Query psy16018
Match_columns 89
No_of_seqs 77 out of 79
Neff 2.8
Searched_HMMs 46136
Date Fri Aug 16 18:49:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16018.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16018hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3938|consensus 100.0 7.2E-29 1.6E-33 198.3 7.1 84 1-85 1-94 (334)
2 PF03925 SeqA: SeqA protein; 83.4 0.68 1.5E-05 35.5 1.5 23 66-88 7-32 (190)
3 PRK11187 replication initiatio 81.5 0.99 2.2E-05 34.6 1.8 23 66-88 7-32 (182)
4 PF13443 HTH_26: Cro/C1-type H 75.8 1.8 3.9E-05 25.2 1.3 20 68-87 41-60 (63)
5 PF02773 S-AdoMet_synt_C: S-ad 75.7 2.6 5.6E-05 31.1 2.4 26 64-89 89-114 (138)
6 cd01807 GDX_N ubiquitin-like d 75.4 3.6 7.8E-05 25.1 2.7 25 59-83 16-40 (74)
7 PF14552 Tautomerase_2: Tautom 73.5 2 4.4E-05 28.1 1.3 20 66-85 45-68 (82)
8 smart00760 Bac_DnaA_C Bacteria 73.1 4.2 9.1E-05 24.4 2.5 22 65-86 1-22 (60)
9 PF11543 UN_NPL4: Nuclear pore 72.7 2.5 5.4E-05 27.5 1.6 24 60-83 20-43 (80)
10 PF00240 ubiquitin: Ubiquitin 70.9 4.4 9.6E-05 23.8 2.3 26 59-84 11-36 (69)
11 cd01803 Ubiquitin Ubiquitin. U 70.4 4.9 0.00011 23.8 2.4 26 59-84 16-41 (76)
12 PF05402 PqqD: Coenzyme PQQ sy 68.9 5.9 0.00013 23.4 2.5 29 60-88 26-54 (68)
13 PF08299 Bac_DnaA_C: Bacterial 66.9 5.4 0.00012 25.0 2.1 22 65-86 1-22 (70)
14 cd01791 Ubl5 UBL5 ubiquitin-li 66.7 4.8 0.0001 25.5 1.9 26 59-84 17-42 (73)
15 PF12833 HTH_18: Helix-turn-he 66.5 7.5 0.00016 23.4 2.7 27 60-86 54-80 (81)
16 cd01796 DDI1_N DNA damage indu 66.3 6.3 0.00014 24.2 2.3 26 59-84 15-40 (71)
17 PF08769 Spo0A_C: Sporulation 65.9 2.6 5.5E-05 28.8 0.6 24 66-89 39-62 (106)
18 cd01794 DC_UbP_C dendritic cel 65.7 6.9 0.00015 24.3 2.5 26 59-84 14-39 (70)
19 cd01793 Fubi Fubi ubiquitin-li 65.7 5.8 0.00013 24.2 2.1 26 59-84 14-39 (74)
20 cd01808 hPLIC_N Ubiquitin-like 65.2 6.9 0.00015 23.7 2.3 25 60-84 16-40 (71)
21 PF12844 HTH_19: Helix-turn-he 63.6 5.9 0.00013 23.0 1.8 20 68-87 42-61 (64)
22 cd01810 ISG15_repeat2 ISG15 ub 63.4 8.7 0.00019 23.5 2.6 26 59-84 14-39 (74)
23 cd00196 UBQ Ubiquitin-like pro 63.4 10 0.00022 19.0 2.5 25 60-84 14-38 (69)
24 cd01792 ISG15_repeat1 ISG15 ub 62.9 8.6 0.00019 24.0 2.5 24 60-83 19-42 (80)
25 cd01804 midnolin_N Ubiquitin-l 62.3 7.5 0.00016 24.4 2.2 25 60-84 18-42 (78)
26 PF01476 LysM: LysM domain; I 61.2 7.4 0.00016 21.0 1.8 19 68-86 7-25 (44)
27 cd01798 parkin_N amino-termina 60.5 8.9 0.00019 23.0 2.2 25 60-84 15-39 (70)
28 COG3057 SeqA Negative regulato 60.4 6.3 0.00014 30.3 1.9 23 66-88 7-32 (181)
29 cd01802 AN1_N ubiquitin-like d 59.4 11 0.00023 25.4 2.6 38 44-83 29-67 (103)
30 PF07027 DUF1318: Protein of u 59.2 8.6 0.00019 26.2 2.2 20 67-86 50-69 (95)
31 PF02071 NSF: Aromatic-di-Alan 57.3 5.9 0.00013 18.4 0.8 10 68-77 3-12 (12)
32 PF14338 Mrr_N: Mrr N-terminal 57.2 10 0.00022 24.3 2.2 23 64-86 20-42 (92)
33 PF06971 Put_DNA-bind_N: Putat 56.2 8.8 0.00019 23.4 1.7 20 69-88 30-49 (50)
34 PF14645 Chibby: Chibby family 55.9 29 0.00063 24.2 4.4 34 43-76 50-86 (116)
35 smart00213 UBQ Ubiquitin homol 55.1 15 0.00032 20.6 2.4 26 59-84 15-40 (64)
36 PHA01976 helix-turn-helix prot 54.2 12 0.00027 21.8 2.1 19 68-86 45-63 (67)
37 PRK02220 4-oxalocrotonate taut 54.1 10 0.00022 22.1 1.6 18 68-85 23-40 (61)
38 cd01806 Nedd8 Nebb8-like ubiq 54.1 16 0.00034 21.6 2.5 24 60-83 17-40 (76)
39 cd01805 RAD23_N Ubiquitin-like 53.7 13 0.00029 22.3 2.2 25 60-84 17-43 (77)
40 PRK01964 4-oxalocrotonate taut 53.1 11 0.00023 22.5 1.6 19 67-85 22-40 (64)
41 PF08281 Sigma70_r4_2: Sigma-7 51.9 12 0.00026 21.2 1.7 18 69-86 28-45 (54)
42 PF12085 DUF3562: Protein of u 51.5 16 0.00034 24.0 2.4 25 64-88 4-28 (66)
43 cd01812 BAG1_N Ubiquitin-like 51.2 20 0.00042 21.1 2.6 24 60-83 16-39 (71)
44 KOG3889|consensus 51.1 10 0.00022 31.9 1.8 37 42-79 202-241 (371)
45 PF13404 HTH_AsnC-type: AsnC-t 50.5 5.9 0.00013 22.9 0.2 24 65-88 15-38 (42)
46 PF01337 Barstar: Barstar (bar 50.5 14 0.00031 23.3 2.0 22 60-81 5-26 (90)
47 PF13647 Glyco_hydro_80: Glyco 50.5 8.4 0.00018 31.2 1.2 24 44-68 201-224 (308)
48 cd01797 NIRF_N amino-terminal 49.5 19 0.00042 22.7 2.5 24 60-83 19-42 (78)
49 TIGR02899 spore_safA spore coa 48.2 17 0.00036 18.9 1.8 17 70-86 7-23 (44)
50 COG4229 Predicted enolase-phos 47.2 9.5 0.00021 30.3 1.0 44 41-85 131-181 (229)
51 PF13560 HTH_31: Helix-turn-he 46.7 19 0.00041 21.2 2.0 19 67-85 44-62 (64)
52 PF01402 RHH_1: Ribbon-helix-h 45.6 25 0.00054 18.9 2.3 22 66-87 10-31 (39)
53 cd00118 LysM Lysin domain, fou 45.6 21 0.00045 17.5 1.8 17 70-86 11-27 (46)
54 PF14566 PTPlike_phytase: Inos 45.4 8.8 0.00019 26.8 0.5 10 42-51 124-133 (149)
55 COG2411 Uncharacterized conser 45.4 11 0.00024 29.2 1.1 27 58-84 71-98 (188)
56 TIGR00013 taut 4-oxalocrotonat 44.9 14 0.00031 21.5 1.3 20 66-85 21-40 (63)
57 cd01809 Scythe_N Ubiquitin-lik 44.0 31 0.00066 20.1 2.7 24 60-83 17-40 (72)
58 PF01381 HTH_3: Helix-turn-hel 43.2 14 0.00031 20.6 1.1 16 69-84 40-55 (55)
59 cd06398 PB1_Joka2 The PB1 doma 43.0 18 0.00038 24.2 1.6 17 65-81 26-42 (91)
60 PRK09685 DNA-binding transcrip 42.6 29 0.00062 25.4 2.8 29 61-89 274-302 (302)
61 PTZ00044 ubiquitin; Provisiona 42.5 32 0.0007 20.6 2.6 25 59-83 16-40 (76)
62 cd05875 Ig6_hNeurofascin_like 41.7 16 0.00034 22.2 1.2 20 45-65 1-20 (77)
63 cd06406 PB1_P67 A PB1 domain i 41.5 18 0.00039 24.3 1.5 22 64-85 21-42 (80)
64 cd05140 Barstar_AU1054-like Ba 40.7 25 0.00054 23.1 2.1 22 60-81 5-26 (86)
65 PF00165 HTH_AraC: Bacterial r 40.5 39 0.00085 18.4 2.6 24 62-86 19-42 (42)
66 cd05142 Barstar Barstar is an 39.9 27 0.00058 23.0 2.1 21 61-81 7-27 (87)
67 PRK06030 hypothetical protein; 39.7 29 0.00063 24.6 2.4 23 64-86 23-45 (124)
68 PF13350 Y_phosphatase3: Tyros 38.3 12 0.00025 25.8 0.2 34 44-88 126-160 (164)
69 PRK10219 DNA-binding transcrip 38.1 39 0.00085 21.4 2.7 26 61-86 80-105 (107)
70 cd05141 Barstar_evA4336-like B 37.8 31 0.00067 21.9 2.1 21 60-80 5-25 (81)
71 cd01769 UBL Ubiquitin-like dom 37.0 39 0.00085 19.0 2.3 23 62-84 16-38 (69)
72 PRK10425 DNase TatD; Provision 36.8 37 0.00081 25.8 2.8 34 54-87 214-247 (258)
73 PF13419 HAD_2: Haloacid dehal 36.7 25 0.00054 22.2 1.6 21 65-85 134-154 (176)
74 cd05749 Ig2_Tyro3_like Second 36.7 23 0.0005 22.2 1.4 19 42-61 13-32 (81)
75 PF07700 HNOB: Heme NO binding 36.5 32 0.0007 24.2 2.2 23 66-88 48-70 (171)
76 PF10545 MADF_DNA_bdg: Alcohol 36.1 26 0.00057 20.7 1.5 23 65-87 24-48 (85)
77 PF07836 DmpG_comm: DmpG-like 35.9 36 0.00078 22.3 2.2 25 63-87 18-42 (66)
78 cd02984 TRX_PICOT TRX domain, 35.5 33 0.00072 20.6 1.9 29 42-74 69-97 (97)
79 COG4001 Predicted metal-bindin 34.5 27 0.00059 24.8 1.6 24 66-89 61-84 (102)
80 cd00489 Barstar_like Barstar i 33.4 39 0.00084 22.0 2.1 21 61-81 6-26 (85)
81 smart00386 HAT HAT (Half-A-TPR 33.2 39 0.00084 16.0 1.6 19 62-80 2-20 (33)
82 PF04760 IF2_N: Translation in 33.0 28 0.00061 20.2 1.3 16 73-88 9-24 (54)
83 PF11784 DUF3320: Protein of u 33.0 34 0.00075 20.5 1.7 21 61-81 24-44 (52)
84 PF10668 Phage_terminase: Phag 32.7 44 0.00095 21.3 2.2 22 64-85 10-40 (60)
85 TIGR03859 PQQ_PqqD coenzyme PQ 32.6 45 0.00097 21.2 2.3 28 59-87 39-66 (81)
86 smart00530 HTH_XRE Helix-turn- 32.6 40 0.00086 16.8 1.7 17 67-83 39-55 (56)
87 cd00491 4Oxalocrotonate_Tautom 32.6 29 0.00063 19.6 1.3 19 67-85 21-39 (58)
88 PF13743 Thioredoxin_5: Thiore 31.7 43 0.00092 23.9 2.2 25 65-89 101-125 (176)
89 PRK11511 DNA-binding transcrip 31.7 59 0.0013 21.8 2.8 27 61-87 84-110 (127)
90 smart00257 LysM Lysin motif. 31.7 47 0.001 15.8 1.8 17 70-86 10-26 (44)
91 smart00342 HTH_ARAC helix_turn 31.5 55 0.0012 18.5 2.3 24 60-83 59-82 (84)
92 COG2169 Ada Adenosine deaminas 31.4 37 0.0008 26.0 2.0 36 49-84 140-178 (187)
93 cd01799 Hoil1_N Ubiquitin-like 31.2 59 0.0013 20.5 2.6 25 59-83 18-42 (75)
94 PF12872 OST-HTH: OST-HTH/LOTU 30.8 25 0.00055 20.9 0.8 18 62-79 46-63 (74)
95 PF13542 HTH_Tnp_ISL3: Helix-t 30.6 43 0.00092 18.7 1.7 19 70-88 30-48 (52)
96 PF11000 DUF2840: Protein of u 30.4 35 0.00075 25.7 1.6 29 59-87 87-117 (149)
97 TIGR02384 RelB_DinJ addiction 28.8 48 0.001 21.6 2.0 24 65-88 12-35 (83)
98 PF05157 T2SE_Nter: Type II se 28.7 54 0.0012 20.0 2.1 24 61-84 4-27 (109)
99 cd01800 SF3a120_C Ubiquitin-li 28.6 73 0.0016 19.5 2.7 24 60-83 14-37 (76)
100 PF14109 GldH_lipo: GldH lipop 28.4 14 0.00031 25.7 -0.6 23 44-68 67-91 (131)
101 PRK05250 S-adenosylmethionine 27.9 54 0.0012 27.8 2.5 25 65-89 321-345 (384)
102 PF08667 BetR: BetR domain; I 27.2 40 0.00088 24.8 1.5 20 65-85 50-69 (147)
103 PRK11449 putative deoxyribonuc 26.8 60 0.0013 24.5 2.4 30 58-87 218-247 (258)
104 PF08383 Maf_N: Maf N-terminal 26.8 23 0.0005 21.0 0.2 20 69-88 12-32 (35)
105 TIGR02681 phage_pRha phage reg 26.8 37 0.0008 23.2 1.2 20 70-89 16-35 (108)
106 TIGR02607 antidote_HigA addict 26.7 65 0.0014 19.1 2.1 19 68-86 48-66 (78)
107 PF02796 HTH_7: Helix-turn-hel 26.6 58 0.0013 18.4 1.8 18 71-88 25-42 (45)
108 smart00482 POLAc DNA polymeras 26.4 9.4 0.0002 28.0 -1.9 35 52-86 30-66 (206)
109 PRK13890 conjugal transfer pro 26.3 57 0.0012 22.3 2.1 20 68-87 48-67 (120)
110 cd06409 PB1_MUG70 The MUG70 pr 26.0 48 0.001 22.3 1.6 27 55-81 7-38 (86)
111 TIGR01034 metK S-adenosylmethi 25.9 62 0.0013 27.4 2.5 25 65-89 318-342 (377)
112 cd00569 HTH_Hin_like Helix-tur 25.6 68 0.0015 14.4 1.7 16 70-85 24-39 (42)
113 PF00432 Prenyltrans: Prenyltr 25.3 32 0.00068 19.3 0.5 31 44-74 8-38 (44)
114 PF13518 HTH_28: Helix-turn-he 25.2 59 0.0013 17.8 1.7 18 69-86 14-31 (52)
115 PRK12534 RNA polymerase sigma 24.9 51 0.0011 22.5 1.6 21 60-85 151-171 (187)
116 PF05099 TerB: Tellurite resis 24.9 45 0.00097 21.8 1.3 21 65-85 116-136 (140)
117 COG0600 TauC ABC-type nitrate/ 24.6 33 0.00071 26.7 0.7 31 59-89 144-174 (258)
118 smart00595 MADF subfamily of S 24.4 61 0.0013 19.9 1.8 22 66-87 26-47 (89)
119 PF08220 HTH_DeoR: DeoR-like h 23.9 58 0.0013 19.3 1.5 23 62-88 13-35 (57)
120 PRK12459 S-adenosylmethionine 23.8 72 0.0016 27.1 2.6 26 64-89 324-349 (386)
121 TIGR01691 enolase-ppase 2,3-di 23.8 50 0.0011 24.6 1.5 22 64-85 152-173 (220)
122 cd05895 Ig_Pro_neuregulin-1 Im 23.6 35 0.00076 20.0 0.5 24 45-68 1-24 (76)
123 cd03409 Chelatase_Class_II Cla 23.5 76 0.0017 19.5 2.1 26 51-77 5-30 (101)
124 PF01026 TatD_DNase: TatD rela 23.5 80 0.0017 23.3 2.5 30 58-87 216-245 (255)
125 PTZ00104 S-adenosylmethionine 23.4 73 0.0016 27.2 2.5 25 65-89 337-361 (398)
126 KOG4812|consensus 23.4 29 0.00063 28.2 0.2 65 10-74 20-84 (262)
127 PF11343 DUF3145: Protein of u 23.2 1.1E+02 0.0024 23.1 3.3 63 18-89 69-144 (158)
128 cd05876 Ig3_L1-CAM Third immun 23.1 41 0.0009 19.7 0.8 16 45-61 1-16 (71)
129 TIGR02875 spore_0_A sporulatio 23.0 59 0.0013 23.1 1.7 24 66-89 189-212 (262)
130 PRK15044 transcriptional regul 23.0 86 0.0019 25.4 2.8 29 61-89 266-294 (295)
131 cd01815 BMSC_UbP_N Ubiquitin-l 23.0 70 0.0015 21.0 1.9 22 62-83 19-43 (75)
132 PRK09393 ftrA transcriptional 22.9 88 0.0019 23.6 2.7 30 60-89 292-321 (322)
133 PF10683 DBD_Tnp_Hermes: Herme 22.6 36 0.00078 22.7 0.5 26 61-86 37-64 (68)
134 PRK00745 4-oxalocrotonate taut 22.5 69 0.0015 18.5 1.7 20 66-85 17-40 (62)
135 PRK09940 transcriptional regul 22.3 76 0.0017 24.7 2.3 28 61-88 207-234 (253)
136 TIGR02950 SigM_subfam RNA poly 22.2 70 0.0015 20.8 1.8 22 59-85 118-139 (154)
137 COG3423 Nlp Predicted transcri 21.8 52 0.0011 22.7 1.1 14 72-85 52-65 (82)
138 PF03517 Voldacs: Regulator of 21.6 58 0.0012 22.6 1.4 20 65-84 91-110 (135)
139 COG1476 Predicted transcriptio 21.6 83 0.0018 20.6 2.0 18 68-85 44-61 (68)
140 smart00421 HTH_LUXR helix_turn 21.5 81 0.0018 16.7 1.7 17 69-85 20-36 (58)
141 PF08598 Sds3: Sds3-like; Int 21.3 31 0.00068 24.6 0.0 28 54-89 176-203 (205)
142 PF10542 Vitelline_membr: Vite 21.1 69 0.0015 19.3 1.4 13 39-51 5-17 (38)
143 COG3384 Aromatic ring-opening 21.0 51 0.0011 26.6 1.1 26 48-74 11-36 (268)
144 cd06170 LuxR_C_like C-terminal 20.9 84 0.0018 16.8 1.7 18 69-86 17-34 (57)
145 COG4031 Predicted metal-bindin 20.9 69 0.0015 25.6 1.8 18 53-76 51-68 (227)
146 PF13936 HTH_38: Helix-turn-he 20.8 26 0.00057 20.0 -0.4 24 65-88 18-41 (44)
147 PF00085 Thioredoxin: Thioredo 20.7 97 0.0021 18.2 2.1 31 42-75 72-102 (103)
148 PF14330 DUF4387: Domain of un 20.7 47 0.001 23.2 0.8 16 71-86 42-57 (99)
149 TIGR01244 conserved hypothetic 20.4 75 0.0016 21.6 1.7 34 44-88 88-121 (135)
150 TIGR01493 HAD-SF-IA-v2 Haloaci 20.3 73 0.0016 21.2 1.6 22 64-85 139-160 (175)
151 PLN02243 S-adenosylmethionine 20.3 95 0.0021 26.4 2.6 25 64-88 328-352 (386)
152 PF10685 KGG: Stress-induced b 20.2 82 0.0018 16.8 1.5 14 62-75 1-15 (23)
153 cd05874 Ig6_NrCAM Sixth immuno 20.0 69 0.0015 19.4 1.3 18 45-63 1-18 (77)
154 TIGR01068 thioredoxin thioredo 20.0 1.5E+02 0.0033 17.2 2.9 33 41-76 68-100 (101)
No 1
>KOG3938|consensus
Probab=99.95 E-value=7.2e-29 Score=198.30 Aligned_cols=84 Identities=43% Similarity=0.723 Sum_probs=64.0
Q ss_pred CCCccCCCCCCCCCCCCCCcCCCCcc----------cccCCCCCCCCCCCCCCceeeeeecccCCCceeccCccchHHHH
Q psy16018 1 MPLFTRKPKKDDHLLDNNNVGEHKSK----------IYNGTKSPAPVTEDSKPKLIFHCQLAHGSPTGLISGFSNVRELY 70 (89)
Q Consensus 1 m~l~~kk~~k~~~~~~~~~~~~~~~~----------~~~g~~~~~p~~~~~~p~LvFh~QLAHGSptg~I~gF~nvkELY 70 (89)
|||+.++-+|.-.......--+-.|. +.++.+ ..+.+++.+|+||||||||||||||+|+||+||+|||
T Consensus 1 M~~~~~~~~k~~~~~~~~~a~~~rs~e~~p~~~~~~~s~~~~-s~s~~~~~~p~LvF~~QLAHGSptg~Ie~fsnv~ELY 79 (334)
T KOG3938|consen 1 MPLQGRPSPKSRPRSEGRGAFNARSGETSPLQPGVPISPNEG-SPSIPPAVRPRLVFHCQLAHGSPTGRIEGFSNVRELY 79 (334)
T ss_pred CCCCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCccCC-CCCCCccCCCceeEeeeeccCCccceecccccHHHHH
Confidence 89998888776665433222111111 112233 2355688999999999999999999999999999999
Q ss_pred HHhhhhhcCChhhHh
Q psy16018 71 QKIAECYEFPAEEVS 85 (89)
Q Consensus 71 ~kIae~f~i~~~eIl 85 (89)
++||+||+|+++|||
T Consensus 80 ~kIAe~F~Is~~dIl 94 (334)
T KOG3938|consen 80 QKIAEAFDISPDDIL 94 (334)
T ss_pred HHHHHHhcCCccceE
Confidence 999999999999997
No 2
>PF03925 SeqA: SeqA protein; InterPro: IPR005621 The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation []. SeqA tetramers are able to aggregate or multimerize in a reversible, concentration-dependent manner []. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor []. The C-terminal domain binds DNA, binding to fully methylated and hemimethylated GATC sequences at oriC. The structure of the C-terminal domain consists of seven alpha-helices and three-stranded beta-sheet.; GO: 0003677 DNA binding, 0032297 negative regulation of DNA-dependent DNA replication initiation; PDB: 3FMT_A 1J3E_A 1XRX_D 1IU3_C 1LRR_D.
Probab=83.37 E-value=0.68 Score=35.52 Aligned_cols=23 Identities=26% Similarity=0.327 Sum_probs=17.4
Q ss_pred hHHHHHHhh---hhhcCChhhHhhhc
Q psy16018 66 VRELYQKIA---ECYEFPAEEVSEDF 88 (89)
Q Consensus 66 vkELY~kIa---e~f~i~~~eIl~~~ 88 (89)
..|||+-|| +.+|=+++||||.+
T Consensus 7 DeELYryIAs~Tq~IGESASdILRRL 32 (190)
T PF03925_consen 7 DEELYRYIASQTQHIGESASDILRRL 32 (190)
T ss_dssp -HHHHHHHHTT-SSTT--HHHHHHHH
T ss_pred cHHHHHHHHHhccccCCCHHHHHHHh
Confidence 479999999 66777999999964
No 3
>PRK11187 replication initiation regulator SeqA; Provisional
Probab=81.47 E-value=0.99 Score=34.56 Aligned_cols=23 Identities=26% Similarity=0.327 Sum_probs=19.8
Q ss_pred hHHHHHHhh---hhhcCChhhHhhhc
Q psy16018 66 VRELYQKIA---ECYEFPAEEVSEDF 88 (89)
Q Consensus 66 vkELY~kIa---e~f~i~~~eIl~~~ 88 (89)
..|||+-|| +..|=+++||||.+
T Consensus 7 DeELYryIAS~Tq~IGESASDILRRL 32 (182)
T PRK11187 7 DEELYRYIASHTQHIGESASDILRRL 32 (182)
T ss_pred cHHHHHHHHHccCccCCCHHHHHHHH
Confidence 479999999 67777999999974
No 4
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=75.80 E-value=1.8 Score=25.21 Aligned_cols=20 Identities=30% Similarity=0.371 Sum_probs=14.8
Q ss_pred HHHHHhhhhhcCChhhHhhh
Q psy16018 68 ELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl~~ 87 (89)
+.-.+||++|++++.||++.
T Consensus 41 ~~l~~ia~~l~~~~~el~~~ 60 (63)
T PF13443_consen 41 DTLEKIAKALNCSPEELFEY 60 (63)
T ss_dssp HHHHHHHHHHT--HHHCTEC
T ss_pred HHHHHHHHHcCCCHHHHhhc
Confidence 34578999999999999863
No 5
>PF02773 S-AdoMet_synt_C: S-adenosylmethionine synthetase, C-terminal domain; InterPro: IPR022630 The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. This entry represents the C-terminal domain of S=adenosylmethionine synthetase and is found in association with PF00438 from PFAM and PF02772 from PFAM. S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP []. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis. In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family. The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance []; GO: 0004478 methionine adenosyltransferase activity; PDB: 3IML_B 1QM4_B 1O9T_B 1O93_A 1O92_B 1O90_A 1FUG_A 1RG9_D 1XRA_A 1P7L_C ....
Probab=75.66 E-value=2.6 Score=31.14 Aligned_cols=26 Identities=12% Similarity=0.300 Sum_probs=20.4
Q ss_pred cchHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 64 SNVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
-+.+||.+-|.++|++.|..|+++|.
T Consensus 89 ~~d~~i~~~I~~~Fdl~P~~II~~L~ 114 (138)
T PF02773_consen 89 ISDEEILEIIKENFDLRPAGIIKELD 114 (138)
T ss_dssp S-HHHHHHHHHHHS--SHHHHHHHCT
T ss_pred chHHHHHHHHHHHhCCcHHHHHHHhC
Confidence 35689999999999999999999763
No 6
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=75.37 E-value=3.6 Score=25.12 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=22.7
Q ss_pred eccCccchHHHHHHhhhhhcCChhh
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~e 83 (89)
.|+...+|.+|-+.|++.+++++++
T Consensus 16 ~v~~~~tV~~lK~~i~~~~gi~~~~ 40 (74)
T cd01807 16 QVSEKESVSTLKKLVSEHLNVPEEQ 40 (74)
T ss_pred EECCCCcHHHHHHHHHHHHCCCHHH
Confidence 4678899999999999999999987
No 7
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=73.51 E-value=2 Score=28.14 Aligned_cols=20 Identities=30% Similarity=0.464 Sum_probs=13.3
Q ss_pred hHHHHHHhh----hhhcCChhhHh
Q psy16018 66 VRELYQKIA----ECYEFPAEEVS 85 (89)
Q Consensus 66 vkELY~kIa----e~f~i~~~eIl 85 (89)
-++||+.|+ +..+|+|+|||
T Consensus 45 K~~ly~~l~~~L~~~~gi~p~Dv~ 68 (82)
T PF14552_consen 45 KKALYRALAERLAEKLGIRPEDVM 68 (82)
T ss_dssp HHHHHHHHHHHHHHHH---GGGEE
T ss_pred HHHHHHHHHHHHHHHcCCCHHHEE
Confidence 467888887 56789999986
No 8
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=73.09 E-value=4.2 Score=24.38 Aligned_cols=22 Identities=18% Similarity=0.487 Sum_probs=19.1
Q ss_pred chHHHHHHhhhhhcCChhhHhh
Q psy16018 65 NVRELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~ 86 (89)
++.++-+.+|+.|+|+++||+.
T Consensus 1 ~~~~I~~~Va~~~~i~~~~i~s 22 (60)
T smart00760 1 TIEEIIEAVAEYFGVKPEDLKS 22 (60)
T ss_pred CHHHHHHHHHHHhCCCHHHHhc
Confidence 4678889999999999999975
No 9
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=72.74 E-value=2.5 Score=27.47 Aligned_cols=24 Identities=29% Similarity=0.416 Sum_probs=16.8
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
|+.=+++.+||++|++.++++...
T Consensus 20 ~~~~~t~~~L~~kI~~~l~~~~~~ 43 (80)
T PF11543_consen 20 VSPSSTLSDLKEKISEQLSIPDSS 43 (80)
T ss_dssp E-TTSBHHHHHHHHHHHS---TTT
T ss_pred cCCcccHHHHHHHHHHHcCCCCcc
Confidence 456678999999999999998654
No 10
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=70.86 E-value=4.4 Score=23.82 Aligned_cols=26 Identities=35% Similarity=0.335 Sum_probs=23.0
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+...+|.+|-+.|++..++|++++
T Consensus 11 ~v~~~~tV~~lK~~i~~~~~~~~~~~ 36 (69)
T PF00240_consen 11 EVDPDDTVADLKQKIAEETGIPPEQQ 36 (69)
T ss_dssp EEETTSBHHHHHHHHHHHHTSTGGGE
T ss_pred EECCCCCHHHhhhhcccccccccccc
Confidence 46678899999999999999999875
No 11
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=70.37 E-value=4.9 Score=23.84 Aligned_cols=26 Identities=12% Similarity=0.210 Sum_probs=21.6
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.++.-.+|.+|.++|++.+++|++++
T Consensus 16 ~v~~~~tV~~lK~~i~~~~g~~~~~q 41 (76)
T cd01803 16 EVEPSDTIENVKAKIQDKEGIPPDQQ 41 (76)
T ss_pred EECCcCcHHHHHHHHHHHhCCCHHHe
Confidence 35556789999999999999998764
No 12
>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=68.92 E-value=5.9 Score=23.45 Aligned_cols=29 Identities=34% Similarity=0.551 Sum_probs=20.7
Q ss_pred ccCccchHHHHHHhhhhhcCChhhHhhhc
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
++|=.++.|+-+.+++.|+++++++-+|.
T Consensus 26 ~~g~~t~~ei~~~l~~~y~~~~~~~~~dv 54 (68)
T PF05402_consen 26 LDGPRTVEEIVDALAEEYDVDPEEAEEDV 54 (68)
T ss_dssp --SSS-HHHHHHHHHHHTT--HHHHHHHH
T ss_pred ccCCCCHHHHHHHHHHHcCCCHHHHHHHH
Confidence 45557899999999999999999887663
No 13
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=66.86 E-value=5.4 Score=24.95 Aligned_cols=22 Identities=14% Similarity=0.501 Sum_probs=17.0
Q ss_pred chHHHHHHhhhhhcCChhhHhh
Q psy16018 65 NVRELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~ 86 (89)
++.++-+.+|+.|++++.||+.
T Consensus 1 t~~~Ii~~Va~~~~v~~~~i~s 22 (70)
T PF08299_consen 1 TIEDIIEAVAEYFGVSVEDIRS 22 (70)
T ss_dssp -HHHHHHHHHHHTT--HHHHHS
T ss_pred CHHHHHHHHHHHHCCCHHHHhC
Confidence 4678889999999999999984
No 14
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=66.73 E-value=4.8 Score=25.45 Aligned_cols=26 Identities=15% Similarity=0.068 Sum_probs=21.5
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+.=.+|.+|.++|++.++++++.+
T Consensus 17 ~v~~~~TV~~LK~~I~~~~~~~~~~q 42 (73)
T cd01791 17 KCNPDDTIGDLKKLIAAQTGTRPEKI 42 (73)
T ss_pred EeCCCCcHHHHHHHHHHHhCCChHHE
Confidence 44555789999999999999999864
No 15
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=66.48 E-value=7.5 Score=23.37 Aligned_cols=27 Identities=15% Similarity=0.304 Sum_probs=22.4
Q ss_pred ccCccchHHHHHHhhhhhcCChhhHhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eIl~ 86 (89)
.-||+|...++...-+.||++|.|+.+
T Consensus 54 ~~Gf~~~~~f~~~fk~~~g~tP~~~r~ 80 (81)
T PF12833_consen 54 ECGFSSQSHFSRAFKRYFGMTPSEYRK 80 (81)
T ss_dssp HTT-SSHHHHHHHHHHHHSS-HHHHHH
T ss_pred HcCCCCHHHHHHHHHHHHCcCHHHHHc
Confidence 459999999999999999999999875
No 16
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=66.32 E-value=6.3 Score=24.22 Aligned_cols=26 Identities=8% Similarity=-0.028 Sum_probs=22.4
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+.-.+|.+|-++|++.+++|+++.
T Consensus 15 ~v~~~~TV~~lK~~I~~~~gip~~~q 40 (71)
T cd01796 15 DVDPDLELENFKALCEAESGIPASQQ 40 (71)
T ss_pred EECCcCCHHHHHHHHHHHhCCCHHHe
Confidence 45667899999999999999999863
No 17
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=65.92 E-value=2.6 Score=28.85 Aligned_cols=24 Identities=33% Similarity=0.534 Sum_probs=19.6
Q ss_pred hHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 66 VRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 66 vkELY~kIae~f~i~~~eIl~~~~ 89 (89)
.|+||-.||+.|+.+++-|=|+.|
T Consensus 39 tK~LYp~IA~k~~TT~s~VERaIR 62 (106)
T PF08769_consen 39 TKELYPDIAKKYGTTPSRVERAIR 62 (106)
T ss_dssp TTTHHHHHHHHTTS-HHHHHHHHH
T ss_pred hhhHHHHHHHHHCCCHHHHHHHHH
Confidence 367999999999999998877654
No 18
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=65.74 E-value=6.9 Score=24.31 Aligned_cols=26 Identities=12% Similarity=0.029 Sum_probs=22.9
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+...+|.+|-++|++.+++|+++.
T Consensus 14 ~v~~~~TV~~lK~~I~~~~gi~~~~q 39 (70)
T cd01794 14 SVSSKDTVGQLKKQLQAAEGVDPCCQ 39 (70)
T ss_pred EECCcChHHHHHHHHHHHhCCCHHHe
Confidence 56778899999999999999998863
No 19
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=65.72 E-value=5.8 Score=24.25 Aligned_cols=26 Identities=15% Similarity=0.238 Sum_probs=22.7
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+.-.+|.++-++|++.+++|+++.
T Consensus 14 ~v~~~~tV~~lK~~i~~~~gip~~~q 39 (74)
T cd01793 14 EVTGQETVSDIKAHVAGLEGIDVEDQ 39 (74)
T ss_pred EECCcCcHHHHHHHHHhhhCCCHHHE
Confidence 45677899999999999999999874
No 20
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=65.21 E-value=6.9 Score=23.67 Aligned_cols=25 Identities=12% Similarity=0.327 Sum_probs=20.5
Q ss_pred ccCccchHHHHHHhhhhhcCChhhH
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
|+.=.+|.+|.++|++.++++++++
T Consensus 16 v~~~~TV~~lK~~I~~~~~i~~~~~ 40 (71)
T cd01808 16 IAEDASVKDFKEAVSKKFKANQEQL 40 (71)
T ss_pred ECCCChHHHHHHHHHHHhCCCHHHE
Confidence 4455689999999999999988753
No 21
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=63.56 E-value=5.9 Score=23.03 Aligned_cols=20 Identities=25% Similarity=0.346 Sum_probs=15.8
Q ss_pred HHHHHhhhhhcCChhhHhhh
Q psy16018 68 ELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl~~ 87 (89)
+.-.+||++|++++++++..
T Consensus 42 ~~l~~i~~~~~v~~~~l~~~ 61 (64)
T PF12844_consen 42 STLKKIAEALGVSLDELFDG 61 (64)
T ss_dssp HHHHHHHHHHTS-HHHHCCC
T ss_pred HHHHHHHHHhCCCHHHHhcc
Confidence 45589999999999998754
No 22
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=63.41 E-value=8.7 Score=23.46 Aligned_cols=26 Identities=15% Similarity=0.151 Sum_probs=22.1
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+.-.+|++|-++|++..+||+++.
T Consensus 14 ~v~~~~tV~~lK~~I~~~~gi~~~~q 39 (74)
T cd01810 14 EVQLTQTVATLKQQVSQRERVQADQF 39 (74)
T ss_pred EECCcChHHHHHHHHHHHhCCCHHHe
Confidence 45667899999999999999998763
No 23
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=63.36 E-value=10 Score=19.02 Aligned_cols=25 Identities=24% Similarity=0.395 Sum_probs=19.8
Q ss_pred ccCccchHHHHHHhhhhhcCChhhH
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
+..-.+++++.++|++.+++++.+.
T Consensus 14 ~~~~~tv~~l~~~i~~~~~~~~~~~ 38 (69)
T cd00196 14 VPSGTTVADLKEKLAKKLGLPPEQQ 38 (69)
T ss_pred cCCCCcHHHHHHHHHHHHCcChHHe
Confidence 3346889999999999998777653
No 24
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=62.89 E-value=8.6 Score=23.98 Aligned_cols=24 Identities=33% Similarity=0.329 Sum_probs=20.3
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
|+.=.+|.||.++|++.+++++++
T Consensus 19 v~~~~TV~~lK~~I~~~~~i~~~~ 42 (80)
T cd01792 19 LRDSMTVSELKQQIAQKIGVPAFQ 42 (80)
T ss_pred cCCCCcHHHHHHHHHHHhCCCHHH
Confidence 455678999999999999998865
No 25
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=62.31 E-value=7.5 Score=24.35 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=20.2
Q ss_pred ccCccchHHHHHHhhhhhcCChhhH
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
++.=.+|.||.++|++.+++++++.
T Consensus 18 v~~~~TV~~LK~~I~~~~~~~~~~q 42 (78)
T cd01804 18 VPPDETVEGLKKRISQRLKVPKERL 42 (78)
T ss_pred ECCcCHHHHHHHHHHHHhCCChHHE
Confidence 3444679999999999999988753
No 26
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=61.22 E-value=7.4 Score=21.04 Aligned_cols=19 Identities=26% Similarity=0.405 Sum_probs=14.4
Q ss_pred HHHHHhhhhhcCChhhHhh
Q psy16018 68 ELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl~ 86 (89)
|-...||..|+++.++|++
T Consensus 7 Dtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 7 DTLWSIAKRYGISVDELME 25 (44)
T ss_dssp --HHHHHHHTTS-HHHHHH
T ss_pred CcHHHHHhhhhhhHhHHHH
Confidence 4467899999999999986
No 27
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=60.51 E-value=8.9 Score=23.04 Aligned_cols=25 Identities=12% Similarity=0.359 Sum_probs=21.8
Q ss_pred ccCccchHHHHHHhhhhhcCChhhH
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
|+.-.+|+++-+.|++..+++++++
T Consensus 15 v~~~~tV~~lK~~i~~~~gi~~~~q 39 (70)
T cd01798 15 VDPDTDIKQLKEVVAKRQGVPPDQL 39 (70)
T ss_pred ECCCChHHHHHHHHHHHHCCCHHHe
Confidence 5577899999999999999998864
No 28
>COG3057 SeqA Negative regulator of replication initiationR [DNA replication, recombination, and repair]
Probab=60.44 E-value=6.3 Score=30.32 Aligned_cols=23 Identities=26% Similarity=0.296 Sum_probs=18.9
Q ss_pred hHHHHHHhh---hhhcCChhhHhhhc
Q psy16018 66 VRELYQKIA---ECYEFPAEEVSEDF 88 (89)
Q Consensus 66 vkELY~kIa---e~f~i~~~eIl~~~ 88 (89)
..|||+-|| .-.|=+.+||||.+
T Consensus 7 DeeLY~YIAS~T~hIGESASDILRRl 32 (181)
T COG3057 7 DEELYSYIASHTKHIGESASDILRRM 32 (181)
T ss_pred cHHHHHHHHHhhhhhcccHHHHHHHH
Confidence 579999999 45666999999964
No 29
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=59.43 E-value=11 Score=25.38 Aligned_cols=38 Identities=21% Similarity=0.232 Sum_probs=28.7
Q ss_pred ceeeeeecccCCCc-eeccCccchHHHHHHhhhhhcCChhh
Q psy16018 44 KLIFHCQLAHGSPT-GLISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 44 ~LvFh~QLAHGSpt-g~I~gF~nvkELY~kIae~f~i~~~e 83 (89)
.+.+-+. .|... =.|+...+|.+|-++|++.++||+++
T Consensus 29 ~I~Vk~l--~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~ 67 (103)
T cd01802 29 ELFIETL--TGTCFELRVSPFETVISVKAKIQRLEGIPVAQ 67 (103)
T ss_pred EEEEEcC--CCCEEEEEeCCCCcHHHHHHHHHHHhCCChHH
Confidence 4444443 35433 35889999999999999999999885
No 30
>PF07027 DUF1318: Protein of unknown function (DUF1318); InterPro: IPR008309 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=59.21 E-value=8.6 Score=26.19 Aligned_cols=20 Identities=40% Similarity=0.567 Sum_probs=17.4
Q ss_pred HHHHHHhhhhhcCChhhHhh
Q psy16018 67 RELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 67 kELY~kIae~f~i~~~eIl~ 86 (89)
+.+|+.||+.-++++++|=.
T Consensus 50 ~~~Y~~iA~~ng~t~~~V~~ 69 (95)
T PF07027_consen 50 RALYQEIAKKNGITVEQVAA 69 (95)
T ss_pred HHHHHHHHHHcCCCHHHHHH
Confidence 57999999999999988744
No 31
>PF02071 NSF: Aromatic-di-Alanine (AdAR) repeat ; InterPro: IPR000744 Regulated exocytosis of neurotransmitters and hormones, as well as intracellular traffic, requires fusion of two lipid bilayers. SNARE proteins are thought to form a protein bridge, the SNARE complex, between an incoming vesicle and the acceptor compartment. SNARE proteins contribute to the specificity of membrane fusion, implying that the mechanisms by which SNAREs are targeted to subcellular compartments are important for specific docking and fusion of vesicles. This mechanism involves a family of conserved proteins, members of which appear to function at all sites of constitutive and regulated secretion in eukaryotes []. Among them are 2 types of cytosolic protein, NSF (N-ethyl-maleimide-sensitive protein) and the SNAPs (alpha-, beta- and gamma-soluble NSF attachment proteins). The yeast vesicular fusion protein, sec17, a cytoplasmic peripheral membrane protein involved in vesicular transport between the endoplasmic reticulum and the golgi apparatus, shows a high degree of sequence similarity to the alpha-SNAP family. SNAP-25 and its non-neuronal homologue Syndet/SNAP-23 are synthesized as soluble proteins in the cytosol. Both SNAP-25 and Syndet/SNAP-23 are palmitoylated at cysteine residues clustered in a loop between two N- and C-terminal coils and palmitoylation is essential for membrane binding and plasma membrane targeting. The C-terminal and the N-terminal helices of SNAP-25, are each targeted to the plasma membrane by two distinct cysteine-rich domains and appear to regulate the availability of SNAP to form complexes with SNARE [].; GO: 0006886 intracellular protein transport
Probab=57.31 E-value=5.9 Score=18.36 Aligned_cols=10 Identities=60% Similarity=1.228 Sum_probs=8.1
Q ss_pred HHHHHhhhhh
Q psy16018 68 ELYQKIAECY 77 (89)
Q Consensus 68 ELY~kIae~f 77 (89)
+-|+++|+||
T Consensus 3 ~~y~~Aa~~y 12 (12)
T PF02071_consen 3 KCYEKAAECY 12 (12)
T ss_pred HHHHHHHhhC
Confidence 3589999987
No 32
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=57.19 E-value=10 Score=24.29 Aligned_cols=23 Identities=30% Similarity=0.642 Sum_probs=19.7
Q ss_pred cchHHHHHHhhhhhcCChhhHhh
Q psy16018 64 SNVRELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl~ 86 (89)
.+.+|+|+.|++.|+++..|.-+
T Consensus 20 ~~~~ei~~~v~~~~~ls~e~~~~ 42 (92)
T PF14338_consen 20 ASRKEIYERVAERFGLSDEERNE 42 (92)
T ss_pred cCHHHHHHHHHHHhCCCHHHHHH
Confidence 57899999999999999887544
No 33
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=56.17 E-value=8.8 Score=23.44 Aligned_cols=20 Identities=25% Similarity=0.378 Sum_probs=16.4
Q ss_pred HHHHhhhhhcCChhhHhhhc
Q psy16018 69 LYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 69 LY~kIae~f~i~~~eIl~~~ 88 (89)
..+.||+..++++.+|=+||
T Consensus 30 SS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 30 SSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHhcccC
Confidence 35789999999999999997
No 34
>PF14645 Chibby: Chibby family
Probab=55.86 E-value=29 Score=24.25 Aligned_cols=34 Identities=26% Similarity=0.221 Sum_probs=22.6
Q ss_pred Cceeee-ee--cccCCCceeccCccchHHHHHHhhhh
Q psy16018 43 PKLIFH-CQ--LAHGSPTGLISGFSNVRELYQKIAEC 76 (89)
Q Consensus 43 p~LvFh-~Q--LAHGSptg~I~gF~nvkELY~kIae~ 76 (89)
-.|||. -| -.+|+.++...+..+.++-.+.+-|-
T Consensus 50 ~~l~F~dG~W~~e~~~~~~~~~~~~~l~~~n~~L~EE 86 (116)
T PF14645_consen 50 QTLVFEDGQWTSESGSGTADGEENQRLRKENQQLEEE 86 (116)
T ss_pred eEEEEECCEEeccCCCcccchhHHHHHHHHHHHHHHH
Confidence 367882 01 34677788888888888777776643
No 35
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=55.10 E-value=15 Score=20.60 Aligned_cols=26 Identities=35% Similarity=0.372 Sum_probs=21.4
Q ss_pred eccCccchHHHHHHhhhhhcCChhhH
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+.=.+|.+|-++|++.+++++.++
T Consensus 15 ~v~~~~tv~~lk~~i~~~~~~~~~~~ 40 (64)
T smart00213 15 EVKPSDTVSELKEKIAELTGIPVEQQ 40 (64)
T ss_pred EECCCCcHHHHHHHHHHHHCCCHHHE
Confidence 45555789999999999999998753
No 36
>PHA01976 helix-turn-helix protein
Probab=54.21 E-value=12 Score=21.83 Aligned_cols=19 Identities=5% Similarity=0.127 Sum_probs=15.7
Q ss_pred HHHHHhhhhhcCChhhHhh
Q psy16018 68 ELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl~ 86 (89)
+...+||++|++++++++.
T Consensus 45 ~~l~~ia~~l~v~~~~l~~ 63 (67)
T PHA01976 45 KTLLRLADALGVTLDWLCG 63 (67)
T ss_pred HHHHHHHHHHCcCHHHHhc
Confidence 3457999999999998864
No 37
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=54.12 E-value=10 Score=22.06 Aligned_cols=18 Identities=17% Similarity=0.326 Sum_probs=12.7
Q ss_pred HHHHHhhhhhcCChhhHh
Q psy16018 68 ELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl 85 (89)
++++.+++++++|+++|.
T Consensus 23 ~it~~l~~~~~~p~~~v~ 40 (61)
T PRK02220 23 DVTAAVSKNTGAPAEHIH 40 (61)
T ss_pred HHHHHHHHHhCcChhhEE
Confidence 344455588999998875
No 38
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=54.11 E-value=16 Score=21.58 Aligned_cols=24 Identities=17% Similarity=0.331 Sum_probs=21.1
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
|+.-.+|.+|-++|++.+++|+++
T Consensus 17 v~~~~tv~~lK~~i~~~~g~~~~~ 40 (76)
T cd01806 17 IEPTDKVERIKERVEEKEGIPPQQ 40 (76)
T ss_pred ECCCCCHHHHHHHHhHhhCCChhh
Confidence 566678999999999999999985
No 39
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=53.69 E-value=13 Score=22.28 Aligned_cols=25 Identities=32% Similarity=0.325 Sum_probs=20.6
Q ss_pred ccCccchHHHHHHhhhhhcC--ChhhH
Q psy16018 60 ISGFSNVRELYQKIAECYEF--PAEEV 84 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i--~~~eI 84 (89)
++.-.+|.+|-+.|++.+++ +++++
T Consensus 17 v~~~~TV~~lK~~i~~~~~i~~~~~~q 43 (77)
T cd01805 17 VDPDDTVAELKEKIEEEKGCDYPPEQQ 43 (77)
T ss_pred ECCCCcHHHHHHHHHHhhCCCCChhHe
Confidence 45567899999999999998 87754
No 40
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=53.07 E-value=11 Score=22.47 Aligned_cols=19 Identities=32% Similarity=0.550 Sum_probs=13.3
Q ss_pred HHHHHHhhhhhcCChhhHh
Q psy16018 67 RELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 67 kELY~kIae~f~i~~~eIl 85 (89)
+++++.+++++++|+++|.
T Consensus 22 ~~it~~l~~~lg~p~~~v~ 40 (64)
T PRK01964 22 REVTEAISATLDVPKERVR 40 (64)
T ss_pred HHHHHHHHHHhCcChhhEE
Confidence 3444455588999999874
No 41
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=51.87 E-value=12 Score=21.18 Aligned_cols=18 Identities=28% Similarity=0.375 Sum_probs=13.6
Q ss_pred HHHHhhhhhcCChhhHhh
Q psy16018 69 LYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 69 LY~kIae~f~i~~~eIl~ 86 (89)
-|+.||+.++++++-|-.
T Consensus 28 s~~eIa~~l~~s~~~v~~ 45 (54)
T PF08281_consen 28 SYAEIAEILGISESTVKR 45 (54)
T ss_dssp -HHHHHHHCTS-HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHH
Confidence 689999999999987743
No 42
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=51.53 E-value=16 Score=24.02 Aligned_cols=25 Identities=40% Similarity=0.468 Sum_probs=21.7
Q ss_pred cchHHHHHHhhhhhcCChhhHhhhc
Q psy16018 64 SNVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
.|+.|+-++||+.-++|.+++.+-|
T Consensus 4 ~~~~e~i~~iA~~t~~P~e~V~~my 28 (66)
T PF12085_consen 4 DNVDEVIRSIAEETGTPAETVRRMY 28 (66)
T ss_pred ccHHHHHHHHHHHHCCCHHHHHHHH
Confidence 5899999999999999999887543
No 43
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=51.22 E-value=20 Score=21.05 Aligned_cols=24 Identities=17% Similarity=0.202 Sum_probs=20.4
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
++.=.+|.+|-++|++.+++|+++
T Consensus 16 v~~~~tv~~lK~~i~~~~gi~~~~ 39 (71)
T cd01812 16 ISSQATFGDLKKMLAPVTGVEPRD 39 (71)
T ss_pred ECCCCcHHHHHHHHHHhhCCChHH
Confidence 455578999999999999999875
No 44
>KOG3889|consensus
Probab=51.11 E-value=10 Score=31.86 Aligned_cols=37 Identities=35% Similarity=0.628 Sum_probs=29.4
Q ss_pred CCceeeeeeccc---CCCceeccCccchHHHHHHhhhhhcC
Q psy16018 42 KPKLIFHCQLAH---GSPTGLISGFSNVRELYQKIAECYEF 79 (89)
Q Consensus 42 ~p~LvFh~QLAH---GSptg~I~gF~nvkELY~kIae~f~i 79 (89)
..--|||| |.| |+-|=.|+||.-+.+|-++--|.|+|
T Consensus 202 ~GiQvfHC-l~h~gtGG~t~lVDgfy~ae~l~~~~Pe~fei 241 (371)
T KOG3889|consen 202 PGIQVFHC-LTHAGTGGDTVLVDGFYCAEKLRNESPEDFEI 241 (371)
T ss_pred CCceEEEe-ecccCCCCceEEEehHHHHHHHHhhChHhhhH
Confidence 34569999 456 44555799999999999999999885
No 45
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=50.52 E-value=5.9 Score=22.91 Aligned_cols=24 Identities=21% Similarity=0.314 Sum_probs=17.8
Q ss_pred chHHHHHHhhhhhcCChhhHhhhc
Q psy16018 65 NVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
|.+..|..||+..++++..|.+.+
T Consensus 15 d~r~s~~~la~~lglS~~~v~~Ri 38 (42)
T PF13404_consen 15 DGRRSYAELAEELGLSESTVRRRI 38 (42)
T ss_dssp -TTS-HHHHHHHHTS-HHHHHHHH
T ss_pred cCCccHHHHHHHHCcCHHHHHHHH
Confidence 345679999999999999998754
No 46
>PF01337 Barstar: Barstar (barnase inhibitor); InterPro: IPR000468 Barstar is a small single chain protein. Barnase is the extracellular ribonuclease IPR001887 from INTERPRO of Bacillus amyloliquefaciens, and barstar its specific intracellular inhibitor [, ]. Expression of barstar is necessary to counter the lethal effect of expressed active barnase. The structure of the barnase-barstar complex is known [].; PDB: 2CX6_A 1B2U_F 1A19_A 1X1U_F 1B27_E 1X1W_F 1BGS_E 1X1Y_D 1B3S_D 1B2S_D ....
Probab=50.50 E-value=14 Score=23.26 Aligned_cols=22 Identities=23% Similarity=0.534 Sum_probs=16.5
Q ss_pred ccCccchHHHHHHhhhhhcCCh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPA 81 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~ 81 (89)
..+.++..++|+.+++++++|.
T Consensus 5 g~~i~~~~~~~~~l~~~l~fP~ 26 (90)
T PF01337_consen 5 GRKIRDKEDFYDALAEALDFPD 26 (90)
T ss_dssp CCC-SSHHHHHHHHHHHTT--T
T ss_pred CCCCCCHHHHHHHHHHHcCCCc
Confidence 3578899999999999999874
No 47
>PF13647 Glyco_hydro_80: Glycosyl hydrolase family 80 of chitosanase A
Probab=50.49 E-value=8.4 Score=31.24 Aligned_cols=24 Identities=46% Similarity=0.695 Sum_probs=20.9
Q ss_pred ceeeeeecccCCCceeccCccchHH
Q psy16018 44 KLIFHCQLAHGSPTGLISGFSNVRE 68 (89)
Q Consensus 44 ~LvFh~QLAHGSptg~I~gF~nvkE 68 (89)
-|-|+.|..-|| .|.|+.|++||.
T Consensus 201 glafqvqvntgs-igsisafssvks 224 (308)
T PF13647_consen 201 GLAFQVQVNTGS-IGSISAFSSVKS 224 (308)
T ss_pred eEEEEEEecccc-ccceehhhhccc
Confidence 478999999887 699999999974
No 48
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=49.52 E-value=19 Score=22.74 Aligned_cols=24 Identities=33% Similarity=0.490 Sum_probs=20.5
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
++.-.+|.++-++|++.+++|+++
T Consensus 19 v~~~~TV~~lK~~i~~~~gi~~~~ 42 (78)
T cd01797 19 LSRLTKVEELREKIQELFNVEPEC 42 (78)
T ss_pred cCCcCcHHHHHHHHHHHhCCCHHH
Confidence 345578999999999999999875
No 49
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=48.19 E-value=17 Score=18.91 Aligned_cols=17 Identities=29% Similarity=0.343 Sum_probs=13.6
Q ss_pred HHHhhhhhcCChhhHhh
Q psy16018 70 YQKIAECYEFPAEEVSE 86 (89)
Q Consensus 70 Y~kIae~f~i~~~eIl~ 86 (89)
...||+.|+++..+|++
T Consensus 7 l~~IA~~~~~~~~~l~~ 23 (44)
T TIGR02899 7 LWKIAKKYGVDFDELIQ 23 (44)
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 45699999999888865
No 50
>COG4229 Predicted enolase-phosphatase [Energy production and conversion]
Probab=47.20 E-value=9.5 Score=30.34 Aligned_cols=44 Identities=32% Similarity=0.457 Sum_probs=32.1
Q ss_pred CCCceeeeeecccCCCceeccCccch-------HHHHHHhhhhhcCChhhHh
Q psy16018 41 SKPKLIFHCQLAHGSPTGLISGFSNV-------RELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 41 ~~p~LvFh~QLAHGSptg~I~gF~nv-------kELY~kIae~f~i~~~eIl 85 (89)
+..+|.|-|--| |-=.+.++||-+. ...|++||+..+++|.|||
T Consensus 131 ~AQkL~Fghs~a-gdL~~lfsGyfDttiG~KrE~~SY~kIa~~iGl~p~eil 181 (229)
T COG4229 131 KAQKLFFGHSDA-GDLNSLFSGYFDTTIGKKRESQSYAKIAGDIGLPPAEIL 181 (229)
T ss_pred hhHHHhhccccc-ccHHhhhcceeeccccccccchhHHHHHHhcCCCchheE
Confidence 356788877522 4445566776543 5689999999999999996
No 51
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=46.68 E-value=19 Score=21.22 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=14.1
Q ss_pred HHHHHHhhhhhcCChhhHh
Q psy16018 67 RELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 67 kELY~kIae~f~i~~~eIl 85 (89)
.+.+.+|+++|+++++++-
T Consensus 44 ~~~l~~l~~~l~~~~~~~~ 62 (64)
T PF13560_consen 44 PDTLQRLARALGVPPDERA 62 (64)
T ss_dssp HHHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHHHCcCHHHHc
Confidence 4588999999999998863
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=45.62 E-value=25 Score=18.89 Aligned_cols=22 Identities=14% Similarity=0.147 Sum_probs=18.3
Q ss_pred hHHHHHHhhhhhcCChhhHhhh
Q psy16018 66 VRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 66 vkELY~kIae~f~i~~~eIl~~ 87 (89)
..+..+++|+..+++.+++++.
T Consensus 10 ~~~~l~~~a~~~g~s~s~~ir~ 31 (39)
T PF01402_consen 10 LYERLDELAKELGRSRSELIRE 31 (39)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHHHH
Confidence 4566778889999999999875
No 53
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=45.61 E-value=21 Score=17.48 Aligned_cols=17 Identities=29% Similarity=0.448 Sum_probs=13.6
Q ss_pred HHHhhhhhcCChhhHhh
Q psy16018 70 YQKIAECYEFPAEEVSE 86 (89)
Q Consensus 70 Y~kIae~f~i~~~eIl~ 86 (89)
...||+.|+++..+|.+
T Consensus 11 ~~~ia~~~~~~~~~~~~ 27 (46)
T cd00118 11 LSSIAQRYGISVEELLK 27 (46)
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 45688889999888865
No 54
>PF14566 PTPlike_phytase: Inositol hexakisphosphate; PDB: 1U24_A 2PSZ_B 3MOZ_A 3D1H_B 2B4P_B 3D1Q_A 2B4O_A 3MMJ_B 1U25_A 1U26_B ....
Probab=45.43 E-value=8.8 Score=26.79 Aligned_cols=10 Identities=50% Similarity=0.830 Sum_probs=7.1
Q ss_pred CCceeeeeec
Q psy16018 42 KPKLIFHCQL 51 (89)
Q Consensus 42 ~p~LvFh~QL 51 (89)
..-|+||||.
T Consensus 124 ~~~l~fhC~~ 133 (149)
T PF14566_consen 124 DTWLHFHCQA 133 (149)
T ss_dssp T-EEEEE-SS
T ss_pred CCeEEEECCC
Confidence 5689999997
No 55
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=45.40 E-value=11 Score=29.22 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=21.5
Q ss_pred eeccCccchHHHHHHhhhhhc-CChhhH
Q psy16018 58 GLISGFSNVRELYQKIAECYE-FPAEEV 84 (89)
Q Consensus 58 g~I~gF~nvkELY~kIae~f~-i~~~eI 84 (89)
.+.+||.|++||-..+.+.|+ +-++|+
T Consensus 71 Ar~DGF~sreELi~~LkriYg~lr~ed~ 98 (188)
T COG2411 71 ARLDGFRSREELIEELKRIYGELRDEDI 98 (188)
T ss_pred HHhcccccHHHHHHHHHHHcCcCCCCce
Confidence 467899999999999999987 454443
No 56
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=44.88 E-value=14 Score=21.47 Aligned_cols=20 Identities=15% Similarity=0.212 Sum_probs=15.8
Q ss_pred hHHHHHHhhhhhcCChhhHh
Q psy16018 66 VRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 66 vkELY~kIae~f~i~~~eIl 85 (89)
++++++.+++++++++++|.
T Consensus 21 ~~~it~~l~~~lg~~~~~v~ 40 (63)
T TIGR00013 21 IEGVTEAMAETLGANLESIV 40 (63)
T ss_pred HHHHHHHHHHHhCCCcccEE
Confidence 46677778899999988764
No 57
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=44.03 E-value=31 Score=20.10 Aligned_cols=24 Identities=33% Similarity=0.378 Sum_probs=19.9
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
++.-.+|.+|-++|++..++++++
T Consensus 17 v~~~~tv~~lK~~i~~~~gi~~~~ 40 (72)
T cd01809 17 VEEEITVLDLKEKIAEEVGIPVEQ 40 (72)
T ss_pred ECCCCcHHHHHHHHHHHHCcCHHH
Confidence 334578999999999999998875
No 58
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=43.24 E-value=14 Score=20.63 Aligned_cols=16 Identities=25% Similarity=0.297 Sum_probs=12.4
Q ss_pred HHHHhhhhhcCChhhH
Q psy16018 69 LYQKIAECYEFPAEEV 84 (89)
Q Consensus 69 LY~kIae~f~i~~~eI 84 (89)
.-.+||++|+++++++
T Consensus 40 ~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 40 TLKKIAKALGVSPEYL 55 (55)
T ss_dssp HHHHHHHHHTSEHHHH
T ss_pred HHHHHHHHHCCCHHHC
Confidence 4467899999988764
No 59
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=42.95 E-value=18 Score=24.22 Aligned_cols=17 Identities=24% Similarity=0.483 Sum_probs=15.5
Q ss_pred chHHHHHHhhhhhcCCh
Q psy16018 65 NVRELYQKIAECYEFPA 81 (89)
Q Consensus 65 nvkELY~kIae~f~i~~ 81 (89)
+..+|++||+++|.|++
T Consensus 26 ~~~~L~~kI~~~f~l~~ 42 (91)
T cd06398 26 NMDGLREKVEELFSLSP 42 (91)
T ss_pred CHHHHHHHHHHHhCCCC
Confidence 67899999999999986
No 60
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=42.62 E-value=29 Score=25.41 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=25.2
Q ss_pred cCccchHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 61 SGFSNVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
-||+|..-.+...-+.||++|.|.-+.+|
T Consensus 274 ~GF~d~s~Fsr~Fkk~~G~sP~~yR~~~~ 302 (302)
T PRK09685 274 WGFSDSSHFSTAFKQRFGVSPGEYRRKFR 302 (302)
T ss_pred hCCCCHHHHHHHHHHHHCcCHHHHHhhcC
Confidence 68999999999899999999999877665
No 61
>PTZ00044 ubiquitin; Provisional
Probab=42.49 E-value=32 Score=20.58 Aligned_cols=25 Identities=8% Similarity=0.024 Sum_probs=21.5
Q ss_pred eccCccchHHHHHHhhhhhcCChhh
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~e 83 (89)
.++.-.+|.+|=++|++..++|+++
T Consensus 16 ~v~~~~tv~~lK~~i~~~~gi~~~~ 40 (76)
T PTZ00044 16 NFEPDNTVQQVKMALQEKEGIDVKQ 40 (76)
T ss_pred EECCCCcHHHHHHHHHHHHCCCHHH
Confidence 4566778999999999999999875
No 62
>cd05875 Ig6_hNeurofascin_like Sixth immunoglobulin (Ig)-like domain of human neurofascin (NF). Ig6_hNeurofascin_like: the sixth immunoglobulin (Ig)-like domain of human neurofascin (NF). NF belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and a cytoplasmic domain. NF has many alternatively spliced isoforms having different temporal expression patterns during development. NF participates in axon subcellular targeting and synapse formation, however little is known of the functions of the different isoforms.
Probab=41.75 E-value=16 Score=22.23 Aligned_cols=20 Identities=30% Similarity=0.587 Sum_probs=13.6
Q ss_pred eeeeeecccCCCceeccCccc
Q psy16018 45 LIFHCQLAHGSPTGLISGFSN 65 (89)
Q Consensus 45 LvFh~QLAHGSptg~I~gF~n 65 (89)
++|+|+ |.|+|+-.|.=+.|
T Consensus 1 ~~l~C~-~~G~P~P~v~W~k~ 20 (77)
T cd05875 1 IIIECE-AKGNPVPTFQWTRN 20 (77)
T ss_pred CEEEEe-ccccCCCEEEEEEC
Confidence 468887 56888777765544
No 63
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=41.45 E-value=18 Score=24.32 Aligned_cols=22 Identities=36% Similarity=0.510 Sum_probs=19.1
Q ss_pred cchHHHHHHhhhhhcCChhhHh
Q psy16018 64 SNVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl 85 (89)
-+..+|+++|++-+.+++++|.
T Consensus 21 ~~y~~L~~ki~~kLkl~~e~i~ 42 (80)
T cd06406 21 LSYATLLQKISSKLELPAEHIT 42 (80)
T ss_pred CCHHHHHHHHHHHhCCCchhcE
Confidence 3678999999999999988875
No 64
>cd05140 Barstar_AU1054-like Barstar_AU1054-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor AU1054 found in Burkholderia cenocepacia. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=40.68 E-value=25 Score=23.14 Aligned_cols=22 Identities=36% Similarity=0.729 Sum_probs=18.7
Q ss_pred ccCccchHHHHHHhhhhhcCCh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPA 81 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~ 81 (89)
.++.++-.++|+.+|++|++|.
T Consensus 5 ~~~i~~~~~l~~~l~~~l~fP~ 26 (86)
T cd05140 5 LSDITSERELHELLKECLGFPG 26 (86)
T ss_pred cccCCCHHHHHHHHHHHcCCch
Confidence 3567888999999999999874
No 65
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=40.54 E-value=39 Score=18.45 Aligned_cols=24 Identities=8% Similarity=0.133 Sum_probs=15.7
Q ss_pred CccchHHHHHHhhhhhcCChhhHhh
Q psy16018 62 GFSNVRELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 62 gF~nvkELY~kIae~f~i~~~eIl~ 86 (89)
|| |..-+.....+.+|+.|.|.++
T Consensus 19 g~-S~~~f~r~Fk~~~g~tp~~y~~ 42 (42)
T PF00165_consen 19 GF-SPSYFSRLFKKETGMTPKQYRR 42 (42)
T ss_dssp TS--HHHHHHHHHHHTSS-HHHHHH
T ss_pred CC-CHHHHHHHHHHHHCcCHHHHhC
Confidence 56 6666777777888888877653
No 66
>cd05142 Barstar Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=39.86 E-value=27 Score=23.01 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=18.1
Q ss_pred cCccchHHHHHHhhhhhcCCh
Q psy16018 61 SGFSNVRELYQKIAECYEFPA 81 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~ 81 (89)
..+++..++|+.++++|++|.
T Consensus 7 ~~i~~~~~f~~~l~~~~~~p~ 27 (87)
T cd05142 7 EEIRSIEDLHQILKKELALPE 27 (87)
T ss_pred ccCCCHHHHHHHHHHHhCCch
Confidence 467888999999999999874
No 67
>PRK06030 hypothetical protein; Provisional
Probab=39.68 E-value=29 Score=24.59 Aligned_cols=23 Identities=9% Similarity=0.200 Sum_probs=20.0
Q ss_pred cchHHHHHHhhhhhcCChhhHhh
Q psy16018 64 SNVRELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl~ 86 (89)
.++.++=+.+|+.|+|+++||+-
T Consensus 23 ~t~d~Ii~~Va~~f~I~~~di~s 45 (124)
T PRK06030 23 ELCEAVIDLLALAFGVSGAEIAS 45 (124)
T ss_pred cCHHHHHHHHHHHhCCCHHHHhC
Confidence 46788889999999999999964
No 68
>PF13350 Y_phosphatase3: Tyrosine phosphatase family; PDB: 1YWF_A 2OZ5_B.
Probab=38.33 E-value=12 Score=25.83 Aligned_cols=34 Identities=26% Similarity=0.737 Sum_probs=21.5
Q ss_pred ceeeeeecccCCC-ceeccCccchHHHHHHhhhhhcCChhhHhhhc
Q psy16018 44 KLIFHCQLAHGSP-TGLISGFSNVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 44 ~LvFh~QLAHGSp-tg~I~gF~nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
.++|||-. |-. ||.+..+ |=.+.|++.++|++||
T Consensus 126 p~l~HC~a--GKDRTG~~~al---------ll~~lGV~~~~I~~DY 160 (164)
T PF13350_consen 126 PVLFHCTA--GKDRTGVVAAL---------LLSLLGVPDEDIIADY 160 (164)
T ss_dssp -EEEE-SS--SSSHHHHHHHH---------HHHHTT--HHHHHHHH
T ss_pred cEEEECCC--CCccHHHHHHH---------HHHHcCCCHHHHHHHH
Confidence 78999984 543 5555443 4477889999999997
No 69
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=38.11 E-value=39 Score=21.44 Aligned_cols=26 Identities=4% Similarity=0.190 Sum_probs=23.0
Q ss_pred cCccchHHHHHHhhhhhcCChhhHhh
Q psy16018 61 SGFSNVRELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~~eIl~ 86 (89)
-||+|..-++...-+.||++|.+.-+
T Consensus 80 ~Gf~~~s~f~~~Fk~~~G~tP~~~r~ 105 (107)
T PRK10219 80 LGYVSQQTFSRVFRRQFDRTPSDYRH 105 (107)
T ss_pred HCCCCHHHHHHHHHHHHCcCHHHHHh
Confidence 48999999999999999999998754
No 70
>cd05141 Barstar_evA4336-like Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=37.75 E-value=31 Score=21.94 Aligned_cols=21 Identities=29% Similarity=0.653 Sum_probs=18.1
Q ss_pred ccCccchHHHHHHhhhhhcCC
Q psy16018 60 ISGFSNVRELYQKIAECYEFP 80 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~ 80 (89)
.++.++..++|+.+|++|++|
T Consensus 5 g~~i~~~~~~~~~l~~~l~fP 25 (81)
T cd05141 5 LSGIADKAALLDALAAALDFP 25 (81)
T ss_pred cccCCCHHHHHHHHHHHcCCC
Confidence 356788899999999999987
No 71
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=36.98 E-value=39 Score=19.01 Aligned_cols=23 Identities=35% Similarity=0.264 Sum_probs=19.0
Q ss_pred CccchHHHHHHhhhhhcCChhhH
Q psy16018 62 GFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 62 gF~nvkELY~kIae~f~i~~~eI 84 (89)
.-.++.+|-+.|++.++++++++
T Consensus 16 ~~~ti~~lK~~i~~~~~~~~~~~ 38 (69)
T cd01769 16 PDDTVAELKAKIAAKEGVPPEQQ 38 (69)
T ss_pred CCChHHHHHHHHHHHHCcChHHE
Confidence 34579999999999999988764
No 72
>PRK10425 DNase TatD; Provisional
Probab=36.84 E-value=37 Score=25.79 Aligned_cols=34 Identities=15% Similarity=0.060 Sum_probs=29.0
Q ss_pred CCCceeccCccchHHHHHHhhhhhcCChhhHhhh
Q psy16018 54 GSPTGLISGFSNVRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 54 GSptg~I~gF~nvkELY~kIae~f~i~~~eIl~~ 87 (89)
|.+.|+...=.++.+.+++||+..+++.+||.+.
T Consensus 214 ~~~~~~~n~P~~i~~v~~~iA~l~~~~~~~v~~~ 247 (258)
T PRK10425 214 PKPASRRNEPAFLPHILQRIAHWRGEDAAWLAAT 247 (258)
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHCcCHHHHHHH
Confidence 4556777777899999999999999999998764
No 73
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=36.72 E-value=25 Score=22.24 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=17.8
Q ss_pred chHHHHHHhhhhhcCChhhHh
Q psy16018 65 NVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl 85 (89)
.-.++|..+.+.++++|.+++
T Consensus 134 p~~~~~~~~~~~~~~~p~~~~ 154 (176)
T PF13419_consen 134 PDPDAYRRALEKLGIPPEEIL 154 (176)
T ss_dssp TSHHHHHHHHHHHTSSGGGEE
T ss_pred hHHHHHHHHHHHcCCCcceEE
Confidence 347899999999999998875
No 74
>cd05749 Ig2_Tyro3_like Second immunoglobulin (Ig)-like domain of Axl/Tyro3 receptor tyrosine kinases (RTKs). Ig2_Tyro3_like: the second immunoglobulin (Ig)-like domain in the Axl/Tyro3 family of receptor tyrosine kinases (RTKs). This family includes Axl (also known as Ark, Ufo, and Tyro7), Tyro3 (also known as Sky, Rse, Brt, Dtk, and Tif), and Mer (also known as Nyk, c-Eyk, and Tyro12). Axl/Tyro3 family receptors have an extracellular portion with two Ig-like domains followed by two fibronectin-types III (FNIII) domains, a membrane-spanning single helix, and a cytoplasmic tyrosine kinase domain. Axl, Tyro3 and Mer are widely expressed in adult tissues, though they show higher expression in the brain, in the lymphatic and vascular systems, and in the testis. Axl, Tyro3, and Mer bind the vitamin K dependent protein Gas6 with high affinity, and in doing so activate their tyrosine kinase activity. Axl/Gas6 signaling may play a part in cell adhesion processes, prevention of apoptosis, and c
Probab=36.67 E-value=23 Score=22.21 Aligned_cols=19 Identities=32% Similarity=0.488 Sum_probs=14.7
Q ss_pred CCceeeeeecccCCCce-ecc
Q psy16018 42 KPKLIFHCQLAHGSPTG-LIS 61 (89)
Q Consensus 42 ~p~LvFh~QLAHGSptg-~I~ 61 (89)
.-...|+|+ |+|.|.- .|.
T Consensus 13 G~~v~l~C~-a~G~P~P~~I~ 32 (81)
T cd05749 13 NTPFNLTCQ-AVGPPEPVEIL 32 (81)
T ss_pred CCCEEEEEE-eeeecCCeEEE
Confidence 346899999 9999976 454
No 75
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=36.48 E-value=32 Score=24.17 Aligned_cols=23 Identities=30% Similarity=0.404 Sum_probs=18.1
Q ss_pred hHHHHHHhhhhhcCChhhHhhhc
Q psy16018 66 VRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 66 vkELY~kIae~f~i~~~eIl~~~ 88 (89)
+..|-+.+|+.-+++.+||+++|
T Consensus 48 ~~~lv~a~a~~~g~~~~~~l~~f 70 (171)
T PF07700_consen 48 TYKLVEAAAEVTGISVEELLEEF 70 (171)
T ss_dssp HHHHHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH
Confidence 44566778899999999999986
No 76
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=36.07 E-value=26 Score=20.66 Aligned_cols=23 Identities=22% Similarity=0.330 Sum_probs=18.6
Q ss_pred chHHHHHHhhhhhc--CChhhHhhh
Q psy16018 65 NVRELYQKIAECYE--FPAEEVSED 87 (89)
Q Consensus 65 nvkELY~kIae~f~--i~~~eIl~~ 87 (89)
...+.|+.||+.++ +++++|.+.
T Consensus 24 ~r~~aw~~Ia~~l~~~~~~~~~~~~ 48 (85)
T PF10545_consen 24 LREEAWQEIARELGKEFSVDDCKKR 48 (85)
T ss_pred HHHHHHHHHHHHHccchhHHHHHHH
Confidence 46789999999999 888877553
No 77
>PF07836 DmpG_comm: DmpG-like communication domain; InterPro: IPR012425 This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain []. The communication domain is thought to play an important role in the heterodimerisation of the enzyme []. Members of this entry heterodimerise with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase [].; GO: 0016833 oxo-acid-lyase activity, 0019439 aromatic compound catabolic process; PDB: 1NVM_E.
Probab=35.91 E-value=36 Score=22.28 Aligned_cols=25 Identities=16% Similarity=0.244 Sum_probs=16.6
Q ss_pred ccchHHHHHHhhhhhcCChhhHhhh
Q psy16018 63 FSNVRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 63 F~nvkELY~kIae~f~i~~~eIl~~ 87 (89)
||+---.-+++|+-|++++-||+..
T Consensus 18 ySsFl~ha~raa~~ygVd~r~il~e 42 (66)
T PF07836_consen 18 YSSFLLHAERAAERYGVDPRDILVE 42 (66)
T ss_dssp -TTHHHHHHHHHHHHT--HHHHHHH
T ss_pred hHHHHHHHHHHHHHhCcCHHHHHHH
Confidence 3444455677889999999999865
No 78
>cd02984 TRX_PICOT TRX domain, PICOT (for PKC-interacting cousin of TRX) subfamily; PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT contains an N-terminal TRX-like domain, which does not contain the catalytic CXXC motif, followed by one to three glutaredoxin domains. The TRX-like domain is required for interaction with PKC theta. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli.
Probab=35.53 E-value=33 Score=20.57 Aligned_cols=29 Identities=28% Similarity=0.527 Sum_probs=22.4
Q ss_pred CCceeeeeecccCCCceeccCccchHHHHHHhh
Q psy16018 42 KPKLIFHCQLAHGSPTGLISGFSNVRELYQKIA 74 (89)
Q Consensus 42 ~p~LvFh~QLAHGSptg~I~gF~nvkELY~kIa 74 (89)
-|.++|--+ |...+++.|+ +.++|.++|+
T Consensus 69 ~Pt~~~~~~---g~~~~~~~g~-~~~~l~~~~~ 97 (97)
T cd02984 69 VPTFVFFRN---GTIVDRVSGA-DPKELAKKVE 97 (97)
T ss_pred ccEEEEEEC---CEEEEEEeCC-CHHHHHHhhC
Confidence 566777754 9999999997 6788888764
No 79
>COG4001 Predicted metal-binding protein [General function prediction only]
Probab=34.54 E-value=27 Score=24.83 Aligned_cols=24 Identities=17% Similarity=0.443 Sum_probs=20.7
Q ss_pred hHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 66 VRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 66 vkELY~kIae~f~i~~~eIl~~~~ 89 (89)
|+.+-++-|++|++...||-|.|+
T Consensus 61 vkkive~garAfgVdee~iRE~~~ 84 (102)
T COG4001 61 VKKIVERGARAFGVDEEDIREQMH 84 (102)
T ss_pred HHHHHHhcchhcCCCHHHHHHHHH
Confidence 677888999999999999988763
No 80
>cd00489 Barstar_like Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it, thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=33.45 E-value=39 Score=22.02 Aligned_cols=21 Identities=10% Similarity=0.346 Sum_probs=17.7
Q ss_pred cCccchHHHHHHhhhhhcCCh
Q psy16018 61 SGFSNVRELYQKIAECYEFPA 81 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~ 81 (89)
+..++..++|+.+|++|++|.
T Consensus 6 ~~i~~~~~f~~~~~~~l~fp~ 26 (85)
T cd00489 6 EDIADWEDFHARLKKKLGFPD 26 (85)
T ss_pred ccCCCHHHHHHHHHHHhCCcc
Confidence 456788999999999999873
No 81
>smart00386 HAT HAT (Half-A-TPR) repeats. Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Probab=33.20 E-value=39 Score=16.02 Aligned_cols=19 Identities=16% Similarity=0.406 Sum_probs=14.5
Q ss_pred CccchHHHHHHhhhhhcCC
Q psy16018 62 GFSNVRELYQKIAECYEFP 80 (89)
Q Consensus 62 gF~nvkELY~kIae~f~i~ 80 (89)
.+..++++|++.-+.+..+
T Consensus 2 ~~~~~r~i~e~~l~~~~~~ 20 (33)
T smart00386 2 DIERARKIYERALEKFPKS 20 (33)
T ss_pred cHHHHHHHHHHHHHHCCCC
Confidence 4667899999988777643
No 82
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=33.03 E-value=28 Score=20.24 Aligned_cols=16 Identities=19% Similarity=0.443 Sum_probs=13.5
Q ss_pred hhhhhcCChhhHhhhc
Q psy16018 73 IAECYEFPAEEVSEDF 88 (89)
Q Consensus 73 Iae~f~i~~~eIl~~~ 88 (89)
+|+.+++++.||++.+
T Consensus 9 lAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 9 LAKELGVPSKEIIKKL 24 (54)
T ss_dssp HHHHHSSSHHHHHHHH
T ss_pred HHHHHCcCHHHHHHHH
Confidence 5888899999998865
No 83
>PF11784 DUF3320: Protein of unknown function (DUF3320); InterPro: IPR021754 This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Probab=33.02 E-value=34 Score=20.50 Aligned_cols=21 Identities=24% Similarity=0.354 Sum_probs=15.8
Q ss_pred cCccchHHHHHHhhhhhcCCh
Q psy16018 61 SGFSNVRELYQKIAECYEFPA 81 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~ 81 (89)
||==...+|+++|++++|++-
T Consensus 24 EgPI~~~~L~~Ri~~a~G~~R 44 (52)
T PF11784_consen 24 EGPIHEDELARRIARAWGLSR 44 (52)
T ss_pred cCCccHHHHHHHHHHHcCccc
Confidence 333456789999999999853
No 84
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=32.71 E-value=44 Score=21.28 Aligned_cols=22 Identities=23% Similarity=0.369 Sum_probs=16.6
Q ss_pred cchHHHHH---------HhhhhhcCChhhHh
Q psy16018 64 SNVRELYQ---------KIAECYEFPAEEVS 85 (89)
Q Consensus 64 ~nvkELY~---------kIae~f~i~~~eIl 85 (89)
...+|||. .||+.++++++.|-
T Consensus 10 dkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 10 DKAFEIYKESNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred HHHHHHHHHhCCCccHHHHHHHHCCCHHHHH
Confidence 34456665 59999999998874
No 85
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=32.64 E-value=45 Score=21.24 Aligned_cols=28 Identities=32% Similarity=0.542 Sum_probs=24.1
Q ss_pred eccCccchHHHHHHhhhhhcCChhhHhhh
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eIl~~ 87 (89)
.|+|=.||.|+.+.+++.|+. ++++-+|
T Consensus 39 lldg~~tv~eI~~~L~~~Y~~-~e~~~~d 66 (81)
T TIGR03859 39 LCDGKRSLAEIIQELAQRFPA-AEEIEDD 66 (81)
T ss_pred HccCCCcHHHHHHHHHHHcCC-hhhHHHH
Confidence 578888999999999999999 7777655
No 86
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=32.60 E-value=40 Score=16.81 Aligned_cols=17 Identities=24% Similarity=0.325 Sum_probs=12.7
Q ss_pred HHHHHHhhhhhcCChhh
Q psy16018 67 RELYQKIAECYEFPAEE 83 (89)
Q Consensus 67 kELY~kIae~f~i~~~e 83 (89)
.+...+|++.|++++.+
T Consensus 39 ~~~~~~i~~~~~~~~~~ 55 (56)
T smart00530 39 LETLKKLAKALGVSLDE 55 (56)
T ss_pred HHHHHHHHHHhCCChhh
Confidence 34457888999998865
No 87
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=32.60 E-value=29 Score=19.64 Aligned_cols=19 Identities=11% Similarity=0.268 Sum_probs=12.9
Q ss_pred HHHHHHhhhhhcCChhhHh
Q psy16018 67 RELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 67 kELY~kIae~f~i~~~eIl 85 (89)
+++++.+++.+++++.+|.
T Consensus 21 ~~i~~~l~~~~g~~~~~v~ 39 (58)
T cd00491 21 ERVTEAVSEILGAPEATIV 39 (58)
T ss_pred HHHHHHHHHHhCcCcccEE
Confidence 4455555688888887764
No 88
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=31.67 E-value=43 Score=23.85 Aligned_cols=25 Identities=32% Similarity=0.347 Sum_probs=19.6
Q ss_pred chHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 65 NVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
|..|+...||+-.||+.++.++|++
T Consensus 101 s~~~~l~~iA~~~gLD~~~F~~d~~ 125 (176)
T PF13743_consen 101 SDEELLLEIAEELGLDVEMFKEDLH 125 (176)
T ss_dssp TSHHHHHHHHHHTT--HHHHHHHHT
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4458899999999999999999874
No 89
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.66 E-value=59 Score=21.81 Aligned_cols=27 Identities=15% Similarity=0.390 Sum_probs=23.9
Q ss_pred cCccchHHHHHHhhhhhcCChhhHhhh
Q psy16018 61 SGFSNVRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~~eIl~~ 87 (89)
-||++..-++...-+.|+++|.+.-+.
T Consensus 84 ~Gf~s~s~F~r~Fkk~~G~tP~~yR~~ 110 (127)
T PRK11511 84 YGFESQQTLTRTFKNYFDVPPHKYRMT 110 (127)
T ss_pred hCCCCHHHHHHHHHHHHCcCHHHHHHh
Confidence 599999999999999999999987543
No 90
>smart00257 LysM Lysin motif.
Probab=31.65 E-value=47 Score=15.84 Aligned_cols=17 Identities=24% Similarity=0.386 Sum_probs=12.2
Q ss_pred HHHhhhhhcCChhhHhh
Q psy16018 70 YQKIAECYEFPAEEVSE 86 (89)
Q Consensus 70 Y~kIae~f~i~~~eIl~ 86 (89)
+..||..|++++.++.+
T Consensus 10 ~~~ia~~~~~~~~~~~~ 26 (44)
T smart00257 10 LSSIARRYGISVSDLLE 26 (44)
T ss_pred HHHHHHHhCCCHHHHHH
Confidence 45678888888777653
No 91
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=31.46 E-value=55 Score=18.48 Aligned_cols=24 Identities=17% Similarity=0.265 Sum_probs=18.4
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
.-||.|...++....+.+|++|.+
T Consensus 59 ~~g~~s~~~f~r~Fk~~~g~sp~~ 82 (84)
T smart00342 59 RVGFSSQSYFSRAFKKLFGVTPSE 82 (84)
T ss_pred HhCCCChHHHHHHHHHHHCcChhh
Confidence 457777888888888888888776
No 92
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=31.43 E-value=37 Score=26.01 Aligned_cols=36 Identities=17% Similarity=0.317 Sum_probs=30.8
Q ss_pred eecccCCCceec---cCccchHHHHHHhhhhhcCChhhH
Q psy16018 49 CQLAHGSPTGLI---SGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 49 ~QLAHGSptg~I---~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.||.||.+.+-+ .||.|.+-.|....+.++.+|.+.
T Consensus 140 ~~L~~g~sv~~a~~daGf~s~s~F~~af~~~~G~~P~~~ 178 (187)
T COG2169 140 KQLRMGASVTDAQIDAGFESSSRFYDAFSKILGMTPTKF 178 (187)
T ss_pred HHHhCCCchhHHHHHhCCCChHHHHHHHHHHcCCChHHH
Confidence 478888866544 699999999999999999999876
No 93
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=31.24 E-value=59 Score=20.53 Aligned_cols=25 Identities=24% Similarity=0.267 Sum_probs=21.0
Q ss_pred eccCccchHHHHHHhhhhhcCChhh
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~e 83 (89)
.|+.-.+|.+|-++|.+.++||+++
T Consensus 18 ~v~~~~TV~~lK~kI~~~~gip~~~ 42 (75)
T cd01799 18 TVRPDMTVAQLKDKVFLDYGFPPAV 42 (75)
T ss_pred EECCCCcHHHHHHHHHHHHCcCHHH
Confidence 3455678999999999999999875
No 94
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=30.83 E-value=25 Score=20.88 Aligned_cols=18 Identities=33% Similarity=0.685 Sum_probs=14.1
Q ss_pred CccchHHHHHHhhhhhcC
Q psy16018 62 GFSNVRELYQKIAECYEF 79 (89)
Q Consensus 62 gF~nvkELY~kIae~f~i 79 (89)
||++..+|-+++.+.|.|
T Consensus 46 G~~~l~~ll~~~~~~~~i 63 (74)
T PF12872_consen 46 GFSSLSELLESLPDVVEI 63 (74)
T ss_dssp TSSSHHHHHHT-TTTEEE
T ss_pred CCCcHHHHHHhCCCeEEE
Confidence 899999999887777765
No 95
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=30.61 E-value=43 Score=18.72 Aligned_cols=19 Identities=16% Similarity=0.230 Sum_probs=15.7
Q ss_pred HHHhhhhhcCChhhHhhhc
Q psy16018 70 YQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 70 Y~kIae~f~i~~~eIl~~~ 88 (89)
++.||+.++++.+-|.+-|
T Consensus 30 ~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIF 48 (52)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 6778999999998887754
No 96
>PF11000 DUF2840: Protein of unknown function (DUF2840); InterPro: IPR021263 This bacterial family of proteins have no known function.
Probab=30.37 E-value=35 Score=25.67 Aligned_cols=29 Identities=28% Similarity=0.469 Sum_probs=25.4
Q ss_pred eccCccchHHHHHHhh--hhhcCChhhHhhh
Q psy16018 59 LISGFSNVRELYQKIA--ECYEFPAEEVSED 87 (89)
Q Consensus 59 ~I~gF~nvkELY~kIa--e~f~i~~~eIl~~ 87 (89)
+++|+.+|+...+.|- |+.||+|.|+--|
T Consensus 87 r~~Gw~kV~~VL~~IDaiEalGidp~dvaPd 117 (149)
T PF11000_consen 87 RIEGWPKVERVLQAIDAIEALGIDPADVAPD 117 (149)
T ss_pred cccCcHHHHHHHHHHhHHHHcCCChhhcChH
Confidence 5799999999999997 9999999987544
No 97
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=28.79 E-value=48 Score=21.59 Aligned_cols=24 Identities=8% Similarity=0.076 Sum_probs=20.2
Q ss_pred chHHHHHHhhhhhcCChhhHhhhc
Q psy16018 65 NVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
.+|+-...|.+.+||++++.++.|
T Consensus 12 ~lK~~a~~i~~~lGl~~s~ai~~f 35 (83)
T TIGR02384 12 ELKKEAYAVFEELGLTPSTAIRMF 35 (83)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 467778888899999999998876
No 98
>PF05157 T2SE_Nter: Type II secretion system (T2SS), protein E, N-terminal domain; InterPro: IPR007831 This domain is found at the N terminus of members of the general secretory system II protein E. Proteins in this subfamily are typically involved in Type IV pilus biogenesis (e.g. Q9X4G8 from SWISSPROT), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (e.g. Q9RF11 from SWISSPROT) [].; GO: 0005524 ATP binding, 0006810 transport; PDB: 2D27_A 2D28_C.
Probab=28.65 E-value=54 Score=20.04 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=15.6
Q ss_pred cCccchHHHHHHhhhhhcCChhhH
Q psy16018 61 SGFSNVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~~eI 84 (89)
.|+-+-+++++.+|+.++++..++
T Consensus 4 ~g~ise~~l~~~la~~~~l~~~~~ 27 (109)
T PF05157_consen 4 LGLISEDQLLEALAEQLGLPFVDL 27 (109)
T ss_dssp TT-S-HHHHHHHHHHHHT--B--G
T ss_pred CCCCCHHHHHHHHHHHhCCCeech
Confidence 467788999999999999987654
No 99
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=28.56 E-value=73 Score=19.52 Aligned_cols=24 Identities=29% Similarity=0.188 Sum_probs=20.6
Q ss_pred ccCccchHHHHHHhhhhhcCChhh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEE 83 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~e 83 (89)
++...+|.+|-++|.+..+||++.
T Consensus 14 v~~~~TV~~lK~~i~~~~gip~~~ 37 (76)
T cd01800 14 LQLSDPVSVLKVKIHEETGMPAGK 37 (76)
T ss_pred ECCCCcHHHHHHHHHHHHCCCHHH
Confidence 456678999999999999999875
No 100
>PF14109 GldH_lipo: GldH lipoprotein
Probab=28.37 E-value=14 Score=25.66 Aligned_cols=23 Identities=30% Similarity=0.563 Sum_probs=17.3
Q ss_pred ceeeeeeccc--CCCceeccCccchHH
Q psy16018 44 KLIFHCQLAH--GSPTGLISGFSNVRE 68 (89)
Q Consensus 44 ~LvFh~QLAH--GSptg~I~gF~nvkE 68 (89)
+=..+|+||. |.+.| +||++++|
T Consensus 67 ~dtl~~~Lad~~G~w~G--~G~~~~~e 91 (131)
T PF14109_consen 67 TDTLECELADPDGKWLG--KGIGDLYE 91 (131)
T ss_pred eeeEEEEEECCCCcEee--eeEeEeEE
Confidence 4578999999 66666 78887655
No 101
>PRK05250 S-adenosylmethionine synthetase; Validated
Probab=27.88 E-value=54 Score=27.77 Aligned_cols=25 Identities=4% Similarity=0.224 Sum_probs=22.4
Q ss_pred chHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 65 NVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
+..+|.+.|.+.|++.|..|+++|.
T Consensus 321 ~~~~i~~~v~~~Fdl~P~~Ii~~L~ 345 (384)
T PRK05250 321 SDEKIEEAVREVFDLRPAGIIKMLD 345 (384)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 4689999999999999999999873
No 102
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=27.25 E-value=40 Score=24.79 Aligned_cols=20 Identities=25% Similarity=0.509 Sum_probs=16.4
Q ss_pred chHHHHHHhhhhhcCChhhHh
Q psy16018 65 NVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl 85 (89)
++.|+ ++||+.|++++++++
T Consensus 50 tl~EI-~~Ia~~fgvS~d~l~ 69 (147)
T PF08667_consen 50 TLEEI-KKIAKHFGVSPDELF 69 (147)
T ss_pred CHHHH-HHHHHHhCcCHHHHH
Confidence 45555 579999999999998
No 103
>PRK11449 putative deoxyribonuclease YjjV; Provisional
Probab=26.82 E-value=60 Score=24.54 Aligned_cols=30 Identities=20% Similarity=0.288 Sum_probs=25.9
Q ss_pred eeccCccchHHHHHHhhhhhcCChhhHhhh
Q psy16018 58 GLISGFSNVRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 58 g~I~gF~nvkELY~kIae~f~i~~~eIl~~ 87 (89)
|+.....++.+.|++||+..+++++|+.+.
T Consensus 218 ~~~n~p~~~~~~~~~ia~l~~~~~~el~~~ 247 (258)
T PRK11449 218 GQPNRPEQAARVFDVLCELRPEPADEIAEV 247 (258)
T ss_pred CCCCCChHHHHHHHHHHHHHCcCHHHHHHH
Confidence 556779999999999999999999988653
No 104
>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=26.78 E-value=23 Score=20.96 Aligned_cols=20 Identities=20% Similarity=0.353 Sum_probs=15.7
Q ss_pred HHHHhh-hhhcCChhhHhhhc
Q psy16018 69 LYQKIA-ECYEFPAEEVSEDF 88 (89)
Q Consensus 69 LY~kIa-e~f~i~~~eIl~~~ 88 (89)
++|.+. ++++++|.|.+|.+
T Consensus 12 ~~Qq~~pe~l~LtpEDAvEaL 32 (35)
T PF08383_consen 12 YQQQMNPEALGLTPEDAVEAL 32 (35)
T ss_pred chhhcChhhcCCCHHHHHHHH
Confidence 456665 99999999998853
No 105
>TIGR02681 phage_pRha phage regulatory protein, rha family. Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that pRha is a phage regulatory protein.
Probab=26.77 E-value=37 Score=23.22 Aligned_cols=20 Identities=15% Similarity=0.262 Sum_probs=17.4
Q ss_pred HHHhhhhhcCChhhHhhhcC
Q psy16018 70 YQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 70 Y~kIae~f~i~~~eIl~~~~ 89 (89)
+-.|||.|+-.-.+||||+|
T Consensus 16 S~~IAe~fgK~H~~VlR~Ir 35 (108)
T TIGR02681 16 SLTMAQMFGKRHDNVIRDIK 35 (108)
T ss_pred HHHHHHHHCcchHHHHHHHH
Confidence 45699999999999999874
No 106
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=26.73 E-value=65 Score=19.11 Aligned_cols=19 Identities=11% Similarity=0.088 Sum_probs=15.4
Q ss_pred HHHHHhhhhhcCChhhHhh
Q psy16018 68 ELYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl~ 86 (89)
+...+||++|+++++.+|.
T Consensus 48 ~~~~~l~~~l~v~~~~l~~ 66 (78)
T TIGR02607 48 DMALRLAKALGTSPEFWLN 66 (78)
T ss_pred HHHHHHHHHcCCCHHHHHH
Confidence 3457999999999988775
No 107
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=26.60 E-value=58 Score=18.44 Aligned_cols=18 Identities=17% Similarity=0.217 Sum_probs=13.0
Q ss_pred HHhhhhhcCChhhHhhhc
Q psy16018 71 QKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 71 ~kIae~f~i~~~eIl~~~ 88 (89)
..||+.|+|+..-|-+-+
T Consensus 25 ~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 25 AEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 468999999988876643
No 108
>smart00482 POLAc DNA polymerase A domain.
Probab=26.42 E-value=9.4 Score=27.95 Aligned_cols=35 Identities=34% Similarity=0.520 Sum_probs=27.1
Q ss_pred ccCC-CceeccCccchHHHHHHhhh-hhcCChhhHhh
Q psy16018 52 AHGS-PTGLISGFSNVRELYQKIAE-CYEFPAEEVSE 86 (89)
Q Consensus 52 AHGS-ptg~I~gF~nvkELY~kIae-~f~i~~~eIl~ 86 (89)
||=| ....++.|.+-.++|..+|. .|+++.+||-.
T Consensus 30 A~ls~D~~l~~~~~~g~D~h~~~A~~~~g~~~~~v~~ 66 (206)
T smart00482 30 AHLSGDENLLEAFNNGGDIHSKTAAQVFGVPEEEVTK 66 (206)
T ss_pred HHHcCCHHHHHHHhcCCCHHHHHHHHHhCCChhhCCH
Confidence 4433 56778888888899999996 78999888753
No 109
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=26.33 E-value=57 Score=22.28 Aligned_cols=20 Identities=25% Similarity=0.368 Sum_probs=16.7
Q ss_pred HHHHHhhhhhcCChhhHhhh
Q psy16018 68 ELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl~~ 87 (89)
+.-.+||++|++++++++..
T Consensus 48 ~~l~kIa~aL~v~~~~L~~~ 67 (120)
T PRK13890 48 KVMEAIADALETPLPLLLES 67 (120)
T ss_pred HHHHHHHHHHCCCHHHHhcc
Confidence 45589999999999998854
No 110
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=25.95 E-value=48 Score=22.30 Aligned_cols=27 Identities=22% Similarity=0.327 Sum_probs=19.7
Q ss_pred CCceeccCcc-----chHHHHHHhhhhhcCCh
Q psy16018 55 SPTGLISGFS-----NVRELYQKIAECYEFPA 81 (89)
Q Consensus 55 Sptg~I~gF~-----nvkELY~kIae~f~i~~ 81 (89)
+|-|++.-|+ ++.||.+.||.-|++..
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~ 38 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDD 38 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCcc
Confidence 3445554443 67999999999998864
No 111
>TIGR01034 metK S-adenosylmethionine synthetase. Tandem isozymes of this S-adenosylmethionine synthetase in E. coli are designated MetK and MetX.
Probab=25.90 E-value=62 Score=27.40 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=22.7
Q ss_pred chHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 65 NVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
+..+|.+.|.+.|++.|..|+++|.
T Consensus 318 ~~~~i~~~v~~~FdlrP~~Ii~~L~ 342 (377)
T TIGR01034 318 SEEELLNVVKENFDLRPGGIIEKLD 342 (377)
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHhC
Confidence 5789999999999999999999874
No 112
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=25.61 E-value=68 Score=14.43 Aligned_cols=16 Identities=13% Similarity=0.077 Sum_probs=10.1
Q ss_pred HHHhhhhhcCChhhHh
Q psy16018 70 YQKIAECYEFPAEEVS 85 (89)
Q Consensus 70 Y~kIae~f~i~~~eIl 85 (89)
+..||+.++++..-|-
T Consensus 24 ~~~ia~~~~is~~tv~ 39 (42)
T cd00569 24 VAEIARRLGVSRSTLY 39 (42)
T ss_pred HHHHHHHHCCCHHHHH
Confidence 4566777777765543
No 113
>PF00432 Prenyltrans: Prenyltransferase and squalene oxidase repeat This Prosite family is a subset of the Pfam family.; InterPro: IPR001330 The beta subunit of the farnesyltransferases is responsible for peptide binding. Squalene-hopene cyclase is a bacterial enzyme that catalyzes the cyclization of squalene into hopene, a key step in hopanoid (triterpenoid) metabolism []. Lanosterol synthase (5.4.99.7 from EC) (oxidosqualene-lanosterol cyclase) catalyzes the cyclization of (S)-2,3-epoxysqualene to lanosterol, the initial precursor of cholesterol, steroid hormones and vitamin D in vertebrates and of ergosterol in fungi []. Cycloartenol synthase () (2,3-epoxysqualene-cycloartenol cyclase) is a plant enzyme that catalyzes the cyclization of (S)-2,3-epoxysqualene to cycloartenol.; GO: 0003824 catalytic activity; PDB: 2IEJ_B 1LD7_B 1LD8_B 2H6G_B 1TN6_B 1S63_B 1MZC_B 2H6I_B 2H6F_B 1JCQ_B ....
Probab=25.31 E-value=32 Score=19.28 Aligned_cols=31 Identities=26% Similarity=0.395 Sum_probs=24.0
Q ss_pred ceeeeeecccCCCceeccCccchHHHHHHhh
Q psy16018 44 KLIFHCQLAHGSPTGLISGFSNVRELYQKIA 74 (89)
Q Consensus 44 ~LvFh~QLAHGSptg~I~gF~nvkELY~kIa 74 (89)
+.+..||..-|+.-++.++...+.--|-.++
T Consensus 8 ~~l~~~Q~~dGGf~~~~~~~~d~~~t~~~~~ 38 (44)
T PF00432_consen 8 RFLLSCQNPDGGFGGRPGGESDTCYTYCALA 38 (44)
T ss_dssp HHHHHTBBTTSSBBSSTTSSBBHHHHHHHHH
T ss_pred HHHHHHCCCCCCCCCCCCCCCChHHHHHHHH
Confidence 4567899999999999999877766665544
No 114
>PF13518 HTH_28: Helix-turn-helix domain
Probab=25.24 E-value=59 Score=17.77 Aligned_cols=18 Identities=17% Similarity=0.194 Sum_probs=13.9
Q ss_pred HHHHhhhhhcCChhhHhh
Q psy16018 69 LYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 69 LY~kIae~f~i~~~eIl~ 86 (89)
-+..||+.|+|+...|-+
T Consensus 14 s~~~~a~~~gis~~tv~~ 31 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYR 31 (52)
T ss_pred CHHHHHHHHCCCHhHHHH
Confidence 456799999999887743
No 115
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=24.89 E-value=51 Score=22.50 Aligned_cols=21 Identities=24% Similarity=0.464 Sum_probs=16.6
Q ss_pred ccCccchHHHHHHhhhhhcCChhhHh
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eIl 85 (89)
++|| -|+.||+.+|+++.-|-
T Consensus 151 ~~g~-----s~~eIA~~lgis~~~v~ 171 (187)
T PRK12534 151 FEGI-----TYEELAARTDTPIGTVK 171 (187)
T ss_pred HcCC-----CHHHHHHHhCCChhHHH
Confidence 5677 68889999999887663
No 116
>PF05099 TerB: Tellurite resistance protein TerB; InterPro: IPR007791 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Direct interaction between DnaK and djlA is needed for the induction of the wcaABCDE operon which is involved in the synthesis of a colanic acid polysaccharide capsule. The colanic acid capsule may help the bacterium survive conditions outside the host [, ]; PDB: 2H5N_D 2JXU_A.
Probab=24.86 E-value=45 Score=21.82 Aligned_cols=21 Identities=24% Similarity=0.445 Sum_probs=14.7
Q ss_pred chHHHHHHhhhhhcCChhhHh
Q psy16018 65 NVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl 85 (89)
.-+++..+||+.++|+.+++-
T Consensus 116 ~E~~~l~~ia~~L~i~~~~~~ 136 (140)
T PF05099_consen 116 EEQEFLRRIAEALGISEEDFQ 136 (140)
T ss_dssp CHHHHHHHHHHHCTS-SS---
T ss_pred HHHHHHHHHHHHcCCCHHHHh
Confidence 456789999999999998764
No 117
>COG0600 TauC ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]
Probab=24.57 E-value=33 Score=26.68 Aligned_cols=31 Identities=10% Similarity=0.071 Sum_probs=27.6
Q ss_pred eccCccchHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
.+.|+.||.+-|-..|+.++.+.-|+++..+
T Consensus 144 t~~Gvr~v~~~~~~~ar~lgas~~~~l~~v~ 174 (258)
T COG0600 144 TLDGVRSVDPDLLELARTLGASRWQILRKVI 174 (258)
T ss_pred HHHHHHhCCHHHHHHHHHcCCCHHHHhHhhc
Confidence 4678999999999999999999999998753
No 118
>smart00595 MADF subfamily of SANT domain.
Probab=24.39 E-value=61 Score=19.86 Aligned_cols=22 Identities=27% Similarity=0.409 Sum_probs=18.5
Q ss_pred hHHHHHHhhhhhcCChhhHhhh
Q psy16018 66 VRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 66 vkELY~kIae~f~i~~~eIl~~ 87 (89)
-+++++.||+.++.+++++...
T Consensus 26 r~~aW~~Ia~~l~~~~~~~~~k 47 (89)
T smart00595 26 KRKAWEEIAEELGLSVEECKKR 47 (89)
T ss_pred HHHHHHHHHHHHCcCHHHHHHH
Confidence 4679999999999998888654
No 119
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=23.90 E-value=58 Score=19.34 Aligned_cols=23 Identities=26% Similarity=0.456 Sum_probs=17.4
Q ss_pred CccchHHHHHHhhhhhcCChhhHhhhc
Q psy16018 62 GFSNVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 62 gF~nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
|+-+++| +|+.|++|.+-|-+|+
T Consensus 13 ~~~s~~e----la~~~~VS~~TiRRDl 35 (57)
T PF08220_consen 13 GKVSVKE----LAEEFGVSEMTIRRDL 35 (57)
T ss_pred CCEEHHH----HHHHHCcCHHHHHHHH
Confidence 4455555 5788999999998886
No 120
>PRK12459 S-adenosylmethionine synthetase; Provisional
Probab=23.79 E-value=72 Score=27.06 Aligned_cols=26 Identities=15% Similarity=0.323 Sum_probs=23.0
Q ss_pred cchHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 64 SNVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
-+..+|.+.|.+.|++.|.-|+++|.
T Consensus 324 ~~~~~i~~~i~~~Fdl~P~~Ii~~L~ 349 (386)
T PRK12459 324 VSDEELTRAVREHFDLRPAGIIEKLN 349 (386)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHcC
Confidence 35788999999999999999999873
No 121
>TIGR01691 enolase-ppase 2,3-diketo-5-methylthio-1-phosphopentane phosphatase. This enzyme is the enolase-phosphatase of methionine salvage, a pathway that regenerates methionine from methylthioadenosine (MTA). Adenosylmethionine (AdoMet) is a donor of different moieties for various processes, including methylation reactions. Use of AdoMet for spermidine biosynthesis, which leads to polyamine biosynthesis, leaves MTA as a by-product that must be cleared. In Bacillus subtilis and related species, this single protein is replaced by separate enzymes with enolase and phosphatase activities.
Probab=23.78 E-value=50 Score=24.64 Aligned_cols=22 Identities=27% Similarity=0.300 Sum_probs=19.4
Q ss_pred cchHHHHHHhhhhhcCChhhHh
Q psy16018 64 SNVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl 85 (89)
-.-.+.|.+|++.++++|+|++
T Consensus 152 KP~p~~y~~i~~~lgv~p~e~l 173 (220)
T TIGR01691 152 KTEAQSYVKIAGQLGSPPREIL 173 (220)
T ss_pred CCCHHHHHHHHHHhCcChhHEE
Confidence 5567899999999999999875
No 122
>cd05895 Ig_Pro_neuregulin-1 Immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. Ig_Pro_neuregulin-1: immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. There are many NRG-1 isoforms which arise from the alternative splicing of mRNA. NRG-1 belongs to the neuregulin gene family, which is comprised of four genes. This group represents NRG-1. NRGs are signaling molecules, which participate in cell-cell interactions in the nervous system, breast, and heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. The NRG-1 protein binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. NRG-1 has multiple functions; for example, in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors; in the peripheral nervous system NRG-1 regulates process
Probab=23.56 E-value=35 Score=19.98 Aligned_cols=24 Identities=25% Similarity=0.450 Sum_probs=13.3
Q ss_pred eeeeeecccCCCceeccCccchHH
Q psy16018 45 LIFHCQLAHGSPTGLISGFSNVRE 68 (89)
Q Consensus 45 LvFh~QLAHGSptg~I~gF~nvkE 68 (89)
|+|.|+...+.|.-.|.=|-|-++
T Consensus 1 ~~L~C~a~~~~p~~~~~W~~~g~~ 24 (76)
T cd05895 1 LVLRCETVSEYPSLRFKWFKNGKE 24 (76)
T ss_pred CEEEEecccCCCCCceEEEECCcc
Confidence 567777655556555544444333
No 123
>cd03409 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III).
Probab=23.49 E-value=76 Score=19.46 Aligned_cols=26 Identities=23% Similarity=0.305 Sum_probs=13.1
Q ss_pred cccCCCceeccCccchHHHHHHhhhhh
Q psy16018 51 LAHGSPTGLISGFSNVRELYQKIAECY 77 (89)
Q Consensus 51 LAHGSptg~I~gF~nvkELY~kIae~f 77 (89)
++|||+... ..-.-+.++.+.+++.+
T Consensus 5 v~HGs~~~s-~~~~~~~~~~~~l~~~~ 30 (101)
T cd03409 5 VGHGSPYKD-PYKKDIEAQAHNLAESL 30 (101)
T ss_pred EECCCCCCc-cHHHHHHHHHHHHHHHC
Confidence 589998651 11123444445554443
No 124
>PF01026 TatD_DNase: TatD related DNase The Pfam entry finds members not in the Prosite definition.; InterPro: IPR001130 This family of proteins are related to a large superfamily of metalloenzymes []. TatD, a member of this family has been shown experimentally to be a DNase enzyme []. Allantoinase 3.5.2.5 from EC, N-isopropylammelide isopropyl amidohydrolase 3.5.1 from EC and the SCN1 protein from fission yeast belong to this family.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters; PDB: 3E2V_B 1XWY_A 3GUW_D 3RCM_A 1ZZM_A 2XIO_A 1J6O_A 2GZX_A 3IPW_A 2Y1H_A ....
Probab=23.47 E-value=80 Score=23.26 Aligned_cols=30 Identities=27% Similarity=0.252 Sum_probs=24.8
Q ss_pred eeccCccchHHHHHHhhhhhcCChhhHhhh
Q psy16018 58 GLISGFSNVRELYQKIAECYEFPAEEVSED 87 (89)
Q Consensus 58 g~I~gF~nvkELY~kIae~f~i~~~eIl~~ 87 (89)
|+...-.++.+.++.||++.+++.+|+.+-
T Consensus 216 ~~~~~p~~i~~~~~~la~~~~~~~e~~~~~ 245 (255)
T PF01026_consen 216 GKPNEPSNIPKVAQALAEIKGISLEELAQI 245 (255)
T ss_dssp TSE--GGGHHHHHHHHHHHHTSTHHHHHHH
T ss_pred CCCCChHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 467778899999999999999999998764
No 125
>PTZ00104 S-adenosylmethionine synthase; Provisional
Probab=23.43 E-value=73 Score=27.16 Aligned_cols=25 Identities=4% Similarity=0.352 Sum_probs=22.4
Q ss_pred chHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 65 NVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
+..+|.+.|.+.|++.|..|+++|.
T Consensus 337 ~~~~i~~~v~~~Fdl~P~~II~~L~ 361 (398)
T PTZ00104 337 DDEDLLEIVQKNFDLRPGDIIKELD 361 (398)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 5678999999999999999999874
No 126
>KOG4812|consensus
Probab=23.38 E-value=29 Score=28.17 Aligned_cols=65 Identities=9% Similarity=0.046 Sum_probs=41.0
Q ss_pred CCCCCCCCCCcCCCCcccccCCCCCCCCCCCCCCceeeeeecccCCCceeccCccchHHHHHHhh
Q psy16018 10 KDDHLLDNNNVGEHKSKIYNGTKSPAPVTEDSKPKLIFHCQLAHGSPTGLISGFSNVRELYQKIA 74 (89)
Q Consensus 10 k~~~~~~~~~~~~~~~~~~~g~~~~~p~~~~~~p~LvFh~QLAHGSptg~I~gF~nvkELY~kIa 74 (89)
..++.+..+--.+|++-+++-...++.....+.|+.+-|.+.-|-+-...-..+..++++|.||-
T Consensus 20 r~t~~~e~ea~~g~~q~d~~~~e~s~l~~~~~~~~~~p~q~~~q~as~~p~~~a~~~p~~~~ki~ 84 (262)
T KOG4812|consen 20 RDTQTVEGEAEIGSDQEDSIEDEGSPLAANEPAPRSVPHQLQVQLASGAPGRHAGILPPPYSKIP 84 (262)
T ss_pred cccCCCccccccCCchhhhhhhccCcccccCCCCccchHHHHHhhccCCchhhcCCCCCcccccc
Confidence 44555555555677776666666554444556667776665555554444457888889998885
No 127
>PF11343 DUF3145: Protein of unknown function (DUF3145); InterPro: IPR021491 This family of proteins with unknown function appear to be restricted to Actinobacteria.
Probab=23.24 E-value=1.1e+02 Score=23.15 Aligned_cols=63 Identities=25% Similarity=0.360 Sum_probs=38.8
Q ss_pred CCcCCCCcccccCCCCCCCCCCCCCCce-eeeeec-ccCCCceeccCcc-----------chHHHHHHhhhhhcCChhhH
Q psy16018 18 NNVGEHKSKIYNGTKSPAPVTEDSKPKL-IFHCQL-AHGSPTGLISGFS-----------NVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 18 ~~~~~~~~~~~~g~~~~~p~~~~~~p~L-vFh~QL-AHGSptg~I~gF~-----------nvkELY~kIae~f~i~~~eI 84 (89)
-||++.+|- |.++.- =+..|.| +||.|. |||. .+=+-. +-.+|...|..+.+-+=+|-
T Consensus 69 fEVTEdps~---g~DG~R---~s~tP~LGi~~a~t~a~Gd---vvv~E~rlRa~~~~a~~~~~~l~~el~~~LG~aWD~e 139 (158)
T PF11343_consen 69 FEVTEDPSP---GVDGER---WSHTPDLGIFHAQTDANGD---VVVPEDRLRAAMERARGDGEDLARELDRALGTAWDDE 139 (158)
T ss_pred EEEEeCCCC---CCCCce---EecCCCCcceeeeecCCCC---EecCHHHHHHHHHHhcCCHHHHHHHHHHHhCCchhhh
Confidence 366777776 554421 2335566 899997 2332 222222 34556667778888888898
Q ss_pred hhhcC
Q psy16018 85 SEDFR 89 (89)
Q Consensus 85 l~~~~ 89 (89)
||-||
T Consensus 140 LEpfR 144 (158)
T PF11343_consen 140 LEPFR 144 (158)
T ss_pred hcccc
Confidence 88887
No 128
>cd05876 Ig3_L1-CAM Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). Ig3_L1-CAM: third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains, five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM.
Probab=23.13 E-value=41 Score=19.69 Aligned_cols=16 Identities=38% Similarity=0.729 Sum_probs=9.3
Q ss_pred eeeeeecccCCCceecc
Q psy16018 45 LIFHCQLAHGSPTGLIS 61 (89)
Q Consensus 45 LvFh~QLAHGSptg~I~ 61 (89)
|+++|+ |+|.|.-.|.
T Consensus 1 ~~L~C~-~~G~P~P~v~ 16 (71)
T cd05876 1 LVLECI-AEGLPTPEVH 16 (71)
T ss_pred CEEEEE-eeEecCCeEE
Confidence 456665 5666665554
No 129
>TIGR02875 spore_0_A sporulation transcription factor Spo0A. Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species.
Probab=23.01 E-value=59 Score=23.10 Aligned_cols=24 Identities=38% Similarity=0.574 Sum_probs=19.2
Q ss_pred hHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 66 VRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 66 vkELY~kIae~f~i~~~eIl~~~~ 89 (89)
-++||-.||+.|+..++-|-+..|
T Consensus 189 tk~lyp~ia~~~~~~~~~ve~~~r 212 (262)
T TIGR02875 189 TKELYPAIAKKYNTTASRVERAIR 212 (262)
T ss_pred HHHHHHHHHHHcCCChHHHHHHHH
Confidence 366999999999999888776543
No 130
>PRK15044 transcriptional regulator SirC; Provisional
Probab=22.97 E-value=86 Score=25.42 Aligned_cols=29 Identities=3% Similarity=0.150 Sum_probs=25.4
Q ss_pred cCccchHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 61 SGFSNVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
-||+|+.-.+...-+.||++|.|..+.++
T Consensus 266 ~GFss~S~FsRaFKk~fG~TPseyRk~~~ 294 (295)
T PRK15044 266 CGYDTPSYFIAIFKRHFKITPLSFMRTMN 294 (295)
T ss_pred hCCCChHHHHHHHHHHHCcCHHHHHHhhc
Confidence 58999999999999999999999887663
No 131
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=22.95 E-value=70 Score=21.02 Aligned_cols=22 Identities=36% Similarity=0.304 Sum_probs=17.6
Q ss_pred CccchHHHHHHhhhhhc--CC-hhh
Q psy16018 62 GFSNVRELYQKIAECYE--FP-AEE 83 (89)
Q Consensus 62 gF~nvkELY~kIae~f~--i~-~~e 83 (89)
|=.+|.+|-++|++.++ ++ +++
T Consensus 19 ~~~TV~~LK~kI~~~~~egi~~~dq 43 (75)
T cd01815 19 GGYQVSTLKQLIAAQLPDSLPDPEL 43 (75)
T ss_pred ccCcHHHHHHHHHHhhccCCCChHH
Confidence 55789999999999974 75 665
No 132
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=22.92 E-value=88 Score=23.58 Aligned_cols=30 Identities=13% Similarity=0.189 Sum_probs=23.4
Q ss_pred ccCccchHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 60 ISGFSNVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 60 I~gF~nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
--||++..-++...-+.|+++|.+.-+.++
T Consensus 292 ~~Gf~~~s~F~r~Fk~~~G~tP~~yr~~~~ 321 (322)
T PRK09393 292 RAGFGSEESLRHHFRRRAATSPAAYRKRFG 321 (322)
T ss_pred HhCCCCHHHHHHHHHHHHCcCHHHHHHHhh
Confidence 358888888888888888888888766553
No 133
>PF10683 DBD_Tnp_Hermes: Hermes transposase DNA-binding domain ; InterPro: IPR018473 This domain confers specific DNA-binding on Hermes transposase [].; PDB: 2BW3_B.
Probab=22.63 E-value=36 Score=22.66 Aligned_cols=26 Identities=19% Similarity=0.455 Sum_probs=20.0
Q ss_pred cCccchHHHHHHhhhhhc--CChhhHhh
Q psy16018 61 SGFSNVRELYQKIAECYE--FPAEEVSE 86 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~--i~~~eIl~ 86 (89)
+||-++-..+=.|+..|| ++.+|+|-
T Consensus 37 sGfk~la~~li~IGA~yG~~V~vd~lLP 64 (68)
T PF10683_consen 37 SGFKKLAQFLINIGATYGENVNVDDLLP 64 (68)
T ss_dssp HHHHHHHHHHHHHHHHH-S-B-HHHHS-
T ss_pred ccHHHHHHHHHHHhHHhcccCCHHHcCC
Confidence 478888888889999999 89999984
No 134
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=22.50 E-value=69 Score=18.48 Aligned_cols=20 Identities=35% Similarity=0.529 Sum_probs=14.1
Q ss_pred hHHHHHHhh----hhhcCChhhHh
Q psy16018 66 VRELYQKIA----ECYEFPAEEVS 85 (89)
Q Consensus 66 vkELY~kIa----e~f~i~~~eIl 85 (89)
.++||+.|. +.|++++++|.
T Consensus 17 k~~l~~~it~~l~~~~~~p~~~v~ 40 (62)
T PRK00745 17 KRKLVEEITRVTVETLGCPPESVD 40 (62)
T ss_pred HHHHHHHHHHHHHHHcCCChhHEE
Confidence 355666665 77899988874
No 135
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=22.32 E-value=76 Score=24.71 Aligned_cols=28 Identities=11% Similarity=0.341 Sum_probs=24.7
Q ss_pred cCccchHHHHHHhhhhhcCChhhHhhhc
Q psy16018 61 SGFSNVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 61 ~gF~nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
-||+|..-.....-+.||++|.+..+.|
T Consensus 207 ~GF~s~S~Fsr~FKr~~G~TPs~yRk~~ 234 (253)
T PRK09940 207 CGYASTSYFIYAFRKHFGNSPKRVSKEY 234 (253)
T ss_pred hCCCCHHHHHHHHHHHHCcCHHHHHHHH
Confidence 4899999999999999999999987765
No 136
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=22.19 E-value=70 Score=20.79 Aligned_cols=22 Identities=27% Similarity=0.428 Sum_probs=17.5
Q ss_pred eccCccchHHHHHHhhhhhcCChhhHh
Q psy16018 59 LISGFSNVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 59 ~I~gF~nvkELY~kIae~f~i~~~eIl 85 (89)
.++|+ -|+.||+.+|+++.-|-
T Consensus 118 ~~~g~-----s~~eIA~~lgis~~tv~ 139 (154)
T TIGR02950 118 EFKEF-----SYKEIAELLNLSLAKVK 139 (154)
T ss_pred hhccC-----cHHHHHHHHCCCHHHHH
Confidence 35677 68999999999987663
No 137
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=21.80 E-value=52 Score=22.68 Aligned_cols=14 Identities=36% Similarity=0.517 Sum_probs=12.3
Q ss_pred HhhhhhcCChhhHh
Q psy16018 72 KIAECYEFPAEEVS 85 (89)
Q Consensus 72 kIae~f~i~~~eIl 85 (89)
-||++.+++|.||-
T Consensus 52 iIA~algv~P~eIW 65 (82)
T COG3423 52 IIADALGVPPEEIW 65 (82)
T ss_pred HHHHHhCCCHHHhC
Confidence 48999999999984
No 138
>PF03517 Voldacs: Regulator of volume decrease after cellular swelling; InterPro: IPR003521 The nucleotide-sensitive chloride conductance regulatory protein (ICln) is found ubiquitously in mammalian (and other) cell types and is postulated to play a critical role in cell volume regulation. Initial studies proposed that ICln was itself a swelling-activated anion channel; however, further studies demonstrated that it is localised primarily to the cell cytoplasm. It has therefore been postulated that activation of cell volume regulation may involve reversible translocation of ICln from the cytoplasm, and its insertion into the plasma membrane. It is not resolved whether the anionic channel involved in cell volume regulation after cell-swelling comprises one or more subunits, and if it does, whether ICln is in fact one of them [].; GO: 0006821 chloride transport, 0006884 cell volume homeostasis; PDB: 1ZYI_A.
Probab=21.62 E-value=58 Score=22.58 Aligned_cols=20 Identities=20% Similarity=0.559 Sum_probs=12.7
Q ss_pred chHHHHHHhhhhhcCChhhH
Q psy16018 65 NVRELYQKIAECYEFPAEEV 84 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eI 84 (89)
.+.++|+.|++|..+.|+.-
T Consensus 91 ~l~~if~Als~C~~LhPD~~ 110 (135)
T PF03517_consen 91 MLDEIFEALSECQELHPDPD 110 (135)
T ss_dssp -HHHHHHHHHHHHH------
T ss_pred HHHHHHHHHHHHHHhCCCCc
Confidence 39999999999999977654
No 139
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=21.59 E-value=83 Score=20.55 Aligned_cols=18 Identities=33% Similarity=0.385 Sum_probs=15.5
Q ss_pred HHHHHhhhhhcCChhhHh
Q psy16018 68 ELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 68 ELY~kIae~f~i~~~eIl 85 (89)
+|=-+||.+|+.+.+||-
T Consensus 44 ~La~kia~~f~~~iedIF 61 (68)
T COG1476 44 ELALKIARVFGKTIEDIF 61 (68)
T ss_pred HHHHHHHHHhCCCHHHHH
Confidence 467799999999999985
No 140
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.48 E-value=81 Score=16.65 Aligned_cols=17 Identities=24% Similarity=0.257 Sum_probs=12.8
Q ss_pred HHHHhhhhhcCChhhHh
Q psy16018 69 LYQKIAECYEFPAEEVS 85 (89)
Q Consensus 69 LY~kIae~f~i~~~eIl 85 (89)
-++.||+.++++..-|-
T Consensus 20 s~~eia~~l~is~~tv~ 36 (58)
T smart00421 20 TNKEIAERLGISEKTVK 36 (58)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 56788888888877654
No 141
>PF08598 Sds3: Sds3-like; InterPro: IPR013907 Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins []. This entry represents the conserved region found in Sds3, Dep1 and BRMS1-homologue p40 proteins. ; PDB: 2XUS_A.
Probab=21.32 E-value=31 Score=24.55 Aligned_cols=28 Identities=32% Similarity=0.635 Sum_probs=0.0
Q ss_pred CCCceeccCccchHHHHHHhhhhhcCChhhHhhhcC
Q psy16018 54 GSPTGLISGFSNVRELYQKIAECYEFPAEEVSEDFR 89 (89)
Q Consensus 54 GSptg~I~gF~nvkELY~kIae~f~i~~~eIl~~~~ 89 (89)
+|+.-.| ||.+... ++.++++||++|+.
T Consensus 176 ~~~~~~~-~~pa~~~-------~~~l~~~eI~eDl~ 203 (205)
T PF08598_consen 176 SGPAPYI-GFPAAPN-------VYMLREEEIEEDLE 203 (205)
T ss_dssp ------------------------------------
T ss_pred cccCCcc-cchhhhh-------ccCCCHHHHHHHHH
Confidence 4544555 7766666 55599999999974
No 142
>PF10542 Vitelline_membr: Vitelline membrane cysteine-rich region; InterPro: IPR013135 In Drosophila melanogaster (Fruit fly) the vitelline membrane (VM) is the first layer of the eggshell produced by the follicular epithelium. It is composed of at least four different proteins. VM proteins are similarly organised with a central highly conserved 38-amino acid domain which is flanked by unrelated regions. Since the surrounding regions have diverged significantly, it is possible that the VM domain is of key importance in VM protein structure [, ]. The VM domain contains three highly conserved cysteines.
Probab=21.13 E-value=69 Score=19.30 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=9.8
Q ss_pred CCCCCceeeeeec
Q psy16018 39 EDSKPKLIFHCQL 51 (89)
Q Consensus 39 ~~~~p~LvFh~QL 51 (89)
|.+.-..||.||-
T Consensus 5 PpCpknY~FSCqp 17 (38)
T PF10542_consen 5 PPCPKNYVFSCQP 17 (38)
T ss_pred CCCCcceeEeccc
Confidence 4456689999993
No 143
>COG3384 Aromatic ring-opening dioxygenase, catalytic LigB subunit related enzyme [Amino acid transport and metabolism]
Probab=21.02 E-value=51 Score=26.64 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=19.8
Q ss_pred eeecccCCCceeccCccchHHHHHHhh
Q psy16018 48 HCQLAHGSPTGLISGFSNVRELYQKIA 74 (89)
Q Consensus 48 h~QLAHGSptg~I~gF~nvkELY~kIa 74 (89)
--=|+||||+=.++. +...+..+.|+
T Consensus 11 ~LflshgsP~~~~~~-n~~~~~l~~lG 36 (268)
T COG3384 11 ALFLSHGSPMLALED-NAATRGLRELG 36 (268)
T ss_pred ceeecCCCcccccCc-cHHHHHHHHHH
Confidence 345899999988887 66666777777
No 144
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=20.91 E-value=84 Score=16.82 Aligned_cols=18 Identities=17% Similarity=0.244 Sum_probs=13.5
Q ss_pred HHHHhhhhhcCChhhHhh
Q psy16018 69 LYQKIAECYEFPAEEVSE 86 (89)
Q Consensus 69 LY~kIae~f~i~~~eIl~ 86 (89)
-++.||+.++++..-|-.
T Consensus 17 s~~eia~~l~~s~~tv~~ 34 (57)
T cd06170 17 TNKEIADILGISEKTVKT 34 (57)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 467888888888876643
No 145
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=20.86 E-value=69 Score=25.55 Aligned_cols=18 Identities=39% Similarity=0.831 Sum_probs=14.7
Q ss_pred cCCCceeccCccchHHHHHHhhhh
Q psy16018 53 HGSPTGLISGFSNVRELYQKIAEC 76 (89)
Q Consensus 53 HGSptg~I~gF~nvkELY~kIae~ 76 (89)
.|-++| ++++||..|||-
T Consensus 51 ~gDedg------~lRNl~erlae~ 68 (227)
T COG4031 51 RGDEDG------SLRNLYERLAER 68 (227)
T ss_pred cCCCcc------hHHHHHHHHHHH
Confidence 499988 678899999953
No 146
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.84 E-value=26 Score=19.99 Aligned_cols=24 Identities=17% Similarity=0.117 Sum_probs=14.7
Q ss_pred chHHHHHHhhhhhcCChhhHhhhc
Q psy16018 65 NVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 65 nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
+--.-+..||+.++.+++=|-+.+
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHHHH
Confidence 333467889999999998886653
No 147
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=20.72 E-value=97 Score=18.24 Aligned_cols=31 Identities=26% Similarity=0.374 Sum_probs=26.1
Q ss_pred CCceeeeeecccCCCceeccCccchHHHHHHhhh
Q psy16018 42 KPKLIFHCQLAHGSPTGLISGFSNVRELYQKIAE 75 (89)
Q Consensus 42 ~p~LvFh~QLAHGSptg~I~gF~nvkELY~kIae 75 (89)
-|.++|... |....++.|..+..+|.+-|.+
T Consensus 72 ~Pt~~~~~~---g~~~~~~~g~~~~~~l~~~i~~ 102 (103)
T PF00085_consen 72 VPTIIFFKN---GKEVKRYNGPRNAESLIEFIEK 102 (103)
T ss_dssp SSEEEEEET---TEEEEEEESSSSHHHHHHHHHH
T ss_pred CCEEEEEEC---CcEEEEEECCCCHHHHHHHHHc
Confidence 578888877 8888999999999999887754
No 148
>PF14330 DUF4387: Domain of unknown function (DUF4387)
Probab=20.71 E-value=47 Score=23.16 Aligned_cols=16 Identities=25% Similarity=0.445 Sum_probs=12.8
Q ss_pred HHhhhhhcCChhhHhh
Q psy16018 71 QKIAECYEFPAEEVSE 86 (89)
Q Consensus 71 ~kIae~f~i~~~eIl~ 86 (89)
+.||+.|++++++|+.
T Consensus 42 ~~ia~Ly~i~~~~I~~ 57 (99)
T PF14330_consen 42 ELIARLYGIDPEDIIK 57 (99)
T ss_pred HHHHHHHCCCHHHEEE
Confidence 3477889999999954
No 149
>TIGR01244 conserved hypothetical protein TIGR01244. No member of this family is characterized. The member from Xylella fastidiosa is a longer protein with an N-terminal region described by this model, followed by a metallo-beta-lactamase family domain and an additional C-terminal region. Members scoring above the trusted cutoff are limited to the proteobacteria.
Probab=20.42 E-value=75 Score=21.64 Aligned_cols=34 Identities=21% Similarity=0.340 Sum_probs=22.2
Q ss_pred ceeeeeecccCCCceeccCccchHHHHHHhhhhhcCChhhHhhhc
Q psy16018 44 KLIFHCQLAHGSPTGLISGFSNVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 44 ~LvFh~QLAHGSptg~I~gF~nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
.++|||- +|.=.|+ ||.-+.-..+++.++|++..
T Consensus 88 pvL~HC~------sG~Rt~~-----l~al~~~~~g~~~~~i~~~~ 121 (135)
T TIGR01244 88 PVLAYCR------SGTRSSL-----LWGFRQAAEGVPVEEIVRRA 121 (135)
T ss_pred CEEEEcC------CChHHHH-----HHHHHHHHcCCCHHHHHHHH
Confidence 4899995 2332344 66555555678999998753
No 150
>TIGR01493 HAD-SF-IA-v2 Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid dehalogenase. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that modelling it with a single alignment is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms : (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only o
Probab=20.30 E-value=73 Score=21.18 Aligned_cols=22 Identities=14% Similarity=0.276 Sum_probs=18.1
Q ss_pred cchHHHHHHhhhhhcCChhhHh
Q psy16018 64 SNVRELYQKIAECYEFPAEEVS 85 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl 85 (89)
---.+.|..+++.++++|+|++
T Consensus 139 KP~p~~f~~~~~~~~~~p~~~l 160 (175)
T TIGR01493 139 KPDPVVYELVFDTVGLPPDRVL 160 (175)
T ss_pred CCCHHHHHHHHHHHCCCHHHeE
Confidence 3467899999999999998864
No 151
>PLN02243 S-adenosylmethionine synthase
Probab=20.27 E-value=95 Score=26.41 Aligned_cols=25 Identities=12% Similarity=0.328 Sum_probs=22.7
Q ss_pred cchHHHHHHhhhhhcCChhhHhhhc
Q psy16018 64 SNVRELYQKIAECYEFPAEEVSEDF 88 (89)
Q Consensus 64 ~nvkELY~kIae~f~i~~~eIl~~~ 88 (89)
-+..+|-+.|.+.|++.|.-|++.|
T Consensus 328 ~~d~~i~~~v~~~Fdlrp~~Ii~~L 352 (386)
T PLN02243 328 IPDKEILKIVKENFDFRPGMIAINL 352 (386)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHhc
Confidence 3678999999999999999999986
No 152
>PF10685 KGG: Stress-induced bacterial acidophilic repeat motif; InterPro: IPR019626 This repeat contains a highly conserved, characteristic sequence motif, KGG, that is recognised by plants and lower eukaryotes. Further downstream from this motif is a Walker A, nucleotide binding motif. YciG is expressed as part of a three-gene operon, yciGFE and this operon is induced by stress and is regulated by RpoS, which controls the general stress-response in E coli. YciG was shown to be important for stationary-phase resistance to thermal stress and in particular to acid stress [].
Probab=20.19 E-value=82 Score=16.77 Aligned_cols=14 Identities=21% Similarity=0.299 Sum_probs=11.8
Q ss_pred Cccc-hHHHHHHhhh
Q psy16018 62 GFSN-VRELYQKIAE 75 (89)
Q Consensus 62 gF~n-vkELY~kIae 75 (89)
||.| .+|.+..||.
T Consensus 1 ~Fa~~d~e~~~eig~ 15 (23)
T PF10685_consen 1 NFASMDPEKAREIGR 15 (23)
T ss_pred CccccCHHHHHHHHH
Confidence 6888 8999998885
No 153
>cd05874 Ig6_NrCAM Sixth immunoglobulin (Ig)-like domain of NrCAM (Ng (neuronglia) CAM-related cell adhesion molecule). Ig6_NrCAM: sixth immunoglobulin (Ig)-like domain of NrCAM (Ng (neuronglia) CAM-related cell adhesion molecule). NrCAM belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and an intracellular domain. NrCAM is primarily expressed in the nervous system.
Probab=20.05 E-value=69 Score=19.36 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=10.5
Q ss_pred eeeeeecccCCCceeccCc
Q psy16018 45 LIFHCQLAHGSPTGLISGF 63 (89)
Q Consensus 45 LvFh~QLAHGSptg~I~gF 63 (89)
++|.|+ |.|+|+-.|.=+
T Consensus 1 ~~l~C~-a~G~P~P~i~W~ 18 (77)
T cd05874 1 IVIQCE-AKGKPPPSFSWT 18 (77)
T ss_pred CEEEee-CcccCCCeEEEE
Confidence 356666 566666666433
No 154
>TIGR01068 thioredoxin thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model.
Probab=20.04 E-value=1.5e+02 Score=17.21 Aligned_cols=33 Identities=24% Similarity=0.255 Sum_probs=25.3
Q ss_pred CCCceeeeeecccCCCceeccCccchHHHHHHhhhh
Q psy16018 41 SKPKLIFHCQLAHGSPTGLISGFSNVRELYQKIAEC 76 (89)
Q Consensus 41 ~~p~LvFh~QLAHGSptg~I~gF~nvkELY~kIae~ 76 (89)
.-|.++|. + .|....++.|+.+.+++-..|.+.
T Consensus 68 ~~P~~~~~-~--~g~~~~~~~g~~~~~~l~~~l~~~ 100 (101)
T TIGR01068 68 SIPTLLLF-K--NGKEVDRSVGALPKAALKQLINKN 100 (101)
T ss_pred cCCEEEEE-e--CCcEeeeecCCCCHHHHHHHHHhh
Confidence 35678877 3 588888999999988888777653
Done!