~~lkrYfqaGG~PE~VI~lLSeny~~ 81 (81)
.+|.|-++-.. .|++|..+-.++..| |+.+-++....=+---|.+-||.-||+
T Consensus 229 ~~hPWv~~~~l-----------~PKSVvRdM~E~amt---------F~dyV~~YgLaRSEGvlLRYLsDAyra 281 (461)
T PF12029_consen 229 RGHPWVGDFEL-----------SPKSVVRDMYERAMT---------FSDYVSRYGLARSEGVLLRYLSDAYRA 281 (461)
T ss_pred hcCCcccCCCC-----------CcchHHHHHHHhhCC---------HHHHHHHhCcchhhhHHHHHHHHHHHH
Confidence 45899875555 499999997777655 333333444444555677778887774
Done!