Query psy13777
Match_columns 121
No_of_seqs 132 out of 1038
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 20:14:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13777.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13777hhsearch_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 9E-39 1.9E-43 266.4 13.8 121 1-121 382-502 (504)
2 PRK13343 F0F1 ATP synthase sub 100.0 2.3E-28 4.9E-33 207.5 14.7 121 1-121 382-502 (502)
3 CHL00059 atpA ATP synthase CF1 100.0 1.1E-27 2.3E-32 202.5 14.4 119 1-119 361-479 (485)
4 TIGR00962 atpA proton transloc 99.9 6E-27 1.3E-31 198.9 14.7 121 1-121 381-501 (501)
5 TIGR03324 alt_F1F0_F1_al alter 99.9 1.6E-25 3.6E-30 189.8 13.8 114 1-114 382-495 (497)
6 PRK09281 F0F1 ATP synthase sub 99.9 7.3E-25 1.6E-29 186.2 14.7 120 1-120 382-501 (502)
7 KOG1353|consensus 99.9 9.1E-26 2E-30 178.8 3.3 59 1-59 282-340 (340)
8 PTZ00185 ATPase alpha subunit; 99.9 7.6E-25 1.7E-29 186.7 7.9 76 1-81 417-492 (574)
9 PRK07165 F0F1 ATP synthase sub 99.9 1.4E-22 3E-27 172.2 13.2 116 1-117 358-475 (507)
10 PF00306 ATP-synt_ab_C: ATP sy 99.9 7.3E-21 1.6E-25 132.9 11.0 82 1-82 7-98 (113)
11 PRK04196 V-type ATP synthase s 98.9 4.9E-09 1.1E-13 88.9 7.8 77 1-81 371-450 (460)
12 TIGR01041 ATP_syn_B_arch ATP s 98.7 3.8E-08 8.3E-13 83.6 7.8 77 1-81 369-448 (458)
13 TIGR01043 ATP_syn_A_arch ATP s 98.4 2E-06 4.4E-11 74.9 10.8 57 4-60 460-523 (578)
14 TIGR02546 III_secr_ATP type II 98.4 6.1E-07 1.3E-11 75.4 7.0 60 1-60 359-421 (422)
15 PRK06315 type III secretion sy 98.3 1.2E-06 2.7E-11 74.2 6.8 59 1-59 379-440 (442)
16 PRK09099 type III secretion sy 98.3 1.9E-06 4E-11 73.1 6.8 59 1-59 377-438 (441)
17 TIGR03498 FliI_clade3 flagella 98.3 2.3E-06 4.9E-11 72.1 6.8 58 1-58 356-416 (418)
18 PRK06936 type III secretion sy 98.2 2.8E-06 6.2E-11 72.0 6.6 59 1-59 376-437 (439)
19 PRK06002 fliI flagellum-specif 98.2 2.5E-06 5.5E-11 72.5 5.2 58 1-63 380-444 (450)
20 PRK07594 type III secretion sy 98.2 5.1E-06 1.1E-10 70.3 6.5 59 1-59 369-430 (433)
21 PRK08149 ATP synthase SpaL; Va 98.1 9.1E-06 2E-10 68.7 6.9 59 1-59 365-426 (428)
22 CHL00060 atpB ATP synthase CF1 98.1 1.3E-05 2.9E-10 68.8 8.0 72 1-72 387-470 (494)
23 PRK12597 F0F1 ATP synthase sub 98.1 1.3E-05 2.8E-10 68.4 7.8 72 1-72 362-445 (461)
24 PRK07721 fliI flagellum-specif 98.1 9.8E-06 2.1E-10 68.6 7.0 56 1-60 372-434 (438)
25 PRK07196 fliI flagellum-specif 98.1 1.1E-05 2.3E-10 68.4 7.0 59 1-59 370-431 (434)
26 PRK05688 fliI flagellum-specif 98.1 1E-05 2.3E-10 68.8 6.7 60 1-60 384-446 (451)
27 TIGR03305 alt_F1F0_F1_bet alte 98.1 1.6E-05 3.4E-10 67.7 7.6 72 1-72 357-440 (449)
28 PRK08472 fliI flagellum-specif 98.0 1.1E-05 2.4E-10 68.3 6.5 59 1-59 371-432 (434)
29 TIGR03496 FliI_clade1 flagella 98.0 9.9E-06 2.2E-10 68.1 5.7 53 1-53 353-408 (411)
30 PRK08972 fliI flagellum-specif 98.0 1.6E-05 3.6E-10 67.5 6.7 59 2-60 379-440 (444)
31 PRK06820 type III secretion sy 97.9 2.3E-05 5.1E-10 66.5 6.8 59 1-59 377-438 (440)
32 PRK14698 V-type ATP synthase s 97.9 2.2E-05 4.9E-10 72.3 6.8 57 4-60 894-957 (1017)
33 TIGR01039 atpD ATP synthase, F 97.9 4.2E-05 9.2E-10 65.3 8.0 72 1-72 362-445 (461)
34 PRK06793 fliI flagellum-specif 97.9 1.7E-05 3.6E-10 67.2 4.9 58 1-58 369-430 (432)
35 TIGR03497 FliI_clade2 flagella 97.8 4.8E-05 1E-09 64.0 6.8 59 1-59 351-412 (413)
36 PRK08927 fliI flagellum-specif 97.8 6.3E-05 1.4E-09 63.9 6.6 61 2-62 375-438 (442)
37 TIGR01026 fliI_yscN ATPase Fli 97.7 7.8E-05 1.7E-09 63.2 6.6 59 1-59 377-438 (440)
38 PRK09280 F0F1 ATP synthase sub 97.6 0.00022 4.9E-09 60.9 7.6 72 1-72 363-446 (463)
39 cd01136 ATPase_flagellum-secre 97.6 7.6E-05 1.6E-09 61.1 4.4 41 1-41 283-326 (326)
40 PRK04192 V-type ATP synthase s 96.7 0.045 9.7E-07 48.3 12.8 57 2-58 461-524 (586)
41 PRK02118 V-type ATP synthase s 96.7 0.0075 1.6E-07 51.4 7.6 62 2-64 353-414 (436)
42 PRK05922 type III secretion sy 96.5 0.0052 1.1E-07 52.3 5.3 58 1-59 369-430 (434)
43 PF09494 Slx4: Slx4 endonuclea 83.5 3.3 7.1E-05 26.0 4.5 44 34-77 4-55 (64)
44 TIGR01040 V-ATPase_V1_B V-type 77.6 10 0.00022 32.9 6.9 49 5-53 379-433 (466)
45 PRK07960 fliI flagellum-specif 66.7 28 0.00061 30.1 7.1 58 2-59 392-452 (455)
46 PF14615 Rsa3: Ribosome-assemb 64.3 23 0.0005 21.2 4.5 40 75-114 2-41 (47)
47 PF09371 Tex_N: Tex-like prote 62.1 16 0.00034 28.0 4.3 50 61-111 36-85 (193)
48 PF02061 Lambda_CIII: Lambda P 61.4 6.4 0.00014 23.3 1.6 25 19-43 19-43 (45)
49 PF03353 Lin-8: Ras-mediated v 60.2 82 0.0018 25.2 8.4 93 3-102 1-96 (313)
50 TIGR01042 V-ATPase_V1_A V-type 58.5 1.4E+02 0.003 26.9 11.9 56 4-59 465-527 (591)
51 KOG1142|consensus 53.4 20 0.00043 28.8 3.7 33 86-118 159-191 (258)
52 PF03847 TFIID_20kDa: Transcri 48.9 19 0.0004 23.0 2.4 31 88-118 6-36 (68)
53 PF03048 Herpes_UL92: UL92 fam 48.8 79 0.0017 24.3 6.2 50 70-119 85-136 (192)
54 cd06940 NR_LBD_REV_ERB The lig 47.7 19 0.00041 26.8 2.6 41 10-56 10-50 (189)
55 PF12844 HTH_19: Helix-turn-he 47.3 27 0.0006 20.8 2.9 40 32-72 1-44 (64)
56 PRK10597 DNA damage-inducible 46.8 23 0.0005 23.6 2.7 51 66-117 12-72 (81)
57 PF05291 Bystin: Bystin; Inte 45.5 74 0.0016 26.2 5.9 81 27-113 46-147 (301)
58 cd07072 NR_LBD_DHR38_like Liga 44.6 17 0.00038 28.3 2.1 48 3-56 23-80 (239)
59 PF04947 Pox_VLTF3: Poxvirus L 41.7 1.5E+02 0.0032 22.2 7.2 87 31-119 12-108 (171)
60 cd07981 TAF12 TATA Binding Pro 40.1 59 0.0013 20.6 3.8 31 88-118 8-38 (72)
61 PF05952 ComX: Bacillus compet 38.7 96 0.0021 19.3 4.4 36 77-113 3-42 (57)
62 PF04353 Rsd_AlgQ: Regulator o 38.3 1.6E+02 0.0036 21.8 6.7 46 51-96 27-78 (153)
63 TIGR03875 RNA_lig_partner RNA 35.5 2.1E+02 0.0047 22.3 8.0 77 8-85 9-106 (206)
64 PF06358 DUF1065: Protein of u 34.1 36 0.00078 23.5 2.1 19 12-30 55-74 (111)
65 PF05542 DUF760: Protein of un 33.1 1.1E+02 0.0025 20.0 4.4 37 78-116 2-38 (86)
66 PF10241 KxDL: Uncharacterized 32.0 1.5E+02 0.0032 19.6 4.8 32 61-92 5-36 (88)
67 PF14022 DUF4238: Protein of u 31.7 1.9E+02 0.0042 21.1 6.0 67 41-113 27-97 (265)
68 PF08112 ATP-synt_E_2: ATP syn 30.8 1.2E+02 0.0026 18.8 3.8 32 65-96 2-33 (56)
69 COG0055 AtpD F0F1-type ATP syn 29.2 1.7E+02 0.0037 25.4 5.7 68 4-71 369-448 (468)
70 PF04967 HTH_10: HTH DNA bindi 28.6 1.3E+02 0.0028 18.2 3.7 26 48-73 2-30 (53)
71 cd03488 Topoisomer_IB_N_htopoI 28.3 3E+02 0.0064 21.7 8.3 72 48-120 36-124 (215)
72 KOG1379|consensus 27.8 23 0.00049 29.5 0.3 28 55-82 248-275 (330)
73 COG3160 Rsd Regulator of sigma 27.7 2.1E+02 0.0046 21.3 5.3 48 49-96 25-78 (162)
74 COG0184 RpsO Ribosomal protein 27.6 1.1E+02 0.0023 20.7 3.6 32 29-60 5-36 (89)
75 cd00660 Topoisomer_IB_N Topois 27.1 3.1E+02 0.0068 21.5 8.3 72 48-120 36-124 (215)
76 KOG1350|consensus 27.0 1.5E+02 0.0032 25.5 4.9 64 6-69 421-496 (521)
77 PF06183 DinI: DinI-like famil 26.2 23 0.00049 22.5 0.0 50 67-117 1-58 (65)
78 PRK06213 enoyl-CoA hydratase; 26.1 2.2E+02 0.0049 21.4 5.6 38 58-95 168-206 (229)
79 KOG0981|consensus 25.9 3.5E+02 0.0076 24.8 7.3 27 95-121 309-335 (759)
80 PF03597 CcoS: Cytochrome oxid 25.2 62 0.0013 19.1 1.8 19 53-71 19-37 (45)
81 PF10392 COG5: Golgi transport 25.1 1.8E+02 0.004 20.3 4.6 45 72-117 42-86 (132)
82 PF08463 EcoEI_R_C: EcoEI R pr 24.9 1.5E+02 0.0032 21.1 4.2 42 71-112 2-45 (164)
83 PF07176 DUF1400: Alpha/beta h 24.8 2.5E+02 0.0053 19.8 5.2 44 9-53 19-67 (127)
84 TIGR03248 galactar-dH20 galact 24.4 1.7E+02 0.0037 25.8 5.1 95 25-119 235-340 (507)
85 COG2183 Tex Transcriptional ac 22.3 1.8E+02 0.0038 27.2 4.9 77 29-111 22-98 (780)
86 PF03965 Penicillinase_R: Peni 22.3 2.5E+02 0.0055 18.8 4.8 80 34-114 22-115 (115)
87 COG5625 Predicted transcriptio 22.2 1.4E+02 0.0031 21.0 3.4 28 30-57 34-61 (113)
88 PF04295 GD_AH_C: D-galactarat 21.9 2.3E+02 0.005 24.2 5.2 96 24-119 125-231 (396)
89 PF02260 FATC: FATC domain; I 21.5 40 0.00088 18.5 0.5 13 45-57 1-13 (33)
90 PF08828 DSX_dimer: Doublesex 21.2 52 0.0011 20.9 1.0 18 18-36 35-52 (62)
91 TIGR00847 ccoS cytochrome oxid 21.0 1.1E+02 0.0023 18.6 2.3 19 53-71 20-38 (51)
92 PF14490 HHH_4: Helix-hairpin- 21.0 2.5E+02 0.0055 18.3 6.2 38 11-48 12-49 (94)
93 PF08236 SRI: SRI (Set2 Rpb1 i 20.5 2.6E+02 0.0057 18.3 5.7 58 60-119 21-80 (88)
94 PF06200 tify: tify domain; I 20.3 5.2 0.00011 22.7 -3.4 27 50-76 5-31 (36)
No 1
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=100.00 E-value=9e-39 Score=266.39 Aligned_cols=121 Identities=49% Similarity=0.798 Sum_probs=119.2
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 80 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~ 80 (121)
||++|||||||++|||||||||++|+++|+||+|++|+||||+|+|+|+++||++|||+++||||+||+++|..|+..++
T Consensus 382 lrl~laqYrel~afsqf~sdLd~~T~~~l~~G~r~~ellkQ~~~~p~sv~~qv~ilya~~~G~ld~v~v~~v~~fe~~l~ 461 (504)
T COG0056 382 LRLILAQYRELEAFSQFGSDLDKATRKQLERGKRLTELLKQPQYSPLSVEEQVLILYAGTNGYLDDVPVEKVADFEKELL 461 (504)
T ss_pred HHHHHHHHHHHHHHHhhcchhCHHHHHHHHccHHHHHHhcCCCCCCccHHHHHHHHHHHhcCcccCCcHHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhccC
Q psy13777 81 AHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANFTG 121 (121)
Q Consensus 81 ~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~f~~ 121 (121)
.|++.+|+++++.|++++.+++++++.++.++++|++.|.|
T Consensus 462 ~~~~~~~~~~~~~I~~~~~l~~~~e~~l~~~i~~f~~~f~~ 502 (504)
T COG0056 462 AYLRSDHKELLEEIRTTKELDDEIEAKLKAAIKEFKKTFAL 502 (504)
T ss_pred HHHHhhHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHhccc
Confidence 99999999999999999999999999999999999999875
No 2
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=99.96 E-value=2.3e-28 Score=207.47 Aligned_cols=121 Identities=34% Similarity=0.548 Sum_probs=118.7
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 80 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~ 80 (121)
+|++||||+|++.|++||+++|+.|+++++||++|+++|||++++|++.++|++.||++++|++|++|+++|+.|+..++
T Consensus 382 lr~~la~y~e~e~~~~~G~~ld~~~~~~i~~~~~i~~~L~Q~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~i~~~~~~~~ 461 (502)
T PRK13343 382 LRLDYAQFLELEAFTRFGGLLDAGTQKQITRGRRLRELLKQPRFSPLSVEEQIALLYALNEGLLDAVPLANIQAFEERLL 461 (502)
T ss_pred HHHHHHHHHHHHHHHHHhhhcCHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhccC
Q psy13777 81 AHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANFTG 121 (121)
Q Consensus 81 ~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~f~~ 121 (121)
+|+++++|++++.|..++.|+++.++.|++++++|.+.|.|
T Consensus 462 ~~~~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~~~~ 502 (502)
T PRK13343 462 EKLDARFAALSLALESPRELDEAWLAALEEILREAGERFAA 502 (502)
T ss_pred HHHHhhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhCC
Confidence 99999999999999999999999999999999999998875
No 3
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=99.95 E-value=1.1e-27 Score=202.52 Aligned_cols=119 Identities=46% Similarity=0.658 Sum_probs=116.7
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 80 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~ 80 (121)
+|++||||+|++.|++|++++|+.|+.+++||++|+++|||++++|+++++|+++|||+++|+||++|+++|..|+..++
T Consensus 361 lr~~la~y~e~e~~~~~~~~~d~~~~~~i~~~~~i~~~L~Q~~~~~~~~~e~~~~l~a~~~g~l~~~~~~~v~~~~~~l~ 440 (485)
T CHL00059 361 LKLELAQFAELEAFAQFASDLDKATQNQLARGQRLRELLKQSQSAPLTVEEQVATIYTGTNGYLDSLEIGQVRKFLVELR 440 (485)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCHHHHHHHHhHHHHHHHhcCCCCCCCCHHHHHHHHHHhccCCcCccCHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13777 81 AHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANF 119 (121)
Q Consensus 81 ~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~f 119 (121)
+|+++++|++++.|..++.++++.++.|++++++|.+.|
T Consensus 441 ~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~ 479 (485)
T CHL00059 441 TYLKTNKPQFQEIISSTKTFTEEAEALLKEAIQEQLELF 479 (485)
T ss_pred HHHHhhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998876
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=99.95 E-value=6e-27 Score=198.90 Aligned_cols=121 Identities=47% Similarity=0.783 Sum_probs=119.1
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 80 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~ 80 (121)
+|..||||+|++.|++||+++|+.++..+++|++|+++|+|++++|+++++|+++|||+++||||++|+++|..|+..+.
T Consensus 381 lr~~la~y~e~~~l~~~g~~ld~~~~~~l~~~~~i~~fL~Q~~~~~~~~~~q~~~l~a~~~G~l~~v~~~~i~~~~~~l~ 460 (501)
T TIGR00962 381 LRLELAQYRELEAFSQFASDLDEATKAQLERGKRLVELLKQPQYKPLPVEEQVVILYAGTKGYLDDIPVDKVRKFEQELL 460 (501)
T ss_pred HHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHhcCCcccccHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhccC
Q psy13777 81 AHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANFTG 121 (121)
Q Consensus 81 ~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~f~~ 121 (121)
+|+++++|++++.|+.++.++++.++.|++++++|.+.|.|
T Consensus 461 ~~l~~~~~~~~~~i~~~~~l~~~~~~~L~~~i~~~~~~f~~ 501 (501)
T TIGR00962 461 DYLDANHPDILEEINTKKKLTEELEDKLKEALKNFKKTFAA 501 (501)
T ss_pred HHHHHhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999988
No 5
>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=99.93 E-value=1.6e-25 Score=189.78 Aligned_cols=114 Identities=26% Similarity=0.468 Sum_probs=111.0
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 80 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~ 80 (121)
+|+.||||+|++.|++||+++|+.|++.+++|++|+++|||++++|+++++|++.|+++++|++|++|+++|..|+..++
T Consensus 382 lr~~la~y~e~e~~~~~G~~ld~~~~~~i~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~~~g~~d~~~~~~v~~~~~~~~ 461 (497)
T TIGR03324 382 LKLAYAQFEELETFARFGARLDENTRKTIEHGRRIRACLKQTQSSPLTVPQQIAILLALTNGLFDGVDLDAMPEAESAIR 461 (497)
T ss_pred HHHHHHHHHHHHHHHHhhhhcCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHH
Q psy13777 81 AHIKSSERGLLESIKKEGKITEDTDAKLKTVVTN 114 (121)
Q Consensus 81 ~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~ 114 (121)
.|++++||++++.|..++.++++.++.+++++++
T Consensus 462 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 (497)
T TIGR03324 462 AAVTSLPADLRERLQSGKKLSDEDREQILDIARG 495 (497)
T ss_pred HHHHhhhHHHHHHHHhcCCCCHHHHHHHHHHHHh
Confidence 9999999999999999999999999999888875
No 6
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=99.93 E-value=7.3e-25 Score=186.23 Aligned_cols=120 Identities=48% Similarity=0.813 Sum_probs=117.3
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 80 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~ 80 (121)
+|..||||+|++.|++||+++|+.++..+++|++|+++|+|+.++|++.++|++++|++++|+||++|.+++..|+..++
T Consensus 382 lr~~la~y~e~~~l~~~g~~l~~~~~~~l~~~~~i~~fL~Q~~~~~~~~~~~~~~~~~~~~G~l~~l~~~~i~~~~~~~~ 461 (502)
T PRK09281 382 LRLDLAQYRELEAFAQFGSDLDEATRAQLERGQRLVELLKQPQYSPLPVEEQVVILYAGTNGYLDDVPVEKVRRFEAELL 461 (502)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHhcCccccCCHHHHHHHHHHHH
Confidence 58899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcc
Q psy13777 81 AHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANFT 120 (121)
Q Consensus 81 ~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~f~ 120 (121)
+|+++++|++++.|..++.++++.++.|++++++|.+.|.
T Consensus 462 ~~l~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~f~ 501 (502)
T PRK09281 462 AYLRSNHADLLEEIRETKDLSDEIEAKLKAAIEEFKKTFA 501 (502)
T ss_pred HHHHHhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999998774
No 7
>KOG1353|consensus
Probab=99.91 E-value=9.1e-26 Score=178.82 Aligned_cols=59 Identities=93% Similarity=1.287 Sum_probs=57.6
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
|||+||||||+++|||||||||++|++.|.||.|++|+|||+||.||.+++||+++||+
T Consensus 282 ~klelaq~revaafaqfgsdlda~tq~~l~rg~rltellkq~qy~p~~~e~qv~~iy~g 340 (340)
T KOG1353|consen 282 LKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYAPLAIEEQVAVIYAG 340 (340)
T ss_pred hhhHHHHHHHHHHHHHhcccccHHHHHHHHhhhHHHHHHhcCCCCCcchhhheeeEecC
Confidence 69999999999999999999999999999999999999999999999999999999984
No 8
>PTZ00185 ATPase alpha subunit; Provisional
Probab=99.91 E-value=7.6e-25 Score=186.70 Aligned_cols=76 Identities=26% Similarity=0.380 Sum_probs=73.1
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFL 80 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~ 80 (121)
+|++||||+||++|||||||||+ ++|+||+|++|+|||++ |+++++||++|||+++||||++|+++|..+|..+.
T Consensus 417 lr~~LaqY~El~~fa~fgsdld~---~~l~rG~r~~ellkQ~~--p~~~~~qv~~l~a~~~g~ld~~~~~~i~~~~~~~~ 491 (574)
T PTZ00185 417 LKGILAEYRKLAADSVGGSQVQT---VPMIRGARFVALFNQKN--PSFFMNALVSLYACLNGYLDDVKVNYAKLYEYLLV 491 (574)
T ss_pred HHHHHHHHHHHHHHHhhcchhhH---HHHHhhHHHHHHHCCCC--CCCHHHHHHHHHHHhcCCcccCcHHHHHHHHHhcc
Confidence 58999999999999999999999 89999999999999999 99999999999999999999999999999998765
Q ss_pred H
Q psy13777 81 A 81 (121)
Q Consensus 81 ~ 81 (121)
+
T Consensus 492 ~ 492 (574)
T PTZ00185 492 N 492 (574)
T ss_pred C
Confidence 4
No 9
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=99.89 E-value=1.4e-22 Score=172.23 Aligned_cols=116 Identities=12% Similarity=0.222 Sum_probs=107.7
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCCh-hHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDP-AKITTFEKEF 79 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~-~~v~~f~~~l 79 (121)
+|..||||+|++.|++||++||+.|++.|++|+++.++|||++|+|+++.+|+++++++++|+|+++|+ ++|..|+..+
T Consensus 358 ~r~~la~Y~e~e~~~~~~~~ld~~~~~~l~~g~~i~~~L~Q~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 437 (507)
T PRK07165 358 ISKIYRAYKRQLKLSMLDYDLNKETSDLLFKGKMIEKMFNQKGFSLYSYRFVLLISKLISWGLLKDVKDEQKALDFIDYL 437 (507)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHhhhhhhCCcHHHHHHHHHHH
Confidence 478999999999999999999999999999999999999999999999999999999999999999999 9999999999
Q ss_pred HHHHHhchhHHHHHHHhcCCCCHHHHH-HHHHHHHHHHH
Q psy13777 80 LAHIKSSERGLLESIKKEGKITEDTDA-KLKTVVTNFLA 117 (121)
Q Consensus 80 ~~~l~~~~~~~~~~i~~~~~l~~~~~~-~l~~~~~~~~~ 117 (121)
++| +.++|++++.|..++.+++++.. -+.-++++|.+
T Consensus 438 ~~~-~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 475 (507)
T PRK07165 438 IEN-DPDAKKIFNKIKNNEDVDDELMKNYFAFLLNQYSD 475 (507)
T ss_pred HHh-hhhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 999 99999999999999999988643 45555666655
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=99.85 E-value=7.3e-21 Score=132.87 Aligned_cols=82 Identities=38% Similarity=0.681 Sum_probs=72.3
Q ss_pred ChhhhhhhHHHHHHHh-hcCC-ccHHHHHHHHhHHHHHHHhhcCCCCCC-------C-HHHHHHHHHHHhhCCCCCCChh
Q psy13777 1 MKLELAQYREVAAFAQ-FGSD-LDAATQQLLNRGVRLTELLKQGQYVPM-------A-IEEQVAVIYCGVRGHLDKLDPA 70 (121)
Q Consensus 1 LkL~LAQyrELeaFaq-FgSd-LD~~Tk~~L~rG~rl~elLKQ~q~~P~-------~-~~eQv~~L~a~~~g~ld~i~~~ 70 (121)
+|+.||||+||++|+| ||+| ||++|+.+|++|++|+++|+|++|+|+ + +.+++.+++++.+|+++++|.+
T Consensus 7 l~~~Laq~~EL~~~~q~vG~d~L~~~~k~~l~~g~~i~e~LkQ~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (113)
T PF00306_consen 7 LKLILAQYRELEEFVQFVGSDALDDEDKLILERGRRIREFLKQNAFDPVPLEKQYVMILEETIDLFYAILRGKFDDIPEE 86 (113)
T ss_dssp HHHHHHHHHHHHHHHHHHTSTCSTHHHHHHHHHHHHHHHHT-BSTTTTTSSHHHHHHHHHHHHHHHHHHHTTTTTTS-GG
T ss_pred HHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHcCCCCCCCCcCcchhhhHHHHHHHHHHHHHhCCCccCCHH
Confidence 5789999999999999 7988 999999999999999999999999999 5 5555556899999999999999
Q ss_pred HHHHHHHHHHHH
Q psy13777 71 KITTFEKEFLAH 82 (121)
Q Consensus 71 ~v~~f~~~l~~~ 82 (121)
.+..+......+
T Consensus 87 ~~~~~~~~~~~~ 98 (113)
T PF00306_consen 87 ELEKIETKDIEK 98 (113)
T ss_dssp GHHHHHHHHHHH
T ss_pred HHHHHhhHHHHH
Confidence 999998877764
No 11
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=98.89 E-value=4.9e-09 Score=88.95 Aligned_cols=77 Identities=18% Similarity=0.303 Sum_probs=70.9
Q ss_pred ChhhhhhhHHHHHHHhh-c-CCccHHHHHHHHhHHHHH-HHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQF-G-SDLDAATQQLLNRGVRLT-ELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEK 77 (121)
Q Consensus 1 LkL~LAQyrELeaFaqF-g-SdLD~~Tk~~L~rG~rl~-elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~ 77 (121)
++..|+||+||..|++| | ++|++.++..+.+|+++. +.|+|+.++|.+.++++..++ ++++++|.+++..|+.
T Consensus 371 l~~~y~~~~~l~~~~~~~G~~~l~d~~~~~~~~~~~~~~~fL~Q~~~~~~~~~~~~~~l~----~~l~~~~~~~l~~~~~ 446 (460)
T PRK04196 371 LYAAYARGKDLRELAAIVGEEALSERDRKYLKFADAFEREFVNQGFDENRSIEETLDLGW----ELLSILPESELKRIKD 446 (460)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHH----HHHhhCCHHHHHHHHH
Confidence 46789999999999999 6 799999999999999997 899999999999999999876 6678999999999999
Q ss_pred HHHH
Q psy13777 78 EFLA 81 (121)
Q Consensus 78 ~l~~ 81 (121)
.+++
T Consensus 447 ~l~~ 450 (460)
T PRK04196 447 EYIE 450 (460)
T ss_pred HHHH
Confidence 9976
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=98.73 E-value=3.8e-08 Score=83.58 Aligned_cols=77 Identities=17% Similarity=0.310 Sum_probs=70.5
Q ss_pred ChhhhhhhHHHHHHHhh-cC-CccHHHHHHHHhHHH-HHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQF-GS-DLDAATQQLLNRGVR-LTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEK 77 (121)
Q Consensus 1 LkL~LAQyrELeaFaqF-gS-dLD~~Tk~~L~rG~r-l~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~ 77 (121)
|+..|++|+||+.+.+| |+ +|++.++..+.+|++ +++.|+|+.++|.+.++++..++ ++++.+|.+.+..|..
T Consensus 369 l~~~y~~~~~L~~i~~~~G~d~l~d~~~~~~~~~~~i~~~fL~Q~~~~~~~~~~~~~~l~----~~l~~~~~~~~~~~~~ 444 (458)
T TIGR01041 369 LYAAYAEGRDLRGLVAIVGEEALSERDRKYLKFADLFERRFVRQGRNENRSIEETLDIGW----ELLSILPESELKRIDE 444 (458)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHH----HHHhhCCHHHHHHHHH
Confidence 35689999999999999 87 999999999999999 58999999999999999999984 5678999999999999
Q ss_pred HHHH
Q psy13777 78 EFLA 81 (121)
Q Consensus 78 ~l~~ 81 (121)
.+++
T Consensus 445 ~~~~ 448 (458)
T TIGR01041 445 EYIE 448 (458)
T ss_pred HHHH
Confidence 9875
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=98.44 E-value=2e-06 Score=74.90 Aligned_cols=57 Identities=21% Similarity=0.326 Sum_probs=53.2
Q ss_pred hhhhhHHHHHHHhh-cCC-ccHHHHHHHHhHHHHHHH-hhcCCCCCC----CHHHHHHHHHHHh
Q psy13777 4 ELAQYREVAAFAQF-GSD-LDAATQQLLNRGVRLTEL-LKQGQYVPM----AIEEQVAVIYCGV 60 (121)
Q Consensus 4 ~LAQyrELeaFaqF-gSd-LD~~Tk~~L~rG~rl~el-LKQ~q~~P~----~~~eQv~~L~a~~ 60 (121)
-|++|+||+.+.|+ |+| |++..+..+.+|+++++. |+|+.|+|+ |.++|+..|.++.
T Consensus 460 lL~~~~el~~iv~lvG~d~L~~~d~~il~~a~~i~e~FLqQ~~~~~~d~~~~~~k~~~~L~~i~ 523 (578)
T TIGR01043 460 LLQKESELQEIVQLVGPDALPERQKLILEVARMIREAFLQQNAFDPVDTYCPPQKQYRILRAIM 523 (578)
T ss_pred HHHHHHHHHHHHhccCCCCCCHHHHHHHHHhHHHHHhhCCCCCCCCccCCCCHHHHHHHHHHHH
Confidence 48999999999999 999 999999999999999976 999999999 9999999887764
No 14
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=98.43 E-value=6.1e-07 Score=75.45 Aligned_cols=60 Identities=22% Similarity=0.295 Sum_probs=56.5
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHh
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~ 60 (121)
+|-.||+|+|++.+.++|+ .+|+.+.+.+.+|.+|.++|+|+.+++.+.++++..|+++-
T Consensus 359 ~~~~l~~y~e~~~li~~g~y~~g~d~~~d~~i~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~~ 421 (422)
T TIGR02546 359 LRRLLATYKEVELLIRLGEYQPGSDPETDDAIDKIDAIRAFLRQSTDEYSPYEETLEQLHALV 421 (422)
T ss_pred HHHHHHhhHHHHHHHHhcCCcCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHHh
Confidence 4678999999999999997 99999999999999999999999999999999999999864
No 15
>PRK06315 type III secretion system ATPase; Provisional
Probab=98.34 E-value=1.2e-06 Score=74.17 Aligned_cols=59 Identities=19% Similarity=0.197 Sum_probs=55.4
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|..||+|+|+|.|.+||. ..|+.+...+.++.+|.+.|+|+.++|++.++++..|..+
T Consensus 379 ~r~~l~~y~e~e~li~~g~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~~ 440 (442)
T PRK06315 379 AREVLAKYKANEMLIRIGEYRRGSDREVDFAIDHIDKLNRFLKQDIHEKTNYEEAAQQLRAI 440 (442)
T ss_pred HHHHHHhhhhhHHHHHhcCCcCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4678999999999999998 9999999999999999999999999999999999887765
No 16
>PRK09099 type III secretion system ATPase; Provisional
Probab=98.29 E-value=1.9e-06 Score=73.09 Aligned_cols=59 Identities=19% Similarity=0.193 Sum_probs=55.3
Q ss_pred ChhhhhhhHHHHHHHhhc---CCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFG---SDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFg---SdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.||+|+|++.+.++| ...|+.+...+.+|.+|.+.|+|+.++|.+.++++..|..+
T Consensus 377 lr~~la~y~e~e~li~iG~y~~g~d~~~d~~i~~~~~i~~fL~Q~~~~~~~~~~t~~~l~~~ 438 (441)
T PRK09099 377 LRQLLAKHREVETLLQVGEYRAGSDPVADEAIAKIDAIRDFLSQRTDEYSDPDATLAALAEL 438 (441)
T ss_pred HHHHHHhhHHHHHHHHhcCccCCCChhHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 467899999999999999 79999999999999999999999999999999999888765
No 17
>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=98.27 E-value=2.3e-06 Score=72.10 Aligned_cols=58 Identities=21% Similarity=0.379 Sum_probs=52.5
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYC 58 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a 58 (121)
+|-.||+|+|++.|.+||. .+|+.+...+++|.+|.+.|+|++++|++.++-+--|..
T Consensus 356 ~r~~l~~y~e~~~~~~~g~y~~g~d~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~ 416 (418)
T TIGR03498 356 LRALLARYEETEDLIRLGAYRKGSDPELDEAIRLVPKIYEFLTQGPDEPTSLQDPFADLAA 416 (418)
T ss_pred HHHHHHhhHHHHHHHHhhCCcCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHh
Confidence 4678999999999999998 699999999999999999999999999998876655543
No 18
>PRK06936 type III secretion system ATPase; Provisional
Probab=98.23 E-value=2.8e-06 Score=71.96 Aligned_cols=59 Identities=24% Similarity=0.307 Sum_probs=55.4
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.||+|+|++.|.++|. .+|+.+.+.+.++.+|.+.|+|+.++|.+.++++..|+.+
T Consensus 376 ~r~~la~y~e~e~li~iG~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~ 437 (439)
T PRK06936 376 LRELLAKYEEVELLLQIGEYQKGQDKEADQAIERIGAIRGFLRQGTHELSHFNETLNLLETL 437 (439)
T ss_pred HHHHHHcchHHHHHHHhcCccCCCCHHHHHHHHhHHHHHHHcCCCCCCCCCHHHHHHHHHHH
Confidence 4678999999999999997 8899999999999999999999999999999999998876
No 19
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=98.18 E-value=2.5e-06 Score=72.48 Aligned_cols=58 Identities=28% Similarity=0.393 Sum_probs=50.2
Q ss_pred ChhhhhhhHHHHHH-----HhhcCC--ccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCC
Q psy13777 1 MKLELAQYREVAAF-----AQFGSD--LDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGH 63 (121)
Q Consensus 1 LkL~LAQyrELeaF-----aqFgSd--LD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ 63 (121)
+|..||+|+|++.| .+|||| +|.++++ |.+|.+.|+|+.++|.+ ++-+.-|..+..|-
T Consensus 380 ~r~~la~y~e~e~li~ig~y~~G~d~~~D~ai~~----~~~i~~fL~Q~~~~~~~-~~~~~~l~~~~~~~ 444 (450)
T PRK06002 380 LKSMIARFEETRDLRLIGGYRAGSDPDLDQAVDL----VPRIYEALRQSPGDPPS-DDAFADLAAALKGA 444 (450)
T ss_pred HHHHHHHHHHHHHHHHhhccccCCChHHHHHHHh----HHHHHHHhCCCCCCCCC-HHHHHHHHHHHhhH
Confidence 47789999999999 699999 8887654 99999999999999999 77777787777664
No 20
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=98.15 E-value=5.1e-06 Score=70.30 Aligned_cols=59 Identities=19% Similarity=0.229 Sum_probs=53.7
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.||+|+|+|.|.+||. ..|+.+.+.+++|.+|++.|+|+..+|++.++-+--|..+
T Consensus 369 ~r~~la~y~e~e~li~~G~y~~g~d~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~ 430 (433)
T PRK07594 369 LRRCLALYQEVELLIRIGEYQRGVDTDTDKAIDTYPDICTFLRQSKDEVCGPELLIEKLHQI 430 (433)
T ss_pred HHHHHHcchHHHHHHHhcCCCCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4678999999999999998 9999999999999999999999999999998876666544
No 21
>PRK08149 ATP synthase SpaL; Validated
Probab=98.10 E-value=9.1e-06 Score=68.72 Aligned_cols=59 Identities=15% Similarity=0.210 Sum_probs=53.1
Q ss_pred ChhhhhhhHHHHHHHhhcCC---ccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSD---LDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSd---LD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.||+|+|++.|.+||.. -|+.+...+.++.+|.+.|+|+.++|.+.++++..|..+
T Consensus 365 ~r~~l~~y~e~e~li~~G~y~~g~~~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~ 426 (428)
T PRK08149 365 FRKLLTRLEELQLFIDLGEYRRGENADNDRAMDKRPALEAFLKQDVAEKSSFSDTLERLNEF 426 (428)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 46789999999999999975 388888899999999999999999999999999887654
No 22
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=98.09 E-value=1.3e-05 Score=68.80 Aligned_cols=72 Identities=21% Similarity=0.353 Sum_probs=65.0
Q ss_pred ChhhhhhhHHHHHH-Hhhc-CCccHHHHHHHHhHHHHHHHhhcCCC----------CCCCHHHHHHHHHHHhhCCCCCCC
Q psy13777 1 MKLELAQYREVAAF-AQFG-SDLDAATQQLLNRGVRLTELLKQGQY----------VPMAIEEQVAVIYCGVRGHLDKLD 68 (121)
Q Consensus 1 LkL~LAQyrELeaF-aqFg-SdLD~~Tk~~L~rG~rl~elLKQ~q~----------~P~~~~eQv~~L~a~~~g~ld~i~ 68 (121)
+|-.||+|+|++.+ +.+| .++++.++..+.+|++|.+.|+|+.| ++.+.++-+..|..+.+|.+|++|
T Consensus 387 ~r~~la~y~e~e~li~~~g~~~ls~~~~~~i~~~~~i~~fL~Q~~f~~e~ft~~~~~~~~~~~~~~~l~~i~~g~~~~~~ 466 (494)
T CHL00060 387 VKQTLQRYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIRGFQLILSGELDGLP 466 (494)
T ss_pred HHHHHHHhHHHHHHHHHhCcccCCHHHHHHHHhHHHHHHHhcCCcchhhcccCCCCcccCHHHHHHHHHHHhCCCccCCC
Confidence 46789999999997 6677 49999999999999999999999944 899999999999999999999999
Q ss_pred hhHH
Q psy13777 69 PAKI 72 (121)
Q Consensus 69 ~~~v 72 (121)
....
T Consensus 467 ~~~~ 470 (494)
T CHL00060 467 EQAF 470 (494)
T ss_pred HHHh
Confidence 8764
No 23
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=98.09 E-value=1.3e-05 Score=68.40 Aligned_cols=72 Identities=22% Similarity=0.343 Sum_probs=65.2
Q ss_pred ChhhhhhhHHHHHHHh-hc-CCccHHHHHHHHhHHHHHHHhhcCC----------CCCCCHHHHHHHHHHHhhCCCCCCC
Q psy13777 1 MKLELAQYREVAAFAQ-FG-SDLDAATQQLLNRGVRLTELLKQGQ----------YVPMAIEEQVAVIYCGVRGHLDKLD 68 (121)
Q Consensus 1 LkL~LAQyrELeaFaq-Fg-SdLD~~Tk~~L~rG~rl~elLKQ~q----------~~P~~~~eQv~~L~a~~~g~ld~i~ 68 (121)
+|-.||+|+|++...+ +| .++|+.+...+.+|++|.+.|+|+. ..+.+.++-+-.|+.+.+|-+|++|
T Consensus 362 ~r~~la~y~e~e~li~i~gy~~l~~~~d~~i~~~~~i~~fL~Q~~~~~~~~t~~~~~~~~~~~~~~~l~~i~~g~~~~~~ 441 (461)
T PRK12597 362 VKRILQRYKELEDVIAILGIDELSAEDKIIVKRARQLQRFLTQPFFVTEAFTGEPGVSVPLEETLDSCERILNGEYDDWS 441 (461)
T ss_pred HHHHHHhhhhHHHHHHHcCCccCCHHHHHHHHhHHHHHHHhCCCcchhhcccCCCCcccCHHHHHHHHHHHhCCCccCCC
Confidence 3668999999999555 77 4899999999999999999999999 6799999999999999999999999
Q ss_pred hhHH
Q psy13777 69 PAKI 72 (121)
Q Consensus 69 ~~~v 72 (121)
....
T Consensus 442 ~~~~ 445 (461)
T PRK12597 442 EESF 445 (461)
T ss_pred HHHH
Confidence 8753
No 24
>PRK07721 fliI flagellum-specific ATP synthase; Validated
Probab=98.09 E-value=9.8e-06 Score=68.60 Aligned_cols=56 Identities=20% Similarity=0.343 Sum_probs=49.8
Q ss_pred ChhhhhhhHHHHHHHhhcC-------CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHh
Q psy13777 1 MKLELAQYREVAAFAQFGS-------DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS-------dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~ 60 (121)
+|-.||+|+|++.|.+||+ ++|.+ +.++.+|.+.|+|+.++|.+.++++..|+.+.
T Consensus 372 ~r~~l~~y~e~~~li~~g~y~~g~~~~~d~a----~~~~~~~~~fl~Q~~~~~~~~~~~~~~l~~~~ 434 (438)
T PRK07721 372 FRELLSTYQNSEDLINIGAYKRGSSREIDEA----IQFYPQIISFLKQGTDEKATFEESIQALLSLF 434 (438)
T ss_pred HHHHHHHhHHHHHHHHhhCCcCCCCHHHHHH----HHhHHHHHHHhCCCCCCCCCHHHHHHHHHHHH
Confidence 4678999999999999998 66655 66799999999999999999999999998875
No 25
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=98.08 E-value=1.1e-05 Score=68.37 Aligned_cols=59 Identities=19% Similarity=0.224 Sum_probs=54.0
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|..||+|+|++.|.+||+ ..|+.+...+.++.+|.+.|+|+.++|.+.++-+--|..+
T Consensus 370 ~r~~~a~y~e~~~li~~g~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~~ 431 (434)
T PRK07196 370 LKQCYADYMAIKPLIPLGGYVAGADPMADQAVHYYPAITQFLRQEVGHPALFSASVEQLTGM 431 (434)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4778999999999999998 9999999999999999999999999999998877666654
No 26
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=98.06 E-value=1e-05 Score=68.76 Aligned_cols=60 Identities=15% Similarity=0.223 Sum_probs=54.7
Q ss_pred ChhhhhhhH---HHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHh
Q psy13777 1 MKLELAQYR---EVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60 (121)
Q Consensus 1 LkL~LAQyr---ELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~ 60 (121)
+|..||+|+ ||..|..|++..|+.+.+.+.++.+|.+.|+|+.++|.+.++++--|..+.
T Consensus 384 ~r~~la~y~~~~dli~~g~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~~~ 446 (451)
T PRK05688 384 FKQLWSRYQQSRDLISVGAYVAGGDPETDLAIARFPHLVQFLRQGLRENVSLAQSREQLAAIF 446 (451)
T ss_pred HHHHHHHHHHHHHHHHHhCccCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHHHh
Confidence 467799999 888999999999999999999999999999999999999999998777653
No 27
>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=98.06 E-value=1.6e-05 Score=67.68 Aligned_cols=72 Identities=21% Similarity=0.371 Sum_probs=66.2
Q ss_pred ChhhhhhhHHHHH-HHhhc-CCccHHHHHHHHhHHHHHHHhhcCCCCC----------CCHHHHHHHHHHHhhCCCCCCC
Q psy13777 1 MKLELAQYREVAA-FAQFG-SDLDAATQQLLNRGVRLTELLKQGQYVP----------MAIEEQVAVIYCGVRGHLDKLD 68 (121)
Q Consensus 1 LkL~LAQyrELea-FaqFg-SdLD~~Tk~~L~rG~rl~elLKQ~q~~P----------~~~~eQv~~L~a~~~g~ld~i~ 68 (121)
+|..||+|+|++. ++.+| .++.+..+..+.+|++|.+.|+|+.|.+ +++++-+-..+.+-+|.+|++|
T Consensus 357 ~~~~l~~y~e~~~li~~~g~~~l~~~~~~~i~~~~~i~~fL~Q~~~~~e~~t~~~g~~v~l~~tl~~~~~il~g~~~~~~ 436 (449)
T TIGR03305 357 VRQTLAQYEELKDIIAMLGLEQLSREDRRVVNRARRLERFLTQPFFTTEQFTGMKGKTVSLEDALDGCERILNDEFQDYP 436 (449)
T ss_pred HHHHHHHHHHHHHHHHhhCCccCCHHHHHHHHHHHHHHHHhCCCCcccccccCCCCceeEHHHHHHHHHHHhcCCcccCC
Confidence 4678999999999 68888 6999999999999999999999999999 9999999999999999999999
Q ss_pred hhHH
Q psy13777 69 PAKI 72 (121)
Q Consensus 69 ~~~v 72 (121)
....
T Consensus 437 ~~~~ 440 (449)
T TIGR03305 437 ERDL 440 (449)
T ss_pred HHHh
Confidence 8753
No 28
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=98.05 E-value=1.1e-05 Score=68.29 Aligned_cols=59 Identities=14% Similarity=0.154 Sum_probs=54.3
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.||+|+|+|.+.++|. ..|+.+.+.+.+|.+|.+.|+|+.++|++.++++.-|..+
T Consensus 371 ~r~~l~~y~e~e~li~~G~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~ 432 (434)
T PRK08472 371 FKRLYSLLKENEVLIRIGAYQKGNDKELDEAISKKEFMEQFLKQNPNELFPFEQTFEQLEEI 432 (434)
T ss_pred HHHHHHhchhHHHHHHhhCccCCCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4678999999999999998 9999999999999999999999999999999998776554
No 29
>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=98.02 E-value=9.9e-06 Score=68.07 Aligned_cols=53 Identities=25% Similarity=0.345 Sum_probs=48.7
Q ss_pred ChhhhhhhHHHHHHHhhc---CCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFG---SDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQV 53 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFg---SdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv 53 (121)
+|-.||+|+|++.+.++| +..|+.+.+.+.+|++|.+.|+|+.++|.+.++-+
T Consensus 353 ~r~~l~~y~e~~~l~~~g~y~~g~d~~~d~~i~~~~~i~~fl~Q~~~~~~~~~~~~ 408 (411)
T TIGR03496 353 FKQLLSRYQENRDLISIGAYQAGSDPELDQAIALYPRIEAFLQQGMRERASFEESL 408 (411)
T ss_pred HHHHHHHhHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHH
Confidence 467899999999999999 78999999999999999999999999999987643
No 30
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=98.00 E-value=1.6e-05 Score=67.47 Aligned_cols=59 Identities=10% Similarity=0.128 Sum_probs=53.6
Q ss_pred hhhhhhhHHHH---HHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHh
Q psy13777 2 KLELAQYREVA---AFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60 (121)
Q Consensus 2 kL~LAQyrELe---aFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~ 60 (121)
|-.||+|+|++ ++..|+++.|+.+.+.+++|.+|.++|+|+.++|.+.++-+.-|..+.
T Consensus 379 r~~ls~y~~~e~li~~g~y~~g~d~~~d~ai~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~~ 440 (444)
T PRK08972 379 KQVYSLYQQNRDLISIGAYKQGSDPRIDNAIRLQPAMNAFLQQTMKEAVPYDMSVNMLKQLA 440 (444)
T ss_pred HHHHHHHHHHHHHHHHhCccCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHHHH
Confidence 56788999988 999999999999999999999999999999999999998877776654
No 31
>PRK06820 type III secretion system ATPase; Validated
Probab=97.95 E-value=2.3e-05 Score=66.46 Aligned_cols=59 Identities=19% Similarity=0.260 Sum_probs=53.7
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.||+|+|++.+.+||+ .+|+.+.+.+.+|.++.+.|+|+.+++.+.++-+-.|+.+
T Consensus 377 ~r~~l~~y~e~~~li~~G~y~~g~d~~~d~~i~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~~ 438 (440)
T PRK06820 377 LRRMLACYQEIELLVRVGEYQAGEDLQADEALQRYPAICAFLQQDHSETAHLETTLEHLAQV 438 (440)
T ss_pred HHHHHHhhhHHHHHHHhhCccCCCCHHHHHHHHhhHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 3667999999999999999 8999999999999999999999999999998877766654
No 32
>PRK14698 V-type ATP synthase subunit A; Provisional
Probab=97.93 E-value=2.2e-05 Score=72.29 Aligned_cols=57 Identities=21% Similarity=0.226 Sum_probs=51.8
Q ss_pred hhhhhHHHHHHHhh-cC-CccHHHHHHHHhHHHHHHH-hhcCCCCC----CCHHHHHHHHHHHh
Q psy13777 4 ELAQYREVAAFAQF-GS-DLDAATQQLLNRGVRLTEL-LKQGQYVP----MAIEEQVAVIYCGV 60 (121)
Q Consensus 4 ~LAQyrELeaFaqF-gS-dLD~~Tk~~L~rG~rl~el-LKQ~q~~P----~~~~eQv~~L~a~~ 60 (121)
-|++|+||+.+.|+ |+ +|++.++.++.+|++|++. |+|+.|+| .|.++|+..|+++.
T Consensus 894 ~l~~~~el~~~i~l~g~~~l~~~d~~~~~~~~~i~e~fL~Q~~~~~~d~~~~~~~~~~~l~~i~ 957 (1017)
T PRK14698 894 LLQKEAELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLL 957 (1017)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhHHHHhccCCCCCCCccccCCCHHHHHHHHHHHH
Confidence 48999999999999 65 5999999999999999975 99999999 79999999988764
No 33
>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=97.93 E-value=4.2e-05 Score=65.27 Aligned_cols=72 Identities=17% Similarity=0.277 Sum_probs=65.2
Q ss_pred ChhhhhhhHHHHHHH-hhc-CCccHHHHHHHHhHHHHHHHhhcCC----------CCCCCHHHHHHHHHHHhhCCCCCCC
Q psy13777 1 MKLELAQYREVAAFA-QFG-SDLDAATQQLLNRGVRLTELLKQGQ----------YVPMAIEEQVAVIYCGVRGHLDKLD 68 (121)
Q Consensus 1 LkL~LAQyrELeaFa-qFg-SdLD~~Tk~~L~rG~rl~elLKQ~q----------~~P~~~~eQv~~L~a~~~g~ld~i~ 68 (121)
+|-.||+|+|++.+. .+| .++++.++..+.+|++|.+.|+|+. .++.+.++.+.-|.++.+|-+|++|
T Consensus 362 ~r~~la~y~e~~~li~i~g~~~lsd~~~~~l~~~~~i~~fL~Q~~~~~~~~t~~~~~~~~~~~~~~~l~~i~~g~~~~~~ 441 (461)
T TIGR01039 362 VQQILQRYKELQDIIAILGMDELSEEDKLTVERARRIQRFLSQPFFVAEVFTGQPGKYVPLKDTIRGFKEILEGKYDHLP 441 (461)
T ss_pred HHHHHHhhhHHHHHHHHhCCccCCHHHHHHHHhHHHHHHHhCCCCchhccccCCCCcccCHHHHHHHHHHHhCCCccCCC
Confidence 366799999999965 566 3799999999999999999999999 8999999999999999999999999
Q ss_pred hhHH
Q psy13777 69 PAKI 72 (121)
Q Consensus 69 ~~~v 72 (121)
.+..
T Consensus 442 ~~~~ 445 (461)
T TIGR01039 442 EQAF 445 (461)
T ss_pred HHHH
Confidence 8864
No 34
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=97.89 E-value=1.7e-05 Score=67.22 Aligned_cols=58 Identities=21% Similarity=0.350 Sum_probs=50.9
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHH----HhHHHHHHHhhcCCCCCCCHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLL----NRGVRLTELLKQGQYVPMAIEEQVAVIYC 58 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L----~rG~rl~elLKQ~q~~P~~~~eQv~~L~a 58 (121)
+|-.||+|+|+|.|.+||+..+.++.... .+|.+|++.|||+.++|++.++-+--|..
T Consensus 369 ~r~~la~y~e~e~~i~~g~y~~g~~~~~d~ai~~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~ 430 (432)
T PRK06793 369 MRKILSIYKENELYFKLGTIQENAENAYIFECKNKVEGINTFLKQGRSDSFQFDDIVEAMHH 430 (432)
T ss_pred HHHHHHhChHHHHHHHhCCccCCCCHHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHh
Confidence 47789999999999999999888887776 69999999999999999999887655543
No 35
>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=97.84 E-value=4.8e-05 Score=64.00 Aligned_cols=59 Identities=20% Similarity=0.289 Sum_probs=52.2
Q ss_pred ChhhhhhhHHHHHHHhhcCCc---cHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDL---DAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdL---D~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.|++|.|++.+.++|+-- |+.+.+.+.+|++|.++|+|+.++|.+.++++..|..+
T Consensus 351 ~r~~l~~y~e~~~li~~g~~~~g~d~~~~~~i~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~ 412 (413)
T TIGR03497 351 LRELLAVYKEAEDLINIGAYKRGSNPKIDEAIRYIEKINSFLKQGIDEKFTFEETVQLLKTL 412 (413)
T ss_pred HHHHHHhhHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHhh
Confidence 356799999999999995422 88899999999999999999999999999999888754
No 36
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=97.78 E-value=6.3e-05 Score=63.94 Aligned_cols=61 Identities=18% Similarity=0.308 Sum_probs=57.6
Q ss_pred hhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhC
Q psy13777 2 KLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRG 62 (121)
Q Consensus 2 kL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g 62 (121)
|--|++|.|++.+.++|+ ..|+.+...+.+|.++.+.|+|+.+++.+.++++-.|+.+.+|
T Consensus 375 r~~l~~y~e~edli~lg~y~~g~d~~~d~ai~~~~~i~~fL~Q~~~e~~~~~~~~~~l~~l~~~ 438 (442)
T PRK08927 375 RQLMATYADMEELIRLGAYRAGSDPEVDEAIRLNPALEAFLRQGKDEATSLAEGYARLAQILGG 438 (442)
T ss_pred HHHHHHHHHHHHHHHhhCCcCCCCHHHHHHHHccHHHHHhcCCCCCCCCCHHHHHHHHHHHhcc
Confidence 667999999999999998 8999999999999999999999999999999999999988765
No 37
>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=97.74 E-value=7.8e-05 Score=63.21 Aligned_cols=59 Identities=19% Similarity=0.253 Sum_probs=52.2
Q ss_pred ChhhhhhhHHHHHHHhhcCCc---cHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDL---DAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdL---D~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|-.||+|+|++.+.++|... |+.+.+.+.+|++|.+.|+|+.++|++.++++--|..+
T Consensus 377 ~r~~l~~y~e~~~li~ig~y~~g~d~~~d~~i~~~~~i~~fL~Q~~~~~~~~~~~~~~l~~~ 438 (440)
T TIGR01026 377 FRELLSKYKDNEDLIRIGAYQRGSDRELDFAIAKYPKLERFLKQGINEKVNFEESLQQLEEI 438 (440)
T ss_pred HHHHHHhhHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHh
Confidence 467899999999999998653 78888889999999999999999999999998776654
No 38
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=97.62 E-value=0.00022 Score=60.93 Aligned_cols=72 Identities=17% Similarity=0.276 Sum_probs=65.2
Q ss_pred ChhhhhhhHHHHHH-Hhhc-CCccHHHHHHHHhHHHHHHHhhcCC----------CCCCCHHHHHHHHHHHhhCCCCCCC
Q psy13777 1 MKLELAQYREVAAF-AQFG-SDLDAATQQLLNRGVRLTELLKQGQ----------YVPMAIEEQVAVIYCGVRGHLDKLD 68 (121)
Q Consensus 1 LkL~LAQyrELeaF-aqFg-SdLD~~Tk~~L~rG~rl~elLKQ~q----------~~P~~~~eQv~~L~a~~~g~ld~i~ 68 (121)
+|-.||+|+|++.. +-+| ..+++.++..+.+|++|.+.|+|+. ..+.+.++-+.-|..+.+|-+|++|
T Consensus 363 ~r~~la~y~e~e~li~i~gy~~~sd~~d~ai~~~~~i~~fL~Q~~~~~~~ft~~~~~~~~~~~~~~~l~~i~~g~~~~~~ 442 (463)
T PRK09280 363 VQQILQRYKELQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFFVAEQFTGSPGKYVPLKDTIRGFKEILEGEYDHLP 442 (463)
T ss_pred HHHHHHHhHHHHHHHHhhCCccCCHHHHHHHHhhHHHHHhccCCcchhhcccCCCCcccCHHHHHHHHHHHhCCCccCCC
Confidence 36679999999995 5677 4799999999999999999999999 9999999999999999999999999
Q ss_pred hhHH
Q psy13777 69 PAKI 72 (121)
Q Consensus 69 ~~~v 72 (121)
..+.
T Consensus 443 ~~~~ 446 (463)
T PRK09280 443 EQAF 446 (463)
T ss_pred HHHH
Confidence 8764
No 39
>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=97.60 E-value=7.6e-05 Score=61.13 Aligned_cols=41 Identities=22% Similarity=0.400 Sum_probs=38.9
Q ss_pred ChhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhc
Q psy13777 1 MKLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQ 41 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ 41 (121)
+|-.|++|+|++.|.+||+ .+|+.+.+.+.||++|.+.|+|
T Consensus 283 ~r~~l~~y~e~~~~i~~g~y~~g~d~~~d~~i~~~~~i~~~l~Q 326 (326)
T cd01136 283 LRELLSAYQEVEDLIRIGAYKKGSDPEVDEAIKLLPKIEAFLKQ 326 (326)
T ss_pred HHHHHHHhHHHHHHHHhcCCCCCCCHHHHHHHHhHHHHHHHhCC
Confidence 4778999999999999998 8999999999999999999998
No 40
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=96.73 E-value=0.045 Score=48.30 Aligned_cols=57 Identities=21% Similarity=0.314 Sum_probs=50.3
Q ss_pred hhhhhhhHHHHHHHhh-cCC-ccHHHHHHHHhHHHHHH-HhhcCCCCCC----CHHHHHHHHHH
Q psy13777 2 KLELAQYREVAAFAQF-GSD-LDAATQQLLNRGVRLTE-LLKQGQYVPM----AIEEQVAVIYC 58 (121)
Q Consensus 2 kL~LAQyrELeaFaqF-gSd-LD~~Tk~~L~rG~rl~e-lLKQ~q~~P~----~~~eQv~~L~a 58 (121)
|--|+.|+|++...+. |.| |.+..+..|+++++|++ .|+|+.|.+. |++.|..+|-+
T Consensus 461 ~~~L~~~~el~eiv~lvG~d~Ls~~d~~~l~~a~~i~~~fL~Q~~f~~~d~~~~l~k~~~~l~~ 524 (586)
T PRK04192 461 MDLLQREAELQEIVRLVGPDALPEEDRLILEVARLIREDFLQQNAFDPVDTYCPPEKQYEMLKL 524 (586)
T ss_pred HHHHHHHHHHHHHHHHhCcccCCHHHHHHHHHHHHHHHhhcCCCCCCCccccccHHHHHHHHHH
Confidence 3458999999999997 997 99999999999999995 9999999999 88988866543
No 41
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=96.70 E-value=0.0075 Score=51.39 Aligned_cols=62 Identities=18% Similarity=0.112 Sum_probs=53.8
Q ss_pred hhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCC
Q psy13777 2 KLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHL 64 (121)
Q Consensus 2 kL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~l 64 (121)
|-.||.|+|++.+.++|.+|++.++..+.+|+++-..|-| |..-.++++-+-..+.+-+++.
T Consensus 353 ~~~~a~y~e~~dli~iG~eLs~~d~~~l~~~~~~e~~~~~-~g~~~~~~etl~~~~~~l~~~~ 414 (436)
T PRK02118 353 IRLYADSREAKEKMAMGFKLSNWDEKLLKFSELFESRLMD-LEVNIPLEEALDLGWKILAQCF 414 (436)
T ss_pred HHHHHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHhhc-CCCcccHHHHHHHHHHHHHHCC
Confidence 5679999999999999999999999999999999999877 4488888888877777766553
No 42
>PRK05922 type III secretion system ATPase; Validated
Probab=96.49 E-value=0.0052 Score=52.26 Aligned_cols=58 Identities=19% Similarity=0.273 Sum_probs=44.7
Q ss_pred ChhhhhhhHHHHHHHhhcCCccHHHHHHHHhHHH----HHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVR----LTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 1 LkL~LAQyrELeaFaqFgSdLD~~Tk~~L~rG~r----l~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
+|..||+|+|+|.|.+||. .++.+...++++.+ |...|+|+..++.+.++-+--|..+
T Consensus 369 ~r~~l~~y~e~edli~~G~-y~~g~d~~~d~a~~~~~~i~~fl~Q~~~~~~~~~~~~~~l~~~ 430 (434)
T PRK05922 369 LRSLLKAYHEALDIIQLGA-YVPGQDAHLDRAVKLLPSIKQFLSQPLSSYCALHNTLKQLEAL 430 (434)
T ss_pred HHHHHHHHHHHHHHHHhcC-CCccCCHHHHHHHHhHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4778999999999999998 77777777888888 6677777777777776655544443
No 43
>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=83.51 E-value=3.3 Score=25.95 Aligned_cols=44 Identities=30% Similarity=0.474 Sum_probs=35.3
Q ss_pred HHHHHhhcCC--------CCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHH
Q psy13777 34 RLTELLKQGQ--------YVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEK 77 (121)
Q Consensus 34 rl~elLKQ~q--------~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~ 77 (121)
+++++.++.+ |+|+.+++-...|-+...|+.+.++...+.+|..
T Consensus 4 ~lt~~I~~~p~l~ekIL~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD 55 (64)
T PF09494_consen 4 ALTKLIRSDPELYEKILMYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLD 55 (64)
T ss_pred HHHHHHHcCHHHHHHHHcCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHH
Confidence 4555555554 9999999999888877788899999999887754
No 44
>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=77.58 E-value=10 Score=32.89 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=36.2
Q ss_pred hhhhHHHHHHHhhcC-----CccHHHHHHHHhHHHH-HHHhhcCCCCCCCHHHHH
Q psy13777 5 LAQYREVAAFAQFGS-----DLDAATQQLLNRGVRL-TELLKQGQYVPMAIEEQV 53 (121)
Q Consensus 5 LAQyrELeaFaqFgS-----dLD~~Tk~~L~rG~rl-~elLKQ~q~~P~~~~eQv 53 (121)
++-|.+.+...+.|. .+.+.....|.++..+ ...|+|+.+++.+.++-.
T Consensus 379 ~~~y~~~~~L~~ig~y~G~d~l~d~a~~~l~~~~~i~~~FL~Q~~~~~~~~~~~l 433 (466)
T TIGR01040 379 YACYAIGKDVQAMKAVVGEEALSSEDLLYLEFLDKFEKNFIAQGPYENRTIFESL 433 (466)
T ss_pred HHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHHHHHHHHhccCcCCCcCHHHHH
Confidence 344544444444444 6777788889999999 889999999999987743
No 45
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=66.67 E-value=28 Score=30.11 Aligned_cols=58 Identities=16% Similarity=0.210 Sum_probs=44.2
Q ss_pred hhhhhhhHHHHHHHhhcC---CccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHH
Q psy13777 2 KLELAQYREVAAFAQFGS---DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCG 59 (121)
Q Consensus 2 kL~LAQyrELeaFaqFgS---dLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~ 59 (121)
|=-|+.|.|++..-+.|. --|+..-+.+.+-.+|.+.|+|+.+++.+.++-+.-|..+
T Consensus 392 r~~l~~Y~~~~dli~ig~y~~G~d~~~D~ai~~~~~i~~fl~Q~~~e~~~~~~~~~~l~~~ 452 (455)
T PRK07960 392 KQLLSSFQRNRDLVSVGAYAKGSDPMLDKAIALWPQLEAFLQQGIFERADWEDSLQALERI 452 (455)
T ss_pred HHHHHHHHHHHHHHHhcCccCCCCHHHHHHHHhHHHHHHHhCCCCCCCcCHHHHHHHHHHh
Confidence 335788999988888743 2344455556677999999999999999999887776654
No 46
>PF14615 Rsa3: Ribosome-assembly protein 3
Probab=64.29 E-value=23 Score=21.18 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHH
Q psy13777 75 FEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTN 114 (121)
Q Consensus 75 f~~~l~~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~ 114 (121)
|.+.+++.+..+..+-++++++...+++.....|.++++.
T Consensus 2 f~~~yl~~~t~efgdDLd~lR~~~dF~~~sl~~Li~aL~~ 41 (47)
T PF14615_consen 2 FRNFYLQRLTDEFGDDLDELRKAPDFTDKSLPLLIDALQQ 41 (47)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Confidence 6777888888899999999999999988777777666654
No 47
>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=62.10 E-value=16 Score=27.95 Aligned_cols=50 Identities=20% Similarity=0.384 Sum_probs=28.9
Q ss_pred hCCCCCCChhHHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHH
Q psy13777 61 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTV 111 (121)
Q Consensus 61 ~g~ld~i~~~~v~~f~~~l~~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~ 111 (121)
.|-+|++.+-.|..--..+. -+......+++.|.+.+.|++++...|..+
T Consensus 36 TG~Lde~~lR~i~~~~~~~~-~L~~Rk~~il~~i~eqgkLt~eL~~~I~~a 85 (193)
T PF09371_consen 36 TGGLDEVQLREIQDRYEYLR-ELEKRKESILKSIEEQGKLTPELKQAIENA 85 (193)
T ss_dssp HTS--HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHTT---HHHHHHHHH-
T ss_pred hCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHcccCCHHHHHHHHhc
Confidence 34455544444444333332 355666789999999999999988887765
No 48
>PF02061 Lambda_CIII: Lambda Phage CIII; InterPro: IPR013056 Bacteriophage lambda regulatory protein CIII is a small protein that plays a role in stabilising the CII transcriptional activator, via a mechanism that is not yet fully understood [, ]. Stabilised CII activates CI, the gene for the repressor protein that prevents transcription of proteins required for lytic development. The central portion of the protein is well conserved and is both necessary and sufficient for the activity of the protein []. Comparative analysis of the CIII sequence in lambda, Bacteriophage HK022 and the lambdoid Enterobacteria phage P22 has led to the suggestion that this central region assumes an amphipathic alpha-helical structure []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=61.37 E-value=6.4 Score=23.28 Aligned_cols=25 Identities=36% Similarity=0.320 Sum_probs=20.8
Q ss_pred CCccHHHHHHHHhHHHHHHHhhcCC
Q psy13777 19 SDLDAATQQLLNRGVRLTELLKQGQ 43 (121)
Q Consensus 19 SdLD~~Tk~~L~rG~rl~elLKQ~q 43 (121)
|=||--|++.-+--+|+.++|.||-
T Consensus 19 SLLdrItRklr~gwKRl~~iLnQpG 43 (45)
T PF02061_consen 19 SLLDRITRKLRDGWKRLWDILNQPG 43 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 4578888887777899999999984
No 49
>PF03353 Lin-8: Ras-mediated vulval-induction antagonist; InterPro: IPR005020 This is a family of Caenorhabditis elegans proteins of unknown function.
Probab=60.23 E-value=82 Score=25.23 Aligned_cols=93 Identities=27% Similarity=0.358 Sum_probs=63.4
Q ss_pred hhhhhhHHHHH--HHhhcCCccHHH-HHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHH
Q psy13777 3 LELAQYREVAA--FAQFGSDLDAAT-QQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEF 79 (121)
Q Consensus 3 L~LAQyrELea--FaqFgSdLD~~T-k~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l 79 (121)
+.|.+|++|+. |..+.+. |... +.+|.-=+..-++.+.....+....+.|++-.-...|.+ +.+..|.......
T Consensus 1 ~t~~~Y~~~~~~~~~~~~~~-~~~~kk~il~~i~~~p~lw~~~~~~~~~~~~~v~v~vy~Rtg~~--~~~~~i~~~~~~a 77 (313)
T PF03353_consen 1 MTLKEYRELEKEKFNKKAKK-DVELKKVILSEIEKFPELWKKKSRVPNEEWEEVAVEVYKRTGKL--VSVKHIRSIFKNA 77 (313)
T ss_pred CCHHHHHHHhhccccccchh-hHHHHHHHHHHHhcChHhhhccCCccHHHHHHHHHHHHHHHhhh--cCHHHHHHHHHHH
Confidence 46889999987 7666555 6655 456666667778888666678888888988777778887 6777777666666
Q ss_pred HHHHHhchhHHHHHHHhcCCCCH
Q psy13777 80 LAHIKSSERGLLESIKKEGKITE 102 (121)
Q Consensus 80 ~~~l~~~~~~~~~~i~~~~~l~~ 102 (121)
-..|+.. +...|... .++.
T Consensus 78 K~~Lr~~---l~~~I~~~-~l~~ 96 (313)
T PF03353_consen 78 KDSLRRR---LRKCIKKK-KLSP 96 (313)
T ss_pred HHHHHHH---HHHHHHHc-CCCH
Confidence 6655543 33334333 4664
No 50
>TIGR01042 V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.
Probab=58.49 E-value=1.4e+02 Score=26.85 Aligned_cols=56 Identities=14% Similarity=0.159 Sum_probs=39.1
Q ss_pred hhhhhHHHHHHHhhcC--CccHHHHHHHHhHHHHH-HHhhcCCC----CCCCHHHHHHHHHHH
Q psy13777 4 ELAQYREVAAFAQFGS--DLDAATQQLLNRGVRLT-ELLKQGQY----VPMAIEEQVAVIYCG 59 (121)
Q Consensus 4 ~LAQyrELeaFaqFgS--dLD~~Tk~~L~rG~rl~-elLKQ~q~----~P~~~~eQv~~L~a~ 59 (121)
-|+.|.|++.-.+-|. .|-+.-+..+...+.++ ..|+|+-| ...|.++|+..|-++
T Consensus 465 lL~~~~el~eiv~l~g~~~l~~~d~~i~~~a~~i~e~FLqQ~a~~~~d~~~~~~kt~~~L~~i 527 (591)
T TIGR01042 465 ILQEEEDLNEIVQLVGKDALAETDKITLEVAKLIKEDFLQQNGYTPYDRFCPFYKTVGMMRNM 527 (591)
T ss_pred HHHHHHHHHHHHHHhCCccCCHHHHHHHHHHHHHHHHhCCCCCCCCccccCCHHHHHHHHHHH
Confidence 4788999999988854 25555566677677776 78899844 446778887665443
No 51
>KOG1142|consensus
Probab=53.38 E-value=20 Score=28.84 Aligned_cols=33 Identities=18% Similarity=0.392 Sum_probs=29.0
Q ss_pred chhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Q psy13777 86 SERGLLESIKKEGKITEDTDAKLKTVVTNFLAN 118 (121)
Q Consensus 86 ~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~ 118 (121)
+..++++.|..+..|+++.++.|.++..+|.+.
T Consensus 159 kl~dLvqqId~~~~LD~dVedlLleiADdFV~s 191 (258)
T KOG1142|consen 159 KLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSS 191 (258)
T ss_pred chhHHHHhhcCcccccHHHHHHHHHHHHHHHHH
Confidence 345788999999999999999999999999874
No 52
>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=48.85 E-value=19 Score=23.04 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=21.6
Q ss_pred hHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Q psy13777 88 RGLLESIKKEGKITEDTDAKLKTVVTNFLAN 118 (121)
Q Consensus 88 ~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~ 118 (121)
.++++.|..+..++++.++.|.+...+|...
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 4677778888899999999999999988764
No 53
>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=48.76 E-value=79 Score=24.34 Aligned_cols=50 Identities=8% Similarity=0.195 Sum_probs=38.8
Q ss_pred hHHHHHHHHHHHHHHhc--hhHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13777 70 AKITTFEKEFLAHIKSS--ERGLLESIKKEGKITEDTDAKLKTVVTNFLANF 119 (121)
Q Consensus 70 ~~v~~f~~~l~~~l~~~--~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~f 119 (121)
+-|......+..|+.+. ++++.++|-.++.|.+++.+.|...++.....|
T Consensus 85 niv~~l~~dv~~y~~~~~~~~~V~~~i~~~g~l~~~i~~~I~~TF~~c~~~~ 136 (192)
T PF03048_consen 85 NIVESLKSDVYSYFSRSNDYAEVKQAIFEDGELKPHIEDLIYFTFNHCFHVF 136 (192)
T ss_pred HHHHHHHHHHHHHHHhcccHHHHHHHHHcCCcccHhHHHHHHHHHHHHHHhh
Confidence 33455666677777444 688999999999999999999999888876654
No 54
>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=47.65 E-value=19 Score=26.82 Aligned_cols=41 Identities=12% Similarity=0.326 Sum_probs=35.0
Q ss_pred HHHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHH
Q psy13777 10 EVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVI 56 (121)
Q Consensus 10 ELeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L 56 (121)
++++|.+|+.-++..-+..++..++| |-|+-++.++|+++|
T Consensus 10 ~~~~~~~~~~~~~~~i~~~V~waK~i------PgF~~L~~~DQi~LL 50 (189)
T cd06940 10 GHEIWEEFSMSFTPAVREVVEFAKRI------PGFRDLSQHDQVTLL 50 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC------CCcccCChhhHHHHH
Confidence 46889999998888888888888877 789999999999775
No 55
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=47.29 E-value=27 Score=20.75 Aligned_cols=40 Identities=23% Similarity=0.250 Sum_probs=24.1
Q ss_pred HHHHHHHhhcCCCCCCCHHHHHH----HHHHHhhCCCCCCChhHH
Q psy13777 32 GVRLTELLKQGQYVPMAIEEQVA----VIYCGVRGHLDKLDPAKI 72 (121)
Q Consensus 32 G~rl~elLKQ~q~~P~~~~eQv~----~L~a~~~g~ld~i~~~~v 72 (121)
|+||+++.++..++--.+++.+- .++...+|-. .++++.+
T Consensus 1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~-~~~~~~l 44 (64)
T PF12844_consen 1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKR-KPSVSTL 44 (64)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS---BHHHH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCc-CCCHHHH
Confidence 89999999999888766666542 3555556643 4444444
No 56
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=46.80 E-value=23 Score=23.58 Aligned_cols=51 Identities=12% Similarity=0.184 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHHHHhchhHHH----------HHHHhcCCCCHHHHHHHHHHHHHHHH
Q psy13777 66 KLDPAKITTFEKEFLAHIKSSERGLL----------ESIKKEGKITEDTDAKLKTVVTNFLA 117 (121)
Q Consensus 66 ~i~~~~v~~f~~~l~~~l~~~~~~~~----------~~i~~~~~l~~~~~~~l~~~~~~~~~ 117 (121)
.+|...+...+.+|.+++...+|+.. ..+.-.+. +++.++.|.+++++..+
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 23332232 23467888888887655
No 57
>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=45.49 E-value=74 Score=26.20 Aligned_cols=81 Identities=17% Similarity=0.168 Sum_probs=61.3
Q ss_pred HHHHhHHHHHHHhhcCCCCCC----------CHHHHHH-----------HHHHHhhCCCCCCChhHHHHHHHHHHHHHHh
Q psy13777 27 QLLNRGVRLTELLKQGQYVPM----------AIEEQVA-----------VIYCGVRGHLDKLDPAKITTFEKEFLAHIKS 85 (121)
Q Consensus 27 ~~L~rG~rl~elLKQ~q~~P~----------~~~eQv~-----------~L~a~~~g~ld~i~~~~v~~f~~~l~~~l~~ 85 (121)
+..+--+++-.+|.-=..-++ +-.|++. -+|++|.=|..+++...+.+|-..++=
T Consensus 46 kVvevY~~vG~~Ls~YrSGkLPKafKiiP~l~nWEeiL~lT~P~~WSp~A~~~aTRiF~SnL~~~~aqrF~~~VLL---- 121 (301)
T PF05291_consen 46 KVVEVYTKVGELLSRYRSGKLPKAFKIIPSLPNWEEILYLTRPEKWSPHAMYEATRIFASNLNEKMAQRFYNLVLL---- 121 (301)
T ss_pred HHHHHHHHHHHHHhhcCCCCCCcCeecccCchhHHHHHHhCChhhccHHHHHHHHHHHhhCCCHHHHHHHHHHHHH----
Confidence 555666667777765444433 3445553 479999999999999999998887763
Q ss_pred chhHHHHHHHhcCCCCHHHHHHHHHHHH
Q psy13777 86 SERGLLESIKKEGKITEDTDAKLKTVVT 113 (121)
Q Consensus 86 ~~~~~~~~i~~~~~l~~~~~~~l~~~~~ 113 (121)
|-+.+.|.++++|+-..-.+|++++-
T Consensus 122 --prvredI~~~KKLn~hly~ALkKaly 147 (301)
T PF05291_consen 122 --PRVREDIAENKKLNYHLYMALKKALY 147 (301)
T ss_pred --HHHHHHHHHcCCcCHHHHHHHHHHHc
Confidence 77889999999999998888888764
No 58
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=44.63 E-value=17 Score=28.32 Aligned_cols=48 Identities=23% Similarity=0.328 Sum_probs=35.1
Q ss_pred hhhhhhHH----------HHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHH
Q psy13777 3 LELAQYRE----------VAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVI 56 (121)
Q Consensus 3 L~LAQyrE----------LeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L 56 (121)
+||+||++ .+.|.+|-.-+...-+..++..++| |-|.-++.++|+++|
T Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~t~~i~~iv~wAK~I------PgF~~L~~~DQi~LL 80 (239)
T cd07072 23 LDYSQYREPSPLEPPMSEAEKVQQFYSLLTSSIDVIKTFAEKI------PGFPDLCKEDQELLF 80 (239)
T ss_pred ccccccCCCCcccCCcchHHHHHHHHHHHHHHHHHHHHHhccC------CCccCCCHHHHHHHH
Confidence 56777774 5666666665666666666666665 789999999999876
No 59
>PF04947 Pox_VLTF3: Poxvirus Late Transcription Factor VLTF3 like ; InterPro: IPR007031 Members of this family are approximately 26 kDa, and are involved in trans-activation of late transcription [].; GO: 0046782 regulation of viral transcription
Probab=41.71 E-value=1.5e+02 Score=22.19 Aligned_cols=87 Identities=13% Similarity=0.146 Sum_probs=57.9
Q ss_pred hHHHHHHHhhcCCCCC---CC--HHHHHHHHHHHhhCCCCCCChhHHHHHHHHHHHHHHhch---hHHHHHHHhc--CCC
Q psy13777 31 RGVRLTELLKQGQYVP---MA--IEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSE---RGLLESIKKE--GKI 100 (121)
Q Consensus 31 rG~rl~elLKQ~q~~P---~~--~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~~~l~~~~---~~~~~~i~~~--~~l 100 (121)
|=-..+++|+|-|+.- +| |-+++.-...-.+=-.++|....|..|.+++- +...+ +.+...+... ..+
T Consensus 12 r~~Hf~e~L~~~q~k~~~~i~~~V~~~l~~~l~k~~i~~~~it~~~V~~~LK~l~--~~K~Y~~v~~I~~~ltg~~p~~l 89 (171)
T PF04947_consen 12 RLNHFREVLRQFQGKQNTTIPDEVYEELRKELKKYNIDISDITKNHVREFLKKLG--YSKYYEHVFLILNILTGKPPPNL 89 (171)
T ss_pred chHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHcCCCHHHcCHHHHHHHHHHcC--CcchHhHHHHHHHHHcCCCCccc
Confidence 3445778888777655 44 46777666666666678899999999988886 23333 3344444332 356
Q ss_pred CHHHHHHHHHHHHHHHHhc
Q psy13777 101 TEDTDAKLKTVVTNFLANF 119 (121)
Q Consensus 101 ~~~~~~~l~~~~~~~~~~f 119 (121)
+.+.++.|...+.++...|
T Consensus 90 s~~~e~~l~~~F~~~~~~~ 108 (171)
T PF04947_consen 90 SSELEERLMIIFDELQKPF 108 (171)
T ss_pred CHHHHHHHHHHHHHHHHHH
Confidence 7888888888888776654
No 60
>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=40.12 E-value=59 Score=20.59 Aligned_cols=31 Identities=19% Similarity=0.438 Sum_probs=24.1
Q ss_pred hHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Q psy13777 88 RGLLESIKKEGKITEDTDAKLKTVVTNFLAN 118 (121)
Q Consensus 88 ~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~ 118 (121)
.+++..|..+..++++..+.|.+..++|...
T Consensus 8 ~~lv~~id~~~~~~~da~~~l~~~~e~fv~~ 38 (72)
T cd07981 8 QELLKEIDPREQLDPDVEELLLEIADDFVDD 38 (72)
T ss_pred HHHHHhhCCCCCcCHHHHHHHHHHHHHHHHH
Confidence 3566777777789999999888888887653
No 61
>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=38.70 E-value=96 Score=19.32 Aligned_cols=36 Identities=14% Similarity=0.285 Sum_probs=24.1
Q ss_pred HHHHHHHHhchhHHHHHHHhcCC----CCHHHHHHHHHHHH
Q psy13777 77 KEFLAHIKSSERGLLESIKKEGK----ITEDTDAKLKTVVT 113 (121)
Q Consensus 77 ~~l~~~l~~~~~~~~~~i~~~~~----l~~~~~~~l~~~~~ 113 (121)
.++..|+.. +|++++.+.+++. +++.....|.++++
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 567788865 4999999988663 56665555555443
No 62
>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=38.30 E-value=1.6e+02 Score=21.76 Aligned_cols=46 Identities=15% Similarity=0.326 Sum_probs=33.6
Q ss_pred HHHHHHHHHhhCCCC------CCChhHHHHHHHHHHHHHHhchhHHHHHHHh
Q psy13777 51 EQVAVIYCGVRGHLD------KLDPAKITTFEKEFLAHIKSSERGLLESIKK 96 (121)
Q Consensus 51 eQv~~L~a~~~g~ld------~i~~~~v~~f~~~l~~~l~~~~~~~~~~i~~ 96 (121)
.|.++.|+--.|.=. ....+.+..|...|.+|+..-|-++.+.|..
T Consensus 27 q~Llv~Yc~L~gl~p~~~~~~~~~~~~l~~FCq~LVDYvSaGHFeIYe~l~~ 78 (153)
T PF04353_consen 27 QQLLVAYCKLAGLKPYKESLTLPSEEALQNFCQQLVDYVSAGHFEIYEQLID 78 (153)
T ss_dssp HHHHHHHHHHHS-------------HHHHHHHHHHHHHHHHHHHTHHHHHHT
T ss_pred HHHHHHHHhHhcCCCCccccCCCCHHHHHHHHHHHHHHHhccchhHHHHHHH
Confidence 567778877777543 3356789999999999999999999988765
No 63
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=35.52 E-value=2.1e+02 Score=22.28 Aligned_cols=77 Identities=18% Similarity=0.210 Sum_probs=55.1
Q ss_pred hHHHHHHHhhc-CCccHHHHHHHHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCC--------------------CC
Q psy13777 8 YREVAAFAQFG-SDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHL--------------------DK 66 (121)
Q Consensus 8 yrELeaFaqFg-SdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~l--------------------d~ 66 (121)
|-.-+...+|| .++.++.+..|+--.+-+=-|.=.-|-|-|+.....-+. -.+|.= -.
T Consensus 9 fTdp~vr~~fg~~~l~ea~~~~l~Lia~arl~l~iscYmPpsVy~El~~fl-~~~~~~~e~~~kl~twv~~KsP~rye~~ 87 (206)
T TIGR03875 9 FTDPELREQLGDEDLCEAVRTFLDLIARARLKLGIECYMPPSVYKELRRFL-ERNGCDPETLAKLDTWVVKKSPNRYEVK 87 (206)
T ss_pred cCCHHHHHHcCCCCHHHHHHHHHHHHHHhhhccCceeecCHHHHHHHHHHH-HhcCCCHHHHHhheeEEEEcCCCeeeee
Confidence 44455667899 899999999888888777777788899988888876543 333332 15
Q ss_pred CChhHHHHHHHHHHHHHHh
Q psy13777 67 LDPAKITTFEKEFLAHIKS 85 (121)
Q Consensus 67 i~~~~v~~f~~~l~~~l~~ 85 (121)
||-.-+-+|...+...++.
T Consensus 88 IPA~i~ye~I~e~R~RInk 106 (206)
T TIGR03875 88 IPAEIFYEYIEEVRERIDK 106 (206)
T ss_pred ccHHHHHHHHHHHHHHHhc
Confidence 6777777777777776643
No 64
>PF06358 DUF1065: Protein of unknown function (DUF1065); InterPro: IPR010470 This entry is represented by Beet necrotic yellow vein virus, p15; it is a family of uncharacterised viral proteins.
Probab=34.08 E-value=36 Score=23.45 Aligned_cols=19 Identities=32% Similarity=0.611 Sum_probs=12.2
Q ss_pred HHHHhhcC-CccHHHHHHHH
Q psy13777 12 AAFAQFGS-DLDAATQQLLN 30 (121)
Q Consensus 12 eaFaqFgS-dLD~~Tk~~L~ 30 (121)
-+|||||. |+-.-....+.
T Consensus 55 nsfaqfggcdipk~va~sis 74 (111)
T PF06358_consen 55 NSFAQFGGCDIPKHVADSIS 74 (111)
T ss_pred hhhhhhCCCCccHHHHHHHH
Confidence 47999965 77665554443
No 65
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=33.10 E-value=1.1e+02 Score=19.99 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=28.1
Q ss_pred HHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Q psy13777 78 EFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFL 116 (121)
Q Consensus 78 ~l~~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~ 116 (121)
.+++|+++-.|+.+..+.+. -++++.+.++..+....
T Consensus 2 ~L~~yi~~l~pe~~~~l~~~--~s~ev~e~m~~~v~~ll 38 (86)
T PF05542_consen 2 DLLQYIQSLKPERIQQLSEP--ASPEVLEAMKQHVSGLL 38 (86)
T ss_pred hHHHHHHHCCHHHHHHhhcc--CCHHHHHHHHHHHHHHH
Confidence 47788988888888877663 57888888877776554
No 66
>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=32.01 E-value=1.5e+02 Score=19.55 Aligned_cols=32 Identities=19% Similarity=0.316 Sum_probs=24.8
Q ss_pred hCCCCCCChhHHHHHHHHHHHHHHhchhHHHH
Q psy13777 61 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLE 92 (121)
Q Consensus 61 ~g~ld~i~~~~v~~f~~~l~~~l~~~~~~~~~ 92 (121)
.+.+|..+++.+-.....+...+......+.+
T Consensus 5 ~~~~d~~d~~~~l~~Q~~~l~~ln~tn~~L~~ 36 (88)
T PF10241_consen 5 TQAVDPEDLDEILALQAQTLGRLNKTNEELLN 36 (88)
T ss_pred HhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788889999999999998888776555443
No 67
>PF14022 DUF4238: Protein of unknown function (DUF4238)
Probab=31.74 E-value=1.9e+02 Score=21.11 Aligned_cols=67 Identities=16% Similarity=0.284 Sum_probs=42.5
Q ss_pred cCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHH-HHHHHHHHHHHhchhHHHHHHHhcCC---CCHHHHHHHHHHHH
Q psy13777 41 QGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKIT-TFEKEFLAHIKSSERGLLESIKKEGK---ITEDTDAKLKTVVT 113 (121)
Q Consensus 41 Q~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~-~f~~~l~~~l~~~~~~~~~~i~~~~~---l~~~~~~~l~~~~~ 113 (121)
.+...+.++... +..++|-+....+.-. ..|+.+ ..+.+..+.+++.|..... ++++....|...+-
T Consensus 27 ~~~~~~~~~~~~-----~~e~~~Y~~~~~~~~~~~iE~~~-~~iE~~~~~~i~~i~~~~~~~~l~~~~~~~l~~F~~ 97 (265)
T PF14022_consen 27 NGKIFPKSPKNI-----CFEKDFYTIKDDDGERDEIEDLL-SEIESEAAPIIDKIIDGRRSSKLTEEDKETLAEFLA 97 (265)
T ss_pred CCceeecCHHHH-----hhhhccccCCCCCchHHHHHHHH-HHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHH
Confidence 344455555532 3344444443333222 666666 7788888999999988776 88888887776654
No 68
>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=30.79 E-value=1.2e+02 Score=18.81 Aligned_cols=32 Identities=9% Similarity=0.306 Sum_probs=26.7
Q ss_pred CCCChhHHHHHHHHHHHHHHhchhHHHHHHHh
Q psy13777 65 DKLDPAKITTFEKEFLAHIKSSERGLLESIKK 96 (121)
Q Consensus 65 d~i~~~~v~~f~~~l~~~l~~~~~~~~~~i~~ 96 (121)
+.|+-..|..|...+.+-++....+++..|+.
T Consensus 2 ~~~~~~~~d~yI~~Lk~kLd~Kk~Eil~~ln~ 33 (56)
T PF08112_consen 2 SEIDKSTIDKYISILKSKLDEKKSEILSNLNM 33 (56)
T ss_pred cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55677788899999999999888898887765
No 69
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=29.17 E-value=1.7e+02 Score=25.41 Aligned_cols=68 Identities=18% Similarity=0.275 Sum_probs=50.1
Q ss_pred hhhhhHHHHHH-HhhcC-CccHHHHHHHHhHHHHHHHhhcCC----------CCCCCHHHHHHHHHHHhhCCCCCCChhH
Q psy13777 4 ELAQYREVAAF-AQFGS-DLDAATQQLLNRGVRLTELLKQGQ----------YVPMAIEEQVAVIYCGVRGHLDKLDPAK 71 (121)
Q Consensus 4 ~LAQyrELeaF-aqFgS-dLD~~Tk~~L~rG~rl~elLKQ~q----------~~P~~~~eQv~~L~a~~~g~ld~i~~~~ 71 (121)
-|.+|.||+.- |=.|= .|.++.|....|.+||...|-||= ...+++.+-+-.+-.+-+|-.|++|...
T Consensus 369 iLqrYkeLqDIIaILGmdELseedk~~V~rArki~~FlSQpF~vAE~FTg~pG~~V~l~dti~~fk~Il~G~yd~~pE~a 448 (468)
T COG0055 369 ILQRYKELQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFFVAEVFTGSPGKYVPLKDTIRGFKRILEGKYDHLPEQA 448 (468)
T ss_pred HHHHHHHHHHHHHHhCchhcChhHHHHHHHHHHHHHHhcCcchhhheecCCCceeeeHHHHHHHHHHHhCCCcccCCHHH
Confidence 46788888764 33453 699999999999999999999973 3445666666666666677777776553
No 70
>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=28.62 E-value=1.3e+02 Score=18.24 Aligned_cols=26 Identities=8% Similarity=0.086 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHhhCCCC---CCChhHHH
Q psy13777 48 AIEEQVAVIYCGVRGHLD---KLDPAKIT 73 (121)
Q Consensus 48 ~~~eQv~~L~a~~~g~ld---~i~~~~v~ 73 (121)
+..+.-++.-|...||+| ++.++.+.
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 344566788899999998 45555544
No 71
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=28.29 E-value=3e+02 Score=21.66 Aligned_cols=72 Identities=14% Similarity=0.219 Sum_probs=40.5
Q ss_pred CHHHHHHHHHHHhhCCCCCCChhHH-HHHHHHHHHHHHhch------------hHH----HHHHHhcCCCCHHHHHHHHH
Q psy13777 48 AIEEQVAVIYCGVRGHLDKLDPAKI-TTFEKEFLAHIKSSE------------RGL----LESIKKEGKITEDTDAKLKT 110 (121)
Q Consensus 48 ~~~eQv~~L~a~~~g~ld~i~~~~v-~~f~~~l~~~l~~~~------------~~~----~~~i~~~~~l~~~~~~~l~~ 110 (121)
+.+|.|+..||..-+ -|-+.-+.. ..|.+.+.+.|.... ..+ ...-...+.+|.+-+..+++
T Consensus 36 peaEEvAtf~a~ml~-t~y~~~~~F~kNFf~Df~~~l~~~~~~~I~~f~kcDF~~i~~~~~~~~e~kK~~tkeEKk~~K~ 114 (215)
T cd03488 36 PEAEEVATFYAKMLE-HDYATKEIFQKNFFKDFKKVMTKEEKVIIKDFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKA 114 (215)
T ss_pred HHHHHHHHHHHHHcC-CccccChHHHHHHHHHHHHHhccccCccccchhhCCCHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 568999999998877 333332222 446555666553221 111 11122345678887777777
Q ss_pred HHHHHHHhcc
Q psy13777 111 VVTNFLANFT 120 (121)
Q Consensus 111 ~~~~~~~~f~ 120 (121)
.-.+..+.|.
T Consensus 115 ek~~~e~~Y~ 124 (215)
T cd03488 115 EKEKLEEEYG 124 (215)
T ss_pred HHHhhhccCC
Confidence 6665555553
No 72
>KOG1379|consensus
Probab=27.77 E-value=23 Score=29.49 Aligned_cols=28 Identities=29% Similarity=0.323 Sum_probs=23.4
Q ss_pred HHHHHhhCCCCCCChhHHHHHHHHHHHH
Q psy13777 55 VIYCGVRGHLDKLDPAKITTFEKEFLAH 82 (121)
Q Consensus 55 ~L~a~~~g~ld~i~~~~v~~f~~~l~~~ 82 (121)
++.+++-|++||+|-+.|..+...+...
T Consensus 248 vIilATDGlfDNl~e~~Il~il~~~~~~ 275 (330)
T KOG1379|consen 248 VIILATDGLFDNLPEKEILSILKGLDAR 275 (330)
T ss_pred EEEEecccccccccHHHHHHHHHHhhcc
Confidence 4567899999999999998888777664
No 73
>COG3160 Rsd Regulator of sigma D [Transcription]
Probab=27.73 E-value=2.1e+02 Score=21.34 Aligned_cols=48 Identities=17% Similarity=0.389 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHhhCCCC------CCChhHHHHHHHHHHHHHHhchhHHHHHHHh
Q psy13777 49 IEEQVAVIYCGVRGHLD------KLDPAKITTFEKEFLAHIKSSERGLLESIKK 96 (121)
Q Consensus 49 ~~eQv~~L~a~~~g~ld------~i~~~~v~~f~~~l~~~l~~~~~~~~~~i~~ 96 (121)
+-.++++-|....|.=- .+..+....|...+++|+..-|-.+.+.|-.
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 34566777776666544 6678889999999999999998888877755
No 74
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=27.57 E-value=1.1e+02 Score=20.70 Aligned_cols=32 Identities=13% Similarity=-0.054 Sum_probs=26.9
Q ss_pred HHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHh
Q psy13777 29 LNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60 (121)
Q Consensus 29 L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~ 60 (121)
-..|..|+.=...+...+.|.++|+++|-.=.
T Consensus 5 ~~~k~~l~~eyg~~~~dtgs~evq~a~Lt~ri 36 (89)
T COG0184 5 SEIKQELRDEYGIPEVDTGSGEVQLALLTERI 36 (89)
T ss_pred HHHHHHHHHHhCCCCCCCCCcHHHHHHHHHHH
Confidence 35788899999999999999999999886543
No 75
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=27.05 E-value=3.1e+02 Score=21.53 Aligned_cols=72 Identities=14% Similarity=0.175 Sum_probs=40.1
Q ss_pred CHHHHHHHHHHHhhCCCCCCChhHH-HHHHHHHHHHHHhc------------hhHH----HHHHHhcCCCCHHHHHHHHH
Q psy13777 48 AIEEQVAVIYCGVRGHLDKLDPAKI-TTFEKEFLAHIKSS------------ERGL----LESIKKEGKITEDTDAKLKT 110 (121)
Q Consensus 48 ~~~eQv~~L~a~~~g~ld~i~~~~v-~~f~~~l~~~l~~~------------~~~~----~~~i~~~~~l~~~~~~~l~~ 110 (121)
+.+|.|+..||..-+ -|-+.-+.. ..|.+.+.+.|... ...+ ...-...+.+|.+-+..+++
T Consensus 36 peaEEvAtf~a~ml~-t~y~~~~~F~kNFf~Df~~~l~~~~~~~i~~f~kcDF~~i~~~~~~~~e~kK~~s~eEKk~~K~ 114 (215)
T cd00660 36 PEAEEVATFFAVMLE-TDYATKEVFRKNFFKDFRKILTKEEKHIIKKLSKCDFTPIYQYFEEEKEKKKAMSKEEKKAIKE 114 (215)
T ss_pred HHHHHHHHHHHHHcC-CccccChHHHHHHHHHHHHHhccccCccccchhhCCCHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 568999999998876 333332222 44555555555222 1111 11122345578887777777
Q ss_pred HHHHHHHhcc
Q psy13777 111 VVTNFLANFT 120 (121)
Q Consensus 111 ~~~~~~~~f~ 120 (121)
.-....+.|.
T Consensus 115 ek~~~e~~Y~ 124 (215)
T cd00660 115 EKEKLEEPYG 124 (215)
T ss_pred HHHhhhccCC
Confidence 6665555453
No 76
>KOG1350|consensus
Probab=27.03 E-value=1.5e+02 Score=25.45 Aligned_cols=64 Identities=19% Similarity=0.315 Sum_probs=43.6
Q ss_pred hhhHHHHHH-HhhcC-CccHHHHHHHHhHHHHHHHhhcC----------CCCCCCHHHHHHHHHHHhhCCCCCCCh
Q psy13777 6 AQYREVAAF-AQFGS-DLDAATQQLLNRGVRLTELLKQG----------QYVPMAIEEQVAVIYCGVRGHLDKLDP 69 (121)
Q Consensus 6 AQyrELeaF-aqFgS-dLD~~Tk~~L~rG~rl~elLKQ~----------q~~P~~~~eQv~~L~a~~~g~ld~i~~ 69 (121)
--|..|..- |=.|- +|.+..|-..+|.++|...|-|| +..-+++++-+-.+-++-+|-.|.+|-
T Consensus 421 Q~YKsLQDIIAILGmDELSEeDkLTV~RARKiqRFLSQPF~VAEvFTG~~GklV~l~~ti~gF~~iL~Ge~D~lPE 496 (521)
T KOG1350|consen 421 QDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGHPGKLVPLEETIRGFKAILEGEYDHLPE 496 (521)
T ss_pred HHHHHHHHHHHHhCchhhchhhhhhHHHHHHHHHHHcCchhhhhhhcCCCCceecHHHHHHHHHHHhcCcccCCch
Confidence 345555433 23343 47778888999999999999987 345566666666677777777777664
No 77
>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=26.16 E-value=23 Score=22.47 Aligned_cols=50 Identities=10% Similarity=0.276 Sum_probs=31.9
Q ss_pred CChhHHHHHHHHHHHHHHhchhHHHHHHHh--------cCCCCHHHHHHHHHHHHHHHH
Q psy13777 67 LDPAKITTFEKEFLAHIKSSERGLLESIKK--------EGKITEDTDAKLKTVVTNFLA 117 (121)
Q Consensus 67 i~~~~v~~f~~~l~~~l~~~~~~~~~~i~~--------~~~l~~~~~~~l~~~~~~~~~ 117 (121)
+|...+..++.+|.+.+...+|+..=+|+. .+.-+++ ++.|.+++++..+
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 467788999999999999999985323332 2222333 8888888887654
No 78
>PRK06213 enoyl-CoA hydratase; Provisional
Probab=26.11 E-value=2.2e+02 Score=21.39 Aligned_cols=38 Identities=16% Similarity=0.239 Sum_probs=26.3
Q ss_pred HHhhCCCCCC-ChhHHHHHHHHHHHHHHhchhHHHHHHH
Q psy13777 58 CGVRGHLDKL-DPAKITTFEKEFLAHIKSSERGLLESIK 95 (121)
Q Consensus 58 a~~~g~ld~i-~~~~v~~f~~~l~~~l~~~~~~~~~~i~ 95 (121)
|...|++|.| |.+++.....++.+.+....|..+..++
T Consensus 168 A~~~Glv~~vv~~~~l~~~a~~~a~~la~~~~~a~~~~K 206 (229)
T PRK06213 168 AVAAGFLDEVVPPEQLLARAQAAARELAGLNMGAHAATK 206 (229)
T ss_pred HHHCCCceeccChHHHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 5678999987 7777777777777767666666554443
No 79
>KOG0981|consensus
Probab=25.90 E-value=3.5e+02 Score=24.76 Aligned_cols=27 Identities=11% Similarity=0.230 Sum_probs=17.0
Q ss_pred HhcCCCCHHHHHHHHHHHHHHHHhccC
Q psy13777 95 KKEGKITEDTDAKLKTVVTNFLANFTG 121 (121)
Q Consensus 95 ~~~~~l~~~~~~~l~~~~~~~~~~f~~ 121 (121)
...+.++.+-+..|++--..+-+.|.|
T Consensus 309 E~rK~mskEEK~~iKeEkek~ee~y~~ 335 (759)
T KOG0981|consen 309 EKRKQMSKEEKLKIKEEKEKLEEKYGW 335 (759)
T ss_pred HHHhhcCHHHHHHHHHHHHHHHHHcCe
Confidence 335567777777777666666665654
No 80
>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=25.17 E-value=62 Score=19.07 Aligned_cols=19 Identities=21% Similarity=0.436 Sum_probs=15.2
Q ss_pred HHHHHHHhhCCCCCCChhH
Q psy13777 53 VAVIYCGVRGHLDKLDPAK 71 (121)
Q Consensus 53 v~~L~a~~~g~ld~i~~~~ 71 (121)
++.++|+.+|=+|+.+-..
T Consensus 19 ~~f~Wavk~GQfdD~e~~a 37 (45)
T PF03597_consen 19 AAFLWAVKSGQFDDLEGPA 37 (45)
T ss_pred HHHHHHHccCCCCCCcchH
Confidence 4678999999999986543
No 81
>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=25.06 E-value=1.8e+02 Score=20.30 Aligned_cols=45 Identities=13% Similarity=0.261 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Q psy13777 72 ITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLA 117 (121)
Q Consensus 72 v~~f~~~l~~~l~~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~ 117 (121)
|....+++...+..+|++++......+.++. ....|+..+.....
T Consensus 42 i~eld~~i~~~v~~~~~~LL~q~~~~~~~~~-~l~~v~~~v~~L~~ 86 (132)
T PF10392_consen 42 IQELDKRIRSQVTSNHEDLLSQASSIEELES-VLQAVRSSVESLQS 86 (132)
T ss_pred HHHHHHHHHHHHHhCHHHHHHHHHhHHHHHH-HHHHHHHHHHHHHH
Confidence 4566677777778889999888877666655 55666655555443
No 82
>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=24.94 E-value=1.5e+02 Score=21.09 Aligned_cols=42 Identities=14% Similarity=0.187 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHhchh--HHHHHHHhcCCCCHHHHHHHHHHH
Q psy13777 71 KITTFEKEFLAHIKSSER--GLLESIKKEGKITEDTDAKLKTVV 112 (121)
Q Consensus 71 ~v~~f~~~l~~~l~~~~~--~~~~~i~~~~~l~~~~~~~l~~~~ 112 (121)
+..+|...+..|+..+.+ +.++.|-.+..++....+.|...+
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 455677777777766643 467788888888888877777765
No 83
>PF07176 DUF1400: Alpha/beta hydrolase of unknown function (DUF1400); InterPro: IPR010802 This domain is specific to cyanobacterial proteins, its function and the function of the proteins it is associated with, are uncharacterised.
Probab=24.80 E-value=2.5e+02 Score=19.76 Aligned_cols=44 Identities=23% Similarity=0.284 Sum_probs=28.2
Q ss_pred HHHHHHHhhcCCccHHHHHHHHh-----HHHHHHHhhcCCCCCCCHHHHH
Q psy13777 9 REVAAFAQFGSDLDAATQQLLNR-----GVRLTELLKQGQYVPMAIEEQV 53 (121)
Q Consensus 9 rELeaFaqFgSdLD~~Tk~~L~r-----G~rl~elLKQ~q~~P~~~~eQv 53 (121)
.+||.||+-|. .++.=+..+.. -+.++++|+.+---+.....|.
T Consensus 19 ~dLe~fa~tG~-~~~~L~~~~~ll~~~~~~~lr~~L~~~~~~~~~~~~~l 67 (127)
T PF07176_consen 19 SDLETFAETGE-ISPELAFYLNLLSPQQRQQLRELLNTPIPIDPVFLSQL 67 (127)
T ss_pred HHHHHHHHcCC-CCHHHHHHHHhcCHhhHHHHHHHHcCCCCCCHHHHHHH
Confidence 58999999876 45554444444 5577778877655544444443
No 84
>TIGR03248 galactar-dH20 galactarate dehydratase. Galactarate dehydratase converts D-galactarate to 5-dehydro-4-deoxyglucarate which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (, GenProp0714).
Probab=24.42 E-value=1.7e+02 Score=25.78 Aligned_cols=95 Identities=9% Similarity=0.051 Sum_probs=71.9
Q ss_pred HHHHHHhH----HHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChh-HHHHHHHHHHHH----HHhchhHH--HHH
Q psy13777 25 TQQLLNRG----VRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPA-KITTFEKEFLAH----IKSSERGL--LES 93 (121)
Q Consensus 25 Tk~~L~rG----~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~-~v~~f~~~l~~~----l~~~~~~~--~~~ 93 (121)
|++.+++| +++.+...+.+-+|+++.+-++-+=++-+.-+..|.-+ -+-.+-..|.++ +-++-||+ .+.
T Consensus 235 ~~~ti~~g~~~~~~l~~~a~~~~R~~~pls~L~vGl~CGGSD~~SGitANPavG~~sD~LV~~GGt~ilsEt~E~~GaE~ 314 (507)
T TIGR03248 235 FAAMIEAIMEMAERRLAKLNRRRRETVPASELVVGMQCGGSDAFSGVTANPAVGFAADLLVRAGATVMFSEVTEVRDAIH 314 (507)
T ss_pred HHHHHHHHHHHHHHHHHHhhhCCcccCCHHHcEEEeecCCCCCccccccChHHHHHHHHHHHcCCeEEecCCcceeChHH
Confidence 55555555 55666778889999999999999999999888888664 455566666653 34556765 566
Q ss_pred HHhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13777 94 IKKEGKITEDTDAKLKTVVTNFLANF 119 (121)
Q Consensus 94 i~~~~~l~~~~~~~l~~~~~~~~~~f 119 (121)
|-....-+++..+++.+.++.+.+.+
T Consensus 315 iL~~Ra~~~ev~~k~~~~i~~~~~y~ 340 (507)
T TIGR03248 315 LLTPRAETAEVAKALVREMDWYDRYL 340 (507)
T ss_pred HHHhhhCCHHHHHHHHHHHHHHHHHH
Confidence 77778889999999999999997754
No 85
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=22.27 E-value=1.8e+02 Score=27.15 Aligned_cols=77 Identities=19% Similarity=0.369 Sum_probs=50.8
Q ss_pred HHhHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhHHHHHHHHHHHHHHhchhHHHHHHHhcCCCCHHHHHHH
Q psy13777 29 LNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKL 108 (121)
Q Consensus 29 L~rG~rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~v~~f~~~l~~~l~~~~~~~~~~i~~~~~l~~~~~~~l 108 (121)
-+++..+.++|..+.--|+=..-== =..|-+|++.+-++..-...+. -|++....+++.|.+-+.++++....|
T Consensus 22 ~~qv~av~~ll~eg~tVPFIarYRk-----e~tg~Lde~qlr~i~~~~~yl~-~L~~Rke~Ilk~IeeqGklTd~L~~~I 95 (780)
T COG2183 22 PAQVEAVIELLDEGNTVPFIARYRK-----EITGGLDEVQLRDLEERLEYLR-ELEERKESILKSIEEQGKLTDELKEQI 95 (780)
T ss_pred HHHHHHHHHHHhcCCceeehhhhcc-----ccCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhccchHHHHHHH
Confidence 3455556666666544443110000 0357778887777776666665 477777889999999999999988888
Q ss_pred HHH
Q psy13777 109 KTV 111 (121)
Q Consensus 109 ~~~ 111 (121)
..+
T Consensus 96 ~~a 98 (780)
T COG2183 96 EAA 98 (780)
T ss_pred HHh
Confidence 774
No 86
>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=22.26 E-value=2.5e+02 Score=18.80 Aligned_cols=80 Identities=13% Similarity=0.173 Sum_probs=44.6
Q ss_pred HHHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCC------------CChhHH-HHHHHHHHHH-HHhchhHHHHHHHhcCC
Q psy13777 34 RLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDK------------LDPAKI-TTFEKEFLAH-IKSSERGLLESIKKEGK 99 (121)
Q Consensus 34 rl~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~------------i~~~~v-~~f~~~l~~~-l~~~~~~~~~~i~~~~~ 99 (121)
-|.+.|.++ +.+-.-.=+.++=-....|++.. ++-++. ......+++. +....+.++..+-.+..
T Consensus 22 eI~~~l~~~-~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~is~~e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~~ 100 (115)
T PF03965_consen 22 EIHEALPEE-RSWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSPLISREEYLAQELRQFLDRLFDGSIPQLVAALVESEE 100 (115)
T ss_dssp HHHHHHCTT-SS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHCT-
T ss_pred HHHHHHHhc-cccchhHHHHHHHHHHhCCceeEeecCCceEEEeCCcHHHHHHHHHHHHHHHHhCCCHHHHHHHHHhcCC
Confidence 355667766 33323333444445566787762 333332 2233333332 34456778888888889
Q ss_pred CCHHHHHHHHHHHHH
Q psy13777 100 ITEDTDAKLKTVVTN 114 (121)
Q Consensus 100 l~~~~~~~l~~~~~~ 114 (121)
+|++..+.|.+.|++
T Consensus 101 ls~~el~~L~~li~e 115 (115)
T PF03965_consen 101 LSPEELEELRKLIDE 115 (115)
T ss_dssp S-HHHHHHHHHHHH-
T ss_pred CCHHHHHHHHHHHcC
Confidence 999999999888764
No 87
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=22.17 E-value=1.4e+02 Score=20.99 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=19.7
Q ss_pred HhHHHHHHHhhcCCCCCCCHHHHHHHHH
Q psy13777 30 NRGVRLTELLKQGQYVPMAIEEQVAVIY 57 (121)
Q Consensus 30 ~rG~rl~elLKQ~q~~P~~~~eQv~~L~ 57 (121)
.+|-||+|+=.+---+-.++-.-|+.+|
T Consensus 34 ~~~mri~ei~rEl~is~rtvr~~v~~l~ 61 (113)
T COG5625 34 GRGMRIREIQRELGISERTVRAAVAVLL 61 (113)
T ss_pred cCCchHHHHHHHHhHHHHHHHHHHHHHH
Confidence 3566888877766666677777777776
No 88
>PF04295 GD_AH_C: D-galactarate dehydratase / Altronate hydrolase, C terminus; InterPro: IPR007392 This domain is found at the C terminus of D-galactarate dehydratase (4.2.1.42 from EC) which is thought to catalyse the reaction D-galactarate = 5-keto-4-deoxy-D-glucarate + H2O, [] and altronate hydrolase (altronic acid hydratase, 4.2.1.7 from EC), which catalyses D-altronate = 2-keto-2-deoxygluconate + H2O []. As purified, both enzymes are catalytically inactive in the absence of added Fe2+, Mn2+, and beta-mercaptoethanol. Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of the single bound Fe2+ ion is unknown. The hydratase has no Fe-S core []. The N-terminal is represented by IPR007389 from INTERPRO.; GO: 0016836 hydro-lyase activity
Probab=21.91 E-value=2.3e+02 Score=24.16 Aligned_cols=96 Identities=20% Similarity=0.277 Sum_probs=70.8
Q ss_pred HHHHHHHhHHH----HHHHhhcCCCCCCCHHHHHHHHHHHhhCCCCCCChhH-HHHHHHHHHHH----HHhchhHHH--H
Q psy13777 24 ATQQLLNRGVR----LTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAK-ITTFEKEFLAH----IKSSERGLL--E 92 (121)
Q Consensus 24 ~Tk~~L~rG~r----l~elLKQ~q~~P~~~~eQv~~L~a~~~g~ld~i~~~~-v~~f~~~l~~~----l~~~~~~~~--~ 92 (121)
.|.+.+++|.+ +.+...+.+-+|+|+.+-++-+=++-+.-+..|.-+- |-.+-..|... +-++-||++ +
T Consensus 125 Gt~~~i~~~~~~~~~l~~~a~~~~R~~~p~s~L~vgl~CGGSD~~SGitaNP~vG~~sD~lv~~GGt~ilsEt~El~GaE 204 (396)
T PF04295_consen 125 GTEDTIEAGVELARELLEEANAQQREPVPLSELVVGLKCGGSDATSGITANPAVGRASDRLVAAGGTAILSETPELIGAE 204 (396)
T ss_pred hHHHHHHHHHHHHHHHHHHhccCCcccccHHHeEEeeecCCCCcccccccChHHHHHHHHHHHcCCEEEEecCccccCHH
Confidence 45556666654 4444557788999999999999999998888886554 34455555542 345567764 7
Q ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13777 93 SIKKEGKITEDTDAKLKTVVTNFLANF 119 (121)
Q Consensus 93 ~i~~~~~l~~~~~~~l~~~~~~~~~~f 119 (121)
.|-....-+++..+++.+.++.+.+.+
T Consensus 205 ~~l~~Ra~~~ev~~k~~~~i~~~~~~~ 231 (396)
T PF04295_consen 205 HILARRAVNPEVADKILALINWFEDYA 231 (396)
T ss_pred HHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 778888889999999999999987754
No 89
>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=21.52 E-value=40 Score=18.45 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=7.2
Q ss_pred CCCCHHHHHHHHH
Q psy13777 45 VPMAIEEQVAVIY 57 (121)
Q Consensus 45 ~P~~~~eQv~~L~ 57 (121)
+|+|+++||--|.
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 4788888886554
No 90
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=21.23 E-value=52 Score=20.94 Aligned_cols=18 Identities=11% Similarity=0.438 Sum_probs=9.9
Q ss_pred cCCccHHHHHHHHhHHHHH
Q psy13777 18 GSDLDAATQQLLNRGVRLT 36 (121)
Q Consensus 18 gSdLD~~Tk~~L~rG~rl~ 36 (121)
|+|++++.++ ++-|++++
T Consensus 35 ~~D~eeA~rr-I~E~~~~v 52 (62)
T PF08828_consen 35 DADVEEASRR-IDEAKNVV 52 (62)
T ss_dssp TT-HHHHHHH-HHH-----
T ss_pred CCCHHHHHHH-HHHHHHHH
Confidence 7899999988 66666654
No 91
>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=21.02 E-value=1.1e+02 Score=18.64 Aligned_cols=19 Identities=32% Similarity=0.431 Sum_probs=15.3
Q ss_pred HHHHHHHhhCCCCCCChhH
Q psy13777 53 VAVIYCGVRGHLDKLDPAK 71 (121)
Q Consensus 53 v~~L~a~~~g~ld~i~~~~ 71 (121)
++.++|+.+|-+|+.+-..
T Consensus 20 ~~f~Wavk~GQfDDle~~a 38 (51)
T TIGR00847 20 VAFLWSLKSGQYDDLKGAA 38 (51)
T ss_pred HHHHHHHccCCCCCCccHH
Confidence 4678999999999996443
No 92
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=20.97 E-value=2.5e+02 Score=18.31 Aligned_cols=38 Identities=21% Similarity=0.300 Sum_probs=27.6
Q ss_pred HHHHHhhcCCccHHHHHHHHhHHHHHHHhhcCCCCCCC
Q psy13777 11 VAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMA 48 (121)
Q Consensus 11 LeaFaqFgSdLD~~Tk~~L~rG~rl~elLKQ~q~~P~~ 48 (121)
+.-+.++|=...-+.+-.-..|....++|+.++|..+.
T Consensus 12 ~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~ 49 (94)
T PF14490_consen 12 MAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIE 49 (94)
T ss_dssp HHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB
T ss_pred HHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHH
Confidence 44566777777777777777899999999999999998
No 93
>PF08236 SRI: SRI (Set2 Rpb1 interacting) domain; InterPro: IPR013257 The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. ; GO: 0018024 histone-lysine N-methyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0034968 histone lysine methylation, 0005694 chromosome; PDB: 2A7O_A 2C5Z_A.
Probab=20.50 E-value=2.6e+02 Score=18.32 Aligned_cols=58 Identities=12% Similarity=0.264 Sum_probs=37.2
Q ss_pred hhCCCCCCChhHHHHHHHHHHHHHHhchhHHHHHH--HhcCCCCHHHHHHHHHHHHHHHHhc
Q psy13777 60 VRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESI--KKEGKITEDTDAKLKTVVTNFLANF 119 (121)
Q Consensus 60 ~~g~ld~i~~~~v~~f~~~l~~~l~~~~~~~~~~i--~~~~~l~~~~~~~l~~~~~~~~~~f 119 (121)
.+.|-+.++-+++..+-..+...+... |+-..- .....+++.....+++.+..+.+.+
T Consensus 21 l~~y~~~~~~ddfK~~ar~lt~~l~~K--E~K~~~~~~~~~~l~~~~~~Kik~fvk~Ym~K~ 80 (88)
T PF08236_consen 21 LNKYRKKLSKDDFKHLARKLTHKLVEK--ELKSCRVNDPPLELSDSKRKKIKKFVKDYMDKF 80 (88)
T ss_dssp HCTTTTT--HHHHHHHHHHHHHHHHHH--HHHHHTT-GGGSS--HHHHHHHHHHHHHHHCCC
T ss_pred HHHccccCCHHHHHHHHHHHHHHHHHH--HHhcCCCCCCccccCHHHHHHHHHHHHHHHHHH
Confidence 466777899999999988888877543 221111 1246789999999988888876643
No 94
>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=20.31 E-value=5.2 Score=22.74 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhhCCCCCCChhHHHHHH
Q psy13777 50 EEQVAVIYCGVRGHLDKLDPAKITTFE 76 (121)
Q Consensus 50 ~eQv~~L~a~~~g~ld~i~~~~v~~f~ 76 (121)
..|.-|.|.+.=-.+|++|.+++.+..
T Consensus 5 ~~qLTIfY~G~V~Vfd~v~~~Ka~~im 31 (36)
T PF06200_consen 5 TAQLTIFYGGQVCVFDDVPPDKAQEIM 31 (36)
T ss_pred CCcEEEEECCEEEEeCCCCHHHHHHHH
Confidence 356667788888889999999887543
Done!