Query psy13775
Match_columns 119
No_of_seqs 112 out of 1025
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 20:11:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13775.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13775hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0056 AtpA F0F1-type ATP syn 100.0 3.7E-28 8.1E-33 200.2 11.5 107 13-119 392-502 (504)
2 PRK13343 F0F1 ATP synthase sub 99.8 7.3E-20 1.6E-24 153.8 11.3 107 13-119 392-502 (502)
3 CHL00059 atpA ATP synthase CF1 99.8 2.3E-19 4.9E-24 150.2 11.0 105 13-117 371-479 (485)
4 TIGR00962 atpA proton transloc 99.8 6.2E-19 1.3E-23 148.4 11.1 107 13-119 391-501 (501)
5 PRK09281 F0F1 ATP synthase sub 99.7 2E-17 4.3E-22 139.3 11.3 107 13-119 392-502 (502)
6 TIGR03324 alt_F1F0_F1_al alter 99.7 1.8E-17 3.9E-22 139.3 10.7 101 13-113 392-496 (497)
7 PTZ00185 ATPase alpha subunit; 99.6 7.2E-16 1.6E-20 130.3 5.4 65 13-79 427-492 (574)
8 PRK07165 F0F1 ATP synthase sub 99.6 4.7E-15 1E-19 124.9 9.1 101 13-114 368-474 (507)
9 KOG1353|consensus 99.4 1.5E-14 3.2E-19 113.6 0.4 45 13-57 292-340 (340)
10 PF00306 ATP-synt_ab_C: ATP sy 99.2 4.1E-11 8.9E-16 82.7 7.0 68 13-80 17-98 (113)
11 PRK04196 V-type ATP synthase s 97.0 0.0012 2.7E-08 55.7 5.0 64 14-81 382-452 (460)
12 TIGR01041 ATP_syn_B_arch ATP s 96.6 0.0035 7.5E-08 53.0 4.7 64 14-81 380-450 (458)
13 TIGR01043 ATP_syn_A_arch ATP s 92.0 0.78 1.7E-05 40.1 7.5 45 14-58 468-523 (578)
14 TIGR02546 III_secr_ATP type II 87.3 0.94 2E-05 37.9 4.3 46 13-58 369-421 (422)
15 PRK06315 type III secretion sy 85.2 1.1 2.3E-05 38.0 3.6 45 13-57 389-440 (442)
16 TIGR03497 FliI_clade2 flagella 84.9 1.1 2.3E-05 37.6 3.4 44 14-57 362-412 (413)
17 PF14615 Rsa3: Ribosome-assemb 82.1 4.6 0.0001 23.9 4.5 41 72-112 1-41 (47)
18 PRK07721 fliI flagellum-specif 81.6 2 4.2E-05 36.3 3.8 45 14-58 383-434 (438)
19 PRK09099 type III secretion sy 81.1 2.2 4.8E-05 36.1 3.9 45 13-57 387-438 (441)
20 PRK06936 type III secretion sy 80.4 2.7 5.8E-05 35.6 4.2 46 12-57 385-437 (439)
21 PRK12597 F0F1 ATP synthase sub 78.1 4.1 8.8E-05 34.7 4.6 56 14-69 374-444 (461)
22 PRK14698 V-type ATP synthase s 77.1 3.2 6.9E-05 38.6 3.9 61 13-73 901-979 (1017)
23 CHL00060 atpB ATP synthase CF1 77.0 4.4 9.5E-05 34.9 4.5 57 13-69 398-469 (494)
24 TIGR01039 atpD ATP synthase, F 76.3 5.2 0.00011 34.2 4.7 56 14-69 374-444 (461)
25 PRK08149 ATP synthase SpaL; Va 75.8 4.3 9.4E-05 34.2 4.1 46 12-57 374-426 (428)
26 KOG1142|consensus 75.2 4.3 9.2E-05 32.2 3.7 32 85-116 160-191 (258)
27 TIGR03498 FliI_clade3 flagella 74.0 5 0.00011 33.7 4.1 44 12-55 365-415 (418)
28 PRK06002 fliI flagellum-specif 73.0 4.3 9.3E-05 34.5 3.4 44 17-61 399-444 (450)
29 PF03847 TFIID_20kDa: Transcri 71.8 4.1 8.9E-05 25.8 2.4 31 86-116 6-36 (68)
30 PRK05688 fliI flagellum-specif 71.0 5.5 0.00012 33.9 3.7 42 16-57 400-445 (451)
31 TIGR03305 alt_F1F0_F1_bet alte 70.4 6.1 0.00013 33.6 3.8 57 13-69 368-439 (449)
32 PRK08472 fliI flagellum-specif 67.8 8.6 0.00019 32.5 4.1 45 13-57 381-432 (434)
33 PF09371 Tex_N: Tex-like prote 65.6 21 0.00046 26.9 5.6 49 60-109 37-85 (193)
34 PF09494 Slx4: Slx4 endonuclea 62.3 16 0.00035 22.4 3.7 37 40-76 20-56 (64)
35 PRK08927 fliI flagellum-specif 61.0 14 0.00029 31.5 4.1 41 20-60 396-438 (442)
36 PRK08972 fliI flagellum-specif 60.6 12 0.00027 31.7 3.8 43 15-57 393-439 (444)
37 PRK07594 type III secretion sy 60.6 13 0.00028 31.5 3.9 44 13-56 379-429 (433)
38 cd07981 TAF12 TATA Binding Pro 59.4 19 0.00042 22.6 3.8 31 86-116 8-38 (72)
39 PF05952 ComX: Bacillus compet 56.0 37 0.0008 20.9 4.4 36 75-111 3-42 (57)
40 PRK09280 F0F1 ATP synthase sub 55.0 27 0.00058 29.9 4.9 57 13-69 374-445 (463)
41 PRK06793 fliI flagellum-specif 54.0 13 0.00029 31.4 2.9 44 12-55 378-429 (432)
42 PF03671 Ufm1: Ubiquitin fold 54.0 4.8 0.0001 26.1 0.3 14 10-23 60-73 (76)
43 TIGR03496 FliI_clade1 flagella 53.4 13 0.00028 31.2 2.8 38 14-51 364-408 (411)
44 PRK07196 fliI flagellum-specif 50.1 26 0.00056 29.7 4.0 45 13-57 380-431 (434)
45 PF05291 Bystin: Bystin; Inte 49.1 60 0.0013 26.4 5.8 55 52-112 94-148 (301)
46 PRK06820 type III secretion sy 48.9 30 0.00065 29.3 4.3 44 13-56 387-437 (440)
47 TIGR01026 fliI_yscN ATPase Fli 46.7 25 0.00054 29.7 3.5 45 13-57 387-438 (440)
48 PF03048 Herpes_UL92: UL92 fam 46.4 93 0.002 23.6 6.2 51 67-117 84-136 (192)
49 PF05542 DUF760: Protein of un 45.4 58 0.0012 21.2 4.4 38 75-114 1-38 (86)
50 PRK10597 DNA damage-inducible 44.0 28 0.0006 22.9 2.7 51 64-115 12-72 (81)
51 KOG1597|consensus 42.5 83 0.0018 25.6 5.7 78 10-89 201-285 (308)
52 PF08112 ATP-synt_E_2: ATP syn 42.4 58 0.0013 19.8 3.7 33 62-94 1-33 (56)
53 PF14802 TMEM192: TMEM192 fami 42.3 54 0.0012 25.5 4.5 36 58-93 198-233 (236)
54 PF10241 KxDL: Uncharacterized 38.3 1.1E+02 0.0024 19.9 5.0 33 59-91 5-37 (88)
55 PF14022 DUF4238: Protein of u 37.5 1.5E+02 0.0032 21.6 6.2 56 56-112 39-98 (265)
56 PRK06213 enoyl-CoA hydratase; 37.2 1.1E+02 0.0025 22.8 5.5 72 36-115 154-226 (229)
57 cd06940 NR_LBD_REV_ERB The lig 36.6 32 0.0007 25.2 2.4 42 9-54 7-50 (189)
58 KOG0981|consensus 34.4 2.1E+02 0.0045 25.8 7.2 27 92-118 308-334 (759)
59 COG2183 Tex Transcriptional ac 33.9 82 0.0018 28.9 4.8 51 58-109 48-98 (780)
60 PF04967 HTH_10: HTH DNA bindi 33.5 95 0.0021 18.5 3.7 26 46-71 2-30 (53)
61 PF08463 EcoEI_R_C: EcoEI R pr 33.5 90 0.0019 22.0 4.3 42 69-110 2-45 (164)
62 PF03965 Penicillinase_R: Peni 33.2 1.3E+02 0.0028 20.0 4.8 31 82-112 85-115 (115)
63 PHA00684 hypothetical protein 32.1 61 0.0013 23.1 3.0 27 58-84 46-72 (128)
64 PRK02118 V-type ATP synthase s 32.1 65 0.0014 27.4 3.7 46 16-61 365-413 (436)
65 PF12581 DUF3756: Protein of u 31.9 16 0.00034 20.8 0.0 17 2-18 25-41 (41)
66 KOG1379|consensus 29.7 20 0.00044 29.4 0.3 28 53-80 248-275 (330)
67 COG3160 Rsd Regulator of sigma 29.6 2E+02 0.0044 21.1 5.4 48 47-94 25-78 (162)
68 COG2854 Ttg2D ABC-type transpo 29.5 1.3E+02 0.0029 23.0 4.8 49 43-93 67-115 (202)
69 PRK07021 fliL flagellar basal 29.2 45 0.00097 24.1 2.1 43 69-111 101-143 (162)
70 PF04353 Rsd_AlgQ: Regulator o 29.1 2.3E+02 0.005 20.7 6.5 47 48-94 26-78 (153)
71 PF10392 COG5: Golgi transport 28.9 1.4E+02 0.0031 20.6 4.5 47 69-116 41-87 (132)
72 PRK05696 fliL flagellar basal 28.5 63 0.0014 23.5 2.8 43 70-112 110-152 (170)
73 PF08006 DUF1700: Protein of u 28.4 1.2E+02 0.0025 22.0 4.2 25 59-83 11-35 (181)
74 PF02260 FATC: FATC domain; I 28.3 25 0.00055 19.0 0.5 13 43-55 1-13 (33)
75 PF03597 CcoS: Cytochrome oxid 27.5 53 0.0012 19.1 1.8 18 51-68 19-36 (45)
76 PF09047 MEF2_binding: MEF2 bi 27.5 65 0.0014 17.6 2.0 20 93-112 4-23 (35)
77 TIGR02698 CopY_TcrY copper tra 26.8 2.2E+02 0.0048 19.7 5.9 34 82-115 86-119 (130)
78 PF06200 tify: tify domain; I 26.7 3.6 7.8E-05 23.0 -3.2 28 47-74 4-31 (36)
79 smart00309 PAH Pancreatic horm 25.7 1.2E+02 0.0025 16.9 2.9 20 63-82 10-29 (36)
80 TIGR00847 ccoS cytochrome oxid 25.4 61 0.0013 19.4 1.8 18 51-68 20-37 (51)
81 PF11771 DUF3314: Protein of u 24.8 26 0.00057 25.8 0.2 14 1-14 56-69 (164)
82 TIGR02308 RNA_lig_T4_1 RNA lig 24.7 1.6E+02 0.0035 24.6 4.8 44 51-94 260-312 (374)
83 PRK11718 anti-RNA polymerase s 24.3 3E+02 0.0065 20.3 8.3 45 48-92 26-76 (161)
84 cd04502 SGNH_hydrolase_like_7 23.8 18 0.00039 25.2 -0.9 37 51-87 53-89 (171)
85 cd01820 PAF_acetylesterase_lik 23.4 21 0.00045 26.2 -0.6 38 50-87 91-128 (214)
86 PF01765 RRF: Ribosome recycli 23.3 2.8E+02 0.0061 19.9 5.4 30 88-117 120-149 (165)
87 cd00126 PAH Pancreatic Hormone 22.9 1.4E+02 0.0031 16.6 2.9 20 63-82 10-29 (36)
88 PF02787 CPSase_L_D3: Carbamoy 22.9 2.6E+02 0.0056 19.3 4.9 42 67-109 43-84 (123)
89 PF06183 DinI: DinI-like famil 22.8 29 0.00062 21.7 0.0 50 65-115 1-58 (65)
90 PF12672 DUF3793: Protein of u 21.5 52 0.0011 24.3 1.2 38 2-39 136-174 (176)
91 cd04329 RNAP_II_Rpb7_N RNAP_II 21.3 41 0.00089 21.5 0.6 23 1-30 6-30 (80)
92 TIGR00496 frr ribosome recycli 21.2 3.4E+02 0.0075 20.0 6.7 33 85-117 123-158 (176)
93 cd01766 Ufm1 Urm1-like ubiquit 21.2 21 0.00046 23.3 -0.8 14 10-23 60-73 (82)
94 cd01136 ATPase_flagellum-secre 21.1 63 0.0014 26.3 1.7 28 13-40 293-325 (326)
95 PF00042 Globin: Globin plant 20.8 1.4E+02 0.0031 18.9 3.2 28 12-39 34-67 (110)
96 PF10615 DUF2470: Protein of u 20.8 1.4E+02 0.003 18.9 3.0 23 72-94 8-30 (83)
97 PRK05697 flagellar basal body- 20.8 86 0.0019 22.2 2.2 42 70-111 77-118 (137)
98 cd04170 EF-G_bact Elongation f 20.7 3.8E+02 0.0082 20.3 5.9 42 69-110 193-235 (268)
99 TIGR03687 pupylate_cterm ubiqu 20.5 1.1E+02 0.0024 16.7 2.1 19 100-118 10-28 (33)
100 PF08362 TetR_C_3: YcdC-like p 20.3 3.3E+02 0.0071 19.4 7.2 90 24-114 46-136 (143)
101 PF09025 YopR_core: YopR Core; 20.3 74 0.0016 23.1 1.7 44 13-57 55-99 (142)
102 cd06932 NR_LBD_PPAR The ligand 20.2 95 0.0021 24.1 2.5 37 14-54 63-101 (259)
No 1
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=99.95 E-value=3.7e-28 Score=200.24 Aligned_cols=107 Identities=36% Similarity=0.604 Sum_probs=104.3
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGL 88 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~ 88 (119)
-+.|||||||| +||++|+||+|++||| |||+|+|+++||++|||+++||||+||+++|.+|+..++.|++.+++++
T Consensus 392 l~afsqf~sdLd~~T~~~l~~G~r~~ellkQ~~~~p~sv~~qv~ilya~~~G~ld~v~v~~v~~fe~~l~~~~~~~~~~~ 471 (504)
T COG0056 392 LEAFSQFGSDLDKATRKQLERGKRLTELLKQPQYSPLSVEEQVLILYAGTNGYLDDVPVEKVADFEKELLAYLRSDHKEL 471 (504)
T ss_pred HHHHHhhcchhCHHHHHHHHccHHHHHHhcCCCCCCccHHHHHHHHHHHhcCcccCCcHHHHHHHHHHHHHHHHhhHHHH
Confidence 47899999999 9999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHhcCC
Q psy13775 89 LESIKKEGKITEDTDAKLKTVVTNFLANFTG 119 (119)
Q Consensus 89 ~~~I~~~~~l~~~~~~~L~~~i~~~~~~f~~ 119 (119)
++.|..++.+++++++.|+.++++|++.|.+
T Consensus 472 ~~~I~~~~~l~~~~e~~l~~~i~~f~~~f~~ 502 (504)
T COG0056 472 LEEIRTTKELDDEIEAKLKAAIKEFKKTFAL 502 (504)
T ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHHHhccc
Confidence 9999999999999999999999999998854
No 2
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=99.82 E-value=7.3e-20 Score=153.83 Aligned_cols=107 Identities=25% Similarity=0.406 Sum_probs=103.5
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGL 88 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~ 88 (119)
-+.|++||+++ .|+++|+||++|+|+| ++|+|+|.++|++.||++++|++|++|+++|.+|++.+++|++++++++
T Consensus 392 ~e~~~~~G~~ld~~~~~~i~~~~~i~~~L~Q~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~i~~~~~~~~~~~~~~~~~~ 471 (502)
T PRK13343 392 LEAFTRFGGLLDAGTQKQITRGRRLRELLKQPRFSPLSVEEQIALLYALNEGLLDAVPLANIQAFEERLLEKLDARFAAL 471 (502)
T ss_pred HHHHHHHhhhcCHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHhhhHHH
Confidence 36799999999 9999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHhcCC
Q psy13775 89 LESIKKEGKITEDTDAKLKTVVTNFLANFTG 119 (119)
Q Consensus 89 ~~~I~~~~~l~~~~~~~L~~~i~~~~~~f~~ 119 (119)
++.|..++.|+++.++.|++++++|.+.|.+
T Consensus 472 ~~~i~~~~~l~~~~~~~l~~~~~~~~~~~~~ 502 (502)
T PRK13343 472 SLALESPRELDEAWLAALEEILREAGERFAA 502 (502)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHhhCC
Confidence 9999999999999999999999999998864
No 3
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=99.80 E-value=2.3e-19 Score=150.22 Aligned_cols=105 Identities=30% Similarity=0.465 Sum_probs=101.7
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGL 88 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~ 88 (119)
-+.|+||++++ .|+.+|+||++|+++| ++++|++.++|+++||++++|+||++|+++|.+|++.+++|+++++|++
T Consensus 371 ~e~~~~~~~~~d~~~~~~i~~~~~i~~~L~Q~~~~~~~~~e~~~~l~a~~~g~l~~~~~~~v~~~~~~l~~~~~~~~~~~ 450 (485)
T CHL00059 371 LEAFAQFASDLDKATQNQLARGQRLRELLKQSQSAPLTVEEQVATIYTGTNGYLDSLEIGQVRKFLVELRTYLKTNKPQF 450 (485)
T ss_pred HHHHHHhhcCCCHHHHHHHHhHHHHHHHhcCCCCCCCCHHHHHHHHHHhccCCcCccCHHHHHHHHHHHHHHHHhhhHHH
Confidence 47899999999 9999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13775 89 LESIKKEGKITEDTDAKLKTVVTNFLANF 117 (119)
Q Consensus 89 ~~~I~~~~~l~~~~~~~L~~~i~~~~~~f 117 (119)
++.|..++.++++.++.|++++++|.+.|
T Consensus 451 ~~~i~~~~~~~~~~~~~l~~~~~~~~~~~ 479 (485)
T CHL00059 451 QEIISSTKTFTEEAEALLKEAIQEQLELF 479 (485)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998876
No 4
>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.
Probab=99.79 E-value=6.2e-19 Score=148.35 Aligned_cols=107 Identities=34% Similarity=0.588 Sum_probs=103.7
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGL 88 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~ 88 (119)
-+.|++||+++ .++..|++|++++++| ++++|++.++|+++||++++||||++|+++|..|+..+++|++++++++
T Consensus 391 ~~~l~~~g~~ld~~~~~~l~~~~~i~~fL~Q~~~~~~~~~~q~~~l~a~~~G~l~~v~~~~i~~~~~~l~~~l~~~~~~~ 470 (501)
T TIGR00962 391 LEAFSQFASDLDEATKAQLERGKRLVELLKQPQYKPLPVEEQVVILYAGTKGYLDDIPVDKVRKFEQELLDYLDANHPDI 470 (501)
T ss_pred HHHHHHHhccCCHHHHHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHhhHHH
Confidence 36899999999 9999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHhcCC
Q psy13775 89 LESIKKEGKITEDTDAKLKTVVTNFLANFTG 119 (119)
Q Consensus 89 ~~~I~~~~~l~~~~~~~L~~~i~~~~~~f~~ 119 (119)
++.|..++.++++.++.|++++++|++.|.|
T Consensus 471 ~~~i~~~~~l~~~~~~~L~~~i~~~~~~f~~ 501 (501)
T TIGR00962 471 LEEINTKKKLTEELEDKLKEALKNFKKTFAA 501 (501)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHhhcC
Confidence 9999999999999999999999999999976
No 5
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=99.73 E-value=2e-17 Score=139.33 Aligned_cols=107 Identities=33% Similarity=0.582 Sum_probs=102.8
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGL 88 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~ 88 (119)
-+.|++||+++ .++..|++|+++.++| ++|+|++.++|++++|++++|+||++|.+++.+|+..+++|++++++++
T Consensus 392 ~~~l~~~g~~l~~~~~~~l~~~~~i~~fL~Q~~~~~~~~~~~~~~~~~~~~G~l~~l~~~~i~~~~~~~~~~l~~~~~~~ 471 (502)
T PRK09281 392 LEAFAQFGSDLDEATRAQLERGQRLVELLKQPQYSPLPVEEQVVILYAGTNGYLDDVPVEKVRRFEAELLAYLRSNHADL 471 (502)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHhcCccccCCHHHHHHHHHHHHHHHHHhhHHH
Confidence 36899999999 9999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHhcCC
Q psy13775 89 LESIKKEGKITEDTDAKLKTVVTNFLANFTG 119 (119)
Q Consensus 89 ~~~I~~~~~l~~~~~~~L~~~i~~~~~~f~~ 119 (119)
++.|..++.++++.++.|++++++|.+.|.+
T Consensus 472 ~~~I~~~~~l~~~~~~~L~~~i~~~~~~f~~ 502 (502)
T PRK09281 472 LEEIRETKDLSDEIEAKLKAAIEEFKKTFAA 502 (502)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999988753
No 6
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=99.73 E-value=1.8e-17 Score=139.25 Aligned_cols=101 Identities=20% Similarity=0.331 Sum_probs=96.9
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGL 88 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~ 88 (119)
-+.|++||+++ .|++.|++|++++++| ++++|++.++|++.|+++++|++|++|+++|.+|+..+++|++++|+++
T Consensus 392 ~e~~~~~G~~ld~~~~~~i~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~~~g~~d~~~~~~v~~~~~~~~~~~~~~~~~~ 471 (497)
T TIGR03324 392 LETFARFGARLDENTRKTIEHGRRIRACLKQTQSSPLTVPQQIAILLALTNGLFDGVDLDAMPEAESAIRAAVTSLPADL 471 (497)
T ss_pred HHHHHHhhhhcCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhhhHHH
Confidence 46799999999 9999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHHHH
Q psy13775 89 LESIKKEGKITEDTDAKLKTVVTNF 113 (119)
Q Consensus 89 ~~~I~~~~~l~~~~~~~L~~~i~~~ 113 (119)
++.|..++.+++++++.|++++++.
T Consensus 472 ~~~~~~~~~~~~~~~~~~~~~~~~~ 496 (497)
T TIGR03324 472 RERLQSGKKLSDEDREQILDIARGA 496 (497)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHhh
Confidence 9999999999999999999988764
No 7
>PTZ00185 ATPase alpha subunit; Provisional
Probab=99.60 E-value=7.2e-16 Score=130.35 Aligned_cols=65 Identities=15% Similarity=0.162 Sum_probs=59.1
Q ss_pred hhHHhhhcCCH-HHHHHHhcccchhhhcCCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHH
Q psy13775 13 GYHYSNFTARI-GLNKSLMLSRRLPILLGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLA 79 (119)
Q Consensus 13 ~~~Fs~Fgsdl-~tr~~L~rG~Rl~ElL~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~ 79 (119)
-++|||||||+ . ++|+||+|++|+|.|-.|+++++||++|||+++||||++|+++|..+|..+.+
T Consensus 427 l~~fa~fgsdld~--~~l~rG~r~~ellkQ~~p~~~~~qv~~l~a~~~g~ld~~~~~~i~~~~~~~~~ 492 (574)
T PTZ00185 427 LAADSVGGSQVQT--VPMIRGARFVALFNQKNPSFFMNALVSLYACLNGYLDDVKVNYAKLYEYLLVN 492 (574)
T ss_pred HHHHHhhcchhhH--HHHHhhHHHHHHHCCCCCCCHHHHHHHHHHHhcCCcccCcHHHHHHHHHhccC
Confidence 47899999999 6 99999999999993333999999999999999999999999999999987654
No 8
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=99.59 E-value=4.7e-15 Score=124.90 Aligned_cols=101 Identities=8% Similarity=0.140 Sum_probs=90.1
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCCh-hhHHHHHHHHHHHHHhchhH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDP-AKITTFEKEFLAHIKSSERG 87 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv-~~I~~fe~~ll~~l~~~~~~ 87 (119)
.+.|++||+++ .|++.|++|+++.|+| ++|+|++..+|+++++++.+|+||++|+ ++|.+|++.+++| +.++++
T Consensus 368 ~e~~~~~~~~ld~~~~~~l~~g~~i~~~L~Q~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~ 446 (507)
T PRK07165 368 QLKLSMLDYDLNKETSDLLFKGKMIEKMFNQKGFSLYSYRFVLLISKLISWGLLKDVKDEQKALDFIDYLIEN-DPDAKK 446 (507)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHhhhhhhCCcHHHHHHHHHHHHHh-hhhhHH
Confidence 46699999999 9999999999999999 9999999999999999999999999999 9999999999999 999999
Q ss_pred HHHHHHhcCCCCHHHH-HHHHHHHHHHH
Q psy13775 88 LLESIKKEGKITEDTD-AKLKTVVTNFL 114 (119)
Q Consensus 88 ~~~~I~~~~~l~~~~~-~~L~~~i~~~~ 114 (119)
+++.|..++.+++++. ..+..++.+|.
T Consensus 447 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 474 (507)
T PRK07165 447 IFNKIKNNEDVDDELMKNYFAFLLNQYS 474 (507)
T ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 9999999999998753 23333444443
No 9
>KOG1353|consensus
Probab=99.44 E-value=1.5e-14 Score=113.64 Aligned_cols=45 Identities=47% Similarity=0.693 Sum_probs=43.0
Q ss_pred hhHHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 13 GYHYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 13 ~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
-++|+|||||| +||+.|+||.|++|+| +||.||.+++||+++||+
T Consensus 292 vaafaqfgsdlda~tq~~l~rg~rltellkq~qy~p~~~e~qv~~iy~g 340 (340)
T KOG1353|consen 292 VAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYAPLAIEEQVAVIYAG 340 (340)
T ss_pred HHHHHHhcccccHHHHHHHHhhhHHHHHHhcCCCCCcchhhheeeEecC
Confidence 37899999999 9999999999999999 999999999999999985
No 10
>PF00306 ATP-synt_ab_C: ATP synthase alpha/beta chain, C terminal domain; InterPro: IPR000793 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the C-terminal domain, which forms a left-handed superhelix composed of 4-5 individual helices. The C-terminal domain can vary between the alpha and beta subunits, and between different ATPases []. ; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 3OAA_U 2F43_B 1MAB_B 1W0K_A 1H8H_B 2WSS_A 1EFR_A 2JIZ_H 1E1Q_A 2V7Q_B ....
Probab=99.22 E-value=4.1e-11 Score=82.68 Aligned_cols=68 Identities=18% Similarity=0.341 Sum_probs=58.7
Q ss_pred hhHHhh-hcCC-H--HHHHHHhcccchhhhc--CCCCCC-------C-HHHHHHHHHHHhcCcCCCCChhhHHHHHHHHH
Q psy13775 13 GYHYSN-FTAR-I--GLNKSLMLSRRLPILL--GQYVPM-------A-IEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 78 (119)
Q Consensus 13 ~~~Fs~-Fgsd-l--~tr~~L~rG~Rl~ElL--~q~~Pl-------s-v~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll 78 (119)
-+.|+| ||+| | .||.+|++|++++|+| ++|+|+ + ..+++.+++.+.+|+++++|.+.+..+.....
T Consensus 17 L~~~~q~vG~d~L~~~~k~~l~~g~~i~e~LkQ~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 (113)
T PF00306_consen 17 LEEFVQFVGSDALDDEDKLILERGRRIREFLKQNAFDPVPLEKQYVMILEETIDLFYAILRGKFDDIPEEELEKIETKDI 96 (113)
T ss_dssp HHHHHHHHTSTCSTHHHHHHHHHHHHHHHHT-BSTTTTTSSHHHHHHHHHHHHHHHHHHHTTTTTTS-GGGHHHHHHHHH
T ss_pred HHHHHHHhhcccchHHHHHHHHHHHHHHHHcCCCCCCCCcCcchhhhHHHHHHHHHHHHHhCCCccCCHHHHHHHhhHHH
Confidence 367999 7988 6 9999999999999988 999999 5 55555568999999999999999999988888
Q ss_pred HH
Q psy13775 79 AH 80 (119)
Q Consensus 79 ~~ 80 (119)
++
T Consensus 97 ~~ 98 (113)
T PF00306_consen 97 EK 98 (113)
T ss_dssp HH
T ss_pred HH
Confidence 74
No 11
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=96.98 E-value=0.0012 Score=55.68 Aligned_cols=64 Identities=14% Similarity=0.191 Sum_probs=55.3
Q ss_pred hHHhhh-cCCH---HHHHHHhcccchh-hhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHH
Q psy13775 14 YHYSNF-TARI---GLNKSLMLSRRLP-ILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHI 81 (119)
Q Consensus 14 ~~Fs~F-gsdl---~tr~~L~rG~Rl~-ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l 81 (119)
..|.+| |+|. .++..+.+|+++. +.| +.+.|.+.++++..++ ++++++|.+++..|+..+++..
T Consensus 382 ~~~~~~~G~~~l~d~~~~~~~~~~~~~~~fL~Q~~~~~~~~~~~~~~l~----~~l~~~~~~~l~~~~~~l~~~~ 452 (460)
T PRK04196 382 RELAAIVGEEALSERDRKYLKFADAFEREFVNQGFDENRSIEETLDLGW----ELLSILPESELKRIKDEYIEKY 452 (460)
T ss_pred HHHHHhcCCCcCCHHHHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHH----HHHhhCCHHHHHHHHHHHHHHh
Confidence 467778 6555 9999999999997 677 8889999999999976 6789999999999999998744
No 12
>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=96.56 E-value=0.0035 Score=53.00 Aligned_cols=64 Identities=14% Similarity=0.180 Sum_probs=55.1
Q ss_pred hHHhhh-cCCH---HHHHHHhcccch-hhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHH
Q psy13775 14 YHYSNF-TARI---GLNKSLMLSRRL-PILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHI 81 (119)
Q Consensus 14 ~~Fs~F-gsdl---~tr~~L~rG~Rl-~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l 81 (119)
..+.+| |+|. .++..+.+|+++ .+.| +.+.|.+.++++..| .++++.+|.+++..|...+++..
T Consensus 380 ~~i~~~~G~d~l~d~~~~~~~~~~~i~~~fL~Q~~~~~~~~~~~~~~l----~~~l~~~~~~~~~~~~~~~~~~~ 450 (458)
T TIGR01041 380 RGLVAIVGEEALSERDRKYLKFADLFERRFVRQGRNENRSIEETLDIG----WELLSILPESELKRIDEEYIEKY 450 (458)
T ss_pred HHHHHhcCCCcCCHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHH----HHHHhhCCHHHHHHHHHHHHHHh
Confidence 456677 8866 999999999995 7888 779999999999999 46788999999999999997744
No 13
>TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=91.96 E-value=0.78 Score=40.13 Aligned_cols=45 Identities=11% Similarity=0.154 Sum_probs=38.9
Q ss_pred hHHhhh-cCC-H--HHHHHHhcccchhhh-c--CCCCCC----CHHHHHHHHHHHh
Q psy13775 14 YHYSNF-TAR-I--GLNKSLMLSRRLPIL-L--GQYVPM----AIEEQVAVIYCGV 58 (119)
Q Consensus 14 ~~Fs~F-gsd-l--~tr~~L~rG~Rl~El-L--~q~~Pl----sv~eQV~iL~a~~ 58 (119)
+-+.|+ |+| | ..|..+++|++++|. | +.|+|+ |.++|+..|.++.
T Consensus 468 ~~iv~lvG~d~L~~~d~~il~~a~~i~e~FLqQ~~~~~~d~~~~~~k~~~~L~~i~ 523 (578)
T TIGR01043 468 QEIVQLVGPDALPERQKLILEVARMIREAFLQQNAFDPVDTYCPPQKQYRILRAIM 523 (578)
T ss_pred HHHHhccCCCCCCHHHHHHHHHhHHHHHhhCCCCCCCCccCCCCHHHHHHHHHHHH
Confidence 457788 999 4 999999999999988 5 889999 9999999887663
No 14
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=87.26 E-value=0.94 Score=37.92 Aligned_cols=46 Identities=9% Similarity=-0.056 Sum_probs=39.6
Q ss_pred hhHHhhhc-----CCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHh
Q psy13775 13 GYHYSNFT-----ARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGV 58 (119)
Q Consensus 13 ~~~Fs~Fg-----sdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~ 58 (119)
-+.+.+|| +|..+.+.+.+|.++.+.| +.+.+.+.++++..|+++-
T Consensus 369 ~~~li~~g~y~~g~d~~~d~~i~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~~ 421 (422)
T TIGR02546 369 VELLIRLGEYQPGSDPETDDAIDKIDAIRAFLRQSTDEYSPYEETLEQLHALV 421 (422)
T ss_pred HHHHHHhcCCcCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHHh
Confidence 45678884 4668889999999999999 8899999999999998763
No 15
>PRK06315 type III secretion system ATPase; Provisional
Probab=85.24 E-value=1.1 Score=37.96 Aligned_cols=45 Identities=9% Similarity=-0.052 Sum_probs=39.2
Q ss_pred hhHHhhhcC-----CHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 13 GYHYSNFTA-----RIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 13 ~~~Fs~Fgs-----dl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
.+.|.+||+ |+.+...+++++++.+.| +.++|.+.++++..|..+
T Consensus 389 ~e~li~~g~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~~ 440 (442)
T PRK06315 389 NEMLIRIGEYRRGSDREVDFAIDHIDKLNRFLKQDIHEKTNYEEAAQQLRAI 440 (442)
T ss_pred hHHHHHhcCCcCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 467888875 559999999999999999 999999999999887654
No 16
>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=84.89 E-value=1.1 Score=37.59 Aligned_cols=44 Identities=14% Similarity=0.181 Sum_probs=38.0
Q ss_pred hHHhhh-----cCCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 14 YHYSNF-----TARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 14 ~~Fs~F-----gsdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
+.+.++ |+|..+.+.+.+|+++.+.| +.++|.+.++++..|..+
T Consensus 362 ~~li~~g~~~~g~d~~~~~~i~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~ 412 (413)
T TIGR03497 362 EDLINIGAYKRGSNPKIDEAIRYIEKINSFLKQGIDEKFTFEETVQLLKTL 412 (413)
T ss_pred HHHHHhcCcccCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHhh
Confidence 455666 77888999999999999999 999999999999888653
No 17
>PF14615 Rsa3: Ribosome-assembly protein 3
Probab=82.05 E-value=4.6 Score=23.87 Aligned_cols=41 Identities=15% Similarity=0.245 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHH
Q psy13775 72 TFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTN 112 (119)
Q Consensus 72 ~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~ 112 (119)
+|.+.+++.+..++.+-+++++....+++.-...|..+++.
T Consensus 1 ~f~~~yl~~~t~efgdDLd~lR~~~dF~~~sl~~Li~aL~~ 41 (47)
T PF14615_consen 1 EFRNFYLQRLTDEFGDDLDELRKAPDFTDKSLPLLIDALQQ 41 (47)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Confidence 47888999999999999999999999999888888777765
No 18
>PRK07721 fliI flagellum-specific ATP synthase; Validated
Probab=81.55 E-value=2 Score=36.29 Aligned_cols=45 Identities=13% Similarity=0.180 Sum_probs=36.4
Q ss_pred hHHhhhcC-----CHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHh
Q psy13775 14 YHYSNFTA-----RIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGV 58 (119)
Q Consensus 14 ~~Fs~Fgs-----dl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~ 58 (119)
+.+.+||+ |+.....+.+++++.+.| +.++|.+.++++..|+.+.
T Consensus 383 ~~li~~g~y~~g~~~~~d~a~~~~~~~~~fl~Q~~~~~~~~~~~~~~l~~~~ 434 (438)
T PRK07721 383 EDLINIGAYKRGSSREIDEAIQFYPQIISFLKQGTDEKATFEESIQALLSLF 434 (438)
T ss_pred HHHHHhhCCcCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHHH
Confidence 45556665 555566688999999999 9999999999999998764
No 19
>PRK09099 type III secretion system ATPase; Provisional
Probab=81.11 E-value=2.2 Score=36.10 Aligned_cols=45 Identities=4% Similarity=-0.160 Sum_probs=38.8
Q ss_pred hhHHhhh-----cCCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 13 GYHYSNF-----TARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 13 ~~~Fs~F-----gsdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
-+.+.++ |+|..+...+++|+++.+.| +.++|.|.++++..|..+
T Consensus 387 ~e~li~iG~y~~g~d~~~d~~i~~~~~i~~fL~Q~~~~~~~~~~t~~~l~~~ 438 (441)
T PRK09099 387 VETLLQVGEYRAGSDPVADEAIAKIDAIRDFLSQRTDEYSDPDATLAALAEL 438 (441)
T ss_pred HHHHHHhcCccCCCChhHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4678888 46778888999999999999 889999999999888655
No 20
>PRK06936 type III secretion system ATPase; Provisional
Probab=80.39 E-value=2.7 Score=35.62 Aligned_cols=46 Identities=7% Similarity=-0.060 Sum_probs=39.5
Q ss_pred hhhHHhhhc-----CCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 12 AGYHYSNFT-----ARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 12 ~~~~Fs~Fg-----sdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
--+.+.+|| +|..+.+.+.++.++.+.| +.+.|.+.++++..|+.+
T Consensus 385 e~e~li~iG~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~ 437 (439)
T PRK06936 385 EVELLLQIGEYQKGQDKEADQAIERIGAIRGFLRQGTHELSHFNETLNLLETL 437 (439)
T ss_pred HHHHHHHhcCccCCCCHHHHHHHHhHHHHHHHcCCCCCCCCCHHHHHHHHHHH
Confidence 346788895 4778888999999999999 889999999999998865
No 21
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=78.06 E-value=4.1 Score=34.72 Aligned_cols=56 Identities=14% Similarity=0.075 Sum_probs=47.5
Q ss_pred hHHhhhcC-CH--HHHHHHhcccchhhhc--CC----------CCCCCHHHHHHHHHHHhcCcCCCCChhh
Q psy13775 14 YHYSNFTA-RI--GLNKSLMLSRRLPILL--GQ----------YVPMAIEEQVAVIYCGVRGHLDKLDPAK 69 (119)
Q Consensus 14 ~~Fs~Fgs-dl--~tr~~L~rG~Rl~ElL--~q----------~~Plsv~eQV~iL~a~~~G~ld~ipv~~ 69 (119)
.+++-+|- .+ .++..+.+|+++.+.| +. ..+.+.++-+--|..+.+|-+|++|...
T Consensus 374 ~li~i~gy~~l~~~~d~~i~~~~~i~~fL~Q~~~~~~~~t~~~~~~~~~~~~~~~l~~i~~g~~~~~~~~~ 444 (461)
T PRK12597 374 DVIAILGIDELSAEDKIIVKRARQLQRFLTQPFFVTEAFTGEPGVSVPLEETLDSCERILNGEYDDWSEES 444 (461)
T ss_pred HHHHHcCCccCCHHHHHHHHhHHHHHHHhCCCcchhhcccCCCCcccCHHHHHHHHHHHhCCCccCCCHHH
Confidence 34555663 33 9999999999999999 66 5699999999999999999999999875
No 22
>PRK14698 V-type ATP synthase subunit A; Provisional
Probab=77.08 E-value=3.2 Score=38.65 Aligned_cols=61 Identities=13% Similarity=0.041 Sum_probs=44.4
Q ss_pred hhHHhhh-cC--CH-HHHHHHhcccchhhh-c--CCCCC----CCHHHHHHHHHHHhc-------CcCCCCChhhHHHH
Q psy13775 13 GYHYSNF-TA--RI-GLNKSLMLSRRLPIL-L--GQYVP----MAIEEQVAVIYCGVR-------GHLDKLDPAKITTF 73 (119)
Q Consensus 13 ~~~Fs~F-gs--dl-~tr~~L~rG~Rl~El-L--~q~~P----lsv~eQV~iL~a~~~-------G~ld~ipv~~I~~f 73 (119)
-+.+.|| |. +. ..|.++++|++|+|. | +.|+| .|.++|+..|+++.. -+-..+|.++|.+.
T Consensus 901 l~~~i~l~g~~~l~~~d~~~~~~~~~i~e~fL~Q~~~~~~d~~~~~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~ 979 (1017)
T PRK14698 901 LQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMDAISRGVPLEEIAKL 979 (1017)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHhHHHHhccCCCCCCCccccCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHhcc
Confidence 3567888 43 33 999999999999987 6 88889 799999999887631 11122567776643
No 23
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=76.97 E-value=4.4 Score=34.91 Aligned_cols=57 Identities=12% Similarity=0.109 Sum_probs=47.7
Q ss_pred hhHHhhhcC-CH--HHHHHHhcccchhhhc--CCC----------CCCCHHHHHHHHHHHhcCcCCCCChhh
Q psy13775 13 GYHYSNFTA-RI--GLNKSLMLSRRLPILL--GQY----------VPMAIEEQVAVIYCGVRGHLDKLDPAK 69 (119)
Q Consensus 13 ~~~Fs~Fgs-dl--~tr~~L~rG~Rl~ElL--~q~----------~Plsv~eQV~iL~a~~~G~ld~ipv~~ 69 (119)
..+.+.+|- .+ .++..+.+|+++.+.| +.| .+.+.++=+..|..+.+|.+|++|.+.
T Consensus 398 e~li~~~g~~~ls~~~~~~i~~~~~i~~fL~Q~~f~~e~ft~~~~~~~~~~~~~~~l~~i~~g~~~~~~~~~ 469 (494)
T CHL00060 398 QDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIRGFQLILSGELDGLPEQA 469 (494)
T ss_pred HHHHHHhCcccCCHHHHHHHHhHHHHHHHhcCCcchhhcccCCCCcccCHHHHHHHHHHHhCCCccCCCHHH
Confidence 344566774 44 9999999999999999 744 888999999999999999999999875
No 24
>TIGR01039 atpD ATP synthase, F1 beta subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.
Probab=76.26 E-value=5.2 Score=34.15 Aligned_cols=56 Identities=11% Similarity=0.051 Sum_probs=47.7
Q ss_pred hHHhhhcCC-H--HHHHHHhcccchhhhc--CC----------CCCCCHHHHHHHHHHHhcCcCCCCChhh
Q psy13775 14 YHYSNFTAR-I--GLNKSLMLSRRLPILL--GQ----------YVPMAIEEQVAVIYCGVRGHLDKLDPAK 69 (119)
Q Consensus 14 ~~Fs~Fgsd-l--~tr~~L~rG~Rl~ElL--~q----------~~Plsv~eQV~iL~a~~~G~ld~ipv~~ 69 (119)
.+++.+|-+ + .++..+++|+++.+.| +. ..+.+.++.+.-|..+.+|-+|++|.++
T Consensus 374 ~li~i~g~~~lsd~~~~~l~~~~~i~~fL~Q~~~~~~~~t~~~~~~~~~~~~~~~l~~i~~g~~~~~~~~~ 444 (461)
T TIGR01039 374 DIIAILGMDELSEEDKLTVERARRIQRFLSQPFFVAEVFTGQPGKYVPLKDTIRGFKEILEGKYDHLPEQA 444 (461)
T ss_pred HHHHHhCCccCCHHHHHHHHhHHHHHHHhCCCCchhccccCCCCcccCHHHHHHHHHHHhCCCccCCCHHH
Confidence 345566633 3 7999999999999999 66 6899999999999999999999999875
No 25
>PRK08149 ATP synthase SpaL; Validated
Probab=75.76 E-value=4.3 Score=34.24 Aligned_cols=46 Identities=4% Similarity=-0.025 Sum_probs=38.8
Q ss_pred hhhHHhhhcC-----CHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 12 AGYHYSNFTA-----RIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 12 ~~~~Fs~Fgs-----dl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
.-+.+.+||+ |+.+...+.++.+|.+.| +.+.|.+.++++..|-..
T Consensus 374 e~e~li~~G~y~~g~~~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~ 426 (428)
T PRK08149 374 ELQLFIDLGEYRRGENADNDRAMDKRPALEAFLKQDVAEKSSFSDTLERLNEF 426 (428)
T ss_pred HHHHHHHcCCCCCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4567888886 557788899999999999 999999999999887543
No 26
>KOG1142|consensus
Probab=75.19 E-value=4.3 Score=32.20 Aligned_cols=32 Identities=19% Similarity=0.403 Sum_probs=28.9
Q ss_pred hhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Q psy13775 85 ERGLLESIKKEGKITEDTDAKLKTVVTNFLAN 116 (119)
Q Consensus 85 ~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~ 116 (119)
-.++++.|..+++|+++.++.|.+++++|+++
T Consensus 160 l~dLvqqId~~~~LD~dVedlLleiADdFV~s 191 (258)
T KOG1142|consen 160 LDDLVQQIDGTTKLDDDVEDLLLEIADDFVSS 191 (258)
T ss_pred hhHHHHhhcCcccccHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999874
No 27
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=73.99 E-value=5 Score=33.69 Aligned_cols=44 Identities=16% Similarity=0.222 Sum_probs=36.1
Q ss_pred hhhHHhhhcC-----CHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHH
Q psy13775 12 AGYHYSNFTA-----RIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIY 55 (119)
Q Consensus 12 ~~~~Fs~Fgs-----dl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~ 55 (119)
-.+.|.+||+ |..+...+++|.+|.+.| +++.|++.++=+--|.
T Consensus 365 e~~~~~~~g~y~~g~d~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~ 415 (418)
T TIGR03498 365 ETEDLIRLGAYRKGSDPELDEAIRLVPKIYEFLTQGPDEPTSLQDPFADLA 415 (418)
T ss_pred HHHHHHHhhCCcCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHH
Confidence 3467888875 448999999999999999 9999999887665554
No 28
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=73.02 E-value=4.3 Score=34.53 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=35.5
Q ss_pred hhhcCCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCc
Q psy13775 17 SNFTARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGH 61 (119)
Q Consensus 17 s~Fgsdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ 61 (119)
.+||||+..-..+.+|.+|.+.| +.++|.+ ++=+.-|..+..|-
T Consensus 399 y~~G~d~~~D~ai~~~~~i~~fL~Q~~~~~~~-~~~~~~l~~~~~~~ 444 (450)
T PRK06002 399 YRAGSDPDLDQAVDLVPRIYEALRQSPGDPPS-DDAFADLAAALKGA 444 (450)
T ss_pred cccCCChHHHHHHHhHHHHHHHhCCCCCCCCC-HHHHHHHHHHHhhH
Confidence 59999986666677899999999 9999999 77666777666553
No 29
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=71.77 E-value=4.1 Score=25.77 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=22.5
Q ss_pred hHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Q psy13775 86 RGLLESIKKEGKITEDTDAKLKTVVTNFLAN 116 (119)
Q Consensus 86 ~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~ 116 (119)
.+++++|..+..++++.++.|.+...+|+.+
T Consensus 6 ~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~ 36 (68)
T PF03847_consen 6 QELVKQIDPNEKLDPDVEELLLELADDFVDD 36 (68)
T ss_dssp HHHHHCC-SS----HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4678888899999999999999999999864
No 30
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=71.00 E-value=5.5 Score=33.88 Aligned_cols=42 Identities=7% Similarity=0.040 Sum_probs=35.3
Q ss_pred Hhhhc--CCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 16 YSNFT--ARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 16 Fs~Fg--sdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
|..|+ +|..+.+.+.++.++.+.| +.++|.+.++++.-|..+
T Consensus 400 ~g~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~~ 445 (451)
T PRK05688 400 VGAYVAGGDPETDLAIARFPHLVQFLRQGLRENVSLAQSREQLAAI 445 (451)
T ss_pred HhCccCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 44454 5559999999999999999 889999999999877655
No 31
>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.
Probab=70.42 E-value=6.1 Score=33.58 Aligned_cols=57 Identities=9% Similarity=0.087 Sum_probs=47.9
Q ss_pred hhHHhhhc-CCH--HHHHHHhcccchhhhc--CCCCC----------CCHHHHHHHHHHHhcCcCCCCChhh
Q psy13775 13 GYHYSNFT-ARI--GLNKSLMLSRRLPILL--GQYVP----------MAIEEQVAVIYCGVRGHLDKLDPAK 69 (119)
Q Consensus 13 ~~~Fs~Fg-sdl--~tr~~L~rG~Rl~ElL--~q~~P----------lsv~eQV~iL~a~~~G~ld~ipv~~ 69 (119)
..+++.+| ..+ ..+..+.+|+++.+.| +.|.+ .++++-+-..+.+-.|.+|++|...
T Consensus 368 ~~li~~~g~~~l~~~~~~~i~~~~~i~~fL~Q~~~~~e~~t~~~g~~v~l~~tl~~~~~il~g~~~~~~~~~ 439 (449)
T TIGR03305 368 KDIIAMLGLEQLSREDRRVVNRARRLERFLTQPFFTTEQFTGMKGKTVSLEDALDGCERILNDEFQDYPERD 439 (449)
T ss_pred HHHHHhhCCccCCHHHHHHHHHHHHHHHHhCCCCcccccccCCCCceeEHHHHHHHHHHHhcCCcccCCHHH
Confidence 34577778 355 6799999999999999 77777 7899999999999999999998764
No 32
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=67.76 E-value=8.6 Score=32.54 Aligned_cols=45 Identities=7% Similarity=-0.026 Sum_probs=37.2
Q ss_pred hhHHhhh-----cCCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 13 GYHYSNF-----TARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 13 ~~~Fs~F-----gsdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
-+.+.+| |+|..+.+.+.+|++|.+.| +.++|++.++++.-|..+
T Consensus 381 ~e~li~~G~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~ 432 (434)
T PRK08472 381 NEVLIRIGAYQKGNDKELDEAISKKEFMEQFLKQNPNELFPFEQTFEQLEEI 432 (434)
T ss_pred HHHHHHhhCccCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 3567777 55668888999999999999 999999999998766543
No 33
>PF09371 Tex_N: Tex-like protein N-terminal domain; InterPro: IPR018974 This presumed domain is found at the N terminus of Q45388 from SWISSPROT. This protein defines a novel family of prokaryotic transcriptional accessory factors []. ; PDB: 2OCE_A 3BZK_A 3BZC_A.
Probab=65.65 E-value=21 Score=26.88 Aligned_cols=49 Identities=20% Similarity=0.393 Sum_probs=29.0
Q ss_pred CcCCCCChhhHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHH
Q psy13775 60 GHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTV 109 (119)
Q Consensus 60 G~ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~ 109 (119)
|=||++.+-.|.+--..+. -|......+++.|...+++++++...|.++
T Consensus 37 G~Lde~~lR~i~~~~~~~~-~L~~Rk~~il~~i~eqgkLt~eL~~~I~~a 85 (193)
T PF09371_consen 37 GGLDEVQLREIQDRYEYLR-ELEKRKESILKSIEEQGKLTPELKQAIENA 85 (193)
T ss_dssp TS--HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHTT---HHHHHHHHH-
T ss_pred CCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHcccCCHHHHHHHHhc
Confidence 4445544444444444443 345556789999999999999998888776
No 34
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=62.32 E-value=16 Score=22.44 Aligned_cols=37 Identities=27% Similarity=0.366 Sum_probs=30.9
Q ss_pred CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHH
Q psy13775 40 GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKE 76 (119)
Q Consensus 40 ~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ 76 (119)
=.|.|+..++=..-|-+...|+.+.++...+.+|.+.
T Consensus 20 L~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~ 56 (64)
T PF09494_consen 20 LMYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLDS 56 (64)
T ss_pred HcCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHHH
Confidence 4699999999888888777788999999998887653
No 35
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=61.05 E-value=14 Score=31.46 Aligned_cols=41 Identities=17% Similarity=0.212 Sum_probs=35.6
Q ss_pred cCCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcC
Q psy13775 20 TARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRG 60 (119)
Q Consensus 20 gsdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G 60 (119)
|+|..+...+.+|.++.+.| +.+.+.+.++++..|+.+.+|
T Consensus 396 g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~l~~~ 438 (442)
T PRK08927 396 GSDPEVDEAIRLNPALEAFLRQGKDEATSLAEGYARLAQILGG 438 (442)
T ss_pred CCCHHHHHHHHccHHHHHhcCCCCCCCCCHHHHHHHHHHHhcc
Confidence 44558888899999999999 888999999999999887655
No 36
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=60.65 E-value=12 Score=31.74 Aligned_cols=43 Identities=7% Similarity=0.104 Sum_probs=35.7
Q ss_pred HHhhhcCCH--HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 15 HYSNFTARI--GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 15 ~Fs~Fgsdl--~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
.+..|++.+ .+.+.+++|.+|.+.| +.++|.+.++=+.-|..+
T Consensus 393 ~~g~y~~g~d~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~ 439 (444)
T PRK08972 393 SIGAYKQGSDPRIDNAIRLQPAMNAFLQQTMKEAVPYDMSVNMLKQL 439 (444)
T ss_pred HHhCccCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 456666555 9999999999999999 999999998877766654
No 37
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=60.58 E-value=13 Score=31.51 Aligned_cols=44 Identities=7% Similarity=-0.099 Sum_probs=36.4
Q ss_pred hhHHhhhcC-----CHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHH
Q psy13775 13 GYHYSNFTA-----RIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYC 56 (119)
Q Consensus 13 ~~~Fs~Fgs-----dl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a 56 (119)
-+.+.+||+ |+.+.+.+++|.+|.+.| +..+|++.++=+.-|..
T Consensus 379 ~e~li~~G~y~~g~d~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~ 429 (433)
T PRK07594 379 VELLIRIGEYQRGVDTDTDKAIDTYPDICTFLRQSKDEVCGPELLIEKLHQ 429 (433)
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 467788875 559999999999999999 99999998876665544
No 38
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=59.39 E-value=19 Score=22.59 Aligned_cols=31 Identities=19% Similarity=0.438 Sum_probs=25.6
Q ss_pred hHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Q psy13775 86 RGLLESIKKEGKITEDTDAKLKTVVTNFLAN 116 (119)
Q Consensus 86 ~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~ 116 (119)
.++++.+..+..++++.++.|.+..++|..+
T Consensus 8 ~~lv~~id~~~~~~~da~~~l~~~~e~fv~~ 38 (72)
T cd07981 8 QELLKEIDPREQLDPDVEELLLEIADDFVDD 38 (72)
T ss_pred HHHHHhhCCCCCcCHHHHHHHHHHHHHHHHH
Confidence 4677777777889999999999999988753
No 39
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=55.98 E-value=37 Score=20.88 Aligned_cols=36 Identities=14% Similarity=0.285 Sum_probs=25.2
Q ss_pred HHHHHHHHhchhHHHHHHHhcCC----CCHHHHHHHHHHHH
Q psy13775 75 KEFLAHIKSSERGLLESIKKEGK----ITEDTDAKLKTVVT 111 (119)
Q Consensus 75 ~~ll~~l~~~~~~~~~~I~~~~~----l~~~~~~~L~~~i~ 111 (119)
.++++||-+ +|++++.+.+++. +|+.....+.++++
T Consensus 3 Q~iV~YLv~-nPevl~kl~~g~asLIGv~~~e~~aIi~~F~ 42 (57)
T PF05952_consen 3 QEIVNYLVQ-NPEVLEKLKEGEASLIGVDKDEQKAIIDAFK 42 (57)
T ss_pred HHHHHHHHH-ChHHHHHHHcCCeeEecCCHHHHHHHHHHHc
Confidence 578899986 4999999988653 56665555555543
No 40
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=55.01 E-value=27 Score=29.91 Aligned_cols=57 Identities=9% Similarity=0.043 Sum_probs=47.5
Q ss_pred hhHHhhhcC-CH--HHHHHHhcccchhhhc--CC----------CCCCCHHHHHHHHHHHhcCcCCCCChhh
Q psy13775 13 GYHYSNFTA-RI--GLNKSLMLSRRLPILL--GQ----------YVPMAIEEQVAVIYCGVRGHLDKLDPAK 69 (119)
Q Consensus 13 ~~~Fs~Fgs-dl--~tr~~L~rG~Rl~ElL--~q----------~~Plsv~eQV~iL~a~~~G~ld~ipv~~ 69 (119)
..+++-+|- .+ .++..|.+|+++.+.| +. ..+.+.++-+.-|..+.+|-+|++|..+
T Consensus 374 e~li~i~gy~~~sd~~d~ai~~~~~i~~fL~Q~~~~~~~ft~~~~~~~~~~~~~~~l~~i~~g~~~~~~~~~ 445 (463)
T PRK09280 374 QDIIAILGMDELSEEDKLTVARARKIQRFLSQPFFVAEQFTGSPGKYVPLKDTIRGFKEILEGEYDHLPEQA 445 (463)
T ss_pred HHHHHhhCCccCCHHHHHHHHhhHHHHHhccCCcchhhcccCCCCcccCHHHHHHHHHHHhCCCccCCCHHH
Confidence 345666663 33 7999999999999999 66 6889999999999999999999999875
No 41
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=54.02 E-value=13 Score=31.40 Aligned_cols=44 Identities=11% Similarity=0.120 Sum_probs=35.1
Q ss_pred hhhHHhhhcCCH--HHHHHH----hcccchhhhc--CCCCCCCHHHHHHHHH
Q psy13775 12 AGYHYSNFTARI--GLNKSL----MLSRRLPILL--GQYVPMAIEEQVAVIY 55 (119)
Q Consensus 12 ~~~~Fs~Fgsdl--~tr~~L----~rG~Rl~ElL--~q~~Plsv~eQV~iL~ 55 (119)
--+.|.+||+.. .++... .+|.+|++.| +.++|++.++=+.-|.
T Consensus 378 e~e~~i~~g~y~~g~~~~~d~ai~~~~~~i~~fl~Q~~~~~~~~~~~~~~l~ 429 (432)
T PRK06793 378 ENELYFKLGTIQENAENAYIFECKNKVEGINTFLKQGRSDSFQFDDIVEAMH 429 (432)
T ss_pred HHHHHHHhCCccCCCCHHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHH
Confidence 346799999988 555555 5999999999 9999999888665554
No 42
>PF03671 Ufm1: Ubiquitin fold modifier 1 protein; InterPro: IPR005375 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1. This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [, ]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms []. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (IPR012462 from INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes []. For further information on ubiquitin, please see Protein of the Month [].; PDB: 1J0G_A 1WXS_A 1L7Y_A.
Probab=54.02 E-value=4.8 Score=26.12 Aligned_cols=14 Identities=21% Similarity=0.366 Sum_probs=11.8
Q ss_pred cchhhHHhhhcCCH
Q psy13775 10 QKAGYHYSNFTARI 23 (119)
Q Consensus 10 ~~~~~~Fs~Fgsdl 23 (119)
|-||-+|-++||+|
T Consensus 60 QTag~vflKhGseL 73 (76)
T PF03671_consen 60 QTAGNVFLKHGSEL 73 (76)
T ss_dssp SBHHHHHHHT-SEE
T ss_pred hhhhhhHhhcCcEe
Confidence 67999999999986
No 43
>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=53.37 E-value=13 Score=31.16 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=30.5
Q ss_pred hHHhhhc-----CCHHHHHHHhcccchhhhc--CCCCCCCHHHHH
Q psy13775 14 YHYSNFT-----ARIGLNKSLMLSRRLPILL--GQYVPMAIEEQV 51 (119)
Q Consensus 14 ~~Fs~Fg-----sdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV 51 (119)
+.+.++| +|..+.+.+.+|+++.+.| +.++|.+.++=+
T Consensus 364 ~~l~~~g~y~~g~d~~~d~~i~~~~~i~~fl~Q~~~~~~~~~~~~ 408 (411)
T TIGR03496 364 RDLISIGAYQAGSDPELDQAIALYPRIEAFLQQGMRERASFEESL 408 (411)
T ss_pred HHHHHhcCCcCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHH
Confidence 5566665 6667888899999999999 889999987643
No 44
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=50.07 E-value=26 Score=29.72 Aligned_cols=45 Identities=9% Similarity=-0.069 Sum_probs=36.9
Q ss_pred hhHHhhhc-----CCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 13 GYHYSNFT-----ARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 13 ~~~Fs~Fg-----sdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
-+.+.+|| +|..+...+.+++++.+.| +.++|.+.++=+--|..+
T Consensus 380 ~~~li~~g~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~~ 431 (434)
T PRK07196 380 IKPLIPLGGYVAGADPMADQAVHYYPAITQFLRQEVGHPALFSASVEQLTGM 431 (434)
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 35677876 5668999999999999999 889999998877666554
No 45
>PF05291 Bystin: Bystin; InterPro: IPR007955 Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy []. This family also includes the Saccharomyces cerevisiae protein ENP1. ENP1 is an essential protein in S. cerevisiae and is localised in the nucleus []. It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective S. cerevisiae cannot synthesise 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits [].
Probab=49.12 E-value=60 Score=26.36 Aligned_cols=55 Identities=18% Similarity=0.177 Sum_probs=47.1
Q ss_pred HHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHH
Q psy13775 52 AVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTN 112 (119)
Q Consensus 52 ~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~ 112 (119)
..+|+++.=|..+++.....+|-+.++= |-+.++|.++++|+--+-..|+.++-.
T Consensus 94 ~A~~~aTRiF~SnL~~~~aqrF~~~VLL------prvredI~~~KKLn~hly~ALkKalyK 148 (301)
T PF05291_consen 94 HAMYEATRIFASNLNEKMAQRFYNLVLL------PRVREDIAENKKLNYHLYMALKKALYK 148 (301)
T ss_pred HHHHHHHHHHhhCCCHHHHHHHHHHHHH------HHHHHHHHHcCCcCHHHHHHHHHHHcC
Confidence 3479999999999999999999888775 678889999999999988888887643
No 46
>PRK06820 type III secretion system ATPase; Validated
Probab=48.86 E-value=30 Score=29.35 Aligned_cols=44 Identities=7% Similarity=-0.022 Sum_probs=35.8
Q ss_pred hhHHhhhc-----CCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHH
Q psy13775 13 GYHYSNFT-----ARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYC 56 (119)
Q Consensus 13 ~~~Fs~Fg-----sdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a 56 (119)
.+.+.+|| +|..+...+.+|.++.+.| +.+++.+.++=+..|+.
T Consensus 387 ~~~li~~G~y~~g~d~~~d~~i~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~ 437 (440)
T PRK06820 387 IELLVRVGEYQAGEDLQADEALQRYPAICAFLQQDHSETAHLETTLEHLAQ 437 (440)
T ss_pred HHHHHHhhCccCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 34577885 4558999999999999999 88999998887766654
No 47
>TIGR01026 fliI_yscN ATPase FliI/YscN family. This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.
Probab=46.65 E-value=25 Score=29.71 Aligned_cols=45 Identities=13% Similarity=0.064 Sum_probs=36.0
Q ss_pred hhHHhhhc-----CCHHHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHH
Q psy13775 13 GYHYSNFT-----ARIGLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 13 ~~~Fs~Fg-----sdl~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~ 57 (119)
-+.+.++| +|..+...+.+|+++.+.| +.|.+.+.++++.-|..+
T Consensus 387 ~~~li~ig~y~~g~d~~~d~~i~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~ 438 (440)
T TIGR01026 387 NEDLIRIGAYQRGSDRELDFAIAKYPKLERFLKQGINEKVNFEESLQQLEEI 438 (440)
T ss_pred HHHHHHhhccccCCCHHHHHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHh
Confidence 35677785 4557777899999999999 999999999998766543
No 48
>PF03048 Herpes_UL92: UL92 family; InterPro: IPR004289 Members of this family are functionally uncharacterised proteins from herpesviruses. The N terminus of these proteins contain 6 conserved cysteines and histidines that might form a zinc binding domain.
Probab=46.42 E-value=93 Score=23.64 Aligned_cols=51 Identities=8% Similarity=0.180 Sum_probs=39.6
Q ss_pred hhhHHHHHHHHHHHHHhc--hhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13775 67 PAKITTFEKEFLAHIKSS--ERGLLESIKKEGKITEDTDAKLKTVVTNFLANF 117 (119)
Q Consensus 67 v~~I~~fe~~ll~~l~~~--~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~f 117 (119)
..-|....+.+..||.+. .+++.++|-.++.|.+.+++.+...+......|
T Consensus 84 ~niv~~l~~dv~~y~~~~~~~~~V~~~i~~~g~l~~~i~~~I~~TF~~c~~~~ 136 (192)
T PF03048_consen 84 VNIVESLKSDVYSYFSRSNDYAEVKQAIFEDGELKPHIEDLIYFTFNHCFHVF 136 (192)
T ss_pred HHHHHHHHHHHHHHHHhcccHHHHHHHHHcCCcccHhHHHHHHHHHHHHHHhh
Confidence 344566677788888755 578889999999999999999998888765544
No 49
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=45.41 E-value=58 Score=21.18 Aligned_cols=38 Identities=16% Similarity=0.283 Sum_probs=29.2
Q ss_pred HHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Q psy13775 75 KEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFL 114 (119)
Q Consensus 75 ~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~ 114 (119)
+.+++|+++-.|+.+..+.+. -+++..+.+++.+....
T Consensus 1 n~L~~yi~~l~pe~~~~l~~~--~s~ev~e~m~~~v~~ll 38 (86)
T PF05542_consen 1 NDLLQYIQSLKPERIQQLSEP--ASPEVLEAMKQHVSGLL 38 (86)
T ss_pred ChHHHHHHHCCHHHHHHhhcc--CCHHHHHHHHHHHHHHH
Confidence 357889999888888888654 58888888887776654
No 50
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=43.96 E-value=28 Score=22.87 Aligned_cols=51 Identities=12% Similarity=0.184 Sum_probs=38.2
Q ss_pred CCChhhHHHHHHHHHHHHHhchhHHH----------HHHHhcCCCCHHHHHHHHHHHHHHHH
Q psy13775 64 KLDPAKITTFEKEFLAHIKSSERGLL----------ESIKKEGKITEDTDAKLKTVVTNFLA 115 (119)
Q Consensus 64 ~ipv~~I~~fe~~ll~~l~~~~~~~~----------~~I~~~~~l~~~~~~~L~~~i~~~~~ 115 (119)
.+|...+..++.++.+.+...+|+.- +.++-.+. +++.++.+.+++++..+
T Consensus 12 ~lp~ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~s~n~lsv~g~-~k~dK~~i~eiLqE~we 72 (81)
T PRK10597 12 PLPAGAIDALAGELSRRIQYAFPDNEGHVSVRYAAANNLSVIGA-TKEDKDRISEILQETWE 72 (81)
T ss_pred CCChhHHHHHHHHHHHHHHhhCCCCCccEEEeecCCCceEecCC-CcchHHHHHHHHHHHHh
Confidence 67888999999999999999999975 33332232 34467888888887755
No 51
>KOG1597|consensus
Probab=42.47 E-value=83 Score=25.63 Aligned_cols=78 Identities=15% Similarity=0.164 Sum_probs=53.9
Q ss_pred cchhhHHhhhcCCH-----HHHHHHhcccchhhhc--CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHH
Q psy13775 10 QKAGYHYSNFTARI-----GLNKSLMLSRRLPILL--GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIK 82 (119)
Q Consensus 10 ~~~~~~Fs~Fgsdl-----~tr~~L~rG~Rl~ElL--~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~ 82 (119)
-.++..-.||=|.| ++....+-+++..|+= +--+|+|++ ++++|.+..=.=..-+..+|...-.---.=++
T Consensus 201 ~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIA--Aa~IYmisqls~~kkt~keI~~vtgVaE~TIr 278 (308)
T KOG1597|consen 201 ISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIA--AAAIYMISQLSDEKKTQKEIGEVTGVAEVTIR 278 (308)
T ss_pred hhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHH--HHHHHHHHHhccCcccHHHHHHHhhhhHHHHH
Confidence 34677788999998 6666667777776665 778999999 78888887755566677777665544444444
Q ss_pred hchhHHH
Q psy13775 83 SSERGLL 89 (119)
Q Consensus 83 ~~~~~~~ 89 (119)
+.+.+++
T Consensus 279 ~sYK~Ly 285 (308)
T KOG1597|consen 279 NSYKDLY 285 (308)
T ss_pred HHHHHHh
Confidence 4444443
No 52
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=42.36 E-value=58 Score=19.84 Aligned_cols=33 Identities=9% Similarity=0.325 Sum_probs=27.5
Q ss_pred CCCCChhhHHHHHHHHHHHHHhchhHHHHHHHh
Q psy13775 62 LDKLDPAKITTFEKEFLAHIKSSERGLLESIKK 94 (119)
Q Consensus 62 ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~ 94 (119)
++.|+-..|..|.+.+...++....+++..|+.
T Consensus 1 m~~~~~~~~d~yI~~Lk~kLd~Kk~Eil~~ln~ 33 (56)
T PF08112_consen 1 MSEIDKSTIDKYISILKSKLDEKKSEILSNLNM 33 (56)
T ss_pred CcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778889999999999999988888887754
No 53
>PF14802 TMEM192: TMEM192 family
Probab=42.32 E-value=54 Score=25.52 Aligned_cols=36 Identities=14% Similarity=0.136 Sum_probs=31.1
Q ss_pred hcCcCCCCChhhHHHHHHHHHHHHHhchhHHHHHHH
Q psy13775 58 VRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIK 93 (119)
Q Consensus 58 ~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~ 93 (119)
..|+=+..+++++-+-++++++|++++...+.++|.
T Consensus 198 e~g~r~~~~~eellEkQadlI~yLk~hn~~L~~ril 233 (236)
T PF14802_consen 198 ELGFRDGSSLEELLEKQADLIRYLKEHNARLSRRIL 233 (236)
T ss_pred ccCCcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 348888889999999999999999998877777764
No 54
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=38.35 E-value=1.1e+02 Score=19.87 Aligned_cols=33 Identities=18% Similarity=0.285 Sum_probs=27.2
Q ss_pred cCcCCCCChhhHHHHHHHHHHHHHhchhHHHHH
Q psy13775 59 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLES 91 (119)
Q Consensus 59 ~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~ 91 (119)
.+.+|..+++.+...+..++..|..++..+.+-
T Consensus 5 ~~~~d~~d~~~~l~~Q~~~l~~ln~tn~~L~~~ 37 (88)
T PF10241_consen 5 TQAVDPEDLDEILALQAQTLGRLNKTNEELLNL 37 (88)
T ss_pred HhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999998876666543
No 55
>PF14022 DUF4238: Protein of unknown function (DUF4238)
Probab=37.49 E-value=1.5e+02 Score=21.56 Aligned_cols=56 Identities=16% Similarity=0.243 Sum_probs=38.7
Q ss_pred HHhcCcCCCCChhhHH-HHHHHHHHHHHhchhHHHHHHHhcCC---CCHHHHHHHHHHHHH
Q psy13775 56 CGVRGHLDKLDPAKIT-TFEKEFLAHIKSSERGLLESIKKEGK---ITEDTDAKLKTVVTN 112 (119)
Q Consensus 56 a~~~G~ld~ipv~~I~-~fe~~ll~~l~~~~~~~~~~I~~~~~---l~~~~~~~L~~~i~~ 112 (119)
+..++|.+....+.-. ..|+.+ ..+....+.+++.|..... ++++....|...+-.
T Consensus 39 ~~e~~~Y~~~~~~~~~~~iE~~~-~~iE~~~~~~i~~i~~~~~~~~l~~~~~~~l~~F~~~ 98 (265)
T PF14022_consen 39 CFEKDFYTIKDDDGERDEIEDLL-SEIESEAAPIIDKIIDGRRSSKLTEEDKETLAEFLAL 98 (265)
T ss_pred hhhhccccCCCCCchHHHHHHHH-HHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHH
Confidence 3445555544444333 677777 8888888899999988776 888888877766543
No 56
>PRK06213 enoyl-CoA hydratase; Provisional
Probab=37.16 E-value=1.1e+02 Score=22.77 Aligned_cols=72 Identities=13% Similarity=0.117 Sum_probs=42.8
Q ss_pred hhhcCCCCCCCHHHHHHHHHHHhcCcCCCC-ChhhHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Q psy13775 36 PILLGQYVPMAIEEQVAVIYCGVRGHLDKL-DPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFL 114 (119)
Q Consensus 36 ~ElL~q~~Plsv~eQV~iL~a~~~G~ld~i-pv~~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~ 114 (119)
++++=...+++.++ |..-|++|.| |.+++.+.-.++.+.+....|..+..++.. +.......+.++++...
T Consensus 154 ~~lll~g~~~~a~e------A~~~Glv~~vv~~~~l~~~a~~~a~~la~~~~~a~~~~K~~--l~~~~~~~l~~~~~~~~ 225 (229)
T PRK06213 154 QRAVINAEMFDPEE------AVAAGFLDEVVPPEQLLARAQAAARELAGLNMGAHAATKLK--VRAAALEAIRAAIEGDA 225 (229)
T ss_pred HHHHHcCcccCHHH------HHHCCCceeccChHHHHHHHHHHHHHHhcCCHHHHHHHHHH--HHHHHHHHHHhchhhhh
Confidence 34442333566543 4456999987 778888888888888877767666544332 33444444555544443
Q ss_pred H
Q psy13775 115 A 115 (119)
Q Consensus 115 ~ 115 (119)
+
T Consensus 226 ~ 226 (229)
T PRK06213 226 A 226 (229)
T ss_pred h
Confidence 3
No 57
>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=36.62 E-value=32 Score=25.24 Aligned_cols=42 Identities=12% Similarity=0.392 Sum_probs=30.0
Q ss_pred ccchhhHHhhhcCCH--HHHHHHhcccchhhhcCCCCCCCHHHHHHHH
Q psy13775 9 PQKAGYHYSNFTARI--GLNKSLMLSRRLPILLGQYVPMAIEEQVAVI 54 (119)
Q Consensus 9 ~~~~~~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL~q~~Plsv~eQV~iL 54 (119)
|.-+-++|.+|+.-. ..+..++.-++| |-|.=++.++|+++|
T Consensus 7 ~~~~~~~~~~~~~~~~~~i~~~V~waK~i----PgF~~L~~~DQi~LL 50 (189)
T cd06940 7 PKSGHEIWEEFSMSFTPAVREVVEFAKRI----PGFRDLSQHDQVTLL 50 (189)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHhcC----CCcccCChhhHHHHH
Confidence 444568899997655 555555544443 899999999999876
No 58
>KOG0981|consensus
Probab=34.44 E-value=2.1e+02 Score=25.83 Aligned_cols=27 Identities=11% Similarity=0.254 Sum_probs=17.4
Q ss_pred HHhcCCCCHHHHHHHHHHHHHHHHhcC
Q psy13775 92 IKKEGKITEDTDAKLKTVVTNFLANFT 118 (119)
Q Consensus 92 I~~~~~l~~~~~~~L~~~i~~~~~~f~ 118 (119)
-+..+.++.+-...|++.-..+-+.|.
T Consensus 308 ~E~rK~mskEEK~~iKeEkek~ee~y~ 334 (759)
T KOG0981|consen 308 KEKRKQMSKEEKLKIKEEKEKLEEKYG 334 (759)
T ss_pred HHHHhhcCHHHHHHHHHHHHHHHHHcC
Confidence 344566777777777777666666554
No 59
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=33.91 E-value=82 Score=28.87 Aligned_cols=51 Identities=18% Similarity=0.418 Sum_probs=41.0
Q ss_pred hcCcCCCCChhhHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHH
Q psy13775 58 VRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTV 109 (119)
Q Consensus 58 ~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~ 109 (119)
..|-+|++.+-+|.+--..+. -|++....+++.|.+.+++++++...+..+
T Consensus 48 ~tg~Lde~qlr~i~~~~~yl~-~L~~Rke~Ilk~IeeqGklTd~L~~~I~~a 98 (780)
T COG2183 48 ITGGLDEVQLRDLEERLEYLR-ELEERKESILKSIEEQGKLTDELKEQIEAA 98 (780)
T ss_pred cCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhccchHHHHHHHHHh
Confidence 347778888888777666666 577777889999999999999988888774
No 60
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=33.55 E-value=95 Score=18.55 Aligned_cols=26 Identities=8% Similarity=0.086 Sum_probs=17.4
Q ss_pred CHHHHHHHHHHHhcCcCC---CCChhhHH
Q psy13775 46 AIEEQVAVIYCGVRGHLD---KLDPAKIT 71 (119)
Q Consensus 46 sv~eQV~iL~a~~~G~ld---~ipv~~I~ 71 (119)
+..+.-++.-|...||+| ++.++++.
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA 30 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELA 30 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHH
Confidence 344556777888999998 45555544
No 61
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=33.53 E-value=90 Score=22.02 Aligned_cols=42 Identities=14% Similarity=0.187 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHHHHhchh--HHHHHHHhcCCCCHHHHHHHHHHH
Q psy13775 69 KITTFEKEFLAHIKSSER--GLLESIKKEGKITEDTDAKLKTVV 110 (119)
Q Consensus 69 ~I~~fe~~ll~~l~~~~~--~~~~~I~~~~~l~~~~~~~L~~~i 110 (119)
+..+|...+..|+..+.+ +.++.|-.+..++....+.|...+
T Consensus 2 ~~~~y~e~~~~~l~~~~~~~~al~~i~~~~~~~~~~L~eL~~~l 45 (164)
T PF08463_consen 2 EAEDYRERFRKYLREHFDDIEALRKIWSNPPLTEADLKELEEKL 45 (164)
T ss_pred CHHHHHHHHHHHHHHHhcCHHHHHHHHcCcccCHHHHHHHHHhC
Confidence 456777777777776532 477778888888888888887765
No 62
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=33.20 E-value=1.3e+02 Score=20.05 Aligned_cols=31 Identities=10% Similarity=0.265 Sum_probs=22.2
Q ss_pred HhchhHHHHHHHhcCCCCHHHHHHHHHHHHH
Q psy13775 82 KSSERGLLESIKKEGKITEDTDAKLKTVVTN 112 (119)
Q Consensus 82 ~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~ 112 (119)
....+.++..+-.+.++|++..+.|.+.+++
T Consensus 85 ~gs~~~l~~~l~~~~~ls~~el~~L~~li~e 115 (115)
T PF03965_consen 85 DGSIPQLVAALVESEELSPEELEELRKLIDE 115 (115)
T ss_dssp TTHHHHHHHHHHHCT-S-HHHHHHHHHHHH-
T ss_pred CCCHHHHHHHHHhcCCCCHHHHHHHHHHHcC
Confidence 3455678888878889999999999888763
No 63
>PHA00684 hypothetical protein
Probab=32.11 E-value=61 Score=23.14 Aligned_cols=27 Identities=15% Similarity=0.164 Sum_probs=24.0
Q ss_pred hcCcCCCCChhhHHHHHHHHHHHHHhc
Q psy13775 58 VRGHLDKLDPAKITTFEKEFLAHIKSS 84 (119)
Q Consensus 58 ~~G~ld~ipv~~I~~fe~~ll~~l~~~ 84 (119)
..|-+..+|++.|..+.++++.|-+++
T Consensus 46 ~~~~l~~~~l~~I~~~V~~Fi~ya~~h 72 (128)
T PHA00684 46 AGTVISTLSLPDIGAAVNRFIAYATAH 72 (128)
T ss_pred cCCccccccHHHHHHHHHHHHHHHHhC
Confidence 378888999999999999999999854
No 64
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=32.09 E-value=65 Score=27.42 Aligned_cols=46 Identities=15% Similarity=0.044 Sum_probs=35.4
Q ss_pred HhhhcCCH--HHHHHHhcccchhhhc-CCCCCCCHHHHHHHHHHHhcCc
Q psy13775 16 YSNFTARI--GLNKSLMLSRRLPILL-GQYVPMAIEEQVAVIYCGVRGH 61 (119)
Q Consensus 16 Fs~Fgsdl--~tr~~L~rG~Rl~ElL-~q~~Plsv~eQV~iL~a~~~G~ 61 (119)
+.++|.+| .++..|.+|+++-..| .|..-.|++|-+-.-+.+-+++
T Consensus 365 li~iG~eLs~~d~~~l~~~~~~e~~~~~~g~~~~~~etl~~~~~~l~~~ 413 (436)
T PRK02118 365 KMAMGFKLSNWDEKLLKFSELFESRLMDLEVNIPLEEALDLGWKILAQC 413 (436)
T ss_pred HHHhhhhcCHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHC
Confidence 44578777 8999999999999998 8778888888777666654443
No 65
>PF12581 DUF3756: Protein of unknown function (DUF3756); InterPro: IPR022230 This domain family is found in viruses, and is approximately 40 amino acids in length. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0070008 serine-type exopeptidase activity
Probab=31.92 E-value=16 Score=20.79 Aligned_cols=17 Identities=35% Similarity=0.714 Sum_probs=14.3
Q ss_pred cccccccccchhhHHhh
Q psy13775 2 EWNVRLLPQKAGYHYSN 18 (119)
Q Consensus 2 ~~~~~~~~~~~~~~Fs~ 18 (119)
||....-|.-||+||-|
T Consensus 25 ewalstepppaGY~~~r 41 (41)
T PF12581_consen 25 EWALSTEPPPAGYAIVR 41 (41)
T ss_pred hhhhccCCCCccccccC
Confidence 78888899999999853
No 66
>KOG1379|consensus
Probab=29.67 E-value=20 Score=29.38 Aligned_cols=28 Identities=29% Similarity=0.323 Sum_probs=23.4
Q ss_pred HHHHHhcCcCCCCChhhHHHHHHHHHHH
Q psy13775 53 VIYCGVRGHLDKLDPAKITTFEKEFLAH 80 (119)
Q Consensus 53 iL~a~~~G~ld~ipv~~I~~fe~~ll~~ 80 (119)
++.+++.|++|+||-+.|..+-..+...
T Consensus 248 vIilATDGlfDNl~e~~Il~il~~~~~~ 275 (330)
T KOG1379|consen 248 VIILATDGLFDNLPEKEILSILKGLDAR 275 (330)
T ss_pred EEEEecccccccccHHHHHHHHHHhhcc
Confidence 3567899999999999998888777764
No 67
>COG3160 Rsd Regulator of sigma D [Transcription]
Probab=29.59 E-value=2e+02 Score=21.10 Aligned_cols=48 Identities=17% Similarity=0.389 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhcCcCC------CCChhhHHHHHHHHHHHHHhchhHHHHHHHh
Q psy13775 47 IEEQVAVIYCGVRGHLD------KLDPAKITTFEKEFLAHIKSSERGLLESIKK 94 (119)
Q Consensus 47 v~eQV~iL~a~~~G~ld------~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~ 94 (119)
.-.++++=|+.-.|+=- .+..+....|+..++.|+..-|=.+.+.|..
T Consensus 25 ~Rk~llvayc~l~gikp~ke~~~plnakaL~~FCq~LvDYlSaGHF~iYe~i~~ 78 (162)
T COG3160 25 VRKHLLVAYCNLVGIKPGKESYMPLNAKALDDFCQSLVDYLSAGHFSIYERILH 78 (162)
T ss_pred HHHHHHHHHHHHhccCccccccCCCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 44567777776666543 6688899999999999999988888877755
No 68
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.54 E-value=1.3e+02 Score=22.98 Aligned_cols=49 Identities=18% Similarity=0.179 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHHHHHHH
Q psy13775 43 VPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIK 93 (119)
Q Consensus 43 ~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~ 93 (119)
.|+--.+=.+-+..+ .+......+++.+|.+.|-.|+.+.+.+.+..-.
T Consensus 67 ~p~vd~~~~a~~vLG--k~~k~aspeQ~~~F~~aF~~yl~q~Y~~aL~~Y~ 115 (202)
T COG2854 67 LPYVDFKYAAKLVLG--KYYKTASPEQRQAFFKAFRTYLEQTYGQALLDYK 115 (202)
T ss_pred hhhhcHHHHHHHHhc--cccccCCHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 344444444455555 7779999999999999999999999988776543
No 69
>PRK07021 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=29.18 E-value=45 Score=24.06 Aligned_cols=43 Identities=9% Similarity=0.166 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHH
Q psy13775 69 KITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVT 111 (119)
Q Consensus 69 ~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~ 111 (119)
+.+..++.++.+|.+..++-+........|.+++.+.+.+.+.
T Consensus 101 ~~p~IRd~ii~~Ls~k~~~~L~~~eGk~~Lk~ei~~~in~~l~ 143 (162)
T PRK07021 101 YLPEVRSRLLLLLSRKHAAELATEEGKQKLAAEIKQTLSQPLV 143 (162)
T ss_pred hCHHHHHHHHHHHhcCCHHHhcCHHHHHHHHHHHHHHHHHHHh
Confidence 3456677888888888777776666665566665555555543
No 70
>PF04353 Rsd_AlgQ: Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; InterPro: IPR007448 This family includes bacterial transcriptional regulators that are thought to act through an interaction with the conserved region 4 of the sigma(70) subunit of RNA polymerase. The Pseudomonas aeruginosa homologue, AlgQ, positively regulates virulence gene expression and is associated with the mucoid phenotype observed in P. aeruginosa isolates from cystic fibrosis patients.; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_A.
Probab=29.13 E-value=2.3e+02 Score=20.70 Aligned_cols=47 Identities=15% Similarity=0.322 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhcCcCCC------CChhhHHHHHHHHHHHHHhchhHHHHHHHh
Q psy13775 48 EEQVAVIYCGVRGHLDK------LDPAKITTFEKEFLAHIKSSERGLLESIKK 94 (119)
Q Consensus 48 ~eQV~iL~a~~~G~ld~------ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~ 94 (119)
-.|.++.|+.-.|+=.. ...+++..|+..+..|+..-|=++.+.|..
T Consensus 26 Rq~Llv~Yc~L~gl~p~~~~~~~~~~~~l~~FCq~LVDYvSaGHFeIYe~l~~ 78 (153)
T PF04353_consen 26 RQQLLVAYCKLAGLKPYKESLTLPSEEALQNFCQQLVDYVSAGHFEIYEQLID 78 (153)
T ss_dssp HHHHHHHHHHHHS-------------HHHHHHHHHHHHHHHHHHHTHHHHHHT
T ss_pred HHHHHHHHHhHhcCCCCccccCCCCHHHHHHHHHHHHHHHhccchhHHHHHHH
Confidence 45778888887776432 356899999999999999998889888765
No 71
>PF10392 COG5: Golgi transport complex subunit 5; InterPro: IPR019465 The conserved oligomeric Golgi (COG) complex is a peripheral membrane complex involved in intra-Golgi protein trafficking. Subunit 5 is located in the smaller, B lobe, together with subunits 6-8, and has been shown to bind subunits 1 and 7 [].
Probab=28.89 E-value=1.4e+02 Score=20.63 Aligned_cols=47 Identities=13% Similarity=0.260 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Q psy13775 69 KITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLAN 116 (119)
Q Consensus 69 ~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~ 116 (119)
.|.+...++-..+..+|.+++......+.++. ....++..+.....+
T Consensus 41 ~i~eld~~i~~~v~~~~~~LL~q~~~~~~~~~-~l~~v~~~v~~L~~s 87 (132)
T PF10392_consen 41 DIQELDKRIRSQVTSNHEDLLSQASSIEELES-VLQAVRSSVESLQSS 87 (132)
T ss_pred HHHHHHHHHHHHHHhCHHHHHHHHHhHHHHHH-HHHHHHHHHHHHHHH
Confidence 35566777777778889999998887766655 666666666555443
No 72
>PRK05696 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=28.52 E-value=63 Score=23.47 Aligned_cols=43 Identities=14% Similarity=0.205 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHH
Q psy13775 70 ITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTN 112 (119)
Q Consensus 70 I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~ 112 (119)
.+..++.++.+|++..++-+........|.+++...+...+..
T Consensus 110 ~p~IRd~i~~~Ls~k~~~~L~~~~gk~~Lr~el~~~i~~~l~~ 152 (170)
T PRK05696 110 IPLIESALLMTFSSATVDQLSTPAGKEELRQKALASVQETLQK 152 (170)
T ss_pred hHHHHHHHHHHHhcCCHHHhcCHHHHHHHHHHHHHHHHHHHHh
Confidence 3346788888998888877776666666666666666665544
No 73
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=28.37 E-value=1.2e+02 Score=21.98 Aligned_cols=25 Identities=12% Similarity=0.069 Sum_probs=21.4
Q ss_pred cCcCCCCChhhHHHHHHHHHHHHHh
Q psy13775 59 RGHLDKLDPAKITTFEKEFLAHIKS 83 (119)
Q Consensus 59 ~G~ld~ipv~~I~~fe~~ll~~l~~ 83 (119)
+.+|.++|.++..+..+.+-+|++.
T Consensus 11 ~~~L~~lp~~e~~e~l~~Y~e~f~d 35 (181)
T PF08006_consen 11 EKYLKKLPEEEREEILEYYEEYFDD 35 (181)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999999975
No 74
>PF02260 FATC: FATC domain; InterPro: IPR003152 The FATC domain is found at the C-terminal end of the PIK-related kinases. Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding; PDB: 2KIT_A 1W1N_A 2KIO_A.
Probab=28.26 E-value=25 Score=18.98 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=7.4
Q ss_pred CCCCHHHHHHHHH
Q psy13775 43 VPMAIEEQVAVIY 55 (119)
Q Consensus 43 ~Plsv~eQV~iL~ 55 (119)
+|+|+++||--|.
T Consensus 1 e~lsv~~qV~~LI 13 (33)
T PF02260_consen 1 EPLSVEQQVDELI 13 (33)
T ss_dssp --S-STHHHHHHH
T ss_pred CCCCHHHHHHHHH
Confidence 4788888887654
No 75
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=27.49 E-value=53 Score=19.07 Aligned_cols=18 Identities=22% Similarity=0.468 Sum_probs=14.7
Q ss_pred HHHHHHHhcCcCCCCChh
Q psy13775 51 VAVIYCGVRGHLDKLDPA 68 (119)
Q Consensus 51 V~iL~a~~~G~ld~ipv~ 68 (119)
++.++|.++|-+|+.+-.
T Consensus 19 ~~f~Wavk~GQfdD~e~~ 36 (45)
T PF03597_consen 19 AAFLWAVKSGQFDDLEGP 36 (45)
T ss_pred HHHHHHHccCCCCCCcch
Confidence 457899999999998654
No 76
>PF09047 MEF2_binding: MEF2 binding; InterPro: IPR015134 The myocyte enhancer factor-2 (MEF2) binding domain, predominantly found in the calcineurin-binding protein CABIN 1, adopts an amphipathic alpha-helical structure, which allows it to bind a hydrophobic groove on the MEF2S domain, forming a triple-helical interaction. Interaction of this domain with MEF2 causes repression of transcription []. ; PDB: 1N6J_G.
Probab=27.48 E-value=65 Score=17.63 Aligned_cols=20 Identities=35% Similarity=0.612 Sum_probs=12.4
Q ss_pred HhcCCCCHHHHHHHHHHHHH
Q psy13775 93 KKEGKITEDTDAKLKTVVTN 112 (119)
Q Consensus 93 ~~~~~l~~~~~~~L~~~i~~ 112 (119)
...+.++++.+.+|+.++-.
T Consensus 4 spkgsiseetkqklk~~ils 23 (35)
T PF09047_consen 4 SPKGSISEETKQKLKSAILS 23 (35)
T ss_dssp --SS---HHHHHHHHHHHHT
T ss_pred CCCCcccHHHHHHHHHHHhh
Confidence 45678999999999988753
No 77
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=26.78 E-value=2.2e+02 Score=19.67 Aligned_cols=34 Identities=9% Similarity=0.202 Sum_probs=26.4
Q ss_pred HhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Q psy13775 82 KSSERGLLESIKKEGKITEDTDAKLKTVVTNFLA 115 (119)
Q Consensus 82 ~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~ 115 (119)
..+...++..+-.++.+|++..+.|.+.|++-.+
T Consensus 86 ~gs~~~ll~~l~~~~~ls~eele~L~~li~~~~~ 119 (130)
T TIGR02698 86 SRKVGAVIADLIEESPLSQTDIEKLEKLLSEKKS 119 (130)
T ss_pred CCCHHHHHHHHHhcCCCCHHHHHHHHHHHHhccc
Confidence 3444567777777888999999999999988654
No 78
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=26.72 E-value=3.6 Score=23.02 Aligned_cols=28 Identities=21% Similarity=0.337 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhcCcCCCCChhhHHHHH
Q psy13775 47 IEEQVAVIYCGVRGHLDKLDPAKITTFE 74 (119)
Q Consensus 47 v~eQV~iL~a~~~G~ld~ipv~~I~~fe 74 (119)
...|..|.|.+.=-.+|++|.+++.+..
T Consensus 4 ~~~qLTIfY~G~V~Vfd~v~~~Ka~~im 31 (36)
T PF06200_consen 4 ETAQLTIFYGGQVCVFDDVPPDKAQEIM 31 (36)
T ss_pred CCCcEEEEECCEEEEeCCCCHHHHHHHH
Confidence 3456667788888889999999887643
No 79
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=25.70 E-value=1.2e+02 Score=16.95 Aligned_cols=20 Identities=15% Similarity=0.326 Sum_probs=16.9
Q ss_pred CCCChhhHHHHHHHHHHHHH
Q psy13775 63 DKLDPAKITTFEKEFLAHIK 82 (119)
Q Consensus 63 d~ipv~~I~~fe~~ll~~l~ 82 (119)
|+.+.+++.++-+++..|+.
T Consensus 10 ~~a~~e~l~~Y~~~L~~Yin 29 (36)
T smart00309 10 DDASPEDLRQYLAALREYIN 29 (36)
T ss_pred CCCCHHHHHHHHHHHHHHHH
Confidence 56788999999999998885
No 80
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus.
Probab=25.43 E-value=61 Score=19.42 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=14.8
Q ss_pred HHHHHHHhcCcCCCCChh
Q psy13775 51 VAVIYCGVRGHLDKLDPA 68 (119)
Q Consensus 51 V~iL~a~~~G~ld~ipv~ 68 (119)
++.++|+++|-+|+++-.
T Consensus 20 ~~f~Wavk~GQfDDle~~ 37 (51)
T TIGR00847 20 VAFLWSLKSGQYDDLKGA 37 (51)
T ss_pred HHHHHHHccCCCCCCccH
Confidence 467899999999998644
No 81
>PF11771 DUF3314: Protein of unknown function (DUF3314) ; InterPro: IPR021748 This small family contains human, mouse and fish members but the function is not known.
Probab=24.85 E-value=26 Score=25.79 Aligned_cols=14 Identities=43% Similarity=0.871 Sum_probs=11.2
Q ss_pred Ccccccccccchhh
Q psy13775 1 MEWNVRLLPQKAGY 14 (119)
Q Consensus 1 ~~~~~~~~~~~~~~ 14 (119)
|.|||...|..+|+
T Consensus 56 MRWNve~~~~~~g~ 69 (164)
T PF11771_consen 56 MRWNVERTPEPSGD 69 (164)
T ss_pred eeeeeecCCCcccC
Confidence 78999999876654
No 82
>TIGR02308 RNA_lig_T4_1 RNA ligase, T4 RnlA family. Members of this family are phage proteins with ATP-dependent RNA ligase activity. Host defense to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL.
Probab=24.67 E-value=1.6e+02 Score=24.63 Aligned_cols=44 Identities=23% Similarity=0.301 Sum_probs=31.9
Q ss_pred HHHHHHHhcCcCCC---------CChhhHHHHHHHHHHHHHhchhHHHHHHHh
Q psy13775 51 VAVIYCGVRGHLDK---------LDPAKITTFEKEFLAHIKSSERGLLESIKK 94 (119)
Q Consensus 51 V~iL~a~~~G~ld~---------ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~ 94 (119)
--++.++.+|-.|+ ..+++|..|++.++.++.+.+..+.+....
T Consensus 260 ~~l~~~vl~g~~DDl~~~~~~~~~~~~~i~~f~~~~~~~~~~~~~~~~~~~~~ 312 (374)
T TIGR02308 260 EKLIYTIIEGATDDLRAMYADDEYSLRKIEAFEETYRSYLDRALFLVTECYNK 312 (374)
T ss_pred HHHHHHHHcCCchhHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677776666 468899999999999998776555544444
No 83
>PRK11718 anti-RNA polymerase sigma 70 factor; Provisional
Probab=24.26 E-value=3e+02 Score=20.35 Aligned_cols=45 Identities=18% Similarity=0.372 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhcCc------CCCCChhhHHHHHHHHHHHHHhchhHHHHHH
Q psy13775 48 EEQVAVIYCGVRGH------LDKLDPAKITTFEKEFLAHIKSSERGLLESI 92 (119)
Q Consensus 48 ~eQV~iL~a~~~G~------ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I 92 (119)
-.|.++.|+.--|+ ..-...+.+..|+..+..|+..-|=++.+.+
T Consensus 26 Rq~LLV~Yc~L~gl~P~~~~~~~~~~~~l~~FC~~LVDYvSaGHFeIYe~l 76 (161)
T PRK11718 26 RQQLLVAYCKLAGIKPGKESLSLPNEKALDDFCQLLVDYVSAGHFEIYEQL 76 (161)
T ss_pred HHHHHHHHHHHhcCCCCcccccCCCHHHHHHHHHHHHHHHcccchHHHHHH
Confidence 45677888877666 1234567799999999999999888888887
No 84
>cd04502 SGNH_hydrolase_like_7 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
Probab=23.78 E-value=18 Score=25.24 Aligned_cols=37 Identities=16% Similarity=0.249 Sum_probs=31.2
Q ss_pred HHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhH
Q psy13775 51 VAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERG 87 (119)
Q Consensus 51 V~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~ 87 (119)
+++|..++|.+....+++.+.+--..+++.+++..|+
T Consensus 53 ~vvi~~G~ND~~~~~~~~~~~~~~~~lv~~i~~~~~~ 89 (171)
T cd04502 53 RVVLYAGDNDLASGRTPEEVLRDFRELVNRIRAKLPD 89 (171)
T ss_pred EEEEEEecCcccCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence 7899999999999999888888888888888765443
No 85
>cd01820 PAF_acetylesterase_like PAF_acetylhydrolase (PAF-AH)_like subfamily of SGNH-hydrolases. Platelet-activating factor (PAF) and PAF-AH are key players in inflammation and in atherosclerosis. PAF-AH is a calcium independent phospholipase A2 which exhibits strong substrate specificity towards PAF, hydrolyzing an acetyl ester at the sn-2 position. PAF-AH also degrades a family of oxidized PAF-like phospholipids with short sn-2 residues. In addition, PAF and PAF-AH are associated with neural migration and mammalian reproduction.
Probab=23.39 E-value=21 Score=26.19 Aligned_cols=38 Identities=13% Similarity=0.115 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhH
Q psy13775 50 QVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERG 87 (119)
Q Consensus 50 QV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~ 87 (119)
.++++.+|+|++....+++.+.+--..+++.+++.+|+
T Consensus 91 d~VvI~~G~ND~~~~~~~~~~~~~l~~ii~~l~~~~P~ 128 (214)
T cd01820 91 KVVVLLIGTNNIGHTTTAEEIAEGILAIVEEIREKLPN 128 (214)
T ss_pred CEEEEEecccccCCCCCHHHHHHHHHHHHHHHHHHCCC
Confidence 57889999999988889999888888888888876554
No 86
>PF01765 RRF: Ribosome recycling factor; InterPro: IPR023584 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth []. Thus ribosomes are 'recycled' and ready for another round of protein synthesis. This entry represents a domain found in ribosome recycling factors.; PDB: 3R8N_Y 1Y69_8 1ISE_A 1EK8_A 1DD5_A 1WIH_A 2Z4L_6 2QBE_6 2V46_Y 1EH1_A ....
Probab=23.31 E-value=2.8e+02 Score=19.89 Aligned_cols=30 Identities=27% Similarity=0.436 Sum_probs=20.3
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13775 88 LLESIKKEGKITEDTDAKLKTVVTNFLANF 117 (119)
Q Consensus 88 ~~~~I~~~~~l~~~~~~~L~~~i~~~~~~f 117 (119)
-++....++.++++....+.+.++...+.|
T Consensus 120 ~lkk~~~~~~~s~D~~~~~~~~iq~l~~~~ 149 (165)
T PF01765_consen 120 KLKKLKKSKEISEDDIKKLEKEIQKLTDKY 149 (165)
T ss_dssp HHHHHHHTTSS-HHHHHHHHHHHHHHHHHH
T ss_pred HHHhhhccCCCCchhhHHHHHHHHHHHHHH
Confidence 334444455689999888888888877665
No 87
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=22.94 E-value=1.4e+02 Score=16.59 Aligned_cols=20 Identities=15% Similarity=0.338 Sum_probs=16.7
Q ss_pred CCCChhhHHHHHHHHHHHHH
Q psy13775 63 DKLDPAKITTFEKEFLAHIK 82 (119)
Q Consensus 63 d~ipv~~I~~fe~~ll~~l~ 82 (119)
|+.+.+++.++-+++..|+.
T Consensus 10 ~~a~~eel~~Y~~~L~~Yin 29 (36)
T cd00126 10 DDASPEELRQYLAALREYIN 29 (36)
T ss_pred CCCCHHHHHHHHHHHHHHHH
Confidence 56788999999999988885
No 88
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=22.91 E-value=2.6e+02 Score=19.34 Aligned_cols=42 Identities=26% Similarity=0.324 Sum_probs=25.2
Q ss_pred hhhHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHH
Q psy13775 67 PAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTV 109 (119)
Q Consensus 67 v~~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~ 109 (119)
+++|.++++.+.++.....++.+.....-| +||...+.+...
T Consensus 43 i~~Iv~~e~~L~~~~~~~~~~~L~~aK~~G-FsD~~IA~l~~~ 84 (123)
T PF02787_consen 43 IKNIVDMEKELKEYLNELDPELLRKAKRLG-FSDRQIARLWGV 84 (123)
T ss_dssp HHHHHHHHHHHHHHGGG--HHHHHHHHHTT---HHHHHHHHTS
T ss_pred HHHHHHHHHHHHHhhccchHHHHHHHHHcC-CCHHHHHhccCC
Confidence 455666677777765555667777776666 788777776554
No 89
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=22.75 E-value=29 Score=21.67 Aligned_cols=50 Identities=10% Similarity=0.276 Sum_probs=31.6
Q ss_pred CChhhHHHHHHHHHHHHHhchhHHHHHHHh--------cCCCCHHHHHHHHHHHHHHHH
Q psy13775 65 LDPAKITTFEKEFLAHIKSSERGLLESIKK--------EGKITEDTDAKLKTVVTNFLA 115 (119)
Q Consensus 65 ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~--------~~~l~~~~~~~L~~~i~~~~~ 115 (119)
+|...+..++.+|.+.+...+|+..=.|.. .+.-+++ ++.+.+++++..+
T Consensus 1 lp~ga~~AL~~EL~kRl~~~yPd~~v~Vr~~s~~~l~v~g~~~~~-k~~i~~iLqe~we 58 (65)
T PF06183_consen 1 LPAGALEALESELTKRLHRQYPDAEVRVRPGSANGLSVSGGKKDD-KERIEEILQEMWE 58 (65)
T ss_dssp --TTHHHHHHHHHHHHHHHH-SS-EEEEEEESS-EEEEES--HHH-HHHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHHHHHCCCceEeeeecccCccccCCcCchH-HHHHHHHHHHHHh
Confidence 477788999999999999998884322222 3322333 8888888887654
No 90
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=21.46 E-value=52 Score=24.30 Aligned_cols=38 Identities=21% Similarity=0.271 Sum_probs=34.1
Q ss_pred cccccccccchhhHHhhhcCCH-HHHHHHhcccchhhhc
Q psy13775 2 EWNVRLLPQKAGYHYSNFTARI-GLNKSLMLSRRLPILL 39 (119)
Q Consensus 2 ~~~~~~~~~~~~~~Fs~Fgsdl-~tr~~L~rG~Rl~ElL 39 (119)
.|-|--=|..|-..|.+|-.-- .....+.+|..+.+|+
T Consensus 136 yWKVY~n~~~a~~~F~~y~~~r~~~~~~~~~G~~l~~l~ 174 (176)
T PF12672_consen 136 YWKVYGNPEEAKKLFERYDKCRERYCRLLEQGKSLEQLL 174 (176)
T ss_pred cCccCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHh
Confidence 4888888999999999998888 9999999999998875
No 91
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=21.29 E-value=41 Score=21.54 Aligned_cols=23 Identities=30% Similarity=0.543 Sum_probs=16.1
Q ss_pred CcccccccccchhhHHhhhcCCH--HHHHHHh
Q psy13775 1 MEWNVRLLPQKAGYHYSNFTARI--GLNKSLM 30 (119)
Q Consensus 1 ~~~~~~~~~~~~~~~Fs~Fgsdl--~tr~~L~ 30 (119)
++++||+-|. +||.++ +...+|.
T Consensus 6 l~d~v~i~P~-------~fg~~l~~~i~~~L~ 30 (80)
T cd04329 6 LEHNILLHPS-------YFGPNLKEYLEQKLL 30 (80)
T ss_pred EEEEEEECHH-------HhCccHHHHHHHHHH
Confidence 4688999886 588888 4444443
No 92
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=21.23 E-value=3.4e+02 Score=19.96 Aligned_cols=33 Identities=21% Similarity=0.490 Sum_probs=23.3
Q ss_pred hhHHHHHHH---hcCCCCHHHHHHHHHHHHHHHHhc
Q psy13775 85 ERGLLESIK---KEGKITEDTDAKLKTVVTNFLANF 117 (119)
Q Consensus 85 ~~~~~~~I~---~~~~l~~~~~~~L~~~i~~~~~~f 117 (119)
..+.++.|. ..+.++++....+.+.++...+.|
T Consensus 123 Rr~~~~~iKk~~k~~~iseD~~k~~~~~iQkltd~~ 158 (176)
T TIGR00496 123 RRDANDKVKKLEKDKEISEDEERRLQEEIQKLTDEY 158 (176)
T ss_pred HHHHHHHHHHHhhcCCCChhHHHHHHHHHHHHHHHH
Confidence 344555554 456799998888888888877665
No 93
>cd01766 Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.
Probab=21.19 E-value=21 Score=23.30 Aligned_cols=14 Identities=21% Similarity=0.366 Sum_probs=13.0
Q ss_pred cchhhHHhhhcCCH
Q psy13775 10 QKAGYHYSNFTARI 23 (119)
Q Consensus 10 ~~~~~~Fs~Fgsdl 23 (119)
|-||.+|-+.||+|
T Consensus 60 qtAGnvflkhgsel 73 (82)
T cd01766 60 QTAGNVFLKHGSEL 73 (82)
T ss_pred hcccceeeecCCEe
Confidence 67999999999998
No 94
>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
Probab=21.14 E-value=63 Score=26.28 Aligned_cols=28 Identities=11% Similarity=0.113 Sum_probs=22.1
Q ss_pred hhHHhhhcC-----CHHHHHHHhcccchhhhcC
Q psy13775 13 GYHYSNFTA-----RIGLNKSLMLSRRLPILLG 40 (119)
Q Consensus 13 ~~~Fs~Fgs-----dl~tr~~L~rG~Rl~ElL~ 40 (119)
-+.|.+||+ |..+.+.++||++|.+.|.
T Consensus 293 ~~~~i~~g~y~~g~d~~~d~~i~~~~~i~~~l~ 325 (326)
T cd01136 293 VEDLIRIGAYKKGSDPEVDEAIKLLPKIEAFLK 325 (326)
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHhHHHHHHHhC
Confidence 467888874 4578888999999998873
No 95
>PF00042 Globin: Globin plant globin signature erythrocruorin family signature alpha hemoglobin signature myoglobin signature thalassemia.; InterPro: IPR000971 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry covers most of the globin family of proteins, but it omits some bacterial globins and the protoglobins. More information about these proteins can be found at Protein of the Month: Haemoglobin [].; GO: 0005506 iron ion binding, 0020037 heme binding; PDB: 2WTH_A 2WTG_A 3A59_G 3FS4_C 3CY5_C 3D1A_B 2RI4_J 3EU1_B 1JEB_A 2Z6N_B ....
Probab=20.85 E-value=1.4e+02 Score=18.91 Aligned_cols=28 Identities=11% Similarity=0.045 Sum_probs=19.4
Q ss_pred hhhHHhhhcC-C----H-HHHHHHhcccchhhhc
Q psy13775 12 AGYHYSNFTA-R----I-GLNKSLMLSRRLPILL 39 (119)
Q Consensus 12 ~~~~Fs~Fgs-d----l-~tr~~L~rG~Rl~ElL 39 (119)
...+|.+|+. . + .+...-.||.|++..|
T Consensus 34 ~~~~F~~~~~~~~~~~l~~~~~~~~h~~~v~~~l 67 (110)
T PF00042_consen 34 YKKLFPKFKDIVPLEELKNNPEFKAHAQRVMEAL 67 (110)
T ss_dssp GGGGGTTGTTTSSHHHHTTSHHHHHHHHHHHHHH
T ss_pred HHhhcccccccchHHHHhccchHHHHHHHHHHHH
Confidence 4567888843 1 1 6667778888888877
No 96
>PF10615 DUF2470: Protein of unknown function (DUF2470); InterPro: IPR019595 This entry represents a putative haem-iron utilisation family of proteins, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however the function of this domain is not known. ; PDB: 3GAS_D 3SWJ_A 2ARZ_B.
Probab=20.84 E-value=1.4e+02 Score=18.88 Aligned_cols=23 Identities=9% Similarity=0.122 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHhchhHHHHHHHh
Q psy13775 72 TFEKEFLAHIKSSERGLLESIKK 94 (119)
Q Consensus 72 ~fe~~ll~~l~~~~~~~~~~I~~ 94 (119)
+++..++++|++.|.+.+..+..
T Consensus 8 ~~~~~ii~HMN~DH~d~l~~~~~ 30 (83)
T PF10615_consen 8 EAAARIIEHMNDDHADDLLLYAR 30 (83)
T ss_dssp HHHHHHHHHHHHH-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHH
Confidence 48899999999999987766654
No 97
>PRK05697 flagellar basal body-associated protein FliL-like protein; Validated
Probab=20.76 E-value=86 Score=22.22 Aligned_cols=42 Identities=5% Similarity=0.146 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHH
Q psy13775 70 ITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVT 111 (119)
Q Consensus 70 I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~ 111 (119)
.+.-++.++..|.+..++-+........|.+++.+.+...+.
T Consensus 77 ~P~IRd~ii~lLs~~t~~eL~t~eGke~Lr~eil~~in~~L~ 118 (137)
T PRK05697 77 DPLIRNALVELLGQQTEDKVKSLTGREEIRQECLKQVNELLE 118 (137)
T ss_pred CHHHHHHHHHHHHcCCHHHhcCHHHHHHHHHHHHHHHHHHHh
Confidence 355677777788877777766666665566666555555554
No 98
>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group
Probab=20.69 E-value=3.8e+02 Score=20.29 Aligned_cols=42 Identities=21% Similarity=0.439 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHH-HHHHHHHHH
Q psy13775 69 KITTFEKEFLAHIKSSERGLLESIKKEGKITED-TDAKLKTVV 110 (119)
Q Consensus 69 ~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~-~~~~L~~~i 110 (119)
.+.+....+++.+....-++++..-+++.++++ +...|.+++
T Consensus 193 ~~~~~~~~l~e~~a~~dd~l~e~yl~~~~~~~~~l~~~l~~~~ 235 (268)
T cd04170 193 EVAEAREELLEAVAETDDELMEKYLEGGELTEEELHAGLRRAL 235 (268)
T ss_pred HHHHHHHHHHHHHhhCCHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 455678888888888888899998888888774 333444443
No 99
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=20.53 E-value=1.1e+02 Score=16.72 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHhcC
Q psy13775 100 EDTDAKLKTVVTNFLANFT 118 (119)
Q Consensus 100 ~~~~~~L~~~i~~~~~~f~ 118 (119)
+++...|.+-.++|.+.|.
T Consensus 10 DeId~vLe~NAe~FV~~fV 28 (33)
T TIGR03687 10 DEIDGVLESNAEEFVRGFV 28 (33)
T ss_pred HHHHHHHHHhHHHHHHHHH
Confidence 4445556666666766663
No 100
>PF08362 TetR_C_3: YcdC-like protein, C-terminal region; InterPro: IPR013573 This entry represents the C-terminal domain found in the hypothetical transcriptional regulators RutR and YcdC (P75899 from SWISSPROT) from Escherichia coli. Both of these proteins are member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. RutR negatively controls the transcription of the rut operon involved in pyrimidine utilization. The C-terminal domains of RutR, YsiA and TetR share a multi-helical, interlocking structure. These proteins also contain helix-turn-helix (HTH) DNA-binding domains.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 3LOC_B.
Probab=20.28 E-value=3.3e+02 Score=19.35 Aligned_cols=90 Identities=12% Similarity=0.140 Sum_probs=50.3
Q ss_pred HHHHHHhcccchhhhc-CCCCCCCHHHHHHHHHHHhcCcCCCCChhhHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHH
Q psy13775 24 GLNKSLMLSRRLPILL-GQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDT 102 (119)
Q Consensus 24 ~tr~~L~rG~Rl~ElL-~q~~Plsv~eQV~iL~a~~~G~ld~ipv~~I~~fe~~ll~~l~~~~~~~~~~I~~~~~l~~~~ 102 (119)
=++..|.-|.++.+.+ ..+.|.--..=.++==-...|.+++|++..+-=..=..-.+-.....+ +..+.....++++.
T Consensus 46 fa~Eii~Gap~L~~~l~~~l~~~~~~~~~~I~~Wi~~G~i~~vdP~hL~f~IWa~TQ~YADf~~Q-i~~~~g~~~~~~~d 124 (143)
T PF08362_consen 46 FANEIIQGAPHLKDYLRERLRPWVDRKVAVIERWIAQGKIAPVDPEHLFFMIWAMTQHYADFAAQ-IRAVLGKSELSEED 124 (143)
T ss_dssp HHHHHHTTSTTTHHHHHTHHHHHHHHHHHHHHHHHHTTSS-S--HHHHHHHHHHHHHHHHHTHHH-HHHHHS--TTSHHH
T ss_pred HHHHHHcCchhhHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHhhhhhhhHHHH-HHHHhCCCCCCHHH
Confidence 4567777778888888 666664322222233345678899998887655444444433222222 23344456688888
Q ss_pred HHHHHHHHHHHH
Q psy13775 103 DAKLKTVVTNFL 114 (119)
Q Consensus 103 ~~~L~~~i~~~~ 114 (119)
.+...+.+..++
T Consensus 125 ~e~a~~~v~~li 136 (143)
T PF08362_consen 125 FEQAAEFVTALI 136 (143)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 888777777654
No 101
>PF09025 YopR_core: YopR Core; InterPro: IPR013349 Proteins in this entry are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yop protein is unusual in that it is released to the extracellular environment rather than injected directly into the target cell as are most Yop proteins.; GO: 0009405 pathogenesis, 0030254 protein secretion by the type III secretion system, 0030257 type III protein secretion system complex; PDB: 1Z21_A.
Probab=20.25 E-value=74 Score=23.08 Aligned_cols=44 Identities=16% Similarity=0.245 Sum_probs=28.0
Q ss_pred hhHHhhhcCCH-HHHHHHhcccchhhhcCCCCCCCHHHHHHHHHHH
Q psy13775 13 GYHYSNFTARI-GLNKSLMLSRRLPILLGQYVPMAIEEQVAVIYCG 57 (119)
Q Consensus 13 ~~~Fs~Fgsdl-~tr~~L~rG~Rl~ElL~q~~Plsv~eQV~iL~a~ 57 (119)
.+.+++||+++ ....-+++-+ ++.+|.+|.|+.--.+-+++.+.
T Consensus 55 ~~L~~~F~g~~~~~~pp~D~~E-Lrall~e~~plg~qkE~~Ll~~l 99 (142)
T PF09025_consen 55 QELLGRFGGRLLPAVPPIDRPE-LRALLREFFPLGAQKEQALLHSL 99 (142)
T ss_dssp HHHHHHHTT--S---HHHHHHH-HHHHHHHHS-SSHHHHHHHHHHH
T ss_pred HHHHHHHhhhccCCCCCcchHH-HHHHHHHhCcchhHHHHHHHHHH
Confidence 46789999999 5666666543 67777889999988777776554
No 102
>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P
Probab=20.23 E-value=95 Score=24.11 Aligned_cols=37 Identities=11% Similarity=0.284 Sum_probs=27.6
Q ss_pred hHHhhhcCCH--HHHHHHhcccchhhhcCCCCCCCHHHHHHHH
Q psy13775 14 YHYSNFTARI--GLNKSLMLSRRLPILLGQYVPMAIEEQVAVI 54 (119)
Q Consensus 14 ~~Fs~Fgsdl--~tr~~L~rG~Rl~ElL~q~~Plsv~eQV~iL 54 (119)
++|.+|.... +.+..++.-++| |-|.=++.++||++|
T Consensus 63 ~~~~~~~~~~~~~i~~vVewAK~I----PgF~~L~~~DQi~LL 101 (259)
T cd06932 63 RLFQRCQVRSVETIRELTEFAKSL----PGFRNLDLNDQVTLL 101 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC----CCcccCChhHHHHHH
Confidence 6788886655 666665555554 889999999999876
Done!