Query psy2555
Match_columns 90
No_of_seqs 103 out of 793
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 19:13:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2555.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2555hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02538 Hydantoinase_B: Hydan 100.0 1.4E-31 3E-36 214.3 10.3 84 2-90 36-119 (527)
2 COG0146 HyuB N-methylhydantoin 100.0 4.3E-31 9.4E-36 212.7 10.2 83 3-90 38-122 (563)
3 PLN02666 5-oxoprolinase 100.0 2.4E-29 5.3E-34 216.6 10.0 84 2-90 778-861 (1275)
4 KOG1939|consensus 99.9 7.9E-25 1.7E-29 182.2 9.6 82 4-90 762-844 (1247)
5 PF10144 SMP_2: Bacterial viru 89.6 0.92 2E-05 33.3 5.0 53 5-88 88-143 (210)
6 TIGR02851 spore_V_T stage V sp 79.3 6.6 0.00014 27.9 5.3 68 5-78 71-145 (180)
7 PRK11477 carbohydrate diacid t 74.3 6.7 0.00015 30.1 4.5 67 5-89 24-94 (385)
8 PRK14061 unknown domain/lipoat 74.1 6.6 0.00014 32.9 4.7 56 5-88 88-143 (562)
9 COG0179 MhpD 2-keto-4-pentenoa 73.0 6.7 0.00014 29.7 4.1 38 30-67 208-248 (266)
10 KOG0673|consensus 72.4 4 8.6E-05 31.2 2.8 46 2-52 185-230 (293)
11 PRK06033 hypothetical protein; 69.5 6.5 0.00014 24.7 2.9 30 24-58 12-41 (83)
12 PF10114 PocR: Sensory domain 68.2 1.7 3.6E-05 29.5 -0.0 73 5-88 23-102 (173)
13 PF15072 DUF4539: Domain of un 67.3 22 0.00048 22.5 5.0 40 3-55 19-58 (86)
14 PRK11246 hypothetical protein; 61.6 17 0.00036 27.1 4.2 55 5-88 88-143 (218)
15 PF00609 DAGK_acc: Diacylglyce 57.5 8.7 0.00019 26.3 2.0 36 49-87 76-120 (161)
16 COG2127 Uncharacterized conser 57.3 6.6 0.00014 26.2 1.3 14 45-58 26-39 (107)
17 PF05651 Diacid_rec: Putative 56.3 26 0.00056 23.8 4.2 68 4-88 18-88 (135)
18 PRK08433 flagellar motor switc 56.2 13 0.00029 24.7 2.7 29 25-58 38-66 (111)
19 PRK08916 flagellar motor switc 55.3 13 0.00029 24.9 2.6 40 24-68 50-91 (116)
20 PRK08983 fliN flagellar motor 55.0 15 0.00032 25.0 2.8 30 24-58 56-85 (127)
21 PRK06788 flagellar motor switc 55.0 13 0.00029 25.0 2.6 32 23-59 38-69 (119)
22 PRK09732 hypothetical protein; 54.8 30 0.00065 23.6 4.3 68 5-87 30-111 (134)
23 PLN02994 1-aminocyclopropane-1 53.2 31 0.00066 23.7 4.2 25 33-60 129-153 (153)
24 PF05708 DUF830: Orthopoxvirus 52.6 7.5 0.00016 25.9 1.0 14 44-57 1-14 (158)
25 PRK03760 hypothetical protein; 52.5 7.2 0.00016 25.9 0.9 50 5-54 61-115 (117)
26 TIGR02754 sod_Ni_protease nick 52.3 27 0.00059 21.1 3.5 12 43-54 10-21 (90)
27 TIGR02480 fliN flagellar motor 51.8 10 0.00023 23.0 1.5 28 27-59 16-43 (77)
28 PF10584 Proteasome_A_N: Prote 50.7 3.3 7.1E-05 20.4 -0.7 14 4-17 2-15 (23)
29 TIGR02303 HpaG-C-term 4-hydrox 50.7 11 0.00024 27.9 1.7 36 29-66 191-227 (245)
30 TIGR03220 catechol_dmpE 2-oxop 50.2 26 0.00057 25.8 3.7 45 11-56 182-229 (255)
31 PF02743 Cache_1: Cache domain 48.0 15 0.00032 21.7 1.7 29 55-88 3-33 (81)
32 PRK09907 toxin MazF; Provision 48.0 16 0.00034 23.8 2.0 15 45-59 7-22 (111)
33 PF01557 FAA_hydrolase: Fumary 47.4 19 0.00042 25.5 2.6 42 13-57 144-185 (218)
34 PRK05698 fliN flagellar motor 47.2 19 0.00041 25.4 2.4 31 23-58 83-113 (155)
35 COG3726 AhpA Uncharacterized m 47.1 18 0.00039 26.8 2.3 55 5-87 88-142 (214)
36 KOG2030|consensus 46.7 26 0.00057 30.9 3.6 23 36-62 518-540 (911)
37 KOG1535|consensus 46.6 37 0.0008 25.3 3.9 38 23-62 157-194 (217)
38 TIGR02305 HpaG-N-term 4-hydrox 46.6 20 0.00044 25.5 2.5 42 13-57 139-180 (205)
39 PRK12764 hypothetical protein; 45.6 16 0.00034 29.9 2.1 33 34-66 169-204 (500)
40 PF02639 DUF188: Uncharacteriz 44.5 16 0.00034 24.8 1.6 28 25-55 32-59 (130)
41 PRK13019 clpS ATP-dependent Cl 43.9 16 0.00034 23.6 1.5 12 48-59 22-33 (94)
42 TIGR02312 HpaH 2-oxo-hepta-3-e 42.3 30 0.00064 25.9 3.0 44 11-55 193-239 (267)
43 TIGR02219 phage_NlpC_fam putat 41.8 34 0.00075 22.7 3.0 12 43-54 75-86 (134)
44 PRK11342 mhpD 2-keto-4-penteno 41.8 32 0.00069 25.5 3.1 44 12-56 187-233 (262)
45 PF02452 PemK: PemK-like prote 40.8 18 0.00039 22.2 1.4 13 46-58 1-13 (110)
46 PRK15203 4-hydroxyphenylacetat 40.7 17 0.00037 29.1 1.5 36 33-68 152-190 (429)
47 PRK10691 hypothetical protein; 40.6 29 0.00063 25.1 2.6 23 43-65 180-203 (219)
48 PF01052 SpoA: Surface present 38.4 19 0.00041 21.4 1.1 27 27-58 16-42 (77)
49 PF01555 N6_N4_Mtase: DNA meth 38.3 38 0.00083 22.9 2.8 31 25-60 171-202 (231)
50 PF02814 UreE_N: UreE urease a 37.6 22 0.00047 20.9 1.3 12 44-55 50-61 (65)
51 smart00702 P4Hc Prolyl 4-hydro 37.4 33 0.00071 23.2 2.4 27 50-78 116-148 (178)
52 PF10948 DUF2635: Protein of u 37.0 23 0.00051 20.1 1.3 13 44-56 34-46 (47)
53 PRK00033 clpS ATP-dependent Cl 36.5 24 0.00051 23.0 1.5 11 49-59 29-39 (100)
54 PRK07963 fliN flagellar motor 35.9 43 0.00094 23.0 2.7 31 23-58 64-94 (137)
55 COG4043 Preprotein translocase 35.8 28 0.0006 23.3 1.7 11 44-54 33-43 (111)
56 TIGR03218 catechol_dmpH 4-oxal 35.5 53 0.0012 24.4 3.4 48 10-59 189-239 (263)
57 PF00877 NLPC_P60: NlpC/P60 fa 35.5 9.3 0.0002 23.8 -0.6 13 43-55 50-62 (105)
58 PF14827 Cache_3: Sensory doma 35.2 48 0.001 21.1 2.8 64 7-88 42-108 (116)
59 PRK00124 hypothetical protein; 35.1 26 0.00057 24.5 1.6 13 43-55 63-75 (151)
60 PRK11524 putative methyltransf 35.0 26 0.00057 26.0 1.7 22 34-60 198-219 (284)
61 PF04968 CHORD: CHORD ; Inter 34.2 23 0.0005 21.4 1.0 8 70-77 29-36 (64)
62 PF11213 DUF3006: Protein of u 33.7 47 0.001 19.9 2.4 13 41-53 30-42 (71)
63 PF13550 Phage-tail_3: Putativ 33.6 27 0.00059 22.9 1.5 13 44-56 139-151 (164)
64 TIGR00113 queA S-adenosylmethi 33.4 25 0.00055 27.7 1.4 15 43-57 47-61 (344)
65 PTZ00414 10 kDa heat shock pro 32.4 45 0.00098 21.8 2.3 17 43-60 61-77 (100)
66 COG0309 HypE Hydrogenase matur 32.2 52 0.0011 26.0 3.0 30 45-89 46-75 (339)
67 PRK00147 queA S-adenosylmethio 32.0 28 0.0006 27.5 1.4 15 43-57 48-62 (342)
68 KOG2183|consensus 31.9 21 0.00045 29.5 0.8 41 27-67 380-438 (492)
69 cd06530 S26_SPase_I The S26 Ty 31.8 69 0.0015 18.9 3.0 11 44-54 13-23 (85)
70 cd03016 PRX_1cys Peroxiredoxin 31.2 1.2E+02 0.0026 21.3 4.5 52 6-58 119-180 (203)
71 PLN02856 fumarylacetoacetase 30.9 29 0.00062 28.2 1.4 28 30-57 329-359 (424)
72 cd04474 RPA1_DBD_A RPA1_DBD_A: 30.9 98 0.0021 19.5 3.7 38 5-54 37-74 (104)
73 PF13651 EcoRI_methylase: Aden 30.8 25 0.00054 27.8 1.0 15 45-59 133-147 (336)
74 COG0809 QueA S-adenosylmethion 30.8 30 0.00065 27.5 1.4 15 43-57 48-62 (348)
75 TIGR02228 sigpep_I_arch signal 30.7 97 0.0021 21.4 3.9 27 44-70 44-70 (158)
76 PRK10838 spr outer membrane li 30.3 47 0.001 23.9 2.3 13 43-55 127-139 (190)
77 PF13180 PDZ_2: PDZ domain; PD 30.2 30 0.00066 20.5 1.1 34 44-77 31-74 (82)
78 PRK01424 S-adenosylmethionine: 30.2 31 0.00068 27.5 1.5 18 40-57 42-59 (366)
79 PRK06933 type III secretion sy 29.9 82 0.0018 24.4 3.7 46 27-77 245-294 (308)
80 PF02938 GAD: GAD domain; Int 29.8 75 0.0016 19.8 3.0 20 31-52 63-82 (95)
81 PF02547 Queuosine_synth: Queu 29.6 24 0.00051 27.8 0.7 15 43-57 47-61 (341)
82 PF02353 CMAS: Mycolic acid cy 29.4 30 0.00066 25.9 1.2 38 4-52 30-67 (273)
83 PF12600 DUF3769: Protein of u 29.4 29 0.00064 28.4 1.2 17 43-59 20-36 (451)
84 cd04480 RPA1_DBD_A_like RPA1_D 29.3 1E+02 0.0022 18.5 3.4 36 6-53 22-57 (86)
85 PF13756 Stimulus_sens_1: Stim 29.1 43 0.00093 21.8 1.8 18 6-23 20-37 (112)
86 cd00989 PDZ_metalloprotease PD 29.0 37 0.00081 19.4 1.4 10 44-53 29-38 (79)
87 PF14811 TPD: Protein of unkno 28.8 44 0.00095 23.1 1.8 24 61-89 62-85 (139)
88 PF13403 Hint_2: Hint domain 28.7 39 0.00084 23.0 1.6 13 43-55 19-31 (147)
89 PF09147 DUF1933: Domain of un 28.6 90 0.002 22.9 3.5 26 2-27 99-127 (201)
90 PLN02164 sulfotransferase 28.4 75 0.0016 24.8 3.3 17 44-60 76-92 (346)
91 PRK08432 flagellar motor switc 28.4 59 0.0013 24.7 2.7 40 24-68 211-252 (283)
92 PLN02376 1-aminocyclopropane-1 28.4 1E+02 0.0023 24.8 4.2 28 30-60 128-155 (496)
93 PF10084 DUF2322: Uncharacteri 28.2 1E+02 0.0022 20.3 3.4 35 7-42 17-51 (100)
94 PF08874 DUF1835: Domain of un 28.0 1.2E+02 0.0027 19.3 3.8 28 30-60 9-36 (124)
95 COG3835 CdaR Sugar diacid util 27.8 73 0.0016 25.6 3.1 72 4-89 20-91 (376)
96 TIGR00523 eIF-1A eukaryotic/ar 27.5 33 0.00071 22.3 1.0 15 44-59 57-71 (99)
97 cd00991 PDZ_archaeal_metallopr 27.4 41 0.00089 19.9 1.4 10 44-53 27-36 (79)
98 cd01285 nucleoside_deaminase N 27.4 1.7E+02 0.0036 18.5 5.3 53 4-56 18-76 (109)
99 cd00990 PDZ_glycyl_aminopeptid 27.1 42 0.00091 19.4 1.3 10 44-53 29-38 (80)
100 cd00714 GFAT Glutamine amidotr 26.8 56 0.0012 23.2 2.2 51 2-52 154-214 (215)
101 PRK11479 hypothetical protein; 26.8 45 0.00097 25.5 1.7 12 43-54 63-74 (274)
102 PLN00139 hypothetical protein; 26.4 64 0.0014 24.8 2.6 21 35-55 276-298 (320)
103 PF05721 PhyH: Phytanoyl-CoA d 26.4 36 0.00079 22.4 1.1 12 44-55 183-194 (211)
104 PRK08666 5'-methylthioadenosin 26.3 40 0.00088 24.8 1.4 13 44-56 91-103 (261)
105 PRK10040 hypothetical protein; 25.7 47 0.001 19.4 1.3 12 46-57 31-42 (52)
106 TIGR00758 UDG_fam4 uracil-DNA 25.4 95 0.0021 21.4 3.1 28 26-55 42-69 (173)
107 PRK00331 glucosamine--fructose 25.3 91 0.002 25.6 3.4 52 2-54 155-217 (604)
108 COG1443 Idi Isopentenyldiphosp 25.2 49 0.0011 24.1 1.6 18 3-20 34-51 (185)
109 COG2230 Cfa Cyclopropane fatty 25.2 1.1E+02 0.0024 23.5 3.6 39 3-52 39-77 (283)
110 COG1956 GAF domain-containing 24.5 56 0.0012 23.3 1.8 34 45-78 89-127 (163)
111 COG2337 MazF Growth inhibitor 24.4 59 0.0013 21.2 1.8 15 45-59 3-18 (112)
112 PRK09216 rplM 50S ribosomal pr 24.0 1.3E+02 0.0029 20.8 3.6 39 8-56 16-60 (144)
113 CHL00159 rpl13 ribosomal prote 23.9 1.3E+02 0.0029 20.8 3.5 40 8-57 17-62 (143)
114 cd00136 PDZ PDZ domain, also c 23.9 54 0.0012 18.3 1.4 9 44-52 30-38 (70)
115 PF05257 CHAP: CHAP domain; I 23.8 49 0.0011 21.1 1.3 31 43-76 61-92 (124)
116 PF07591 PT-HINT: Pretoxin HIN 23.7 26 0.00057 23.3 0.0 18 43-60 12-29 (130)
117 cd04459 Rho_CSD Rho_CSD: Rho p 23.4 77 0.0017 19.2 2.0 17 35-53 33-49 (68)
118 TIGR01641 phageSPP1_gp7 phage 23.2 90 0.0019 19.5 2.4 27 47-73 78-108 (108)
119 smart00065 GAF Domain present 23.0 1.1E+02 0.0023 17.7 2.7 19 64-87 91-109 (149)
120 TIGR01697 PNPH-PUNA-XAPA inosi 23.0 56 0.0012 23.9 1.6 13 44-56 98-110 (248)
121 cd00992 PDZ_signaling PDZ doma 22.9 57 0.0012 18.7 1.4 10 44-53 43-52 (82)
122 COG2002 AbrB Regulators of sta 22.8 1.5E+02 0.0032 18.4 3.3 16 35-52 20-35 (89)
123 COG1671 Uncharacterized protei 22.7 56 0.0012 23.0 1.5 12 44-55 63-74 (150)
124 KOG4146|consensus 22.5 87 0.0019 20.6 2.2 36 23-58 34-76 (101)
125 TIGR02551 SpaO_YscQ type III s 22.5 52 0.0011 24.8 1.4 31 23-58 141-171 (298)
126 TIGR03633 arc_protsome_A prote 22.4 50 0.0011 23.5 1.2 17 1-17 1-17 (224)
127 COG1015 DeoB Phosphopentomutas 22.4 1.1E+02 0.0024 24.8 3.2 23 43-65 320-348 (397)
128 PF00391 PEP-utilizers: PEP-ut 22.3 35 0.00076 20.6 0.3 40 6-54 31-76 (80)
129 PF08541 ACP_syn_III_C: 3-Oxoa 22.2 1.8E+02 0.0039 17.3 3.6 11 43-53 64-74 (90)
130 PF09142 TruB_C: tRNA Pseudour 21.9 75 0.0016 18.3 1.7 14 6-19 28-41 (56)
131 PF02668 TauD: Taurine catabol 21.9 46 0.001 23.2 0.9 12 44-55 224-235 (258)
132 PF08741 YwhD: YwhD family; I 21.8 55 0.0012 23.4 1.3 28 50-77 7-38 (163)
133 PHA02813 hypothetical protein; 21.8 1.2E+02 0.0025 24.3 3.2 33 50-82 127-171 (354)
134 KOG1170|consensus 21.7 67 0.0015 28.8 2.0 36 50-88 689-730 (1099)
135 cd01674 Homoaconitase_Swivel H 21.7 1.4E+02 0.0031 20.4 3.3 32 30-61 24-59 (129)
136 PF05382 Amidase_5: Bacterioph 21.6 67 0.0015 22.2 1.7 13 44-56 75-87 (145)
137 PF01505 Vault: Major Vault Pr 21.6 55 0.0012 17.8 1.0 19 44-65 25-43 (43)
138 PRK05967 cystathionine beta-ly 21.4 1.2E+02 0.0026 24.0 3.2 29 31-62 89-117 (395)
139 PRK13699 putative methylase; P 21.1 1.3E+02 0.0028 21.7 3.2 22 34-60 153-174 (227)
140 KOG4207|consensus 21.1 1.1E+02 0.0023 23.3 2.7 29 29-60 25-53 (256)
141 PF03260 Lipoprotein_11: Lepid 20.9 1.1E+02 0.0023 23.4 2.7 20 66-90 193-212 (253)
142 PF02311 AraC_binding: AraC-li 20.9 51 0.0011 20.1 0.9 12 44-55 44-55 (136)
143 PRK08202 purine nucleoside pho 20.8 67 0.0015 24.0 1.7 14 44-57 120-133 (272)
144 PHA03200 uracil DNA glycosylas 20.8 99 0.0022 23.5 2.6 20 50-70 88-107 (255)
145 PF08918 PhoQ_Sensor: PhoQ Sen 20.8 58 0.0013 23.6 1.3 19 7-25 77-95 (180)
146 PRK06666 fliM flagellar motor 20.5 86 0.0019 23.8 2.2 26 27-57 266-291 (337)
147 PF00122 E1-E2_ATPase: E1-E2 A 20.5 57 0.0012 22.7 1.2 25 43-70 50-74 (230)
148 COG0791 Spr Cell wall-associat 20.4 85 0.0018 21.7 2.0 12 44-55 138-149 (197)
149 PF00717 Peptidase_S24: Peptid 20.3 61 0.0013 18.2 1.1 12 43-54 9-20 (70)
150 PF02721 DUF223: Domain of unk 20.3 1E+02 0.0022 19.1 2.2 19 35-53 18-36 (95)
151 PRK13261 ureE urease accessory 20.2 71 0.0015 22.0 1.6 12 44-55 55-66 (159)
152 COG3971 2-keto-4-pentenoate hy 20.1 1.5E+02 0.0032 22.8 3.4 48 8-55 185-234 (264)
153 PF11814 DUF3335: Peptidase_C3 20.1 74 0.0016 23.5 1.7 14 46-59 155-168 (207)
No 1
>PF02538 Hydantoinase_B: Hydantoinase B/oxoprolinase; InterPro: IPR003692 An appreciable fraction of the sulphur present in mammals occurs in the form of glutathione. The synthesis of glutathione and its utilization take place by the reactions of the gamma-glutamyl cycle, which include those catalysed by gamma-glutamylcysteine and glutathione synthetases, gamma-glutamyl transpeptidase, cysteinylglycinase, gamma-glutamyl cyclotransferease, and 5-oxoprolinase []. This family includes N-methylhydantoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase 3.5.2.9 from EC which catalyses the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to hydantoinase_A.; GO: 0003824 catalytic activity
Probab=99.97 E-value=1.4e-31 Score=214.33 Aligned_cols=84 Identities=42% Similarity=0.647 Sum_probs=81.2
Q ss_pred CCceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCCC
Q psy2555 2 NNFVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEE 81 (90)
Q Consensus 2 ~~d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~~ 81 (90)
++||+|+|+|++|++++|+.++|+|++++..++|.+++++.++|+|||||++||||.||+|++|+++++||||+|||
T Consensus 36 ~~D~~~aI~d~~G~~va~~~~ip~h~~~~~~~v~~~~~~~~~~i~~GDv~i~NDPy~Gg~H~~Dv~~~~PVF~~Gel--- 112 (527)
T PF02538_consen 36 AGDFSCAIFDADGRLVAQSEGIPVHVGSMPFAVKAILEYFEDGIRPGDVFITNDPYIGGTHLPDVTVVMPVFHDGEL--- 112 (527)
T ss_pred hcccceeeECCCCCeEEcCCCCcEEEechHHHHHHHHHhccCCCCCCCEEEEcCcccCCccCCccEEEEeEEeCCce---
Confidence 58999999999999999999999999999999999999887899999999999999999999999999999999988
Q ss_pred ccEEEEEeC
Q psy2555 82 GPVFFVANR 90 (90)
Q Consensus 82 ~lv~~~a~~ 90 (90)
++|++++
T Consensus 113 --v~~~~~~ 119 (527)
T PF02538_consen 113 --VGWAASR 119 (527)
T ss_pred --EEEEeee
Confidence 9999875
No 2
>COG0146 HyuB N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=99.97 E-value=4.3e-31 Score=212.71 Aligned_cols=83 Identities=48% Similarity=0.789 Sum_probs=80.2
Q ss_pred CceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCC--CCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCC
Q psy2555 3 NFVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKG--NFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVE 80 (90)
Q Consensus 3 ~d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~--~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~ 80 (90)
.||||||||++|+++||++++|+|+|+|...||.+++++.+ +|+|||||++||||.|||||||+++++|||++|+|
T Consensus 38 lD~scAI~d~~G~lVA~a~hipVHlGsM~~~vk~~i~~~~~~~~l~pGDV~~~NdPy~GgTHLpDvt~~~PvF~~~~l-- 115 (563)
T COG0146 38 LDFSCAIFDAEGNLVAQAPHIPVHLGSMSVSVKAMIRNNKENPDLEPGDVFITNDPYIGGTHLPDVTLVTPVFHDGKL-- 115 (563)
T ss_pred cceeEEEECCCCCeeccCCCCeEEecccHHHHHHHHHhhccCCCCCCCCEEEecCcccCCccCCceeEEeeeEeCCeE--
Confidence 69999999999999999999999999999999999999875 89999999999999999999999999999999987
Q ss_pred CccEEEEEeC
Q psy2555 81 EGPVFFVANR 90 (90)
Q Consensus 81 ~~lv~~~a~~ 90 (90)
+||+++|
T Consensus 116 ---i~~va~r 122 (563)
T COG0146 116 ---IGYVANR 122 (563)
T ss_pred ---EEEEEec
Confidence 9999986
No 3
>PLN02666 5-oxoprolinase
Probab=99.96 E-value=2.4e-29 Score=216.64 Aligned_cols=84 Identities=58% Similarity=1.007 Sum_probs=81.1
Q ss_pred CCceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCCC
Q psy2555 2 NNFVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEE 81 (90)
Q Consensus 2 ~~d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~~ 81 (90)
++||+|+|+|++|++++|+.++|+|+|+|..+++.++++|+++|+|||||++||||.||+|+||+++++|||++|||
T Consensus 778 ~~D~s~ai~d~~G~lva~~~~ip~hlgsm~~~v~~~l~~~~~~l~pGDV~i~NDPy~GgtHl~Dv~~~~PVF~~G~l--- 854 (1275)
T PLN02666 778 RLDFSCALFGPDGGLVANAPHVPVHLGAMSSTVRWQLEYWGENLNEGDVLVTNHPQAGGSHLPDITVITPVFRDGKI--- 854 (1275)
T ss_pred ccccceEEECCCCCeeecCCCceEEeecCHHHHHHHHHhccCCCCCCCEEEEcCCcCCCCcCCceEEEeCeEECCEE---
Confidence 58999999999999999999999999999999999999998789999999999999999999999999999999987
Q ss_pred ccEEEEEeC
Q psy2555 82 GPVFFVANR 90 (90)
Q Consensus 82 ~lv~~~a~~ 90 (90)
++|++++
T Consensus 855 --v~f~a~~ 861 (1275)
T PLN02666 855 --VFFVASR 861 (1275)
T ss_pred --EEEEEEe
Confidence 9999985
No 4
>KOG1939|consensus
Probab=99.92 E-value=7.9e-25 Score=182.16 Aligned_cols=82 Identities=65% Similarity=1.070 Sum_probs=79.8
Q ss_pred ceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCC-CCCCCc
Q psy2555 4 FVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDS-QPVEEG 82 (90)
Q Consensus 4 d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~G-el~~~~ 82 (90)
|||||||+++|.++|.++++|+|+|+|+.+|++.+++|+++|+||||+++|+|-.||+||||+|++.|||.++ ++
T Consensus 762 DfSCALF~pdGgLVANAPHvPvhLGsMqt~V~~Q~k~~~~kLk~GDVlltNHP~aGG~HLPDiTvITPvF~~~~~~---- 837 (1247)
T KOG1939|consen 762 DFSCALFSPDGGLVANAPHVPVHLGSMQTTVKWQLKHWGEKLKPGDVLLTNHPSAGGSHLPDITVITPVFDKGHEP---- 837 (1247)
T ss_pred cceeEeEcCCCCeeccCCCCceeecchHHHHHHHHHHhccCCCCCcEEEecCCCCCCccCCCceEEeeeecCCCcE----
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999988 55
Q ss_pred cEEEEEeC
Q psy2555 83 PVFFVANR 90 (90)
Q Consensus 83 lv~~~a~~ 90 (90)
+||+|+|
T Consensus 838 -vF~vAsR 844 (1247)
T KOG1939|consen 838 -VFFVASR 844 (1247)
T ss_pred -EEEEecc
Confidence 9999987
No 5
>PF10144 SMP_2: Bacterial virulence factor haemolysin; InterPro: IPR019305 This entry represents a group of bacterial proteins that are membrane proteins that effect the expression of haemolysin under anaerobic conditions [].
Probab=89.60 E-value=0.92 Score=33.27 Aligned_cols=53 Identities=21% Similarity=0.560 Sum_probs=33.7
Q ss_pred eeeEEeCCCCCeeeecCC-CceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCC--CCCCCeEEEEeeeeCCCCCCC
Q psy2555 5 VSKESFGPDGGLVSNAPH-IPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGG--SHLPDLTVITPVFIDSQPVEE 81 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g-~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg--tHl~D~~~~~PVF~~Gel~~~ 81 (90)
+.++|||.+|..+|++.. .| ++..+ + + |-|-.+. .| -++.||+.++++
T Consensus 88 ldAsIYd~~G~lLA~S~~~~~---------vr~~L---~--l--------d~~~~~~~~~q----q~VepI~~~~~~--- 138 (210)
T PF10144_consen 88 LDASIYDADGVLLAQSGESVS---------VRERL---G--L--------DGPEAGSYGRQ----QIVEPIYSDDGP--- 138 (210)
T ss_pred eEEEEECCCCCEEEEcCCCcc---------hhhhh---c--C--------CcccccccCCc----eEEEEeccCCCe---
Confidence 468999999999998642 22 23322 1 1 2222221 22 489999999977
Q ss_pred ccEEEEE
Q psy2555 82 GPVFFVA 88 (90)
Q Consensus 82 ~lv~~~a 88 (90)
+||+=
T Consensus 139 --~GflR 143 (210)
T PF10144_consen 139 --LGFLR 143 (210)
T ss_pred --eEEEE
Confidence 99963
No 6
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=79.28 E-value=6.6 Score=27.95 Aligned_cols=68 Identities=9% Similarity=0.065 Sum_probs=44.1
Q ss_pred eeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCC---CCCCCCC----CCeEEEEeeeeCCC
Q psy2555 5 VSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHP---KAGGSHL----PDLTVITPVFIDSQ 77 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDP---y~GgtHl----~D~~~~~PVF~~Ge 77 (90)
++++|.|++.=+.+.+.|---|.+. . +....++ -|+.|.+++.++- |.+.++. --..++.|++.+|+
T Consensus 71 ~aVaITDr~~ILA~~G~g~d~~~~~-~--is~~t~~---~i~~gk~~~~~~~~~~~i~c~~~~~~~l~s~ii~Pl~~~g~ 144 (180)
T TIGR02851 71 HIVLITDRDTVIAVAGVSKKEYLNK-P--ISDELED---TMEERKTVILSDTKDGPIEIIDGQEFEYTSQVIAPIIAEGD 144 (180)
T ss_pred CEEEEECCCcEEEEECCChhhcCCC-c--cCHHHHH---HHHcCCEEEecCCccceeccccCCCCCcceEEEEEEEECCe
Confidence 4788999887777677776666555 2 2222222 2677888766653 3444422 24899999999997
Q ss_pred C
Q psy2555 78 P 78 (90)
Q Consensus 78 l 78 (90)
.
T Consensus 145 v 145 (180)
T TIGR02851 145 P 145 (180)
T ss_pred E
Confidence 6
No 7
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=74.25 E-value=6.7 Score=30.13 Aligned_cols=67 Identities=12% Similarity=0.256 Sum_probs=43.6
Q ss_pred eeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCC----CCCCCCCCCeEEEEeeeeCCCCCC
Q psy2555 5 VSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHP----KAGGSHLPDLTVITPVFIDSQPVE 80 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDP----y~GgtHl~D~~~~~PVF~~Gel~~ 80 (90)
+..-|.|.+|.++|.+. |--+|+.....+.++ +.|+.+..+.- |.| +. -.+-.||+++|++
T Consensus 24 ~ninimd~~G~IIaS~d--~~Rig~~HegA~~~~-------~~~~~~~i~~~~~~~~~g-~k---~GiN~Pi~~~~~v-- 88 (385)
T PRK11477 24 TNINVMDARGRIIGSGD--RERIGELHEGALLVL-------SQGRVVDIDDAVARHLHG-VR---QGINLPLRLEGEI-- 88 (385)
T ss_pred CCeEEECCCCEEEecCC--hHHcccccHHHHHHH-------hcCCeeeecHHHHhhcCC-CC---cCceeeEEECCEE--
Confidence 45678999999998653 455777776665553 34555555543 333 21 2466899999987
Q ss_pred CccEEEEEe
Q psy2555 81 EGPVFFVAN 89 (90)
Q Consensus 81 ~~lv~~~a~ 89 (90)
+|+++.
T Consensus 89 ---iGvIgI 94 (385)
T PRK11477 89 ---VGVIGL 94 (385)
T ss_pred ---EEEEec
Confidence 988763
No 8
>PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional
Probab=74.05 E-value=6.6 Score=32.85 Aligned_cols=56 Identities=16% Similarity=0.342 Sum_probs=35.8
Q ss_pred eeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCCCccE
Q psy2555 5 VSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEEGPV 84 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~~~lv 84 (90)
+.++|||++|.++|++..- ..+|..+ + .|-|-.++ ..-.-++.|||.++.+ +
T Consensus 88 lDAsiY~~~G~lla~s~~~--------~~~r~~l---~----------l~~~~~~~--~~~qQiVePi~~~~~~-----~ 139 (562)
T PRK14061 88 LDAGVYDEQGDLIARSGES--------VEVRDRL---A----------LDGKKAGG--YFNQQIVEPIAGKNGP-----L 139 (562)
T ss_pred eeeeeecCCCCEEEecCCc--------ccHHHHh---c----------CCCcccCC--ccceeEEEEecCCCCc-----e
Confidence 4689999999999986421 1234433 2 22333321 2235689999999876 9
Q ss_pred EEEE
Q psy2555 85 FFVA 88 (90)
Q Consensus 85 ~~~a 88 (90)
||+=
T Consensus 140 GflR 143 (562)
T PRK14061 140 GYLR 143 (562)
T ss_pred EEEE
Confidence 9963
No 9
>COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=72.96 E-value=6.7 Score=29.70 Aligned_cols=38 Identities=24% Similarity=0.233 Sum_probs=26.3
Q ss_pred hHHHHHHHHHhcC--CCCCCCcEEEecCCCC-CCCCCCCeE
Q psy2555 30 MQEAVKFQIDHRK--GNFKKGSVILSNHPKA-GGSHLPDLT 67 (90)
Q Consensus 30 ~~~~v~~~~~~~~--~~l~~GDv~i~NDPy~-GgtHl~D~~ 67 (90)
|-..+..++++.. -+|+||||+.|-=|=. |-.|.-|..
T Consensus 208 Mi~~i~~lI~~lS~~~tL~pGDvI~TGTP~Gvg~l~~GD~v 248 (266)
T COG0179 208 MIFSIPELIAYLSRFMTLEPGDVILTGTPSGVGFLKPGDVV 248 (266)
T ss_pred cccCHHHHHHHHhCCcccCCCCEEEeCCCCCcccCCCCCEE
Confidence 4444555555554 4799999999999975 446777743
No 10
>KOG0673|consensus
Probab=72.41 E-value=4 Score=31.21 Aligned_cols=46 Identities=22% Similarity=0.312 Sum_probs=32.5
Q ss_pred CCceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEE
Q psy2555 2 NNFVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVIL 52 (90)
Q Consensus 2 ~~d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i 52 (90)
++..||.+|-+.|++ +.|+|..+.+.+.. ..++.+.- +++|||.+=
T Consensus 185 ~GelScq~YQrS~dm---glGVPFnIASYsLL-T~miAhv~-gl~pgdfiH 230 (293)
T KOG0673|consen 185 NGELSCQMYQRSGDM---GLGVPFNIASYSLL-TCMIAHVC-GLKPGDFIH 230 (293)
T ss_pred CCeeeehhhhhcccc---ccCccchhHHHHHH-HHHHHHHh-CCCCCceEE
Confidence 356778888887776 56889888876543 55566653 799999763
No 11
>PRK06033 hypothetical protein; Validated
Probab=69.50 E-value=6.5 Score=24.68 Aligned_cols=30 Identities=23% Similarity=0.315 Sum_probs=23.0
Q ss_pred ceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCC
Q psy2555 24 PVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKA 58 (90)
Q Consensus 24 p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~ 58 (90)
.+-+|.....++.++ +|++|||+-.|-+..
T Consensus 12 ~v~Lg~~~i~l~dlL-----~L~~GDVI~L~~~~~ 41 (83)
T PRK06033 12 MVVLGRSSMPIHQVL-----RMGRGAVIPLDATEA 41 (83)
T ss_pred EEEEecccccHHHHh-----CCCCCCEEEeCCCCC
Confidence 344677777777776 799999999987654
No 12
>PF10114 PocR: Sensory domain found in PocR; InterPro: IPR018771 This entry is thought to act as a sensory domain in histidine kinases catalysing the reaction: ATP + protein L-histidine = ADP + protein N- phospho-L-histidine.
Probab=68.20 E-value=1.7 Score=29.54 Aligned_cols=73 Identities=15% Similarity=0.239 Sum_probs=40.6
Q ss_pred eeeEEeCCCCCeeeecCCCceeecchH---H---HHHHHHHhcC-CCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCC
Q psy2555 5 VSKESFGPDGGLVSNAPHIPVHLGSMQ---E---AVKFQIDHRK-GNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQ 77 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g~p~~~g~~~---~---~v~~~~~~~~-~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Ge 77 (90)
.++.|+|.+|+.+.+..+.+-|..-+. . .++..-.... ...+.|..++.- -|..=+.+..||+.+|+
T Consensus 23 l~~~i~d~~G~~l~~~~~~~~fC~~~~~~~~~~~~C~~~~~~~~~~a~~~~~~~i~~------C~~GL~~~~~PI~~~g~ 96 (173)
T PF10114_consen 23 LSIVIVDPDGNPLTQPSNFCPFCKLIRSSPEGRERCRESDRRLAEQAMKKGEPYIYR------CHAGLVDIAVPIIVDGE 96 (173)
T ss_pred CcEEEEeCCCCEEeeCCCchhhhhHHhcCCcccccCHHHHHHHHHHhhccCCCEEEE------cCcCceeeeeeEEECCE
Confidence 578899999999966555444432111 0 1111111111 234444333332 35555678999999998
Q ss_pred CCCCccEEEEE
Q psy2555 78 PVEEGPVFFVA 88 (90)
Q Consensus 78 l~~~~lv~~~a 88 (90)
+ +|+..
T Consensus 97 ~-----iG~i~ 102 (173)
T PF10114_consen 97 Y-----IGYII 102 (173)
T ss_pred E-----EEEEE
Confidence 7 88754
No 13
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=67.26 E-value=22 Score=22.54 Aligned_cols=40 Identities=15% Similarity=0.247 Sum_probs=31.8
Q ss_pred CceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecC
Q psy2555 3 NFVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNH 55 (90)
Q Consensus 3 ~d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~ND 55 (90)
.|+..-+-|+.|++=+. +| +.+++++++.|.+|=+++.-|
T Consensus 19 ~D~~v~l~DpTG~i~~t-----iH--------~~v~~~y~~~l~~GavLlLk~ 58 (86)
T PF15072_consen 19 EDAFVVLKDPTGEIRGT-----IH--------RKVLEEYGDELSPGAVLLLKD 58 (86)
T ss_pred CCeEEEEECCCCcEEEE-----Ee--------HHHHhhcCCccccCEEEEEee
Confidence 48888889999987542 34 788888888899999999754
No 14
>PRK11246 hypothetical protein; Provisional
Probab=61.62 E-value=17 Score=27.09 Aligned_cols=55 Identities=15% Similarity=0.317 Sum_probs=34.4
Q ss_pred eeeEEeCCCCCeeeecC-CCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCCCcc
Q psy2555 5 VSKESFGPDGGLVSNAP-HIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEEGP 83 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~-g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~~~l 83 (90)
+.++|||++|.++|++. .+ .+|..+. . ++=.+| +|. . .-++-||+.+++.
T Consensus 88 lDAsIY~~~G~llA~S~~~~---------~~re~L~-L-d~~~~~-------s~~--~----qQiVEPI~~~~~~----- 138 (218)
T PRK11246 88 LDASVYDEQGDLIARSGESV---------NVRDRLA-L-DGKKAG-------SYF--N----QQIVEPIAGKNGP----- 138 (218)
T ss_pred eeEEEECCCCCEEEecCCCc---------cHHHHhC-C-CCcccc-------ccC--C----CceEEEecCCCCc-----
Confidence 57899999999999864 22 2333321 1 222223 221 2 3489999999976
Q ss_pred EEEEE
Q psy2555 84 VFFVA 88 (90)
Q Consensus 84 v~~~a 88 (90)
+||+=
T Consensus 139 lGFlR 143 (218)
T PRK11246 139 LGFLR 143 (218)
T ss_pred eeEEE
Confidence 99974
No 15
>PF00609 DAGK_acc: Diacylglycerol kinase accessory domain; InterPro: IPR000756 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The DAG kinase domain is assumed to be an accessory domain. Upon cell stimulation, DAG kinase converts DAG into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. It catalyses the reaction: ATP + 1,2-diacylglycerol = ADP + 1,2-diacylglycerol 3-phosphate. The enzyme is stimulated by calcium and phosphatidylserine and phosphorylated by protein kinase C. This domain is always associated with IPR001206 from INTERPRO.; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway
Probab=57.53 E-value=8.7 Score=26.30 Aligned_cols=36 Identities=25% Similarity=0.222 Sum_probs=25.9
Q ss_pred cEEEecCCCCC-CCCCCCe--------EEEEeeeeCCCCCCCccEEEE
Q psy2555 49 SVILSNHPKAG-GSHLPDL--------TVITPVFIDSQPVEEGPVFFV 87 (90)
Q Consensus 49 Dv~i~NDPy~G-gtHl~D~--------~~~~PVF~~Gel~~~~lv~~~ 87 (90)
-++++|=|+.+ |.++-.- .+..|-+.||.| |++++.
T Consensus 76 ~iv~lNIpSy~gG~~~W~~~~~~~~~~~~~~~~~~Dg~l---EVvg~~ 120 (161)
T PF00609_consen 76 SIVFLNIPSYGGGVDLWGNSKPDRSKLKFKKQSMDDGKL---EVVGFR 120 (161)
T ss_pred EEEEEccccccCCcccccCCcccccccccccccccCceE---EEEEEc
Confidence 47899999864 5544333 356788889998 888875
No 16
>COG2127 Uncharacterized conserved protein [Function unknown]
Probab=57.32 E-value=6.6 Score=26.17 Aligned_cols=14 Identities=36% Similarity=0.131 Sum_probs=11.3
Q ss_pred CCCCcEEEecCCCC
Q psy2555 45 FKKGSVILSNHPKA 58 (90)
Q Consensus 45 l~~GDv~i~NDPy~ 58 (90)
-..=+|++.||||+
T Consensus 26 p~~ykVillNDd~T 39 (107)
T COG2127 26 PKMYKVILLNDDYT 39 (107)
T ss_pred CCceeEEEecCCCc
Confidence 34558999999997
No 17
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=56.29 E-value=26 Score=23.77 Aligned_cols=68 Identities=12% Similarity=0.239 Sum_probs=45.2
Q ss_pred ceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCc-EEEecCC--CCCCCCCCCeEEEEeeeeCCCCCC
Q psy2555 4 FVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGS-VILSNHP--KAGGSHLPDLTVITPVFIDSQPVE 80 (90)
Q Consensus 4 d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GD-v~i~NDP--y~GgtHl~D~~~~~PVF~~Gel~~ 80 (90)
++..-|.|.+|..+|. +-|--+|+...+.+.+++. ++ +.++++- -..|++ -.+-.||+++|++
T Consensus 18 ~~~inimd~~G~IIAS--td~~RIG~~HegA~~~i~~-------~~~~~i~~~~~~~~~g~k---~GinlPI~~~g~~-- 83 (135)
T PF05651_consen 18 GYNINIMDENGIIIAS--TDPERIGTFHEGAKEVIRT-------NKEIEITEEDAEQYPGVK---PGINLPIIFNGEV-- 83 (135)
T ss_pred CCCEEEECCCcEEEec--CChhhcCccCHHHHHHHHc-------CCcccccHhHHhhccCCC---cceeeeEEECCEE--
Confidence 3567799999999976 4566788888887777652 22 3344443 122333 2367899999987
Q ss_pred CccEEEEE
Q psy2555 81 EGPVFFVA 88 (90)
Q Consensus 81 ~~lv~~~a 88 (90)
+|-++
T Consensus 84 ---iGviG 88 (135)
T PF05651_consen 84 ---IGVIG 88 (135)
T ss_pred ---EEEEE
Confidence 87654
No 18
>PRK08433 flagellar motor switch protein; Validated
Probab=56.22 E-value=13 Score=24.69 Aligned_cols=29 Identities=34% Similarity=0.476 Sum_probs=22.2
Q ss_pred eeecchHHHHHHHHHhcCCCCCCCcEEEecCCCC
Q psy2555 25 VHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKA 58 (90)
Q Consensus 25 ~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~ 58 (90)
+-+|.....++.++ +|++|||+..+-|..
T Consensus 38 v~LG~t~itl~dlL-----~Lq~GDVI~Ld~~~~ 66 (111)
T PRK08433 38 AELGTTQISLLEIL-----KFEKGSVIDLEKPAG 66 (111)
T ss_pred EEEecccccHHHHh-----CCCCCCEEEeCCCCC
Confidence 34666677777775 699999999987764
No 19
>PRK08916 flagellar motor switch protein; Reviewed
Probab=55.31 E-value=13 Score=24.92 Aligned_cols=40 Identities=18% Similarity=0.156 Sum_probs=27.1
Q ss_pred ceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCC--CCCCCeEE
Q psy2555 24 PVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGG--SHLPDLTV 68 (90)
Q Consensus 24 p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg--tHl~D~~~ 68 (90)
.+-+|.....++.++ +|++|||+-+|-+..-- .+.++..+
T Consensus 50 tv~LG~~~ltl~ELL-----~L~~GDVI~Ld~~~~e~V~I~Vng~~~ 91 (116)
T PRK08916 50 SAVLGRSKMDVGQLL-----KLGPGSVLELDRKVGEAIDIYVNNRLV 91 (116)
T ss_pred EEEEecccccHHHHh-----cCCCCCEEEcCCCCCCCEEEEECCEEE
Confidence 455677777777775 69999999998766532 34444333
No 20
>PRK08983 fliN flagellar motor switch protein; Validated
Probab=54.97 E-value=15 Score=25.00 Aligned_cols=30 Identities=13% Similarity=0.284 Sum_probs=23.2
Q ss_pred ceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCC
Q psy2555 24 PVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKA 58 (90)
Q Consensus 24 p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~ 58 (90)
-+-+|.....++.++ +|++|||+.+|-+..
T Consensus 56 ~v~LG~t~ltl~dlL-----~L~~GDVI~Ld~~~d 85 (127)
T PRK08983 56 SMEVGRSFISIRNLL-----QLNQGSVVELDRVAG 85 (127)
T ss_pred EEEEecCcccHHHHh-----CCCCCCEEEeCCCCC
Confidence 445666677777775 799999999998765
No 21
>PRK06788 flagellar motor switch protein; Validated
Probab=54.95 E-value=13 Score=25.00 Aligned_cols=32 Identities=19% Similarity=0.181 Sum_probs=25.2
Q ss_pred CceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCC
Q psy2555 23 IPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAG 59 (90)
Q Consensus 23 ~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~G 59 (90)
+.+-+|.....++.++ +|++|||+-+|-+..-
T Consensus 38 v~aeLG~t~ltl~DlL-----~L~vGDVI~Ldk~~~d 69 (119)
T PRK06788 38 LGVKLGKASITLGDVK-----QLKVGDVLEVEKNLGH 69 (119)
T ss_pred EEEEEecceecHHHHh-----CCCCCCEEEeCCcCCC
Confidence 3456777888888876 6999999999977653
No 22
>PRK09732 hypothetical protein; Provisional
Probab=54.82 E-value=30 Score=23.56 Aligned_cols=68 Identities=19% Similarity=0.139 Sum_probs=39.3
Q ss_pred eeeEEeCCCCCeeeecC--CCceeecchHHHHHHHHH--hcC-------CCCCCCcEEEecCCCCCCCCCCCeEEE---E
Q psy2555 5 VSKESFGPDGGLVSNAP--HIPVHLGSMQEAVKFQID--HRK-------GNFKKGSVILSNHPKAGGSHLPDLTVI---T 70 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~--g~p~~~g~~~~~v~~~~~--~~~-------~~l~~GDv~i~NDPy~GgtHl~D~~~~---~ 70 (90)
.+.+|.|+.|.+++... +-+. .+...+.+.... .+. +.+++|...+.+ .+.++.+ .
T Consensus 30 v~iaVvD~~G~l~a~~RmDgA~~--~s~~iA~~KA~TAa~~~~~T~~~~~~~~~g~~~~~~--------~~~~~~~~GG~ 99 (134)
T PRK09732 30 VSIAVADDGGHLLALSRMDDCAP--IAAYISQEKARTAALGRRETKGYEEMVNNGRTAFVT--------APLLTSLEGGV 99 (134)
T ss_pred EEEEEEcCCCCEEEEEEcCCCcc--ccHHHHHHHHHHHHHcCCCHHHHHHHHccCchhhcc--------CCCEEEeCCee
Confidence 57899999999998543 4443 444444433221 122 245667644432 2344333 5
Q ss_pred eeeeCCCCCCCccEEEE
Q psy2555 71 PVFIDSQPVEEGPVFFV 87 (90)
Q Consensus 71 PVF~~Gel~~~~lv~~~ 87 (90)
||..+|++ ||=+
T Consensus 100 Pi~~~g~v-----iGAI 111 (134)
T PRK09732 100 PVVVDGQI-----IGAV 111 (134)
T ss_pred EEeECCEE-----EEEE
Confidence 99889976 7644
No 23
>PLN02994 1-aminocyclopropane-1-carboxylate synthase
Probab=53.22 E-value=31 Score=23.73 Aligned_cols=25 Identities=16% Similarity=0.091 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCCCCCcEEEecCCCCCC
Q psy2555 33 AVKFQIDHRKGNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 33 ~v~~~~~~~~~~l~~GDv~i~NDPy~Gg 60 (90)
++..++..+ ..|||.++.-+||..+
T Consensus 129 al~~l~~~l---~dpGD~VlVp~P~Y~~ 153 (153)
T PLN02994 129 ANEIIMFCI---ADPGDAFLVPTPYYAA 153 (153)
T ss_pred HHHHHHHHH---cCCCCEEEEeCCCCCC
Confidence 444444433 5789999999998753
No 24
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); PDB: 2IF6_B 3KW0_C.
Probab=52.58 E-value=7.5 Score=25.87 Aligned_cols=14 Identities=21% Similarity=0.536 Sum_probs=7.9
Q ss_pred CCCCCcEEEecCCC
Q psy2555 44 NFKKGSVILSNHPK 57 (90)
Q Consensus 44 ~l~~GDv~i~NDPy 57 (90)
.+++|||++.+-+.
T Consensus 1 ~l~~GDIil~~~~~ 14 (158)
T PF05708_consen 1 KLQTGDIILTRGKS 14 (158)
T ss_dssp ---TT-EEEEEE-S
T ss_pred CCCCeeEEEEECCc
Confidence 47999999998763
No 25
>PRK03760 hypothetical protein; Provisional
Probab=52.48 E-value=7.2 Score=25.93 Aligned_cols=50 Identities=10% Similarity=0.045 Sum_probs=31.6
Q ss_pred eeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcC-----CCCCCCcEEEec
Q psy2555 5 VSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRK-----GNFKKGSVILSN 54 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~-----~~l~~GDv~i~N 54 (90)
....-.|++|++++...--|.-.......+++++|--. -++++||.+-..
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~~~gi~~Gd~v~~~ 115 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIRVLKVEVGDEIEWI 115 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHHHcCCCCCCEEEEe
Confidence 44567899999998755556544333334556655322 269999998654
No 26
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=52.28 E-value=27 Score=21.13 Aligned_cols=12 Identities=17% Similarity=0.235 Sum_probs=8.9
Q ss_pred CCCCCCcEEEec
Q psy2555 43 GNFKKGSVILSN 54 (90)
Q Consensus 43 ~~l~~GDv~i~N 54 (90)
+.|++||+++.|
T Consensus 10 P~l~~GD~vlv~ 21 (90)
T TIGR02754 10 PTLPPGDRIIVV 21 (90)
T ss_pred CccCCCCEEEEE
Confidence 357788888877
No 27
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=51.84 E-value=10 Score=23.02 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=20.4
Q ss_pred ecchHHHHHHHHHhcCCCCCCCcEEEecCCCCC
Q psy2555 27 LGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAG 59 (90)
Q Consensus 27 ~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~G 59 (90)
+|.....++.++ +|++||++-.|-+...
T Consensus 16 Lg~~~itl~ell-----~L~~Gdvi~L~~~~~~ 43 (77)
T TIGR02480 16 LGRTRITLGDLL-----KLGEGSVIELDKLAGE 43 (77)
T ss_pred EeceEeEHHHHh-----cCCCCCEEEcCCCCCC
Confidence 555555666664 7999999999876653
No 28
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=50.75 E-value=3.3 Score=20.41 Aligned_cols=14 Identities=43% Similarity=0.581 Sum_probs=11.9
Q ss_pred ceeeEEeCCCCCee
Q psy2555 4 FVSKESFGPDGGLV 17 (90)
Q Consensus 4 d~~~~i~d~~G~~v 17 (90)
|.++.+|+++||+.
T Consensus 2 D~~~t~FSp~Grl~ 15 (23)
T PF10584_consen 2 DRSITTFSPDGRLF 15 (23)
T ss_dssp SSSTTSBBTTSSBH
T ss_pred CCCceeECCCCeEE
Confidence 67788999999986
No 29
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (TIGR02305). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=50.67 E-value=11 Score=27.89 Aligned_cols=36 Identities=25% Similarity=0.407 Sum_probs=21.2
Q ss_pred chHHHHHHHHHhcCCCCCCCcEEEecCCCCCC-CCCCCe
Q psy2555 29 SMQEAVKFQIDHRKGNFKKGSVILSNHPKAGG-SHLPDL 66 (90)
Q Consensus 29 ~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg-tHl~D~ 66 (90)
.....+..+.+. ..|+|||++++=-|-..+ ....|.
T Consensus 191 ~v~~Li~~ls~~--~tL~pGDvIlTGTp~g~~~l~~GD~ 227 (245)
T TIGR02303 191 SVAELIEYLSEF--MTLEPGDVILTGTPKGLSDVKPGDV 227 (245)
T ss_pred CHHHHHHHHhcC--CCcCCCCEEEcCCCCCCeEcCCCCE
Confidence 334444444332 479999999998875322 344453
No 30
>TIGR03220 catechol_dmpE 2-oxopent-4-enoate hydratase. Members of this protein family are 2-oxopent-4-enoate hydratase, which is also called 2-hydroxypent-2,4-dienoate hydratase. It is closely related to another gene found in the same operon, 4-oxalocrotonate decarboxylase, with which it interacts closely.
Probab=50.17 E-value=26 Score=25.82 Aligned_cols=45 Identities=31% Similarity=0.343 Sum_probs=28.0
Q ss_pred CCCCCeeeecCCCceeecchHHHHHHHHHhc---CCCCCCCcEEEecCC
Q psy2555 11 GPDGGLVSNAPHIPVHLGSMQEAVKFQIDHR---KGNFKKGSVILSNHP 56 (90)
Q Consensus 11 d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~---~~~l~~GDv~i~NDP 56 (90)
..+|+.+.++.+- -.+|....++.++.+++ +..|++||++++=-|
T Consensus 182 ~vnG~~~~~g~~~-~~lg~p~~~l~~L~~~l~~~g~~L~aGdiV~TGt~ 229 (255)
T TIGR03220 182 EKNGEIVSTGAGA-AALGSPVNAVAWLANTLGRLGIPLKAGEVILSGSL 229 (255)
T ss_pred EECCEEEeecchh-hccCCHHHHHHHHHHHHHHcCCCCCCCCEEECCCC
Confidence 3467666554331 12344555666666654 358999999999865
No 31
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=47.95 E-value=15 Score=21.67 Aligned_cols=29 Identities=21% Similarity=0.395 Sum_probs=20.5
Q ss_pred CCCCC-CCCCCCeEEEEeeee-CCCCCCCccEEEEE
Q psy2555 55 HPKAG-GSHLPDLTVITPVFI-DSQPVEEGPVFFVA 88 (90)
Q Consensus 55 DPy~G-gtHl~D~~~~~PVF~-~Gel~~~~lv~~~a 88 (90)
+||.. .+..+=+++.+||+. +|++ +|.++
T Consensus 3 ~py~~~~~~~~vi~~s~pi~~~~g~~-----~Gvv~ 33 (81)
T PF02743_consen 3 EPYVDAATGQPVITISVPIYDDDGKI-----IGVVG 33 (81)
T ss_dssp --EEETTTTEEEEEEEEEEEETTTEE-----EEEEE
T ss_pred cCEEeCCCCcEEEEEEEEEECCCCCE-----EEEEE
Confidence 67754 366677899999999 8876 87654
No 32
>PRK09907 toxin MazF; Provisional
Probab=47.95 E-value=16 Score=23.83 Aligned_cols=15 Identities=27% Similarity=0.512 Sum_probs=13.3
Q ss_pred CCCCcEEEec-CCCCC
Q psy2555 45 FKKGSVILSN-HPKAG 59 (90)
Q Consensus 45 l~~GDv~i~N-DPy~G 59 (90)
++.|||++.| ||-.|
T Consensus 7 ~~rGdI~~vdl~P~~G 22 (111)
T PRK09907 7 PDMGDLIWVDFDPTKG 22 (111)
T ss_pred CCCCcEEEEECCCCCC
Confidence 7899999999 79886
No 33
>PF01557 FAA_hydrolase: Fumarylacetoacetate (FAA) hydrolase family Mutations in Swiss:P16930 cause inherited tyrosinemia type I.; InterPro: IPR002529 Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation []. This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders [, ]. The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole []. FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures []. This entry represents the C-terminal domain of fumarylacetoacetase, as well as other domains that share a homologous sequence, including: 5-carboxymethyl-2-hydroxymuconate delta-isomerase (CHM isomerase; 5.3.3.10 from EC), which catalyses the conversion of 5-carboxymethyl-2-hydroxymuconate to 5-carboxy-2-oxohept-3-enedioate []. 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase (OPET decarboxylase; 4.1.1.68 from EC), which catalyses the conversion of 5-oxopent-3-ene-1,2,5-tricarboxylate to 2-oxohept-3-enedioate and carbon dioxide. Bifunctional enzyme HpcE (OPET decarboxylase 4.1.1.68 from EC/HHDD isomerase 5.3.3.10 from EC), which is a duplication consisting of a tandem repeat of two FAH C-terminal-like domains. This enzyme is responsible for the degradation of 4-hydroxyphenylacetate, a product of tyrosine and phenylalanine metabolism also released by lignin catabolism []. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1SAW_B 3LZK_B 3S52_B 2WQT_Q 1SV6_C 2DFU_B 1WZO_D 3QDF_A 1GTT_B 1I7O_C ....
Probab=47.44 E-value=19 Score=25.45 Aligned_cols=42 Identities=24% Similarity=0.416 Sum_probs=26.8
Q ss_pred CCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCC
Q psy2555 13 DGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPK 57 (90)
Q Consensus 13 ~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy 57 (90)
+|+.+.++.. --.++....++.++.+.. .|++||++++--|-
T Consensus 144 nG~~~~~~~~-~~~~~~~~~ll~~ls~~~--~L~aGdvI~TGt~~ 185 (218)
T PF01557_consen 144 NGEVVQSGST-SDMLGDPAELLAWLSRGL--TLRAGDVILTGTPT 185 (218)
T ss_dssp TTEEEEEEEG-GGBSSSHHHHHHHHHTTS---B-TTEEEEEEESS
T ss_pred CCEEEEeccc-hhHHhhHHHHHHHHhCCC--CCCcceEEEcCCcC
Confidence 6777665543 233556666777743333 79999999999984
No 34
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=47.17 E-value=19 Score=25.42 Aligned_cols=31 Identities=23% Similarity=0.379 Sum_probs=23.9
Q ss_pred CceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCC
Q psy2555 23 IPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKA 58 (90)
Q Consensus 23 ~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~ 58 (90)
+.+-+|.....++.++ +|++|||+-+|-+..
T Consensus 83 lsveLG~t~itlrdLL-----~L~~GDVI~Ldk~~~ 113 (155)
T PRK05698 83 ISMEVGSTDINIRNLL-----QLNQGSVIELDRLAG 113 (155)
T ss_pred EEEEEecCcccHHHHh-----CCCCCCEEEeCCCCC
Confidence 4456677777778776 699999999987654
No 35
>COG3726 AhpA Uncharacterized membrane protein affecting hemolysin expression [General function prediction only]
Probab=47.10 E-value=18 Score=26.81 Aligned_cols=55 Identities=18% Similarity=0.204 Sum_probs=32.2
Q ss_pred eeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCCCccE
Q psy2555 5 VSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEEGPV 84 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~~~lv 84 (90)
+-++|||.+|+++|.+. +.. -||.. .+ .|-|-.|..-. .-++-||..++-+ .
T Consensus 88 ldAsIY~~~g~LlA~ag-------~~~-~vR~~---l~----------Ldg~~~g~y~n--qQiVEPI~~~~gi-----~ 139 (214)
T COG3726 88 LDASIYDEDGDLLARAG-------SSV-NVRDR---LA----------LDGKTAGLYFN--QQIVEPIAGKNGI-----L 139 (214)
T ss_pred eeceeecccchhHHhcc-------ccc-chhhh---hh----------cCCCCCccccc--ceeecccccCCCc-----c
Confidence 45789999999998643 111 12222 22 23333332111 4688999988855 8
Q ss_pred EEE
Q psy2555 85 FFV 87 (90)
Q Consensus 85 ~~~ 87 (90)
||+
T Consensus 140 GfL 142 (214)
T COG3726 140 GFL 142 (214)
T ss_pred eeE
Confidence 886
No 36
>KOG2030|consensus
Probab=46.69 E-value=26 Score=30.90 Aligned_cols=23 Identities=13% Similarity=0.332 Sum_probs=16.6
Q ss_pred HHHHhcCCCCCCCcEEEecCCCCCCCC
Q psy2555 36 FQIDHRKGNFKKGSVILSNHPKAGGSH 62 (90)
Q Consensus 36 ~~~~~~~~~l~~GDv~i~NDPy~GgtH 62 (90)
-++++| |+|||+|++|| ..|.+|
T Consensus 518 llvkky---~~~~DiY~had-~~gaSs 540 (911)
T KOG2030|consen 518 LLVKKY---LEPGDIYVHAD-LHGASS 540 (911)
T ss_pred HHHHhh---CCCCCeEEecc-cCCCce
Confidence 345555 89999999999 455443
No 37
>KOG1535|consensus
Probab=46.61 E-value=37 Score=25.28 Aligned_cols=38 Identities=16% Similarity=0.260 Sum_probs=25.0
Q ss_pred CceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCC
Q psy2555 23 IPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSH 62 (90)
Q Consensus 23 ~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtH 62 (90)
+-..+......+.++-+.+ .+.||||+++--|-.-|-+
T Consensus 157 T~~mifkip~li~~is~~~--tL~~GDvILTGTP~GVg~v 194 (217)
T KOG1535|consen 157 TSLMIFKIPDLISRLSQIM--TLEPGDVILTGTPEGVGEV 194 (217)
T ss_pred hhhheecHHHHHHHHhhhe--eecCCCEEEecCCCccccc
Confidence 3344455555555554444 7999999999999864433
No 38
>TIGR02305 HpaG-N-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (TIGR02303). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=46.60 E-value=20 Score=25.49 Aligned_cols=42 Identities=14% Similarity=0.189 Sum_probs=24.3
Q ss_pred CCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCC
Q psy2555 13 DGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPK 57 (90)
Q Consensus 13 ~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy 57 (90)
+|+.+.++.+- -.+++....+..+.+. ..|++||++++=-|=
T Consensus 139 ng~~~~~g~~~-~~~~~~~~li~~ls~~--~~L~aGdvI~TGT~~ 180 (205)
T TIGR02305 139 NGKPAQSNNTS-NLVRSAAQLISELSEF--MTLNPGDVLLLGTPE 180 (205)
T ss_pred CCEEEEeeCHH-HhCcCHHHHHHHHhCC--CCcCCCCEEEeCCCC
Confidence 56655443321 1134444444444432 479999999998864
No 39
>PRK12764 hypothetical protein; Provisional
Probab=45.56 E-value=16 Score=29.91 Aligned_cols=33 Identities=18% Similarity=0.290 Sum_probs=20.7
Q ss_pred HHHHHHhcC--CCCCCCcEEEecCCCCCC-CCCCCe
Q psy2555 34 VKFQIDHRK--GNFKKGSVILSNHPKAGG-SHLPDL 66 (90)
Q Consensus 34 v~~~~~~~~--~~l~~GDv~i~NDPy~Gg-tHl~D~ 66 (90)
+..+++++. -.|+|||++++=-|-..+ ....|.
T Consensus 169 v~~LI~~lS~~~tL~pGDvIlTGTp~g~~~l~pGD~ 204 (500)
T PRK12764 169 FAQLVADLSQLLTLEEGDVILTGTPAGSSVAAPGDV 204 (500)
T ss_pred HHHHHHHHhcCCCcCCCCEEEeCCCCCCeecCCCCE
Confidence 344444443 479999999999885322 344443
No 40
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=44.54 E-value=16 Score=24.81 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=17.8
Q ss_pred eeecchHHHHHHHHHhcCCCCCCCcEEEecC
Q psy2555 25 VHLGSMQEAVKFQIDHRKGNFKKGSVILSNH 55 (90)
Q Consensus 25 ~~~g~~~~~v~~~~~~~~~~l~~GDv~i~ND 55 (90)
+.+.+-..++..-+- ...++||+++|+|
T Consensus 32 i~Vd~g~DaaD~~I~---~~~~~gDiVITqD 59 (130)
T PF02639_consen 32 IVVDSGFDAADFYIV---NHAKPGDIVITQD 59 (130)
T ss_pred EEECCCCChHHHHHH---HcCCCCCEEEECC
Confidence 344444445433322 4689999999999
No 41
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=43.90 E-value=16 Score=23.61 Aligned_cols=12 Identities=25% Similarity=0.058 Sum_probs=9.9
Q ss_pred CcEEEecCCCCC
Q psy2555 48 GSVILSNHPKAG 59 (90)
Q Consensus 48 GDv~i~NDPy~G 59 (90)
=-|++.||+|..
T Consensus 22 ykViL~NDd~~t 33 (94)
T PRK13019 22 YKVIVLNDDFNT 33 (94)
T ss_pred eEEEEEcCCCCC
Confidence 359999999974
No 42
>TIGR02312 HpaH 2-oxo-hepta-3-ene-1,7-dioic acid hydratase. This model represents the enzyme which hydrates the double bond of 2-oxo-hepta-3-ene-1,7-dioic acid to form 4-hydroxy-2-oxo-heptane-1,7-dioic acid in the catabolism of 4-hydroxyphenylacetic acid. The gene for this enzyme is generally found adjacent to other genes of this pathway in an apparent operon.
Probab=42.33 E-value=30 Score=25.85 Aligned_cols=44 Identities=16% Similarity=0.209 Sum_probs=26.8
Q ss_pred CCCCCeeeecCCCceeecchHHHHHHHHHhc---CCCCCCCcEEEecC
Q psy2555 11 GPDGGLVSNAPHIPVHLGSMQEAVKFQIDHR---KGNFKKGSVILSNH 55 (90)
Q Consensus 11 d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~---~~~l~~GDv~i~ND 55 (90)
..+|+.+.++.+-.+ +|....++.++.+++ +..|++||++++=-
T Consensus 193 ~~nG~~~~~g~~~~~-lg~P~~al~wL~~~l~~~G~~L~aGdiV~TGs 239 (267)
T TIGR02312 193 YRNGVVEETGLAAGV-LNHPANGVAWLANKLAPWGETLEAGQVVLAGS 239 (267)
T ss_pred EECCEEEEEechhhh-cCCHHHHHHHHHHHHHHcCCCCCCCCEEECCC
Confidence 456777666543211 344444555665544 35799999999874
No 43
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=41.83 E-value=34 Score=22.71 Aligned_cols=12 Identities=17% Similarity=0.307 Sum_probs=10.6
Q ss_pred CCCCCCcEEEec
Q psy2555 43 GNFKKGSVILSN 54 (90)
Q Consensus 43 ~~l~~GDv~i~N 54 (90)
++++|||+++.+
T Consensus 75 ~~~qpGDlvff~ 86 (134)
T TIGR02219 75 DAAQPGDVLVFR 86 (134)
T ss_pred hcCCCCCEEEEe
Confidence 579999999986
No 44
>PRK11342 mhpD 2-keto-4-pentenoate hydratase; Provisional
Probab=41.79 E-value=32 Score=25.48 Aligned_cols=44 Identities=18% Similarity=0.196 Sum_probs=24.7
Q ss_pred CCCCeeeecCCCceeecchHHHHHHHHHhc---CCCCCCCcEEEecCC
Q psy2555 12 PDGGLVSNAPHIPVHLGSMQEAVKFQIDHR---KGNFKKGSVILSNHP 56 (90)
Q Consensus 12 ~~G~~va~~~g~p~~~g~~~~~v~~~~~~~---~~~l~~GDv~i~NDP 56 (90)
.+|+.+.++.+-- .++....++.++.+++ +..|++||++++=-|
T Consensus 187 vng~~~q~g~~~~-~lg~p~~~l~~L~~~l~~~g~~L~aGdvV~TGt~ 233 (262)
T PRK11342 187 RNNEEVSSGRGSE-CLGHPLNAAVWLARKMASLGEPLRAGDIILTGAL 233 (262)
T ss_pred ECCEEEEEEcHHH-hccCHHHHHHHHHHHHHHcCCCcCCCCEEEcCCC
Confidence 3566655443211 1233334444444443 257999999999876
No 45
>PF02452 PemK: PemK-like protein; InterPro: IPR003477 PemK is a growth inhibitor in Escherichia coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. It is responsible for mediating cell death through inhibiting protein synthesis through the cleavage of single-stranded RNA. PemK is part of the PemK-PemI system, where PemI is an antitoxin that inhibits the action of the PemK toxin []. PemK homologues have been found in a wide range of bacteria, which together form an endonuclease family that interfere with mRNA function. This family consists of the PemK protein in addition to ChpA, ChpB, Kid and MazF.; GO: 0003677 DNA binding; PDB: 1M1F_A 2C06_A 3NFC_F 1UB4_B 1NE8_A.
Probab=40.76 E-value=18 Score=22.23 Aligned_cols=13 Identities=23% Similarity=0.652 Sum_probs=9.2
Q ss_pred CCCcEEEecCCCC
Q psy2555 46 KKGSVILSNHPKA 58 (90)
Q Consensus 46 ~~GDv~i~NDPy~ 58 (90)
++|||++.+.|..
T Consensus 1 k~GdI~~v~~p~~ 13 (110)
T PF02452_consen 1 KRGDIVWVDFPDF 13 (110)
T ss_dssp STTEEEEEE-S--
T ss_pred CCceEEEEECCCC
Confidence 6899999999855
No 46
>PRK15203 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase; Provisional
Probab=40.69 E-value=17 Score=29.11 Aligned_cols=36 Identities=17% Similarity=0.166 Sum_probs=23.3
Q ss_pred HHHHHHHhcC--CCCCCCcEEEecCCCCC-CCCCCCeEE
Q psy2555 33 AVKFQIDHRK--GNFKKGSVILSNHPKAG-GSHLPDLTV 68 (90)
Q Consensus 33 ~v~~~~~~~~--~~l~~GDv~i~NDPy~G-gtHl~D~~~ 68 (90)
.+..++.++. -+|+|||++++==|=-. -.+..|...
T Consensus 152 ~~~~lis~lS~~~tL~pGDvI~TGTP~g~~~l~~GD~v~ 190 (429)
T PRK15203 152 NAAQLLSALSEFATLNPGDAILLGTPQARVEIQPGDRVR 190 (429)
T ss_pred CHHHHHHHHhCCCCcCCCCEEEcCCCCCceECCCCCEEE
Confidence 3445555544 37999999999998642 245555543
No 47
>PRK10691 hypothetical protein; Provisional
Probab=40.65 E-value=29 Score=25.12 Aligned_cols=23 Identities=26% Similarity=0.457 Sum_probs=16.1
Q ss_pred CCCCCCcEEEecCCCCCC-CCCCC
Q psy2555 43 GNFKKGSVILSNHPKAGG-SHLPD 65 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy~Gg-tHl~D 65 (90)
..|++||++++=-|-..+ ....|
T Consensus 180 ~tL~aGDvI~TGTp~g~~~l~~GD 203 (219)
T PRK10691 180 FTLRAGDVVLTGTPEGVGPLQSGD 203 (219)
T ss_pred CccCCCCEEEcCCCCCCEECCCCC
Confidence 379999999998875432 34444
No 48
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=38.36 E-value=19 Score=21.42 Aligned_cols=27 Identities=30% Similarity=0.411 Sum_probs=15.7
Q ss_pred ecchHHHHHHHHHhcCCCCCCCcEEEecCCCC
Q psy2555 27 LGSMQEAVKFQIDHRKGNFKKGSVILSNHPKA 58 (90)
Q Consensus 27 ~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~ 58 (90)
++.....++.++ +|++||++-.+.|-.
T Consensus 16 l~~~~l~l~el~-----~L~~Gdvi~l~~~~~ 42 (77)
T PF01052_consen 16 LGEASLTLGELL-----NLKVGDVIPLDKPAD 42 (77)
T ss_dssp EEEEEEEHHHHH-----C--TT-EEEECCESS
T ss_pred EEeeEeEHHHHh-----cCCCCCEEEeCCCCC
Confidence 343344455553 799999999999844
No 49
>PF01555 N6_N4_Mtase: DNA methylase; InterPro: IPR002941 This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. This family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. N-4 cytosine-specific DNA methylases (2.1.1.113 from EC) [] are enzymes that specifically methylate the amino group at the C-4 position of cytosines in DNA. Such enzymes are found as components of type II restriction-modification systems in prokaryotes. Such enzymes recognise a specific sequence in DNA and methylate a cytosine in that sequence. By this action they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2ZIF_A 2ZIE_A 2ZIG_A 1NW6_A 1NW8_A 1NW7_A 1NW5_A 1EG2_A 1BOO_A 1G60_B ....
Probab=38.34 E-value=38 Score=22.93 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=16.5
Q ss_pred eeecchHH-HHHHHHHhcCCCCCCCcEEEecCCCCCC
Q psy2555 25 VHLGSMQE-AVKFQIDHRKGNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 25 ~~~g~~~~-~v~~~~~~~~~~l~~GDv~i~NDPy~Gg 60 (90)
.|-...+. .++.+++.+. .|||+++ |||.|+
T Consensus 171 ~h~~~kP~~l~~~lI~~~t---~~gdiVl--DpF~GS 202 (231)
T PF01555_consen 171 KHPTQKPVELIERLIKAST---NPGDIVL--DPFAGS 202 (231)
T ss_dssp --TT-S-HHHHHHHHHHHS----TT-EEE--ETT-TT
T ss_pred ceeecCCHHHHHHHHHhhh---ccceeee--hhhhcc
Confidence 34444333 4477777663 6799987 999874
No 50
>PF02814 UreE_N: UreE urease accessory protein, N-terminal domain; InterPro: IPR004029 Urease and other nickel metalloenzymes are synthesised as precursors devoid of the metalloenzyme active site. These precursors then undergo a complex post-translational maturation process that requires a number of accessory proteins. Members of this group are nickel-binding proteins required for urease metallocentre assembly []. They are believed to function as metallochaperones to deliver nickel to urease apoprotein [, ]. It has been shown by yeast two-hybrid analysis that UreE forms a dimeric complex with UreG in Helicobacter pylori []. The UreDFG-apoenzyme complex has also been shown to exist [, ] and is believed to be, with the addition of UreE, the assembly system for active urease []. The complexes, rather than the individual proteins, presumably bind to UreB via UreE/H recognition sites. The structure of Klebsiella aerogenes UreE reveals a unique two-domain architecture.The N-terminal domain is structurally related to a heat shock protein, while the C-terminal domain shows homology to the Atx1 copper metallochaperone [, ]. Significantly, the metal-binding sites in UreE and Atx1 are distinct in location and types of residues despite the relationship between these proteins and the mechanism for UreE activation of urease is proposed to be different from the thiol ligand exchange mechanism used by the copper metallochaperones. The N-terminal domain is termed the peptide-binding domain. Deletion of this domain does not eliminate enzymatic activity, and the truncated protein can still activate urease [].; GO: 0016151 nickel ion binding, 0006461 protein complex assembly, 0019627 urea metabolic process; PDB: 3NXZ_B 3TJA_B 3LA0_B 3TJ9_B 3NY0_A 3L9Z_A 3TJ8_A 1EAR_A 1EB0_A 1GMU_B ....
Probab=37.58 E-value=22 Score=20.88 Aligned_cols=12 Identities=17% Similarity=0.468 Sum_probs=8.5
Q ss_pred CCCCCcEEEecC
Q psy2555 44 NFKKGSVILSNH 55 (90)
Q Consensus 44 ~l~~GDv~i~ND 55 (90)
.|++||++...|
T Consensus 50 ~L~~GDvL~~d~ 61 (65)
T PF02814_consen 50 VLRDGDVLYLDD 61 (65)
T ss_dssp T--TTEEEEECT
T ss_pred ccCCCCEEEeCC
Confidence 499999999876
No 51
>smart00702 P4Hc Prolyl 4-hydroxylase alpha subunit homologues. Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.
Probab=37.45 E-value=33 Score=23.23 Aligned_cols=27 Identities=22% Similarity=0.450 Sum_probs=16.4
Q ss_pred EEEecCCCCCC-CCCCCeE-----EEEeeeeCCCC
Q psy2555 50 VILSNHPKAGG-SHLPDLT-----VITPVFIDSQP 78 (90)
Q Consensus 50 v~i~NDPy~Gg-tHl~D~~-----~~~PVF~~Gel 78 (90)
++.+||++.|| +..++.. .++|. .|.+
T Consensus 116 ~~yLn~~~~GG~~~f~~~~~~~~~~v~P~--~G~~ 148 (178)
T smart00702 116 LLYLNDVEEGGELVFPGLGLMVCATVKPK--KGDL 148 (178)
T ss_pred EEEeccCCcCceEEecCCCCccceEEeCC--CCcE
Confidence 45678999877 5555443 45663 4554
No 52
>PF10948 DUF2635: Protein of unknown function (DUF2635); InterPro: IPR024400 This family consists of uncharacterised proteins found in bacteria and bacteriophages. It includes protein Gp38 from Enterobacteria phage Mu.
Probab=37.03 E-value=23 Score=20.14 Aligned_cols=13 Identities=15% Similarity=0.284 Sum_probs=10.6
Q ss_pred CCCCCcEEEecCC
Q psy2555 44 NFKKGSVILSNHP 56 (90)
Q Consensus 44 ~l~~GDv~i~NDP 56 (90)
-+++|||++.+-+
T Consensus 34 Rl~dGDV~~v~~~ 46 (47)
T PF10948_consen 34 RLADGDVVEVTPK 46 (47)
T ss_pred hhhcCCEEEecCC
Confidence 4899999998754
No 53
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=36.52 E-value=24 Score=23.03 Aligned_cols=11 Identities=27% Similarity=0.320 Sum_probs=9.3
Q ss_pred cEEEecCCCCC
Q psy2555 49 SVILSNHPKAG 59 (90)
Q Consensus 49 Dv~i~NDPy~G 59 (90)
=|++.||+|..
T Consensus 29 ~ViL~NDd~nt 39 (100)
T PRK00033 29 KVLLHNDDYTP 39 (100)
T ss_pred EEEEEcCCCCC
Confidence 48999999974
No 54
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=35.88 E-value=43 Score=23.05 Aligned_cols=31 Identities=23% Similarity=0.374 Sum_probs=23.5
Q ss_pred CceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCC
Q psy2555 23 IPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKA 58 (90)
Q Consensus 23 ~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~ 58 (90)
+.+-+|.....++.++ +|++|||+-++-+..
T Consensus 64 lsveLG~t~itlrdLL-----~L~~GDVI~Ld~~~~ 94 (137)
T PRK07963 64 LTVELGRTRMTIKELL-----RLTQGSVVALDGLAG 94 (137)
T ss_pred EEEEEecccccHHHHh-----CCCCCCEEEeCCCCC
Confidence 3455677777777776 699999999987654
No 55
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.83 E-value=28 Score=23.30 Aligned_cols=11 Identities=36% Similarity=0.531 Sum_probs=10.4
Q ss_pred CCCCCcEEEec
Q psy2555 44 NFKKGSVILSN 54 (90)
Q Consensus 44 ~l~~GDv~i~N 54 (90)
.++|||.++.|
T Consensus 33 ~ik~GD~IiF~ 43 (111)
T COG4043 33 QIKPGDKIIFN 43 (111)
T ss_pred CCCCCCEEEEc
Confidence 69999999999
No 56
>TIGR03218 catechol_dmpH 4-oxalocrotonate decarboxylase. Members of this protein family are 4-oxalocrotonate decarboxylase. Note that this protein, as characterized (indirectly) in Pseudomonas sp. strain CF600, was inactive except when coexpressed with DmpE, 2-oxopent-4-enoate hydratase, a homologous protein from the same operon. Both of these enzymes are active in the degradation of catechol, a common intermediate in the degradation of aromatic compounds such as benzoate, toluene, phenol, dimethylphenol (dmp), salicylate, etc.
Probab=35.54 E-value=53 Score=24.43 Aligned_cols=48 Identities=25% Similarity=0.324 Sum_probs=28.2
Q ss_pred eCCCCCeeeecCCCceeecchHHHHHHHHHhc---CCCCCCCcEEEecCCCCC
Q psy2555 10 FGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHR---KGNFKKGSVILSNHPKAG 59 (90)
Q Consensus 10 ~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~---~~~l~~GDv~i~NDPy~G 59 (90)
+..+|+.+.++.|-.+ +|.-..++.+++++. +..+++||++++- .|.+
T Consensus 189 l~~~g~~v~~g~g~~~-lG~P~~al~wL~~~l~~~G~~L~aG~iV~tG-s~t~ 239 (263)
T TIGR03218 189 MEKNGEVVAMGAGAAV-LGHPAAAVAMLANHLAERGEEIPAGSFIMSG-GITE 239 (263)
T ss_pred EEECCEEEEeeccccc-CCCHHHHHHHHHHHHHHcCCCCCCCCEEECC-cCcC
Confidence 3457777766544211 243344555555544 3579999999986 3443
No 57
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=35.53 E-value=9.3 Score=23.85 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=10.9
Q ss_pred CCCCCCcEEEecC
Q psy2555 43 GNFKKGSVILSNH 55 (90)
Q Consensus 43 ~~l~~GDv~i~ND 55 (90)
.+++|||+++...
T Consensus 50 ~~~~pGDlif~~~ 62 (105)
T PF00877_consen 50 SELQPGDLIFFKG 62 (105)
T ss_dssp GG-TTTEEEEEEG
T ss_pred hcCCcccEEEEeC
Confidence 5799999999988
No 58
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=35.17 E-value=48 Score=21.09 Aligned_cols=64 Identities=22% Similarity=0.319 Sum_probs=36.9
Q ss_pred eEEeCCCCCeeeecCCCceeecchHH--HHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeee-eCCCCCCCcc
Q psy2555 7 KESFGPDGGLVSNAPHIPVHLGSMQE--AVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVF-IDSQPVEEGP 83 (90)
Q Consensus 7 ~~i~d~~G~~va~~~g~p~~~g~~~~--~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF-~~Gel~~~~l 83 (90)
..|.|++|..++.+ -|-.+|..-. .++. -| .|--+..-.+..+ -+=+..+.||+ .+|++
T Consensus 42 i~v~D~~g~~l~~s--~~~~iG~~~~~~~~~~-------aL-~G~~~~~~~~~~~---~~~~~~~~PV~d~~g~v----- 103 (116)
T PF14827_consen 42 IVVTDRDGIVLAHS--DPERIGDRYSDEDVRK-------AL-QGKSYTSVSQGTG---GPSLRAFAPVYDSDGKV----- 103 (116)
T ss_dssp EEEECTTSBECE-S--SCCCTTSB-SSCCHCH-------HC-CT--EEEEEECTT---CEEEEEEEEEE-TTS-E-----
T ss_pred EEEEcCCCCEEEcC--ChHHcCCcccCCChhh-------hh-cCCceEEeeecCC---ceEEEEEEeeECCCCcE-----
Confidence 35899999998865 3434443111 1111 23 4444555444444 45678999999 89987
Q ss_pred EEEEE
Q psy2555 84 VFFVA 88 (90)
Q Consensus 84 v~~~a 88 (90)
+|++.
T Consensus 104 iG~V~ 108 (116)
T PF14827_consen 104 IGVVS 108 (116)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 99875
No 59
>PRK00124 hypothetical protein; Validated
Probab=35.08 E-value=26 Score=24.50 Aligned_cols=13 Identities=15% Similarity=0.432 Sum_probs=11.5
Q ss_pred CCCCCCcEEEecC
Q psy2555 43 GNFKKGSVILSNH 55 (90)
Q Consensus 43 ~~l~~GDv~i~ND 55 (90)
...++||+++|+|
T Consensus 63 ~~~~~gDiVIT~D 75 (151)
T PRK00124 63 QLAEKGDIVITQD 75 (151)
T ss_pred HhCCCCCEEEeCC
Confidence 3589999999999
No 60
>PRK11524 putative methyltransferase; Provisional
Probab=35.01 E-value=26 Score=25.98 Aligned_cols=22 Identities=32% Similarity=0.465 Sum_probs=16.2
Q ss_pred HHHHHHhcCCCCCCCcEEEecCCCCCC
Q psy2555 34 VKFQIDHRKGNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 34 v~~~~~~~~~~l~~GDv~i~NDPy~Gg 60 (90)
++.+++.+. .|||+++ |||.|+
T Consensus 198 ~erlI~~~S---~~GD~VL--DPF~GS 219 (284)
T PRK11524 198 LKRIILASS---NPGDIVL--DPFAGS 219 (284)
T ss_pred HHHHHHHhC---CCCCEEE--ECCCCC
Confidence 356665553 7999998 999874
No 61
>PF04968 CHORD: CHORD ; InterPro: IPR007051 Cysteine- and histidine-rich domains (CHORDs) are 60-amino acid modules that bind two zinc ions. They are usually arranged in tandem and are found in all tested eukaryotes, with the exception of yeast, where they are involved in processes ranging from pressure sensing in the heart to maintenance of diploidy in fungi, and exhibit distinct protein-protein interaction specificity. Six cysteine and two histidine residues are invariant within the CHORD domain. Three other residues are also invariant and some positions are confined to positive, negative, or aromatic amino acids [, ]. Silencing of the Caenorhabditis elegansCHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development. The CHORD domain is sometimes found N-terminal to the CS domain, IPR007052 from INTERPRO, in metazoan proteins, but occurs separately from the CS domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains []. ; PDB: 2XCM_E 2YRT_A.
Probab=34.15 E-value=23 Score=21.42 Aligned_cols=8 Identities=38% Similarity=0.750 Sum_probs=6.0
Q ss_pred EeeeeCCC
Q psy2555 70 TPVFIDSQ 77 (90)
Q Consensus 70 ~PVF~~Ge 77 (90)
.||||||.
T Consensus 29 ~PvFHeg~ 36 (64)
T PF04968_consen 29 PPVFHEGM 36 (64)
T ss_dssp -EEEETTE
T ss_pred CceecCCc
Confidence 69999983
No 62
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=33.70 E-value=47 Score=19.89 Aligned_cols=13 Identities=23% Similarity=0.197 Sum_probs=11.0
Q ss_pred cCCCCCCCcEEEe
Q psy2555 41 RKGNFKKGSVILS 53 (90)
Q Consensus 41 ~~~~l~~GDv~i~ 53 (90)
++.+.++|||+..
T Consensus 30 LP~~~keGDvl~i 42 (71)
T PF11213_consen 30 LPEGAKEGDVLEI 42 (71)
T ss_pred CCCCCCcccEEEE
Confidence 4578999999977
No 63
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=33.60 E-value=27 Score=22.90 Aligned_cols=13 Identities=23% Similarity=0.363 Sum_probs=12.3
Q ss_pred CCCCCcEEEecCC
Q psy2555 44 NFKKGSVILSNHP 56 (90)
Q Consensus 44 ~l~~GDv~i~NDP 56 (90)
.++|||++-.++|
T Consensus 139 ~l~pGDvi~l~~~ 151 (164)
T PF13550_consen 139 ALEPGDVIALSDD 151 (164)
T ss_pred cCCCCCEEEEEeC
Confidence 6899999999999
No 64
>TIGR00113 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase. This model describes the enzyme for S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). QueA synthesizes Queuosine which is usually in the first position of the anticodon of tRNAs specific for asparagine, aspartate, histidine, and tyrosine.
Probab=33.45 E-value=25 Score=27.73 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=12.9
Q ss_pred CCCCCCcEEEecCCC
Q psy2555 43 GNFKKGSVILSNHPK 57 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy 57 (90)
+=++|||+++.||-.
T Consensus 47 ~~l~~gDlLV~NdTk 61 (344)
T TIGR00113 47 DFFNEGDLLVLNNTK 61 (344)
T ss_pred hhcCCCCEEEEeCcE
Confidence 458999999999965
No 65
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=32.41 E-value=45 Score=21.80 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=13.5
Q ss_pred CCCCCCcEEEecCCCCCC
Q psy2555 43 GNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy~Gg 60 (90)
..+++||.++.+. |.|.
T Consensus 61 ~~Vk~GD~Vl~~~-y~Gt 77 (100)
T PTZ00414 61 PTVKVGDTVLLPE-FGGS 77 (100)
T ss_pred ceecCCCEEEEcC-CCCc
Confidence 4699999999865 8763
No 66
>COG0309 HypE Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=32.22 E-value=52 Score=26.04 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=20.8
Q ss_pred CCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCCCccEEEEEe
Q psy2555 45 FKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEEGPVFFVAN 89 (90)
Q Consensus 45 l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~~~lv~~~a~ 89 (90)
+.++.+.++-|||. +.|+|..|+. +||.|.
T Consensus 46 l~~~~la~tTD~~~----------i~P~ff~~~d-----iG~lAV 75 (339)
T COG0309 46 LGDGVLAFTTDPFV----------IDPLFFPGGD-----IGKLAV 75 (339)
T ss_pred cCCceEEEEeCCeE----------ecccccCCCc-----eEEEEE
Confidence 44445777778775 5778877766 898763
No 67
>PRK00147 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=32.03 E-value=28 Score=27.50 Aligned_cols=15 Identities=13% Similarity=0.414 Sum_probs=12.9
Q ss_pred CCCCCCcEEEecCCC
Q psy2555 43 GNFKKGSVILSNHPK 57 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy 57 (90)
+=++|||+++.||-.
T Consensus 48 ~~l~~gDlLV~NdTk 62 (342)
T PRK00147 48 DYLNPGDLLVFNDTR 62 (342)
T ss_pred hhcCCCCEEEEEcCe
Confidence 458999999999965
No 68
>KOG2183|consensus
Probab=31.94 E-value=21 Score=29.46 Aligned_cols=41 Identities=20% Similarity=0.228 Sum_probs=26.7
Q ss_pred ecchHHHHHHHHHhcCCCCCC--------C-------cEEEec---CCCCCCCCCCCeE
Q psy2555 27 LGSMQEAVKFQIDHRKGNFKK--------G-------SVILSN---HPKAGGSHLPDLT 67 (90)
Q Consensus 27 ~g~~~~~v~~~~~~~~~~l~~--------G-------Dv~i~N---DPy~GgtHl~D~~ 67 (90)
-..+..-.+.+++.|+-..+| | -+++.| |||+||.++.|+.
T Consensus 380 ~fn~~~y~e~C~~~~~v~prP~wi~t~fgg~~l~~~SNiIFSNG~LDPWSGGGV~~nis 438 (492)
T KOG2183|consen 380 PFNSESYQEGCMQTFGVTPRPKWITTEFGGADLSAFSNIIFSNGLLDPWSGGGVLKNIS 438 (492)
T ss_pred CCCHHHHHHHHHHhcCCCCCCcceehhhccccchhhcceeeeCCCcCCccCcCeecccc
Confidence 334566667777777522222 2 567776 9999998887763
No 69
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=31.76 E-value=69 Score=18.89 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.9
Q ss_pred CCCCCcEEEec
Q psy2555 44 NFKKGSVILSN 54 (90)
Q Consensus 44 ~l~~GDv~i~N 54 (90)
.+++||+++.+
T Consensus 13 ~i~~gd~v~v~ 23 (85)
T cd06530 13 TLQPGDLVLVN 23 (85)
T ss_pred cccCCCEEEEE
Confidence 35555555554
No 70
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=31.18 E-value=1.2e+02 Score=21.26 Aligned_cols=52 Identities=21% Similarity=0.245 Sum_probs=29.9
Q ss_pred eeEEeCCCCCeeeecCCCceeecc-hHHH---HHHH--HHhcC----CCCCCCcEEEecCCCC
Q psy2555 6 SKESFGPDGGLVSNAPHIPVHLGS-MQEA---VKFQ--IDHRK----GNFKKGSVILSNHPKA 58 (90)
Q Consensus 6 ~~~i~d~~G~~va~~~g~p~~~g~-~~~~---v~~~--~~~~~----~~l~~GDv~i~NDPy~ 58 (90)
++-|.|++|++.....+ |...|. .... ++.+ .++.+ .+|+|||-.+...|-.
T Consensus 119 ~~fiID~~G~I~~~~~~-~~~~gr~~~ell~~l~~lq~~~~~~~~~p~~w~~g~~~~~~~~~~ 180 (203)
T cd03016 119 AVFIIDPDKKIRLILYY-PATTGRNFDEILRVVDALQLTDKHKVATPANWKPGDDVIVPPSVS 180 (203)
T ss_pred EEEEECCCCeEEEEEec-CCCCCCCHHHHHHHHHHHhhHhhcCcCcCCCCCCCCceecCCCCC
Confidence 46788999987765322 223332 2222 2221 11122 4899999998887765
No 71
>PLN02856 fumarylacetoacetase
Probab=30.94 E-value=29 Score=28.15 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=18.8
Q ss_pred hHHHHHHHHHhc-C--CCCCCCcEEEecCCC
Q psy2555 30 MQEAVKFQIDHR-K--GNFKKGSVILSNHPK 57 (90)
Q Consensus 30 ~~~~v~~~~~~~-~--~~l~~GDv~i~NDPy 57 (90)
|...+..++.++ . -+|+|||++.+==|=
T Consensus 329 M~ws~~qlIah~~s~g~tL~pGDLi~TGTps 359 (424)
T PLN02856 329 LYWTLAQQLAHHTVNGCNLRPGDLLGSGTIS 359 (424)
T ss_pred cCCCHHHHHHHHHhCCeecCCCCEEEeCCCC
Confidence 344445555542 1 489999999998884
No 72
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=30.92 E-value=98 Score=19.52 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=21.7
Q ss_pred eeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEec
Q psy2555 5 VSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSN 54 (90)
Q Consensus 5 ~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~N 54 (90)
|..-|.|.+|..+. +-... ..+++|.+.|++|+|+...
T Consensus 37 ~~~~l~De~~~~I~--------~t~~~----~~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 37 FSFDLLDEDGGEIR--------ATFFN----DAVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred EEEEEEECCCCEEE--------EEEeh----HHHHHhhcccccccEEEEe
Confidence 45556676555442 21122 3344455679999998753
No 73
>PF13651 EcoRI_methylase: Adenine-specific methyltransferase EcoRI
Probab=30.83 E-value=25 Score=27.79 Aligned_cols=15 Identities=20% Similarity=0.459 Sum_probs=13.2
Q ss_pred CCCCcEEEecCCCCC
Q psy2555 45 FKKGSVILSNHPKAG 59 (90)
Q Consensus 45 l~~GDv~i~NDPy~G 59 (90)
+++.||++||=||+-
T Consensus 133 l~eADIVVTNPPFSL 147 (336)
T PF13651_consen 133 LKEADIVVTNPPFSL 147 (336)
T ss_pred HhcCCEEEeCCCcHH
Confidence 578999999999973
No 74
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=30.75 E-value=30 Score=27.48 Aligned_cols=15 Identities=13% Similarity=0.414 Sum_probs=12.8
Q ss_pred CCCCCCcEEEecCCC
Q psy2555 43 GNFKKGSVILSNHPK 57 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy 57 (90)
+-|+|||+++.||--
T Consensus 48 dyl~~GD~LVfNdTr 62 (348)
T COG0809 48 DYLNPGDLLVFNDTR 62 (348)
T ss_pred hhcCCCCEEEEecCe
Confidence 458999999999954
No 75
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=30.67 E-value=97 Score=21.43 Aligned_cols=27 Identities=19% Similarity=0.370 Sum_probs=13.5
Q ss_pred CCCCCcEEEecCCCCCCCCCCCeEEEE
Q psy2555 44 NFKKGSVILSNHPKAGGSHLPDLTVIT 70 (90)
Q Consensus 44 ~l~~GDv~i~NDPy~GgtHl~D~~~~~ 70 (90)
.+++||.++.+-.........|+.+++
T Consensus 44 tl~~GD~vlv~~~~~~~~~~GDIVvf~ 70 (158)
T TIGR02228 44 TFNTGDLILVTGADPNDIQVGDVITYK 70 (158)
T ss_pred CccCCCEEEEEecccCCCCCCCEEEEE
Confidence 456666666654111234445555554
No 76
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=30.25 E-value=47 Score=23.94 Aligned_cols=13 Identities=15% Similarity=0.480 Sum_probs=10.6
Q ss_pred CCCCCCcEEEecC
Q psy2555 43 GNFKKGSVILSNH 55 (90)
Q Consensus 43 ~~l~~GDv~i~ND 55 (90)
.+++|||+++...
T Consensus 127 ~~lqpGDLVfF~~ 139 (190)
T PRK10838 127 SKLRTGDLVLFRA 139 (190)
T ss_pred CCCCCCcEEEECC
Confidence 4799999998763
No 77
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=30.19 E-value=30 Score=20.47 Aligned_cols=34 Identities=26% Similarity=0.409 Sum_probs=18.1
Q ss_pred CCCCCcEEEecC--CCCC--------CCCCCCeEEEEeeeeCCC
Q psy2555 44 NFKKGSVILSNH--PKAG--------GSHLPDLTVITPVFIDSQ 77 (90)
Q Consensus 44 ~l~~GDv~i~ND--Py~G--------gtHl~D~~~~~PVF~~Ge 77 (90)
+|++||+++.=| |-.. ..+.++-++-.=|..+|+
T Consensus 31 Gl~~GD~I~~ing~~v~~~~~~~~~l~~~~~g~~v~l~v~R~g~ 74 (82)
T PF13180_consen 31 GLQPGDIILAINGKPVNSSEDLVNILSKGKPGDTVTLTVLRDGE 74 (82)
T ss_dssp TS-TTEEEEEETTEESSSHHHHHHHHHCSSTTSEEEEEEEETTE
T ss_pred CCCCCcEEEEECCEEcCCHHHHHHHHHhCCCCCEEEEEEEECCE
Confidence 699999998522 1111 145555555555555554
No 78
>PRK01424 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=30.16 E-value=31 Score=27.54 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=14.1
Q ss_pred hcCCCCCCCcEEEecCCC
Q psy2555 40 HRKGNFKKGSVILSNHPK 57 (90)
Q Consensus 40 ~~~~~l~~GDv~i~NDPy 57 (90)
.+.+=++|||+++.||-.
T Consensus 42 dl~~~L~~GDlLV~NdTk 59 (366)
T PRK01424 42 NIIDYLKEGDLLVFNNSK 59 (366)
T ss_pred HHHhhcCCCCEEEEeccE
Confidence 333458999999999965
No 79
>PRK06933 type III secretion system protein; Validated
Probab=29.90 E-value=82 Score=24.41 Aligned_cols=46 Identities=17% Similarity=0.129 Sum_probs=28.7
Q ss_pred ecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCC--CCCCCeEEEE--eeeeCCC
Q psy2555 27 LGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGG--SHLPDLTVIT--PVFIDSQ 77 (90)
Q Consensus 27 ~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg--tHl~D~~~~~--PVF~~Ge 77 (90)
+|.....++.++ +|++|||+-.|-+..+. ...++..+.+ ++-.+|+
T Consensus 245 LG~~~ltl~eLl-----~L~~GdVi~L~~~~~~~V~I~vng~~i~~Gelv~v~~~ 294 (308)
T PRK06933 245 VGRQTLDLHTLT-----SLQPGSLIDLTTPVDGEVRLLANGRLLGHGRLVEIQGR 294 (308)
T ss_pred EecccccHHHHh-----cCCCCCEEEcCCCCCCCEEEEECCEEEEEEEEEEECCE
Confidence 444444555543 79999999999887653 4555554443 4444554
No 80
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=29.83 E-value=75 Score=19.81 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=12.1
Q ss_pred HHHHHHHHHhcCCCCCCCcEEE
Q psy2555 31 QEAVKFQIDHRKGNFKKGSVIL 52 (90)
Q Consensus 31 ~~~v~~~~~~~~~~l~~GDv~i 52 (90)
..-.+.+++++ ++++||+++
T Consensus 63 e~~~~~l~~~~--~a~~GD~ll 82 (95)
T PF02938_consen 63 EEELKALIERL--GAKPGDLLL 82 (95)
T ss_dssp HHHHHHHHHHT--T--TTEEEE
T ss_pred HHHHHHHHHHh--CCCCCCEEE
Confidence 34456666666 699999965
No 81
>PF02547 Queuosine_synth: Queuosine biosynthesis protein; InterPro: IPR003699 This entry represents the queuosine biosynthesis proteins QueA. Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine. The hypermodified nucleoside is found in bacteria and eukaryotes []. Queuosine is synthesized de novo exclusively in bacteria; for eukaryotes the compound is a nutrient factor. Queuosine biosynthesis protein, or S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (QueA) catalyses the formation of the 2,3-epoxy-4,5-dihydroxycyclopentane ring of the Q precursor epoxyqueuosine (oQ). S-adenosyl-L-methionine (AdoMet) reacts with 7-aminomethyl-7-deazaguanine of tRNA at position 34 to yield adenine, methionine, and a modified tRNA with oQ at position 34. QueA consists of two domains: domain 1 has 3 layers alpha/beta/alpha, while domain 2 is a closed beta-barrel with Greek-key topology [].; GO: 0016740 transferase activity, 0016853 isomerase activity, 0008616 queuosine biosynthetic process; PDB: 1WDI_A 1VKY_B 1YY3_A.
Probab=29.58 E-value=24 Score=27.83 Aligned_cols=15 Identities=20% Similarity=0.468 Sum_probs=10.9
Q ss_pred CCCCCCcEEEecCCC
Q psy2555 43 GNFKKGSVILSNHPK 57 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy 57 (90)
+=|+|||+++.||-.
T Consensus 47 ~~L~~GDlLV~NdTk 61 (341)
T PF02547_consen 47 DYLRPGDLLVFNDTK 61 (341)
T ss_dssp GG--TTEEEEEEEEE
T ss_pred HhhCCCCEEEEeCCE
Confidence 458999999999954
No 82
>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4). All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....
Probab=29.41 E-value=30 Score=25.88 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=13.8
Q ss_pred ceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEE
Q psy2555 4 FVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVIL 52 (90)
Q Consensus 4 d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i 52 (90)
-+|||+++...+.+.+++ ..-++.++++. +++||+-++
T Consensus 30 ~YS~~~~~~~~~~Le~AQ---------~~k~~~~~~~~--~l~~G~~vL 67 (273)
T PF02353_consen 30 KYSCAYFDEGDDTLEEAQ---------ERKLDLLCEKL--GLKPGDRVL 67 (273)
T ss_dssp --S----SSTT--HHHHH---------HHHHHHHHTTT--T--TT-EEE
T ss_pred CCCCeecCCchhhHHHHH---------HHHHHHHHHHh--CCCCCCEEE
Confidence 467788877555553322 22234444444 699999766
No 83
>PF12600 DUF3769: Protein of unknown function (DUF3769); InterPro: IPR022244 This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 560 and 931 amino acids in length.
Probab=29.39 E-value=29 Score=28.37 Aligned_cols=17 Identities=24% Similarity=0.389 Sum_probs=15.1
Q ss_pred CCCCCCcEEEecCCCCC
Q psy2555 43 GNFKKGSVILSNHPKAG 59 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy~G 59 (90)
++|+-=+|-++||||+-
T Consensus 20 ~gW~a~~~~~TNDPf~P 36 (451)
T PF12600_consen 20 NGWKAENVRFTNDPFSP 36 (451)
T ss_pred CCcEEeeeEEcCCCCCc
Confidence 57999999999999984
No 84
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=29.32 E-value=1e+02 Score=18.54 Aligned_cols=36 Identities=11% Similarity=-0.037 Sum_probs=22.4
Q ss_pred eeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEe
Q psy2555 6 SKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILS 53 (90)
Q Consensus 6 ~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~ 53 (90)
..-|.|.+|..+- ...- +..+++|.+-|++|.++..
T Consensus 22 ~miL~De~G~~I~--------a~i~----~~~~~~f~~~L~eg~vy~i 57 (86)
T cd04480 22 EMVLVDEKGNRIH--------ATIP----KRLAAKFRPLLKEGKWYTI 57 (86)
T ss_pred EEEEEcCCCCEEE--------EEEC----HHHHHhhhhhceeCCEEEE
Confidence 4457787776542 1111 4446667677999998874
No 85
>PF13756 Stimulus_sens_1: Stimulus-sensing domain
Probab=29.13 E-value=43 Score=21.83 Aligned_cols=18 Identities=22% Similarity=0.599 Sum_probs=13.8
Q ss_pred eeEEeCCCCCeeeecCCC
Q psy2555 6 SKESFGPDGGLVSNAPHI 23 (90)
Q Consensus 6 ~~~i~d~~G~~va~~~g~ 23 (90)
-+=|||++|.+++-+..+
T Consensus 20 RARlyd~dG~Ll~DSr~l 37 (112)
T PF13756_consen 20 RARLYDPDGNLLADSRVL 37 (112)
T ss_pred eEEEECCCCCEEeecccc
Confidence 356999999999966543
No 86
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=29.01 E-value=37 Score=19.43 Aligned_cols=10 Identities=40% Similarity=0.647 Sum_probs=8.8
Q ss_pred CCCCCcEEEe
Q psy2555 44 NFKKGSVILS 53 (90)
Q Consensus 44 ~l~~GDv~i~ 53 (90)
+|++||+++.
T Consensus 29 gl~~GD~I~~ 38 (79)
T cd00989 29 GLKAGDRILA 38 (79)
T ss_pred CCCCCCEEEE
Confidence 6999999985
No 87
>PF14811 TPD: Protein of unknown function TPD sequence-motif
Probab=28.78 E-value=44 Score=23.13 Aligned_cols=24 Identities=21% Similarity=0.506 Sum_probs=20.8
Q ss_pred CCCCCeEEEEeeeeCCCCCCCccEEEEEe
Q psy2555 61 SHLPDLTVITPVFIDSQPVEEGPVFFVAN 89 (90)
Q Consensus 61 tHl~D~~~~~PVF~~Gel~~~~lv~~~a~ 89 (90)
.-.||+.+-.||-.+|.+ |-|.=|
T Consensus 62 ~kTPDi~l~~Pi~i~g~~-----V~WIES 85 (139)
T PF14811_consen 62 DKTPDIKLEVPIAINGHV-----VNWIES 85 (139)
T ss_pred CCCCCEEecCCceECCeE-----Eeeeeh
Confidence 569999999999999977 888654
No 88
>PF13403 Hint_2: Hint domain
Probab=28.66 E-value=39 Score=23.03 Aligned_cols=13 Identities=15% Similarity=0.511 Sum_probs=12.2
Q ss_pred CCCCCCcEEEecC
Q psy2555 43 GNFKKGSVILSNH 55 (90)
Q Consensus 43 ~~l~~GDv~i~ND 55 (90)
++|++||.+++-|
T Consensus 19 e~L~~GD~V~T~d 31 (147)
T PF13403_consen 19 EDLRPGDRVLTRD 31 (147)
T ss_pred eccCCCCEEEecC
Confidence 6899999999998
No 89
>PF09147 DUF1933: Domain of unknown function (DUF1933); InterPro: IPR015230 This domain is predominantly found in carbapenam synthetase, and is composed of two antiparallel six-stranded beta-sheets that form a sandwich, flanked on each side by two alpha-helices. Their exact function has not, as yet, been determined []. ; PDB: 1Q19_A 1Q15_D.
Probab=28.63 E-value=90 Score=22.94 Aligned_cols=26 Identities=19% Similarity=0.106 Sum_probs=17.6
Q ss_pred CCceeeEEeCCCCCee--eecCC-Cceee
Q psy2555 2 NNFVSKESFGPDGGLV--SNAPH-IPVHL 27 (90)
Q Consensus 2 ~~d~~~~i~d~~G~~v--a~~~g-~p~~~ 27 (90)
-+||+.-|=|++|++. ..+.| -|+|+
T Consensus 99 EGdfcffiE~kng~L~l~Tds~G~~pv~l 127 (201)
T PF09147_consen 99 EGDFCFFIEDKNGELTLITDSRGFNPVYL 127 (201)
T ss_dssp -SSEEEEEEETTSEEEEEE-SSSSS-EEE
T ss_pred cCceEEEEecCCCcEEEEecCCCCceEEE
Confidence 3799999999999754 45566 47776
No 90
>PLN02164 sulfotransferase
Probab=28.45 E-value=75 Score=24.84 Aligned_cols=17 Identities=18% Similarity=0.428 Sum_probs=15.7
Q ss_pred CCCCCcEEEecCCCCCC
Q psy2555 44 NFKKGSVILSNHPKAGG 60 (90)
Q Consensus 44 ~l~~GDv~i~NDPy~Gg 60 (90)
..+|+||||.--|-+|.
T Consensus 76 ~~r~~DV~laSyPKsGT 92 (346)
T PLN02164 76 QARPNDFLVCSYPKTGT 92 (346)
T ss_pred CCCCCCEEEEcCCCchh
Confidence 68999999999999985
No 91
>PRK08432 flagellar motor switch protein FliY; Validated
Probab=28.43 E-value=59 Score=24.66 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=27.0
Q ss_pred ceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCC--CCCCCeEE
Q psy2555 24 PVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGG--SHLPDLTV 68 (90)
Q Consensus 24 p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg--tHl~D~~~ 68 (90)
.+-+|.....++.++ +|++|||+-.|-+..-- .+.++..+
T Consensus 211 ~v~lG~~~~~i~dlL-----~L~~GdVI~Ld~~~~~pv~v~v~~~~~ 252 (283)
T PRK08432 211 RVRIGQKKMLLKDVL-----SMDIGSVVELNQLANDPLEILVDDKVI 252 (283)
T ss_pred EEEEecCcccHHHHh-----CCCCCCEEEeCCCCCCcEEEEECCEEE
Confidence 345666666777775 69999999999887532 34444433
No 92
>PLN02376 1-aminocyclopropane-1-carboxylate synthase
Probab=28.38 E-value=1e+02 Score=24.81 Aligned_cols=28 Identities=18% Similarity=0.059 Sum_probs=20.8
Q ss_pred hHHHHHHHHHhcCCCCCCCcEEEecCCCCCC
Q psy2555 30 MQEAVKFQIDHRKGNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 30 ~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg 60 (90)
...++..++..+ .+|||.++.-+||..+
T Consensus 128 a~~al~~l~~~l---~~pGD~Vlv~~P~Y~~ 155 (496)
T PLN02376 128 ATGANETIMFCL---ADPGDVFLIPSPYYAA 155 (496)
T ss_pred hHHHHHHHHHHh---CCCCCEEEECCCCccc
Confidence 344556666555 5799999999999865
No 93
>PF10084 DUF2322: Uncharacterized protein conserved in bacteria (DUF2322); InterPro: IPR016755 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.17 E-value=1e+02 Score=20.33 Aligned_cols=35 Identities=20% Similarity=0.263 Sum_probs=26.9
Q ss_pred eEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcC
Q psy2555 7 KESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRK 42 (90)
Q Consensus 7 ~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~ 42 (90)
.-|+|.+|+.++.-+..|.-.||+... .++.++|+
T Consensus 17 l~l~d~~g~~v~~I~n~pGk~GSL~VY-~~La~~fg 51 (100)
T PF10084_consen 17 LDLLDADGNVVAHIENKPGKLGSLAVY-NALAQKFG 51 (100)
T ss_pred eEeecCCCcEEEEecCCCCcceeHHHH-HHHHHHhC
Confidence 458899999999888899999987633 55556664
No 94
>PF08874 DUF1835: Domain of unknown function (DUF1835); InterPro: IPR014973 This group of proteins are functionally uncharacterised.
Probab=28.00 E-value=1.2e+02 Score=19.28 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=20.0
Q ss_pred hHHHHHHHHHhcCCCCCCCcEEEecCCCCCC
Q psy2555 30 MQEAVKFQIDHRKGNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 30 ~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg 60 (90)
....+|..++.-+ .+|||+..+|+++=|
T Consensus 9 ~a~sLk~a~~~~g---~~~~Vi~~~d~lsiG 36 (124)
T PF08874_consen 9 AAGSLKQALKQSG---FEGDVICFRDDLSIG 36 (124)
T ss_pred hHHHHHHHHHhcC---CCCcEEEEeCCCccc
Confidence 4445566655432 899999999999844
No 95
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=27.75 E-value=73 Score=25.59 Aligned_cols=72 Identities=15% Similarity=0.191 Sum_probs=39.8
Q ss_pred ceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCCCCCCCCCeEEEEeeeeCCCCCCCcc
Q psy2555 4 FVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKAGGSHLPDLTVITPVFIDSQPVEEGP 83 (90)
Q Consensus 4 d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtHl~D~~~~~PVF~~Gel~~~~l 83 (90)
|++.-+.|++|..++.+ =|-=+|......-- -+++++++..-+--..-.+--=-.+=.|||++|++
T Consensus 20 ~~nInVMd~~GvIIgSg--d~~Rigq~HEGAll-------al~e~R~V~Id~~~a~~l~gVkpGINLPi~~~~~v----- 85 (376)
T COG3835 20 DYNINVMDADGVIIGSG--DPERIGQLHEGALL-------ALKERRVVEIDQAVARKLKGVKPGINLPIRFDGKV----- 85 (376)
T ss_pred cccceEECCCCeEEecC--ChHHhcchhhHHHH-------HHhcCcEEEeeHHHHHHhcCCCCCCCcceEecCce-----
Confidence 56778899999999754 34334443332211 25566666555432110010011244699999987
Q ss_pred EEEEEe
Q psy2555 84 VFFVAN 89 (90)
Q Consensus 84 v~~~a~ 89 (90)
||-.+.
T Consensus 86 VGViGI 91 (376)
T COG3835 86 VGVIGI 91 (376)
T ss_pred EEEEec
Confidence 886653
No 96
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=27.52 E-value=33 Score=22.31 Aligned_cols=15 Identities=20% Similarity=0.362 Sum_probs=12.9
Q ss_pred CCCCCcEEEecCCCCC
Q psy2555 44 NFKKGSVILSNHPKAG 59 (90)
Q Consensus 44 ~l~~GDv~i~NDPy~G 59 (90)
-|++||.++. +||-.
T Consensus 57 wI~~GD~VlV-sp~d~ 71 (99)
T TIGR00523 57 WIREGDVVIV-KPWEF 71 (99)
T ss_pred EecCCCEEEE-EEccC
Confidence 4899999999 89964
No 97
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=27.44 E-value=41 Score=19.88 Aligned_cols=10 Identities=40% Similarity=0.574 Sum_probs=8.9
Q ss_pred CCCCCcEEEe
Q psy2555 44 NFKKGSVILS 53 (90)
Q Consensus 44 ~l~~GDv~i~ 53 (90)
+|++||+++.
T Consensus 27 GL~~GDiI~~ 36 (79)
T cd00991 27 VLHTGDVIYS 36 (79)
T ss_pred CCCCCCEEEE
Confidence 6999999985
No 98
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=27.40 E-value=1.7e+02 Score=18.47 Aligned_cols=53 Identities=8% Similarity=0.023 Sum_probs=29.9
Q ss_pred ceeeEEeCCCCCeeeecCC-Cc----eeecchHHHHHHHHHhcC-CCCCCCcEEEecCC
Q psy2555 4 FVSKESFGPDGGLVSNAPH-IP----VHLGSMQEAVKFQIDHRK-GNFKKGSVILSNHP 56 (90)
Q Consensus 4 d~~~~i~d~~G~~va~~~g-~p----~~~g~~~~~v~~~~~~~~-~~l~~GDv~i~NDP 56 (90)
-+.+.|++++|++++.+.. .+ ...=+-..+++.+.++.. ..++.-++|.+-.|
T Consensus 18 ~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~EP 76 (109)
T cd01285 18 PFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEP 76 (109)
T ss_pred cEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCCC
Confidence 3678999999999987632 21 111122334455555443 24566666666555
No 99
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=27.06 E-value=42 Score=19.38 Aligned_cols=10 Identities=10% Similarity=0.375 Sum_probs=8.8
Q ss_pred CCCCCcEEEe
Q psy2555 44 NFKKGSVILS 53 (90)
Q Consensus 44 ~l~~GDv~i~ 53 (90)
+|++||+++.
T Consensus 29 Gl~~GD~I~~ 38 (80)
T cd00990 29 GLVAGDELVA 38 (80)
T ss_pred CCCCCCEEEE
Confidence 6999999985
No 100
>cd00714 GFAT Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. In humans, GFAT catalyzes the first and rate-limiting step of hexosamine metabolism, the conversion of D-fructose-6P (Fru6P) into D-glucosamine-6P using L-glutamine as a nitrogen source. The end product of this pathway, UDP-N-acetyl glucosamine, is a major building block of the bacterial peptidoglycan and fungal chitin.
Probab=26.83 E-value=56 Score=23.23 Aligned_cols=51 Identities=12% Similarity=0.223 Sum_probs=29.9
Q ss_pred CCceeeEEeCCC--CCeeeecCCCceeecchH------HHHHHHHHhcC--CCCCCCcEEE
Q psy2555 2 NNFVSKESFGPD--GGLVSNAPHIPVHLGSMQ------EAVKFQIDHRK--GNFKKGSVIL 52 (90)
Q Consensus 2 ~~d~~~~i~d~~--G~~va~~~g~p~~~g~~~------~~v~~~~~~~~--~~l~~GDv~i 52 (90)
.+.|+.+++|.+ +++++....-|.+++-.. +=.+.+.++.. ..|++||++.
T Consensus 154 ~G~fa~~~~d~~~~~~l~~~RD~~PL~~~~~~~~~~~aSE~~al~~~~~~~~~~~~~~~~~ 214 (215)
T cd00714 154 EGAYALAVISKDEPDEIVAARNGSPLVIGIGDGENFVASDAPALLEHTRRVIYLEDGDIAV 214 (215)
T ss_pred ccceEEEEEEeCCCCEEEEEECCCCcEEEEcCCeEEEEECHHHHHHhcCEEEEECCCCEEe
Confidence 467899999974 367776656677765211 11123332222 3678888764
No 101
>PRK11479 hypothetical protein; Provisional
Probab=26.78 E-value=45 Score=25.54 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=10.3
Q ss_pred CCCCCCcEEEec
Q psy2555 43 GNFKKGSVILSN 54 (90)
Q Consensus 43 ~~l~~GDv~i~N 54 (90)
.+++|||+++..
T Consensus 63 ~~LqpGDLVFfs 74 (274)
T PRK11479 63 PDLKPGDLLFSS 74 (274)
T ss_pred hhCCCCCEEEEe
Confidence 579999999964
No 102
>PLN00139 hypothetical protein; Provisional
Probab=26.40 E-value=64 Score=24.80 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=14.5
Q ss_pred HHHHHhcC--CCCCCCcEEEecC
Q psy2555 35 KFQIDHRK--GNFKKGSVILSNH 55 (90)
Q Consensus 35 ~~~~~~~~--~~l~~GDv~i~ND 55 (90)
+.+++... -.|++|||++.+-
T Consensus 276 ~~~~~~~~~~~~Wq~GDvl~iDN 298 (320)
T PLN00139 276 GQIIEEESIQFKWEKGDVLFLDN 298 (320)
T ss_pred HHHHHHhhccCCCCCCCEEEEeC
Confidence 44444432 4799999999875
No 103
>PF05721 PhyH: Phytanoyl-CoA dioxygenase (PhyH); InterPro: IPR008775 This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [].; PDB: 3GJA_A 3EMR_A 3OBZ_A 2OPW_A 3NNL_B 3NNF_A 3NNM_B 3NNJ_A 2FCV_B 2FCU_A ....
Probab=26.36 E-value=36 Score=22.42 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=10.0
Q ss_pred CCCCCcEEEecC
Q psy2555 44 NFKKGSVILSNH 55 (90)
Q Consensus 44 ~l~~GDv~i~ND 55 (90)
.+++||+++.|-
T Consensus 183 ~~~~Gdvl~~~~ 194 (211)
T PF05721_consen 183 PMKAGDVLFFHS 194 (211)
T ss_dssp -BSTTEEEEEET
T ss_pred ecCCCeEEEEcC
Confidence 689999999875
No 104
>PRK08666 5'-methylthioadenosine phosphorylase; Validated
Probab=26.30 E-value=40 Score=24.84 Aligned_cols=13 Identities=23% Similarity=0.478 Sum_probs=11.8
Q ss_pred CCCCCcEEEecCC
Q psy2555 44 NFKKGSVILSNHP 56 (90)
Q Consensus 44 ~l~~GDv~i~NDP 56 (90)
++++||+++.+|=
T Consensus 91 ~l~~GDiVi~~d~ 103 (261)
T PRK08666 91 NMKPGDFVILDQF 103 (261)
T ss_pred CCCCCCEEeehhh
Confidence 7999999999985
No 105
>PRK10040 hypothetical protein; Provisional
Probab=25.70 E-value=47 Score=19.36 Aligned_cols=12 Identities=17% Similarity=0.230 Sum_probs=9.8
Q ss_pred CCCcEEEecCCC
Q psy2555 46 KKGSVILSNHPK 57 (90)
Q Consensus 46 ~~GDv~i~NDPy 57 (90)
-.|+.|++||--
T Consensus 31 C~g~~FvCnDGS 42 (52)
T PRK10040 31 CTGGKFVCNDGS 42 (52)
T ss_pred ccCCEEEeCCCc
Confidence 469999999943
No 106
>TIGR00758 UDG_fam4 uracil-DNA glycosylase, family 4. This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity.
Probab=25.40 E-value=95 Score=21.40 Aligned_cols=28 Identities=11% Similarity=0.207 Sum_probs=22.2
Q ss_pred eecchHHHHHHHHHhcCCCCCCCcEEEecC
Q psy2555 26 HLGSMQEAVKFQIDHRKGNFKKGSVILSNH 55 (90)
Q Consensus 26 ~~g~~~~~v~~~~~~~~~~l~~GDv~i~ND 55 (90)
|.|..+..++.+++.. ++.+.|++++|=
T Consensus 42 f~g~sG~~L~~~l~~~--gl~~~~vy~t~~ 69 (173)
T TIGR00758 42 FVGRAGKLLDEMLAAI--GLSRENVYITNV 69 (173)
T ss_pred CcChHHHHHHHHHHHc--CCCcccEEEecc
Confidence 5676777778888766 588999999986
No 107
>PRK00331 glucosamine--fructose-6-phosphate aminotransferase; Reviewed
Probab=25.27 E-value=91 Score=25.57 Aligned_cols=52 Identities=12% Similarity=0.091 Sum_probs=33.5
Q ss_pred CCceeeEEeCCC--CCeeeecCCCceeecchH---------HHHHHHHHhcCCCCCCCcEEEec
Q psy2555 2 NNFVSKESFGPD--GGLVSNAPHIPVHLGSMQ---------EAVKFQIDHRKGNFKKGSVILSN 54 (90)
Q Consensus 2 ~~d~~~~i~d~~--G~~va~~~g~p~~~g~~~---------~~v~~~~~~~~~~l~~GDv~i~N 54 (90)
.+.|+.+++|++ +++++...+-|.++|--. .++...-+.+ -.++||+++..+
T Consensus 155 ~G~~a~~~~d~~~~~~l~~~Rd~~PL~~g~~~~~~~~aSE~~al~~~~~~~-~~l~pg~~~~i~ 217 (604)
T PRK00331 155 EGAYALAVIDKDEPDTIVAARNGSPLVIGLGEGENFLASDALALLPYTRRV-IYLEDGEIAVLT 217 (604)
T ss_pred cCeeEEEEEecCCCCEEEEEECCCceEEEEcCCeEEEEECHHHHHHhcCEE-EEECCCeEEEEE
Confidence 467999999986 467776667788776321 1222221222 369999988875
No 108
>COG1443 Idi Isopentenyldiphosphate isomerase [Lipid metabolism]
Probab=25.23 E-value=49 Score=24.11 Aligned_cols=18 Identities=22% Similarity=0.191 Sum_probs=15.2
Q ss_pred CceeeEEeCCCCCeeeec
Q psy2555 3 NFVSKESFGPDGGLVSNA 20 (90)
Q Consensus 3 ~d~~~~i~d~~G~~va~~ 20 (90)
.-||+-|||.+|+++.|.
T Consensus 34 rAFS~~lFne~g~LLltr 51 (185)
T COG1443 34 RAFSSFLFNERGQLLLTR 51 (185)
T ss_pred hhhheeEECCCCceeeeh
Confidence 358999999999988764
No 109
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=25.22 E-value=1.1e+02 Score=23.47 Aligned_cols=39 Identities=15% Similarity=0.187 Sum_probs=24.8
Q ss_pred CceeeEEeCCCCCeeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEE
Q psy2555 3 NFVSKESFGPDGGLVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVIL 52 (90)
Q Consensus 3 ~d~~~~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i 52 (90)
+-+||+.|.....++.+++ ...++.+++++ .|+||+-+|
T Consensus 39 ~~Yscayf~~~~~tL~eAQ---------~~k~~~~~~kl--~L~~G~~lL 77 (283)
T COG2230 39 MTYSCAYFEDPDMTLEEAQ---------RAKLDLILEKL--GLKPGMTLL 77 (283)
T ss_pred CceeeEEeCCCCCChHHHH---------HHHHHHHHHhc--CCCCCCEEE
Confidence 4578888887665544332 22345555555 599999887
No 110
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=24.48 E-value=56 Score=23.34 Aligned_cols=34 Identities=18% Similarity=0.361 Sum_probs=20.0
Q ss_pred CCCCcEEEecCCCCCCCCCC-----CeEEEEeeeeCCCC
Q psy2555 45 FKKGSVILSNHPKAGGSHLP-----DLTVITPVFIDSQP 78 (90)
Q Consensus 45 l~~GDv~i~NDPy~GgtHl~-----D~~~~~PVF~~Gel 78 (90)
.+.|.+.+..|-..--.|.. -==++.|||.+|++
T Consensus 89 ~~~~~t~~V~DV~~~~ghiaCD~as~SEIVvPi~~~g~~ 127 (163)
T COG1956 89 AATGETVRVDDVHAFPGHIACDAASNSEIVVPIFKDGKL 127 (163)
T ss_pred HhcCCeEEecccccCCCccccccccCceEEEEEEECCEE
Confidence 45556666666543222332 12368899999987
No 111
>COG2337 MazF Growth inhibitor [Signal transduction mechanisms]
Probab=24.43 E-value=59 Score=21.25 Aligned_cols=15 Identities=33% Similarity=0.623 Sum_probs=12.5
Q ss_pred CCCCcEEEec-CCCCC
Q psy2555 45 FKKGSVILSN-HPKAG 59 (90)
Q Consensus 45 l~~GDv~i~N-DPy~G 59 (90)
++.||++..| +|+.|
T Consensus 3 ~~rg~i~~~~l~p~~g 18 (112)
T COG2337 3 PKRGDIYLVDLGPVVG 18 (112)
T ss_pred cccccEEEecCCCccc
Confidence 5789999999 88865
No 112
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=24.00 E-value=1.3e+02 Score=20.78 Aligned_cols=39 Identities=21% Similarity=0.313 Sum_probs=22.7
Q ss_pred EEeCCCCCeeeecCCCceeecchHHHHHHHHH-h----cCCCCCCCc-EEEecCC
Q psy2555 8 ESFGPDGGLVSNAPHIPVHLGSMQEAVKFQID-H----RKGNFKKGS-VILSNHP 56 (90)
Q Consensus 8 ~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~-~----~~~~l~~GD-v~i~NDP 56 (90)
-|.|++|.. +|-+...|...+. + |..+...|| |++.|-=
T Consensus 16 ~viDA~~~~----------lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViNa~ 60 (144)
T PRK09216 16 YVIDAEGKV----------LGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAE 60 (144)
T ss_pred EEEeCCCCc----------hHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEeCc
Confidence 356666655 4555555655554 2 335677898 5566643
No 113
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=23.91 E-value=1.3e+02 Score=20.80 Aligned_cols=40 Identities=18% Similarity=0.236 Sum_probs=22.3
Q ss_pred EEeCCCCCeeeecCCCceeecchHHHHHHHHH-h----cCCCCCCCc-EEEecCCC
Q psy2555 8 ESFGPDGGLVSNAPHIPVHLGSMQEAVKFQID-H----RKGNFKKGS-VILSNHPK 57 (90)
Q Consensus 8 ~i~d~~G~~va~~~g~p~~~g~~~~~v~~~~~-~----~~~~l~~GD-v~i~NDPy 57 (90)
-|.|++|.. +|-+..-|...+. + |..+...|| |++.|-=-
T Consensus 17 ~viDA~~~~----------lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViNa~k 62 (143)
T CHL00159 17 YIIDAKDQT----------LGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEK 62 (143)
T ss_pred EEEeCCCCc----------hHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEecce
Confidence 355666655 4555555555554 2 334677788 55666433
No 114
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=23.89 E-value=54 Score=18.30 Aligned_cols=9 Identities=44% Similarity=0.815 Sum_probs=8.3
Q ss_pred CCCCCcEEE
Q psy2555 44 NFKKGSVIL 52 (90)
Q Consensus 44 ~l~~GDv~i 52 (90)
.|++||+++
T Consensus 30 gl~~GD~I~ 38 (70)
T cd00136 30 GLQAGDVIL 38 (70)
T ss_pred CCCCCCEEE
Confidence 699999997
No 115
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=23.84 E-value=49 Score=21.15 Aligned_cols=31 Identities=13% Similarity=0.274 Sum_probs=15.5
Q ss_pred CCCCCCcEEEec-CCCCCCCCCCCeEEEEeeeeCC
Q psy2555 43 GNFKKGSVILSN-HPKAGGSHLPDLTVITPVFIDS 76 (90)
Q Consensus 43 ~~l~~GDv~i~N-DPy~GgtHl~D~~~~~PVF~~G 76 (90)
...++||+++.+ .+..+-.| +.++.=|..+|
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GH---VaIV~~v~~~~ 92 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGH---VAIVESVNDGG 92 (124)
T ss_dssp S---TTEEEEEEECTTTTT-E---EEEEEEE-TTS
T ss_pred cccccceEEEeccCCCCCCCe---EEEEEEECCCC
Confidence 578999999994 33333355 45555554343
No 116
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=23.72 E-value=26 Score=23.33 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=0.0
Q ss_pred CCCCCCcEEEecCCCCCC
Q psy2555 43 GNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy~Gg 60 (90)
++|++||.++.=||-.|.
T Consensus 12 e~I~~GD~Vls~d~~tg~ 29 (130)
T PF07591_consen 12 EDIKVGDRVLSYDEETGE 29 (130)
T ss_dssp ------------------
T ss_pred cccccccccccccccccc
Confidence 689999999999998874
No 117
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=23.36 E-value=77 Score=19.20 Aligned_cols=17 Identities=24% Similarity=0.421 Sum_probs=13.2
Q ss_pred HHHHHhcCCCCCCCcEEEe
Q psy2555 35 KFQIDHRKGNFKKGSVILS 53 (90)
Q Consensus 35 ~~~~~~~~~~l~~GDv~i~ 53 (90)
...+++| +|+.||.+.-
T Consensus 33 ~~~Irr~--~LR~GD~V~G 49 (68)
T cd04459 33 PSQIRRF--NLRTGDTVVG 49 (68)
T ss_pred HHHHHHh--CCCCCCEEEE
Confidence 4566667 5999999875
No 118
>TIGR01641 phageSPP1_gp7 phage putative head morphogenesis protein, SPP1 gp7 family. This model describes a region of about 110 amino acids found exclusively in phage-related proteins, internally or toward the C-terminus. One member, gp7 of phage SPP1, appears involved in head morphogenesis.
Probab=23.24 E-value=90 Score=19.53 Aligned_cols=27 Identities=19% Similarity=0.233 Sum_probs=22.5
Q ss_pred CCcEEEecCCCCCC----CCCCCeEEEEeee
Q psy2555 47 KGSVILSNHPKAGG----SHLPDLTVITPVF 73 (90)
Q Consensus 47 ~GDv~i~NDPy~Gg----tHl~D~~~~~PVF 73 (90)
.|=+|-.+||..|. .|.+.=+.+.|||
T Consensus 78 dG~~~~~d~~~~~~~~pp~h~~CRC~~~pv~ 108 (108)
T TIGR01641 78 NGKIFKVDDAVPGVNAPPLHPNCRCTLAPVP 108 (108)
T ss_pred CCcEEecCCCCcCCcCCCCCCCcCCeeeeCC
Confidence 57788899998654 7999999999986
No 119
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=23.00 E-value=1.1e+02 Score=17.69 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=14.8
Q ss_pred CCeEEEEeeeeCCCCCCCccEEEE
Q psy2555 64 PDLTVITPVFIDSQPVEEGPVFFV 87 (90)
Q Consensus 64 ~D~~~~~PVF~~Gel~~~~lv~~~ 87 (90)
..-.+..|++.+|++ +|..
T Consensus 91 ~~s~~~~Pl~~~~~~-----~G~l 109 (149)
T smart00065 91 VRSFLAVPLVADGEL-----VGVL 109 (149)
T ss_pred eeeEEEeeeeecCEE-----EEEE
Confidence 456788999999976 7754
No 120
>TIGR01697 PNPH-PUNA-XAPA inosine guanosine and xanthosine phosphorylase family. Sequences from Clostridium and Thermotoga fall between these last two clades and are uncharacterized with respect to substrate range and operon.
Probab=22.98 E-value=56 Score=23.92 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=11.8
Q ss_pred CCCCCcEEEecCC
Q psy2555 44 NFKKGSVILSNHP 56 (90)
Q Consensus 44 ~l~~GDv~i~NDP 56 (90)
++++||+++.+|-
T Consensus 98 ~l~~GDiVI~~~~ 110 (248)
T TIGR01697 98 DFKPGDLMIIKDH 110 (248)
T ss_pred CCCCCCEEEEhhh
Confidence 6999999999986
No 121
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=22.88 E-value=57 Score=18.66 Aligned_cols=10 Identities=30% Similarity=0.557 Sum_probs=8.5
Q ss_pred CCCCCcEEEe
Q psy2555 44 NFKKGSVILS 53 (90)
Q Consensus 44 ~l~~GDv~i~ 53 (90)
.+++||+++.
T Consensus 43 gl~~GD~I~~ 52 (82)
T cd00992 43 GLRVGDRILE 52 (82)
T ss_pred CCCCCCEEEE
Confidence 6999999874
No 122
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=22.77 E-value=1.5e+02 Score=18.36 Aligned_cols=16 Identities=25% Similarity=0.231 Sum_probs=10.6
Q ss_pred HHHHHhcCCCCCCCcEEE
Q psy2555 35 KFQIDHRKGNFKKGSVIL 52 (90)
Q Consensus 35 ~~~~~~~~~~l~~GDv~i 52 (90)
+.+.+.+ +|++||++.
T Consensus 20 keiR~~l--gi~~Gd~le 35 (89)
T COG2002 20 KEIREAL--GIKEGDVLE 35 (89)
T ss_pred HHHHHHh--CCCCCCEEE
Confidence 4444445 599999764
No 123
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.70 E-value=56 Score=23.02 Aligned_cols=12 Identities=17% Similarity=0.404 Sum_probs=10.7
Q ss_pred CCCCCcEEEecC
Q psy2555 44 NFKKGSVILSNH 55 (90)
Q Consensus 44 ~l~~GDv~i~ND 55 (90)
--++||+++|.|
T Consensus 63 ~a~~gDlVVT~D 74 (150)
T COG1671 63 LAEKGDLVVTAD 74 (150)
T ss_pred hCCCCCEEEECc
Confidence 468999999999
No 124
>KOG4146|consensus
Probab=22.52 E-value=87 Score=20.63 Aligned_cols=36 Identities=22% Similarity=0.389 Sum_probs=21.7
Q ss_pred Cceeecc-hHHHHHHHHHhcC------CCCCCCcEEEecCCCC
Q psy2555 23 IPVHLGS-MQEAVKFQIDHRK------GNFKKGSVILSNHPKA 58 (90)
Q Consensus 23 ~p~~~g~-~~~~v~~~~~~~~------~~l~~GDv~i~NDPy~ 58 (90)
-|.-+|. +.+..+..+++.+ +.++||=+.+.||--+
T Consensus 34 ~~~tvgdll~yi~~~~ie~r~~lFi~~gsvrpGii~lINd~DW 76 (101)
T KOG4146|consen 34 SPATVGDLLDYIFGKYIETRDSLFIHHGSVRPGIIVLINDMDW 76 (101)
T ss_pred CcccHHHHHHHHHHHHhcCCcceEeeCCcCcCcEEEEEeccch
Confidence 3555654 3334444554422 4789999999998643
No 125
>TIGR02551 SpaO_YscQ type III secretion system apparatus protein YscQ/HrcQ. Genes in this family are found in type III secretion operons. The gene (YscQ) in Yersinia is essential for YOPs secretion, while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid, and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae.
Probab=22.47 E-value=52 Score=24.77 Aligned_cols=31 Identities=26% Similarity=0.459 Sum_probs=21.7
Q ss_pred CceeecchHHHHHHHHHhcCCCCCCCcEEEecCCCC
Q psy2555 23 IPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNHPKA 58 (90)
Q Consensus 23 ~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~ 58 (90)
++..+|....+.+.. ..+++|||++...++.
T Consensus 141 ~~l~lG~~~Ls~~~L-----~~L~~GDvLl~~~~~~ 171 (298)
T TIGR02551 141 VRLEIGSSRLALDEL-----RSLEVGDVLLLDNPSA 171 (298)
T ss_pred EEEEEccEEecHHHH-----hccCCCCEEeeccccc
Confidence 345566555555444 4799999999998865
No 126
>TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit. This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.
Probab=22.39 E-value=50 Score=23.46 Aligned_cols=17 Identities=35% Similarity=0.450 Sum_probs=15.1
Q ss_pred CCCceeeEEeCCCCCee
Q psy2555 1 MNNFVSKESFGPDGGLV 17 (90)
Q Consensus 1 ~~~d~~~~i~d~~G~~v 17 (90)
|.-|+...+|+++||+.
T Consensus 1 ~~~~~~~~~f~p~Grl~ 17 (224)
T TIGR03633 1 MGYDRAITVFSPDGRLY 17 (224)
T ss_pred CCCCCCCceECCCCeEe
Confidence 66789999999999987
No 127
>COG1015 DeoB Phosphopentomutase [Carbohydrate transport and metabolism]
Probab=22.35 E-value=1.1e+02 Score=24.77 Aligned_cols=23 Identities=26% Similarity=0.647 Sum_probs=18.5
Q ss_pred CCCCCCcEEEe-----cCCCCCCC-CCCC
Q psy2555 43 GNFKKGSVILS-----NHPKAGGS-HLPD 65 (90)
Q Consensus 43 ~~l~~GDv~i~-----NDPy~Ggt-Hl~D 65 (90)
+.|+|+|++|. |||=++|| |.-.
T Consensus 320 ~~l~edDlLiiTADHGnDPT~~gTdHTRE 348 (397)
T COG1015 320 ENLREDDLLIITADHGNDPTWGGTDHTRE 348 (397)
T ss_pred HhcCCCCEEEEecCCCCCCCCCCCCcccc
Confidence 58999999986 99988665 6554
No 128
>PF00391 PEP-utilizers: PEP-utilising enzyme, mobile domain; InterPro: IPR008279 A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related [, , , ]. All these enzymes share the same catalytic mechanism: they bind PEP and transfer the phosphoryl group from it to a histidine residue. This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it []. It is often found associated with the pyruvate phosphate dikinase, PEP/pyruvate-binding domain (IPR002192 from INTERPRO) at its N terminus.; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0016310 phosphorylation; PDB: 2X0S_A 2OLS_A 2HRO_A 2E28_A 2WQD_A 3T05_D 3T0T_D 3T07_B 2DIK_A 2FM4_A ....
Probab=22.27 E-value=35 Score=20.63 Aligned_cols=40 Identities=18% Similarity=0.315 Sum_probs=26.1
Q ss_pred eeEEeCCCCC------eeeecCCCceeecchHHHHHHHHHhcCCCCCCCcEEEec
Q psy2555 6 SKESFGPDGG------LVSNAPHIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSN 54 (90)
Q Consensus 6 ~~~i~d~~G~------~va~~~g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~N 54 (90)
..+|...+|. ++|.+.|+|.-++.-... ..+++||.+..|
T Consensus 31 ~~Giv~~~Gg~~SH~aIlAr~~giP~ivg~~~~~---------~~i~~g~~v~lD 76 (80)
T PF00391_consen 31 VAGIVTEEGGPTSHAAILARELGIPAIVGVGDAT---------EAIKDGDWVTLD 76 (80)
T ss_dssp SSEEEESSSSTTSHHHHHHHHTT-EEEESTTTHH---------HHSCTTEEEEEE
T ss_pred eEEEEEEcCCccchHHHHHHHcCCCEEEeeccHh---------hccCCCCEEEEE
Confidence 4567777665 455677899888874211 258889988874
No 129
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=22.24 E-value=1.8e+02 Score=17.26 Aligned_cols=11 Identities=36% Similarity=0.625 Sum_probs=9.1
Q ss_pred CCCCCCcEEEe
Q psy2555 43 GNFKKGSVILS 53 (90)
Q Consensus 43 ~~l~~GDv~i~ 53 (90)
+.++|||.++.
T Consensus 64 g~~~~Gd~vl~ 74 (90)
T PF08541_consen 64 GRIKPGDRVLL 74 (90)
T ss_dssp TSSCTTEEEEE
T ss_pred CCCCCCCEEEE
Confidence 47999999875
No 130
>PF09142 TruB_C: tRNA Pseudouridine synthase II, C terminal; InterPro: IPR015225 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1SGV_B.
Probab=21.88 E-value=75 Score=18.29 Aligned_cols=14 Identities=43% Similarity=0.731 Sum_probs=9.3
Q ss_pred eeEEeCCCCCeeee
Q psy2555 6 SKESFGPDGGLVSN 19 (90)
Q Consensus 6 ~~~i~d~~G~~va~ 19 (90)
.++.++++|+++|.
T Consensus 28 ~~aa~~pdG~lvAL 41 (56)
T PF09142_consen 28 PVAAFAPDGRLVAL 41 (56)
T ss_dssp -EEEE-TTS-EEEE
T ss_pred eEEEECCCCcEEEE
Confidence 46889999999984
No 131
>PF02668 TauD: Taurine catabolism dioxygenase TauD, TfdA family; InterPro: IPR003819 This family consists of TauD/TfdA taurine catabolism dioxygenases. The Escherichia coli tauD gene is required for the utilization of taurine (2-aminoethanesulphonic acid) as a sulphur source and is expressed only under conditions of sulphate starvation. TauD is an alpha-ketoglutarate-dependent dioxygenase catalyzing the oxygenolytic release of sulphite from taurine []. The 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. (strain RASC) also belongs to this family []. TfdA from Ralstonia eutropha (Alcaligenes eutrophus) is a 2,4-D monooxygenase [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3SWT_B 3R1J_A 1GVG_A 1DRT_A 1DS1_A 1DS0_A 1DRY_A 3V15_A 3PVJ_D 3V17_A ....
Probab=21.86 E-value=46 Score=23.24 Aligned_cols=12 Identities=8% Similarity=0.539 Sum_probs=8.9
Q ss_pred CCCCCcEEEecC
Q psy2555 44 NFKKGSVILSNH 55 (90)
Q Consensus 44 ~l~~GDv~i~ND 55 (90)
.|++||++|.|.
T Consensus 224 ~~~~GDlli~dN 235 (258)
T PF02668_consen 224 RWQPGDLLIWDN 235 (258)
T ss_dssp E--TTEEEEEET
T ss_pred cCCCceEEEEcC
Confidence 699999999886
No 132
>PF08741 YwhD: YwhD family; InterPro: IPR014852 The members of this entry are currently uncharacterised. They are around 170 amino acids in length.
Probab=21.79 E-value=55 Score=23.36 Aligned_cols=28 Identities=32% Similarity=0.550 Sum_probs=20.5
Q ss_pred EEEecCCCC--CC--CCCCCeEEEEeeeeCCC
Q psy2555 50 VILSNHPKA--GG--SHLPDLTVITPVFIDSQ 77 (90)
Q Consensus 50 v~i~NDPy~--Gg--tHl~D~~~~~PVF~~Ge 77 (90)
-||.|||-- || .=.-|+.-++|||.|+|
T Consensus 7 nIi~~d~tdgH~G~g~Gsi~L~nvspViID~e 38 (163)
T PF08741_consen 7 NIIKNDSTDGHGGFGAGSISLNNVSPVIIDVE 38 (163)
T ss_pred EEecCCCCCCCCCcceeeEeccccccEEEecC
Confidence 478999973 33 45567777899999964
No 133
>PHA02813 hypothetical protein; Provisional
Probab=21.76 E-value=1.2e+02 Score=24.30 Aligned_cols=33 Identities=24% Similarity=0.438 Sum_probs=24.8
Q ss_pred EEEecCCCCCC-C--CCC---------CeEEEEeeeeCCCCCCCc
Q psy2555 50 VILSNHPKAGG-S--HLP---------DLTVITPVFIDSQPVEEG 82 (90)
Q Consensus 50 v~i~NDPy~Gg-t--Hl~---------D~~~~~PVF~~Gel~~~~ 82 (90)
++.+|+|..|| | +.+ |+.+-.++.|+|..|+++
T Consensus 127 LLYLN~~~~GGeT~f~~~~~tsI~~g~dlLFdh~l~Heg~~V~sG 171 (354)
T PHA02813 127 VLYLNNTSKGGNTNIHIKDNTIFSTKNDVLFDKTLNHSSDIITDG 171 (354)
T ss_pred EEEEeccCCCCceEEEcCCCceEeecceEEEecccccCCcEeccC
Confidence 45689999987 2 555 777788888998776665
No 134
>KOG1170|consensus
Probab=21.73 E-value=67 Score=28.82 Aligned_cols=36 Identities=31% Similarity=0.374 Sum_probs=27.0
Q ss_pred EEEecCC-CCCC-----CCCCCeEEEEeeeeCCCCCCCccEEEEE
Q psy2555 50 VILSNHP-KAGG-----SHLPDLTVITPVFIDSQPVEEGPVFFVA 88 (90)
Q Consensus 50 v~i~NDP-y~Gg-----tHl~D~~~~~PVF~~Gel~~~~lv~~~a 88 (90)
|+|.|=| |.|| +---|-.+..|-|.|+.| |.|+..+
T Consensus 689 IviLNIpSyaGGtNFWGsnk~dd~f~apSfDDriL---EVVAvFG 730 (1099)
T KOG1170|consen 689 IVILNIPSYAGGTNFWGSNKDDDEFTAPSFDDRIL---EVVAVFG 730 (1099)
T ss_pred eEEEecccccCcccccCCCCCCCcccCCCccccee---EEeeeeh
Confidence 6777877 5675 456788899999999987 6666443
No 135
>cd01674 Homoaconitase_Swivel Homoaconitase swivel domain. This family includes homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases. This is the swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.
Probab=21.71 E-value=1.4e+02 Score=20.44 Aligned_cols=32 Identities=16% Similarity=0.287 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhcC----CCCCCCcEEEecCCCCCCC
Q psy2555 30 MQEAVKFQIDHRK----GNFKKGSVILSNHPKAGGS 61 (90)
Q Consensus 30 ~~~~v~~~~~~~~----~~l~~GDv~i~NDPy~Ggt 61 (90)
.....+++++.+. ..+++|||++.-.=|-.|+
T Consensus 24 ~e~la~~~~e~~dp~f~~~v~~gdilVaG~nFG~GS 59 (129)
T cd01674 24 PEKMAEVCMENYDSEFSTKTKQGDILVSGFNFGTGS 59 (129)
T ss_pred HHHHHHhhcccCCchhhhcCCCCCEEEeCCccCCCC
Confidence 4556677777764 4689999999999887553
No 136
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=21.64 E-value=67 Score=22.24 Aligned_cols=13 Identities=15% Similarity=0.534 Sum_probs=11.3
Q ss_pred CCCCCcEEEecCC
Q psy2555 44 NFKKGSVILSNHP 56 (90)
Q Consensus 44 ~l~~GDv~i~NDP 56 (90)
+++.|||+|...+
T Consensus 75 ~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 75 NLQRGDIFIWGRR 87 (145)
T ss_pred cccCCCEEEEcCC
Confidence 6899999998776
No 137
>PF01505 Vault: Major Vault Protein repeat; InterPro: IPR002499 Vaults are the largest ribonucleoprotein particles known, having a mass of approximately 13 MDa. They are multi-subunit structures that may act as scaffolds for proteins involved in signal transduction and may also play a role in nucleo-cytoplasmic transport. Vaults are present in most normal tissues, but are more highly expressed in epithelial cells with secretory and excretory functions, as well as in cells chronically exposed to xenobiotics, such as bronchial cells and cells lining the intestine []. Overexpression of these proteins is linked with multidrug-resistance in cancer cells. The mammalian vault structure is highly regular and consists of approximately 96 molecules of the 100 kDa major vault protein (MVP), 2 molecules of the 240 kDa minor vault protein TEP1, 8 molecules of the 193 kDa minor vault protein VPARP and at least 6 copies of a small untranslated RNA of 88-141 bases. The MVP molecules form the core of the complex, which is a barrel-like structure with an invaginated waist and two protruding caps. The complex can unfold into two symmetrical flower-like structures with 8 petals each supposedly consisting of 6 MVP molecules []. The MVP protein is composed of two distinct domains []. The N-terminal domain contains ~8 copies of the vault repeat (or MVP repeat) in tandem. The MVP repeat is composed of ~53 amino acids and forms a structural part of the vault wall. The C-terminal part of MVP may be involved in oligomerization and be located in the vault cap, while the MVP repeats in the N-terminal part can be packed like staves in a barrel to form the vault wall. The 3D structure of the repeat forms a fold that consists of a three stranded (B) antiparallel beta-sheet in a unique topology B2-B1-B3 and two loops. MVP repeats can be interaction-mediating modules, as MVP repeats 3 and 4 bind VPARP, which is one of the other vault proteins.; PDB: 3GF5_A 3GNG_A 3GNF_B 2ZUO_G 2QZV_B 2ZV5_c 2ZV4_Y 1Y7X_A.
Probab=21.60 E-value=55 Score=17.78 Aligned_cols=19 Identities=32% Similarity=0.513 Sum_probs=14.2
Q ss_pred CCCCCcEEEecCCCCCCCCCCC
Q psy2555 44 NFKKGSVILSNHPKAGGSHLPD 65 (90)
Q Consensus 44 ~l~~GDv~i~NDPy~GgtHl~D 65 (90)
.-++||.++..-| +++.|+
T Consensus 25 ~R~~Ge~WLv~gP---~~YiP~ 43 (43)
T PF01505_consen 25 KRKAGEEWLVTGP---GTYIPR 43 (43)
T ss_dssp EECTTEEEEEESS---SEECST
T ss_pred EEeCCCEEEEeCC---eeEcCC
Confidence 4688999999888 555553
No 138
>PRK05967 cystathionine beta-lyase; Provisional
Probab=21.35 E-value=1.2e+02 Score=23.98 Aligned_cols=29 Identities=14% Similarity=-0.046 Sum_probs=21.1
Q ss_pred HHHHHHHHHhcCCCCCCCcEEEecCCCCCCCC
Q psy2555 31 QEAVKFQIDHRKGNFKKGSVILSNHPKAGGSH 62 (90)
Q Consensus 31 ~~~v~~~~~~~~~~l~~GDv~i~NDPy~GgtH 62 (90)
..++..++..+ ++|||-++..+|..+++.
T Consensus 89 ~aAi~~~l~al---l~~GD~Vlv~~~~Y~~~~ 117 (395)
T PRK05967 89 LAAVTVPFLGF---LSPGDHALIVDSVYYPTR 117 (395)
T ss_pred HHHHHHHHHHh---cCCCCEEEEccCCcHHHH
Confidence 34555555444 899999999999887754
No 139
>PRK13699 putative methylase; Provisional
Probab=21.13 E-value=1.3e+02 Score=21.74 Aligned_cols=22 Identities=23% Similarity=0.377 Sum_probs=15.5
Q ss_pred HHHHHHhcCCCCCCCcEEEecCCCCCC
Q psy2555 34 VKFQIDHRKGNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 34 v~~~~~~~~~~l~~GDv~i~NDPy~Gg 60 (90)
++.+++.+ -++||+++ |||.|+
T Consensus 153 ~~~~i~~~---s~~g~~vl--Dpf~Gs 174 (227)
T PRK13699 153 LQPLIESF---THPNAIVL--DPFAGS 174 (227)
T ss_pred HHHHHHHh---CCCCCEEE--eCCCCC
Confidence 35566655 36999877 999874
No 140
>KOG4207|consensus
Probab=21.11 E-value=1.1e+02 Score=23.25 Aligned_cols=29 Identities=7% Similarity=0.161 Sum_probs=23.6
Q ss_pred chHHHHHHHHHhcCCCCCCCcEEEecCCCCCC
Q psy2555 29 SMQEAVKFQIDHRKGNFKKGSVILSNHPKAGG 60 (90)
Q Consensus 29 ~~~~~v~~~~~~~~~~l~~GDv~i~NDPy~Gg 60 (90)
+.+..++.+.++|+ +-|||+|--|+|+..
T Consensus 25 Tspd~LrrvFekYG---~vgDVyIPrdr~Tr~ 53 (256)
T KOG4207|consen 25 TSPDDLRRVFEKYG---RVGDVYIPRDRYTRQ 53 (256)
T ss_pred CCHHHHHHHHHHhC---cccceeccccccccc
Confidence 45667788999886 569999999999863
No 141
>PF03260 Lipoprotein_11: Lepidopteran low molecular weight (30 kD) lipoprotein; InterPro: IPR004943 This family includes Lepidopteran low molecular weight (30 kDa) lipoprotein, which is an extracellular protein of unknown function. Biosynthesis occurs in a stage-dependent fashion in the fat body. ; GO: 0005576 extracellular region; PDB: 3PUB_B.
Probab=20.90 E-value=1.1e+02 Score=23.42 Aligned_cols=20 Identities=30% Similarity=0.514 Sum_probs=16.6
Q ss_pred eEEEEeeeeCCCCCCCccEEEEEeC
Q psy2555 66 LTVITPVFIDSQPVEEGPVFFVANR 90 (90)
Q Consensus 66 ~~~~~PVF~~Gel~~~~lv~~~a~~ 90 (90)
...+.|+-++|++ ++|.-+|
T Consensus 193 ~WyLqP~~~~~~l-----LFfI~NR 212 (253)
T PF03260_consen 193 QWYLQPVKYNGEL-----LFFIYNR 212 (253)
T ss_dssp -EEEEEEEETTEE-----EEEEEET
T ss_pred EEEEEeEEeCCee-----EEEEEeh
Confidence 4688999999987 9998776
No 142
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=20.86 E-value=51 Score=20.07 Aligned_cols=12 Identities=25% Similarity=0.384 Sum_probs=7.5
Q ss_pred CCCCCcEEEecC
Q psy2555 44 NFKKGSVILSNH 55 (90)
Q Consensus 44 ~l~~GDv~i~ND 55 (90)
.++|||+++.|-
T Consensus 44 ~l~~g~~~li~p 55 (136)
T PF02311_consen 44 PLKPGDLFLIPP 55 (136)
T ss_dssp EE-TT-EEEE-T
T ss_pred EEECCEEEEecC
Confidence 589999999873
No 143
>PRK08202 purine nucleoside phosphorylase; Provisional
Probab=20.82 E-value=67 Score=23.98 Aligned_cols=14 Identities=21% Similarity=0.458 Sum_probs=12.0
Q ss_pred CCCCCcEEEecCCC
Q psy2555 44 NFKKGSVILSNHPK 57 (90)
Q Consensus 44 ~l~~GDv~i~NDPy 57 (90)
++++||+++.+|=.
T Consensus 120 ~l~~GDiVi~~d~i 133 (272)
T PRK08202 120 DFGPGDLMLISDHI 133 (272)
T ss_pred CCCCCCEEEEchhh
Confidence 69999999999853
No 144
>PHA03200 uracil DNA glycosylase; Provisional
Probab=20.82 E-value=99 Score=23.52 Aligned_cols=20 Identities=25% Similarity=0.238 Sum_probs=14.1
Q ss_pred EEEecCCCCCCCCCCCeEEEE
Q psy2555 50 VILSNHPKAGGSHLPDLTVIT 70 (90)
Q Consensus 50 v~i~NDPy~GgtHl~D~~~~~ 70 (90)
||+-.|||.+ .+..=+++-.
T Consensus 88 VIlGQDPYh~-gqA~GLaFSV 107 (255)
T PHA03200 88 VIVGQDPYHD-GSACGLAFGT 107 (255)
T ss_pred EEEecCCCCC-CccceEEEEe
Confidence 7899999998 5555444443
No 145
>PF08918 PhoQ_Sensor: PhoQ Sensor; InterPro: IPR015014 The PhoQ Sensor is required for the virulence of various Gram-negative bacteria by allowing interaction of PhoPQ with the intracellular membrane, resulting in remodelling of the bacterial cell surface and subsequent bacterial resistance to host antimicrobial peptides. The domain contains a major flat acidic surface, which binds to at least 3 calcium ions, neutralising the domain's negative charge and allowing interaction with the negatively charged membrane []. ; GO: 0004673 protein histidine kinase activity, 0005524 ATP binding, 0046872 metal ion binding, 0000160 two-component signal transduction system (phosphorelay), 0018106 peptidyl-histidine phosphorylation, 0016020 membrane; PDB: 1YAX_D 3BQA_B 3BQ8_B.
Probab=20.81 E-value=58 Score=23.59 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=13.4
Q ss_pred eEEeCCCCCeeeecCCCce
Q psy2555 7 KESFGPDGGLVSNAPHIPV 25 (90)
Q Consensus 7 ~~i~d~~G~~va~~~g~p~ 25 (90)
+-|||.+|+++++...+|.
T Consensus 77 ~~IYD~~G~lLW~qr~vP~ 95 (180)
T PF08918_consen 77 VLIYDENGKLLWRQRDVPE 95 (180)
T ss_dssp EEEEETTS-EEEESS--HH
T ss_pred EEEEcCCCcEEEecCccHH
Confidence 4699999999998777663
No 146
>PRK06666 fliM flagellar motor switch protein FliM; Validated
Probab=20.55 E-value=86 Score=23.80 Aligned_cols=26 Identities=31% Similarity=0.483 Sum_probs=18.7
Q ss_pred ecchHHHHHHHHHhcCCCCCCCcEEEecCCC
Q psy2555 27 LGSMQEAVKFQIDHRKGNFKKGSVILSNHPK 57 (90)
Q Consensus 27 ~g~~~~~v~~~~~~~~~~l~~GDv~i~NDPy 57 (90)
+|.....++.++ +|++|||+-.|-+.
T Consensus 266 L~~~~i~l~dll-----~L~vGDVI~L~~~~ 291 (337)
T PRK06666 266 LGEIKLTLSEIL-----NLKVGDVIPLEKPA 291 (337)
T ss_pred EecceeeHHHHh-----CCCCCCEEEeCCCC
Confidence 444455555554 79999999999875
No 147
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=20.46 E-value=57 Score=22.71 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=18.3
Q ss_pred CCCCCCcEEEecCCCCCCCCCCCeEEEE
Q psy2555 43 GNFKKGSVILSNHPKAGGSHLPDLTVIT 70 (90)
Q Consensus 43 ~~l~~GDv~i~NDPy~GgtHl~D~~~~~ 70 (90)
.+++|||+++.+. |-.=+.|..++.
T Consensus 50 ~~L~~GDiI~l~~---g~~vPaD~~ll~ 74 (230)
T PF00122_consen 50 SELVPGDIIILKA---GDIVPADGILLE 74 (230)
T ss_dssp GGT-TTSEEEEET---TEBESSEEEEEE
T ss_pred hhccceeeeeccc---ccccccCcccee
Confidence 4799999999865 446677777776
No 148
>COG0791 Spr Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]
Probab=20.41 E-value=85 Score=21.67 Aligned_cols=12 Identities=17% Similarity=0.551 Sum_probs=10.9
Q ss_pred CCCCCcEEEecC
Q psy2555 44 NFKKGSVILSNH 55 (90)
Q Consensus 44 ~l~~GDv~i~ND 55 (90)
++++||+++.|.
T Consensus 138 ~~~~GDlvff~~ 149 (197)
T COG0791 138 DLQPGDLVFFNT 149 (197)
T ss_pred hCCCCCEEEEec
Confidence 589999999997
No 149
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=20.33 E-value=61 Score=18.22 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=9.9
Q ss_pred CCCCCCcEEEec
Q psy2555 43 GNFKKGSVILSN 54 (90)
Q Consensus 43 ~~l~~GDv~i~N 54 (90)
+.+++||+++.+
T Consensus 9 P~i~~Gd~v~v~ 20 (70)
T PF00717_consen 9 PTIKDGDIVLVD 20 (70)
T ss_dssp GTSSTTEEEEEE
T ss_pred cCeeCCCEEEEE
Confidence 468899999887
No 150
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=20.30 E-value=1e+02 Score=19.05 Aligned_cols=19 Identities=32% Similarity=0.281 Sum_probs=13.1
Q ss_pred HHHHHhcCCCCCCCcEEEe
Q psy2555 35 KFQIDHRKGNFKKGSVILS 53 (90)
Q Consensus 35 ~~~~~~~~~~l~~GDv~i~ 53 (90)
+..+++|...|+||.++..
T Consensus 18 ~~~~~~f~~~l~Eg~~y~i 36 (95)
T PF02721_consen 18 KELVDKFKDSLKEGSWYTI 36 (95)
T ss_pred HHHHHHHHhhcccCCEEEe
Confidence 4455556667899998764
No 151
>PRK13261 ureE urease accessory protein UreE; Provisional
Probab=20.23 E-value=71 Score=22.03 Aligned_cols=12 Identities=17% Similarity=0.523 Sum_probs=11.2
Q ss_pred CCCCCcEEEecC
Q psy2555 44 NFKKGSVILSNH 55 (90)
Q Consensus 44 ~l~~GDv~i~ND 55 (90)
.|++||++..+|
T Consensus 55 ~L~dGDvL~~d~ 66 (159)
T PRK13261 55 VLRDGDVLFLDD 66 (159)
T ss_pred ccCCCCEEEeCC
Confidence 599999999998
No 152
>COG3971 2-keto-4-pentenoate hydratase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.15 E-value=1.5e+02 Score=22.81 Aligned_cols=48 Identities=10% Similarity=0.093 Sum_probs=26.8
Q ss_pred EEeCCCCCeeeecC--CCceeecchHHHHHHHHHhcCCCCCCCcEEEecC
Q psy2555 8 ESFGPDGGLVSNAP--HIPVHLGSMQEAVKFQIDHRKGNFKKGSVILSNH 55 (90)
Q Consensus 8 ~i~d~~G~~va~~~--g~p~~~g~~~~~v~~~~~~~~~~l~~GDv~i~ND 55 (90)
++.+++|.....+. +++-|--.--......+..++..|+-|||+++-.
T Consensus 185 ~~l~rng~~~e~g~~aavLghP~~a~~wLAn~~a~~G~~Lk~G~IVl~Gs 234 (264)
T COG3971 185 ATLYRNGVEEETGVGAAVLGHPAAALAWLANKLAAYGVPLKAGDIVLTGS 234 (264)
T ss_pred ceeeecCEEEEeeechhhcCCcHHHHHHHHHHHHHcCCCcccCcEEecCc
Confidence 45566776665433 3444432212222333445667899999998743
No 153
>PF11814 DUF3335: Peptidase_C39 like family; InterPro: IPR021770 This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Probab=20.13 E-value=74 Score=23.48 Aligned_cols=14 Identities=7% Similarity=0.257 Sum_probs=12.4
Q ss_pred CCCcEEEecCCCCC
Q psy2555 46 KKGSVILSNHPKAG 59 (90)
Q Consensus 46 ~~GDv~i~NDPy~G 59 (90)
.++|.++.||||..
T Consensus 155 ~d~~~vyihDP~~d 168 (207)
T PF11814_consen 155 VDDDFVYIHDPDVD 168 (207)
T ss_pred ecCCEEEEeCCCCC
Confidence 47899999999986
Done!