Query 032049
Match_columns 148
No_of_seqs 118 out of 1063
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:54:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032049.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032049hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00086 40S ribosomal protein 100.0 1.2E-60 2.5E-65 368.0 14.4 145 4-148 3-147 (147)
2 PLN00210 40S ribosomal protein 100.0 7.4E-61 1.6E-65 367.0 13.0 139 10-148 3-141 (141)
3 PRK00474 rps9p 30S ribosomal p 100.0 1.6E-57 3.5E-62 346.0 13.7 133 9-148 2-134 (134)
4 TIGR03627 arch_S9P archaeal ri 100.0 1.5E-56 3.2E-61 339.2 13.2 130 11-148 1-130 (130)
5 COG0103 RpsI Ribosomal protein 100.0 2.6E-55 5.7E-60 330.9 12.4 125 11-148 5-130 (130)
6 CHL00079 rps9 ribosomal protei 100.0 1.2E-54 2.7E-59 328.7 13.3 125 11-148 4-130 (130)
7 PRK00132 rpsI 30S ribosomal pr 100.0 1.8E-54 4E-59 327.8 13.4 127 9-148 3-130 (130)
8 PF00380 Ribosomal_S9: Ribosom 100.0 2.3E-53 4.9E-58 318.4 6.1 120 16-148 1-121 (121)
9 KOG1753 40S ribosomal protein 100.0 1.9E-46 4E-51 283.1 11.3 141 8-148 5-145 (145)
10 KOG1697 Mitochondrial/chloropl 100.0 3.7E-45 8E-50 301.1 10.5 132 4-148 143-275 (275)
11 KOG0058 Peptide exporter, ABC 94.8 0.029 6.4E-07 53.1 3.6 78 15-96 503-621 (716)
12 COG2274 SunT ABC-type bacterio 89.1 1.1 2.4E-05 42.6 6.5 100 16-118 509-656 (709)
13 TIGR03797 NHPM_micro_ABC2 NHPM 88.4 1.7 3.7E-05 40.2 7.0 103 17-122 490-639 (686)
14 COG4988 CydD ABC-type transpor 88.1 0.25 5.4E-06 45.8 1.4 99 15-115 356-500 (559)
15 PRK10790 putative multidrug tr 87.4 1.1 2.4E-05 40.5 5.2 100 16-117 377-522 (592)
16 PLN03130 ABC transporter C fam 87.0 0.27 5.8E-06 50.4 1.1 98 16-115 1275-1418(1622)
17 COG4608 AppF ABC-type oligopep 87.0 0.24 5.1E-06 42.0 0.6 82 10-100 43-129 (268)
18 PLN03232 ABC transporter C fam 85.6 0.71 1.5E-05 46.9 3.2 96 18-116 1274-1416(1495)
19 TIGR02868 CydC thiol reductant 84.1 3.4 7.3E-05 36.8 6.5 49 66-117 458-516 (529)
20 KOG0055 Multidrug/pheromone ex 83.0 1.8 3.9E-05 43.6 4.6 85 29-116 1042-1171(1228)
21 PRK10787 DNA-binding ATP-depen 82.6 4.6 0.0001 38.8 7.1 69 24-97 614-691 (784)
22 KOG0055 Multidrug/pheromone ex 81.2 3 6.5E-05 42.1 5.4 86 29-117 405-535 (1228)
23 PTZ00265 multidrug resistance 79.0 3.4 7.3E-05 42.2 5.1 101 15-117 1260-1404(1466)
24 COG1750 Archaeal serine protea 78.3 5 0.00011 37.5 5.6 72 24-97 55-132 (579)
25 COG1132 MdlB ABC-type multidru 77.6 2.8 6E-05 37.8 3.7 99 15-115 364-509 (567)
26 PTZ00243 ABC transporter; Prov 76.5 1.2 2.7E-05 45.5 1.2 26 19-44 1349-1377(1560)
27 TIGR00957 MRP_assoc_pro multi 75.7 5.2 0.00011 40.9 5.4 96 18-116 1324-1466(1522)
28 COG1124 DppF ABC-type dipeptid 75.1 1.1 2.4E-05 37.7 0.5 45 15-59 42-111 (252)
29 PF13541 ChlI: Subunit ChlI of 74.2 10 0.00022 28.3 5.4 71 25-98 3-73 (121)
30 COG3842 PotA ABC-type spermidi 74.1 6.9 0.00015 34.4 5.1 14 29-42 57-70 (352)
31 TIGR03796 NHPM_micro_ABC1 NHPM 72.6 11 0.00023 35.1 6.3 53 67-122 604-666 (710)
32 PF03755 YicC_N: YicC-like fam 69.7 18 0.00039 27.7 6.1 81 9-97 1-90 (159)
33 TIGR01271 CFTR_protein cystic 68.2 9 0.0002 39.2 5.1 31 66-97 1341-1371(1490)
34 TIGR00763 lon ATP-dependent pr 64.2 15 0.00031 35.1 5.4 74 25-98 619-696 (775)
35 TIGR02903 spore_lon_C ATP-depe 62.0 15 0.00032 34.3 5.0 63 29-98 474-540 (615)
36 COG1125 OpuBA ABC-type proline 54.6 9.7 0.00021 32.9 2.2 24 27-50 51-74 (309)
37 TIGR00416 sms DNA repair prote 54.5 25 0.00054 31.6 5.0 47 50-98 337-385 (454)
38 KOG3288 OTU-like cysteine prot 52.8 15 0.00031 31.6 3.0 32 65-96 272-303 (307)
39 PF02601 Exonuc_VII_L: Exonucl 52.2 15 0.00032 30.8 3.0 51 47-97 54-106 (319)
40 cd03214 ABC_Iron-Siderophores_ 49.8 21 0.00045 27.2 3.2 81 29-117 51-143 (180)
41 TIGR02653 Lon_rel_chp conserve 49.1 49 0.0011 31.7 6.1 72 23-97 514-592 (675)
42 PF05362 Lon_C: Lon protease ( 48.9 77 0.0017 25.6 6.5 55 24-78 46-104 (204)
43 COG4604 CeuD ABC-type enteroch 48.3 14 0.00031 30.9 2.3 41 29-75 53-93 (252)
44 PRK15317 alkyl hydroperoxide r 45.8 24 0.00052 31.6 3.5 58 33-90 172-232 (517)
45 TIGR03140 AhpF alkyl hydropero 44.9 23 0.0005 31.8 3.2 24 67-90 210-233 (515)
46 cd03216 ABC_Carb_Monos_I This 38.9 41 0.00089 25.2 3.4 35 82-117 85-128 (163)
47 PRK00286 xseA exodeoxyribonucl 36.2 38 0.00082 29.8 3.1 30 47-79 175-204 (438)
48 cd03247 ABCC_cytochrome_bd The 34.3 37 0.00081 25.6 2.5 34 83-117 102-144 (178)
49 COG3526 Uncharacterized protei 33.5 35 0.00077 24.6 2.1 23 21-43 36-61 (99)
50 TIGR00958 3a01208 Conjugate Tr 33.2 28 0.0006 32.7 1.9 28 67-96 606-634 (711)
51 PF02120 Flg_hook: Flagellar h 32.6 27 0.00059 23.2 1.3 53 62-125 21-73 (85)
52 COG4531 ZnuA ABC-type Zn2+ tra 32.4 18 0.0004 31.3 0.6 49 81-134 158-206 (318)
53 TIGR00237 xseA exodeoxyribonuc 31.9 47 0.001 29.6 3.1 49 47-97 169-218 (432)
54 PF06905 FAIM1: Fas apoptotic 31.2 61 0.0013 25.9 3.3 35 11-46 53-92 (177)
55 TIGR01193 bacteriocin_ABC ABC- 30.9 29 0.00063 32.2 1.7 48 67-117 600-657 (708)
56 PRK11174 cysteine/glutathione 30.9 35 0.00076 30.8 2.1 49 66-117 473-531 (588)
57 TIGR00764 lon_rel lon-related 30.8 1.4E+02 0.0031 27.9 6.1 64 31-97 450-514 (608)
58 PF09428 DUF2011: Fungal prote 29.3 18 0.0004 27.5 0.0 22 25-46 2-24 (131)
59 PRK06617 2-octaprenyl-6-methox 28.5 41 0.00088 28.5 2.0 19 71-89 3-21 (374)
60 COG4104 Uncharacterized conser 28.3 49 0.0011 24.2 2.1 18 25-42 58-75 (98)
61 TIGR01424 gluta_reduc_2 glutat 28.3 44 0.00094 29.2 2.2 22 69-90 2-23 (446)
62 TIGR00255 conserved hypothetic 28.3 1.8E+02 0.0038 24.9 5.8 81 9-97 2-91 (291)
63 PRK11820 hypothetical protein; 27.6 2.1E+02 0.0045 24.4 6.1 81 9-97 2-91 (288)
64 PRK06185 hypothetical protein; 27.3 42 0.00092 28.3 1.9 22 66-89 5-26 (407)
65 PRK11823 DNA repair protein Ra 27.2 1.2E+02 0.0026 27.1 4.8 47 50-98 323-371 (446)
66 COG2884 FtsE Predicted ATPase 27.0 79 0.0017 26.3 3.3 15 28-42 53-67 (223)
67 PF01808 AICARFT_IMPCHas: AICA 26.4 44 0.00096 29.0 1.9 43 48-93 266-315 (315)
68 cd03483 MutL_Trans_MLH1 MutL_T 26.4 19 0.00041 26.5 -0.4 11 33-43 51-61 (127)
69 PTZ00367 squalene epoxidase; P 26.4 77 0.0017 29.3 3.6 39 49-89 15-53 (567)
70 PF01479 S4: S4 domain; Inter 26.2 37 0.0008 20.3 1.0 13 31-43 25-37 (48)
71 PRK08849 2-octaprenyl-3-methyl 26.0 49 0.0011 28.0 2.0 19 72-90 6-24 (384)
72 TIGR00368 Mg chelatase-related 25.6 1.7E+02 0.0036 26.8 5.5 68 27-97 20-87 (499)
73 PF08194 DIM: DIM protein; In 25.6 43 0.00092 20.3 1.1 10 31-40 23-32 (36)
74 PRK08013 oxidoreductase; Provi 25.3 43 0.00093 28.6 1.6 22 67-90 3-24 (400)
75 cd03482 MutL_Trans_MutL MutL_T 24.8 23 0.00051 25.9 -0.1 11 33-43 47-57 (123)
76 COG0644 FixC Dehydrogenases (f 24.3 64 0.0014 27.7 2.5 23 67-91 3-25 (396)
77 TIGR02204 MsbA_rel ABC transpo 24.1 44 0.00096 30.0 1.5 50 67-117 465-522 (576)
78 TIGR03375 type_I_sec_LssB type 23.9 49 0.0011 30.7 1.8 49 66-117 589-647 (694)
79 TIGR02032 GG-red-SF geranylger 23.9 52 0.0011 25.8 1.7 18 72-89 3-20 (295)
80 PRK08163 salicylate hydroxylas 23.6 61 0.0013 27.2 2.2 20 70-89 5-24 (396)
81 COG1148 HdrA Heterodisulfide r 23.4 61 0.0013 30.5 2.3 34 52-89 111-144 (622)
82 PRK06996 hypothetical protein; 23.3 53 0.0011 28.0 1.8 22 67-90 11-32 (398)
83 PRK06753 hypothetical protein; 23.1 63 0.0014 26.9 2.2 19 71-89 2-20 (373)
84 PRK08773 2-octaprenyl-3-methyl 22.9 54 0.0012 27.7 1.7 21 67-89 6-26 (392)
85 PF03764 EFG_IV: Elongation fa 22.7 2.8E+02 0.0061 19.5 7.0 76 20-96 28-114 (120)
86 PF13510 Fer2_4: 2Fe-2S iron-s 22.6 55 0.0012 22.3 1.4 19 33-51 5-23 (82)
87 TIGR03329 Phn_aa_oxid putative 22.5 62 0.0013 28.4 2.1 25 67-91 22-46 (460)
88 COG4559 ABC-type hemin transpo 22.4 49 0.0011 28.0 1.3 22 26-47 50-71 (259)
89 PRK08020 ubiF 2-octaprenyl-3-m 22.3 64 0.0014 27.1 2.0 22 66-89 4-25 (391)
90 PRK11160 cysteine/glutathione 22.1 60 0.0013 29.5 2.0 48 68-117 465-521 (574)
91 cd03222 ABC_RNaseL_inhibitor T 22.1 77 0.0017 24.6 2.4 36 81-117 73-117 (177)
92 cd01121 Sms Sms (bacterial rad 22.0 1.3E+02 0.0027 26.5 3.9 32 64-96 340-371 (372)
93 PF02359 CDC48_N: Cell divisio 22.0 1E+02 0.0022 20.9 2.8 32 6-38 30-65 (87)
94 PRK10157 putative oxidoreducta 22.0 60 0.0013 28.3 1.9 22 67-90 5-26 (428)
95 PF00475 IGPD: Imidazoleglycer 21.9 3.9E+02 0.0084 20.8 7.1 70 20-94 70-144 (145)
96 cd03229 ABC_Class3 This class 21.8 70 0.0015 24.1 2.0 34 83-117 104-146 (178)
97 PHA01748 hypothetical protein 21.8 1.2E+02 0.0026 19.7 2.9 18 78-96 25-42 (60)
98 PF10865 DUF2703: Domain of un 21.6 44 0.00095 25.1 0.8 17 30-46 61-77 (120)
99 TIGR01846 type_I_sec_HlyB type 21.6 58 0.0013 30.2 1.8 49 67-117 582-639 (694)
100 PRK08850 2-octaprenyl-6-methox 21.3 57 0.0012 27.8 1.6 19 72-90 7-25 (405)
101 PRK07588 hypothetical protein; 21.3 72 0.0016 26.9 2.2 19 71-89 2-20 (391)
102 PF01494 FAD_binding_3: FAD bi 21.1 82 0.0018 25.2 2.4 19 71-89 3-21 (356)
103 PRK07045 putative monooxygenas 21.0 80 0.0017 26.6 2.4 21 67-89 5-25 (388)
104 PRK11445 putative oxidoreducta 21.0 73 0.0016 26.8 2.2 18 72-89 4-21 (351)
105 PRK10015 oxidoreductase; Provi 20.9 65 0.0014 28.2 1.9 22 67-90 5-26 (429)
106 PRK07364 2-octaprenyl-6-methox 20.8 64 0.0014 27.3 1.8 21 67-89 18-38 (415)
107 smart00363 S4 S4 RNA-binding d 20.6 59 0.0013 18.9 1.1 12 31-42 25-36 (60)
108 PRK11176 lipid transporter ATP 20.4 71 0.0015 28.8 2.1 49 67-117 469-526 (582)
109 COG1561 Uncharacterized stress 20.0 1.6E+02 0.0035 25.4 4.0 70 22-97 8-91 (290)
No 1
>PTZ00086 40S ribosomal protein S16; Provisional
Probab=100.00 E-value=1.2e-60 Score=367.97 Aligned_cols=145 Identities=64% Similarity=1.121 Sum_probs=139.2
Q ss_pred cCCCCCceEEEeeeccceEEEEEEEeCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEecCCccchH
Q 032049 4 AKAGPVESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQI 83 (148)
Q Consensus 4 ~~~~~~~~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa 83 (148)
.+-.+.+.|+++||||||+|+|++.+|+|+|+|||+|+++||++.++++|++||.+++.+.+++|||+|+|+|||+||||
T Consensus 3 ~~~~~~~~v~~~GrRKtAiArv~l~~G~G~i~INg~~l~~y~~~~~r~~i~~Pl~~~~~~~~~~~Di~i~V~GGG~sgQA 82 (147)
T PTZ00086 3 EKTTKLKQVQTFGKKKTAVAVALVTKGKGLIRVNGVPLDLINPETLRAKVFEPLLLVGKERFSRLDIRVRVRGGGQVAQA 82 (147)
T ss_pred ccccCCcceEEeeecCCceEEEEEEcCCceEEECCcCHHHhCcHHHHHHHHHHHHHhCcCccCceeEEEEEEcCCHHHHH
Confidence 34567789999999999999999999999999999999999998899999999999987557899999999999999999
Q ss_pred HHHHHHHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 84 YAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 84 ~AIr~aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
+||||||||||+.|++.|.|+..++.||++|+.||+||||+|||+|||||||++||||+||||||
T Consensus 83 ~Air~aIaRAL~~~~~~~~~~~~r~~Lk~~~~~ydrglLtrD~R~~ERKK~G~~kARk~~Q~SkR 147 (147)
T PTZ00086 83 YAIRQAIAKGLVAYYQKYVDEATKAELKDKLLAYDRSLLVADPRRCEPKKFGGPGARARFQKSYR 147 (147)
T ss_pred HHHHHHHHHHHHHHhcccCChHHHHHHHHHHhhccCCcccCCccccccCcCCCcccccccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999998
No 2
>PLN00210 40S ribosomal protein S16; Provisional
Probab=100.00 E-value=7.4e-61 Score=366.95 Aligned_cols=139 Identities=97% Similarity=1.509 Sum_probs=135.3
Q ss_pred ceEEEeeeccceEEEEEEEeCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHH
Q 032049 10 ESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 10 ~~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~a 89 (148)
+.++++||||||+|+|++.||+|+|+|||+|+++|+++.++++|++||.+++.+.+++|||+|+|+|||+||||+|||||
T Consensus 3 ~~~~~~GrRKta~Arv~~~~G~G~i~INg~~~~~y~~~~~r~~i~~Pl~~~~~~~~~~~Di~~~V~GGG~sgQa~Air~a 82 (141)
T PLN00210 3 ESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVQPEILRFKAFEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQS 82 (141)
T ss_pred cceeeeccCCCceEEEEEECCCceEEECCCcHHHHCCHHHHHHHHHHHHHhCccccCceeEEEEEEcCCHhHHHHHHHHH
Confidence 57999999999999999999999999999999999999999999999999997667899999999999999999999999
Q ss_pred HHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 90 IAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 90 iAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
|||||+.|+++|.||+.++.||+.|++||+||||+|||+|||||||++||||+||||||
T Consensus 83 iaraL~~~~~~~~~~~~r~~Lk~~l~~yd~glLtrD~R~~ERKK~G~~kARk~~Q~Skr 141 (141)
T PLN00210 83 IAKALVAYYQKYVDEQSKKEIKDILLRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 141 (141)
T ss_pred HHHHHHHhcccccChhHHHHHHHHHHhccCCCccCCchhhccCcCCccccccccccccC
Confidence 99999999999999999999999999999999999999999999999999999999998
No 3
>PRK00474 rps9p 30S ribosomal protein S9P; Reviewed
Probab=100.00 E-value=1.6e-57 Score=345.99 Aligned_cols=133 Identities=50% Similarity=0.831 Sum_probs=124.7
Q ss_pred CceEEEeeeccceEEEEEEEeCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHH
Q 032049 9 VESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQ 88 (148)
Q Consensus 9 ~~~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~ 88 (148)
++.++++||||||+|+|+|.||+|+|+|||+|+++|+++.++++|++||.+++.+.+++|||+|+|+|||+||||+||||
T Consensus 2 ~~~~~~~GrRKta~A~v~l~~G~G~i~VNg~~~~~y~~~~~r~~i~~Pl~~~~~~~~~~~di~i~V~GGG~sgQa~Air~ 81 (134)
T PRK00474 2 MKVVITSGKRKTAIARATIREGKGRVRINGVPLELIEPELARLKIMEPLILAGEDLRSKVDIDVNVEGGGIMGQADAART 81 (134)
T ss_pred CceEEEEeeCCCeEEEEEEEcCceEEEECCEeHHHHCCHHHHHHHHHHHHHhCccccCCccEEEEEEcCChhHHHHHHHH
Confidence 57789999999999999999999999999999999998999999999999998444699999999999999999999999
Q ss_pred HHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 89 SIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 89 aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
||||||+.|++ ++ +|++.|++||+||||+|||++||||||++||||+||||||
T Consensus 82 aIaraL~~~~~---~~----~~r~~lk~~d~glLtrD~R~~ERKK~G~~kARk~~Q~SkR 134 (134)
T PRK00474 82 AIARGLVEWTG---DM----ELKDAFLAYDRTLLVGDPRRTEPKKWGGKGARAKRQKSYR 134 (134)
T ss_pred HHHHHHHHhcc---CH----HHHHHHHHhcCCCcccCchhhccCcCCCccccccccccCC
Confidence 99999999853 33 5888889999999999999999999999999999999998
No 4
>TIGR03627 arch_S9P archaeal ribosomal protein S9P. This model describes exclusively the archaeal ribosomal protein S9P. Homologous eukaryotic and bacterial ribosomal proteins are excluded from this model.
Probab=100.00 E-value=1.5e-56 Score=339.20 Aligned_cols=130 Identities=52% Similarity=0.811 Sum_probs=121.0
Q ss_pred eEEEeeeccceEEEEEEEeCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHHH
Q 032049 11 SVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 11 ~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~ai 90 (148)
+++++|+||||+|+|+|.||+|+|+|||+|+++|++..++++|++||.+++. .+++|||+|+|+|||+||||+||||||
T Consensus 1 ~~~~~GrRKta~A~v~l~~G~G~i~VNg~~~~~y~~~~~r~~i~~Pl~~~~~-~~~~~Dv~i~V~GGG~sgQa~Air~aI 79 (130)
T TIGR03627 1 VVITSGKRKTAIARATIREGKGRVRINGVPVELYPPELARLKIMEPLILAGD-IAKEVDIDVKVSGGGIMGQADAARTAI 79 (130)
T ss_pred CeEEEeeCCCeEEEEEEEcCceEEEECCEeHHHhCCHHHHHHHHHHHHHHhc-cccCccEEEEEEcCChhHHHHHHHHHH
Confidence 3789999999999999999999999999999999988999999999999972 248999999999999999999999999
Q ss_pred HHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 91 AKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 91 AraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
||||+.|++ + ++|++.|++||+||||+|||++||||||++||||+||||||
T Consensus 80 araL~~~~~---~----~~~r~~lk~~d~glLtrD~R~~ERKK~G~~kARk~~Q~SkR 130 (130)
T TIGR03627 80 ARGLVEFTG---D----KELRDAFRAYDRTLLVNDPRRKEPKKPGGRGARAKRQKSYR 130 (130)
T ss_pred HHHHHHhcc---C----HHHHHHHHHhcCCCccCCchhhccCcCCCccccccccccCC
Confidence 999999853 2 35888888899999999999999999999999999999998
No 5
>COG0103 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-55 Score=330.91 Aligned_cols=125 Identities=45% Similarity=0.659 Sum_probs=116.1
Q ss_pred eEEEeeeccceEEEEEEEeCceeEEEcCeeccccCC-HHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHH
Q 032049 11 SVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 11 ~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~-~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~a 89 (148)
+++++||||+|+|+|+|.||+|+|+|||+|+++||+ +.++++|++||.+++. .++|||+|+|+|||+||||+|||||
T Consensus 5 ~~~~tGkRK~AvArv~l~~g~G~i~vNg~~~e~yf~~e~~r~~i~~Pl~l~~~--~~~~Di~v~V~GGG~~GQA~AiR~g 82 (130)
T COG0103 5 QVYTTGKRKSAVARVRLVPGKGKITVNGRPLELYFPRETLRMKIMQPLLLTGT--VGKFDIDVTVKGGGISGQAGAIRHG 82 (130)
T ss_pred eeeeeccccceEEEEEEEcCCcEEEECCcCHHHhcchHHHHHHHhhhHHHhCc--cccccEEEEEecCCchHHHHHHHHH
Confidence 789999999999999999999999999999999987 7899999999999997 4999999999999999999999999
Q ss_pred HHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 90 IAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 90 iAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
|||||++| +++ ||+.|++| ||||+|||++||||||++|||++||||||
T Consensus 83 IaRAL~~~-----~~~----lr~~lk~~--g~LtrD~R~~ErKK~G~~kARr~~Q~SkR 130 (130)
T COG0103 83 IARALVEY-----DPE----LRPALKKA--GLLTRDPRRVERKKYGLKKARRRPQFSKR 130 (130)
T ss_pred HHHHHHHH-----CHH----HHHHHHHC--CCcccCccccccccccccccccccccccC
Confidence 99999998 555 44455554 79999999999999999999999999998
No 6
>CHL00079 rps9 ribosomal protein S9
Probab=100.00 E-value=1.2e-54 Score=328.71 Aligned_cols=125 Identities=38% Similarity=0.402 Sum_probs=116.9
Q ss_pred eEEEeeeccceEEEEEEEeCceeEEEcCeeccccCC--HHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHH
Q 032049 11 SVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEP--EILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQ 88 (148)
Q Consensus 11 ~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~--~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~ 88 (148)
+++++|+||||+|+|+|.||+|+|+|||+|+++||+ ..++++|++||.+++. +++|||+|+|+|||+||||+||||
T Consensus 4 ~~~~~GrRKta~Arv~l~~G~G~i~INg~~~~~yf~~~~~~~~~v~~Pl~~~~~--~~~~Di~i~V~GGG~sgQa~Air~ 81 (130)
T CHL00079 4 LYIGTGRRKTAVAQVRLVPGSGEIIINGKPAEEYLQYNPNYLNAIKAPLKLLGL--ENKYDIIVKVKGGGLTGQAEAIRL 81 (130)
T ss_pred EEEEEeeCCCeEEEEEEEcCCcEEEECCCcHHHHCCcCHHHHHHHHHHHHHhCc--CCceeEEEEEEcCChhHHHHHHHH
Confidence 568999999999999999999999999999999987 4567899999999996 489999999999999999999999
Q ss_pred HHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 89 SIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 89 aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
||||||++| +|+.++.||+. ||||+|||+|||||||++||||+||||||
T Consensus 82 aIaraLv~~-----~~~~k~~Lk~~------glLtrD~R~~ERKK~G~~kARk~~Q~SkR 130 (130)
T CHL00079 82 GLARALCKI-----NPENRKSLKKE------GFLTRDARIKERKKYGLKKARKAPQFSKR 130 (130)
T ss_pred HHHHHHHHH-----CHHHHHHHHHc------CCcccCCcccccCcCCCcccccccccCCC
Confidence 999999998 56677778875 99999999999999999999999999998
No 7
>PRK00132 rpsI 30S ribosomal protein S9; Reviewed
Probab=100.00 E-value=1.8e-54 Score=327.76 Aligned_cols=127 Identities=38% Similarity=0.475 Sum_probs=118.7
Q ss_pred CceEEEeeeccceEEEEEEEeCceeEEEcCeeccccCC-HHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHH
Q 032049 9 VESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIR 87 (148)
Q Consensus 9 ~~~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~-~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr 87 (148)
....+++||||+|+|+|++.||+|+|+|||+|+++||+ ..++++|++||.+++.. ++|||+|+|+|||+||||+|||
T Consensus 3 ~~~~~~~GrRK~a~A~v~l~~G~G~i~INg~~~~~yf~~~~~r~~i~~Pl~~~~~~--~~~Di~i~V~GGG~sgQa~Air 80 (130)
T PRK00132 3 EVQYYGTGRRKTAVARVRLKPGSGKITVNGRDLEEYFPRETLRMVVRQPLELTETE--GKFDVYVTVKGGGISGQAGAIR 80 (130)
T ss_pred cceEEEEeeCCCeEEEEEEEcCccEEEECCEeHHHHcCCHHHHHHHHHHHHHhCcc--CceeEEEEEEcCCHHHHHHHHH
Confidence 34568999999999999999999999999999999875 78999999999999964 8999999999999999999999
Q ss_pred HHHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 88 QSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 88 ~aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
|||||||+.| +|+.++.||.. ||||+|||+|||||||++||||+||||||
T Consensus 81 ~aiaraLv~~-----~~~~r~~Lk~~------glLtrD~R~~ErKK~G~~kARk~~q~skR 130 (130)
T PRK00132 81 HGIARALLEY-----DPDLRPALKKA------GFLTRDARMVERKKYGLKKARRAPQFSKR 130 (130)
T ss_pred HHHHHHHHHH-----CHHHHHHHHHC------CCcccCchhhccCcCCCcccccccccccC
Confidence 9999999998 56777778875 99999999999999999999999999998
No 8
>PF00380 Ribosomal_S9: Ribosomal protein S9/S16; InterPro: IPR000754 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian; plant; and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a beta-alpha-beta fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V46_I 3T1H_I 3MR8_I 3F1G_I 3D5C_I 3D5A_I 2WDG_I 3MS0_I 2WDM_I 2J02_I ....
Probab=100.00 E-value=2.3e-53 Score=318.37 Aligned_cols=120 Identities=47% Similarity=0.615 Sum_probs=107.1
Q ss_pred eeccceEEEEEEEeCceeEEEcCeeccccCC-HHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHHHHHHH
Q 032049 16 GRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKAL 94 (148)
Q Consensus 16 GrRKta~A~v~l~~G~G~I~INg~~l~~y~~-~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL 94 (148)
|+||||+|+|+|.||+|+|.|||+|+++||+ ..++++|++||.+++. +++|||+|+|+|||+||||+||||||||||
T Consensus 1 GkRK~a~A~v~l~~G~G~i~INg~~l~~yf~~~~~r~~il~Pl~~~~~--~~~~di~~~V~GGG~~gQa~Air~aiaraL 78 (121)
T PF00380_consen 1 GKRKTAIARVWLKPGSGKIRINGKPLEEYFPNPYLREKILEPLELTGT--LGKFDIFANVKGGGISGQAGAIRLAIARAL 78 (121)
T ss_dssp EEETTEEEEEEEEESSSEEEETTSEHHHHSSSTTTGCCTTHHHHCTTT--STSEEEEEEEESSSHHHHHHHHHHHHHHHH
T ss_pred CCCceEEEEEEEEeCceEEEECCEEHHHhcCcHhHHHHHHHHHHHhCc--CCeeeEEEEEecCcEeeehHHHHHHHHHHH
Confidence 8999999999999999999999999987775 6799999999999997 489999999999999999999999999999
Q ss_pred HHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 95 VAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 95 ~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
+.|++ +.++.||+. ||||+|||+|||||||++||||+||||||
T Consensus 79 ~~~~~-----~~~~~Lk~~------glLt~D~R~~ErKK~G~~kARk~~q~skR 121 (121)
T PF00380_consen 79 VKFNP-----SLKPELKKA------GLLTRDPRRVERKKPGRKKARKKPQWSKR 121 (121)
T ss_dssp HHHHT-----TCHHHHCTT------TTTS-BS-S-SS-CTTSSSSSBSSCTST-
T ss_pred HHHhH-----HHHHHHhhC------CceeecchhccccCCCCCCcccccccccC
Confidence 99964 456677765 99999999999999999999999999998
No 9
>KOG1753 consensus 40S ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-46 Score=283.09 Aligned_cols=141 Identities=80% Similarity=1.289 Sum_probs=139.8
Q ss_pred CCceEEEeeeccceEEEEEEEeCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHH
Q 032049 8 PVESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIR 87 (148)
Q Consensus 8 ~~~~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr 87 (148)
++++++.+|++|+|+|.+.++.|+|.|.|||.|++.+.+.+++.+++||+.+++.+++..+||.|+|+|||.++|.+|||
T Consensus 5 ~~qSvq~fG~KK~AtAva~ck~G~glikvNg~ple~ie~~~L~~Kl~Epvlllgk~rfa~vdi~v~~~ggghvsqiyair 84 (145)
T KOG1753|consen 5 PLQSVQVFGRKKTATAVAHCKHGSGLIKVNGRPLELIEPEILRYKLLEPVLLLGKERFAGVDIRVRVKGGGHVSQIYAIR 84 (145)
T ss_pred cccceeeeccccceEEEEEeecCceEEEECCcchHhccHHHHHHHHhhhHhhhhhhhhCCCceEEEEecCchHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 88 QSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 88 ~aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
++||+||++|+++|+||..+.++|+.|.+||+.||+.|||+.|+||+|+++||+++|.|||
T Consensus 85 qa~~kalvayyqkyvDE~skkeiKd~li~yDrtlLVADprr~esKKFGGpGAraryQksyr 145 (145)
T KOG1753|consen 85 QAIAKALVAYYQKYVDEQSKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR 145 (145)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHhCCceEEEcCcccccccccCCcchHHHhhhhcC
Confidence 9999999999999999999999999999999999999999999999999999999999998
No 10
>KOG1697 consensus Mitochondrial/chloroplast ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-45 Score=301.10 Aligned_cols=132 Identities=30% Similarity=0.366 Sum_probs=123.5
Q ss_pred cCCCCCceEEEeeeccceEEEEEEEeCceeEEEcCeeccccCC-HHHHHHHHhHHHHhcccccceecEEEEEecCCccch
Q 032049 4 AKAGPVESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQ 82 (148)
Q Consensus 4 ~~~~~~~~v~~~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~-~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQ 82 (148)
+...|...+.++|+||+|+|+|++.||+|+|.|||++++.||+ ..+|+.++.||.+++. +++|||+++|+|||.|||
T Consensus 143 ~~g~~~~~~~~~g~rK~a~A~V~v~~GtGk~~vNg~~~~~yF~~~~~Re~ll~Pl~~~~~--lg~~dv~atv~GGG~sgq 220 (275)
T KOG1697|consen 143 ESGKPEVRIIAVGRRKCARATVKVQPGTGKFDVNGRDLDVYFQHLQHREQLLYPLAVSES--LGKYDVTATVSGGGPSGQ 220 (275)
T ss_pred ccCCCceeeeeccceecceeEEEEecCceeEEecchhHHhHhccchhHHHHhhhHHHhcc--ccceeEEEEecCCCccch
Confidence 3344667899999999999999999999999999999998886 6799999999999985 599999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCCCCcccccCcccccC
Q 032049 83 IYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR 148 (148)
Q Consensus 83 a~AIr~aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~G~~kARk~~q~SkR 148 (148)
|+||+||||+||+.| +|+.++.||.+ ||||+|+|.+||||+|++||||+|||+||
T Consensus 221 agAI~~gia~aL~~~-----~p~~~~~lr~a------GlLTrD~R~vERKK~gq~kARkk~tW~KR 275 (275)
T KOG1697|consen 221 AGAIRLGIAKALASF-----EPDLIEPLRLA------GLLTRDPRVVERKKPGQPKARKKPTWKKR 275 (275)
T ss_pred hHHHHHHHHHHHHhc-----CHHHhhHHHhc------CccccchHhhhhccCCccccccccccccC
Confidence 999999999999997 67888999998 99999999999999999999999999998
No 11
>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.77 E-value=0.029 Score=53.05 Aligned_cols=78 Identities=29% Similarity=0.390 Sum_probs=55.6
Q ss_pred eeeccceEEEEEEE---eCceeEEEcCeeccccCCHHHHHHHH----hHHHHh---------------------------
Q 032049 15 FGRKKTAVAVTYCK---RGRGLIKINGCPIELVEPEILRFKAY----EPILLL--------------------------- 60 (148)
Q Consensus 15 ~GrRKta~A~v~l~---~G~G~I~INg~~l~~y~~~~~r~~i~----~PL~~~--------------------------- 60 (148)
.|.=|+++|.-.+. |-+|.|.++|+|+.+|.+.++|.+|- ||+.+.
T Consensus 503 SGsGKSTiasLL~rfY~PtsG~IllDG~~i~~~~~~~lr~~Ig~V~QEPvLFs~sI~eNI~YG~~~~t~e~i~~AAk~AN 582 (716)
T KOG0058|consen 503 SGSGKSTIASLLLRFYDPTSGRILLDGVPISDINHKYLRRKIGLVGQEPVLFSGSIRENIAYGLDNATDEEIEAAAKMAN 582 (716)
T ss_pred CCCCHHHHHHHHHHhcCCCCCeEEECCeehhhcCHHHHHHHeeeeeccceeecccHHHHHhcCCCCCCHHHHHHHHHHhC
Confidence 45567777644433 78999999999999999988886642 233221
Q ss_pred ------cccccceecEEEEEecCCcc-chHHHHHHHHHHHHHH
Q 032049 61 ------GRHRFAGVDMRIRVKGGGHT-SQIYAIRQSIAKALVA 96 (148)
Q Consensus 61 ------~~~~~~~~di~i~V~GGG~s-gQa~AIr~aiAraL~~ 96 (148)
+.. +.||-.|--+|-=+| ||-+ |.||||||+.
T Consensus 583 ah~FI~~~p--~gY~T~VGEkG~qLSGGQKQ--RIAIARALlr 621 (716)
T KOG0058|consen 583 AHEFITNFP--DGYNTVVGEKGSQLSGGQKQ--RIAIARALLR 621 (716)
T ss_pred hHHHHHhCc--cccccccCCccccccchHHH--HHHHHHHHhc
Confidence 121 578888877876666 5776 7899999986
No 12
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=89.12 E-value=1.1 Score=42.56 Aligned_cols=100 Identities=24% Similarity=0.291 Sum_probs=64.8
Q ss_pred eeccceEEEEEE---EeCceeEEEcCeeccccCCHHHHH------------------------------HHHhHHHHhcc
Q 032049 16 GRKKTAVAVTYC---KRGRGLIKINGCPIELVEPEILRF------------------------------KAYEPILLLGR 62 (148)
Q Consensus 16 GrRKta~A~v~l---~~G~G~I~INg~~l~~y~~~~~r~------------------------------~i~~PL~~~~~ 62 (148)
|-=|+..++... .|-.|.|.+||.++.++....+|+ ++++...+++.
T Consensus 509 GsGKSTL~KLL~gly~p~~G~I~~dg~dl~~i~~~~lR~~ig~V~Q~~~Lf~gSI~eNi~l~~p~~~~e~i~~A~~~ag~ 588 (709)
T COG2274 509 GSGKSTLLKLLLGLYKPQQGRILLDGVDLNDIDLASLRRQVGYVLQDPFLFSGSIRENIALGNPEATDEEIIEAAQLAGA 588 (709)
T ss_pred CCCHHHHHHHHhcCCCCCCceEEECCEeHHhcCHHHHHhheeEEcccchhhcCcHHHHHhcCCCCCCHHHHHHHHHHhCc
Confidence 334666664433 367899999999987655444443 33334443331
Q ss_pred c-----ccceecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhcC
Q 032049 63 H-----RFAGVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRYD 118 (148)
Q Consensus 63 ~-----~~~~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~yd 118 (148)
+ .=..||-.+.-.|.++| ||-+ |+||||||+. .|+ -.|++.+..+-+.|.+..
T Consensus 589 ~~fI~~lP~gy~t~v~E~G~~LSGGQrQ--rlalARaLl~-~P~ILlLDEaTSaLD~~sE~~I~~~L~~~~ 656 (709)
T COG2274 589 HEFIENLPMGYDTPVGEGGANLSGGQRQ--RLALARALLS-KPKILLLDEATSALDPETEAIILQNLLQIL 656 (709)
T ss_pred HHHHHhcccccccccccCCCCCCHHHHH--HHHHHHHhcc-CCCEEEEeCcccccCHhHHHHHHHHHHHHh
Confidence 1 01478888888899998 5777 7899999984 333 236677777777777665
No 13
>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif
Probab=88.35 E-value=1.7 Score=40.18 Aligned_cols=103 Identities=19% Similarity=0.212 Sum_probs=57.8
Q ss_pred eccceEEEEEE---EeCceeEEEcCeeccccC------------------CHHHHHHH-----------HhHHHHhcccc
Q 032049 17 RKKTAVAVTYC---KRGRGLIKINGCPIELVE------------------PEILRFKA-----------YEPILLLGRHR 64 (148)
Q Consensus 17 rRKta~A~v~l---~~G~G~I~INg~~l~~y~------------------~~~~r~~i-----------~~PL~~~~~~~ 64 (148)
-=||+.++..+ .|-+|.|.|||+++.++. +.+.++.+ .+-+..++.+.
T Consensus 490 sGKSTLlklL~gl~~p~~G~I~idg~~i~~~~~~~lr~~i~~v~Q~~~lf~gTI~eNi~~~~~~~~e~i~~al~~a~l~~ 569 (686)
T TIGR03797 490 SGKSTLLRLLLGFETPESGSVFYDGQDLAGLDVQAVRRQLGVVLQNGRLMSGSIFENIAGGAPLTLDEAWEAARMAGLAE 569 (686)
T ss_pred CCHHHHHHHHhCCCCCCCCEEEECCEEcCcCCHHHHHhccEEEccCCccCcccHHHHHhcCCCCCHHHHHHHHHHcCcHH
Confidence 34555554332 256799999999986432 22233322 23333333210
Q ss_pred -----cceecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhcCCCce
Q 032049 65 -----FAGVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRYDRTLL 122 (148)
Q Consensus 65 -----~~~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~yd~glL 122 (148)
=..||-.+.-.|...| ||.+ |+||||||+.- |. -.|++....+.+.|.+.++..+
T Consensus 570 ~i~~lp~G~dt~ige~G~~LSGGQrQ--RialARAll~~-p~iLiLDEpTS~LD~~te~~i~~~L~~~~~T~I 639 (686)
T TIGR03797 570 DIRAMPMGMHTVISEGGGTLSGGQRQ--RLLIARALVRK-PRILLFDEATSALDNRTQAIVSESLERLKVTRI 639 (686)
T ss_pred HHHhccccccccccCCCCCCCHHHHH--HHHHHHHHhcC-CCEEEEeCCccCCCHHHHHHHHHHHHHhCCeEE
Confidence 0356665555555555 5554 88999999863 33 2366667777777776544433
No 14
>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]
Probab=88.07 E-value=0.25 Score=45.79 Aligned_cols=99 Identities=25% Similarity=0.319 Sum_probs=56.0
Q ss_pred eeeccceEEEEEE---EeCceeEEEcCeeccccCCHHHHHHHH------------------------------hHHHHhc
Q 032049 15 FGRKKTAVAVTYC---KRGRGLIKINGCPIELVEPEILRFKAY------------------------------EPILLLG 61 (148)
Q Consensus 15 ~GrRKta~A~v~l---~~G~G~I~INg~~l~~y~~~~~r~~i~------------------------------~PL~~~~ 61 (148)
+|-=|++...+.+ .|..|+|.|||.++.+..+..+++++. +-+.-++
T Consensus 356 SGaGKSTLl~lL~G~~~~~~G~I~vng~~l~~l~~~~~~k~i~~v~Q~p~lf~gTireNi~l~~~~~s~e~i~~al~~a~ 435 (559)
T COG4988 356 SGAGKSTLLNLLLGFLAPTQGEIRVNGIDLRDLSPEAWRKQISWVSQNPYLFAGTIRENILLARPDASDEEIIAALDQAG 435 (559)
T ss_pred CCCCHHHHHHHHhCcCCCCCceEEECCccccccCHHHHHhHeeeeCCCCccccccHHHHhhccCCcCCHHHHHHHHHHhc
Confidence 3444555544433 357899999999887655444443332 2222222
Q ss_pred cccc----ceecEEEEEecCCccc-hHHHHHHHHHHHHHHhhhh--------cCChhhHHHHHHHhh
Q 032049 62 RHRF----AGVDMRIRVKGGGHTS-QIYAIRQSIAKALVAFYQK--------YVDEQSKKEIKDILV 115 (148)
Q Consensus 62 ~~~~----~~~di~i~V~GGG~sg-Qa~AIr~aiAraL~~~~~~--------~~~~~~~~~Lk~~l~ 115 (148)
...+ +.+|-.+-=.|-|+|| | |-|+|+||||+.-.+- ..|.+....+...+.
T Consensus 436 l~~~v~~p~GLdt~ige~G~~LSgGQ--~QRlaLARAll~~~~l~llDEpTA~LD~etE~~i~~~l~ 500 (559)
T COG4988 436 LLEFVPKPDGLDTVIGEGGAGLSGGQ--AQRLALARALLSPASLLLLDEPTAHLDAETEQIILQALQ 500 (559)
T ss_pred HHHhhcCCCcccchhccCCCCCCHHH--HHHHHHHHHhcCCCCEEEecCCccCCCHhHHHHHHHHHH
Confidence 1100 2456666667777774 5 5599999999864211 235555555555544
No 15
>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=87.43 E-value=1.1 Score=40.48 Aligned_cols=100 Identities=15% Similarity=0.241 Sum_probs=55.4
Q ss_pred eeccceEEEEEE---EeCceeEEEcCeecccc------------------CCHHHH-----------HHHHhHHHHhccc
Q 032049 16 GRKKTAVAVTYC---KRGRGLIKINGCPIELV------------------EPEILR-----------FKAYEPILLLGRH 63 (148)
Q Consensus 16 GrRKta~A~v~l---~~G~G~I~INg~~l~~y------------------~~~~~r-----------~~i~~PL~~~~~~ 63 (148)
|.=|++..+..+ .|.+|.|.+||.++.++ |+.+.+ +.+.+-+..++.+
T Consensus 377 GsGKSTLl~lL~gl~~p~~G~I~idg~~i~~~~~~~l~~~i~~v~Q~~~lF~~Ti~~NI~~~~~~~d~~i~~a~~~~gl~ 456 (592)
T PRK10790 377 GSGKSTLASLLMGYYPLTEGEIRLDGRPLSSLSHSVLRQGVAMVQQDPVVLADTFLANVTLGRDISEEQVWQALETVQLA 456 (592)
T ss_pred CCCHHHHHHHHhcccCCCCceEEECCEEhhhCCHHHHHhheEEEccCCccccchHHHHHHhCCCCCHHHHHHHHHHcCcH
Confidence 334555443332 36679999999988643 222333 2233333333311
Q ss_pred ----cc-ceecEEEEEecCCccchHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 64 ----RF-AGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 64 ----~~-~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
.+ +.+|-.+.-.|...|| -+.=|+||||||+.- ++ ..|++....+.+.|.++
T Consensus 457 ~~i~~lp~Gldt~i~e~g~~LSG-GqrQRialARaLl~~-~~illlDEpts~LD~~t~~~i~~~l~~~ 522 (592)
T PRK10790 457 ELARSLPDGLYTPLGEQGNNLSV-GQKQLLALARVLVQT-PQILILDEATANIDSGTEQAIQQALAAV 522 (592)
T ss_pred HHHHhccccccccccCCCCCCCH-HHHHHHHHHHHHHhC-CCEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 01 3577766655666664 234599999999863 22 23666666666655543
No 16
>PLN03130 ABC transporter C family member; Provisional
Probab=87.03 E-value=0.27 Score=50.40 Aligned_cols=98 Identities=23% Similarity=0.255 Sum_probs=53.2
Q ss_pred eeccceEEEEEEE---eCceeEEEcCeeccccCCHHHH-----------------------------HHHHhHHHHhccc
Q 032049 16 GRKKTAVAVTYCK---RGRGLIKINGCPIELVEPEILR-----------------------------FKAYEPILLLGRH 63 (148)
Q Consensus 16 GrRKta~A~v~l~---~G~G~I~INg~~l~~y~~~~~r-----------------------------~~i~~PL~~~~~~ 63 (148)
|-=|++.+.+.+. |.+|.|.|||+++.++....+| +++.+.+..++..
T Consensus 1275 GSGKSTLl~lL~rl~~p~~G~I~IDG~dI~~i~l~~LR~~IsiVpQdp~LF~GTIreNLd~~~~~tdeei~~Al~~a~l~ 1354 (1622)
T PLN03130 1275 GAGKSSMLNALFRIVELERGRILIDGCDISKFGLMDLRKVLGIIPQAPVLFSGTVRFNLDPFNEHNDADLWESLERAHLK 1354 (1622)
T ss_pred CCCHHHHHHHHhCcCCCCCceEEECCEecccCCHHHHHhccEEECCCCccccccHHHHhCcCCCCCHHHHHHHHHHcCcH
Confidence 3346666544443 6789999999998654332222 2233334333211
Q ss_pred c----c-ceecEEEEEecCCccchHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhh
Q 032049 64 R----F-AGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILV 115 (148)
Q Consensus 64 ~----~-~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~ 115 (148)
. + ..+|-.|.-.|.-.| .=+-=|++|||||+.- ++ -+|.+....+.+.|.
T Consensus 1355 ~~I~~lp~GLdt~Vge~G~nLS-gGQrQrlaLARALLr~-p~ILILDEATSaLD~~Te~~Iq~~I~ 1418 (1622)
T PLN03130 1355 DVIRRNSLGLDAEVSEAGENFS-VGQRQLLSLARALLRR-SKILVLDEATAAVDVRTDALIQKTIR 1418 (1622)
T ss_pred HHHHhCccccCccccCCCCCCC-HHHHHHHHHHHHHHcC-CCEEEEECCCCCCCHHHHHHHHHHHH
Confidence 0 1 356765544444444 3334589999999963 32 235555555555544
No 17
>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]
Probab=86.96 E-value=0.24 Score=42.05 Aligned_cols=82 Identities=23% Similarity=0.182 Sum_probs=55.2
Q ss_pred ceEEEeeeccceEEEEEEE---eCceeEEEcCeeccccCCHHHHHHHHhHHHHhc--ccccceecEEEEEecCCccchHH
Q 032049 10 ESVQCFGRKKTAVAVTYCK---RGRGLIKINGCPIELVEPEILRFKAYEPILLLG--RHRFAGVDMRIRVKGGGHTSQIY 84 (148)
Q Consensus 10 ~~v~~~GrRKta~A~v~l~---~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~--~~~~~~~di~i~V~GGG~sgQa~ 84 (148)
.-|--+|.=||..+++.+. |.+|.|..+|+++..+......+.+.+-|..++ .+.+.+|+-.. .| ||-+
T Consensus 43 glVGESG~GKSTlgr~i~~L~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhel--SG----GQrQ 116 (268)
T COG4608 43 GLVGESGCGKSTLGRLILGLEEPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHEL--SG----GQRQ 116 (268)
T ss_pred EEEecCCCCHHHHHHHHHcCcCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCccc--Cc----hhhh
Confidence 3444567778888876654 678999999999887765445566777777655 22345666533 33 3544
Q ss_pred HHHHHHHHHHHHhhhh
Q 032049 85 AIRQSIAKALVAFYQK 100 (148)
Q Consensus 85 AIr~aiAraL~~~~~~ 100 (148)
|.+|||||. .+|+
T Consensus 117 --Ri~IARALa-l~P~ 129 (268)
T COG4608 117 --RIGIARALA-LNPK 129 (268)
T ss_pred --hHHHHHHHh-hCCc
Confidence 889999997 3454
No 18
>PLN03232 ABC transporter C family member; Provisional
Probab=85.63 E-value=0.71 Score=46.91 Aligned_cols=96 Identities=20% Similarity=0.245 Sum_probs=54.4
Q ss_pred ccceEEEEEEE---eCceeEEEcCeeccccCCH------------------HHH-----------HHHHhHHHHhcccc-
Q 032049 18 KKTAVAVTYCK---RGRGLIKINGCPIELVEPE------------------ILR-----------FKAYEPILLLGRHR- 64 (148)
Q Consensus 18 RKta~A~v~l~---~G~G~I~INg~~l~~y~~~------------------~~r-----------~~i~~PL~~~~~~~- 64 (148)
=|++.+.+.+. |-+|.|.|||.|+.++... +.| +++.+.+..++...
T Consensus 1274 GKSTL~~lL~rl~~p~~G~I~IdG~di~~i~~~~lR~~i~iVpQdp~LF~gTIr~NL~~~~~~sdeei~~al~~a~l~~~ 1353 (1495)
T PLN03232 1274 GKSSMLNALFRIVELEKGRIMIDDCDVAKFGLTDLRRVLSIIPQSPVLFSGTVRFNIDPFSEHNDADLWEALERAHIKDV 1353 (1495)
T ss_pred CHHHHHHHHhCCCcCCCceEEECCEEhhhCCHHHHHhhcEEECCCCeeeCccHHHHcCCCCCCCHHHHHHHHHHcCCHHH
Confidence 46666544442 6689999999998643322 222 22344444333210
Q ss_pred ---c-ceecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhh
Q 032049 65 ---F-AGVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVR 116 (148)
Q Consensus 65 ---~-~~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~ 116 (148)
+ ..+|-.+.-.|...| ||-+ |++|||||+.- ++ -.|.+....+.+.|.+
T Consensus 1354 I~~lp~GLdt~v~e~G~~LSgGQrQ--rlaLARALLr~-~~ILILDEATSaLD~~Te~~Iq~~L~~ 1416 (1495)
T PLN03232 1354 IDRNPFGLDAEVSEGGENFSVGQRQ--LLSLARALLRR-SKILVLDEATASVDVRTDSLIQRTIRE 1416 (1495)
T ss_pred HHhCcCCCCceecCCCCCCCHHHHH--HHHHHHHHHhC-CCEEEEECCcccCCHHHHHHHHHHHHH
Confidence 1 366766655555565 3555 88999999863 22 2355555555555443
No 19
>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.
Probab=84.11 E-value=3.4 Score=36.81 Aligned_cols=49 Identities=22% Similarity=0.290 Sum_probs=32.7
Q ss_pred ceecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 66 AGVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 66 ~~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
+.||-.+--.|...| ||.+ |+||||||+.- ++ ..|++....+.+.|.+.
T Consensus 458 ~GldT~ige~G~~LSGGQrQ--RiaiARall~~-~~iliLDE~TSaLD~~te~~I~~~l~~~ 516 (529)
T TIGR02868 458 DGLDTVLGEGGARLSGGERQ--RLALARALLAD-APILLLDEPTEHLDAGTESELLEDLLAA 516 (529)
T ss_pred ccccchhccccCcCCHHHHH--HHHHHHHHhcC-CCEEEEeCCcccCCHHHHHHHHHHHHHh
Confidence 356776665565566 4555 99999999863 22 24677777777776654
No 20
>KOG0055 consensus Multidrug/pheromone exporter, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]
Probab=83.04 E-value=1.8 Score=43.63 Aligned_cols=85 Identities=31% Similarity=0.447 Sum_probs=52.9
Q ss_pred eCceeEEEcCeeccccCCHHHHHHHH----hHHHHhc--------------------------ccc-----cceecEEEE
Q 032049 29 RGRGLIKINGCPIELVEPEILRFKAY----EPILLLG--------------------------RHR-----FAGVDMRIR 73 (148)
Q Consensus 29 ~G~G~I~INg~~l~~y~~~~~r~~i~----~PL~~~~--------------------------~~~-----~~~~di~i~ 73 (148)
|-+|.|.|+|.++..+....+|.++- ||..+-+ ... =..||-.|-
T Consensus 1042 p~~G~V~IDg~dik~lnl~~LR~~i~lVsQEP~LF~~TIrENI~YG~~~vs~~eIi~Aak~ANaH~FI~sLP~GyDT~vG 1121 (1228)
T KOG0055|consen 1042 PDAGKVKIDGVDIKDLNLKWLRKQIGLVSQEPVLFNGTIRENIAYGSEEVSEEEIIEAAKLANAHNFISSLPQGYDTRVG 1121 (1228)
T ss_pred CCCCeEEECCcccccCCHHHHHHhcceeccCchhhcccHHHHHhccCCCCCHHHHHHHHHHhhhHHHHhcCcCcccCccC
Confidence 45799999999998887666665531 3443322 000 146787666
Q ss_pred EecCCcc-chHHHHHHHHHHHHHHhhhhc---------CChhhHHHHHHHhhh
Q 032049 74 VKGGGHT-SQIYAIRQSIAKALVAFYQKY---------VDEQSKKEIKDILVR 116 (148)
Q Consensus 74 V~GGG~s-gQa~AIr~aiAraL~~~~~~~---------~~~~~~~~Lk~~l~~ 116 (148)
-+|.=+| ||.+ |.||||||+. +|+- .|.++...+.++|-.
T Consensus 1122 erG~QLSGGQKQ--RIAIARAilR-nPkILLLDEATSALDseSErvVQeALd~ 1171 (1228)
T KOG0055|consen 1122 ERGVQLSGGQKQ--RIAIARAILR-NPKILLLDEATSALDSESERVVQEALDR 1171 (1228)
T ss_pred cccCcCCchHHH--HHHHHHHHHc-CCCeeeeeccchhhhhhhHHHHHHHHHH
Confidence 6666665 4655 9999999996 4541 244455556666543
No 21
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=82.62 E-value=4.6 Score=38.77 Aligned_cols=69 Identities=17% Similarity=0.272 Sum_probs=41.7
Q ss_pred EEEEEeCceeEEEcCeeccccCCHHHHHHHHhHHHHh---------cccccceecEEEEEecCCccchHHHHHHHHHHHH
Q 032049 24 VTYCKRGRGLIKINGCPIELVEPEILRFKAYEPILLL---------GRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKAL 94 (148)
Q Consensus 24 ~v~l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~---------~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL 94 (148)
.+...||+|++.++|. +.+.. ++.+...+..+ +.+.+.++||++.|-||....---++-+|++-||
T Consensus 614 E~~~~~g~g~~~~tG~-lg~vm----kes~~~A~~~~~~~~~~~~~~~~~~~~~Di~i~v~~g~~~~dgpsagla~~~Al 688 (784)
T PRK10787 614 ETACVPGKGKLTYTGS-LGEVM----QESIQAALTVVRARAEKLGINPDFYEKRDIHVHVPEGATPKDGPSAGIAMCTAL 688 (784)
T ss_pred EEEEecCCceEEEecC-cHHHH----HHHHHHHHHHHHHHHHHcCCCcccccCceEEEEecCCCCCCCCCchHHHHHHHH
Confidence 3445689999999994 43322 22222222221 1223468899999999877644445666777777
Q ss_pred HHh
Q 032049 95 VAF 97 (148)
Q Consensus 95 ~~~ 97 (148)
+..
T Consensus 689 ~S~ 691 (784)
T PRK10787 689 VSC 691 (784)
T ss_pred HHH
Confidence 665
No 22
>KOG0055 consensus Multidrug/pheromone exporter, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]
Probab=81.23 E-value=3 Score=42.11 Aligned_cols=86 Identities=27% Similarity=0.331 Sum_probs=53.6
Q ss_pred eCceeEEEcCeeccccCCHHHHHHH----HhHHHHhcc-------------------------------cccceecEEEE
Q 032049 29 RGRGLIKINGCPIELVEPEILRFKA----YEPILLLGR-------------------------------HRFAGVDMRIR 73 (148)
Q Consensus 29 ~G~G~I~INg~~l~~y~~~~~r~~i----~~PL~~~~~-------------------------------~~~~~~di~i~ 73 (148)
|-+|.|.|+|.++..+....+|.+| -+|+.+..+ .....||-.|-
T Consensus 405 P~~G~V~idG~di~~~~~~~lr~~iglV~QePvlF~~tI~eNI~~G~~dat~~~i~~a~k~ana~~fi~~lp~g~~T~vg 484 (1228)
T KOG0055|consen 405 PTSGEVLIDGEDIRNLNLKWLRSQIGLVSQEPVLFATTIRENIRYGKPDATREEIEEAAKAANAHDFILKLPDGYDTLVG 484 (1228)
T ss_pred CCCceEEEcCccchhcchHHHHhhcCeeeechhhhcccHHHHHhcCCCcccHHHHHHHHHHccHHHHHHhhHHhhccccc
Confidence 5679999999999988777777653 245544321 00135666555
Q ss_pred EecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 74 VKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 74 V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
-+|-=+| || --|.||||||+. +|+ ..|++.+....++|.+.
T Consensus 485 e~g~qLSGGQ--KQRIAIARalv~-~P~ILLLDEaTSaLD~~se~~Vq~ALd~~ 535 (1228)
T KOG0055|consen 485 ERGVQLSGGQ--KQRIAIARALVR-NPKILLLDEATSALDAESERVVQEALDKA 535 (1228)
T ss_pred CCCCCCChHH--HHHHHHHHHHHh-CCCEEEecCcccccCHHHHHHHHHHHHHh
Confidence 4443344 34 459999999985 444 23666666666665443
No 23
>PTZ00265 multidrug resistance protein (mdr1); Provisional
Probab=79.04 E-value=3.4 Score=42.24 Aligned_cols=101 Identities=19% Similarity=0.149 Sum_probs=58.7
Q ss_pred eeeccceEEEEEEEeCceeEEEcCeeccccCCHHHHHH------------------------------HHhHHHHhcccc
Q 032049 15 FGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFK------------------------------AYEPILLLGRHR 64 (148)
Q Consensus 15 ~GrRKta~A~v~l~~G~G~I~INg~~l~~y~~~~~r~~------------------------------i~~PL~~~~~~~ 64 (148)
.+.++++.-.-...|-+|.|.|||.++.+|....+|.. |.+.+..++.+.
T Consensus 1260 ~~~~~~~~~~~~~~~~~G~I~idG~di~~~~~~~lR~~i~~V~Qep~LF~gTIreNI~~g~~~at~eeI~~A~k~A~l~~ 1339 (1466)
T PTZ00265 1260 LTKEGGSGEDSTVFKNSGKILLDGVDICDYNLKDLRNLFSIVSQEPMLFNMSIYENIKFGKEDATREDVKRACKFAAIDE 1339 (1466)
T ss_pred cccccccccccccCCCCCeEEECCEEHHhCCHHHHHhhccEeCCCCccccccHHHHHhcCCCCCCHHHHHHHHHHcCCHH
Confidence 34455554444455779999999999865543222222 222222222100
Q ss_pred ----c-ceecEEEEEecCCccchHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 65 ----F-AGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 65 ----~-~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
+ ..||-.|--+|..+|| =+.=|+||||||+. .|. -.|++....+.+.|.+.
T Consensus 1340 fI~~LP~GydT~VGe~G~~LSG-GQkQRIaIARALlr-~p~ILLLDEaTSaLD~~sE~~I~~~L~~~ 1404 (1466)
T PTZ00265 1340 FIESLPNKYDTNVGPYGKSLSG-GQKQRIAIARALLR-EPKILLLDEATSSLDSNSEKLIEKTIVDI 1404 (1466)
T ss_pred HHHhCccccCCccCCCCCcCCH-HHHHHHHHHHHHhc-CCCEEEEeCcccccCHHHHHHHHHHHHHH
Confidence 1 4677766666666763 23459999999986 333 23666666777776654
No 24
>COG1750 Archaeal serine proteases [General function prediction only]
Probab=78.32 E-value=5 Score=37.52 Aligned_cols=72 Identities=19% Similarity=0.227 Sum_probs=52.6
Q ss_pred EEEEEeCceeEEEcCeecccc-CCHHHHHHHHhHHHHhcccccceecEEEEEecC-----CccchHHHHHHHHHHHHHHh
Q 032049 24 VTYCKRGRGLIKINGCPIELV-EPEILRFKAYEPILLLGRHRFAGVDMRIRVKGG-----GHTSQIYAIRQSIAKALVAF 97 (148)
Q Consensus 24 ~v~l~~G~G~I~INg~~l~~y-~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GG-----G~sgQa~AIr~aiAraL~~~ 97 (148)
.|.+.||+|.+.|-+-|+.+. .....|-.....+.++|.+ +.+||+++.|+-+ |+|+ -+++..|+=-+|.-|
T Consensus 55 ~vtv~pG~G~v~v~t~P~t~~d~~~SArvAa~~A~~~~Gvd-~ssyd~~i~v~a~~pVVGgPSa-gg~mtva~~~~~~~~ 132 (579)
T COG1750 55 SVTVTPGDGRVYVATFPYTQIDMQGSARVAAGVALRLAGVD-MSSYDVYIAVEADSPVVGGPSA-GGYMTVAIYAALMGW 132 (579)
T ss_pred eeeecCCCceEEeecCCCchhccchhhHHHHHHHHHhhCCC-ccceeEEEEEecCCCeecCccc-chHhHHHHHHHHhCC
Confidence 344579999999999999987 5566777788889999987 5999999999743 3443 235555555555443
No 25
>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]
Probab=77.56 E-value=2.8 Score=37.81 Aligned_cols=99 Identities=24% Similarity=0.276 Sum_probs=55.5
Q ss_pred eeeccceEEEEEEE---eCceeEEEcCeeccccCCHHHHHHH------------------------------HhHHHHhc
Q 032049 15 FGRKKTAVAVTYCK---RGRGLIKINGCPIELVEPEILRFKA------------------------------YEPILLLG 61 (148)
Q Consensus 15 ~GrRKta~A~v~l~---~G~G~I~INg~~l~~y~~~~~r~~i------------------------------~~PL~~~~ 61 (148)
+|-=|++.++..+. |-+|.|.|||.++.++....+|..| .+.+..++
T Consensus 364 sGsGKSTl~~LL~r~~~~~~G~I~idg~dI~~i~~~~lr~~I~~V~Qd~~LF~~TI~~NI~~g~~~at~eei~~a~k~a~ 443 (567)
T COG1132 364 SGSGKSTLIKLLLRLYDPTSGEILIDGIDIRDISLDSLRKRIGIVSQDPLLFSGTIRENIALGRPDATDEEIEEALKLAN 443 (567)
T ss_pred CCCCHHHHHHHHhccCCCCCCeEEECCEehhhcCHHHHHHhccEEcccceeecccHHHHHhcCCCCCCHHHHHHHHHHhC
Confidence 34446666544332 5689999999998766554444333 22232221
Q ss_pred cc----cc-ceecEEEEEecCCccchHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhh
Q 032049 62 RH----RF-AGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILV 115 (148)
Q Consensus 62 ~~----~~-~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~ 115 (148)
.+ .+ +.||-.|.-.|...| .=+--|+||||||+.- ++ ..|.+....+.+.+.
T Consensus 444 ~~d~I~~lp~g~dt~vge~G~~LS-gGQrQrlaiARall~~-~~ILILDEaTSalD~~tE~~I~~~l~ 509 (567)
T COG1132 444 AHEFIANLPDGYDTIVGERGVNLS-GGQRQRLAIARALLRN-PPILILDEATSALDTETEALIQDALK 509 (567)
T ss_pred hHHHHHhCcccccceecCCCccCC-HHHHHHHHHHHHHhcC-CCEEEEeccccccCHHhHHHHHHHHH
Confidence 10 01 257776663333344 3445699999999863 32 235555556666553
No 26
>PTZ00243 ABC transporter; Provisional
Probab=76.51 E-value=1.2 Score=45.53 Aligned_cols=26 Identities=27% Similarity=0.441 Sum_probs=17.1
Q ss_pred cceEEEEEEE---eCceeEEEcCeecccc
Q 032049 19 KTAVAVTYCK---RGRGLIKINGCPIELV 44 (148)
Q Consensus 19 Kta~A~v~l~---~G~G~I~INg~~l~~y 44 (148)
|++.+...+. |-+|.|.|||+++..+
T Consensus 1349 KSTLl~lLlrl~~p~~G~I~IDG~di~~i 1377 (1560)
T PTZ00243 1349 KSTLLLTFMRMVEVCGGEIRVNGREIGAY 1377 (1560)
T ss_pred HHHHHHHHhCCCCCCCcEEEECCEEcccC
Confidence 5555443332 4579999999998643
No 27
>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP). This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.
Probab=75.70 E-value=5.2 Score=40.94 Aligned_cols=96 Identities=20% Similarity=0.231 Sum_probs=53.5
Q ss_pred ccceEEEEEEE---eCceeEEEcCeeccccCC------------------HHHHH-----------HHHhHHHHhcccc-
Q 032049 18 KKTAVAVTYCK---RGRGLIKINGCPIELVEP------------------EILRF-----------KAYEPILLLGRHR- 64 (148)
Q Consensus 18 RKta~A~v~l~---~G~G~I~INg~~l~~y~~------------------~~~r~-----------~i~~PL~~~~~~~- 64 (148)
=|++...+.+. |-+|.|.|||.++.++.. .+.|+ ++.+-|..++...
T Consensus 1324 GKSTL~~lL~rl~~~~~G~I~IdG~dI~~i~~~~LR~~i~iVpQdp~LF~gTIr~NLdp~~~~sdeei~~al~~a~l~~~ 1403 (1522)
T TIGR00957 1324 GKSSLTLGLFRINESAEGEIIIDGLNIAKIGLHDLRFKITIIPQDPVLFSGSLRMNLDPFSQYSDEEVWWALELAHLKTF 1403 (1522)
T ss_pred CHHHHHHHHhcCccCCCCeEEECCEEccccCHHHHHhcCeEECCCCcccCccHHHHcCcccCCCHHHHHHHHHHcCcHHH
Confidence 46666544332 567999999998764322 22222 2333333333110
Q ss_pred ---c-ceecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhh
Q 032049 65 ---F-AGVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVR 116 (148)
Q Consensus 65 ---~-~~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~ 116 (148)
+ +.+|-.|.-.|...| ||-+ |++|||||+.- ++ -+|.+....+.+.|.+
T Consensus 1404 I~~lp~GLdt~v~e~G~~LSgGQrQ--rl~LARALLr~-~~ILiLDEaTSalD~~Te~~Iq~~l~~ 1466 (1522)
T TIGR00957 1404 VSALPDKLDHECAEGGENLSVGQRQ--LVCLARALLRK-TKILVLDEATAAVDLETDNLIQSTIRT 1466 (1522)
T ss_pred HhhCccCCCceecCCCCcCCHHHHH--HHHHHHHHHcC-CCEEEEECCcccCCHHHHHHHHHHHHH
Confidence 1 456766655555666 3555 88999999863 22 2355555555555544
No 28
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=75.14 E-value=1.1 Score=37.74 Aligned_cols=45 Identities=24% Similarity=0.337 Sum_probs=31.4
Q ss_pred eeeccceEEEEEE---EeCceeEEEcCeeccc--------------c-------CC-HHHHHHHHhHHHH
Q 032049 15 FGRKKTAVAVTYC---KRGRGLIKINGCPIEL--------------V-------EP-EILRFKAYEPILL 59 (148)
Q Consensus 15 ~GrRKta~A~v~l---~~G~G~I~INg~~l~~--------------y-------~~-~~~r~~i~~PL~~ 59 (148)
+|.=|++.+++.+ .|-+|.|.++|+++.. | +| ......+.+||..
T Consensus 42 SGsGKSTL~r~l~Gl~~p~~G~I~~~G~~~~~~~~~~~~~~~VQmVFQDp~~SLnP~~tv~~~l~Epl~~ 111 (252)
T COG1124 42 SGSGKSTLARLLAGLEKPSSGSILLDGKPLAPKKRAKAFYRPVQMVFQDPYSSLNPRRTVGRILSEPLRP 111 (252)
T ss_pred CCCCHHHHHHHHhcccCCCCceEEECCcccCccccchhhccceeEEecCCccccCcchhHHHHHhhhhcc
Confidence 5667888887654 4788999999965432 1 22 2356778889886
No 29
>PF13541 ChlI: Subunit ChlI of Mg-chelatase
Probab=74.18 E-value=10 Score=28.25 Aligned_cols=71 Identities=20% Similarity=0.190 Sum_probs=52.0
Q ss_pred EEEEeCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHHHHHHHHHhh
Q 032049 25 TYCKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFY 98 (148)
Q Consensus 25 v~l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~ 98 (148)
|.+.+|--.+.|-|.|-... ...++.|..-|.-.+.. +...||+|++.+||+-=+--+.-+|||-||+.-+
T Consensus 3 v~~~~Glp~~~ivGl~~~av--~esr~Rv~~al~~~g~~-~p~~~i~VNlap~~l~k~g~~~DLaIA~ailsa~ 73 (121)
T PF13541_consen 3 VDISRGLPSFNIVGLPDTAV--KESRERVRSALKNSGFP-FPNQDITVNLAPADLKKEGPAFDLAIAIAILSAF 73 (121)
T ss_pred EEEcCCCCceEEecCchHHH--HHHHHHHHHHHHhcCCC-CCcceeeeEEEeCCEEEeeeeehHHHHHHHHHhC
Confidence 33444544577777665433 23455667777777764 6899999999999999888999999999998754
No 30
>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=74.08 E-value=6.9 Score=34.37 Aligned_cols=14 Identities=29% Similarity=0.401 Sum_probs=11.4
Q ss_pred eCceeEEEcCeecc
Q 032049 29 RGRGLIKINGCPIE 42 (148)
Q Consensus 29 ~G~G~I~INg~~l~ 42 (148)
|.+|.|.+||+++.
T Consensus 57 p~~G~I~l~G~~i~ 70 (352)
T COG3842 57 PSSGEILLDGEDIT 70 (352)
T ss_pred CCCceEEECCEECC
Confidence 56799999998763
No 31
>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.
Probab=72.59 E-value=11 Score=35.07 Aligned_cols=53 Identities=32% Similarity=0.359 Sum_probs=33.7
Q ss_pred eecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhcCCCce
Q 032049 67 GVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRYDRTLL 122 (148)
Q Consensus 67 ~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~yd~glL 122 (148)
.||-.+.-.|...| || -=|+||||||+.- |+ -.|+.....+-+.|.+.++..+
T Consensus 604 gl~t~i~e~G~~LSGGQ--rQRiaLARall~~-p~iliLDEptS~LD~~te~~i~~~l~~~~~T~I 666 (710)
T TIGR03796 604 GYDAELAEGGANLSGGQ--RQRLEIARALVRN-PSILILDEATSALDPETEKIIDDNLRRRGCTCI 666 (710)
T ss_pred cccceeccCCCCCCHHH--HHHHHHHHHHhhC-CCEEEEECccccCCHHHHHHHHHHHHhcCCEEE
Confidence 56766665666666 45 4589999999863 33 2366666667666665444443
No 32
>PF03755 YicC_N: YicC-like family, N-terminal region ; InterPro: IPR013527 Proteins in this entry are homologues of YicC (P23839 from SWISSPROT) from Escherichia coli. Although it is relatively poorly characterised YicC has been shown to be important for cells in the stationary phase, and essential for growth at high temperatures []. This domain is found at the N-terminal region of these proteins.
Probab=69.70 E-value=18 Score=27.72 Aligned_cols=81 Identities=21% Similarity=0.284 Sum_probs=47.0
Q ss_pred CceEEEeeeccceEEEEEEEeCceeEE-----EcCeeccccC--CHHHH--HHHHhHHHHhcccccceecEEEEEecCCc
Q 032049 9 VESVQCFGRKKTAVAVTYCKRGRGLIK-----INGCPIELVE--PEILR--FKAYEPILLLGRHRFAGVDMRIRVKGGGH 79 (148)
Q Consensus 9 ~~~v~~~GrRKta~A~v~l~~G~G~I~-----INg~~l~~y~--~~~~r--~~i~~PL~~~~~~~~~~~di~i~V~GGG~ 79 (148)
|+++.++|+-- ...+.+.|. ||++-++... |..+. +.-+.-+.--... -+++||.|+++..+.
T Consensus 1 i~SMTGfgr~~-------~~~~~~~~~vEikSvN~R~Ldi~~rlP~~l~~lE~~ir~~i~~~l~-RGkV~v~i~~~~~~~ 72 (159)
T PF03755_consen 1 IKSMTGFGRAE-------AETDGGSISVEIKSVNHRFLDISIRLPRELSSLEPEIRKLIRKKLS-RGKVEVSIRVERSSE 72 (159)
T ss_pred CcCcCCCceeE-------EecCCeEEEEEEEecccCceeeEEeCCHHHHHHHHHHHHHHHHhcc-cceEEEEEEEEECcc
Confidence 35566666543 333445544 6999887643 44332 1111111111122 289999999999886
Q ss_pred cchHHHHHHHHHHHHHHh
Q 032049 80 TSQIYAIRQSIAKALVAF 97 (148)
Q Consensus 80 sgQa~AIr~aiAraL~~~ 97 (148)
+...-.|-.++++++...
T Consensus 73 ~~~~~~in~~l~~~y~~~ 90 (159)
T PF03755_consen 73 SAVELRINEELAKAYYEA 90 (159)
T ss_pred cCCCcccCHHHHHHHHHH
Confidence 666666777777776654
No 33
>TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR). The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.
Probab=68.20 E-value=9 Score=39.20 Aligned_cols=31 Identities=10% Similarity=0.007 Sum_probs=20.2
Q ss_pred ceecEEEEEecCCccchHHHHHHHHHHHHHHh
Q 032049 66 AGVDMRIRVKGGGHTSQIYAIRQSIAKALVAF 97 (148)
Q Consensus 66 ~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~ 97 (148)
+.+|..|.-.|..+| .=+-=+++|||||+.-
T Consensus 1341 ~GLdt~v~e~G~nLS-gGQrQrL~LARALLr~ 1371 (1490)
T TIGR01271 1341 DKLDFVLVDGGYVLS-NGHKQLMCLARSILSK 1371 (1490)
T ss_pred cccccccccCCCcCC-HHHHHHHHHHHHHhCC
Confidence 456776665454555 3334489999999863
No 34
>TIGR00763 lon ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
Probab=64.15 E-value=15 Score=35.12 Aligned_cols=74 Identities=19% Similarity=0.209 Sum_probs=43.4
Q ss_pred EEEEeCceeEEEcCeeccccCCH--HHHHHHHhHHHHhcc--cccceecEEEEEecCCccchHHHHHHHHHHHHHHhh
Q 032049 25 TYCKRGRGLIKINGCPIELVEPE--ILRFKAYEPILLLGR--HRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFY 98 (148)
Q Consensus 25 v~l~~G~G~I~INg~~l~~y~~~--~~r~~i~~PL~~~~~--~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~ 98 (148)
|.+.+|.|.+.|.|.+-..+... ....-+..-+.-.+. +.|.++||+|+|-+|.....--+.-+|||-||++..
T Consensus 619 ~~~~~G~~~~~~tG~~~~~~kES~~~a~~~v~~~~~~~~~~~~~~~~~di~v~~~~g~~~k~Gpsa~laia~al~sa~ 696 (775)
T TIGR00763 619 TTKVAGKGSLELTGQLGDVMKESAQIALTYVRSIAADLGISPNFFEKADIHLHVPEGATPKDGPSAGITMATALLSLA 696 (775)
T ss_pred EEEeCCCceEEEeCCchHHHHHHHHHHHHHHHHHHHHcCCCccccCCeEEEEEcCCcccCCCCCcchHHHHHHHHHHc
Confidence 34458999999999654444321 111112222222222 124688999999998777555556677777776653
No 35
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=62.04 E-value=15 Score=34.26 Aligned_cols=63 Identities=16% Similarity=0.360 Sum_probs=41.9
Q ss_pred eCceeEEEcCeeccccCCHHHHHHHHhHHH----HhcccccceecEEEEEecCCccchHHHHHHHHHHHHHHhh
Q 032049 29 RGRGLIKINGCPIELVEPEILRFKAYEPIL----LLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFY 98 (148)
Q Consensus 29 ~G~G~I~INg~~l~~y~~~~~r~~i~~PL~----~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~ 98 (148)
||.|.|..+|....+ .++.|...+. .++.+ +..+||+|++-||+ --.--+.-+|||-||+...
T Consensus 474 pg~~~vgl~~~~~~e-----~kerv~~A~~~l~~~~g~~-~~~~di~vnl~~~~-~k~gpsadLaia~ailSa~ 540 (615)
T TIGR02903 474 PGKGTVRFNDTAGSM-----AKDSVFNAASVIRKITGKD-LSNYDIHVNVIGGG-RIDGPSAGAAITLCMISAI 540 (615)
T ss_pred CCCceEeeCCcchHH-----HHHHHHHHHHHHHHhCCCC-CCCeeEEEEcCCCC-CCCCchHHHHHHHHHHHhc
Confidence 566677666644333 3444555555 45553 68999999999887 4555677788888887653
No 36
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=54.59 E-value=9.7 Score=32.93 Aligned_cols=24 Identities=33% Similarity=0.405 Sum_probs=17.8
Q ss_pred EEeCceeEEEcCeeccccCCHHHH
Q 032049 27 CKRGRGLIKINGCPIELVEPEILR 50 (148)
Q Consensus 27 l~~G~G~I~INg~~l~~y~~~~~r 50 (148)
+.|.+|.|.|||+++.++.+..+|
T Consensus 51 iept~G~I~i~g~~i~~~d~~~LR 74 (309)
T COG1125 51 IEPTSGEILIDGEDISDLDPVELR 74 (309)
T ss_pred cCCCCceEEECCeecccCCHHHHH
Confidence 446789999999999876544333
No 37
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=54.47 E-value=25 Score=31.58 Aligned_cols=47 Identities=23% Similarity=0.270 Sum_probs=36.1
Q ss_pred HHHHHhHH--HHhcccccceecEEEEEecCCccchHHHHHHHHHHHHHHhh
Q 032049 50 RFKAYEPI--LLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFY 98 (148)
Q Consensus 50 r~~i~~PL--~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~ 98 (148)
|..++..+ .-.+.. +...||+|++- ||+-=+--|.-+|||-||+.-+
T Consensus 337 r~~~~~Avl~k~~g~~-~~~~di~vNl~-ggl~~~~~~~DLaia~ailss~ 385 (454)
T TIGR00416 337 RLALLLAVLEKRLGLP-LADQDVFLNVA-GGVKVSEPAADLALLIAIVSSF 385 (454)
T ss_pred HHHHHHHHHHHhcCCC-CCCceEEEEcc-CCcccCCccccHHHHHHHHHhC
Confidence 66666666 455653 68999999999 7777777788899999988754
No 38
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=52.78 E-value=15 Score=31.63 Aligned_cols=32 Identities=25% Similarity=0.100 Sum_probs=27.9
Q ss_pred cceecEEEEEecCCccchHHHHHHHHHHHHHH
Q 032049 65 FAGVDMRIRVKGGGHTSQIYAIRQSIAKALVA 96 (148)
Q Consensus 65 ~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~ 96 (148)
..+|-+.|.|=+=|++||.+|.+||-|-+=+.
T Consensus 272 t~~ftlRC~~Cq~glvGq~ea~eHA~~TGH~n 303 (307)
T KOG3288|consen 272 TAKFTLRCMVCQMGLVGQKEAAEHAKATGHVN 303 (307)
T ss_pred ccceEEEeeecccceeeHHHHHHHHHhcCCCc
Confidence 36899999999999999999999998876544
No 39
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=52.17 E-value=15 Score=30.80 Aligned_cols=51 Identities=20% Similarity=0.261 Sum_probs=32.2
Q ss_pred HHHHHHHHhHHHHhcccc-cceecEEEEEecCCccchHHH-HHHHHHHHHHHh
Q 032049 47 EILRFKAYEPILLLGRHR-FAGVDMRIRVKGGGHTSQIYA-IRQSIAKALVAF 97 (148)
Q Consensus 47 ~~~r~~i~~PL~~~~~~~-~~~~di~i~V~GGG~sgQa~A-Ir~aiAraL~~~ 97 (148)
+..-..|..-|...+... ...||+.|.++|||-..--.+ =-..+||||..+
T Consensus 54 ~~A~~~I~~al~~~~~~~~~~~~Dviii~RGGGs~eDL~~FN~e~varai~~~ 106 (319)
T PF02601_consen 54 EGAAASIVSALRKANEMGQADDFDVIIIIRGGGSIEDLWAFNDEEVARAIAAS 106 (319)
T ss_pred cchHHHHHHHHHHHHhccccccccEEEEecCCCChHHhcccChHHHHHHHHhC
Confidence 345566777788776431 127999999999996543322 134566666654
No 40
>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.
Probab=49.83 E-value=21 Score=27.17 Aligned_cols=81 Identities=23% Similarity=0.176 Sum_probs=44.8
Q ss_pred eCceeEEEcCeeccccCCHHHHHHHHh---HHHHhcccccceecEEEEEecCCccchHHHHHHHHHHHHHHhhhh-----
Q 032049 29 RGRGLIKINGCPIELVEPEILRFKAYE---PILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK----- 100 (148)
Q Consensus 29 ~G~G~I~INg~~l~~y~~~~~r~~i~~---PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~----- 100 (148)
|-+|.|.+||.++..+.+...+..+-. -+..++.+ ...+ . .....+.-+.-|++|||||+. .|.
T Consensus 51 ~~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~--~~~~----~-~~~~LS~G~~qrl~laral~~-~p~llllD 122 (180)
T cd03214 51 PSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLA--HLAD----R-PFNELSGGERQRVLLARALAQ-EPPILLLD 122 (180)
T ss_pred CCCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCH--hHhc----C-CcccCCHHHHHHHHHHHHHhc-CCCEEEEe
Confidence 567999999999876544332222211 12222221 1111 1 122333345678999999985 333
Q ss_pred ----cCChhhHHHHHHHhhhc
Q 032049 101 ----YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 101 ----~~~~~~~~~Lk~~l~~y 117 (148)
-.|+..+..+.+.|.++
T Consensus 123 EP~~~LD~~~~~~~~~~l~~~ 143 (180)
T cd03214 123 EPTSHLDIAHQIELLELLRRL 143 (180)
T ss_pred CCccCCCHHHHHHHHHHHHHH
Confidence 23666677777776655
No 41
>TIGR02653 Lon_rel_chp conserved hypothetical protein. This model describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to Pfam model pfam05362, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of E. coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST].
Probab=49.11 E-value=49 Score=31.72 Aligned_cols=72 Identities=15% Similarity=0.091 Sum_probs=43.9
Q ss_pred EEEEEEeCceeEEEcCeeccccCCH-------HHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHHHHHHHH
Q 032049 23 AVTYCKRGRGLIKINGCPIELVEPE-------ILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALV 95 (148)
Q Consensus 23 A~v~l~~G~G~I~INg~~l~~y~~~-------~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~ 95 (148)
-.+.+.+|+|++.++|..+.+...+ +++. -..-|.. +. .+.++||++-|--|...+-.-.+-+|++-|||
T Consensus 514 IE~~~~~G~Gkl~lTG~~lg~vmKESa~~A~sy~ks-~a~~l~~-~~-~~~~~DiHIHvpega~pkdGpSAGia~~~AL~ 590 (675)
T TIGR02653 514 FEVQVSAGSGKHSVSGLGSNTTAKESIRVAFDYFKG-NLVRISA-SA-KFSEHDYHLHVVDLHNTGPSTEASLAALIALC 590 (675)
T ss_pred EEEEEeCCCCceeeccCCchHHHHHHHHHHHHHHHH-hHHhcCC-Cc-ccCcceEEEECCCCCCCCCCchhHHHHHHHHH
Confidence 3455669999999999555432211 1111 1111221 12 36899999999877766666666667777776
Q ss_pred Hh
Q 032049 96 AF 97 (148)
Q Consensus 96 ~~ 97 (148)
..
T Consensus 591 Sa 592 (675)
T TIGR02653 591 SA 592 (675)
T ss_pred HH
Confidence 64
No 42
>PF05362 Lon_C: Lon protease (S16) C-terminal proteolytic domain; InterPro: IPR008269 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature defines the C-terminal proteolytic domain of the archael, bacterial and eukaryotic Lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (Lon protease family, clan SF). In the eukaryotes the majority of the proteins are located in the mitochondrial matrix [, ]. In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response [].; GO: 0004176 ATP-dependent peptidase activity, 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1Z0E_E 1Z0G_E 1Z0T_F 1Z0C_A 1Z0V_A 1Z0B_A 1Z0W_A 2KJP_A 2X36_F 3K1J_B ....
Probab=48.93 E-value=77 Score=25.57 Aligned_cols=55 Identities=18% Similarity=0.229 Sum_probs=28.1
Q ss_pred EEEEEeCceeEEEcCeeccccCCH--HHHHHHHhHHHH--hcccccceecEEEEEecCC
Q 032049 24 VTYCKRGRGLIKINGCPIELVEPE--ILRFKAYEPILL--LGRHRFAGVDMRIRVKGGG 78 (148)
Q Consensus 24 ~v~l~~G~G~I~INg~~l~~y~~~--~~r~~i~~PL~~--~~~~~~~~~di~i~V~GGG 78 (148)
.+.+.+|+|.+.+.|.--+.+... .....+..=+.- .+.+.+.++|+++.+..|+
T Consensus 46 E~~~~~G~G~l~~tG~lg~v~kES~~~A~~~~k~~~~~~~~~~~~~~~~dihi~~~~~~ 104 (204)
T PF05362_consen 46 EAQVIPGKGKLIITGNLGDVMKESAKIAFSYLKANLKRIGIDPSNFDNYDIHIHVPDGA 104 (204)
T ss_dssp EEEEEESSSEEEEESSBHHHHHHHHHHHHHHHHHHHHCCSSTCCHHGCEEEEEEESSTT
T ss_pred EEeeccCcceeEeecccchhHHHHHHHHHHHHHhhhcccccccccccceeEEEeccccc
Confidence 445568999999998643322211 011111111111 1122346899999997543
No 43
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=48.29 E-value=14 Score=30.94 Aligned_cols=41 Identities=22% Similarity=0.387 Sum_probs=31.0
Q ss_pred eCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEe
Q 032049 29 RGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVK 75 (148)
Q Consensus 29 ~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~ 75 (148)
..+|+|+|+|.++..+....+-.+ |.++..+ +.++...+|+
T Consensus 53 ~d~G~i~i~g~~~~~~~s~~LAk~----lSILkQ~--N~i~~rlTV~ 93 (252)
T COG4604 53 KDSGEITIDGLELTSTPSKELAKK----LSILKQE--NHINSRLTVR 93 (252)
T ss_pred ccCceEEEeeeecccCChHHHHHH----HHHHHhh--chhhheeEHH
Confidence 468999999999999987655443 5555555 6888888874
No 44
>PRK15317 alkyl hydroperoxide reductase subunit F; Provisional
Probab=45.78 E-value=24 Score=31.64 Aligned_cols=58 Identities=19% Similarity=0.052 Sum_probs=31.4
Q ss_pred eEEEcCeeccc-cCC-HHHHHHHHhHHHHhccc-ccceecEEEEEecCCccchHHHHHHHH
Q 032049 33 LIKINGCPIEL-VEP-EILRFKAYEPILLLGRH-RFAGVDMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 33 ~I~INg~~l~~-y~~-~~~r~~i~~PL~~~~~~-~~~~~di~i~V~GGG~sgQa~AIr~ai 90 (148)
.+.|||..+.. -.+ ..+.+.+..|....... .-...+.++.|=|||..|-+-|+.++-
T Consensus 172 ~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dvvIIGgGpaGl~aA~~la~ 232 (517)
T PRK15317 172 TVFLNGEEFGQGRMTLEEILAKLDTGAAARAAEELNAKDPYDVLVVGGGPAGAAAAIYAAR 232 (517)
T ss_pred EEEECCcEEEecCCCHHHHHHHHhccccccchhhcccCCCCCEEEECCCHHHHHHHHHHHH
Confidence 36788876543 122 33444555433211000 002334446777999999998887753
No 45
>TIGR03140 AhpF alkyl hydroperoxide reductase, F subunit. This enzyme is the partner of the peroxiredoxin (alkyl hydroperoxide reductase) AhpC which contains the peroxide-reactive cysteine. AhpF contains the reductant (NAD(P)H) binding domain (pfam00070) and presumably acts to resolve the disulfide which forms after oxidation of the active site cysteine in AphC. This proteins contains two paired conserved cysteine motifs, CxxCP and CxHCDGP.
Probab=44.86 E-value=23 Score=31.79 Aligned_cols=24 Identities=25% Similarity=0.192 Sum_probs=18.6
Q ss_pred eecEEEEEecCCccchHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~ai 90 (148)
..+.++.|=|||..|-+-|+.++-
T Consensus 210 ~~~~dVvIIGgGpAGl~AA~~la~ 233 (515)
T TIGR03140 210 LDPYDVLVVGGGPAGAAAAIYAAR 233 (515)
T ss_pred cCCCCEEEECCCHHHHHHHHHHHH
Confidence 344556788999999999888765
No 46
>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=38.88 E-value=41 Score=25.23 Aligned_cols=35 Identities=14% Similarity=0.093 Sum_probs=25.1
Q ss_pred hHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 82 QIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 82 Qa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
.-+.-|.+|||||+. .|+ ..|+..+..+.+.|.++
T Consensus 85 ~G~~qrl~laral~~-~p~illlDEP~~~LD~~~~~~l~~~l~~~ 128 (163)
T cd03216 85 VGERQMVEIARALAR-NARLLILDEPTAALTPAEVERLFKVIRRL 128 (163)
T ss_pred HHHHHHHHHHHHHhc-CCCEEEEECCCcCCCHHHHHHHHHHHHHH
Confidence 344679999999985 333 24777788888877766
No 47
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=36.15 E-value=38 Score=29.85 Aligned_cols=30 Identities=23% Similarity=0.211 Sum_probs=22.1
Q ss_pred HHHHHHHHhHHHHhcccccceecEEEEEecCCc
Q 032049 47 EILRFKAYEPILLLGRHRFAGVDMRIRVKGGGH 79 (148)
Q Consensus 47 ~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~ 79 (148)
+..-..|..-|...+.. + ||+.|.++|||-
T Consensus 175 ~~A~~~i~~al~~~~~~--~-~Dviii~RGGGS 204 (438)
T PRK00286 175 EGAAASIVAAIERANAR--G-EDVLIVARGGGS 204 (438)
T ss_pred ccHHHHHHHHHHHhcCC--C-CCEEEEecCCCC
Confidence 33455677778777642 4 999999999994
No 48
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=34.25 E-value=37 Score=25.63 Aligned_cols=34 Identities=12% Similarity=0.169 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 83 IYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 83 a~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
-+.-|.+|||||+. .|. -.|+..+..+.+.|.++
T Consensus 102 G~~qrv~laral~~-~p~~lllDEP~~~LD~~~~~~l~~~l~~~ 144 (178)
T cd03247 102 GERQRLALARILLQ-DAPIVLLDEPTVGLDPITERQLLSLIFEV 144 (178)
T ss_pred HHHHHHHHHHHHhc-CCCEEEEECCcccCCHHHHHHHHHHHHHH
Confidence 35789999999985 333 23666677777766654
No 49
>COG3526 Uncharacterized protein conserved in bacteria [Posttranslational modification, protein turnover, chaperones]
Probab=33.55 E-value=35 Score=24.64 Aligned_cols=23 Identities=22% Similarity=0.147 Sum_probs=18.5
Q ss_pred eEEEEEEEeCce---eEEEcCeeccc
Q 032049 21 AVAVTYCKRGRG---LIKINGCPIEL 43 (148)
Q Consensus 21 a~A~v~l~~G~G---~I~INg~~l~~ 43 (148)
-+..|-|.||+| +|++||.-+.+
T Consensus 36 dlgeV~L~PgTGG~FeI~~dg~~iWe 61 (99)
T COG3526 36 DLGEVALIPGTGGVFEITCDGVLIWE 61 (99)
T ss_pred hhheEEEecCCCceEEEEECCEEEEE
Confidence 356789999998 58899988765
No 50
>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein.
Probab=33.17 E-value=28 Score=32.66 Aligned_cols=28 Identities=39% Similarity=0.501 Sum_probs=18.6
Q ss_pred eecEEEEEecCCcc-chHHHHHHHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHT-SQIYAIRQSIAKALVA 96 (148)
Q Consensus 67 ~~di~i~V~GGG~s-gQa~AIr~aiAraL~~ 96 (148)
.+|-.+.-.|.-.| || .=|+||||||+.
T Consensus 606 GldT~ige~G~~LSGGQ--kQRlalARALl~ 634 (711)
T TIGR00958 606 GYDTEVGEKGSQLSGGQ--KQRIAIARALVR 634 (711)
T ss_pred ccCCcccCCCCcCCHHH--HHHHHHHHHHhc
Confidence 46765554444454 44 559999999986
No 51
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=32.63 E-value=27 Score=23.22 Aligned_cols=53 Identities=23% Similarity=0.333 Sum_probs=33.5
Q ss_pred ccccceecEEEEEecCCccchHHHHHHHHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceecc
Q 032049 62 RHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVAD 125 (148)
Q Consensus 62 ~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D 125 (148)
.+.|+.++|.+.+.|++++.+..+=.......|-... +.|+..|.+ .|+-..+
T Consensus 21 p~~LG~v~v~l~~~~~~l~v~~~~~~~~~~~~L~~~~---------~~L~~~L~~--~G~~~~~ 73 (85)
T PF02120_consen 21 PPELGSVEVKLRLQGGNLSVQFTAENPETKELLRQNL---------PELKERLQA--QGLEVVN 73 (85)
T ss_dssp SGGG--EEEEEEEETTEEEEEEE--SSHHHHHHHHTH---------HHHHHHHHT--TT-EEEE
T ss_pred ccccCcEEEEEEEeCCEEEEEEEECCHHHHHHHHHHH---------HHHHHHHHH--CCCCeEE
Confidence 3457999999999999999998887777777776542 245555544 3665443
No 52
>COG4531 ZnuA ABC-type Zn2+ transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]
Probab=32.41 E-value=18 Score=31.32 Aligned_cols=49 Identities=22% Similarity=0.225 Sum_probs=39.5
Q ss_pred chHHHHHHHHHHHHHHhhhhcCChhhHHHHHHHhhhcCCCceeccCCCcccCCC
Q 032049 81 SQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKF 134 (148)
Q Consensus 81 gQa~AIr~aiAraL~~~~~~~~~~~~~~~Lk~~l~~yd~glLt~D~R~~ERKK~ 134 (148)
+-+.++..+|+..|.+. ||+.+..+..+|++|++.|--.|--.+|.=||
T Consensus 158 ~~ak~~A~~i~~~L~e~-----dp~~~a~y~aNlk~f~~~La~~d~~i~~~L~p 206 (318)
T COG4531 158 AIAKAVAAAIAKKLAEL-----DPQNAAKYDANLKDFEAQLAALDKKVGEELAP 206 (318)
T ss_pred hHHHHHHHHHHHHHHhh-----ChhhHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 56788999999999986 78889999999999988777777666665443
No 53
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=31.91 E-value=47 Score=29.60 Aligned_cols=49 Identities=22% Similarity=0.302 Sum_probs=29.8
Q ss_pred HHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHH-HHHHHHHHHHh
Q 032049 47 EILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAI-RQSIAKALVAF 97 (148)
Q Consensus 47 ~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AI-r~aiAraL~~~ 97 (148)
+..-..|..-|...+.. ..+|+.|.++|||-..==-+. -..+||||..+
T Consensus 169 ~~a~~~i~~al~~~~~~--~~~dviii~RGGGs~eDL~~Fn~e~~~rai~~~ 218 (432)
T TIGR00237 169 EGAVQSIVESIELANTK--NECDVLIVGRGGGSLEDLWSFNDEKVARAIFLS 218 (432)
T ss_pred ccHHHHHHHHHHHhhcC--CCCCEEEEecCCCCHHHhhhcCcHHHHHHHHcC
Confidence 34455677778766643 569999999999965321111 13455555443
No 54
>PF06905 FAIM1: Fas apoptotic inhibitory molecule (FAIM1); InterPro: IPR010695 This family consists of several fas apoptotic inhibitory molecule (FAIM) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology [].; GO: 0043066 negative regulation of apoptosis; PDB: 3MX7_A 2KW1_A 2KD2_A.
Probab=31.21 E-value=61 Score=25.93 Aligned_cols=35 Identities=14% Similarity=0.210 Sum_probs=20.1
Q ss_pred eEEEeeeccceEEEEEEE--eCce---eEEEcCeeccccCC
Q 032049 11 SVQCFGRKKTAVAVTYCK--RGRG---LIKINGCPIELVEP 46 (148)
Q Consensus 11 ~v~~~GrRKta~A~v~l~--~G~G---~I~INg~~l~~y~~ 46 (148)
-.+.+|.+++ .|.+.+. +|.. .+.|||+|++.|..
T Consensus 53 e~F~ig~~~~-k~~I~I~~~~g~~YeYsL~VdGksl~ky~e 92 (177)
T PF06905_consen 53 ETFTIGGKNT-KCEINIEAVSGFAYEYSLEVDGKSLKKYKE 92 (177)
T ss_dssp EEEEETTTTE-EEEEEEEEETTTEEEEEEEETTEEEEE--S
T ss_pred cEEEECCCce-EEEEEEEecCCceEEEEEEECCEEHHHHHH
Confidence 3456776533 3444444 4432 47899999999854
No 55
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=30.95 E-value=29 Score=32.23 Aligned_cols=48 Identities=25% Similarity=0.360 Sum_probs=31.2
Q ss_pred eecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 67 GVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 67 ~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
.||..+.-.|..+| ||.+ |+||||||+.- |. -.|++....+.+.|.++
T Consensus 600 gldt~i~e~G~~LSgGQrQ--RialARall~~-p~iliLDE~Ts~LD~~te~~i~~~L~~~ 657 (708)
T TIGR01193 600 GYQTELSEEGSSISGGQKQ--RIALARALLTD-SKVLILDESTSNLDTITEKKIVNNLLNL 657 (708)
T ss_pred ccCcEecCCCCCCCHHHHH--HHHHHHHHhhC-CCEEEEeCccccCCHHHHHHHHHHHHHh
Confidence 56766655565666 4544 88999999863 32 23666666777766654
No 56
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=30.89 E-value=35 Score=30.81 Aligned_cols=49 Identities=24% Similarity=0.306 Sum_probs=31.9
Q ss_pred ceecEEEEEecCCcc-chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 66 AGVDMRIRVKGGGHT-SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 66 ~~~di~i~V~GGG~s-gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
+.||-.|--+|..+| ||. =|+||||||+.- |+ ..|++....+.+.|.+.
T Consensus 473 ~G~dT~vge~G~~LSGGQr--QRialARAll~~-~~IliLDE~TSaLD~~te~~i~~~l~~~ 531 (588)
T PRK11174 473 QGLDTPIGDQAAGLSVGQA--QRLALARALLQP-CQLLLLDEPTASLDAHSEQLVMQALNAA 531 (588)
T ss_pred cccccccccCCCCCCHHHH--HHHHHHHHHhcC-CCEEEEeCCccCCCHHHHHHHHHHHHHH
Confidence 356776666666677 454 499999999863 33 23666666666666553
No 57
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=30.83 E-value=1.4e+02 Score=27.87 Aligned_cols=64 Identities=17% Similarity=0.116 Sum_probs=38.6
Q ss_pred ceeEEEcCeeccccCCHHHHHHHHhHHH-HhcccccceecEEEEEecCCccchHHHHHHHHHHHHHHh
Q 032049 31 RGLIKINGCPIELVEPEILRFKAYEPIL-LLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAF 97 (148)
Q Consensus 31 ~G~I~INg~~l~~y~~~~~r~~i~~PL~-~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~ 97 (148)
.|.+.+.|.+-...... .+.+..-|. ..+. .+..+||+|++.+|..--.-.+.-+|||-||+..
T Consensus 450 ~g~~~~~Gl~g~~~kEs--~~~~~a~l~~~~~~-~~~~~~i~I~l~~~~~~k~G~sadlaia~AilSa 514 (608)
T TIGR00764 450 EGRIIATGKLGEIAKEA--VTNVSALIKKYTGE-DISNYDIHIQFLQTYEGVEGDSASISVATAVISA 514 (608)
T ss_pred CceEEEecCcHHHHHHH--HHHHHHHHHHhhCC-CCCCceEEEEeCCCCCCCCCCchHHHHHHHHHHH
Confidence 46677777543333211 122333333 4554 3689999999987776555556677777777765
No 58
>PF09428 DUF2011: Fungal protein of unknown function (DUF2011); InterPro: IPR018555 This is a family of fungal proteins whose function is unknown.
Probab=29.25 E-value=18 Score=27.45 Aligned_cols=22 Identities=9% Similarity=0.039 Sum_probs=18.3
Q ss_pred EEEEeCc-eeEEEcCeeccccCC
Q 032049 25 TYCKRGR-GLIKINGCPIELVEP 46 (148)
Q Consensus 25 v~l~~G~-G~I~INg~~l~~y~~ 46 (148)
|.|.+-+ |.+.+|.+|.++||.
T Consensus 2 I~Lreps~~~~i~~~RP~sYYfa 24 (131)
T PF09428_consen 2 ISLREPSPEEFIVNERPLSYYFA 24 (131)
T ss_pred ceecCCCCCccccCCCCCcceeC
Confidence 5677666 899999999999984
No 59
>PRK06617 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated
Probab=28.51 E-value=41 Score=28.47 Aligned_cols=19 Identities=16% Similarity=0.235 Sum_probs=15.4
Q ss_pred EEEEecCCccchHHHHHHH
Q 032049 71 RIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 71 ~i~V~GGG~sgQa~AIr~a 89 (148)
+|.|-|||++|.+-|+.++
T Consensus 3 dV~IvGgG~~Gl~~A~~L~ 21 (374)
T PRK06617 3 NTVILGCGLSGMLTALSFA 21 (374)
T ss_pred cEEEECCCHHHHHHHHHHH
Confidence 3577899999999887664
No 60
>COG4104 Uncharacterized conserved protein [Function unknown]
Probab=28.33 E-value=49 Score=24.20 Aligned_cols=18 Identities=33% Similarity=0.510 Sum_probs=15.0
Q ss_pred EEEEeCceeEEEcCeecc
Q 032049 25 TYCKRGRGLIKINGCPIE 42 (148)
Q Consensus 25 v~l~~G~G~I~INg~~l~ 42 (148)
..+.+|+-.+.|||+|+.
T Consensus 58 ~~I~~Gs~tv~InGkpaA 75 (98)
T COG4104 58 CVIAEGSSTVKINGKPAA 75 (98)
T ss_pred CeEEeccceEEECCEEeE
Confidence 347789999999999975
No 61
>TIGR01424 gluta_reduc_2 glutathione-disulfide reductase, plant. The tripeptide glutathione is an important reductant, e.g., for maintaining the cellular thiol/disulfide status and for protecting against reactive oxygen species such as hydrogen peroxide. Glutathione-disulfide reductase regenerates reduced glutathione from oxidized glutathione (glutathione disulfide) + NADPH. This model represents one of two closely related subfamilies of glutathione-disulfide reductase. Both are closely related to trypanothione reductase, and separate models are built so each of the three can describe proteins with conserved function. This model describes glutathione-disulfide reductases of plants and some bacteria, including cyanobacteria.
Probab=28.33 E-value=44 Score=29.23 Aligned_cols=22 Identities=23% Similarity=0.119 Sum_probs=17.8
Q ss_pred cEEEEEecCCccchHHHHHHHH
Q 032049 69 DMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 69 di~i~V~GGG~sgQa~AIr~ai 90 (148)
|.++.|=|||..|-+-|++.|-
T Consensus 2 ~yDvvVIG~GpaG~~aA~~aa~ 23 (446)
T TIGR01424 2 DYDLFVIGAGSGGVRAARLAAN 23 (446)
T ss_pred cccEEEECCCHHHHHHHHHHHh
Confidence 3445788999999999998873
No 62
>TIGR00255 conserved hypothetical protein TIGR00255. The apparent ortholog from Aquifex aeolicus as reported is split into two consecutive reading frames.
Probab=28.33 E-value=1.8e+02 Score=24.86 Aligned_cols=81 Identities=15% Similarity=0.146 Sum_probs=41.5
Q ss_pred CceEEEeeeccceEEEEEEEeCceeE-----EEcCeeccccC--CHHHH--HHHHhHHHHhcccccceecEEEEEecCCc
Q 032049 9 VESVQCFGRKKTAVAVTYCKRGRGLI-----KINGCPIELVE--PEILR--FKAYEPILLLGRHRFAGVDMRIRVKGGGH 79 (148)
Q Consensus 9 ~~~v~~~GrRKta~A~v~l~~G~G~I-----~INg~~l~~y~--~~~~r--~~i~~PL~~~~~~~~~~~di~i~V~GGG~ 79 (148)
++++.++|+--.+. +.+.+ .||++-++..+ |..+. +.-+.-+.--... -+++|++++++..+.
T Consensus 2 i~SMTGfgr~~~~~-------~~~~~~vEikSVN~R~Ldi~~rlP~~l~~lE~~ir~~i~~~l~-RGkV~v~i~~~~~~~ 73 (291)
T TIGR00255 2 IRSMTGFARLEKKI-------DWGSASVELKSVNQRFLEFKFRLPEQFRGLELDLRELIRQYIT-RGKIECFLRVEYKEL 73 (291)
T ss_pred CCCccCcCceeEec-------CCeEEEEEEEecccCceeeeeeCCHHHHHHHHHHHHHHHHhcc-CceEEEEEEEEEcCc
Confidence 46777888754331 12222 27999887642 43322 1111111111122 289999999985443
Q ss_pred cchHHHHHHHHHHHHHHh
Q 032049 80 TSQIYAIRQSIAKALVAF 97 (148)
Q Consensus 80 sgQa~AIr~aiAraL~~~ 97 (148)
....-.|-..+++++...
T Consensus 74 ~~~~~~id~~l~~~y~~~ 91 (291)
T TIGR00255 74 VPSELFLNNPLAIEAISA 91 (291)
T ss_pred CCCCcccCHHHHHHHHHH
Confidence 333334556666665543
No 63
>PRK11820 hypothetical protein; Provisional
Probab=27.55 E-value=2.1e+02 Score=24.43 Aligned_cols=81 Identities=19% Similarity=0.256 Sum_probs=41.8
Q ss_pred CceEEEeeeccceEEEEEEEeCceeEE-----EcCeeccccC--CHHHH--HHHHhHHHHhcccccceecEEEEEecCCc
Q 032049 9 VESVQCFGRKKTAVAVTYCKRGRGLIK-----INGCPIELVE--PEILR--FKAYEPILLLGRHRFAGVDMRIRVKGGGH 79 (148)
Q Consensus 9 ~~~v~~~GrRKta~A~v~l~~G~G~I~-----INg~~l~~y~--~~~~r--~~i~~PL~~~~~~~~~~~di~i~V~GGG~ 79 (148)
++++.++|+--.+ .+.+.++ ||++-++..+ |..+. +.-+.-+.--... -+++||.++++.-+.
T Consensus 2 i~SMTGfgr~~~~-------~~~~~~~vEikSVN~R~Ldi~~rlP~~~~~lE~~ir~~i~~~~~-RGkV~v~v~~~~~~~ 73 (288)
T PRK11820 2 IKSMTGFGRAEIK-------GEWGSVTVELRSVNHRYLDLNFRLPEQLRSLEPELRERIRKRLS-RGKVEVSLRLERDES 73 (288)
T ss_pred CCCccCcCeeeEe-------cCCeEEEEEEeecccCceeeeeeCCHHHHHHHHHHHHHHHHhCc-CceEEEEEEEEECCC
Confidence 4677788875433 1122332 7999887642 43322 1111111111122 289999999985543
Q ss_pred cchHHHHHHHHHHHHHHh
Q 032049 80 TSQIYAIRQSIAKALVAF 97 (148)
Q Consensus 80 sgQa~AIr~aiAraL~~~ 97 (148)
....-.+-.++++++...
T Consensus 74 ~~~~~~vd~~l~~~y~~~ 91 (288)
T PRK11820 74 AQGELSLNEDLAKQYLEA 91 (288)
T ss_pred ccCCcccCHHHHHHHHHH
Confidence 333334566666665543
No 64
>PRK06185 hypothetical protein; Provisional
Probab=27.26 E-value=42 Score=28.35 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=17.0
Q ss_pred ceecEEEEEecCCccchHHHHHHH
Q 032049 66 AGVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 66 ~~~di~i~V~GGG~sgQa~AIr~a 89 (148)
..+| |.|-|||++|-+-|+.++
T Consensus 5 ~~~d--V~IvGgG~~Gl~~A~~La 26 (407)
T PRK06185 5 ETTD--CCIVGGGPAGMMLGLLLA 26 (407)
T ss_pred cccc--EEEECCCHHHHHHHHHHH
Confidence 3556 467899999999887764
No 65
>PRK11823 DNA repair protein RadA; Provisional
Probab=27.21 E-value=1.2e+02 Score=27.11 Aligned_cols=47 Identities=21% Similarity=0.225 Sum_probs=34.1
Q ss_pred HHHHHhHH--HHhcccccceecEEEEEecCCccchHHHHHHHHHHHHHHhh
Q 032049 50 RFKAYEPI--LLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFY 98 (148)
Q Consensus 50 r~~i~~PL--~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~ 98 (148)
|-.++..+ .-.+.. +...||+|++- ||+-=+--|.-+|||-||+.-.
T Consensus 323 Rv~~~~Avl~~~~g~~-~~~~~i~vnla-~~~~k~g~~~DLaIa~ailsa~ 371 (446)
T PRK11823 323 RLAMLLAVLEKRLGLP-LGDQDVYVNVV-GGLKITEPAADLAVALAIASSL 371 (446)
T ss_pred HHHHHHHHHHHHcCCC-CCCccEEEEcc-CCcccCCccccHHHHHHHHHhc
Confidence 43334555 455653 68999999999 7777666688889998888753
No 66
>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]
Probab=26.95 E-value=79 Score=26.30 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=11.7
Q ss_pred EeCceeEEEcCeecc
Q 032049 28 KRGRGLIKINGCPIE 42 (148)
Q Consensus 28 ~~G~G~I~INg~~l~ 42 (148)
.|..|+|.+||.++.
T Consensus 53 ~pt~G~i~~~~~dl~ 67 (223)
T COG2884 53 RPTRGKILVNGHDLS 67 (223)
T ss_pred cCCCceEEECCeecc
Confidence 356799999998763
No 67
>PF01808 AICARFT_IMPCHas: AICARFT/IMPCHase bienzyme; InterPro: IPR002695 This is a family of bifunctional enzymes catalysing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalysed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase 2.1.2.3 from EC (AICARFT), this enzyme catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate []. The last step is catalysed by IMP (Inosine monophosphate) cyclohydrolase 3.5.4.10 from EC (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP [].; GO: 0003937 IMP cyclohydrolase activity, 0004643 phosphoribosylaminoimidazolecarboxamide formyltransferase activity, 0006164 purine nucleotide biosynthetic process; PDB: 1ZCZ_A 1PL0_D 1PKX_C 1P4R_B 1G8M_B 2IU3_B 2B1I_A 2B1G_D 1OZ0_B 1M9N_B ....
Probab=26.42 E-value=44 Score=29.03 Aligned_cols=43 Identities=21% Similarity=0.136 Sum_probs=32.1
Q ss_pred HHHHHHHhHHHHhcccccceecEEEEEe-------cCCccchHHHHHHHHHHH
Q 032049 48 ILRFKAYEPILLLGRHRFAGVDMRIRVK-------GGGHTSQIYAIRQSIAKA 93 (148)
Q Consensus 48 ~~r~~i~~PL~~~~~~~~~~~di~i~V~-------GGG~sgQa~AIr~aiAra 93 (148)
...+.++.-+.++. +-+=|-.|.++ |.|++...+|+++|+.||
T Consensus 266 ~e~~dL~FAwkv~k---~vKSNAIv~ak~~~tvGIGaGQ~sRVda~~iA~~KA 315 (315)
T PF01808_consen 266 EELEDLLFAWKVVK---HVKSNAIVLAKDGQTVGIGAGQMSRVDAARIAIEKA 315 (315)
T ss_dssp HHHHHHHHHHHHHH---CSSSSEEEEEETTEEEEEEESSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHh---hcccceEEEEeCCeEEEeCCCCcchHHHHHHHHhhC
Confidence 34556777777764 24556666665 889999999999999886
No 68
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=26.41 E-value=19 Score=26.53 Aligned_cols=11 Identities=27% Similarity=0.341 Sum_probs=9.3
Q ss_pred eEEEcCeeccc
Q 032049 33 LIKINGCPIEL 43 (148)
Q Consensus 33 ~I~INg~~l~~ 43 (148)
.+.|||+|+..
T Consensus 51 ~~fVNgR~V~~ 61 (127)
T cd03483 51 ILFINNRLVEC 61 (127)
T ss_pred EEEEcCCEecC
Confidence 48899999975
No 69
>PTZ00367 squalene epoxidase; Provisional
Probab=26.38 E-value=77 Score=29.32 Aligned_cols=39 Identities=15% Similarity=0.146 Sum_probs=25.5
Q ss_pred HHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHH
Q 032049 49 LRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 49 ~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~a 89 (148)
+.+.++.=+..... ..+.+.+|.|-|||+.|-+-|+.++
T Consensus 15 ~~~~~~~~~~~~~~--~~~~~~dViIVGaGiaGlalA~aLa 53 (567)
T PTZ00367 15 LLNRILSRLRFKPA--RTNYDYDVIIVGGSIAGPVLAKALS 53 (567)
T ss_pred HHHHHHHHHccCcc--ccccCccEEEECCCHHHHHHHHHHH
Confidence 34455555555332 2345666788999999999876654
No 70
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=26.19 E-value=37 Score=20.27 Aligned_cols=13 Identities=31% Similarity=0.549 Sum_probs=11.1
Q ss_pred ceeEEEcCeeccc
Q 032049 31 RGLIKINGCPIEL 43 (148)
Q Consensus 31 ~G~I~INg~~l~~ 43 (148)
.|.|+|||+.+.+
T Consensus 25 ~g~V~VNg~~v~~ 37 (48)
T PF01479_consen 25 QGRVKVNGKVVKD 37 (48)
T ss_dssp TTTEEETTEEESS
T ss_pred CCEEEECCEEEcC
Confidence 5889999999874
No 71
>PRK08849 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional
Probab=25.97 E-value=49 Score=28.04 Aligned_cols=19 Identities=32% Similarity=0.382 Sum_probs=15.9
Q ss_pred EEEecCCccchHHHHHHHH
Q 032049 72 IRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 72 i~V~GGG~sgQa~AIr~ai 90 (148)
|.|-|||++|-+-|+.++-
T Consensus 6 v~IvGgG~aGl~~A~~L~~ 24 (384)
T PRK08849 6 IAVVGGGMVGAATALGFAK 24 (384)
T ss_pred EEEECcCHHHHHHHHHHHh
Confidence 5788999999999987753
No 72
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=25.59 E-value=1.7e+02 Score=26.81 Aligned_cols=68 Identities=22% Similarity=0.175 Sum_probs=46.3
Q ss_pred EEeCceeEEEcCeeccccCCHHHHHHHHhHHHHhcccccceecEEEEEecCCccchHHHHHHHHHHHHHHh
Q 032049 27 CKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAF 97 (148)
Q Consensus 27 l~~G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~~ 97 (148)
+.+|-+.+.|=|.|-... ..-++.|...|.=.+.. +...||+|++--||+-=.--+.=+|||-||+.-
T Consensus 20 ~~~Glp~f~ivGl~d~~v--~Es~erVr~al~n~g~~-~p~~~I~VNlaPggl~k~g~~~DLaIA~ailsa 87 (499)
T TIGR00368 20 ISKGLPGITIVGLPETTV--KESRERVKSAIKNSGFH-FPAKRITINLAPADLPKEGGRFDLPIAIGILAA 87 (499)
T ss_pred EcCCCcceEEecCcHHHH--HHHHHHHHHHHHhcCCC-CCCeeEEEEecCCCeeccCccccHHHHHHHHHh
Confidence 334544566656554322 12345577777777774 789999999987887766667788888888765
No 73
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=25.57 E-value=43 Score=20.26 Aligned_cols=10 Identities=40% Similarity=0.408 Sum_probs=8.2
Q ss_pred ceeEEEcCee
Q 032049 31 RGLIKINGCP 40 (148)
Q Consensus 31 ~G~I~INg~~ 40 (148)
.|++.|||+=
T Consensus 23 pG~ViING~C 32 (36)
T PF08194_consen 23 PGNVIINGKC 32 (36)
T ss_pred CCeEEECcee
Confidence 5899999974
No 74
>PRK08013 oxidoreductase; Provisional
Probab=25.33 E-value=43 Score=28.61 Aligned_cols=22 Identities=27% Similarity=0.336 Sum_probs=16.9
Q ss_pred eecEEEEEecCCccchHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~ai 90 (148)
.|| |.|-|||++|.+-|+.++-
T Consensus 3 ~~d--V~IvGaGpaGl~~A~~La~ 24 (400)
T PRK08013 3 SVD--VVIAGGGMVGLAVACGLQG 24 (400)
T ss_pred cCC--EEEECcCHHHHHHHHHHhh
Confidence 455 4778999999998877643
No 75
>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.
Probab=24.78 E-value=23 Score=25.87 Aligned_cols=11 Identities=18% Similarity=0.223 Sum_probs=9.2
Q ss_pred eEEEcCeeccc
Q 032049 33 LIKINGCPIEL 43 (148)
Q Consensus 33 ~I~INg~~l~~ 43 (148)
-|.|||+|+..
T Consensus 47 ~ifVN~R~V~~ 57 (123)
T cd03482 47 YFYVNGRMVRD 57 (123)
T ss_pred EEEEcCcEECC
Confidence 48899999874
No 76
>COG0644 FixC Dehydrogenases (flavoproteins) [Energy production and conversion]
Probab=24.35 E-value=64 Score=27.70 Aligned_cols=23 Identities=26% Similarity=0.286 Sum_probs=18.3
Q ss_pred eecEEEEEecCCccchHHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSIA 91 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~aiA 91 (148)
.|| |.|-|+|++|-+-|+++|=+
T Consensus 3 ~~D--VvIVGaGPAGs~aA~~la~~ 25 (396)
T COG0644 3 EYD--VVIVGAGPAGSSAARRLAKA 25 (396)
T ss_pred eee--EEEECCchHHHHHHHHHHHc
Confidence 455 47789999999998887755
No 77
>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein. This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.
Probab=24.10 E-value=44 Score=29.95 Aligned_cols=50 Identities=20% Similarity=0.197 Sum_probs=27.0
Q ss_pred eecEEEEEecCCccchHHHHHHHHHHHHHHhhhh--------cCChhhHHHHHHHhhhc
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK--------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~--------~~~~~~~~~Lk~~l~~y 117 (148)
.+|..+.-.|--.|| -+.=|++|||||+.--+- -.|++.+..+.+.|.+.
T Consensus 465 gl~t~i~~~g~~LSg-Gq~Qrl~laRal~~~~~ililDEpts~lD~~~~~~i~~~l~~~ 522 (576)
T TIGR02204 465 GYDTYLGERGVTLSG-GQRQRIAIARAILKDAPILLLDEATSALDAESEQLVQQALETL 522 (576)
T ss_pred CCCceeCCCCCcCCH-HHHHHHHHHHHHHhCCCeEEEeCcccccCHHHHHHHHHHHHHH
Confidence 345443222333432 346699999999863211 23666666666555543
No 78
>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
Probab=23.86 E-value=49 Score=30.72 Aligned_cols=49 Identities=31% Similarity=0.456 Sum_probs=32.4
Q ss_pred ceecEEEEEecCCccc-hHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 66 AGVDMRIRVKGGGHTS-QIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 66 ~~~di~i~V~GGG~sg-Qa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
..||-.+.-.|...|| | -=|+||||||+.- |+ -.|++....+.+.|.+.
T Consensus 589 ~gl~T~i~e~G~~LSgGQ--rQRlalARall~~-p~iliLDE~Ts~LD~~te~~i~~~l~~~ 647 (694)
T TIGR03375 589 DGLDMQIGERGRSLSGGQ--RQAVALARALLRD-PPILLLDEPTSAMDNRSEERFKDRLKRW 647 (694)
T ss_pred ccccceecCCCCCCCHHH--HHHHHHHHHHhcC-CCEEEEeCCCCCCCHHHHHHHHHHHHHH
Confidence 3577766656666664 5 4599999999863 33 23666777777776654
No 79
>TIGR02032 GG-red-SF geranylgeranyl reductase family. This model represents a subfamily which includes geranylgeranyl reductases involved in chlorophyll and bacteriochlorophyll biosynthesis as well as other related enzymes which may also act on geranylgeranyl groups or related substrates.
Probab=23.85 E-value=52 Score=25.83 Aligned_cols=18 Identities=28% Similarity=0.337 Sum_probs=15.0
Q ss_pred EEEecCCccchHHHHHHH
Q 032049 72 IRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 72 i~V~GGG~sgQa~AIr~a 89 (148)
|.|-|||++|-+-|+.++
T Consensus 3 v~IiGaG~aGl~~A~~l~ 20 (295)
T TIGR02032 3 VVVVGAGPAGASAAYRLA 20 (295)
T ss_pred EEEECCCHHHHHHHHHHH
Confidence 577899999999887764
No 80
>PRK08163 salicylate hydroxylase; Provisional
Probab=23.60 E-value=61 Score=27.22 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=16.3
Q ss_pred EEEEEecCCccchHHHHHHH
Q 032049 70 MRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 70 i~i~V~GGG~sgQa~AIr~a 89 (148)
..|.|-|||++|-+-|+.++
T Consensus 5 ~~V~IvGaGiaGl~~A~~L~ 24 (396)
T PRK08163 5 TPVLIVGGGIGGLAAALALA 24 (396)
T ss_pred CeEEEECCcHHHHHHHHHHH
Confidence 45688899999999887764
No 81
>COG1148 HdrA Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]
Probab=23.43 E-value=61 Score=30.53 Aligned_cols=34 Identities=24% Similarity=0.348 Sum_probs=24.1
Q ss_pred HHHhHHHHhcccccceecEEEEEecCCccchHHHHHHH
Q 032049 52 KAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 52 ~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr~a 89 (148)
..++||+-.. -..+=.+.|-|||++|-.-|+-+|
T Consensus 111 r~le~le~~~----~~v~~svLVIGGGvAGitAAl~La 144 (622)
T COG1148 111 RKLEPLEEIK----VEVSKSVLVIGGGVAGITAALELA 144 (622)
T ss_pred hhcCChhhHH----HhhccceEEEcCcHHHHHHHHHHH
Confidence 3466776543 244556889999999998877665
No 82
>PRK06996 hypothetical protein; Provisional
Probab=23.30 E-value=53 Score=28.02 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=17.7
Q ss_pred eecEEEEEecCCccchHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~ai 90 (148)
.+| |.|-|||++|.+-|+.++-
T Consensus 11 ~~d--v~IvGgGpaG~~~A~~L~~ 32 (398)
T PRK06996 11 DFD--IAIVGAGPVGLALAGWLAR 32 (398)
T ss_pred CCC--EEEECcCHHHHHHHHHHhc
Confidence 455 5778999999999988764
No 83
>PRK06753 hypothetical protein; Provisional
Probab=23.11 E-value=63 Score=26.91 Aligned_cols=19 Identities=21% Similarity=0.204 Sum_probs=15.7
Q ss_pred EEEEecCCccchHHHHHHH
Q 032049 71 RIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 71 ~i~V~GGG~sgQa~AIr~a 89 (148)
.|.|-|||++|-+-|+.++
T Consensus 2 ~V~IvGgG~aGl~~A~~L~ 20 (373)
T PRK06753 2 KIAIIGAGIGGLTAAALLQ 20 (373)
T ss_pred EEEEECCCHHHHHHHHHHH
Confidence 4678899999999887764
No 84
>PRK08773 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Validated
Probab=22.89 E-value=54 Score=27.70 Aligned_cols=21 Identities=24% Similarity=0.336 Sum_probs=16.6
Q ss_pred eecEEEEEecCCccchHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~a 89 (148)
.+| |.|-|||++|-+-|+.++
T Consensus 6 ~~d--V~IvGaG~aGl~~A~~La 26 (392)
T PRK08773 6 RRD--AVIVGGGVVGAACALALA 26 (392)
T ss_pred CCC--EEEECcCHHHHHHHHHHh
Confidence 455 577899999999887764
No 85
>PF03764 EFG_IV: Elongation factor G, domain IV; InterPro: IPR005517 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, appears to be essential for the structural transition to take place. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3J0E_H 1FNM_A 3IZP_E 2OM7_L 1KTV_A 2J7K_A 2BM1_A 2BM0_A 2BV3_A 1ZM3_E ....
Probab=22.65 E-value=2.8e+02 Score=19.46 Aligned_cols=76 Identities=16% Similarity=0.128 Sum_probs=42.0
Q ss_pred ceEEEEEEE--e--CceeEEEcCeeccccCCHHHHHHHHhHHHHh---ccc-ccceecEEEEEecCCc---cchHHHHHH
Q 032049 20 TAVAVTYCK--R--GRGLIKINGCPIELVEPEILRFKAYEPILLL---GRH-RFAGVDMRIRVKGGGH---TSQIYAIRQ 88 (148)
Q Consensus 20 ta~A~v~l~--~--G~G~I~INg~~l~~y~~~~~r~~i~~PL~~~---~~~-~~~~~di~i~V~GGG~---sgQa~AIr~ 88 (148)
.-.|++.+. | |+|.+.+|..+...+.. .++..|.+=+.-. |.. .+--.||.|++..+-. ..-..|++.
T Consensus 28 ~~~a~v~~~~~P~~~~~~~~~~~~~~~~l~~-~~~~ai~~G~~~a~~~Gpl~g~pv~~v~v~l~~~~~~~~~s~~~a~~~ 106 (120)
T PF03764_consen 28 RQFAKVILRVEPLEGGGNIFVDETEGGQLPK-EFQDAIEEGFQSALSSGPLCGYPVTDVKVTLTDGEYHEVDSSPGAFRA 106 (120)
T ss_dssp EEEEEEEEEEEETSTSSEEEEESSSTTSSGG-GGHHHHHHHHHHHHCSSTTTSSEB-SEEEEEEEEEC-TTTBSHHHHHH
T ss_pred CceEEEEEEEeecccCCceeeeccccccccH-HHHHHHhhhhhheecccccCCCceEEEEEEEEEeeecCCcCCHHHHHH
Confidence 344555554 4 56899999987554432 2222233323211 111 1245678888766553 233678888
Q ss_pred HHHHHHHH
Q 032049 89 SIAKALVA 96 (148)
Q Consensus 89 aiAraL~~ 96 (148)
|.++|+-+
T Consensus 107 aa~~a~~~ 114 (120)
T PF03764_consen 107 AARRAFRE 114 (120)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88888765
No 86
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=22.55 E-value=55 Score=22.32 Aligned_cols=19 Identities=32% Similarity=0.434 Sum_probs=13.3
Q ss_pred eEEEcCeeccccCCHHHHH
Q 032049 33 LIKINGCPIELVEPEILRF 51 (148)
Q Consensus 33 ~I~INg~~l~~y~~~~~r~ 51 (148)
.|+|||++++-+....+.+
T Consensus 5 ~i~idG~~v~~~~G~til~ 23 (82)
T PF13510_consen 5 TITIDGKPVEVPPGETILE 23 (82)
T ss_dssp EEEETTEEEEEEET-BHHH
T ss_pred EEEECCEEEEEcCCCHHHH
Confidence 5889999998776654433
No 87
>TIGR03329 Phn_aa_oxid putative aminophosphonate oxidoreductase. This clade of sequences are members of the pfam01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW.
Probab=22.50 E-value=62 Score=28.41 Aligned_cols=25 Identities=24% Similarity=0.274 Sum_probs=19.2
Q ss_pred eecEEEEEecCCccchHHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSIA 91 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~aiA 91 (148)
..+.+|.|-|||++|-+-|..++=+
T Consensus 22 ~~~~DVvIIGgGi~Gls~A~~La~~ 46 (460)
T TIGR03329 22 DTQADVCIVGGGFTGLWTAIMIKQQ 46 (460)
T ss_pred CceeCEEEECCCHHHHHHHHHHHHh
Confidence 4445678889999999988887543
No 88
>COG4559 ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=22.36 E-value=49 Score=28.04 Aligned_cols=22 Identities=27% Similarity=0.492 Sum_probs=18.3
Q ss_pred EEEeCceeEEEcCeeccccCCH
Q 032049 26 YCKRGRGLIKINGCPIELVEPE 47 (148)
Q Consensus 26 ~l~~G~G~I~INg~~l~~y~~~ 47 (148)
.+.|.+|++.+||+++.++.+.
T Consensus 50 el~p~~G~v~~~g~~l~~~~~~ 71 (259)
T COG4559 50 ELSPDSGEVTLNGVPLNSWPPE 71 (259)
T ss_pred ccCCCCCeEeeCCcChhhCCHH
Confidence 3456789999999999999874
No 89
>PRK08020 ubiF 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed
Probab=22.26 E-value=64 Score=27.12 Aligned_cols=22 Identities=23% Similarity=0.422 Sum_probs=17.2
Q ss_pred ceecEEEEEecCCccchHHHHHHH
Q 032049 66 AGVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 66 ~~~di~i~V~GGG~sgQa~AIr~a 89 (148)
..||| .|-|||++|-+-|+.++
T Consensus 4 ~~~dV--iIvGgG~aGl~~A~~La 25 (391)
T PRK08020 4 QPTDI--AIVGGGMVGAALALGLA 25 (391)
T ss_pred ccccE--EEECcCHHHHHHHHHHh
Confidence 35665 66899999999887764
No 90
>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=22.15 E-value=60 Score=29.52 Aligned_cols=48 Identities=19% Similarity=0.219 Sum_probs=29.8
Q ss_pred ecEEEEEecCCccchHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 68 VDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 68 ~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
||-.+.-.|.-.| .-+.=|+||||||+. .|+ ..|++....+.+.|.++
T Consensus 465 ldT~vge~g~~LS-gGqrqRialARall~-~~~ililDE~ts~lD~~t~~~i~~~l~~~ 521 (574)
T PRK11160 465 LNAWLGEGGRQLS-GGEQRRLGIARALLH-DAPLLLLDEPTEGLDAETERQILELLAEH 521 (574)
T ss_pred cCchhcCCCCCCC-HHHHHHHHHHHHHhc-CCCEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 4544433333344 345669999999986 333 24677777787777665
No 91
>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=22.13 E-value=77 Score=24.64 Aligned_cols=36 Identities=25% Similarity=0.222 Sum_probs=23.2
Q ss_pred chHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 81 SQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 81 gQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
+.-+.-|.+|||||+.- |. -.|+..+..+.+.|.++
T Consensus 73 SgGq~qrv~laral~~~-p~lllLDEPts~LD~~~~~~l~~~l~~~ 117 (177)
T cd03222 73 SGGELQRVAIAAALLRN-ATFYLFDEPSAYLDIEQRLNAARAIRRL 117 (177)
T ss_pred CHHHHHHHHHHHHHhcC-CCEEEEECCcccCCHHHHHHHHHHHHHH
Confidence 33446799999999852 33 23666677666666554
No 92
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=22.02 E-value=1.3e+02 Score=26.47 Aligned_cols=32 Identities=28% Similarity=0.298 Sum_probs=25.7
Q ss_pred ccceecEEEEEecCCccchHHHHHHHHHHHHHH
Q 032049 64 RFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVA 96 (148)
Q Consensus 64 ~~~~~di~i~V~GGG~sgQa~AIr~aiAraL~~ 96 (148)
.+.+.||+++|-||=.. +--|+-+|||-||+.
T Consensus 340 ~~~~~dv~~~~~gg~~~-~e~~~dla~~~a~~s 371 (372)
T cd01121 340 PLADQDVFVNVAGGLKI-TEPAADLAVALAIVS 371 (372)
T ss_pred CccCCCEEEEccCCeec-cCcHHHHHHHHHHHc
Confidence 36899999999876555 666899999998874
No 93
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=22.02 E-value=1e+02 Score=20.94 Aligned_cols=32 Identities=31% Similarity=0.514 Sum_probs=22.1
Q ss_pred CCCCceEEEeeeccceEEEEEEEe----CceeEEEcC
Q 032049 6 AGPVESVQCFGRKKTAVAVTYCKR----GRGLIKING 38 (148)
Q Consensus 6 ~~~~~~v~~~GrRKta~A~v~l~~----G~G~I~INg 38 (148)
..+...+.-.|+|| ++|.|+-.. +.|.|.+|+
T Consensus 30 l~~gd~v~i~g~~~-tv~~v~~~~~~~~~~g~I~l~~ 65 (87)
T PF02359_consen 30 LFPGDVVLISGKRK-TVAFVFPDRPDDSPPGVIRLSG 65 (87)
T ss_dssp T-TTEEEEEETTTE-EEEEEEEECCSTTCTTEEEE-H
T ss_pred CCCccEEEEeCCce-EEEEEEECCCCCCCCCEEEECH
Confidence 44557788899777 778888763 468888876
No 94
>PRK10157 putative oxidoreductase FixC; Provisional
Probab=22.01 E-value=60 Score=28.33 Aligned_cols=22 Identities=18% Similarity=0.196 Sum_probs=18.1
Q ss_pred eecEEEEEecCCccchHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~ai 90 (148)
+||| .|-|||++|.+-|+.+|-
T Consensus 5 ~~DV--iIVGaGpAG~~aA~~La~ 26 (428)
T PRK10157 5 IFDA--IIVGAGLAGSVAALVLAR 26 (428)
T ss_pred cCcE--EEECcCHHHHHHHHHHHh
Confidence 5775 678999999999988764
No 95
>PF00475 IGPD: Imidazoleglycerol-phosphate dehydratase; InterPro: IPR000807 Imidazoleglycerol-phosphate dehydratase is the enzyme that catalyses the seventh step in the biosynthesis of histidine in bacteria, fungi and plants. In most organisms it is a monofunctional protein of about 22 to 29 kD. In some bacteria such as Escherichia coli, it is the C-terminal domain of a bifunctional protein that include a histidinol-phosphatase domain [].; GO: 0004424 imidazoleglycerol-phosphate dehydratase activity, 0000105 histidine biosynthetic process; PDB: 2F1D_G 2AE8_A 1RHY_B.
Probab=21.90 E-value=3.9e+02 Score=20.77 Aligned_cols=70 Identities=26% Similarity=0.236 Sum_probs=40.6
Q ss_pred ceEEEEEEE-eCceeEEEcCeecccc---CCHHHHHHHHhHHHHhcccccceecEEEEEe-cCCccchHHHHHHHHHHHH
Q 032049 20 TAVAVTYCK-RGRGLIKINGCPIELV---EPEILRFKAYEPILLLGRHRFAGVDMRIRVK-GGGHTSQIYAIRQSIAKAL 94 (148)
Q Consensus 20 ta~A~v~l~-~G~G~I~INg~~l~~y---~~~~~r~~i~~PL~~~~~~~~~~~di~i~V~-GGG~sgQa~AIr~aiAraL 94 (148)
+|.|+|.+- -|.+-...|+..-.+. ++-.+-+..++-|..- .+.++.+.+. |.-.-=+++|+--|++|||
T Consensus 70 EaL~~v~vDlsGRp~l~~~~~~~~~~iG~~~~el~~~F~~sla~~-----~~~tlHi~~~~G~N~HH~~Ea~FKa~grAL 144 (145)
T PF00475_consen 70 EALARVAVDLSGRPYLVFNGEFPREKIGDFDTELVEHFFRSLANN-----AGITLHIRVLYGENDHHIIEAIFKAFGRAL 144 (145)
T ss_dssp TEEEEEEEEESSS-EEEEE---SSSEETTEETTHHHHHHHHHHHH-----HTEEEEEEEEE-SSHHHHHHHHHHHHHHHH
T ss_pred hhhheeEEEecCCceEEEecccCccccCCCChhhHHHHHHHHHHh-----CCceEEEEEEeCCChHHHHHHHHHHHHHHh
Confidence 345555553 3444444443332222 1222334456656432 5788999998 8888889999999999997
No 96
>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=21.84 E-value=70 Score=24.15 Aligned_cols=34 Identities=21% Similarity=0.279 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 83 IYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 83 a~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
-+.-|.+||+||+.- |. -.|+..+..|.+.|.++
T Consensus 104 G~~qr~~la~al~~~-p~llilDEP~~~LD~~~~~~l~~~l~~~ 146 (178)
T cd03229 104 GQQQRVALARALAMD-PDVLLLDEPTSALDPITRREVRALLKSL 146 (178)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 346789999999863 33 13666777777766654
No 97
>PHA01748 hypothetical protein
Probab=21.84 E-value=1.2e+02 Score=19.69 Aligned_cols=18 Identities=33% Similarity=0.420 Sum_probs=13.7
Q ss_pred CccchHHHHHHHHHHHHHH
Q 032049 78 GHTSQIYAIRQSIAKALVA 96 (148)
Q Consensus 78 G~sgQa~AIr~aiAraL~~ 96 (148)
|. ..+++||.||-..+-.
T Consensus 25 g~-~RSE~Ir~Ai~~~~~~ 42 (60)
T PHA01748 25 GL-NRSEAIRKAIEKMVKD 42 (60)
T ss_pred CC-CHHHHHHHHHHHHHHH
Confidence 45 5999999999866544
No 98
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=21.60 E-value=44 Score=25.07 Aligned_cols=17 Identities=41% Similarity=0.464 Sum_probs=13.5
Q ss_pred CceeEEEcCeeccccCC
Q 032049 30 GRGLIKINGCPIELVEP 46 (148)
Q Consensus 30 G~G~I~INg~~l~~y~~ 46 (148)
.+=.|.|||+|++++..
T Consensus 61 ~S~~I~inG~piE~~l~ 77 (120)
T PF10865_consen 61 ESPTIRINGRPIEDLLG 77 (120)
T ss_pred CCCeeeECCEehhHhhC
Confidence 46689999999987643
No 99
>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.
Probab=21.58 E-value=58 Score=30.24 Aligned_cols=49 Identities=24% Similarity=0.246 Sum_probs=31.5
Q ss_pred eecEEEEEecCCccchHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
.+|-.+.-.|...|| =+-=|++|||||+.- |. -.|++.+..+.+.|.++
T Consensus 582 gl~t~i~~~g~~LSg-Gq~qri~lARall~~-~~ililDEpts~LD~~~~~~i~~~l~~~ 639 (694)
T TIGR01846 582 GYNTEVGEKGANLSG-GQRQRIAIARALVGN-PRILIFDEATSALDYESEALIMRNMREI 639 (694)
T ss_pred ccCcEecCCCCCCCH-HHHHHHHHHHHHHhC-CCEEEEECCCcCCCHHHHHHHHHHHHHH
Confidence 567666655555553 334589999999863 22 23666677777776655
No 100
>PRK08850 2-octaprenyl-6-methoxyphenol hydroxylase; Validated
Probab=21.32 E-value=57 Score=27.81 Aligned_cols=19 Identities=21% Similarity=0.296 Sum_probs=15.6
Q ss_pred EEEecCCccchHHHHHHHH
Q 032049 72 IRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 72 i~V~GGG~sgQa~AIr~ai 90 (148)
|.|-|||++|.+-|+.++-
T Consensus 7 V~IvGaG~~Gl~~A~~L~~ 25 (405)
T PRK08850 7 VAIIGGGMVGLALAAALKE 25 (405)
T ss_pred EEEECccHHHHHHHHHHHh
Confidence 5778999999999877643
No 101
>PRK07588 hypothetical protein; Provisional
Probab=21.26 E-value=72 Score=26.90 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=15.8
Q ss_pred EEEEecCCccchHHHHHHH
Q 032049 71 RIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 71 ~i~V~GGG~sgQa~AIr~a 89 (148)
.|.|-|||++|-+-|+.++
T Consensus 2 ~V~IVGgG~aGl~~A~~L~ 20 (391)
T PRK07588 2 KVAISGAGIAGPTLAYWLR 20 (391)
T ss_pred eEEEECccHHHHHHHHHHH
Confidence 3678899999999988765
No 102
>PF01494 FAD_binding_3: FAD binding domain; InterPro: IPR002938 Monooxygenases incorporate one hydroxyl group into substrates and are found in many metabolic pathways. In this reaction, two atoms of dioxygen are reduced to one hydroxyl group and one H2O molecule by the concomitant oxidation of NAD(P)H []. P-hydroxybenzoate hydroxylase from Pseudomonas fluorescens contains this sequence motif (present in in flavoprotein hydroxylases) with a putative dual function in FAD and NADPH binding [].; PDB: 2Y6R_B 2XYO_C 2Y6Q_C 3P9U_D 2XDO_C 1FOH_D 1PN0_A 3IHG_C 2QA2_A 2VOU_C ....
Probab=21.10 E-value=82 Score=25.17 Aligned_cols=19 Identities=16% Similarity=0.295 Sum_probs=11.6
Q ss_pred EEEEecCCccchHHHHHHH
Q 032049 71 RIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 71 ~i~V~GGG~sgQa~AIr~a 89 (148)
.|-|-|||++|-+-|+.++
T Consensus 3 dV~IvGaG~aGl~~A~~L~ 21 (356)
T PF01494_consen 3 DVAIVGAGPAGLAAALALA 21 (356)
T ss_dssp EEEEE--SHHHHHHHHHHH
T ss_pred eEEEECCCHHHHHHHHHHH
Confidence 3467899999987655443
No 103
>PRK07045 putative monooxygenase; Reviewed
Probab=21.05 E-value=80 Score=26.60 Aligned_cols=21 Identities=24% Similarity=0.291 Sum_probs=16.9
Q ss_pred eecEEEEEecCCccchHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~a 89 (148)
.|| |.|-|||++|-+-|+.++
T Consensus 5 ~~~--V~IiGgGpaGl~~A~~L~ 25 (388)
T PRK07045 5 PVD--VLINGSGIAGVALAHLLG 25 (388)
T ss_pred eeE--EEEECCcHHHHHHHHHHH
Confidence 455 578899999999887765
No 104
>PRK11445 putative oxidoreductase; Provisional
Probab=21.02 E-value=73 Score=26.77 Aligned_cols=18 Identities=17% Similarity=0.167 Sum_probs=14.9
Q ss_pred EEEecCCccchHHHHHHH
Q 032049 72 IRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 72 i~V~GGG~sgQa~AIr~a 89 (148)
|.|-|||++|-+-|+.+|
T Consensus 4 V~IvGaGpaGl~~A~~La 21 (351)
T PRK11445 4 VAIIGLGPAGSALARLLA 21 (351)
T ss_pred EEEECCCHHHHHHHHHHh
Confidence 578899999999987653
No 105
>PRK10015 oxidoreductase; Provisional
Probab=20.85 E-value=65 Score=28.23 Aligned_cols=22 Identities=23% Similarity=0.258 Sum_probs=17.5
Q ss_pred eecEEEEEecCCccchHHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSI 90 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~ai 90 (148)
.|| |.|-|||++|-+-|+.+|=
T Consensus 5 ~~D--ViIVGgGpAG~~aA~~LA~ 26 (429)
T PRK10015 5 KFD--AIVVGAGVAGSVAALVMAR 26 (429)
T ss_pred ccC--EEEECcCHHHHHHHHHHHh
Confidence 456 5788999999999888753
No 106
>PRK07364 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated
Probab=20.83 E-value=64 Score=27.30 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=16.7
Q ss_pred eecEEEEEecCCccchHHHHHHH
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQS 89 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~a 89 (148)
.|| |.|-|||++|-+-|+.++
T Consensus 18 ~~d--V~IvGaG~aGl~~A~~L~ 38 (415)
T PRK07364 18 TYD--VAIVGGGIVGLTLAAALK 38 (415)
T ss_pred ccC--EEEECcCHHHHHHHHHHh
Confidence 455 578899999999887764
No 107
>smart00363 S4 S4 RNA-binding domain.
Probab=20.55 E-value=59 Score=18.86 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=10.0
Q ss_pred ceeEEEcCeecc
Q 032049 31 RGLIKINGCPIE 42 (148)
Q Consensus 31 ~G~I~INg~~l~ 42 (148)
.|.|.|||.+..
T Consensus 25 ~g~i~vng~~~~ 36 (60)
T smart00363 25 QGRVKVNGKKVT 36 (60)
T ss_pred cCCEEECCEEec
Confidence 578999999873
No 108
>PRK11176 lipid transporter ATP-binding/permease protein; Provisional
Probab=20.40 E-value=71 Score=28.76 Aligned_cols=49 Identities=27% Similarity=0.248 Sum_probs=29.4
Q ss_pred eecEEEEEecCCccchHHHHHHHHHHHHHHhhhh---------cCChhhHHHHHHHhhhc
Q 032049 67 GVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQK---------YVDEQSKKEIKDILVRY 117 (148)
Q Consensus 67 ~~di~i~V~GGG~sgQa~AIr~aiAraL~~~~~~---------~~~~~~~~~Lk~~l~~y 117 (148)
.+|..+.-.|--.|| -+.=|++|||||+.- +. ..|++....+.+.|.+.
T Consensus 469 Gldt~ig~~g~~LSG-GqrQRi~LARall~~-~~ililDEptsaLD~~t~~~i~~~l~~~ 526 (582)
T PRK11176 469 GLDTVIGENGVLLSG-GQRQRIAIARALLRD-SPILILDEATSALDTESERAIQAALDEL 526 (582)
T ss_pred ccCceeCCCCCcCCH-HHHHHHHHHHHHHhC-CCEEEEECccccCCHHHHHHHHHHHHHH
Confidence 456655544433442 345589999999873 22 34666666666666553
No 109
>COG1561 Uncharacterized stress-induced protein [Function unknown]
Probab=20.02 E-value=1.6e+02 Score=25.42 Aligned_cols=70 Identities=24% Similarity=0.250 Sum_probs=39.9
Q ss_pred EEEEEEEeCceeEE-----EcCeeccccC--CHHHH-------HHHHhHHHHhcccccceecEEEEEecCCccchHHHHH
Q 032049 22 VAVTYCKRGRGLIK-----INGCPIELVE--PEILR-------FKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIR 87 (148)
Q Consensus 22 ~A~v~l~~G~G~I~-----INg~~l~~y~--~~~~r-------~~i~~PL~~~~~~~~~~~di~i~V~GGG~sgQa~AIr 87 (148)
.|++....|.+.+. ||++-++.+| |..++ +.+..-| .+ +++++++++.+-=.+..--.|-
T Consensus 8 far~e~~~~~~~~~~ElrSVN~r~Le~~~RLP~~l~~lE~~lR~~i~~~i-----sR-Gkie~~l~~~~~~~~~~~l~in 81 (290)
T COG1561 8 FARAEKEGGWYSAAVELRSVNGRYLETRFRLPEQLRGLEPALRELISSRI-----SR-GKVECTLRIEREESAQKELEIN 81 (290)
T ss_pred hhhccccCCCeEEEEEEeeccccchhHhhcCCHhhHHhhHHHHHHHHHHh-----cC-CceEEEEEeecccccccceeeC
Confidence 34445555566554 7999888765 43333 3222222 12 8999999986655444444555
Q ss_pred HHHHHHHHHh
Q 032049 88 QSIAKALVAF 97 (148)
Q Consensus 88 ~aiAraL~~~ 97 (148)
-.++++++..
T Consensus 82 ~~ll~~~~~~ 91 (290)
T COG1561 82 EDLLKQLVTL 91 (290)
T ss_pred HHHHHHHHHH
Confidence 5556655544
Done!