Query psy4809
Match_columns 89
No_of_seqs 101 out of 383
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 18:17:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4809.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4809hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00148 PROF Profilin binds ac 100.0 3E-35 6.6E-40 190.4 12.4 89 1-89 39-127 (127)
2 PTZ00316 profilin; Provisional 100.0 5.3E-35 1.2E-39 193.3 12.4 89 1-89 39-150 (150)
3 smart00392 PROF Profilin. Bind 100.0 2.4E-34 5.3E-39 186.5 12.1 89 1-89 41-129 (129)
4 KOG1755|consensus 100.0 1.9E-30 4.1E-35 167.4 10.7 89 1-89 39-128 (128)
5 PF00235 Profilin: Profilin; 100.0 2.1E-30 4.6E-35 165.3 9.9 84 1-84 38-121 (121)
6 PHA02610 uvsY.-2 hypothetical 82.2 2.2 4.7E-05 23.7 2.8 31 50-80 4-36 (53)
7 COG3382 Solo B3/4 domain (OB-f 79.0 9.5 0.00021 27.2 5.9 35 53-87 181-215 (229)
8 PF09176 Mpt_N: Methylene-tetr 68.2 3.2 6.9E-05 25.0 1.2 30 1-30 21-53 (81)
9 PF10886 DUF2685: Protein of u 66.1 10 0.00023 21.1 2.9 32 50-81 4-37 (54)
10 PF05952 ComX: Bacillus compet 63.2 7.4 0.00016 21.9 2.0 18 1-18 29-46 (57)
11 COG1157 FliI Flagellar biosynt 60.2 12 0.00025 29.3 3.2 34 56-89 219-253 (441)
12 cd01132 F1_ATPase_alpha F1 ATP 59.3 16 0.00034 26.7 3.7 34 56-89 127-161 (274)
13 cd01134 V_A-ATPase_A V/A-type 57.6 14 0.00029 28.2 3.2 34 56-89 220-254 (369)
14 COG1660 Predicted P-loop-conta 57.1 26 0.00056 25.8 4.4 33 55-88 240-272 (286)
15 PF02021 UPF0102: Uncharacteri 56.4 30 0.00065 20.8 4.1 67 20-87 11-78 (93)
16 PF12965 DUF3854: Domain of un 56.0 29 0.00062 22.3 4.2 36 54-89 66-103 (130)
17 PRK00394 transcription factor; 55.7 38 0.00083 23.0 4.9 43 43-89 42-84 (179)
18 PRK05922 type III secretion sy 54.3 19 0.00041 28.0 3.5 35 55-89 212-247 (434)
19 TIGR01043 ATP_syn_A_arch ATP s 54.2 17 0.00037 29.3 3.4 34 56-89 285-319 (578)
20 PF08513 LisH: LisH; InterPro 54.1 9.9 0.00022 17.8 1.3 10 80-89 7-16 (27)
21 PF13734 Inhibitor_I69: Spi pr 54.1 45 0.00097 20.5 4.6 81 2-87 8-92 (96)
22 PF11389 Porin_OmpL1: Leptospi 52.2 28 0.00061 25.1 3.9 49 12-60 30-79 (267)
23 PF03129 HGTP_anticodon: Antic 52.1 36 0.00077 19.7 3.9 30 57-89 1-30 (94)
24 PRK04192 V-type ATP synthase s 51.2 20 0.00043 29.0 3.3 34 56-89 290-324 (586)
25 PF08479 POTRA_2: POTRA domain 49.6 23 0.00049 20.1 2.6 22 68-89 31-52 (76)
26 smart00667 LisH Lissencephaly 47.8 12 0.00026 17.3 1.1 13 77-89 7-19 (34)
27 PF03668 ATP_bind_2: P-loop AT 47.7 48 0.001 24.4 4.6 34 55-89 239-272 (284)
28 PRK06936 type III secretion sy 47.3 24 0.00052 27.5 3.1 34 56-89 218-252 (439)
29 TIGR01042 V-ATPase_V1_A V-type 47.0 26 0.00055 28.4 3.3 34 56-89 291-325 (591)
30 COG2139 RPL21A Ribosomal prote 47.0 35 0.00075 21.3 3.2 24 45-68 57-80 (98)
31 cd00861 ProRS_anticodon_short 46.6 48 0.001 18.9 3.8 19 71-89 14-32 (94)
32 TIGR02764 spore_ybaN_pdaB poly 46.3 47 0.001 21.9 4.2 30 58-89 153-182 (191)
33 PRK02821 hypothetical protein; 45.3 48 0.0011 19.6 3.6 42 6-47 6-51 (77)
34 cd01133 F1-ATPase_beta F1 ATP 45.1 29 0.00062 25.3 3.1 34 56-89 128-163 (274)
35 PRK08972 fliI flagellum-specif 45.0 27 0.00059 27.2 3.1 34 56-89 218-252 (444)
36 PF03859 CG-1: CG-1 domain; I 44.9 27 0.00058 22.5 2.6 49 1-49 9-65 (118)
37 TIGR03496 FliI_clade1 flagella 44.9 28 0.0006 26.7 3.2 34 56-89 193-227 (411)
38 PF02770 Acyl-CoA_dh_M: Acyl-C 44.8 23 0.00049 18.8 2.0 17 21-37 24-40 (52)
39 PF08356 EF_assoc_2: EF hand a 44.5 17 0.00036 22.2 1.6 29 1-29 4-34 (89)
40 PF07244 Surf_Ag_VNR: Surface 44.1 30 0.00064 19.1 2.6 22 68-89 32-53 (78)
41 PRK09099 type III secretion sy 43.8 32 0.00069 26.7 3.3 34 56-89 219-253 (441)
42 PRK08927 fliI flagellum-specif 43.7 29 0.00064 27.0 3.1 34 56-89 214-248 (442)
43 TIGR03497 FliI_clade2 flagella 43.6 31 0.00068 26.5 3.3 34 56-89 193-227 (413)
44 cd01136 ATPase_flagellum-secre 43.4 29 0.00062 25.9 3.0 34 56-89 125-159 (326)
45 PRK00468 hypothetical protein; 42.9 62 0.0014 18.9 3.8 42 6-47 5-50 (75)
46 COG3377 Uncharacterized conser 41.9 84 0.0018 19.4 4.4 16 22-37 5-20 (95)
47 PRK08472 fliI flagellum-specif 41.9 40 0.00086 26.2 3.6 34 56-89 212-246 (434)
48 TIGR03498 FliI_clade3 flagella 41.3 35 0.00076 26.3 3.2 34 56-89 196-230 (418)
49 PRK14675 hypothetical protein; 40.9 63 0.0014 20.7 3.9 69 19-88 22-91 (125)
50 PRK09280 F0F1 ATP synthase sub 40.9 36 0.00079 26.7 3.3 34 56-89 203-238 (463)
51 PF00656 Peptidase_C14: Caspas 40.7 49 0.0011 22.2 3.7 33 57-89 2-36 (248)
52 cd00320 cpn10 Chaperonin 10 Kd 40.1 21 0.00046 21.6 1.6 18 21-38 71-88 (93)
53 PF00006 ATP-synt_ab: ATP synt 40.1 35 0.00075 23.8 2.8 34 56-89 71-105 (215)
54 PRK12597 F0F1 ATP synthase sub 40.1 31 0.00068 26.9 2.8 34 56-89 202-237 (461)
55 PTZ00414 10 kDa heat shock pro 40.1 29 0.00063 21.6 2.2 18 21-38 76-93 (100)
56 COG1832 Predicted CoA-binding 39.9 52 0.0011 21.8 3.5 30 54-89 15-44 (140)
57 PRK07721 fliI flagellum-specif 39.7 44 0.00095 25.9 3.6 34 56-89 214-248 (438)
58 PHA02119 hypothetical protein 39.6 21 0.00045 21.2 1.4 12 78-89 57-68 (87)
59 cd04516 TBP_eukaryotes eukaryo 39.3 1.2E+02 0.0026 20.5 5.4 39 47-89 47-85 (174)
60 PF07799 DUF1643: Protein of u 39.3 51 0.0011 20.8 3.4 34 56-89 13-46 (136)
61 PRK00364 groES co-chaperonin G 39.2 23 0.0005 21.5 1.7 18 21-38 72-89 (95)
62 KOG0141|consensus 39.2 43 0.00094 25.6 3.3 42 21-62 183-227 (421)
63 PF02789 Peptidase_M17_N: Cyto 39.0 88 0.0019 18.9 4.5 34 55-88 52-86 (126)
64 cd00032 CASc Caspase, interleu 38.7 68 0.0015 22.3 4.2 33 57-89 11-46 (243)
65 TIGR00725 conserved hypothetic 38.4 67 0.0014 21.2 3.9 29 61-89 4-32 (159)
66 COG3512 CRISPR-associated prot 38.0 57 0.0012 20.6 3.2 30 60-89 9-38 (116)
67 PRK05688 fliI flagellum-specif 37.7 41 0.00088 26.3 3.1 33 57-89 225-258 (451)
68 PRK08149 ATP synthase SpaL; Va 37.2 49 0.0011 25.7 3.4 34 56-89 207-241 (428)
69 PLN00062 TATA-box-binding prot 36.9 1.4E+02 0.0029 20.4 5.5 40 46-89 46-85 (179)
70 PRK06820 type III secretion sy 36.8 45 0.00098 25.9 3.2 34 56-89 219-253 (440)
71 CHL00060 atpB ATP synthase CF1 36.5 47 0.001 26.3 3.3 33 56-88 227-260 (494)
72 cd00862 ProRS_anticodon_zinc P 36.3 91 0.002 21.2 4.4 33 57-89 12-44 (202)
73 TIGR03305 alt_F1F0_F1_bet alte 35.9 49 0.0011 25.9 3.3 34 56-89 197-232 (449)
74 TIGR01041 ATP_syn_B_arch ATP s 35.7 48 0.0011 25.9 3.2 34 56-89 203-238 (458)
75 cd04955 GT1_like_6 This family 35.4 78 0.0017 22.0 4.1 31 59-89 3-33 (363)
76 TIGR00460 fmt methionyl-tRNA f 35.3 1.8E+02 0.0038 21.2 7.0 33 2-37 216-248 (313)
77 TIGR01752 flav_long flavodoxin 35.3 86 0.0019 20.4 4.1 35 54-88 77-111 (167)
78 PRK04196 V-type ATP synthase s 34.9 51 0.0011 25.7 3.3 34 56-89 205-240 (460)
79 TIGR00962 atpA proton transloc 34.9 52 0.0011 26.0 3.3 34 56-89 219-253 (501)
80 cd04518 TBP_archaea archaeal T 34.9 1.4E+02 0.0031 20.1 5.8 41 45-89 45-85 (174)
81 PRK14533 groES co-chaperonin G 34.1 39 0.00086 20.5 2.1 18 21-38 67-84 (91)
82 PF09314 DUF1972: Domain of un 33.7 81 0.0017 21.6 3.8 33 56-88 2-34 (185)
83 PF14553 YqbF: YqbF, hypotheti 33.7 41 0.00089 17.8 1.8 14 76-89 21-34 (43)
84 PRK09281 F0F1 ATP synthase sub 33.2 57 0.0012 25.8 3.3 34 56-89 220-254 (502)
85 PF00166 Cpn10: Chaperonin 10 32.9 41 0.00088 20.2 2.0 18 21-38 71-88 (93)
86 cd01135 V_A-ATPase_B V/A-type 32.8 60 0.0013 23.7 3.2 34 56-89 131-166 (276)
87 TIGR01039 atpD ATP synthase, F 32.6 60 0.0013 25.5 3.3 34 56-89 202-237 (461)
88 PRK14698 V-type ATP synthase s 32.5 49 0.0011 28.5 3.0 34 56-89 719-753 (1017)
89 PF02911 Formyl_trans_C: Formy 32.3 1.1E+02 0.0023 17.8 7.0 33 2-37 14-46 (100)
90 PRK12359 flavodoxin FldB; Prov 32.2 1E+02 0.0022 20.7 4.0 35 54-88 78-112 (172)
91 PRK07594 type III secretion sy 31.6 68 0.0015 24.9 3.4 33 57-89 212-245 (433)
92 TIGR03324 alt_F1F0_F1_al alter 31.0 59 0.0013 25.8 3.0 34 56-89 220-254 (497)
93 COG4702 Uncharacterized conser 30.9 85 0.0018 21.4 3.4 38 48-85 119-158 (168)
94 PRK08105 flavodoxin; Provision 30.8 60 0.0013 21.0 2.7 22 68-89 10-31 (149)
95 PF03358 FMN_red: NADPH-depend 30.5 1.3E+02 0.0029 18.7 4.2 26 63-88 6-31 (152)
96 PF13439 Glyco_transf_4: Glyco 30.2 1.1E+02 0.0023 18.7 3.7 21 69-89 10-30 (177)
97 PRK09273 hypothetical protein; 30.2 83 0.0018 22.2 3.4 29 61-89 3-31 (211)
98 PF08357 SEFIR: SEFIR domain; 30.0 54 0.0012 20.7 2.3 18 72-89 13-31 (150)
99 cd03792 GT1_Trehalose_phosphor 29.8 88 0.0019 22.5 3.7 29 61-89 2-30 (372)
100 COG1938 Archaeal enzymes of AT 29.7 1.2E+02 0.0027 21.8 4.3 33 56-88 75-107 (244)
101 PRK09271 flavodoxin; Provision 29.5 1.2E+02 0.0026 19.6 3.9 20 69-88 10-29 (160)
102 PF10653 Phage-A118_gp45: Prot 29.4 37 0.00081 18.9 1.3 15 73-87 38-52 (62)
103 cd08053 Yqbg Putative Head-Tai 29.1 70 0.0015 19.8 2.7 22 67-88 48-69 (121)
104 cd03823 GT1_ExpE7_like This fa 29.0 96 0.0021 21.1 3.6 31 59-89 3-33 (359)
105 KOG3222|consensus 28.9 54 0.0012 22.8 2.3 16 74-89 177-192 (195)
106 PRK13343 F0F1 ATP synthase sub 28.9 82 0.0018 25.0 3.5 34 56-89 220-254 (502)
107 PF09907 DUF2136: Uncharacteri 28.8 73 0.0016 18.7 2.6 13 23-35 40-52 (76)
108 COG2945 Predicted hydrolase of 28.5 76 0.0017 22.4 3.0 33 57-89 28-61 (210)
109 COG1058 CinA Predicted nucleot 28.3 64 0.0014 23.3 2.7 34 56-89 2-35 (255)
110 PRK01064 hypothetical protein; 28.1 1.3E+02 0.0029 17.7 4.2 42 6-47 5-50 (78)
111 COG4535 CorC Putative Mg2+ and 28.1 1.4E+02 0.003 22.0 4.3 40 2-42 232-275 (293)
112 PRK06703 flavodoxin; Provision 27.9 1.4E+02 0.0031 18.8 4.1 27 59-88 4-30 (151)
113 CHL00059 atpA ATP synthase CF1 27.5 76 0.0016 25.1 3.1 34 56-89 199-233 (485)
114 cd04517 TLF TBP-like factors ( 27.4 2E+02 0.0043 19.4 5.6 40 46-89 46-85 (174)
115 COG2885 OmpA Outer membrane pr 26.9 1.5E+02 0.0033 19.6 4.2 15 74-88 137-151 (190)
116 PRK02118 V-type ATP synthase s 26.6 86 0.0019 24.5 3.2 33 56-88 196-229 (436)
117 PHA02755 hypothetical protein; 26.3 43 0.00092 20.3 1.2 21 59-79 9-29 (96)
118 KOG4048|consensus 26.0 89 0.0019 21.5 2.9 43 41-83 82-126 (201)
119 COG1647 Esterase/lipase [Gener 25.9 53 0.0012 23.7 1.9 15 75-89 29-43 (243)
120 PF00352 TBP: Transcription fa 25.9 1.5E+02 0.0032 17.3 5.9 38 47-88 49-86 (86)
121 PRK09267 flavodoxin FldA; Vali 25.7 1.6E+02 0.0035 19.0 4.1 35 54-88 79-113 (169)
122 PF11513 TA0956: Thermoplasma 25.4 1.8E+02 0.0039 18.2 5.1 38 49-89 66-104 (110)
123 COG3403 Uncharacterized conser 25.2 1.2E+02 0.0026 21.9 3.5 32 57-88 52-83 (257)
124 PRK12678 transcription termina 25.1 83 0.0018 26.0 3.0 32 58-89 471-503 (672)
125 TIGR01026 fliI_yscN ATPase Fli 24.9 93 0.002 24.1 3.2 32 58-89 221-253 (440)
126 PF13856 Gifsy-2: ATP-binding 24.6 70 0.0015 19.1 2.0 18 20-37 68-85 (95)
127 PRK14688 hypothetical protein; 24.6 1.5E+02 0.0032 18.9 3.6 68 20-88 21-89 (121)
128 PF02233 PNTB: NAD(P) transhyd 24.6 59 0.0013 25.6 2.0 19 70-88 320-338 (463)
129 TIGR01040 V-ATPase_V1_B V-type 24.6 85 0.0018 24.8 2.9 34 56-89 212-247 (466)
130 PRK05569 flavodoxin; Provision 24.3 1.8E+02 0.004 17.9 4.1 27 59-88 4-30 (141)
131 PRK06793 fliI flagellum-specif 24.1 1E+02 0.0022 24.0 3.2 32 58-89 214-246 (432)
132 PF07485 DUF1529: Domain of Un 24.1 75 0.0016 20.4 2.2 37 1-43 65-101 (123)
133 smart00538 POP4 A domain found 23.9 1.8E+02 0.0038 17.6 3.9 16 47-62 29-44 (92)
134 PRK03298 hypothetical protein; 23.7 2.2E+02 0.0048 20.3 4.6 67 3-86 105-171 (224)
135 PRK05723 flavodoxin; Provision 23.4 97 0.0021 20.2 2.7 22 68-89 9-30 (151)
136 PF04320 DUF469: Protein with 23.3 41 0.00089 21.0 0.8 26 2-29 28-53 (101)
137 PF01868 UPF0086: Domain of un 22.9 93 0.002 18.6 2.3 35 27-64 13-47 (89)
138 TIGR03072 release_prfH putativ 22.7 2.7E+02 0.0059 19.4 5.3 37 50-86 130-166 (200)
139 TIGR01754 flav_RNR ribonucleot 22.7 1.8E+02 0.004 18.1 3.8 20 69-88 10-29 (140)
140 PRK02983 lysS lysyl-tRNA synth 22.6 5E+02 0.011 22.8 7.2 58 31-89 256-313 (1094)
141 PF03665 UPF0172: Uncharacteri 22.3 76 0.0016 21.9 2.1 22 6-28 12-33 (196)
142 PRK09004 FMN-binding protein M 22.3 1.1E+02 0.0023 19.7 2.7 22 68-89 10-31 (146)
143 PF04960 Glutaminase: Glutamin 21.9 2.4E+02 0.0053 20.7 4.7 45 41-85 234-282 (286)
144 PRK07960 fliI flagellum-specif 21.8 1.1E+02 0.0023 24.1 3.0 18 72-89 248-265 (455)
145 COG1837 Predicted RNA-binding 21.8 1.9E+02 0.0041 17.1 3.8 42 6-47 5-50 (76)
146 PF14080 DUF4261: Domain of un 21.7 1.7E+02 0.0038 16.7 3.8 25 64-88 16-40 (77)
147 PRK03879 ribonuclease P protei 21.5 1.8E+02 0.0039 17.8 3.4 13 21-33 31-43 (96)
148 PF06580 His_kinase: Histidine 21.5 1E+02 0.0022 17.9 2.2 17 70-86 29-45 (82)
149 PRK05416 glmZ(sRNA)-inactivati 21.5 2.4E+02 0.0051 20.5 4.6 33 55-89 242-274 (288)
150 cd03530 Rieske_NirD_small_Baci 21.5 1.6E+02 0.0035 17.1 3.2 22 22-43 16-37 (98)
151 PF00649 Copper-fist: Copper f 21.4 99 0.0021 16.1 1.9 13 24-36 2-14 (40)
152 PF15643 Tox-PL-2: Papain fold 21.4 1E+02 0.0022 19.3 2.3 20 69-88 17-36 (100)
153 PRK00971 glutaminase; Provisio 21.2 2.9E+02 0.0063 20.6 5.0 45 41-85 255-303 (307)
154 COG0234 GroS Co-chaperonin Gro 21.2 83 0.0018 19.5 1.9 18 21-38 72-89 (96)
155 PF02696 UPF0061: Uncharacteri 21.1 2.9E+02 0.0063 21.9 5.2 48 39-87 163-211 (487)
156 cd03416 CbiX_SirB_N Sirohydroc 21.0 1.7E+02 0.0037 17.1 3.3 26 59-87 3-28 (101)
157 COG4725 IME4 Transcriptional a 21.0 1.6E+02 0.0035 20.3 3.4 54 29-82 102-156 (198)
158 KOG2500|consensus 21.0 1.2E+02 0.0027 21.9 2.9 31 9-39 68-98 (253)
159 smart00115 CASc Caspase, inter 21.0 1.7E+02 0.0036 20.4 3.6 33 57-89 10-44 (241)
160 PF13399 LytR_C: LytR cell env 21.0 95 0.0021 17.9 2.1 29 57-89 2-30 (90)
161 COG1654 BirA Biotin operon rep 20.8 99 0.0021 18.3 2.1 19 71-89 30-48 (79)
162 TIGR03814 Gln_ase glutaminase 20.7 3.2E+02 0.007 20.3 5.1 45 41-85 248-296 (300)
163 PRK12356 glutaminase; Reviewed 20.6 3.1E+02 0.0068 20.5 5.1 45 41-85 259-307 (319)
164 PF11314 DUF3117: Protein of u 20.5 64 0.0014 17.6 1.1 14 1-14 35-48 (51)
165 PF13822 ACC_epsilon: Acyl-CoA 20.5 71 0.0015 17.8 1.4 13 2-14 12-24 (62)
166 PF08269 Cache_2: Cache domain 20.1 45 0.00097 19.5 0.5 18 22-39 49-66 (95)
167 cd07321 Extradiol_Dioxygenase_ 20.1 28 0.0006 20.4 -0.4 17 1-19 35-51 (77)
No 1
>cd00148 PROF Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway.
Probab=100.00 E-value=3e-35 Score=190.44 Aligned_cols=89 Identities=48% Similarity=0.772 Sum_probs=87.4
Q ss_pred CCHHHHHHHHhhcCCCccccccceEEcceEEEEEEecCcEEEEecCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHH
Q psy4809 1 LSKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGTDKVIRAKLGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKL 80 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~l 80 (89)
++|+|+++|+++|+||+.++++||+|+|+||+++|+|++.+++|++++|++++||+|+||||+|+++++|++|+++|++|
T Consensus 39 ~t~~E~~~i~~~f~d~~~~~~~Gi~l~G~KY~~l~~d~~~i~~kk~~~Gi~i~kT~~~ivi~~y~e~~~~g~~~~~v~~l 118 (127)
T cd00148 39 LTPEEVGTLVAGFKDPDGVFSTGLTLGGQKYMVIRADDRSIYGKKGAGGVVIVKTKQALVIGMYEEGVQPGQANKVVEKL 118 (127)
T ss_pred cCHHHHHHHHHHccCccccccCCEEECCeEEEEEecCccEEEeeeCCCeEEEEECCCEEEEEEcCCCCCHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCC
Q psy4809 81 GDYLVSCGY 89 (89)
Q Consensus 81 AdyL~~~gy 89 (89)
||||+++||
T Consensus 119 adYL~~~gy 127 (127)
T cd00148 119 ADYLRSQGY 127 (127)
T ss_pred HHHHHHcCC
Confidence 999999998
No 2
>PTZ00316 profilin; Provisional
Probab=100.00 E-value=5.3e-35 Score=193.33 Aligned_cols=89 Identities=25% Similarity=0.483 Sum_probs=85.2
Q ss_pred CCHHHHHHHHhhcCCCccccccceEEcceEEEEEEe----cCcEEEEecCCceEEEEEcCceEEEEEeCC----------
Q psy4809 1 LSKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSG----TDKVIRAKLGKVGVHCMKTQQAVVISLYED---------- 66 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~----d~~~i~~kkg~~G~~i~KT~~aiiIg~y~~---------- 66 (89)
|+|+|+++|+++|+||+.++++||+|+|+||+++|+ |++.+|+||+++|+|++||+||+|||+|++
T Consensus 39 lspeE~~~I~~~F~d~~~l~~~Gi~l~G~KY~~lr~~~d~d~~~i~gKKg~~G~~i~kT~qaiiI~~y~~~~~~~~~~~~ 118 (150)
T PTZ00316 39 PQPEEVAHILKCLGNFSLVQSSGVTIYGVKFFGLQSGTEGDMKYIFFKKGAAGGCIYTSKQTAIIAVYGNPGDTSSLQQD 118 (150)
T ss_pred cCHHHHHHHHHHhcCCccccCCCEEEcceEEEEEEeccCCCcceEEEecCCCeEEEEEcCCEEEEEEeCCcccccccccc
Confidence 689999999999999999999999999999999998 457899999999999999999999999999
Q ss_pred ---------CCChhhHHHHHHHHHHHHHhCCC
Q psy4809 67 ---------PIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 67 ---------~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
+++|++|+.+||+|||||++.||
T Consensus 119 ~~~~~~~~~~~~pg~~~~~Ve~LadYL~~~gy 150 (150)
T PTZ00316 119 LEKNEAHAVAVNPADCNTTVKRIAEYLISLDY 150 (150)
T ss_pred cccccccccccCHHHHHHHHHHHHHHHHHcCC
Confidence 57999999999999999999998
No 3
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=100.00 E-value=2.4e-34 Score=186.46 Aligned_cols=89 Identities=38% Similarity=0.661 Sum_probs=87.1
Q ss_pred CCHHHHHHHHhhcCCCccccccceEEcceEEEEEEecCcEEEEecCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHH
Q psy4809 1 LSKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGTDKVIRAKLGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKL 80 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~l 80 (89)
++|+|+++|++.|+||+.++++||+|+|+||+++|+|++.+++||+++|++++||+|+||||+|+++++|++|+++|++|
T Consensus 41 ~~~~E~~~i~~~f~~~~~~~~~Gi~l~G~Ky~~~~~d~~~i~~kk~~~Gv~i~kT~~aivI~~y~e~~~~g~~~~~v~~l 120 (129)
T smart00392 41 ITPEEIAAIAALFNSLAAVFSNGLTLGGQKYMVIRADDRSIMGKKGAGGVVIVKTKQALIIGMYKEGVQPGQANKTVEKL 120 (129)
T ss_pred CCHHHHHHHHHHccCcchhccCCeEECCeEEEEEEecCcEEEeecCCceEEEEECCCEEEEEECCCCCChHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCC
Q psy4809 81 GDYLVSCGY 89 (89)
Q Consensus 81 AdyL~~~gy 89 (89)
||||+++||
T Consensus 121 adYL~~~Gy 129 (129)
T smart00392 121 ADYLRSSGY 129 (129)
T ss_pred HHHHHHcCC
Confidence 999999998
No 4
>KOG1755|consensus
Probab=99.97 E-value=1.9e-30 Score=167.45 Aligned_cols=89 Identities=40% Similarity=0.709 Sum_probs=86.6
Q ss_pred CCHHHHHHHHhhcCCCccccccceEEcceEEEEEEec-CcEEEEecCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHH
Q psy4809 1 LSKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGT-DKVIRAKLGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEK 79 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d-~~~i~~kkg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~ 79 (89)
++|+|+..+++.|+||+.++.+|++|+|+||+++|.| +.++++|++.+||+|.||.+++|+++|+|+++|++|+++||.
T Consensus 39 ~~~~e~~~~v~~F~d~~~~~~~Gl~L~Gqkylv~~ge~~~~~~gk~~~~gv~i~kT~~~li~~~y~e~v~~g~~~k~ve~ 118 (128)
T KOG1755|consen 39 VKPSEIPAIVAGFKDPGGLAGTGLTLGGQKYLVVRGEEGRVIRGKEGTGGVTIKKTGQALIFSIYKEGVQPGQCNKVVES 118 (128)
T ss_pred ccHHHHHHHHhcccCcccccccceeecccEEEEEecccceEEecccCCCcEEEEEcceEEEEEEcCCCCCHHHHHHHHHH
Confidence 5799999999999999999999999999999999999 678999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCC
Q psy4809 80 LGDYLVSCGY 89 (89)
Q Consensus 80 lAdyL~~~gy 89 (89)
|||||+++||
T Consensus 119 LadYL~~~gy 128 (128)
T KOG1755|consen 119 LADYLRESGY 128 (128)
T ss_pred HHHHHHhcCC
Confidence 9999999998
No 5
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=99.97 E-value=2.1e-30 Score=165.34 Aligned_cols=84 Identities=40% Similarity=0.706 Sum_probs=81.3
Q ss_pred CCHHHHHHHHhhcCCCccccccceEEcceEEEEEEecCcEEEEecCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHH
Q psy4809 1 LSKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGTDKVIRAKLGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKL 80 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~l 80 (89)
++|+|++.|++.|++|+.++.+||+|+|+||+++|.|++.+++|++++|++++||++++|||+|+++++|++|+++|++|
T Consensus 38 ~~~~E~~~i~~~f~~~~~~~~~gi~l~G~kY~~~~~d~~~i~~k~~~~G~~i~kt~~~ivIg~y~~~~~~~~~~~~v~~l 117 (121)
T PF00235_consen 38 ISPEEAKAIIKAFNNPSKFPSNGITLGGKKYIVLRADDNSIYGKKGKGGIIIVKTKQAIVIGMYDESIQPGNCNKAVEKL 117 (121)
T ss_dssp CSHHHHHHHHHHHHSSSHHHHH-EEETTEEEEEEEEETTEEEEEETTEEEEEEECSSEEEEEEEETTSTHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCchhcccCCeEEcCcEeEEEecCCceEEeeCCCCcEEEEECCCEEEEEEeCCCCCHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHH
Q psy4809 81 GDYL 84 (89)
Q Consensus 81 AdyL 84 (89)
||||
T Consensus 118 A~yL 121 (121)
T PF00235_consen 118 ADYL 121 (121)
T ss_dssp HHHH
T ss_pred HhhC
Confidence 9998
No 6
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=82.15 E-value=2.2 Score=23.66 Aligned_cols=31 Identities=26% Similarity=0.414 Sum_probs=24.1
Q ss_pred EEEEEcC--ceEEEEEeCCCCChhhHHHHHHHH
Q psy4809 50 VHCMKTQ--QAVVISLYEDPIQPQQAASVVEKL 80 (89)
Q Consensus 50 ~~i~KT~--~aiiIg~y~~~~~~~~~~~~ve~l 80 (89)
+++.|++ .++.|-+-..+.+||.|...++.+
T Consensus 4 CvvCK~Pi~~al~v~T~~Gpvh~g~C~~y~~e~ 36 (53)
T PHA02610 4 CVVCKQPIEKALVVETEKGPVHPGPCYNYVEEL 36 (53)
T ss_pred eeeeCCchhhceEEecCCCCCCChhHHHHHHhc
Confidence 3455655 677788888889999999988776
No 7
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=79.02 E-value=9.5 Score=27.23 Aligned_cols=35 Identities=14% Similarity=0.191 Sum_probs=31.6
Q ss_pred EEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhC
Q psy4809 53 MKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSC 87 (89)
Q Consensus 53 ~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~ 87 (89)
..|+.+++|+..-+++.-....++.+.|+++|...
T Consensus 181 ~~Tk~~l~I~e~vp~~~~~~l~~a~~~l~~~l~~~ 215 (229)
T COG3382 181 ESTKNVLLIAEGVPGVEVEDLVEALDSLADLLEKL 215 (229)
T ss_pred hccceEEEEEecCCCccHHHHHHHHHHHHHHHHHh
Confidence 56899999999999999889999999999999863
No 8
>PF09176 Mpt_N: Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; InterPro: IPR015259 Prokaryotic methylene-tetrahydromethanopterin dehydrogenase catalyses the dehydrogenation of methylene-tetrahydromethanopterin during growth on one-carbon compounds such as methanol. It can also catalyse the reversible dehydrogenation of methylene-tetrahydrofolate, though at much lower efficiency []. The pterin domain of this protein is composed of two alpha-beta segments found at the N- and C-terminal ends of the polypeptide respectivly. This entry represents the N-terminal segment of the pterin domain, with a core comprising three alpha/beta/alpha layers in which each sheet contains four strands. ; PDB: 1LUA_A 1LU9_C.
Probab=68.20 E-value=3.2 Score=25.04 Aligned_cols=30 Identities=27% Similarity=0.450 Sum_probs=20.8
Q ss_pred CCHHHHHHHHhh--c-CCCccccccceEEcceE
Q psy4809 1 LSKDELGKLVQG--F-EKQDILTSSGVTLAGNR 30 (89)
Q Consensus 1 ~s~~E~~~i~~~--f-~~~~~~~~~Gi~l~G~k 30 (89)
++++|+..|+.. | ..|+.+..+||.+||..
T Consensus 21 V~~~~V~~LvqdaIFsR~P~~~~~TaiFIGG~d 53 (81)
T PF09176_consen 21 VTPDEVRGLVQDAIFSRGPKDLKRTAIFIGGRD 53 (81)
T ss_dssp --TTTHHHHHHHHHSSS-GGGGGGEEEEEE-S-
T ss_pred cCHHHhhhhhcceeEccCCcCCceeEEEECCcc
Confidence 578889999873 5 57778889999999963
No 9
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=66.11 E-value=10 Score=21.11 Aligned_cols=32 Identities=25% Similarity=0.378 Sum_probs=23.4
Q ss_pred EEEEEcC--ceEEEEEeCCCCChhhHHHHHHHHH
Q psy4809 50 VHCMKTQ--QAVVISLYEDPIQPQQAASVVEKLG 81 (89)
Q Consensus 50 ~~i~KT~--~aiiIg~y~~~~~~~~~~~~ve~lA 81 (89)
+++.|++ .++.+-+-..+.+||.|...++.+.
T Consensus 4 CvVCKqpi~~a~~v~T~~G~VH~g~C~~y~~e~~ 37 (54)
T PF10886_consen 4 CVVCKQPIDDALVVETESGPVHPGVCAQYLEELP 37 (54)
T ss_pred eeeeCCccCcceEEEcCCCccCcHHHHHHHHhcc
Confidence 3455554 5677777777889999999888763
No 10
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=63.15 E-value=7.4 Score=21.93 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=15.0
Q ss_pred CCHHHHHHHHhhcCCCcc
Q psy4809 1 LSKDELGKLVQGFEKQDI 18 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~ 18 (89)
+++.|.++|+++|++...
T Consensus 29 v~~~e~~aIi~~F~~~~~ 46 (57)
T PF05952_consen 29 VDKDEQKAIIDAFKDEES 46 (57)
T ss_pred CCHHHHHHHHHHHccccc
Confidence 578999999999976554
No 11
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=60.22 E-value=12 Score=29.26 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=25.6
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|+++-|++. ..-++......+|+|++++|.
T Consensus 219 rsViVvATSD~s~l~R~~aa~~At~IAEyFRDqG~ 253 (441)
T COG1157 219 RSVVVVATSDESALMRLKAAFTATTIAEYFRDQGK 253 (441)
T ss_pred ceEEEEECCCCCHHHHHHHHHHHHHHHHHHHhCCC
Confidence 4566677777764 445678888899999999983
No 12
>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.
Probab=59.31 E-value=16 Score=26.66 Aligned_cols=34 Identities=24% Similarity=0.281 Sum_probs=25.0
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++..+++. ..-.+-.+.-.+|+||+++|+
T Consensus 127 ~tvvv~~t~d~~~~~r~~a~~~a~aiAE~fr~~G~ 161 (274)
T cd01132 127 YTIVVAATASDPAPLQYLAPYTGCAMGEYFMDNGK 161 (274)
T ss_pred eeEEEEeCCCCchhHHHHHHHHHHHHHHHHHHCCC
Confidence 3467777777765 334567778899999999885
No 13
>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.
Probab=57.58 E-value=14 Score=28.24 Aligned_cols=34 Identities=12% Similarity=0.322 Sum_probs=24.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|.+..+++. ..-.+-.+.-.+|+|++++||
T Consensus 220 rtvlV~nts~~p~~~R~~s~yta~tiAEYfrd~G~ 254 (369)
T cd01134 220 RTVLIANTSNMPVAAREASIYTGITIAEYFRDMGY 254 (369)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4567777777764 334466667779999999986
No 14
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=57.13 E-value=26 Score=25.83 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=25.8
Q ss_pred cCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 55 TQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 55 T~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
.++.+.||+..-+.+- .....+|+||+||++.|
T Consensus 240 gks~lTIaIGCTGGqH-RSV~iae~La~~l~~~~ 272 (286)
T COG1660 240 GKSYLTIAIGCTGGQH-RSVYIAEQLAEYLRARG 272 (286)
T ss_pred CCeEEEEEEccCCCcc-chHHHHHHHHHHHHhcc
Confidence 4678889987766543 46778999999999875
No 15
>PF02021 UPF0102: Uncharacterised protein family UPF0102; InterPro: IPR003509 The proteins in this entry are functionally uncharacterised.; PDB: 3FOV_A.
Probab=56.42 E-value=30 Score=20.85 Aligned_cols=67 Identities=16% Similarity=0.193 Sum_probs=33.8
Q ss_pred cccceEEcceEEEEEEecCcEEEEecCCce-EEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhC
Q psy4809 20 TSSGVTLAGNRYIYLSGTDKVIRAKLGKVG-VHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSC 87 (89)
Q Consensus 20 ~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~G-~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~ 87 (89)
...|..+-...|.+-+.+ =.|.++++..- |+-+||.+.--.+.-.+.+++.....-......||...
T Consensus 11 ~~~G~~IL~rN~r~~~GE-IDiIa~~~~~lvfVEVK~R~~~~~~~~~~~v~~~K~~ri~~~A~~yL~~~ 78 (93)
T PF02021_consen 11 ERKGYRILERNWRCRRGE-IDIIARDGDTLVFVEVKTRSSSSFGSPEEAVDPRKQRRIRRAAEYYLAEN 78 (93)
T ss_dssp HHTT-EEEEEEEEETTEE-EEEEEEETTEEEEEEEEE--------------HHHHHHHHHHHHHHHHH-
T ss_pred HHCCCEEeeeeecCCCCc-EeEEEEEcccEEEEEEEEeecccccCHHHHChHHHHHHHHHHHHHHHHHC
Confidence 457888888888883333 23666666555 45579998766666666677777766666666677664
No 16
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=56.04 E-value=29 Score=22.34 Aligned_cols=36 Identities=22% Similarity=0.381 Sum_probs=28.1
Q ss_pred EcCceEEEEEeCCCC--ChhhHHHHHHHHHHHHHhCCC
Q psy4809 54 KTQQAVVISLYEDPI--QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 54 KT~~aiiIg~y~~~~--~~~~~~~~ve~lAdyL~~~gy 89 (89)
....-++|++-.|.. +-.+++.+..+|++.|.+.|.
T Consensus 66 ~~gr~v~iaFD~D~~~~Tn~~V~~a~~~l~~~L~~~G~ 103 (130)
T PF12965_consen 66 KPGREVYIAFDADTKPKTNKNVRRAIKRLGKLLKEAGC 103 (130)
T ss_pred cCCceEEEEecCCCccchhHHHHHHHHHHHHHHHHCCC
Confidence 345778888877744 336899999999999999874
No 17
>PRK00394 transcription factor; Reviewed
Probab=55.69 E-value=38 Score=23.00 Aligned_cols=43 Identities=12% Similarity=0.080 Sum_probs=32.7
Q ss_pred EecCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 43 AKLGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 43 ~kkg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+..+.-+.|..+.+.++.|... ...+..+++++++.|++.||
T Consensus 42 l~~Pk~t~lIf~sGKiv~tGa~S----~~~a~~a~~~~~~~l~~~g~ 84 (179)
T PRK00394 42 LEDPKIAALIFRSGKVVCTGAKS----VEDLHEAVKIIIKKLKELGI 84 (179)
T ss_pred ecCCceEEEEEcCCcEEEEccCC----HHHHHHHHHHHHHHHHHcCC
Confidence 33445667777888887777543 45899999999999999886
No 18
>PRK05922 type III secretion system ATPase; Validated
Probab=54.30 E-value=19 Score=27.96 Aligned_cols=35 Identities=11% Similarity=0.188 Sum_probs=27.2
Q ss_pred cCceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 55 TQQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 55 T~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
.++.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 212 ~rTVlv~atsd~~~~~r~~a~~~a~tiAEyfrd~G~ 247 (434)
T PRK05922 212 QRTIIIASPAHETAPTKVIAGRAAMTIAEYFRDQGH 247 (434)
T ss_pred cceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 34677888888765 455688888999999999885
No 19
>TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=54.20 E-value=17 Score=29.28 Aligned_cols=34 Identities=12% Similarity=0.322 Sum_probs=23.6
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|.++-+++. ..-.+--+.-.+|+|++++||
T Consensus 285 RTvlVanTSn~p~~aR~~s~ytg~TiAEYfRD~G~ 319 (578)
T TIGR01043 285 RTVLIANTSNMPVAAREASIYTGITIAEYFRDMGY 319 (578)
T ss_pred ceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 3566666666665 233455666779999999997
No 20
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=54.12 E-value=9.9 Score=17.81 Aligned_cols=10 Identities=60% Similarity=1.049 Sum_probs=7.8
Q ss_pred HHHHHHhCCC
Q psy4809 80 LGDYLVSCGY 89 (89)
Q Consensus 80 lAdyL~~~gy 89 (89)
+-|||.++||
T Consensus 7 I~~YL~~~Gy 16 (27)
T PF08513_consen 7 IYDYLVENGY 16 (27)
T ss_dssp HHHHHHHCT-
T ss_pred HHHHHHHCCc
Confidence 4689999997
No 21
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=54.10 E-value=45 Score=20.52 Aligned_cols=81 Identities=11% Similarity=0.135 Sum_probs=37.2
Q ss_pred CHHHHHHHHhhcCCCccccccceEEcceEEEEEEec-CcEEEEecCCceEEEEEcC--ceEEEEEeCCCCC-hhhHHHHH
Q psy4809 2 SKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGT-DKVIRAKLGKVGVHCMKTQ--QAVVISLYEDPIQ-PQQAASVV 77 (89)
Q Consensus 2 s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d-~~~i~~kkg~~G~~i~KT~--~aiiIg~y~~~~~-~~~~~~~v 77 (89)
|++|+..|+..|-....-...-+...... ...+ +--|+-- +.+|++|+--. ..=|+|+-+++.- ..+. ..-
T Consensus 8 t~~eA~~IA~~F~~~~~~~k~~~~~~~~s---~~~~~~~YI~N~-~~~GFVIVSgDdr~~~ILaYS~~G~fd~~~~-n~~ 82 (96)
T PF13734_consen 8 TEKEALQIAKTFVQKNGQSKTKLRTRSTS---TPSDTPYYIFND-NNKGFVIVSGDDRMGPILAYSDEGSFDTNNA-NVR 82 (96)
T ss_dssp -HHHHHHHHHHHHH--------EE----T---TT-SSSEEEEEE-TTS-EEEEESBTTS-SEEEEESSS----T-H-HHH
T ss_pred CHHHHHHHHHHHHHhcccccceeEecccC---CCCCCcEEEEEc-CCCEEEEEECCCCccceeEEcCCCCcCccch-hHH
Confidence 78999999998832111111111111110 0000 1124444 67788887744 4668899888863 3333 355
Q ss_pred HHHHHHHHhC
Q psy4809 78 EKLGDYLVSC 87 (89)
Q Consensus 78 e~lAdyL~~~ 87 (89)
.-|+.|+.+.
T Consensus 83 ~~l~~y~~~i 92 (96)
T PF13734_consen 83 PGLQAYLEQI 92 (96)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 6677776653
No 22
>PF11389 Porin_OmpL1: Leptospira porin protein OmpL1; InterPro: IPR021058 OmpL1 is a member of the outer membrane (OM) proteins in the mammalian pathogen Leptospira, related proteins are restricted to the Spirochaetes. Specifically, it is a porin [].
Probab=52.22 E-value=28 Score=25.12 Aligned_cols=49 Identities=12% Similarity=0.007 Sum_probs=31.6
Q ss_pred hcCCCccccccceEEcceEEEEEEecCcEEEEecCCceEEEEE-cCceEE
Q psy4809 12 GFEKQDILTSSGVTLAGNRYIYLSGTDKVIRAKLGKVGVHCMK-TQQAVV 60 (89)
Q Consensus 12 ~f~~~~~~~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~G~~i~K-T~~aii 60 (89)
+|.||.+...+|=.++=-.=..+-+|++.+-.++..+|++-.| |+.+++
T Consensus 30 ~~~~~~k~~~~~~~~gv~~r~aI~aENrLitL~~tt~g~I~a~~tngaM~ 79 (267)
T PF11389_consen 30 CVQNPYKPAGEGNYTGVLPRKAIIAENRLITLDRTTGGLINAKSTNGAMT 79 (267)
T ss_pred cccCCCCcCCcCcceeecccccccccceEEEEecccCceeeeeeccCcee
Confidence 3456665555555544222223445677788888999999999 887765
No 23
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=52.06 E-value=36 Score=19.67 Aligned_cols=30 Identities=20% Similarity=0.329 Sum_probs=21.6
Q ss_pred ceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
|++||.+..+ .......+.++++.|++.|+
T Consensus 1 qv~Ii~~~~~---~~~~~~~a~~l~~~L~~~gi 30 (94)
T PF03129_consen 1 QVVIIPVGKK---DEEIIEYAQELANKLRKAGI 30 (94)
T ss_dssp SEEEEESSCS---HHHHHHHHHHHHHHHHHTTS
T ss_pred CEEEEEeCCC---cHHHHHHHHHHHHHHHHCCC
Confidence 3556665554 34577889999999999874
No 24
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=51.20 E-value=20 Score=28.98 Aligned_cols=34 Identities=12% Similarity=0.302 Sum_probs=24.2
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|.+.-+++. ....+--+.-.+|+|++++||
T Consensus 290 RTvlVanTSn~Pv~aR~~s~ytgiTiAEYfRd~G~ 324 (586)
T PRK04192 290 RTVLIANTSNMPVAAREASIYTGITIAEYYRDMGY 324 (586)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 4566667777664 334466667789999999997
No 25
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=49.60 E-value=23 Score=20.15 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=17.6
Q ss_pred CChhhHHHHHHHHHHHHHhCCC
Q psy4809 68 IQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 68 ~~~~~~~~~ve~lAdyL~~~gy 89 (89)
+.....+..+..+.+++++.||
T Consensus 31 l~~~~l~~~~~~l~~~y~~~GY 52 (76)
T PF08479_consen 31 LTLADLQQLADALTNYYREKGY 52 (76)
T ss_dssp B-HHHHHHHHHHHHHHHHHTT-
T ss_pred cCHHHHHHHHHHHHHHHHHcCc
Confidence 3556788999999999999998
No 26
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=47.79 E-value=12 Score=17.28 Aligned_cols=13 Identities=31% Similarity=0.595 Sum_probs=10.3
Q ss_pred HHHHHHHHHhCCC
Q psy4809 77 VEKLGDYLVSCGY 89 (89)
Q Consensus 77 ve~lAdyL~~~gy 89 (89)
..-+.+||...||
T Consensus 7 ~~lI~~yL~~~g~ 19 (34)
T smart00667 7 NRLILEYLLRNGY 19 (34)
T ss_pred HHHHHHHHHHcCH
Confidence 3458999999987
No 27
>PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This entry represents UPF0042 nucleotide-binding proteins. This is a family of putative P-loop ATPases [], as they contain an ATP-binding site and display ATPase and GTPase activities.; GO: 0005524 ATP binding
Probab=47.72 E-value=48 Score=24.39 Aligned_cols=34 Identities=21% Similarity=0.287 Sum_probs=26.5
Q ss_pred cCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 55 TQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 55 T~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.++.+.||...-+.+- .....+|.||++|++.||
T Consensus 239 gk~~ltIaiGCTGG~H-RSV~iae~La~~L~~~~~ 272 (284)
T PF03668_consen 239 GKSYLTIAIGCTGGQH-RSVAIAERLAERLREKGY 272 (284)
T ss_pred CCceEEEEEEcCCCcC-cHHHHHHHHHHHHHhcCC
Confidence 4667888887766533 567789999999999875
No 28
>PRK06936 type III secretion system ATPase; Provisional
Probab=47.29 E-value=24 Score=27.46 Aligned_cols=34 Identities=18% Similarity=0.373 Sum_probs=23.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 218 rtvvv~atsd~p~~~R~~a~~~a~tiAEyfrd~G~ 252 (439)
T PRK06936 218 KAVLVVATSDRPSMERAKAGFVATSIAEYFRDQGK 252 (439)
T ss_pred eeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3566677776654 223466667779999999885
No 29
>TIGR01042 V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=47.05 E-value=26 Score=28.42 Aligned_cols=34 Identities=18% Similarity=0.341 Sum_probs=23.9
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|.+.-+++. ....+.-+.-.+|+|++++||
T Consensus 291 rtvlVa~tsd~p~~~R~~s~ytg~tiAEYfRD~G~ 325 (591)
T TIGR01042 291 RTTLVANTSNMPVAAREASIYTGITLAEYFRDMGY 325 (591)
T ss_pred ceEEEEEcCCCCHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4566666666664 334566667779999999997
No 30
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=46.96 E-value=35 Score=21.29 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=21.5
Q ss_pred cCCceEEEEEcCceEEEEEeCCCC
Q psy4809 45 LGKVGVHCMKTQQAVVISLYEDPI 68 (89)
Q Consensus 45 kg~~G~~i~KT~~aiiIg~y~~~~ 68 (89)
.|..|.++-++..|++|.+++.+.
T Consensus 57 ~G~TG~Vvg~~g~ay~V~v~~G~k 80 (98)
T COG2139 57 QGKTGTVVGVRGRAYKVEVYDGNK 80 (98)
T ss_pred cCcceEEEeccCCEEEEEEecCCc
Confidence 479999999999999999998764
No 31
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=46.60 E-value=48 Score=18.95 Aligned_cols=19 Identities=26% Similarity=0.270 Sum_probs=15.8
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q psy4809 71 QQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 71 ~~~~~~ve~lAdyL~~~gy 89 (89)
......+.++|+.|++.|+
T Consensus 14 ~~~~~~a~~la~~Lr~~g~ 32 (94)
T cd00861 14 EVQQELAEKLYAELQAAGV 32 (94)
T ss_pred HHHHHHHHHHHHHHHHCCC
Confidence 4577788999999999885
No 32
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=46.28 E-value=47 Score=21.92 Aligned_cols=30 Identities=17% Similarity=0.314 Sum_probs=20.7
Q ss_pred eEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 58 AVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 58 aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.||+ +++.. ......++...+-++|++.||
T Consensus 153 ~Iil-~Hd~~-~~~~t~~~l~~~i~~l~~~Gy 182 (191)
T TIGR02764 153 DIIL-LHASD-SAKQTVKALPTIIKKLKEKGY 182 (191)
T ss_pred CEEE-EeCCC-CcHhHHHHHHHHHHHHHHCCC
Confidence 3444 45422 233566789999999999998
No 33
>PRK02821 hypothetical protein; Provisional
Probab=45.33 E-value=48 Score=19.55 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=25.5
Q ss_pred HHHHHhhc-CCCccccccceEEcceEEEEEEecC---cEEEEecCC
Q psy4809 6 LGKLVQGF-EKQDILTSSGVTLAGNRYIYLSGTD---KVIRAKLGK 47 (89)
Q Consensus 6 ~~~i~~~f-~~~~~~~~~Gi~l~G~kY~~~r~d~---~~i~~kkg~ 47 (89)
+..|+..+ ++|.++.-+-..-.+...+.+++++ +.+.||+|.
T Consensus 6 v~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr 51 (77)
T PRK02821 6 VEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGR 51 (77)
T ss_pred HHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCc
Confidence 34455555 6787765554444455556677654 468888775
No 34
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=45.07 E-value=29 Score=25.29 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=23.2
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhC-CC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSC-GY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~-gy 89 (89)
++.+|++..+++. ..-.+..+.-.+|+||+++ |+
T Consensus 128 ~tvvv~~t~d~~~~~r~~~~~~a~~~AEyfr~~~g~ 163 (274)
T cd01133 128 KTALVYGQMNEPPGARARVALTGLTMAEYFRDEEGQ 163 (274)
T ss_pred eeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 3456667777654 3334667777899999987 74
No 35
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=44.98 E-value=27 Score=27.25 Aligned_cols=34 Identities=12% Similarity=0.224 Sum_probs=23.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|+++.|+
T Consensus 218 rtvvv~atsd~p~~~R~~a~~~A~tiAEyfrd~G~ 252 (444)
T PRK08972 218 RSVVVAAPADTSPLMRLKGCETATTIAEYFRDQGL 252 (444)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3456666666654 334577777789999999885
No 36
>PF03859 CG-1: CG-1 domain; InterPro: IPR005559 CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein []. CG-1 domains are associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin-binding domain and ankyrins [].; GO: 0005516 calmodulin binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=44.90 E-value=27 Score=22.49 Aligned_cols=49 Identities=14% Similarity=0.175 Sum_probs=27.2
Q ss_pred CCHHHHHHHHhhcC------CCccccccc--eEEcceEEEEEEecCcEEEEecCCce
Q psy4809 1 LSKDELGKLVQGFE------KQDILTSSG--VTLAGNRYIYLSGTDKVIRAKLGKVG 49 (89)
Q Consensus 1 ~s~~E~~~i~~~f~------~~~~~~~~G--i~l~G~kY~~~r~d~~~i~~kkg~~G 49 (89)
++|+|+..|+..++ .|...+++| +-++-.+-..-|-|+..+.-||++.+
T Consensus 9 l~~~Ei~~IL~n~~~~~~~~~~~~rP~sGslfLf~Rk~~r~fRkDG~~WrKkkdgkt 65 (118)
T PF03859_consen 9 LKPEEIAFILLNYEKFQIWLEPPNRPPSGSLFLFNRKVVRFFRKDGHNWRKKKDGKT 65 (118)
T ss_pred CCHHHHHHHHHhHHhCCcccCCCCCCCCceEEEEEchHhhhhhcccceeEEcCCCCc
Confidence 57999999998764 222333333 22222222224456667777776544
No 37
>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=44.88 E-value=28 Score=26.73 Aligned_cols=34 Identities=18% Similarity=0.232 Sum_probs=23.6
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 193 ~tvvv~~tsd~~~~~r~~a~~~a~tiAEyfr~~G~ 227 (411)
T TIGR03496 193 RSVVVAATADESPLMRLRAAFYATAIAEYFRDQGK 227 (411)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 3456666666654 334567777889999999885
No 38
>PF02770 Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle domain; InterPro: IPR006091 Acyl-CoA dehydrogenases (1.3.99.3 from EC) are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [] prefers branched-chain substrates. The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents the middle beta-barrel domain found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO; 1.3.3.6 from EC) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [].; GO: 0003995 acyl-CoA dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 3MDD_B 1UDY_C 3MDE_B 2UXW_A 3B96_A 1SIQ_A 1SIR_A 2R0N_A 2R0M_A 2D29_B ....
Probab=44.84 E-value=23 Score=18.78 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=14.8
Q ss_pred ccceEEcceEEEEEEec
Q psy4809 21 SSGVTLAGNRYIYLSGT 37 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d 37 (89)
.+|+.|+|+|+++..+.
T Consensus 24 ~~~~~L~G~K~~v~~~~ 40 (52)
T PF02770_consen 24 GDGYVLNGEKRFVSNAP 40 (52)
T ss_dssp TTEEEEEEEEEEEETTT
T ss_pred cceEEEeeEEEEECCcC
Confidence 57899999999998765
No 39
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=44.53 E-value=17 Score=22.23 Aligned_cols=29 Identities=28% Similarity=0.376 Sum_probs=20.4
Q ss_pred CCHHHHHHHHhhcC--CCccccccceEEcce
Q psy4809 1 LSKDELGKLVQGFE--KQDILTSSGVTLAGN 29 (89)
Q Consensus 1 ~s~~E~~~i~~~f~--~~~~~~~~Gi~l~G~ 29 (89)
++++|+..|..... -|.....+||++.|-
T Consensus 4 L~~~el~~ik~~v~~~~~~gv~~~GiT~~GF 34 (89)
T PF08356_consen 4 LQPQELEDIKKVVRENIPDGVNDNGITLDGF 34 (89)
T ss_pred CCHHHHHHHHHHHHHHCCCCcCCCccchhhH
Confidence 57888888887652 445566788888774
No 40
>PF07244 Surf_Ag_VNR: Surface antigen variable number repeat; InterPro: IPR010827 This motif is found primarily in bacterial surface antigens, normally as variable number repeats at the N terminus. The C terminus of these proteins is normally represented by IPR000184 from INTERPRO. There may also be a relationship to haemolysin activator HlyB (IPR005565 from INTERPRO). The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.; GO: 0019867 outer membrane; PDB: 2X8X_X 3MC8_A 3OG5_A 3MC9_B 2QCZ_B 3EFC_A 3Q6B_A 2QDF_A 2V9H_A.
Probab=44.13 E-value=30 Score=19.12 Aligned_cols=22 Identities=32% Similarity=0.671 Sum_probs=19.5
Q ss_pred CChhhHHHHHHHHHHHHHhCCC
Q psy4809 68 IQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 68 ~~~~~~~~~ve~lAdyL~~~gy 89 (89)
..+....+...+|.+++.+.||
T Consensus 32 ~~~~~i~~~~~~l~~~y~~~Gy 53 (78)
T PF07244_consen 32 FNPEKIEEDIERLQDYYKDKGY 53 (78)
T ss_dssp ECHHHHHHHHHHHHHHHHTTSC
T ss_pred eCHHHHHHHHHHHHHHHHHcCC
Confidence 3677889999999999999998
No 41
>PRK09099 type III secretion system ATPase; Provisional
Probab=43.76 E-value=32 Score=26.75 Aligned_cols=34 Identities=21% Similarity=0.326 Sum_probs=23.9
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 219 rtvvv~~tsd~p~~~r~~a~~~a~tiAEyfrd~G~ 253 (441)
T PRK09099 219 RSVVVCATSDRSSIERAKAAYVATAIAEYFRDRGL 253 (441)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4566777777754 333466677789999999885
No 42
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=43.70 E-value=29 Score=27.00 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=25.0
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|+++.|+
T Consensus 214 rsvvv~atsd~~~~~r~~a~~~a~tiAEyfrd~G~ 248 (442)
T PRK08927 214 RSVVVVATSDEPALMRRQAAYLTLAIAEYFRDQGK 248 (442)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 4566777777654 334577888889999999885
No 43
>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=43.58 E-value=31 Score=26.46 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=24.7
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|+++.|+
T Consensus 193 ~~v~v~~tsd~~~~~r~~~~~~a~tiAEyfr~~G~ 227 (413)
T TIGR03497 193 RSVVVVATSDQPALMRLKAAFTATAIAEYFRDQGK 227 (413)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 4567777777754 333566778889999999885
No 44
>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
Probab=43.39 E-value=29 Score=25.86 Aligned_cols=34 Identities=18% Similarity=0.288 Sum_probs=24.0
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++..+++. ..-.+..+.-.+|+||+++|+
T Consensus 125 rtvvv~~t~d~~~~~r~~~~~~a~~~AEyfr~~g~ 159 (326)
T cd01136 125 RSVVVVATSDESPLLRVKAAYTATAIAEYFRDQGK 159 (326)
T ss_pred eEEEEEcCCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3456677777754 334566777789999999874
No 45
>PRK00468 hypothetical protein; Provisional
Probab=42.91 E-value=62 Score=18.91 Aligned_cols=42 Identities=10% Similarity=0.177 Sum_probs=22.7
Q ss_pred HHHHHhhc-CCCccccccceEEcceEEEEEEecC---cEEEEecCC
Q psy4809 6 LGKLVQGF-EKQDILTSSGVTLAGNRYIYLSGTD---KVIRAKLGK 47 (89)
Q Consensus 6 ~~~i~~~f-~~~~~~~~~Gi~l~G~kY~~~r~d~---~~i~~kkg~ 47 (89)
+..|+..+ ++|+.+.-+-..-+..-.+.++.++ +.++||+|.
T Consensus 5 v~~iv~~LVd~Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr 50 (75)
T PRK00468 5 VETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGR 50 (75)
T ss_pred HHHHHHHhcCCCCeEEEEEEeCCCeEEEEEEEChhhCcceecCCCh
Confidence 44555655 6788765553322233233455543 468887765
No 46
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=41.89 E-value=84 Score=19.43 Aligned_cols=16 Identities=13% Similarity=0.403 Sum_probs=14.3
Q ss_pred cceEEcceEEEEEEec
Q psy4809 22 SGVTLAGNRYIYLSGT 37 (89)
Q Consensus 22 ~Gi~l~G~kY~~~r~d 37 (89)
+-|.++|++|..++.|
T Consensus 5 ~~i~i~gk~~l~~~~~ 20 (95)
T COG3377 5 EPIDIEGKKFLGLKVD 20 (95)
T ss_pred eeEeeCCeEEEEEEec
Confidence 5688999999999998
No 47
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=41.86 E-value=40 Score=26.19 Aligned_cols=34 Identities=15% Similarity=0.275 Sum_probs=24.0
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+......+|+|++++|+
T Consensus 212 ~tvvV~atsddsp~~R~~~~~~a~~iAEyFrd~G~ 246 (434)
T PRK08472 212 NTVIVVATSDDSPLMRKYGAFCAMSVAEYFKNQGL 246 (434)
T ss_pred ceEEEEECCCCCHHHhhHHHHHHHHHHHHHHHcCC
Confidence 4566777777754 333455567899999999885
No 48
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=41.33 E-value=35 Score=26.29 Aligned_cols=34 Identities=21% Similarity=0.335 Sum_probs=23.8
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 196 ~tvvv~atsd~~~~~r~~a~~~a~~iAEyfrd~G~ 230 (418)
T TIGR03498 196 RSVVVVATSDESPLMRRQAAYTATAIAEYFRDQGK 230 (418)
T ss_pred eeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3456677777654 233466677889999999884
No 49
>PRK14675 hypothetical protein; Provisional
Probab=40.92 E-value=63 Score=20.65 Aligned_cols=69 Identities=14% Similarity=0.123 Sum_probs=47.6
Q ss_pred ccccceEEcceEEEEEEecCcEEEEecCCc-eEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 19 LTSSGVTLAGNRYIYLSGTDKVIRAKLGKV-GVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 19 ~~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~-G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
+...|+.+-...|.+-..+ =.|+++++.. =|+=+||.+.--.|.-.+.+++............||.+++
T Consensus 22 L~~~G~~il~rn~r~~~GE-IDlIa~d~~~lvFVEVK~R~~~~~g~~~~aV~~~K~~ri~~~A~~yL~~~~ 91 (125)
T PRK14675 22 LKGLRYKIVERNFRCRCGE-IDIIARDGKTLVFVEVKTRKNYAYGVPQLAVTPFKQRQISKAALTWLAKKK 91 (125)
T ss_pred HHHCCCEEEEEEEeCCCCe-EEEEEEeCCEEEEEEEEeccCCCCcChHHcCCHHHHHHHHHHHHHHHHHCC
Confidence 3467999988888774333 2356666432 3455788877667776777888888777777777887765
No 50
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=40.88 E-value=36 Score=26.67 Aligned_cols=34 Identities=18% Similarity=0.263 Sum_probs=24.0
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHh-CCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVS-CGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~-~gy 89 (89)
++.+|++..+++. ..-.+..+.-.+|+|+++ +|+
T Consensus 203 rsvvV~atsd~p~~~r~~a~~~a~tiAEyfrd~~G~ 238 (463)
T PRK09280 203 KTALVFGQMNEPPGARLRVALTGLTMAEYFRDVEGQ 238 (463)
T ss_pred eeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4566667666654 334566778889999999 875
No 51
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=40.72 E-value=49 Score=22.22 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=24.8
Q ss_pred ceEEEEEeCCCC--ChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDPI--QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~~--~~~~~~~~ve~lAdyL~~~gy 89 (89)
.|||||...-+. .-..|..-++.|++.|.+.||
T Consensus 2 ~AliIg~~~y~~~~~L~~~~~D~~~~~~~L~~~gf 36 (248)
T PF00656_consen 2 RALIIGVNYYQNPPPLPGAVNDAEAMAEALEKLGF 36 (248)
T ss_dssp EEEEEEESSTSSTCHCTTHHHHHHHHHHHHHHTTE
T ss_pred EEEEEEeeCCCCCCCCCCHHHHHHHHHHHHHHcCC
Confidence 488988866443 224588999999999988775
No 52
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=40.12 E-value=21 Score=21.59 Aligned_cols=18 Identities=33% Similarity=0.654 Sum_probs=15.4
Q ss_pred ccceEEcceEEEEEEecC
Q psy4809 21 SSGVTLAGNRYIYLSGTD 38 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d~ 38 (89)
.+-+.++|++|+++|.+|
T Consensus 71 g~~v~~~~~~y~i~~~~D 88 (93)
T cd00320 71 GTEVKLDGEEYLILRESD 88 (93)
T ss_pred ceEEEECCEEEEEEEHHH
Confidence 456889999999999875
No 53
>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 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. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....
Probab=40.11 E-value=35 Score=23.79 Aligned_cols=34 Identities=18% Similarity=0.288 Sum_probs=22.6
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+....-.+|+|++++|+
T Consensus 71 ~t~vv~~t~~~~~~~r~~~~~~a~t~AEyfrd~G~ 105 (215)
T PF00006_consen 71 RTVVVAATSDEPPAARYRAPYTALTIAEYFRDQGK 105 (215)
T ss_dssp GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTS
T ss_pred ccccccccchhhHHHHhhhhccchhhhHHHhhcCC
Confidence 3466667766654 223466667788999999885
No 54
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=40.10 E-value=31 Score=26.95 Aligned_cols=34 Identities=12% Similarity=0.140 Sum_probs=24.8
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhC-CC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSC-GY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~-gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++++ |+
T Consensus 202 rsvvv~atsd~~~~~R~~a~~~a~tiAEyfrd~~G~ 237 (461)
T PRK12597 202 KTVMVYGQMNEPPGARMRVVLTGLTIAEYLRDEEKE 237 (461)
T ss_pred eeEEEecCCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4566777777764 3446778888899999987 74
No 55
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=40.08 E-value=29 Score=21.59 Aligned_cols=18 Identities=17% Similarity=0.425 Sum_probs=15.3
Q ss_pred ccceEEcceEEEEEEecC
Q psy4809 21 SSGVTLAGNRYIYLSGTD 38 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d~ 38 (89)
.+-+.++|++|+++|.+|
T Consensus 76 Gtevk~dg~ey~i~~e~D 93 (100)
T PTZ00414 76 GSSVKVEGEEFFLYNEDS 93 (100)
T ss_pred CcEEEECCEEEEEEEhHH
Confidence 456899999999999875
No 56
>COG1832 Predicted CoA-binding protein [General function prediction only]
Probab=39.91 E-value=52 Score=21.80 Aligned_cols=30 Identities=23% Similarity=0.517 Sum_probs=24.1
Q ss_pred EcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 54 KTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 54 KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
++|+--|||..+++..|+ ...++||.++||
T Consensus 15 ~~K~IAvVG~S~~P~r~s------y~V~kyL~~~GY 44 (140)
T COG1832 15 SAKTIAVVGASDKPDRPS------YRVAKYLQQKGY 44 (140)
T ss_pred hCceEEEEecCCCCCccH------HHHHHHHHHCCC
Confidence 467777899988887764 567899999998
No 57
>PRK07721 fliI flagellum-specific ATP synthase; Validated
Probab=39.68 E-value=44 Score=25.88 Aligned_cols=34 Identities=18% Similarity=0.353 Sum_probs=24.2
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.++++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 214 r~v~vv~~~~~~~~~r~~~~~~a~~iAEyfr~~g~ 248 (438)
T PRK07721 214 RSIVVVATSDQPALMRIKGAYTATAIAEYFRDQGL 248 (438)
T ss_pred CeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 3456677666654 334577788889999999885
No 58
>PHA02119 hypothetical protein
Probab=39.62 E-value=21 Score=21.17 Aligned_cols=12 Identities=50% Similarity=0.855 Sum_probs=9.7
Q ss_pred HHHHHHHHhCCC
Q psy4809 78 EKLGDYLVSCGY 89 (89)
Q Consensus 78 e~lAdyL~~~gy 89 (89)
..+.|||++.||
T Consensus 57 ~divdylr~lgy 68 (87)
T PHA02119 57 KDIVDYLRSLGY 68 (87)
T ss_pred HHHHHHHHHccc
Confidence 457799999887
No 59
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=39.29 E-value=1.2e+02 Score=20.48 Aligned_cols=39 Identities=10% Similarity=0.148 Sum_probs=28.6
Q ss_pred CceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 47 KVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 47 ~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
+.=+.|..+.+.++-|.. +...+..+++++++.|++.||
T Consensus 47 k~t~lIF~SGKiviTGak----s~e~a~~a~~~i~~~L~~~g~ 85 (174)
T cd04516 47 KTTALIFSSGKMVCTGAK----SEDDSKLAARKYARIIQKLGF 85 (174)
T ss_pred cEEEEEECCCeEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 333566667776666643 346789999999999999886
No 60
>PF07799 DUF1643: Protein of unknown function (DUF1643); InterPro: IPR012441 This entry is represented by Bacteriophage D3, Orf41.6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The members of this family are all sequences found within hypothetical proteins expressed by various bacteria, archaea and phage. The region concerned is approximately 150 residues long.
Probab=39.27 E-value=51 Score=20.81 Aligned_cols=34 Identities=12% Similarity=0.279 Sum_probs=22.5
Q ss_pred CceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
+.+++|++++....+...=.++.++-.+.+..||
T Consensus 13 ~~~~~I~lNPS~A~~~~~D~T~~~~~~~a~~~gy 46 (136)
T PF07799_consen 13 PPLLFIGLNPSTADAEKDDPTIRRCINFARRWGY 46 (136)
T ss_pred CEEEEEEeCCCCCCCcCCCHHHHHHHHHHhhcCC
Confidence 5688899998876655444555555555566665
No 61
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=39.20 E-value=23 Score=21.54 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=15.0
Q ss_pred ccceEEcceEEEEEEecC
Q psy4809 21 SSGVTLAGNRYIYLSGTD 38 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d~ 38 (89)
..-+.++|++|+++|.+|
T Consensus 72 g~ev~~~~~~y~iv~~~D 89 (95)
T PRK00364 72 GTEVKIDGEEYLILRESD 89 (95)
T ss_pred CeEEEECCEEEEEEEHHH
Confidence 346889999999999875
No 62
>KOG0141|consensus
Probab=39.19 E-value=43 Score=25.55 Aligned_cols=42 Identities=19% Similarity=0.323 Sum_probs=30.9
Q ss_pred ccceEEcceEEEEEEecC-c--EEEEecCCceEEEEEcCceEEEE
Q psy4809 21 SSGVTLAGNRYIYLSGTD-K--VIRAKLGKVGVHCMKTQQAVVIS 62 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d~-~--~i~~kkg~~G~~i~KT~~aiiIg 62 (89)
.+...|+|.|+.+....+ + .+|+|-+.+++--.+--+++||=
T Consensus 183 g~~yiLNGsK~witNG~~advliVyAkTd~~a~~~~hGIt~FiVE 227 (421)
T KOG0141|consen 183 GDDYILNGSKFWITNGPDADVLIVYAKTDHSAVPPSHGITAFIVE 227 (421)
T ss_pred CCcEEecCcEEEEecCCCCcEEEEEEecCCCCCCCcCceEEEEEc
Confidence 468899999999988643 2 57898777776666666677764
No 63
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=39.03 E-value=88 Score=18.87 Aligned_cols=34 Identities=6% Similarity=0.084 Sum_probs=28.6
Q ss_pred cCceEEEEEeCCC-CChhhHHHHHHHHHHHHHhCC
Q psy4809 55 TQQAVVISLYEDP-IQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 55 T~~aiiIg~y~~~-~~~~~~~~~ve~lAdyL~~~g 88 (89)
.++.++||..+.. .++....++...++..|.+.+
T Consensus 52 ~~~v~lvGlG~~~~~~~~~~r~a~~~~~~~l~~~~ 86 (126)
T PF02789_consen 52 AKRVLLVGLGKKEKLTAESLRKAGAAAARALKKLK 86 (126)
T ss_dssp CSEEEEEEEESCTGBCHHHHHHHHHHHHHHHHHTT
T ss_pred ccEEEEEECCCcCcCCHHHHHHHHHHHHHHHhhCC
Confidence 4678899999887 588899999999999998754
No 64
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=38.68 E-value=68 Score=22.33 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=23.8
Q ss_pred ceEEEEE--eCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISL--YEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~--y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
-|+||+. |..+. .......-++.|++-|++.||
T Consensus 11 ~aLII~n~~f~~~~~~r~g~~~D~~~l~~~f~~lgF 46 (243)
T cd00032 11 LALIINNENFDKGLKDRDGTDVDAENLTKLFESLGY 46 (243)
T ss_pred EEEEEechhcCCCCCCCCChHHHHHHHHHHHHHCCC
Confidence 4778887 44422 334566889999999999987
No 65
>TIGR00725 conserved hypothetical protein, DprA/Smf-related, family 1. This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of PFAM model pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE.
Probab=38.37 E-value=67 Score=21.18 Aligned_cols=29 Identities=17% Similarity=0.258 Sum_probs=21.6
Q ss_pred EEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 61 ISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 61 Ig~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
|+++..+..+....+++.+|++.|.+.|+
T Consensus 4 I~V~gss~~~~~~~~~A~~lg~~La~~g~ 32 (159)
T TIGR00725 4 IGVIGSSNKSEELYEIAYRLGKELAKKGH 32 (159)
T ss_pred EEEEeCCCCChHHHHHHHHHHHHHHHCCC
Confidence 44554444455889999999999998874
No 66
>COG3512 CRISPR-associated protein, Cas2 homolog [Defense mechanisms]
Probab=37.98 E-value=57 Score=20.65 Aligned_cols=30 Identities=20% Similarity=0.507 Sum_probs=26.4
Q ss_pred EEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 60 VISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 60 iIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
+|-++|-|.....-.++..++-+.|.+-||
T Consensus 9 ~ilmFDlPt~t~~erKaa~kFR~fLlk~Gy 38 (116)
T COG3512 9 MILMFDLPTDTAAERKAANKFRQFLLKDGY 38 (116)
T ss_pred eeeEeeCCcccHHHHHHHHHHHHHHHHhhH
Confidence 577889888888889999999999999887
No 67
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=37.71 E-value=41 Score=26.30 Aligned_cols=33 Identities=24% Similarity=0.284 Sum_probs=22.0
Q ss_pred ceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
+.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 225 svvv~atsd~~p~~r~~a~~~a~aiAEyfrd~G~ 258 (451)
T PRK05688 225 SVVVASPADDAPLMRLRAAMYCTRIAEYFRDKGK 258 (451)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 345555555543 333466777889999999885
No 68
>PRK08149 ATP synthase SpaL; Validated
Probab=37.15 E-value=49 Score=25.67 Aligned_cols=34 Identities=18% Similarity=0.181 Sum_probs=24.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
+..+|++.-+++. ..-.+..+...+|+|++++|+
T Consensus 207 ~~~vV~~~sd~p~~~r~~a~~~a~tiAE~fr~~G~ 241 (428)
T PRK08149 207 KCVLVYATSDFSSVDRCNAALVATTVAEYFRDQGK 241 (428)
T ss_pred ceEEEEECCCCCHHHHHhHHHHHHHHHHHHHHcCC
Confidence 3456677776654 233577788889999999884
No 69
>PLN00062 TATA-box-binding protein; Provisional
Probab=36.85 E-value=1.4e+02 Score=20.37 Aligned_cols=40 Identities=10% Similarity=0.130 Sum_probs=29.7
Q ss_pred CCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 46 GKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 46 g~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+.-+.|..+.+.++-|.- +...+..++.++++.|++.||
T Consensus 46 Pk~t~lIF~SGKiviTGak----s~e~a~~a~~~~~~~L~~lg~ 85 (179)
T PLN00062 46 PKTTALIFASGKMVCTGAK----SEHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred CcEEEEEECCCeEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 3445667777777766643 446789999999999999886
No 70
>PRK06820 type III secretion system ATPase; Validated
Probab=36.81 E-value=45 Score=25.94 Aligned_cols=34 Identities=18% Similarity=0.369 Sum_probs=23.3
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 219 rtvvv~atsd~p~~~r~~a~~~a~tiAEyfrd~G~ 253 (440)
T PRK06820 219 RTVVVVATSDRPALERLKGLSTATTIAEYFRDRGK 253 (440)
T ss_pred eEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3566677666654 233455677789999999885
No 71
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=36.50 E-value=47 Score=26.31 Aligned_cols=33 Identities=12% Similarity=0.245 Sum_probs=25.1
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~g 88 (89)
++.+|++..+++. ..-.+..+.-.+|+|++.+|
T Consensus 227 rsvvv~atsd~p~~~R~~a~~~A~tiAEyfrd~g 260 (494)
T CHL00060 227 KVALVYGQMNEPPGARMRVGLTALTMAEYFRDVN 260 (494)
T ss_pred ceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 4678888888875 33457777788999999876
No 72
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=36.29 E-value=91 Score=21.24 Aligned_cols=33 Identities=15% Similarity=0.288 Sum_probs=23.9
Q ss_pred ceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
|.+||-..++..........+.++++-|++.|+
T Consensus 12 qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Gi 44 (202)
T cd00862 12 QVVIVPIGIKDEKREEVLEAADELAERLKAAGI 44 (202)
T ss_pred eEEEEEecCCccchHHHHHHHHHHHHHHHHCCC
Confidence 667777765533334577889999999998874
No 73
>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.
Probab=35.86 E-value=49 Score=25.86 Aligned_cols=34 Identities=9% Similarity=0.179 Sum_probs=24.9
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHh-CCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVS-CGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~-~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++. +|+
T Consensus 197 rtvvv~~ts~~~~~~r~~~~~~a~tiAEyfrd~~G~ 232 (449)
T TIGR03305 197 NTVMVFGQMNEPPGARFRVGHTALTMAEYFRDDEKQ 232 (449)
T ss_pred eEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4567777777764 334577788889999997 775
No 74
>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=35.69 E-value=48 Score=25.88 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=24.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHH-hCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLV-SCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~-~~gy 89 (89)
++.+|++.-+++. ..-.+-.+.-.+|+|++ ++|+
T Consensus 203 rtvvv~atsd~p~~~R~~a~~~a~tiAEyfr~d~G~ 238 (458)
T TIGR01041 203 RAVVFLNLADDPAVERIVTPRMALTAAEYLAFEKDM 238 (458)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHccCC
Confidence 4567777777764 33456777778999999 6885
No 75
>cd04955 GT1_like_6 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=35.44 E-value=78 Score=22.03 Aligned_cols=31 Identities=26% Similarity=0.252 Sum_probs=23.1
Q ss_pred EEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 59 VVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 59 iiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.||+.+.-+...|-....+..||+.|.+.|+
T Consensus 3 ~~i~~~~~~~~~gG~~~~~~~la~~L~~~g~ 33 (363)
T cd04955 3 AIIGTRGIPAKYGGFETFVEELAPRLVARGH 33 (363)
T ss_pred EEEecCcCCcccCcHHHHHHHHHHHHHhcCC
Confidence 4566655455556677889999999999885
No 76
>TIGR00460 fmt methionyl-tRNA formyltransferase. The top-scoring characterized proteins other than methionyl-tRNA formyltransferase (fmt) itself are formyltetrahydrofolate dehydrogenases. The mitochondrial methionyl-tRNA formyltransferases are so divergent that, in a multiple alignment of bacterial fmt, mitochondrial fmt, and formyltetrahydrofolate dehydrogenases, the mitochondrial fmt appears the most different. However, because both bacterial and mitochondrial fmt are included in the seed alignment, all credible fmt sequences score higher than any non-fmt sequence. This enzyme modifies Met on initiator tRNA to f-Met.
Probab=35.31 E-value=1.8e+02 Score=21.24 Aligned_cols=33 Identities=15% Similarity=0.174 Sum_probs=22.9
Q ss_pred CHHHHHHHHhhcCCCccccccceEEcceEEEEEEec
Q psy4809 2 SKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGT 37 (89)
Q Consensus 2 s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d 37 (89)
+.+++..++.+|. |- ..-=..++|+++.+.++.
T Consensus 216 ~a~~I~~~iRA~~-p~--pga~~~~~g~~i~i~~a~ 248 (313)
T TIGR00460 216 SAEELLNKIRALN-PW--PTAWLTFEGKNIKIHKAK 248 (313)
T ss_pred CHHHHHHHHhccC-CC--CceEEEECCEEEEEEEEE
Confidence 4678889999985 32 112247889999988754
No 77
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=35.30 E-value=86 Score=20.44 Aligned_cols=35 Identities=11% Similarity=0.061 Sum_probs=25.6
Q ss_pred EcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 54 KTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 54 KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
+.++..++|.++....+..-..++..|.+.|.+.|
T Consensus 77 ~gk~v~~fg~g~~~~y~~~f~~a~~~l~~~l~~~G 111 (167)
T TIGR01752 77 TGKTVALFGLGDQEGYSETFCDGMGILYDKIKARG 111 (167)
T ss_pred CCCEEEEEecCCCCcccHHHHHHHHHHHHHHHHcC
Confidence 34677888887765555566777888888888876
No 78
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=34.90 E-value=51 Score=25.74 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=23.9
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHH-hCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLV-SCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~-~~gy 89 (89)
++.+|++.-+++. ..-.+-.+.-.+|+|++ ++|+
T Consensus 205 rtvvV~atsd~p~~~R~~a~~~a~tiAEyfr~d~G~ 240 (460)
T PRK04196 205 RSVVFLNLADDPAIERILTPRMALTAAEYLAFEKGM 240 (460)
T ss_pred eEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4566677776764 23356677778999999 6875
No 79
>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.
Probab=34.90 E-value=52 Score=26.03 Aligned_cols=34 Identities=18% Similarity=0.121 Sum_probs=23.1
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+-.+...+|+|++.+|+
T Consensus 219 ~tvvV~atsd~p~~~r~~a~~~a~aiAEyfrd~G~ 253 (501)
T TIGR00962 219 YTIVVAATASDSASLQYLAPYTGCTMAEYFRDNGK 253 (501)
T ss_pred eeEEEEecCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3456667766654 223456677889999999884
No 80
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=34.87 E-value=1.4e+02 Score=20.10 Aligned_cols=41 Identities=12% Similarity=0.111 Sum_probs=30.6
Q ss_pred cCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 45 LGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 45 kg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
..+.-+.|..+.+.++.|. .+...+..+++++++.|++.||
T Consensus 45 ~Pk~t~lIF~SGKiv~tGa----ks~~~a~~a~~~~~~~L~~~g~ 85 (174)
T cd04518 45 DPKIAALIFRSGKMVCTGA----KSVEDLHRAVKEIIKKLKDYGI 85 (174)
T ss_pred CCcEEEEEECCCeEEEEcc----CCHHHHHHHHHHHHHHHHhcCC
Confidence 3455566777777777664 3456899999999999999885
No 81
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=34.08 E-value=39 Score=20.52 Aligned_cols=18 Identities=17% Similarity=0.442 Sum_probs=15.1
Q ss_pred ccceEEcceEEEEEEecC
Q psy4809 21 SSGVTLAGNRYIYLSGTD 38 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d~ 38 (89)
.+-+.++|++|+++|.+|
T Consensus 67 g~ev~~~~~~y~iv~e~D 84 (91)
T PRK14533 67 GTEIKIDDEDYIIIDVND 84 (91)
T ss_pred CeEEEECCEEEEEEEhHh
Confidence 456889999999999874
No 82
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=33.70 E-value=81 Score=21.60 Aligned_cols=33 Identities=27% Similarity=0.286 Sum_probs=27.1
Q ss_pred CceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 56 QQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 56 ~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
++-.|||+-.=|..-|---+.||+|+.+|.+.|
T Consensus 2 kkIaIiGtrGIPa~YGGfET~ve~L~~~l~~~g 34 (185)
T PF09314_consen 2 KKIAIIGTRGIPARYGGFETFVEELAPRLVSKG 34 (185)
T ss_pred ceEEEEeCCCCCcccCcHHHHHHHHHHHHhcCC
Confidence 455688888777777788899999999998865
No 83
>PF14553 YqbF: YqbF, hypothetical protein domain; PDB: 2HJQ_A.
Probab=33.68 E-value=41 Score=17.84 Aligned_cols=14 Identities=29% Similarity=0.487 Sum_probs=10.2
Q ss_pred HHHHHHHHHHhCCC
Q psy4809 76 VVEKLGDYLVSCGY 89 (89)
Q Consensus 76 ~ve~lAdyL~~~gy 89 (89)
+.+++++||.++++
T Consensus 21 V~kk~y~YL~~ne~ 34 (43)
T PF14553_consen 21 VSKKIYNYLNDNEF 34 (43)
T ss_dssp E-HHHHHHHHHSTT
T ss_pred hhHHHHHHHhcCCc
Confidence 45788999998764
No 84
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=33.22 E-value=57 Score=25.81 Aligned_cols=34 Identities=24% Similarity=0.282 Sum_probs=24.0
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+-.+.-.+|+|++..|+
T Consensus 220 ~tvvv~atsd~p~~~r~~a~~~a~tiAEyfrd~G~ 254 (502)
T PRK09281 220 YTIVVAATASDPAPLQYLAPYAGCAMGEYFMDNGK 254 (502)
T ss_pred ceEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4566777776654 333566777789999999885
No 85
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=32.90 E-value=41 Score=20.20 Aligned_cols=18 Identities=22% Similarity=0.591 Sum_probs=15.2
Q ss_pred ccceEEcceEEEEEEecC
Q psy4809 21 SSGVTLAGNRYIYLSGTD 38 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d~ 38 (89)
..-+.++|++|+++|.++
T Consensus 71 g~~v~~~~~~~~~~~~~d 88 (93)
T PF00166_consen 71 GTEVKFDGEKYLIVREDD 88 (93)
T ss_dssp SEEEEETTEEEEEEEGGG
T ss_pred ceEEEECCEEEEEEEHHH
Confidence 457888999999999875
No 86
>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.
Probab=32.76 E-value=60 Score=23.74 Aligned_cols=34 Identities=18% Similarity=0.298 Sum_probs=23.1
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhC-CC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSC-GY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~-gy 89 (89)
++.+|++.-+++. ..-.+-.+.-.+|+|++.. |+
T Consensus 131 ~tv~v~~t~~~~~~~r~~a~~~a~aiAEyfrd~~g~ 166 (276)
T cd01135 131 RVVLFLNLANDPTIERIITPRMALTTAEYLAYEKGK 166 (276)
T ss_pred eEEEEEecCCCCHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4566667777764 2234666677799999986 63
No 87
>TIGR01039 atpD ATP synthase, F1 beta subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.
Probab=32.61 E-value=60 Score=25.50 Aligned_cols=34 Identities=18% Similarity=0.259 Sum_probs=24.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHh-CCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVS-CGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~-~gy 89 (89)
++.+|++.-+++. ..-.+..+.-.+|+|++. .|+
T Consensus 202 rtvvV~atsd~p~~~R~~a~~~a~tiAEyfrd~~G~ 237 (461)
T TIGR01039 202 KTALVYGQMNEPPGARMRVALTGLTMAEYFRDEQGQ 237 (461)
T ss_pred eeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4567777777764 334567788899999998 674
No 88
>PRK14698 V-type ATP synthase subunit A; Provisional
Probab=32.53 E-value=49 Score=28.51 Aligned_cols=34 Identities=12% Similarity=0.322 Sum_probs=23.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|.+.-+++. ..-.+--+.-.+|+|++++||
T Consensus 719 rtvlv~~ts~~p~~~R~~s~y~a~tiAEyfrd~G~ 753 (1017)
T PRK14698 719 RTVLIANTSNMPVAAREASIYTGITIAEYFRDMGY 753 (1017)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4556666666654 233466667779999999997
No 89
>PF02911 Formyl_trans_C: Formyl transferase, C-terminal domain; InterPro: IPR005793 Methionyl-tRNA formyltransferase (2.1.2.9 from EC) transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. This family also includes formyltetrahydrofolate dehydrogenases, which produce formate from formyl-tetrahydrofolate. These enzymes contain an N-terminal domain in common with other formyl transferase enzymes (IPR002376 from INTERPRO). The C-terminal domain has an open beta-barrel fold [].; GO: 0016742 hydroxymethyl-, formyl- and related transferase activity, 0009058 biosynthetic process; PDB: 3RFO_D 1Z7E_C 2BLN_A 1YRW_A 1FMT_A 2FMT_B 3Q0I_A 3R8X_A 3TQQ_A 2BW0_A ....
Probab=32.28 E-value=1.1e+02 Score=17.82 Aligned_cols=33 Identities=24% Similarity=0.284 Sum_probs=23.3
Q ss_pred CHHHHHHHHhhcCCCccccccceEEcceEEEEEEec
Q psy4809 2 SKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGT 37 (89)
Q Consensus 2 s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d 37 (89)
+.+|+..++.+|. |-. .-=..++|++..+.++.
T Consensus 14 ~A~~I~~~vRal~-p~p--ga~~~~~~~~i~i~~~~ 46 (100)
T PF02911_consen 14 SAEEIYNLVRALN-PYP--GAFTTFNGKRIKILKAE 46 (100)
T ss_dssp BHHHHHHHHHHTT-TTT---EEEEETTEEEEEEEEE
T ss_pred CHHHHHHHHhCCC-CCC--CEEEeeCCeEEEEEeee
Confidence 5688999999996 432 11235699999888874
No 90
>PRK12359 flavodoxin FldB; Provisional
Probab=32.25 E-value=1e+02 Score=20.72 Aligned_cols=35 Identities=11% Similarity=0.030 Sum_probs=27.7
Q ss_pred EcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 54 KTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 54 KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
+-|+..+.|.++....+..=..++..|.+.|++.|
T Consensus 78 ~gK~vAlFG~Gd~~~y~~~f~~a~~~l~~~l~~~G 112 (172)
T PRK12359 78 EGKIVALYGMGDQLGYGEWFLDALGMLHDKLAPKG 112 (172)
T ss_pred CCCEEEEEeCCCCccchHHHHHHHHHHHHHHHhCC
Confidence 34567788888866677778889999999998765
No 91
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=31.58 E-value=68 Score=24.93 Aligned_cols=33 Identities=15% Similarity=0.319 Sum_probs=22.0
Q ss_pred ceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
+.++++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 212 tv~vv~tsd~p~~~r~~a~~~a~tiAEyfrd~G~ 245 (433)
T PRK07594 212 CVIVVATSDRPALERVRALFVATTIAEFFRDNGK 245 (433)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 445566655544 233466668889999999885
No 92
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=30.96 E-value=59 Score=25.80 Aligned_cols=34 Identities=21% Similarity=0.241 Sum_probs=22.4
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+-.+...+|+|++++|+
T Consensus 220 ~tvvV~atsd~p~~~r~~ap~~a~aiAEyfrd~G~ 254 (497)
T TIGR03324 220 YTIVVVTEGNDPPGLQYIAPYAATSIGEHFMEQGR 254 (497)
T ss_pred eeEEEEeCCCCCHHHHHHHHHHHHHHHHHHHhCCC
Confidence 3456666666643 223455667789999999885
No 93
>COG4702 Uncharacterized conserved protein [Function unknown]
Probab=30.89 E-value=85 Score=21.36 Aligned_cols=38 Identities=26% Similarity=0.156 Sum_probs=30.3
Q ss_pred ceEEEEEcCceEEEEEeCCCC--ChhhHHHHHHHHHHHHH
Q psy4809 48 VGVHCMKTQQAVVISLYEDPI--QPQQAASVVEKLGDYLV 85 (89)
Q Consensus 48 ~G~~i~KT~~aiiIg~y~~~~--~~~~~~~~ve~lAdyL~ 85 (89)
+|-+..+.+++.+||...-+. +...=+-+|..||+.|-
T Consensus 119 GG~fpI~vk~ag~iG~v~VSGlpqreDHnlvv~aL~~~lg 158 (168)
T COG4702 119 GGGFPIQVKGAGVIGVVTVSGLPQREDHNLVVRALADHLG 158 (168)
T ss_pred cCceeEEEeccceEEEEEecCCCcccchhHHHHHHHHHhC
Confidence 566777778899999888775 55678899999999874
No 94
>PRK08105 flavodoxin; Provisional
Probab=30.84 E-value=60 Score=20.99 Aligned_cols=22 Identities=23% Similarity=0.093 Sum_probs=18.7
Q ss_pred CChhhHHHHHHHHHHHHHhCCC
Q psy4809 68 IQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 68 ~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+.|++...+++|++.|++.|+
T Consensus 10 S~tGnte~~A~~l~~~l~~~g~ 31 (149)
T PRK08105 10 TVYGNALLVAEEAEAILTAQGH 31 (149)
T ss_pred cCchHHHHHHHHHHHHHHhCCC
Confidence 4678999999999999988764
No 95
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=30.49 E-value=1.3e+02 Score=18.73 Aligned_cols=26 Identities=15% Similarity=0.331 Sum_probs=19.8
Q ss_pred EeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 63 LYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 63 ~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
.+..+-..+++...++.+++.|.+.|
T Consensus 6 i~gS~r~~~~t~~l~~~~~~~l~~~g 31 (152)
T PF03358_consen 6 INGSPRKNSNTRKLAEAVAEQLEEAG 31 (152)
T ss_dssp EESSSSTTSHHHHHHHHHHHHHHHTT
T ss_pred EECcCCCCCHHHHHHHHHHHHHHHcC
Confidence 34444467899999999999998765
No 96
>PF13439 Glyco_transf_4: Glycosyltransferase Family 4; PDB: 2JJM_E 3MBO_C 2GEJ_A 2GEK_A.
Probab=30.24 E-value=1.1e+02 Score=18.67 Aligned_cols=21 Identities=29% Similarity=0.184 Sum_probs=17.3
Q ss_pred ChhhHHHHHHHHHHHHHhCCC
Q psy4809 69 QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 69 ~~~~~~~~ve~lAdyL~~~gy 89 (89)
..|=+...+..|+++|.+.|+
T Consensus 10 ~~GG~e~~~~~l~~~l~~~G~ 30 (177)
T PF13439_consen 10 NIGGAERVVLNLARALAKRGH 30 (177)
T ss_dssp SSSHHHHHHHHHHHHHHHTT-
T ss_pred CCChHHHHHHHHHHHHHHCCC
Confidence 456788899999999999885
No 97
>PRK09273 hypothetical protein; Provisional
Probab=30.23 E-value=83 Score=22.23 Aligned_cols=29 Identities=24% Similarity=0.224 Sum_probs=24.0
Q ss_pred EEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 61 ISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 61 Ig~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
||.=.+..|+.......+.|.+||.+.||
T Consensus 3 iali~e~sqa~kn~~i~~~L~~~L~~~G~ 31 (211)
T PRK09273 3 IALINENSQAAKNAIIYEALKKVADPKGH 31 (211)
T ss_pred EEeecccchhhhhHHHHHHHHHHHHHCCC
Confidence 55667777887888889999999999886
No 98
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=29.97 E-value=54 Score=20.72 Aligned_cols=18 Identities=22% Similarity=0.314 Sum_probs=14.8
Q ss_pred hHHHHHHHHHHHHHhC-CC
Q psy4809 72 QAASVVEKLGDYLVSC-GY 89 (89)
Q Consensus 72 ~~~~~ve~lAdyL~~~-gy 89 (89)
.-...|.+||++|++. |+
T Consensus 13 ~h~~~V~~la~~L~~~~g~ 31 (150)
T PF08357_consen 13 EHKEWVLALAEFLRQNCGI 31 (150)
T ss_pred HHHHHHHHHHHHHHhccCC
Confidence 3468899999999998 74
No 99
>cd03792 GT1_Trehalose_phosphorylase Trehalose phosphorylase (TP) reversibly catalyzes trehalose synthesis and degradation from alpha-glucose-1-phosphate (alpha-Glc-1-P) and glucose. The catalyzing activity includes the phosphorolysis of trehalose, which produce alpha-Glc-1-P and glucose, and the subsequent synthesis of trehalose. This family is most closely related to the GT1 family of glycosyltransferases.
Probab=29.77 E-value=88 Score=22.47 Aligned_cols=29 Identities=10% Similarity=0.060 Sum_probs=22.5
Q ss_pred EEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 61 ISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 61 Ig~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
|+++......|-....+..++++|.+.|+
T Consensus 2 i~~~~~~~~~GGv~~~~~~l~~~l~~~g~ 30 (372)
T cd03792 2 VLHVNSTPYGGGVAEILHSLVPLMRDLGV 30 (372)
T ss_pred eEEEeCCCCCCcHHHHHHHHHHHHHHcCC
Confidence 34555555667789999999999999875
No 100
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=29.68 E-value=1.2e+02 Score=21.83 Aligned_cols=33 Identities=15% Similarity=0.283 Sum_probs=28.5
Q ss_pred CceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 56 QQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 56 ~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
..-+++.+.+-++.|..-++....+++|+.++|
T Consensus 75 ~~~~~~~~~dv~I~p~~i~e~s~~v~~w~~~~~ 107 (244)
T COG1938 75 SDGVLALVSDVPIPPAVIYEISNAVVEWAEENG 107 (244)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHHHHHHHcC
Confidence 445677788889999999999999999999876
No 101
>PRK09271 flavodoxin; Provisional
Probab=29.51 E-value=1.2e+02 Score=19.64 Aligned_cols=20 Identities=10% Similarity=0.179 Sum_probs=17.1
Q ss_pred ChhhHHHHHHHHHHHHHhCC
Q psy4809 69 QPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 69 ~~~~~~~~ve~lAdyL~~~g 88 (89)
..|+..+.++.+|+.|...|
T Consensus 10 ~tGnTe~~A~~ia~~l~~~g 29 (160)
T PRK09271 10 LSGNTREVAREIEERCEEAG 29 (160)
T ss_pred CCchHHHHHHHHHHHHHhCC
Confidence 55789999999999998866
No 102
>PF10653 Phage-A118_gp45: Protein gp45 of Bacteriophage A118; InterPro: IPR018915 The proteins in this entry represents Gp45 in Listeria phage A118 (Bacteriophage A118) and related proteins; Gp45 is thought to have a function in the phage tail-fibre system.
Probab=29.38 E-value=37 Score=18.90 Aligned_cols=15 Identities=27% Similarity=0.401 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHhC
Q psy4809 73 AASVVEKLGDYLVSC 87 (89)
Q Consensus 73 ~~~~ve~lAdyL~~~ 87 (89)
...-+++|+||+.+.
T Consensus 38 ietgcekm~dyieel 52 (62)
T PF10653_consen 38 IETGCEKMTDYIEEL 52 (62)
T ss_pred hhhhhHHHHHHHHHH
Confidence 345689999998763
No 103
>cd08053 Yqbg Putative Head-Tail Connector Protein Yqbg from Bacillus subtilis and similar proteins. The uncharacterized Bacillus subtilis Yqbg protein, whose gene is part of the unusual genetic element called skin, shows a similar structure to the connector proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. gp6 and gp15 are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. They form dodecameric ring structures that comprise the middle ring of the connector, located between the portal protein (attached to the head) and the gp7/gp16 ring (attached to the tail). The Yqbg gene is surrounded with genes similar to genes in the Bacillus subtilis prophage-like element PBSX, which encode for proteins comprising contractile-tailed phage-like particles that are produced upon mitomycin C treatment. Yqbg likely acts as a
Probab=29.07 E-value=70 Score=19.81 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=18.8
Q ss_pred CCChhhHHHHHHHHHHHHHhCC
Q psy4809 67 PIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 67 ~~~~~~~~~~ve~lAdyL~~~g 88 (89)
+..|..+..|+..+|+|+...|
T Consensus 48 ~~~~e~vk~A~c~~ae~~~~~~ 69 (121)
T cd08053 48 PEIPEEVKLAVCALAEYIALID 69 (121)
T ss_pred ccccHHHHHHHHHHHHHHHHhC
Confidence 5578899999999999998754
No 104
>cd03823 GT1_ExpE7_like This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II).
Probab=28.96 E-value=96 Score=21.14 Aligned_cols=31 Identities=23% Similarity=0.246 Sum_probs=21.9
Q ss_pred EEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 59 VVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 59 iiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
++|..+--+...|-....+..|++.|.+.||
T Consensus 3 l~i~~~~~~~~~gG~~~~~~~l~~~L~~~g~ 33 (359)
T cd03823 3 LVVNHLYPPRSVGGAEVVAHDLAEALAKRGH 33 (359)
T ss_pred eEEcccCCcccccchHHHHHHHHHHHHhcCC
Confidence 4455444444455678889999999998875
No 105
>KOG3222|consensus
Probab=28.95 E-value=54 Score=22.81 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHhCCC
Q psy4809 74 ASVVEKLGDYLVSCGY 89 (89)
Q Consensus 74 ~~~ve~lAdyL~~~gy 89 (89)
..|+++|.+||.++|+
T Consensus 177 y~A~~klk~yl~~~g~ 192 (195)
T KOG3222|consen 177 YRALAKLKEYLAENGV 192 (195)
T ss_pred HHHHHHHHHHHHhcCc
Confidence 5789999999999884
No 106
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=28.91 E-value=82 Score=25.02 Aligned_cols=34 Identities=21% Similarity=0.196 Sum_probs=21.9
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+-.+...+|+|++++|+
T Consensus 220 ~tvvV~atsd~~~~~r~~ap~~a~aiAEyfrd~G~ 254 (502)
T PRK13343 220 YTTVVVAEASDPPGLQYLAPFAGCAIAEYFRDQGQ 254 (502)
T ss_pred eeEEEEecccccHHHHHHHHHHHHHHHHHHHhCCC
Confidence 4456666666643 222355567778999999884
No 107
>PF09907 DUF2136: Uncharacterized protein conserved in bacteria (DUF2136); InterPro: IPR018669 HigB (YgjN) is the toxin of the HigB-HigA toxin-antitoxin system, acting as a translation-dependent mRNA interferase. HigB inhibits protein synthesis by cleaving translated mRNAs within the coding region []. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=28.76 E-value=73 Score=18.69 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=9.8
Q ss_pred ceEEcceEEEEEE
Q psy4809 23 GVTLAGNRYIYLS 35 (89)
Q Consensus 23 Gi~l~G~kY~~~r 35 (89)
=|.++|.+|.++-
T Consensus 40 vFnI~GN~yRlI~ 52 (76)
T PF09907_consen 40 VFNIGGNKYRLIA 52 (76)
T ss_pred EEEcCCCcEEEEE
Confidence 4678888888754
No 108
>COG2945 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]
Probab=28.51 E-value=76 Score=22.41 Aligned_cols=33 Identities=21% Similarity=0.323 Sum_probs=27.1
Q ss_pred ceEEEEEeCCCCChh-hHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDPIQPQ-QAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~~~~~-~~~~~ve~lAdyL~~~gy 89 (89)
..|.+.-++.+...| +-|+.|..+|.-|.+.||
T Consensus 28 ~~iAli~HPHPl~gGtm~nkvv~~la~~l~~~G~ 61 (210)
T COG2945 28 APIALICHPHPLFGGTMNNKVVQTLARALVKRGF 61 (210)
T ss_pred CceEEecCCCccccCccCCHHHHHHHHHHHhCCc
Confidence 566677778887665 599999999999999986
No 109
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=28.27 E-value=64 Score=23.34 Aligned_cols=34 Identities=18% Similarity=0.215 Sum_probs=28.9
Q ss_pred CceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.++-||.+.+|=.+....++-.--||++|.+.|+
T Consensus 2 ~~a~iI~vG~ElL~G~ivdtNa~~la~~L~~~G~ 35 (255)
T COG1058 2 MKAEIIAVGDELLSGRIVDTNAAFLADELTELGV 35 (255)
T ss_pred ceEEEEEEccceecCceecchHHHHHHHHHhcCc
Confidence 3577889999977877788888999999999986
No 110
>PRK01064 hypothetical protein; Provisional
Probab=28.14 E-value=1.3e+02 Score=17.66 Aligned_cols=42 Identities=17% Similarity=0.170 Sum_probs=20.1
Q ss_pred HHHHHhhc-CCCccccccceEEcceEEEEEEecC---cEEEEecCC
Q psy4809 6 LGKLVQGF-EKQDILTSSGVTLAGNRYIYLSGTD---KVIRAKLGK 47 (89)
Q Consensus 6 ~~~i~~~f-~~~~~~~~~Gi~l~G~kY~~~r~d~---~~i~~kkg~ 47 (89)
+..|+..+ ++|+.+.-+-..-++.-.+-++.++ +.+.||+|.
T Consensus 5 v~~iv~~LVd~Pe~V~V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~ 50 (78)
T PRK01064 5 LAYIVKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGR 50 (78)
T ss_pred HHHHHHHhcCCCCeEEEEEEeCCCEEEEEEEECcccceEEECCCCc
Confidence 34555555 6787665442211222233344432 457776654
No 111
>COG4535 CorC Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]
Probab=28.06 E-value=1.4e+02 Score=21.96 Aligned_cols=40 Identities=10% Similarity=0.243 Sum_probs=27.6
Q ss_pred CHHHHHHHHh----hcCCCccccccceEEcceEEEEEEecCcEEE
Q psy4809 2 SKDELGKLVQ----GFEKQDILTSSGVTLAGNRYIYLSGTDKVIR 42 (89)
Q Consensus 2 s~~E~~~i~~----~f~~~~~~~~~Gi~l~G~kY~~~r~d~~~i~ 42 (89)
|.+|+.+|-. +|..... +.+-+.++|-.|.+.++|.+.+.
T Consensus 232 sDeevDTIGGLVm~afGhLP~-RGE~i~i~~~~FkV~~ADsRrv~ 275 (293)
T COG4535 232 SDEEVDTIGGLVMQAFGHLPA-RGEKIDIGGYQFKVARADSRRVI 275 (293)
T ss_pred ChhhhhhhhHHHHHHhccCCC-CCCEEEEcceEEEEeecccceEE
Confidence 5667666543 4433222 45779999999999999987644
No 112
>PRK06703 flavodoxin; Provisional
Probab=27.87 E-value=1.4e+02 Score=18.77 Aligned_cols=27 Identities=7% Similarity=0.130 Sum_probs=20.0
Q ss_pred EEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 59 VVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 59 iiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
++|.++. ..|++...++.+|+.|...|
T Consensus 4 v~IiY~S---~tGnT~~iA~~ia~~l~~~g 30 (151)
T PRK06703 4 ILIAYAS---MSGNTEDIADLIKVSLDAFD 30 (151)
T ss_pred EEEEEEC---CCchHHHHHHHHHHHHHhcC
Confidence 4455544 45889999999999997765
No 113
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=27.54 E-value=76 Score=25.13 Aligned_cols=34 Identities=21% Similarity=0.213 Sum_probs=22.2
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
++.+|++.-+++. ..-.+-.+...+|+|++.+|+
T Consensus 199 ~tvvV~atad~~~~~r~~ap~~a~aiAEyfr~~G~ 233 (485)
T CHL00059 199 YTIVVAETADSPATLQYLAPYTGAALAEYFMYRGR 233 (485)
T ss_pred ceEEEEeCCCCCHHHHHHHHHHHhhHHHHHHHcCC
Confidence 3456666655543 223456667789999999884
No 114
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=27.40 E-value=2e+02 Score=19.37 Aligned_cols=40 Identities=8% Similarity=0.184 Sum_probs=29.1
Q ss_pred CCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 46 GKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 46 g~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+.-+.|..+.+.++.|. .+...+..+++++++.|++.||
T Consensus 46 Pk~t~lIF~sGKiviTGa----ks~~~~~~a~~~~~~~l~~~g~ 85 (174)
T cd04517 46 PRATASVWSSGKITITGA----TSEEEAKQAARRAARLLQKLGF 85 (174)
T ss_pred CcEEEEEECCCeEEEEcc----CCHHHHHHHHHHHHHHHHHcCC
Confidence 344556666777666654 3456899999999999998875
No 115
>COG2885 OmpA Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]
Probab=26.89 E-value=1.5e+02 Score=19.64 Aligned_cols=15 Identities=47% Similarity=0.660 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHhCC
Q psy4809 74 ASVVEKLGDYLVSCG 88 (89)
Q Consensus 74 ~~~ve~lAdyL~~~g 88 (89)
..-.+.+++||.+.|
T Consensus 137 ~rRA~aV~~~L~~~G 151 (190)
T COG2885 137 ERRAEAVADYLVSQG 151 (190)
T ss_pred HHHHHHHHHHHHHcC
Confidence 344556666666655
No 116
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=26.57 E-value=86 Score=24.45 Aligned_cols=33 Identities=12% Similarity=0.152 Sum_probs=24.6
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~g 88 (89)
++++|++.-+++. ..-.+-.+.-.+|+||+..|
T Consensus 196 rtvlv~~~adep~~~R~~~~~~AltiAEyfrd~g 229 (436)
T PRK02118 196 RTVMFIHTASDPPVECLLVPDMALAVAEKFALEG 229 (436)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 5677788888875 33456677778999999886
No 117
>PHA02755 hypothetical protein; Provisional
Probab=26.32 E-value=43 Score=20.33 Aligned_cols=21 Identities=33% Similarity=0.485 Sum_probs=16.8
Q ss_pred EEEEEeCCCCChhhHHHHHHH
Q psy4809 59 VVISLYEDPIQPQQAASVVEK 79 (89)
Q Consensus 59 iiIg~y~~~~~~~~~~~~ve~ 79 (89)
+-||.|++.+|.....++.|.
T Consensus 9 m~igsypdavqgsp~~e~aee 29 (96)
T PHA02755 9 MAIGSYPDAVQGSPAAEAAEE 29 (96)
T ss_pred cccccCcccccCChHHHHHHH
Confidence 458999999998887777665
No 118
>KOG4048|consensus
Probab=26.01 E-value=89 Score=21.54 Aligned_cols=43 Identities=16% Similarity=0.118 Sum_probs=34.4
Q ss_pred EEEec--CCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHH
Q psy4809 41 IRAKL--GKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDY 83 (89)
Q Consensus 41 i~~kk--g~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdy 83 (89)
=||+| +-+|.+|.++..+=...+-+-+.-|-+..+-|.+.-.|
T Consensus 82 HyG~KivglgG~FiIqkG~a~~hvm~dFs~cP~nsdeEVnkWL~f 126 (201)
T KOG4048|consen 82 HYGKKIVGLGGQFIIQKGKARLHVMADFSSCPLNSDEEVNKWLHF 126 (201)
T ss_pred hcCcccccccceEEEeccccccccccccCCCCCCCHHHHHHHHhH
Confidence 47887 77899999998888888888777888888888776555
No 119
>COG1647 Esterase/lipase [General function prediction only]
Probab=25.95 E-value=53 Score=23.69 Aligned_cols=15 Identities=47% Similarity=0.711 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHhCCC
Q psy4809 75 SVVEKLGDYLVSCGY 89 (89)
Q Consensus 75 ~~ve~lAdyL~~~gy 89 (89)
.-|.-||+||.++||
T Consensus 29 ~Dvr~Lgr~L~e~Gy 43 (243)
T COG1647 29 RDVRMLGRYLNENGY 43 (243)
T ss_pred HHHHHHHHHHHHCCc
Confidence 358899999999998
No 120
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=25.87 E-value=1.5e+02 Score=17.30 Aligned_cols=38 Identities=21% Similarity=0.251 Sum_probs=29.2
Q ss_pred CceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 47 KVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 47 ~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
+--+.+..|.+.+|.|. .++..+..+++++.+.|.+.|
T Consensus 49 ~~t~~IF~sGki~itGa----ks~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 49 KATVLIFSSGKIVITGA----KSEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp TEEEEEETTSEEEEEEE----SSHHHHHHHHHHHHHHHHHTT
T ss_pred cEEEEEEcCCEEEEEec----CCHHHHHHHHHHHHHHHHHcC
Confidence 44566777777777775 356689999999999998865
No 121
>PRK09267 flavodoxin FldA; Validated
Probab=25.69 E-value=1.6e+02 Score=18.96 Aligned_cols=35 Identities=11% Similarity=0.114 Sum_probs=24.7
Q ss_pred EcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 54 KTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 54 KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
+.+...++++++....+..-..++..|.+.|.+.|
T Consensus 79 ~~k~vaifg~g~~~~~~~~~~~~~~~l~~~l~~~g 113 (169)
T PRK09267 79 SGKKVALFGLGDQEDYAEYFCDAMGTLYDIVEPRG 113 (169)
T ss_pred CCCEEEEEecCCCCcchHHHHHHHHHHHHHHHHCC
Confidence 34567777777655555556677888999888765
No 122
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=25.40 E-value=1.8e+02 Score=18.17 Aligned_cols=38 Identities=13% Similarity=0.308 Sum_probs=22.8
Q ss_pred eEEEEEc-CceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 49 GVHCMKT-QQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 49 G~~i~KT-~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
|++++-. ++.+=|.+.+-. .|..+.++..++-.+..||
T Consensus 66 GFvviN~dKK~mSvsFsdid---eNmK~~i~ei~kkykd~Gy 104 (110)
T PF11513_consen 66 GFVVINKDKKMMSVSFSDID---ENMKNSIEEIVKKYKDSGY 104 (110)
T ss_dssp EEEEEETTTTEEEEEE-S-----CCHHHHHHHHHHHHHCCS-
T ss_pred EEEEEecCCeEEEEEecchh---HHHHHHHHHHHHHhhcCCc
Confidence 5555544 444445544322 2558889999999999987
No 123
>COG3403 Uncharacterized conserved protein [Function unknown]
Probab=25.19 E-value=1.2e+02 Score=21.92 Aligned_cols=32 Identities=19% Similarity=0.238 Sum_probs=27.6
Q ss_pred ceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 57 QAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 57 ~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
..+.|+++.+.-.|..+..-...||+|+..++
T Consensus 52 ~q~~iavvgdl~~p~aa~gla~~Laey~t~~~ 83 (257)
T COG3403 52 DQLRIAVVGDLRSPSAAXGLAPLLAEYGTISR 83 (257)
T ss_pred CCeeEEeccCCCCchhhhhhHHHHHHHhhhcc
Confidence 46789999999999999999999999988763
No 124
>PRK12678 transcription termination factor Rho; Provisional
Probab=25.09 E-value=83 Score=25.96 Aligned_cols=32 Identities=22% Similarity=0.310 Sum_probs=23.8
Q ss_pred eEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 58 AVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 58 aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
-||.++++++. ..-.+...+-.+|+||+++|+
T Consensus 471 eVVasT~D~p~~~~~~~a~~ai~~Ae~fre~G~ 503 (672)
T PRK12678 471 EVIASTFDRPPSDHTTVAELAIERAKRLVELGK 503 (672)
T ss_pred eEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 36777777765 234577777789999999985
No 125
>TIGR01026 fliI_yscN ATPase FliI/YscN family. This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.
Probab=24.93 E-value=93 Score=24.14 Aligned_cols=32 Identities=19% Similarity=0.284 Sum_probs=20.7
Q ss_pred eEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 58 AVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 58 aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+|++.-+++. ..-.+..++-.+|+|++++|+
T Consensus 221 vvv~~~~d~~p~~r~~~~~~a~t~AE~frd~G~ 253 (440)
T TIGR01026 221 VVVVATSDQSPLLRLKGAYVATAIAEYFRDQGK 253 (440)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 34455555543 223466777789999999885
No 126
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=24.65 E-value=70 Score=19.08 Aligned_cols=18 Identities=17% Similarity=0.230 Sum_probs=14.7
Q ss_pred cccceEEcceEEEEEEec
Q psy4809 20 TSSGVTLAGNRYIYLSGT 37 (89)
Q Consensus 20 ~~~Gi~l~G~kY~~~r~d 37 (89)
..+-+.++|+.|.+.+..
T Consensus 68 ~gd~v~~dG~~y~V~~~~ 85 (95)
T PF13856_consen 68 RGDRVVIDGESYTVTRFQ 85 (95)
T ss_dssp TT-EEEETTEEEEEEEEE
T ss_pred CCCEEEECCeEEEEeEEe
Confidence 457899999999999875
No 127
>PRK14688 hypothetical protein; Provisional
Probab=24.64 E-value=1.5e+02 Score=18.87 Aligned_cols=68 Identities=13% Similarity=0.191 Sum_probs=44.6
Q ss_pred cccceEEcceEEEEEEecCcEEEEecCCc-eEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 20 TSSGVTLAGNRYIYLSGTDKVIRAKLGKV-GVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 20 ~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~-G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
...|..+-...|.+-+.+ =.|.++++.. =|+=+||.+.--.|.-.+.+++.....-...-..||.+.+
T Consensus 21 ~~~Gy~Il~rN~r~~~GE-IDiIa~~~~~lVFVEVK~R~~~~~g~~~eaV~~~K~~ri~~aA~~yL~~~~ 89 (121)
T PRK14688 21 KGMGYSIIQTNCRLPEGE-IDIVGQDGEYLVFIEVRTKRRLGYGLPAESVTPRKKAHLMASAESYIQKHR 89 (121)
T ss_pred HHCCCEEEEEEeeCCCCc-EeEEEeeCCEEEEEEEEecCCCCCCChHHcCCHHHHHHHHHHHHHHHHhCC
Confidence 457888888888774433 2355665443 3455788766555655566788777777777777887654
No 128
>PF02233 PNTB: NAD(P) transhydrogenase beta subunit; InterPro: IPR012136 NAD(P) transhydrogenase catalyses the transfer of reducing equivalents between NAD(H) and NADP(H), coupled to the translocation of protons across a membrane []. It is an integral membrane protein found in most organisms except for yeasts, plants and some bacterial species. In bacterial species it is located in the cytoplasmic membrane, while in mitochondria it is located in the inner membrane. Under most physiological conditions this enzyme synthesises NADPH, driven by consumption of the proton electrochemical gradient. The resulting NADPH is subsequently used for biosynthetic reactions or the reduction of glutathione. The global structure of this enzyme is similar in all organisms, consisting of three distinct domains, though the polypeptide composition can vary. Domain I binds NAD(+)/NADH, domain II is a hydrophobic membrane-spanning domain, and domain III binds NADP(+)/NADPH. Domain I is composed of two subdomains, both of which form a Rossman fold, while domain III consists of a single Rossman fold where the NADP(+) is flipped relative to the normal orientation of bound nucleotides within the Rossman fold [, , ]. Several residues within these domains are thought to make functionally important interdomain contacts for hydride transfer between these domains []. Proton translocation occurs through domain II and is thought to induce conformational changes which are transmitted across domain III to the site of hydride transfer between domains I and III. This entry represents the beta subunit found in bacterial two-subunit NADP(H) transhydrogenases. This subunit forms domain III and part of the transmembrane domain II. ; GO: 0008750 NAD(P)+ transhydrogenase (AB-specific) activity, 0050661 NADP binding, 0055114 oxidation-reduction process, 0016021 integral to membrane; PDB: 1PT9_A 1DJL_A 1U31_B 2BRU_C 1PTJ_C 1HZZ_C 2FRD_C 2FSV_C 1XLT_C 1U2G_C ....
Probab=24.59 E-value=59 Score=25.61 Aligned_cols=19 Identities=37% Similarity=0.410 Sum_probs=16.7
Q ss_pred hhhHHHHHHHHHHHHHhCC
Q psy4809 70 PQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 70 ~~~~~~~ve~lAdyL~~~g 88 (89)
-.+|+.+|.+|+|+|++.|
T Consensus 320 vAqAQ~~v~el~~~L~~~G 338 (463)
T PF02233_consen 320 VAQAQHAVAELADLLEERG 338 (463)
T ss_dssp HCTTHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHhCC
Confidence 3589999999999999987
No 129
>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=24.57 E-value=85 Score=24.75 Aligned_cols=34 Identities=18% Similarity=0.393 Sum_probs=24.3
Q ss_pred CceEEEEEeCCCC-ChhhHHHHHHHHHHHHH-hCCC
Q psy4809 56 QQAVVISLYEDPI-QPQQAASVVEKLGDYLV-SCGY 89 (89)
Q Consensus 56 ~~aiiIg~y~~~~-~~~~~~~~ve~lAdyL~-~~gy 89 (89)
++.+|++.-+++. ..-.+-.+.-.+|+|++ +.|+
T Consensus 212 rtvvv~atsd~p~~~R~~a~~~a~tiAEyfr~~~G~ 247 (466)
T TIGR01040 212 RVCLFLNLANDPTIERIITPRLALTTAEYLAYQCEK 247 (466)
T ss_pred eEEEEEECCCCCHHHHHHHHhhhHHHHHHHHHhcCC
Confidence 5677777777754 33456677777999999 6774
No 130
>PRK05569 flavodoxin; Provisional
Probab=24.26 E-value=1.8e+02 Score=17.92 Aligned_cols=27 Identities=15% Similarity=0.187 Sum_probs=19.5
Q ss_pred EEEEEeCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 59 VVISLYEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 59 iiIg~y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
++|.++. ..|+....++.+++-|.+.|
T Consensus 4 i~iiY~S---~tGnT~~iA~~i~~~~~~~g 30 (141)
T PRK05569 4 VSIIYWS---CGGNVEVLANTIADGAKEAG 30 (141)
T ss_pred EEEEEEC---CCCHHHHHHHHHHHHHHhCC
Confidence 3444444 26788999999999887765
No 131
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=24.10 E-value=1e+02 Score=23.95 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=21.8
Q ss_pred eEEEEEeCCCC-ChhhHHHHHHHHHHHHHhCCC
Q psy4809 58 AVVISLYEDPI-QPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 58 aiiIg~y~~~~-~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+|++..+++. ..-.+..+.-.+|+|++++|.
T Consensus 214 vvv~~tsd~s~~~r~ra~~~a~~iAEyfr~~G~ 246 (432)
T PRK06793 214 VVVVATSDESHLMQLRAAKLATSIAEYFRDQGN 246 (432)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 45666666643 223477777789999999874
No 132
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=24.06 E-value=75 Score=20.40 Aligned_cols=37 Identities=14% Similarity=0.314 Sum_probs=26.1
Q ss_pred CCHHHHHHHHhhcCCCccccccceEEcceEEEEEEecCcEEEE
Q psy4809 1 LSKDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGTDKVIRA 43 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d~~~i~~ 43 (89)
+.++|+..+++++ +.+||.+--.+=-.+..+++.+|.
T Consensus 65 ll~~EV~pvi~aL------~~~GI~vtAlHNH~l~e~Prl~ym 101 (123)
T PF07485_consen 65 LLEDEVNPVISAL------RKNGIEVTALHNHWLFEQPRLFYM 101 (123)
T ss_pred ecHHHHHHHHHHH------HHCCceEEEEecccccCCCCEEEE
Confidence 4678888888765 456887776666666677776654
No 133
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=23.85 E-value=1.8e+02 Score=17.58 Aligned_cols=16 Identities=19% Similarity=0.241 Sum_probs=7.3
Q ss_pred CceEEEEEcCceEEEE
Q psy4809 47 KVGVHCMKTQQAVVIS 62 (89)
Q Consensus 47 ~~G~~i~KT~~aiiIg 62 (89)
-.|+++--|+..++|-
T Consensus 29 i~GiVv~ET~nt~~I~ 44 (92)
T smart00538 29 IEGIVVDETRNTLKIE 44 (92)
T ss_pred cEEEEEEeeeeEEEEE
Confidence 3444444444444443
No 134
>PRK03298 hypothetical protein; Provisional
Probab=23.75 E-value=2.2e+02 Score=20.35 Aligned_cols=67 Identities=19% Similarity=0.212 Sum_probs=41.9
Q ss_pred HHHHHHHHhhcCCCccccccceEEcceEEEEEEecCcEEEEecCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHH
Q psy4809 3 KDELGKLVQGFEKQDILTSSGVTLAGNRYIYLSGTDKVIRAKLGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGD 82 (89)
Q Consensus 3 ~~E~~~i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d~~~i~~kkg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAd 82 (89)
..+++.++. ++|+ +...|+.+-++.|.+ ..-+=.|.++...+..+++--|.- | --.+|++|..
T Consensus 105 Ea~Lq~~la--e~p~-~i~~G~~lv~rE~~t-~~G~IDil~rD~~G~~V~vEvKRr---~----------~idaV~QL~R 167 (224)
T PRK03298 105 EAHLQELLA--EHIE-TLGEGYTLVRREYPT-AIGPVDLLCRDADGGTVAVEIKRR---G----------EIDGVEQLTR 167 (224)
T ss_pred HHHHHHHHH--hCHH-HhcCCCEEEEEEecC-CCCceeEEEEcCCCCEEEEEEEec---C----------CccHHHHHHH
Confidence 456666665 6774 458899998877744 222334888776666666544432 0 1237888888
Q ss_pred HHHh
Q psy4809 83 YLVS 86 (89)
Q Consensus 83 yL~~ 86 (89)
|+.-
T Consensus 168 Yve~ 171 (224)
T PRK03298 168 YLEL 171 (224)
T ss_pred HHHH
Confidence 8753
No 135
>PRK05723 flavodoxin; Provisional
Probab=23.42 E-value=97 Score=20.18 Aligned_cols=22 Identities=18% Similarity=0.211 Sum_probs=18.3
Q ss_pred CChhhHHHHHHHHHHHHHhCCC
Q psy4809 68 IQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 68 ~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+.|++...+++|++.|.+.|+
T Consensus 9 S~tG~ae~~A~~la~~l~~~g~ 30 (151)
T PRK05723 9 SVYGTAEEVARHAESLLKAAGF 30 (151)
T ss_pred cCchHHHHHHHHHHHHHHHCCC
Confidence 4678999999999999987663
No 136
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=23.33 E-value=41 Score=21.03 Aligned_cols=26 Identities=19% Similarity=0.609 Sum_probs=20.2
Q ss_pred CHHHHHHHHhhcCCCccccccceEEcce
Q psy4809 2 SKDELGKLVQGFEKQDILTSSGVTLAGN 29 (89)
Q Consensus 2 s~~E~~~i~~~f~~~~~~~~~Gi~l~G~ 29 (89)
++++..++++.|=| .+-++|+.++|-
T Consensus 28 ~~e~~D~~~D~fId--~Ie~~gL~~~Gg 53 (101)
T PF04320_consen 28 SEEQIDAFVDAFID--VIEPNGLAFGGG 53 (101)
T ss_pred CHHHHHHHHHHHHH--HHHhCCCEEecC
Confidence 67888999998865 455788888874
No 137
>PF01868 UPF0086: Domain of unknown function UPF0086; InterPro: IPR002730 The p29 subunit (also known as Rpp29 or Pop4) of the related ribonucleoproteins ribonuclease (RNase) P and RNase MRP can be found in both eukaryotes and arachea []. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex []. Rpp29 (3.1.26.5 from EC) catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits. RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA (approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor (approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits Mth Rpp29, a homologue of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme []. In Saccharomyces cerevisiae (Baker's yeast), RNase P consists of 9 protein subunits (Pop1, Pop3-8, Rpr2 and Rpp1), while in humans there are 10 subunits (Rpp14, 20, 21, 25, 29, 30, 38, 40, hPop1, 5). RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA []. RNase MRP also cleaves primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits and is highly related to RNase P (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1).; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0006364 rRNA processing, 0006379 mRNA cleavage, 0008033 tRNA processing, 0000172 ribonuclease MRP complex, 0030677 ribonuclease P complex; PDB: 1V76_B 2ZAE_C 1OQK_A 2KI7_A 1TSF_A 1TS9_A 1PC0_A.
Probab=22.90 E-value=93 Score=18.61 Aligned_cols=35 Identities=17% Similarity=0.226 Sum_probs=17.3
Q ss_pred cceEEEEEEecCcEEEEecCCceEEEEEcCceEEEEEe
Q psy4809 27 AGNRYIYLSGTDKVIRAKLGKVGVHCMKTQQAVVISLY 64 (89)
Q Consensus 27 ~G~kY~~~r~d~~~i~~kkg~~G~~i~KT~~aiiIg~y 64 (89)
-|-+-.+++..+.++. |-.|+++.-|+..++|-.-
T Consensus 13 ~G~~i~V~~s~~pslv---G~~GiVV~ETknt~~I~t~ 47 (89)
T PF01868_consen 13 IGAKIEVVRSKNPSLV---GIEGIVVDETKNTFVIVTE 47 (89)
T ss_dssp TT-EEEEEEESSCCCT---TEEEEEEEEETTEEEEEET
T ss_pred cCCEEEEEEcCCCCcc---CCEEEEEEcccceEEEEec
Confidence 3444455555443322 2456666666666665543
No 138
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=22.72 E-value=2.7e+02 Score=19.35 Aligned_cols=37 Identities=11% Similarity=0.073 Sum_probs=26.2
Q ss_pred EEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHh
Q psy4809 50 VHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVS 86 (89)
Q Consensus 50 ~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~ 86 (89)
|.+...++-|+|-.-++..|..|=..|.+.|...|.+
T Consensus 130 Vrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~l~~ 166 (200)
T TIGR03072 130 VRATHLASGISVKVQSERSQHANKRLATLLLAVRLAD 166 (200)
T ss_pred EEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHH
Confidence 4555555556666666667778888899999888764
No 139
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.
Probab=22.69 E-value=1.8e+02 Score=18.13 Aligned_cols=20 Identities=25% Similarity=0.298 Sum_probs=16.2
Q ss_pred ChhhHHHHHHHHHHHHHhCC
Q psy4809 69 QPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 69 ~~~~~~~~ve~lAdyL~~~g 88 (89)
..|+..+.++.+|+.|...|
T Consensus 10 ~tGnTe~iA~~ia~~l~~~g 29 (140)
T TIGR01754 10 LSGNTEEVAFMIQDYLQKDG 29 (140)
T ss_pred CCChHHHHHHHHHHHHhhCC
Confidence 55788999999999887655
No 140
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=22.61 E-value=5e+02 Score=22.80 Aligned_cols=58 Identities=10% Similarity=0.111 Sum_probs=39.6
Q ss_pred EEEEEecCcEEEEecCCceEEEEEcCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 31 YIYLSGTDKVIRAKLGKVGVHCMKTQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 31 Y~~~r~d~~~i~~kkg~~G~~i~KT~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
|+.++.|...++. ....+++.+....-..|++.|-=..|..-..+++.+.++-+..|+
T Consensus 256 ~la~~~Dk~~~fs-~~g~a~i~Yrv~~~~~i~~GDPvG~~e~~~~~i~~F~~~a~~~g~ 313 (1094)
T PRK02983 256 YFATRRDKSVVFA-PSGRAAITYRVEVGVCLASGDPVGDPEAWPQAIDAWLALARTYGW 313 (1094)
T ss_pred eeeecCCceEEEC-CCCCEEEEEEEECCEEEEECCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 4555656555554 334677777777666666655444778888999999998887764
No 141
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=22.34 E-value=76 Score=21.86 Aligned_cols=22 Identities=14% Similarity=0.170 Sum_probs=15.8
Q ss_pred HHHHHhhcCCCccccccceEEcc
Q psy4809 6 LGKLVQGFEKQDILTSSGVTLAG 28 (89)
Q Consensus 6 ~~~i~~~f~~~~~~~~~Gi~l~G 28 (89)
.+.++.+++.|.. .-+|+-||-
T Consensus 12 ~K~~LHaaKyP~~-aVnGvLlg~ 33 (196)
T PF03665_consen 12 AKMILHAAKYPHC-AVNGVLLGK 33 (196)
T ss_pred HHHHHHhccCCCC-ceeeEEEec
Confidence 4667788888754 458888874
No 142
>PRK09004 FMN-binding protein MioC; Provisional
Probab=22.28 E-value=1.1e+02 Score=19.73 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=18.3
Q ss_pred CChhhHHHHHHHHHHHHHhCCC
Q psy4809 68 IQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 68 ~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.+.|++....++|++.|++.|+
T Consensus 10 S~tGnae~~A~~l~~~~~~~g~ 31 (146)
T PRK09004 10 STLGGAEYVADHLAEKLEEAGF 31 (146)
T ss_pred cCchHHHHHHHHHHHHHHHcCC
Confidence 4678999999999999987763
No 143
>PF04960 Glutaminase: Glutaminase; InterPro: IPR015868 Glutaminases (3.5.1.2 from EC) deaminate glutamine to glutamate. In Bacillus subtilis, glutaminase is encoded by glnA, which is part of an operon, glnA-glnT (formerly ybgJ-ybgH), where glnT encodes a glutamine transporter. The glnA-glnT operon is regulated by the 2-component system GlnK-GlnL in response to glutamine []. This entry represents the core structural motif of a family of glutaminases that include GlnA, which are characterised by their beta-lactamase-like topology, containing a cluster of alpha-helices and an alpha/beta sandwich. This family describes the enzyme glutaminase, from a larger family that includes serine-dependent beta-lactamases and penicillin-binding proteins. Many bacteria have two isozymes. This model is based on selected known glutaminases and their homologs within prokaryotes, with the exclusion of highly-derived (long branch) and architecturally varied homologs, so as to achieve conservative assignments. A sharp drop in scores occurs below 250, and cutoffs are set accordingly. The enzyme converts glutamine to glutamate, with the release of ammonia. Members tend to be described as glutaminase A (glsA), where B (glsB) is unknown and may not be homologous (as in Rhizobium etli. Some species have two isozymes that may both be designated A (GlsA1 and GlsA2). ; GO: 0004359 glutaminase activity, 0006541 glutamine metabolic process; PDB: 2OSU_B 3BRM_A 3AGF_B 1MKI_B 2PBY_C 3SS5_D 3SS3_A 3SS4_C 3UO9_C 3UNW_C ....
Probab=21.91 E-value=2.4e+02 Score=20.71 Aligned_cols=45 Identities=22% Similarity=0.285 Sum_probs=32.3
Q ss_pred EEEecCCceEEEEEcCceEEEEEeCCCCC-hhh---HHHHHHHHHHHHH
Q psy4809 41 IRAKLGKVGVHCMKTQQAVVISLYEDPIQ-PQQ---AASVVEKLGDYLV 85 (89)
Q Consensus 41 i~~kkg~~G~~i~KT~~aiiIg~y~~~~~-~~~---~~~~ve~lAdyL~ 85 (89)
+=+|.|-+|.++.--+.-+=||.|..+.. .|| ...+.|.|++.|.
T Consensus 234 lPaKSGVgGgilavvPg~~gIav~SP~LD~~GNSv~G~~~le~ls~~~~ 282 (286)
T PF04960_consen 234 LPAKSGVGGGILAVVPGRMGIAVYSPPLDEKGNSVRGMKALEQLSERLG 282 (286)
T ss_dssp S-EEE-TTSEEEEEETTTEEEEEE-SEB-TTSSBHHHHHHHHHHHHHHT
T ss_pred CccccCCCceEEEEeCCCcEEEEECCCCCCCCCcHHHHHHHHHHHHHhC
Confidence 45788988888888898899999988773 344 6677788887764
No 144
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=21.83 E-value=1.1e+02 Score=24.07 Aligned_cols=18 Identities=17% Similarity=0.274 Sum_probs=14.6
Q ss_pred hHHHHHHHHHHHHHhCCC
Q psy4809 72 QAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 72 ~~~~~ve~lAdyL~~~gy 89 (89)
.+..+.-.+|+|+++.|+
T Consensus 248 ~~~~~a~tiAEyfrd~G~ 265 (455)
T PRK07960 248 QGAAYATRIAEDFRDRGQ 265 (455)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 466677889999999885
No 145
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=21.77 E-value=1.9e+02 Score=17.09 Aligned_cols=42 Identities=14% Similarity=0.085 Sum_probs=25.6
Q ss_pred HHHHHhhc-CCCccccccceEEcceEEEEEEecC---cEEEEecCC
Q psy4809 6 LGKLVQGF-EKQDILTSSGVTLAGNRYIYLSGTD---KVIRAKLGK 47 (89)
Q Consensus 6 ~~~i~~~f-~~~~~~~~~Gi~l~G~kY~~~r~d~---~~i~~kkg~ 47 (89)
+..|+..| ++|..+.-+-.-......+-++.++ +.+.||+|.
T Consensus 5 v~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GR 50 (76)
T COG1837 5 VEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGR 50 (76)
T ss_pred HHHHHHHhcCCccceEEEEEecCCeEEEEEEECcccccceecCCCh
Confidence 34455555 7888775544444556566666653 468887765
No 146
>PF14080 DUF4261: Domain of unknown function (DUF4261)
Probab=21.66 E-value=1.7e+02 Score=16.68 Aligned_cols=25 Identities=12% Similarity=0.336 Sum_probs=20.7
Q ss_pred eCCCCChhhHHHHHHHHHHHHHhCC
Q psy4809 64 YEDPIQPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 64 y~~~~~~~~~~~~ve~lAdyL~~~g 88 (89)
......|.........+|.||.+.|
T Consensus 16 ~~~~~~p~ev~~~l~~ia~Yil~~~ 40 (77)
T PF14080_consen 16 HFSDLDPEEVYNFLYNIAYYILENG 40 (77)
T ss_pred EcCCCCHHHHHHHHHHHHHHHHcCC
Confidence 3456788899999999999998875
No 147
>PRK03879 ribonuclease P protein component 1; Validated
Probab=21.54 E-value=1.8e+02 Score=17.77 Aligned_cols=13 Identities=15% Similarity=0.176 Sum_probs=6.3
Q ss_pred ccceEEcceEEEE
Q psy4809 21 SSGVTLAGNRYIY 33 (89)
Q Consensus 21 ~~Gi~l~G~kY~~ 33 (89)
-+|+.+.-++-.+
T Consensus 31 i~GiVv~ETknt~ 43 (96)
T PRK03879 31 IKGRVVDETRNTL 43 (96)
T ss_pred ceEEEEEeceeEE
Confidence 3455555554443
No 148
>PF06580 His_kinase: Histidine kinase; InterPro: IPR010559 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain IPR003594 from INTERPRO and/or IPR003660 from INTERPRO.; GO: 0000155 two-component sensor activity, 0000160 two-component signal transduction system (phosphorelay), 0016021 integral to membrane
Probab=21.53 E-value=1e+02 Score=17.88 Aligned_cols=17 Identities=29% Similarity=0.505 Sum_probs=14.9
Q ss_pred hhhHHHHHHHHHHHHHh
Q psy4809 70 PQQAASVVEKLGDYLVS 86 (89)
Q Consensus 70 ~~~~~~~ve~lAdyL~~ 86 (89)
+..+...+..|+++|+-
T Consensus 29 ~~~~~~~i~~ls~~lRy 45 (82)
T PF06580_consen 29 PEKASEMILSLSDLLRY 45 (82)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 67889999999999984
No 149
>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional
Probab=21.53 E-value=2.4e+02 Score=20.54 Aligned_cols=33 Identities=21% Similarity=0.304 Sum_probs=24.5
Q ss_pred cCceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 55 TQQAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 55 T~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
.++.+.||+...+.+. .....+|+||++|. .||
T Consensus 242 g~~~~~i~igCtGG~H-RSV~~~e~l~~~l~-~~~ 274 (288)
T PRK05416 242 GKSYLTIAIGCTGGQH-RSVAIAERLAERLS-KGY 274 (288)
T ss_pred CCCEEEEEEecCCCcc-cHHHHHHHHHHHHh-CCC
Confidence 4567888888776643 47788999999994 454
No 150
>cd03530 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.
Probab=21.50 E-value=1.6e+02 Score=17.09 Aligned_cols=22 Identities=18% Similarity=0.199 Sum_probs=17.2
Q ss_pred cceEEcceEEEEEEecCcEEEE
Q psy4809 22 SGVTLAGNRYIYLSGTDKVIRA 43 (89)
Q Consensus 22 ~Gi~l~G~kY~~~r~d~~~i~~ 43 (89)
..+.++|+...+.|.+++.+++
T Consensus 16 ~~~~~~g~~i~l~r~~~g~~~A 37 (98)
T cd03530 16 RKVQTGGGEIAVFRTADDEVFA 37 (98)
T ss_pred EEEEECCEEEEEEEeCCCCEEE
Confidence 4678899999999987555555
No 151
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=21.41 E-value=99 Score=16.14 Aligned_cols=13 Identities=23% Similarity=0.473 Sum_probs=9.8
Q ss_pred eEEcceEEEEEEe
Q psy4809 24 VTLAGNRYIYLSG 36 (89)
Q Consensus 24 i~l~G~kY~~~r~ 36 (89)
+.++|+||-|...
T Consensus 2 ili~g~KyAC~~C 14 (40)
T PF00649_consen 2 ILIDGEKYACESC 14 (40)
T ss_dssp EEETTEEEEETTT
T ss_pred eeECCeEEEhhhh
Confidence 4689999988553
No 152
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=21.39 E-value=1e+02 Score=19.30 Aligned_cols=20 Identities=20% Similarity=0.305 Sum_probs=17.4
Q ss_pred ChhhHHHHHHHHHHHHHhCC
Q psy4809 69 QPQQAASVVEKLGDYLVSCG 88 (89)
Q Consensus 69 ~~~~~~~~ve~lAdyL~~~g 88 (89)
...+|.+-...|.++|++.|
T Consensus 17 ~~~qC~~cA~Al~~~L~~~g 36 (100)
T PF15643_consen 17 KIFQCVECASALKQFLKQAG 36 (100)
T ss_pred CceehHHHHHHHHHHHHHCC
Confidence 46789999999999999876
No 153
>PRK00971 glutaminase; Provisional
Probab=21.23 E-value=2.9e+02 Score=20.55 Aligned_cols=45 Identities=18% Similarity=0.240 Sum_probs=33.7
Q ss_pred EEEecCCceEEEEEcCceEEEEEeCCCCC-hhh---HHHHHHHHHHHHH
Q psy4809 41 IRAKLGKVGVHCMKTQQAVVISLYEDPIQ-PQQ---AASVVEKLGDYLV 85 (89)
Q Consensus 41 i~~kkg~~G~~i~KT~~aiiIg~y~~~~~-~~~---~~~~ve~lAdyL~ 85 (89)
+=+|.|-+|.++.--+.-.-||.|..+.. .|| ..++.+.|++.|.
T Consensus 255 lPaKSGVgGgIlavvPg~~gIav~SP~LD~~GNSv~G~~~le~ls~~~~ 303 (307)
T PRK00971 255 LPAKSGVGGGILAVVPGEMAIAVWSPELDAKGNSLAGTAALERLSQRLG 303 (307)
T ss_pred CccccCCcceEEEEeCCCcEEEEECCCcCCCCCCHHHHHHHHHHHHHhC
Confidence 45788988878877888889999998873 344 5667777777663
No 154
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=83 Score=19.54 Aligned_cols=18 Identities=33% Similarity=0.676 Sum_probs=15.0
Q ss_pred ccceEEcceEEEEEEecC
Q psy4809 21 SSGVTLAGNRYIYLSGTD 38 (89)
Q Consensus 21 ~~Gi~l~G~kY~~~r~d~ 38 (89)
.+-+.++|++|++++.+|
T Consensus 72 G~evk~dgeeylil~e~D 89 (96)
T COG0234 72 GTEVKIDGEEYLILSESD 89 (96)
T ss_pred CcEEEECCEEEEEechHH
Confidence 467889999999999765
No 155
>PF02696 UPF0061: Uncharacterized ACR, YdiU/UPF0061 family; InterPro: IPR003846 The proteins in this entry are functionally uncharacterised.
Probab=21.06 E-value=2.9e+02 Score=21.89 Aligned_cols=48 Identities=13% Similarity=0.214 Sum_probs=30.6
Q ss_pred cEEEEecCCceEEEEE-cCceEEEEEeCCCCChhhHHHHHHHHHHHHHhC
Q psy4809 39 KVIRAKLGKVGVHCMK-TQQAVVISLYEDPIQPQQAASVVEKLGDYLVSC 87 (89)
Q Consensus 39 ~~i~~kkg~~G~~i~K-T~~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~ 87 (89)
..++.-+..-|.+++. .++.|=+|+++=-...+. .+.+.+|+||.++.
T Consensus 163 ~~v~r~~~ep~Avv~RvA~S~iR~GsFe~~~~~~~-~~~l~~L~dy~i~~ 211 (487)
T PF02696_consen 163 EPVRRETPEPGAVVTRVAPSHIRFGSFEYFAYRGD-PEGLRQLADYVIKR 211 (487)
T ss_pred eeEEcCCCCCceEEEeccccceeeeeeehhhhcCC-HHHHHHHHHHHHHH
Confidence 3444334334555555 567777999987544333 45688999998864
No 156
>cd03416 CbiX_SirB_N Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both are found in a wide range of bacteria. This subgroup also contains single domain proteins from archaea and bacteria which may represent the ancestral form of class II chelatases before domain duplication occurred.
Probab=21.03 E-value=1.7e+02 Score=17.06 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=17.5
Q ss_pred EEEEEeCCCCChhhHHHHHHHHHHHHHhC
Q psy4809 59 VVISLYEDPIQPQQAASVVEKLGDYLVSC 87 (89)
Q Consensus 59 iiIg~y~~~~~~~~~~~~ve~lAdyL~~~ 87 (89)
+++++.... + .++..++.+++.|.+.
T Consensus 3 vlv~hGS~~--~-~~~~~~~~l~~~l~~~ 28 (101)
T cd03416 3 LLVGHGSRD--P-RAAEALEALAERLRER 28 (101)
T ss_pred EEEEcCCCC--H-HHHHHHHHHHHHHHhh
Confidence 445554432 2 6778999999998764
No 157
>COG4725 IME4 Transcriptional activator, adenine-specific DNA methyltransferase [Signal transduction mechanisms / Transcription]
Probab=21.03 E-value=1.6e+02 Score=20.34 Aligned_cols=54 Identities=13% Similarity=0.258 Sum_probs=39.7
Q ss_pred eEEEEEEecCcEEEEecCCceEEEEEcCceEEEEEeCCCC-ChhhHHHHHHHHHH
Q psy4809 29 NRYIYLSGTDKVIRAKLGKVGVHCMKTQQAVVISLYEDPI-QPQQAASVVEKLGD 82 (89)
Q Consensus 29 ~kY~~~r~d~~~i~~kkg~~G~~i~KT~~aiiIg~y~~~~-~~~~~~~~ve~lAd 82 (89)
+-|-+-...++++.|-+|+---+-..+...||+.+-.|.. .|.....-+|+||-
T Consensus 102 tGhwlr~S~Eh~~vg~~GNpK~~~~~~~i~li~S~~RE~SRKP~E~y~i~ErL~~ 156 (198)
T COG4725 102 TGHWLRTSGEHVFVGTLGNPKQSHVPPTISLIVSMTRETSRKPDELYGIAERLAG 156 (198)
T ss_pred cceeecCCCcEEEEEecCCchhhcCCCceEEEEccchhhccCCHHHHHHHHHhCC
Confidence 4444333446677787777666666777789999998876 78889999999874
No 158
>KOG2500|consensus
Probab=21.01 E-value=1.2e+02 Score=21.87 Aligned_cols=31 Identities=13% Similarity=0.063 Sum_probs=19.6
Q ss_pred HHhhcCCCccccccceEEcceEEEEEEecCc
Q psy4809 9 LVQGFEKQDILTSSGVTLAGNRYIYLSGTDK 39 (89)
Q Consensus 9 i~~~f~~~~~~~~~Gi~l~G~kY~~~r~d~~ 39 (89)
++++|-|+....+---.+.-.+|+++|.+|+
T Consensus 68 fA~c~id~~~~~avEav~DSSRYFViRv~dg 98 (253)
T KOG2500|consen 68 FAQCPIDEGPGNAVEAVSDSSRYFVIRVEDG 98 (253)
T ss_pred hhhCcccCCCCccceeecccceEEEEEEeCC
Confidence 4455555544333344567889999999853
No 159
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=20.98 E-value=1.7e+02 Score=20.42 Aligned_cols=33 Identities=21% Similarity=0.204 Sum_probs=22.5
Q ss_pred ceEEEEEeCCC--CChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDP--IQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~--~~~~~~~~~ve~lAdyL~~~gy 89 (89)
-||||+...=. ........-++.|++-|++.||
T Consensus 10 ~alII~n~~f~~~~~r~g~~~D~~~l~~~f~~lgF 44 (241)
T smart00115 10 LALIINNENFHSLPRRNGTDVDAENLTELFQSLGY 44 (241)
T ss_pred EEEEEECccCCCCcCCCCcHHHHHHHHHHHHHCCC
Confidence 46777665432 2333456689999999999987
No 160
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=20.98 E-value=95 Score=17.92 Aligned_cols=29 Identities=17% Similarity=0.250 Sum_probs=18.8
Q ss_pred ceEEEEEeCCCCChhhHHHHHHHHHHHHHhCCC
Q psy4809 57 QAVVISLYEDPIQPQQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 57 ~aiiIg~y~~~~~~~~~~~~ve~lAdyL~~~gy 89 (89)
+.+-|-+++.+..+|.+ .++++.|++.||
T Consensus 2 ~~v~V~VlNgt~~~GlA----~~~a~~L~~~Gf 30 (90)
T PF13399_consen 2 SDVRVEVLNGTGVSGLA----ARVADALRNRGF 30 (90)
T ss_pred CceEEEEEECcCCcCHH----HHHHHHHHHCCC
Confidence 34556777777766655 456677777776
No 161
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=20.82 E-value=99 Score=18.31 Aligned_cols=19 Identities=21% Similarity=-0.015 Sum_probs=16.2
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q psy4809 71 QQAASVVEKLGDYLVSCGY 89 (89)
Q Consensus 71 ~~~~~~ve~lAdyL~~~gy 89 (89)
|....+|++-.+-|++.||
T Consensus 30 giSRtaVwK~Iq~Lr~~G~ 48 (79)
T COG1654 30 GISRTAVWKHIQQLREEGV 48 (79)
T ss_pred CccHHHHHHHHHHHHHhCC
Confidence 5578899999999999886
No 162
>TIGR03814 Gln_ase glutaminase A. This family describes the enzyme glutaminase, from a larger family that includes serine-dependent beta-lactamases and penicillin-binding proteins. Many bacteria have two isozymes. This model is based on selected known glutaminases and their homologs within prokaryotes, with the exclusion of highly-derived (long branch) and architecturally varied homologs, so as to achieve conservative assignments. A sharp drop in scores occurs below 250, and cutoffs are set accordingly. The enzyme converts glutamine to glutamate, with the release of ammonia. Members tend to be described as glutaminase A (glsA), where B (glsB) is unknown and may not be homologous (as in Rhizobium etli). Some species have two isozymes that may both be designated A (GlsA1 and GlsA2).
Probab=20.73 E-value=3.2e+02 Score=20.29 Aligned_cols=45 Identities=18% Similarity=0.194 Sum_probs=33.9
Q ss_pred EEEecCCceEEEEEcCceEEEEEeCCCCC-hhh---HHHHHHHHHHHHH
Q psy4809 41 IRAKLGKVGVHCMKTQQAVVISLYEDPIQ-PQQ---AASVVEKLGDYLV 85 (89)
Q Consensus 41 i~~kkg~~G~~i~KT~~aiiIg~y~~~~~-~~~---~~~~ve~lAdyL~ 85 (89)
+=+|.|-+|-++.--+.-.-||.|..+.. .|| ...+.+.|++.|.
T Consensus 248 lPaKSGVgGgIlavvPg~~gIav~SP~LD~~GNSv~G~~~le~ls~~~~ 296 (300)
T TIGR03814 248 LPAKSGVGGGILAVVPGKMGIAVFSPALDAAGNSVAGQKALELLSEKLG 296 (300)
T ss_pred CccccCccceEEEEeCCceEEEEECCCcCCCCCCHHHHHHHHHHHHHhC
Confidence 45788888888888888889999998873 344 5567777777663
No 163
>PRK12356 glutaminase; Reviewed
Probab=20.57 E-value=3.1e+02 Score=20.53 Aligned_cols=45 Identities=18% Similarity=0.196 Sum_probs=34.2
Q ss_pred EEEecCCceEEEEEcCceEEEEEeCCCCC-hhh---HHHHHHHHHHHHH
Q psy4809 41 IRAKLGKVGVHCMKTQQAVVISLYEDPIQ-PQQ---AASVVEKLGDYLV 85 (89)
Q Consensus 41 i~~kkg~~G~~i~KT~~aiiIg~y~~~~~-~~~---~~~~ve~lAdyL~ 85 (89)
+=+|.|-+|-++.--+.-.=||.|..+.. .|| ...+.|.|++.|.
T Consensus 259 lPaKSGVgGgIlavvPg~~gIav~SP~LD~~GNSv~G~~~le~ls~~~~ 307 (319)
T PRK12356 259 LPGKSGVGGGILAVVPGKMGIAAFSPPLDSAGNSVRGQKAVAYVADKLG 307 (319)
T ss_pred CccccCccceeEEEeCCceEEEEECCCcCCCCCcHHHHHHHHHHHHHhC
Confidence 45788988888888888889999998873 344 5667777777763
No 164
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=20.50 E-value=64 Score=17.64 Aligned_cols=14 Identities=29% Similarity=0.420 Sum_probs=11.4
Q ss_pred CCHHHHHHHHhhcC
Q psy4809 1 LSKDELGKLVQGFE 14 (89)
Q Consensus 1 ~s~~E~~~i~~~f~ 14 (89)
++++|++.|.+++.
T Consensus 35 l~~~Ea~~L~~~l~ 48 (51)
T PF11314_consen 35 LNPDEAKELGEALK 48 (51)
T ss_pred eCHHHHHHHHHHHH
Confidence 58999999988764
No 165
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=20.49 E-value=71 Score=17.85 Aligned_cols=13 Identities=23% Similarity=0.383 Sum_probs=11.2
Q ss_pred CHHHHHHHHhhcC
Q psy4809 2 SKDELGKLVQGFE 14 (89)
Q Consensus 2 s~~E~~~i~~~f~ 14 (89)
|++|+.+|+..|.
T Consensus 12 t~eElAAL~aVla 24 (62)
T PF13822_consen 12 TDEELAALTAVLA 24 (62)
T ss_pred CHHHHHHHHHHHH
Confidence 7899999998874
No 166
>PF08269 Cache_2: Cache domain; InterPro: IPR013163 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 []. This entry is composed of the type 2 Cache domain.; PDB: 2QHK_A 4EXO_A.
Probab=20.08 E-value=45 Score=19.53 Aligned_cols=18 Identities=17% Similarity=0.521 Sum_probs=9.4
Q ss_pred cceEEcceEEEEEEecCc
Q psy4809 22 SGVTLAGNRYIYLSGTDK 39 (89)
Q Consensus 22 ~Gi~l~G~kY~~~r~d~~ 39 (89)
+.+++++.-|+++-..+.
T Consensus 49 ~~~r~~~~gY~fi~d~~g 66 (95)
T PF08269_consen 49 RALRYGGDGYFFIYDMDG 66 (95)
T ss_dssp HH--SBTTB--EEE-TTS
T ss_pred hccccCCCCeEEEEeCCC
Confidence 577778888888877654
No 167
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=20.08 E-value=28 Score=20.40 Aligned_cols=17 Identities=24% Similarity=0.345 Sum_probs=11.7
Q ss_pred CCHHHHHHHHhhcCCCccc
Q psy4809 1 LSKDELGKLVQGFEKQDIL 19 (89)
Q Consensus 1 ~s~~E~~~i~~~f~~~~~~ 19 (89)
||++|.++|.+ .|...+
T Consensus 35 Lt~eE~~al~~--rD~~~L 51 (77)
T cd07321 35 LTPEEKAALLA--RDVGAL 51 (77)
T ss_pred CCHHHHHHHHc--CCHHHH
Confidence 57888888887 454444
Done!