Query 033676
Match_columns 114
No_of_seqs 129 out of 1021
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 05:01:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10733 hflB ATP-dependent me 99.8 6E-21 1.3E-25 162.7 8.8 94 1-95 503-598 (644)
2 CHL00176 ftsH cell division pr 99.8 2.3E-20 5E-25 159.2 9.2 100 1-100 533-633 (638)
3 COG0465 HflB ATP-dependent Zn 99.8 1.9E-19 4E-24 152.3 8.9 93 1-95 500-593 (596)
4 PF01434 Peptidase_M41: Peptid 99.7 1.5E-18 3.3E-23 130.4 5.6 89 1-89 123-213 (213)
5 KOG0734 AAA+-type ATPase conta 99.7 3.9E-18 8.3E-23 143.1 8.3 83 1-93 652-735 (752)
6 TIGR01241 FtsH_fam ATP-depende 99.7 2.4E-16 5.2E-21 130.5 7.8 90 1-91 404-495 (495)
7 KOG0731 AAA+-type ATPase conta 99.6 3E-16 6.6E-21 135.5 7.8 93 1-98 661-754 (774)
8 PF10415 FumaraseC_C: Fumarase 84.1 3.2 7E-05 24.9 4.5 41 53-93 10-50 (55)
9 smart00114 CARD Caspase recrui 83.8 3.5 7.7E-05 26.4 4.9 37 56-92 4-46 (88)
10 cd08327 CARD_RAIDD Caspase act 82.6 4.1 8.8E-05 27.2 4.9 38 55-92 3-47 (94)
11 PF07104 DUF1366: Protein of u 79.0 9.9 0.00021 26.4 6.0 45 40-85 71-115 (116)
12 cd08329 CARD_BIRC2_BIRC3 Caspa 78.7 5.4 0.00012 26.4 4.5 35 58-92 8-49 (94)
13 cd08332 CARD_CASP2 Caspase act 78.6 7.3 0.00016 25.5 5.1 37 56-92 4-46 (90)
14 PF14327 CSTF2_hinge: Hinge do 77.6 4.3 9.4E-05 26.3 3.7 59 33-91 25-83 (84)
15 cd08326 CARD_CASP9 Caspase act 76.1 7.2 0.00016 25.3 4.4 35 58-92 2-42 (84)
16 PF13801 Metal_resist: Heavy-m 70.7 23 0.0005 22.7 6.0 49 43-92 47-95 (125)
17 cd08323 CARD_APAF1 Caspase act 69.3 9.9 0.00021 24.8 3.9 25 68-92 16-40 (86)
18 PF12209 SAC3: Leucine permeas 68.0 29 0.00064 22.3 6.6 43 34-77 6-48 (79)
19 cd08324 CARD_NOD1_CARD4 Caspas 66.8 8.5 0.00019 25.4 3.1 37 58-94 7-43 (85)
20 cd08785 CARD_CARD9-like Caspas 65.7 17 0.00038 23.7 4.5 36 58-93 2-43 (86)
21 cd08810 CARD_BCL10 Caspase act 64.6 20 0.00043 23.4 4.6 34 59-92 3-42 (84)
22 PF00619 CARD: Caspase recruit 62.8 18 0.00039 22.4 4.1 31 61-91 11-41 (85)
23 PF07028 DUF1319: Protein of u 58.8 55 0.0012 23.1 6.2 56 45-100 50-108 (126)
24 PF00901 Orbi_VP5: Orbivirus o 54.2 64 0.0014 27.8 6.9 48 46-93 141-188 (508)
25 PF01411 tRNA-synt_2c: tRNA sy 53.6 37 0.00079 29.3 5.6 52 44-95 345-396 (552)
26 PRK15054 nitrate reductase 2 s 49.7 50 0.0011 25.5 5.3 40 55-94 120-159 (231)
27 PRK13710 plasmid maintenance p 48.4 69 0.0015 20.3 6.2 50 31-87 21-70 (72)
28 COG2811 NtpF Archaeal/vacuolar 47.9 89 0.0019 21.5 6.9 43 36-78 20-62 (108)
29 cd08330 CARD_ASC_NALP1 Caspase 47.6 66 0.0014 20.5 4.9 34 60-93 9-42 (82)
30 cd08325 CARD_CASP1-like Caspas 47.5 32 0.00068 22.1 3.4 29 64-92 14-42 (83)
31 PHA02571 a-gt.4 hypothetical p 47.0 93 0.002 21.4 6.4 35 39-73 17-51 (109)
32 PF01343 Peptidase_S49: Peptid 46.5 28 0.00062 24.4 3.3 53 31-87 77-129 (154)
33 PRK03963 V-type ATP synthase s 43.9 1.2E+02 0.0026 21.9 6.9 38 38-75 11-48 (198)
34 PRK13902 alaS alanyl-tRNA synt 43.9 76 0.0016 29.2 6.2 51 44-97 396-446 (900)
35 TIGR03826 YvyF flagellar opero 43.3 65 0.0014 22.9 4.7 48 42-93 20-70 (137)
36 PRK01584 alanyl-tRNA synthetas 42.4 75 0.0016 27.9 5.8 53 43-95 350-402 (594)
37 PRK05932 RNA polymerase factor 41.4 87 0.0019 26.4 5.9 35 44-78 292-329 (455)
38 TIGR02395 rpoN_sigma RNA polym 40.9 85 0.0018 26.2 5.7 36 43-78 266-304 (429)
39 TIGR00344 alaS alanine--tRNA l 40.3 97 0.0021 28.3 6.3 51 44-95 347-397 (851)
40 PF05527 DUF758: Domain of unk 40.1 1.4E+02 0.003 22.4 6.2 50 39-89 28-87 (186)
41 PF09551 Spore_II_R: Stage II 40.0 1.3E+02 0.0029 21.2 7.2 44 38-81 21-70 (130)
42 COG4453 Uncharacterized protei 38.6 1E+02 0.0022 20.7 4.8 47 35-93 18-72 (95)
43 PRK03963 V-type ATP synthase s 38.0 1.4E+02 0.0031 21.5 6.0 19 40-58 24-42 (198)
44 PF07011 DUF1313: Protein of u 37.7 57 0.0012 21.6 3.4 31 42-72 3-33 (87)
45 KOG2751 Beclin-like protein [S 37.6 95 0.0021 26.4 5.5 56 31-87 137-194 (447)
46 PF04368 DUF507: Protein of un 36.8 1.1E+02 0.0024 22.7 5.3 42 38-79 48-89 (183)
47 PF03979 Sigma70_r1_1: Sigma-7 36.8 73 0.0016 20.1 3.8 26 65-90 6-31 (82)
48 KOG0188 Alanyl-tRNA synthetase 36.4 69 0.0015 29.2 4.7 51 44-94 355-405 (895)
49 PRK08475 F0F1 ATP synthase sub 36.2 1.6E+02 0.0035 21.1 6.6 48 39-86 72-119 (167)
50 PRK02292 V-type ATP synthase s 35.8 1.7E+02 0.0036 21.1 7.1 38 37-74 20-57 (188)
51 PF10398 DUF2443: Protein of u 35.8 69 0.0015 20.7 3.5 32 32-75 45-76 (79)
52 PF07369 DUF1488: Protein of u 35.2 77 0.0017 19.8 3.7 25 54-78 48-72 (83)
53 PF04757 Pex2_Pex12: Pex2 / Pe 35.2 90 0.0019 22.8 4.6 40 43-82 1-49 (229)
54 TIGR02499 HrpE_YscL_not type I 34.6 1.5E+02 0.0033 20.4 5.6 24 45-68 14-37 (166)
55 PRK14135 recX recombination re 34.2 2.1E+02 0.0045 21.7 6.6 59 31-92 39-97 (263)
56 PF06428 Sec2p: GDP/GTP exchan 34.0 1.5E+02 0.0032 19.9 5.4 44 36-79 14-64 (100)
57 PF09687 PRESAN: Plasmodium RE 33.7 1.4E+02 0.0029 19.4 7.1 51 43-93 64-114 (129)
58 PRK06718 precorrin-2 dehydroge 33.5 1.1E+02 0.0024 22.5 4.9 38 33-70 127-164 (202)
59 COG0013 AlaS Alanyl-tRNA synth 33.3 77 0.0017 29.2 4.6 54 43-96 348-401 (879)
60 TIGR03683 A-tRNA_syn_arch alan 31.9 1.5E+02 0.0032 27.4 6.1 51 44-97 400-450 (902)
61 TIGR02837 spore_II_R stage II 31.4 2.2E+02 0.0047 21.1 7.0 31 53-83 77-107 (168)
62 TIGR01470 cysG_Nterm siroheme 31.3 1.2E+02 0.0025 22.5 4.7 39 33-71 127-165 (205)
63 PF10849 DUF2654: Protein of u 30.3 60 0.0013 20.7 2.5 21 68-90 39-59 (70)
64 TIGR00706 SppA_dom signal pept 29.5 1E+02 0.0022 22.7 4.1 52 33-88 134-185 (207)
65 PF04120 Iron_permease: Low af 29.4 1.4E+02 0.0029 21.2 4.5 46 49-94 59-108 (132)
66 PF08681 DUF1778: Protein of u 28.7 99 0.0021 19.5 3.4 19 48-66 28-46 (80)
67 PRK09173 F0F1 ATP synthase sub 28.4 2.1E+02 0.0046 20.0 7.1 39 40-78 64-102 (159)
68 cd00211 PTS_IIA_fru PTS_IIA, P 28.4 1.2E+02 0.0026 19.8 4.0 28 64-91 15-42 (136)
69 cd07215 Pat17_PNPLA8_PNPLA9_li 27.4 62 0.0013 25.6 2.7 34 42-75 296-329 (329)
70 PHA00743 helix-turn-helix prot 27.2 1E+02 0.0023 18.3 3.0 39 41-80 3-41 (51)
71 KOG0450 2-oxoglutarate dehydro 27.0 65 0.0014 29.4 3.0 36 58-93 526-561 (1017)
72 PRK09098 type III secretion sy 26.9 2.9E+02 0.0062 21.1 6.4 27 40-66 46-72 (233)
73 cd07018 S49_SppA_67K_type Sign 26.6 1.6E+02 0.0035 21.8 4.8 51 33-87 152-202 (222)
74 PF08838 DUF1811: Protein of u 26.5 83 0.0018 21.4 2.8 28 32-60 2-29 (102)
75 PF03909 BSD: BSD domain ; I 26.3 1.1E+02 0.0024 18.1 3.2 35 53-89 13-47 (62)
76 COG3937 Uncharacterized conser 26.1 1.7E+02 0.0037 20.1 4.3 30 63-92 21-50 (108)
77 COG4847 Uncharacterized protei 26.1 1.4E+02 0.0031 20.2 3.8 40 39-78 55-99 (103)
78 TIGR02609 doc_partner putative 25.9 1.1E+02 0.0024 19.0 3.2 15 59-73 60-74 (74)
79 PRK00117 recX recombination re 25.5 2.1E+02 0.0045 19.9 4.9 28 51-78 11-38 (157)
80 PRK01194 V-type ATP synthase s 25.4 2.7E+02 0.0059 20.3 7.1 36 40-75 12-47 (185)
81 cd01671 CARD Caspase activatio 25.3 1.6E+02 0.0035 17.7 3.9 27 66-92 13-39 (80)
82 cd07979 TAF9 TATA Binding Prot 25.2 2.3E+02 0.0049 19.3 5.5 45 43-92 21-65 (117)
83 PF02671 PAH: Paired amphipath 24.9 80 0.0017 17.6 2.2 21 53-73 24-44 (47)
84 PF11401 Tetrabrachion: Tetrab 24.6 1.5E+02 0.0033 17.0 6.5 36 37-72 4-39 (49)
85 cd04768 HTH_BmrR-like Helix-Tu 24.5 1.7E+02 0.0037 18.8 4.1 33 44-76 61-93 (96)
86 PRK01558 V-type ATP synthase s 24.5 2.9E+02 0.0063 20.3 6.4 26 40-65 29-54 (198)
87 PF01023 S_100: S-100/ICaBP ty 24.5 38 0.00082 19.2 0.8 17 77-93 21-37 (44)
88 PF10397 ADSL_C: Adenylosuccin 24.5 55 0.0012 20.5 1.6 44 46-93 23-67 (81)
89 PRK05562 precorrin-2 dehydroge 24.5 3.2E+02 0.007 20.8 6.7 37 33-70 143-179 (223)
90 PTZ00015 histone H4; Provision 24.3 2.3E+02 0.005 19.1 5.7 49 46-94 45-96 (102)
91 COG0353 RecR Recombinational D 24.2 1.1E+02 0.0024 23.2 3.4 28 51-78 23-50 (198)
92 PF00676 E1_dh: Dehydrogenase 24.1 1.4E+02 0.003 23.5 4.1 28 32-59 266-293 (300)
93 PRK01005 V-type ATP synthase s 23.9 3.2E+02 0.0069 20.5 6.4 19 47-65 41-59 (207)
94 PRK12595 bifunctional 3-deoxy- 23.8 4E+02 0.0086 21.7 6.9 52 38-91 12-76 (360)
95 PF11460 DUF3007: Protein of u 23.8 1.9E+02 0.0041 19.8 4.2 32 61-92 68-101 (104)
96 smart00544 MA3 Domain in DAP-5 23.6 1.8E+02 0.0039 18.8 4.1 47 43-93 35-81 (113)
97 TIGR00496 frr ribosome recycli 23.3 3E+02 0.0066 20.1 7.4 56 32-91 94-149 (176)
98 PF11553 DUF3231: Protein of u 23.3 2E+02 0.0044 20.2 4.6 24 42-69 44-67 (166)
99 PHA02734 coat protein; Provisi 23.2 1E+02 0.0023 21.9 2.9 41 33-73 92-132 (149)
100 cd08819 CARD_MDA5_2 Caspase ac 23.0 1.1E+02 0.0025 20.2 2.9 25 68-92 21-45 (88)
101 COG2315 MmcQ Uncharacterized p 22.6 90 0.002 21.6 2.5 24 43-66 89-112 (118)
102 PRK09665 PTS system galactitol 22.6 1.2E+02 0.0025 21.1 3.1 32 63-94 14-45 (150)
103 cd08787 CARD_NOD2_1_CARD15 Cas 22.5 98 0.0021 20.4 2.5 24 66-89 19-42 (87)
104 PF02885 Glycos_trans_3N: Glyc 22.2 1E+02 0.0022 18.5 2.5 25 69-93 3-27 (66)
105 PRK00252 alaS alanyl-tRNA synt 22.2 2.5E+02 0.0055 25.7 5.8 53 44-96 340-392 (865)
106 PLN00035 histone H4; Provision 22.1 2.6E+02 0.0057 18.9 5.7 49 46-94 44-95 (103)
107 PF11815 DUF3336: Domain of un 22.0 2.1E+02 0.0046 20.1 4.4 45 49-93 98-142 (145)
108 PF01991 vATP-synt_E: ATP synt 21.8 3E+02 0.0064 19.4 7.1 13 44-56 19-31 (198)
109 PRK06397 V-type ATP synthase s 21.8 2.7E+02 0.0059 19.0 5.3 35 40-74 20-54 (111)
110 COG2180 NarJ Nitrate reductase 21.6 2.1E+02 0.0046 21.3 4.5 45 55-99 126-170 (179)
111 PF02187 GAS2: Growth-Arrest-S 21.4 48 0.001 21.2 0.9 14 40-53 1-14 (73)
112 PRK10250 hypothetical protein; 20.9 1.1E+02 0.0024 20.7 2.7 24 43-66 93-116 (122)
113 PRK07417 arogenate dehydrogena 20.9 3.8E+02 0.0082 20.4 5.9 42 48-92 228-269 (279)
114 smart00803 TAF TATA box bindin 20.3 2.2E+02 0.0048 17.3 5.4 47 32-90 18-64 (65)
115 PRK06545 prephenate dehydrogen 20.2 3.6E+02 0.0077 21.5 5.9 44 46-92 228-271 (359)
116 TIGR01791 CM_archaeal chorisma 20.1 2.3E+02 0.0051 17.6 7.2 52 39-91 8-72 (83)
117 COG4029 Uncharacterized protei 20.1 2.3E+02 0.0049 20.3 4.1 16 77-92 123-138 (142)
118 PRK02292 V-type ATP synthase s 20.0 3.4E+02 0.0074 19.4 7.0 31 41-71 13-43 (188)
No 1
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.84 E-value=6e-21 Score=162.68 Aligned_cols=94 Identities=24% Similarity=0.382 Sum_probs=83.1
Q ss_pred CccccCCCC-CCcccccCCCCchhHHH-HhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 1 MVTTFGMSE-IGPWSLVDGSQSGDVIM-RMMARNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 1 MV~~~GMS~-lG~v~~~~~~~~~~fl~-~~~~~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
||++||||+ +|++.|...+.. .|++ .....+.||++|++.||.||++||++||++|++||++|++.|++||++|+++
T Consensus 503 mv~~~Gms~~lg~~~~~~~~~~-~~lg~~~~~~~~~s~~~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~ 581 (644)
T PRK10733 503 MVTQWGFSEKLGPLLYAEEEGE-VFLGRSVAKAKHMSDETARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKY 581 (644)
T ss_pred HHHHhCCCccccchhhcccccc-cccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence 899999999 999999765421 2664 3445678999999999999999999999999999999999999999999999
Q ss_pred hcCCHHHHHHHhhcccC
Q 033676 79 ETMSGDEFRAILSEFVE 95 (114)
Q Consensus 79 EtL~g~e~~~ll~~~~~ 95 (114)
|||+++||++++.....
T Consensus 582 etl~~~ei~~i~~~~~~ 598 (644)
T PRK10733 582 ETIDAPQIDDLMARRDV 598 (644)
T ss_pred ceeCHHHHHHHHhcCCC
Confidence 99999999999987643
No 2
>CHL00176 ftsH cell division protein; Validated
Probab=99.82 E-value=2.3e-20 Score=159.20 Aligned_cols=100 Identities=40% Similarity=0.671 Sum_probs=86.5
Q ss_pred CccccCCCCCCcccccCCCCchhHHHH-hhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 033676 1 MVTTFGMSEIGPWSLVDGSQSGDVIMR-MMARNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKE 79 (114)
Q Consensus 1 MV~~~GMS~lG~v~~~~~~~~~~fl~~-~~~~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~E 79 (114)
||++||||++||++|...+....|++. +...+.||+++++.||.||+++|+.||++|++||++|++.|++||++|+++|
T Consensus 533 mv~~~Gm~~~g~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~iD~ev~~~l~~~~~~a~~iL~~~~~~l~~la~~Lle~E 612 (638)
T CHL00176 533 MVTRFGMSSIGPISLESNNSTDPFLGRFMQRNSEYSEEIADKIDMEVRSILHTCYQYAYQILKDNRVLIDLLVELLLQKE 612 (638)
T ss_pred HHHHhCCCcCCceeecCCCCcccccccccccccCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhC
Confidence 899999999999999765421126643 4456789999999999999999999999999999999999999999999999
Q ss_pred cCCHHHHHHHhhcccCCCCcC
Q 033676 80 TMSGDEFRAILSEFVEIPSEN 100 (114)
Q Consensus 80 tL~g~e~~~ll~~~~~~~~~~ 100 (114)
||+++||+++++.+...|+.+
T Consensus 613 tl~~~ei~~il~~~~~~~~~~ 633 (638)
T CHL00176 613 TIDGDEFREIVNSYTILPPKK 633 (638)
T ss_pred ccCHHHHHHHHhhcCCCCCCc
Confidence 999999999998876655443
No 3
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.80 E-value=1.9e-19 Score=152.30 Aligned_cols=93 Identities=35% Similarity=0.526 Sum_probs=85.2
Q ss_pred CccccCCCC-CCcccccCCCCchhHHHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 033676 1 MVTTFGMSE-IGPWSLVDGSQSGDVIMRMMARNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKE 79 (114)
Q Consensus 1 MV~~~GMS~-lG~v~~~~~~~~~~fl~~~~~~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~E 79 (114)
||++||||+ +|++.|...++. |++.....++||++|++.||.||+++++.||+++++||.+|++.++.+++.|+++|
T Consensus 500 mVt~~Gms~~lG~v~~~~~~~~--flg~~~~~~~~Se~ta~~ID~evk~ii~~~y~~a~~il~~~~~~l~~~~~~Lle~E 577 (596)
T COG0465 500 MVTEYGMSAKLGPVAYEQVEGV--FLGRYQKAKNYSEETAQEIDREVKDIIDEAYERAKELLNENKDALETLAEMLLEKE 577 (596)
T ss_pred hhhhcCcchhhCceehhhcccc--cccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 899999999 999999887543 88554477899999999999999999999999999999999999999999999999
Q ss_pred cCCHHHHHHHhhcccC
Q 033676 80 TMSGDEFRAILSEFVE 95 (114)
Q Consensus 80 tL~g~e~~~ll~~~~~ 95 (114)
||++++|+.|+.....
T Consensus 578 ti~~~~i~~i~~~~~~ 593 (596)
T COG0465 578 TIDAEEIKDILAGRKL 593 (596)
T ss_pred ccCHHHHHHHHhcccC
Confidence 9999999999976643
No 4
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=99.75 E-value=1.5e-18 Score=130.40 Aligned_cols=89 Identities=37% Similarity=0.562 Sum_probs=72.3
Q ss_pred CccccCCCC-CCcccccCCCCchhHH-HHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 1 MVTTFGMSE-IGPWSLVDGSQSGDVI-MRMMARNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 1 MV~~~GMS~-lG~v~~~~~~~~~~fl-~~~~~~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
||..||||+ +|++.+........|+ +.+....++|+.+...+|.+|+++|+.+|++|++||++||+.|++||+.|+++
T Consensus 123 mv~~~Gm~~~~g~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~ 202 (213)
T PF01434_consen 123 MVASYGMGDSLGLLSYSPNDDDEVFLGREWNSRRPMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEK 202 (213)
T ss_dssp HHHTST-TTTTTSS-SEEEE-S-SSS-E---EEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH
T ss_pred HHHHhCCCCCCceeeeeccccccccccccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence 789999999 9999987643211144 22334568999999999999999999999999999999999999999999999
Q ss_pred hcCCHHHHHHH
Q 033676 79 ETMSGDEFRAI 89 (114)
Q Consensus 79 EtL~g~e~~~l 89 (114)
|+|+++||++|
T Consensus 203 ~~L~~~ei~~I 213 (213)
T PF01434_consen 203 ETLSGEEIEEI 213 (213)
T ss_dssp SEEEHHHHHHH
T ss_pred CeeCHHHHhhC
Confidence 99999999976
No 5
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.74 E-value=3.9e-18 Score=143.14 Aligned_cols=83 Identities=37% Similarity=0.578 Sum_probs=76.8
Q ss_pred CccccCCCC-CCcccccCCCCchhHHHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 033676 1 MVTTFGMSE-IGPWSLVDGSQSGDVIMRMMARNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKE 79 (114)
Q Consensus 1 MV~~~GMS~-lG~v~~~~~~~~~~fl~~~~~~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~E 79 (114)
||++||||+ +||+++....++ ..++++|...||.||++||.++|+||+.||+.|...++.||++||++|
T Consensus 652 MVt~fGMSd~vG~v~~~~~~~~----------~s~~~~t~~lidaEi~~lL~~sYeRak~iL~~h~kEl~~LA~ALleYE 721 (752)
T KOG0734|consen 652 MVTKFGMSDKVGPVTLSAEDNS----------SSLSPRTQELIDAEIKRLLRDSYERAKSILKTHKKELHALAEALLEYE 721 (752)
T ss_pred HHHHcCccccccceeeeccCCC----------CCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 899999999 999999876422 467888999999999999999999999999999999999999999999
Q ss_pred cCCHHHHHHHhhcc
Q 033676 80 TMSGDEFRAILSEF 93 (114)
Q Consensus 80 tL~g~e~~~ll~~~ 93 (114)
||+++||.+++.+.
T Consensus 722 TL~A~eik~vl~g~ 735 (752)
T KOG0734|consen 722 TLDAKEIKRVLKGK 735 (752)
T ss_pred cCCHHHHHHHHhcc
Confidence 99999999999755
No 6
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=99.66 E-value=2.4e-16 Score=130.47 Aligned_cols=90 Identities=32% Similarity=0.536 Sum_probs=78.7
Q ss_pred CccccCCCC-CCcccccCCCCchhHHH-HhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 1 MVTTFGMSE-IGPWSLVDGSQSGDVIM-RMMARNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 1 MV~~~GMS~-lG~v~~~~~~~~~~fl~-~~~~~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
||++|||++ +|++++...... .|++ .+...+.||+.+...+|.+|+++|+.+|++|++||++|++.|++||++|+++
T Consensus 404 mv~~~Gm~~~~g~~~~~~~~~~-~~l~~~~~~~~~~s~~~~~~id~~v~~lL~~a~~ra~~lL~~~~~~l~~la~~Ll~~ 482 (495)
T TIGR01241 404 MVTEWGMSDKLGPVAYGSDGGD-VFLGRGFAKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKALLEK 482 (495)
T ss_pred HHHHhCCCcccCceeeccCccc-cccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHc
Confidence 789999999 999999764311 2552 2344679999999999999999999999999999999999999999999999
Q ss_pred hcCCHHHHHHHhh
Q 033676 79 ETMSGDEFRAILS 91 (114)
Q Consensus 79 EtL~g~e~~~ll~ 91 (114)
|+|+++||++|++
T Consensus 483 e~L~~~ei~~il~ 495 (495)
T TIGR01241 483 ETITREEIKELLA 495 (495)
T ss_pred CeeCHHHHHHHhC
Confidence 9999999999874
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.65 E-value=3e-16 Score=135.55 Aligned_cols=93 Identities=45% Similarity=0.552 Sum_probs=83.8
Q ss_pred CccccCCCC-CCcccccCCCCchhHHHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 033676 1 MVTTFGMSE-IGPWSLVDGSQSGDVIMRMMARNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKE 79 (114)
Q Consensus 1 MV~~~GMS~-lG~v~~~~~~~~~~fl~~~~~~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~E 79 (114)
||++||||+ +|++++.... .+.+...++||+.+++.||.||++|++.||++|.++|++|++.|++||+.|+++|
T Consensus 661 ~V~~~Gms~kig~~~~~~~~-----~~~~~~~~p~s~~~~~~Id~ev~~lv~~ay~~~~~ll~~n~~~l~~ia~~LLeke 735 (774)
T KOG0731|consen 661 MVASFGMSEKIGPISFQMLL-----PGDESFRKPYSEKTAQLIDTEVRRLVQKAYERTKELLRTNRDKLDKIAEVLLEKE 735 (774)
T ss_pred HHHHcCcccccCceeccCcc-----cccccccCccchhHHHHHHHHHHHHHhhHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 799999999 9999994432 1234457899999999999999999999999999999999999999999999999
Q ss_pred cCCHHHHHHHhhcccCCCC
Q 033676 80 TMSGDEFRAILSEFVEIPS 98 (114)
Q Consensus 80 tL~g~e~~~ll~~~~~~~~ 98 (114)
+|+++++.++++.++..++
T Consensus 736 ~l~~ee~~~ll~~~~~~~~ 754 (774)
T KOG0731|consen 736 VLTGEEIIALLGERPPGMP 754 (774)
T ss_pred hccHHHHHHHhccCCCccc
Confidence 9999999999999887764
No 8
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=84.14 E-value=3.2 Score=24.91 Aligned_cols=41 Identities=22% Similarity=0.293 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 53 AYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 53 ~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
-|++|-+|-++-...=..+.+.++++.-|+.+++.++++..
T Consensus 10 GYe~aa~iAk~A~~~g~svre~v~~~g~lt~ee~d~ll~p~ 50 (55)
T PF10415_consen 10 GYEKAAEIAKEALAEGRSVREVVLEEGLLTEEELDELLDPE 50 (55)
T ss_dssp HHHHHHHHHHHHHHHT--HHHHHHHTTSS-HHHHHHHTSHH
T ss_pred ccHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHcCHH
Confidence 36666666666555556778888899999999999999754
No 9
>smart00114 CARD Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
Probab=83.85 E-value=3.5 Score=26.36 Aligned_cols=37 Identities=27% Similarity=0.431 Sum_probs=29.0
Q ss_pred HHHHHHHHhHHHH------HHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 56 IALSQIRNNREAI------DKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 56 ~a~~iL~~nr~~L------~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
+.+++|..||..| +-+-+.|+++.+|+.++...+-..
T Consensus 4 ~~r~~L~k~r~~l~~~l~~~~vld~L~~~~Vlt~~e~e~i~~~ 46 (88)
T smart00114 4 RDKRLLRRNRVRLGEELGVDGLLDYLVEKNVLTEKEIEAIKAA 46 (88)
T ss_pred HHHHHHHHhHHHHHHHcchhHHHHHHHHcCCCCHHHHHHHHcc
Confidence 4456667776655 568999999999999999988653
No 10
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=82.58 E-value=4.1 Score=27.16 Aligned_cols=38 Identities=13% Similarity=0.259 Sum_probs=29.2
Q ss_pred HHHHHHHHHhHHHHHH-------HHHHHHHHhcCCHHHHHHHhhc
Q 033676 55 EIALSQIRNNREAIDK-------IVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 55 ~~a~~iL~~nr~~L~~-------la~~Lle~EtL~g~e~~~ll~~ 92 (114)
++-+++|.+||..|-+ +.+.|+++++||.++...|-..
T Consensus 3 e~hr~~Lr~~R~~Lv~dl~~~~~v~~~L~~~gIlT~~~~e~I~a~ 47 (94)
T cd08327 3 PKHKQLLRSQRLELSAELLVDGLVIQYLYQEGILTESHVEEIESQ 47 (94)
T ss_pred HHHHHHHHHHHHHHHHHccchHHHHHHHHhCCCCCHHHHHHHHcc
Confidence 3556788888876653 5567999999999999988753
No 11
>PF07104 DUF1366: Protein of unknown function (DUF1366); InterPro: IPR009796 This entry is represented by Streptococcus phage 7201, Orf40. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 130 residues in length. One of the sequences in this family, from phage Sfi11 (O80186 from SWISSPROT) is known as Gp149. The function of this family is unknown.
Probab=79.01 E-value=9.9 Score=26.42 Aligned_cols=45 Identities=11% Similarity=0.394 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHH
Q 033676 40 ADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDE 85 (114)
Q Consensus 40 ~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e 85 (114)
..+|+.+.++ +++-+++.+.++.....|..+...|.++|+++.++
T Consensus 71 ~kvd~~l~k~-~~~~~K~e~~~k~~~~tl~~lI~~~~~~~~~~de~ 115 (116)
T PF07104_consen 71 QKVDEKLEKM-KAQIDKVEKATKTAQATLNDLIATLYEKEVLTDED 115 (116)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCC
Confidence 4556444444 78888899999999999999999999999998765
No 12
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=78.69 E-value=5.4 Score=26.38 Aligned_cols=35 Identities=34% Similarity=0.508 Sum_probs=27.2
Q ss_pred HHHHHHhHHHH-------HHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 58 LSQIRNNREAI-------DKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 58 ~~iL~~nr~~L-------~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
+.+|+.||..| +-|.+.|+++..|+.++...|-..
T Consensus 8 ~~~L~~~R~~Lv~~l~~v~~ilD~Ll~~~Vlt~ee~e~I~~~ 49 (94)
T cd08329 8 LSLIRKNRMALFQHLTSVLPILDSLLSANVITEQEYDVIKQK 49 (94)
T ss_pred HHHHHHhHHHHHHHHhhhHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 34666666654 568899999999999999988654
No 13
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=78.59 E-value=7.3 Score=25.47 Aligned_cols=37 Identities=19% Similarity=0.379 Sum_probs=29.4
Q ss_pred HHHHHHHHhHHHH------HHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 56 IALSQIRNNREAI------DKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 56 ~a~~iL~~nr~~L------~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
+-+++|.+||..| +.|.+.|+++.+||.++...|-+.
T Consensus 4 ~hR~~L~~~r~~Lv~~l~~~~v~~~L~~~gvlt~~~~~~I~~~ 46 (90)
T cd08332 4 RHREALKKNRVKLAKELVLDELLIHLLQKDILTDSMAESIMAK 46 (90)
T ss_pred HHHHHHHHhHHHHHHHCCHHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 4466777777665 569999999999999999988754
No 14
>PF14327 CSTF2_hinge: Hinge domain of cleavage stimulation factor subunit 2; PDB: 4EBA_G.
Probab=77.63 E-value=4.3 Score=26.27 Aligned_cols=59 Identities=19% Similarity=0.224 Sum_probs=42.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhh
Q 033676 33 SMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILS 91 (114)
Q Consensus 33 ~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~ 91 (114)
.++..-..++-.+.+.++...-++++++|.+|-..--+++++++.---++.+-+..++.
T Consensus 25 ~l~~~ql~ell~~mK~l~~~~p~~ar~lL~~nPqLa~Al~qa~l~lg~vd~~v~~~~l~ 83 (84)
T PF14327_consen 25 SLPPEQLYELLSQMKQLAQQNPEQARQLLQQNPQLAYALFQALLLLGMVDPDVVQSILK 83 (84)
T ss_dssp TSHHHHHHHHHHHHHHHHC----HHHHHHHS-THHHHHHHHHHHHTSS-SSSCHHH---
T ss_pred hCCHHHHHHHHHHHHHHHHhCHHHHHHHHHHCcHHHHHHHHHHHHhCCCCHHHHHhhcc
Confidence 45555567788899999999999999999999999999999999988888777766653
No 15
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=76.11 E-value=7.2 Score=25.30 Aligned_cols=35 Identities=17% Similarity=0.292 Sum_probs=27.1
Q ss_pred HHHHHHhHHHH------HHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 58 LSQIRNNREAI------DKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 58 ~~iL~~nr~~L------~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
+++|.+||..| +.+-+.|+++.++|.++...|-..
T Consensus 2 R~lL~~~r~~Lv~~l~~~~v~~~L~~~~Vlt~~~~e~I~~~ 42 (84)
T cd08326 2 RQILRRHRARLVEELQPKYLWDHLLSRGVFTPDMIEEIQAA 42 (84)
T ss_pred HHHHHHhHHHHHHHCCHHHHHHHHHhcCCCCHHHHHHHHcC
Confidence 35566666554 569999999999999999988753
No 16
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=70.70 E-value=23 Score=22.68 Aligned_cols=49 Identities=20% Similarity=0.217 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
-.+++.+.++.+..+..+-.+.+..-..+ ..|+..++.|.+.|++++..
T Consensus 47 ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l-~~ll~~~~~D~~~i~a~~~~ 95 (125)
T PF13801_consen 47 QAKLRALMDEFRQEMRALRQELRAARQEL-RALLAAPPPDEAAIEALLEE 95 (125)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCSSS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHcCCCCCHHHHHHHHHH
Confidence 56777888888877777777666666665 45667889999999988754
No 17
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=69.29 E-value=9.9 Score=24.85 Aligned_cols=25 Identities=16% Similarity=0.246 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 68 IDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 68 L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
.+.|.+.|+++.+||.++.+.|-..
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~ 40 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSK 40 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcC
Confidence 3669999999999999999998754
No 18
>PF12209 SAC3: Leucine permease transcriptional regulator helical domain; InterPro: IPR024293 This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [].; PDB: 3FWC_N 3FWB_B.
Probab=68.01 E-value=29 Score=22.29 Aligned_cols=43 Identities=12% Similarity=0.268 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 033676 34 MSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLE 77 (114)
Q Consensus 34 ~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle 77 (114)
+++-..+.++.|+..++..+.++...- ..++..++.|++.|..
T Consensus 6 ~~~ii~~vV~~el~~~l~~~l~~~n~~-~~R~~iI~sLs~ELy~ 48 (79)
T PF12209_consen 6 YSQIIQDVVHSELSKILKNLLRRQNAR-KERKQIIDSLSEELYD 48 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH-H---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHH
Confidence 445567789999999999987774433 4556778989888854
No 19
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=66.83 E-value=8.5 Score=25.41 Aligned_cols=37 Identities=11% Similarity=0.118 Sum_probs=28.8
Q ss_pred HHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhccc
Q 033676 58 LSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFV 94 (114)
Q Consensus 58 ~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~ 94 (114)
++.|-.+....+-+.+.|+++..|+.++...+.....
T Consensus 7 Re~LV~rI~~v~plLD~Ll~n~~it~E~y~~V~a~~T 43 (85)
T cd08324 7 RELLVTHIRNTQCLVDNLLKNDYFSTEDAEIVCACPT 43 (85)
T ss_pred HHHHHHHHHhhHHHHHHHhccCCccHHHHHHHHhCCC
Confidence 3455556666678999999999999999998876543
No 20
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=65.74 E-value=17 Score=23.72 Aligned_cols=36 Identities=11% Similarity=0.211 Sum_probs=28.2
Q ss_pred HHHHHHhHHHH------HHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 58 LSQIRNNREAI------DKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 58 ~~iL~~nr~~L------~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
+++|+.||..| +.+.+.|.++..||.++.+.|....
T Consensus 2 ~~~L~~~R~~L~~~l~~~~l~d~L~q~~VLt~~d~EeI~~~~ 43 (86)
T cd08785 2 WEALEGMRHRLTRKINPSRLTPYLRQCKVLDEQDEEEVLSSP 43 (86)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHhcCCCCHHHHHHHhCCC
Confidence 34566666654 4589999999999999999998743
No 21
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by asso
Probab=64.58 E-value=20 Score=23.42 Aligned_cols=34 Identities=18% Similarity=0.297 Sum_probs=26.1
Q ss_pred HHHHHhHHHH------HHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 59 SQIRNNREAI------DKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 59 ~iL~~nr~~L------~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
++|++||..| +.+.+.|+++..||.++.+.+...
T Consensus 3 ~~L~~~R~~L~~~L~~~~l~d~L~s~~ILt~~d~EeI~~~ 42 (84)
T cd08810 3 EVLEELRHYLCDKIIADRHFDYLRSKRILTRDDCEEISCR 42 (84)
T ss_pred HHHHHHHHHHHHHhcHHHHHHHHHHcCCCCHHHHHHHhcc
Confidence 3455555443 568999999999999999999863
No 22
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=62.83 E-value=18 Score=22.38 Aligned_cols=31 Identities=23% Similarity=0.517 Sum_probs=25.4
Q ss_pred HHHhHHHHHHHHHHHHHHhcCCHHHHHHHhh
Q 033676 61 IRNNREAIDKIVEVLLEKETMSGDEFRAILS 91 (114)
Q Consensus 61 L~~nr~~L~~la~~Lle~EtL~g~e~~~ll~ 91 (114)
|.++...++.+.+.|+++.+|+.+|...|..
T Consensus 11 Lv~~l~~~~~ild~L~~~~vlt~~e~e~I~~ 41 (85)
T PF00619_consen 11 LVEDLDDLDDILDHLLSRGVLTEEEYEEIRS 41 (85)
T ss_dssp HHHHSSHHHHHHHHHHHTTSSSHHHHHHHHT
T ss_pred HHHHhCcHHHHHHHHHHCCCCCHHHHHHHHc
Confidence 3334446788999999999999999999876
No 23
>PF07028 DUF1319: Protein of unknown function (DUF1319); InterPro: IPR010746 This entry is represented by Commelina yellow mottle virus, Orf1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses.
Probab=58.78 E-value=55 Score=23.12 Aligned_cols=56 Identities=7% Similarity=0.193 Sum_probs=39.5
Q ss_pred HHHHHHHHHH---HHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccCCCCcC
Q 033676 45 AVKRLSDRAY---EIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVEIPSEN 100 (114)
Q Consensus 45 eV~~il~~~y---~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~~~~~~ 100 (114)
.+..|+..+. +..+.-+..=...|..|....+++-.|+.+|+++++-.-..+|+-.
T Consensus 50 ~~~ki~~~Qr~~l~~l~~~l~~l~~eL~~Lr~~~l~rRPLtk~dVeeLV~~IseQPK~I 108 (126)
T PF07028_consen 50 NLSKIQESQRSELKELKQELDVLSKELQALRKEYLERRPLTKEDVEELVLRISEQPKFI 108 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCcHHH
Confidence 3444444433 3334445555677888999999999999999999997776666643
No 24
>PF00901 Orbi_VP5: Orbivirus outer capsid protein VP5; InterPro: IPR000145 The orbivirus VP5 protein is one of the two proteins (with VP2) which make up the virus particle outer capsid. Cryoelectron microscopy indicates that VP5 is a trimer suggesting that there are 360 copies of VP5 per virion [].; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=54.23 E-value=64 Score=27.81 Aligned_cols=48 Identities=10% Similarity=0.262 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 46 VKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 46 V~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
--++|+.+.+-..+|++.....|++|+++|.+.+.+-..+=++++..+
T Consensus 141 q~~~LekAl~~~~~i~~~E~~~l~~L~~AL~kE~~~Rt~dE~~mv~~y 188 (508)
T PF00901_consen 141 QIEILEKALKSYGKIVKEENKQLDRLARALQKESRERTQDERKMVEEY 188 (508)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence 446778888888889999999999999999999988877777777654
No 25
>PF01411 tRNA-synt_2c: tRNA synthetases class II (A); InterPro: IPR018164 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Alanyl-tRNA synthetase (6.1.1.7 from EC) is an alpha4 tetramer that belongs to class IIc. ; GO: 0000166 nucleotide binding, 0004813 alanine-tRNA ligase activity, 0005524 ATP binding, 0006419 alanyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3HY1_A 3HXZ_C 3HXY_A 3HXU_A 3HY0_B 3HXV_A 3HXX_A 3HXW_A 2E1B_A 2ZZG_B ....
Probab=53.55 E-value=37 Score=29.27 Aligned_cols=52 Identities=15% Similarity=0.265 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccC
Q 033676 44 AAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVE 95 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~ 95 (114)
..|.++|..-+++=.+.|.+-...|+++.+.|-++.+|+|+++-.|.+.++-
T Consensus 345 ~~I~~ii~~EE~~F~~TL~~G~~~l~~~i~~~~~~~~lsge~aF~LYDTyGf 396 (552)
T PF01411_consen 345 DYIKDIIKEEEERFLKTLERGLKLLEKLIKKLKKKKELSGEDAFKLYDTYGF 396 (552)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSEE-HHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccCCChHHheeehhccCC
Confidence 5789999999999999999999999999999888999999999999887753
No 26
>PRK15054 nitrate reductase 2 subunit delta; Provisional
Probab=49.68 E-value=50 Score=25.55 Aligned_cols=40 Identities=18% Similarity=0.028 Sum_probs=34.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhccc
Q 033676 55 EIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFV 94 (114)
Q Consensus 55 ~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~ 94 (114)
+.++.+|..++..|+.|...|-+.++--..=|..++.-.+
T Consensus 120 ~~a~~~L~~~~~iLe~L~~rL~~~~SpYa~l~~all~l~~ 159 (231)
T PRK15054 120 DQAKEGLLNVAPILALLGGRLKQREAPWYALFDALLQLAG 159 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHhC
Confidence 5678899999999999999999999999998988875443
No 27
>PRK13710 plasmid maintenance protein CcdA; Provisional
Probab=48.40 E-value=69 Score=20.29 Aligned_cols=50 Identities=20% Similarity=0.222 Sum_probs=36.1
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHH
Q 033676 31 RNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFR 87 (114)
Q Consensus 31 ~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~ 87 (114)
.-+.|......|.++++++ ++...+.+|++.++.+.+..-++- +-.++++
T Consensus 21 giNlS~~~e~~L~~~~~~~------~~~~W~~eN~eai~~~n~~ve~~G-~~~de~R 70 (72)
T PRK13710 21 DVNISGLVNTAMQNEARRL------RAERWKAENREGMAEVARFIEMNG-SFADENR 70 (72)
T ss_pred CCcHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHhC-CcHHhcC
Confidence 3577888888888888884 556677799999999887655544 4444443
No 28
>COG2811 NtpF Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]
Probab=47.92 E-value=89 Score=21.46 Aligned_cols=43 Identities=19% Similarity=0.279 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 36 EKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 36 e~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
+..-+..-++-+++|..+-++++.|+.+--...+.+++.+++.
T Consensus 20 d~~IeeAkEe~~~~i~eAr~eareiieeaE~eA~~~~~e~l~~ 62 (108)
T COG2811 20 DEEIEEAKEEAEQIIKEAREEAREIIEEAEEEAEKLAQEILEE 62 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444566677888999999999999999988888888877764
No 29
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=47.59 E-value=66 Score=20.49 Aligned_cols=34 Identities=15% Similarity=0.316 Sum_probs=25.9
Q ss_pred HHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 60 QIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 60 iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
-|.++-..++.|.+.|+++..|+.++...+....
T Consensus 9 ~Li~~v~~v~~ilD~L~~~~Vit~e~~~~I~a~~ 42 (82)
T cd08330 9 ALIARVTNVDPILDKLHGKKVITQEQYSEVRAEK 42 (82)
T ss_pred HHHHHHhhHHHHHHHHHHCCCCCHHHHHHHHcCC
Confidence 3444444567889999999999999999887644
No 30
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=47.50 E-value=32 Score=22.07 Aligned_cols=29 Identities=28% Similarity=0.508 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 64 NREAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 64 nr~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
.++.++-+-+.|+++.+|+.+|.+.+-..
T Consensus 14 ~~~~i~~llD~Ll~~~Vl~~~E~e~i~~~ 42 (83)
T cd08325 14 GKGVINGLLDDLLEKNVLNEEEMEKIKEE 42 (83)
T ss_pred hHhhHHHHHHHHHHcCCCCHHHHHHHHhc
Confidence 46678899999999999999999988764
No 31
>PHA02571 a-gt.4 hypothetical protein; Provisional
Probab=47.04 E-value=93 Score=21.44 Aligned_cols=35 Identities=17% Similarity=0.203 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 033676 39 AADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVE 73 (114)
Q Consensus 39 ~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~ 73 (114)
.+.+++.=.++-..+..+|.++|+.|+..+.+|-.
T Consensus 17 ee~~~~~q~~~e~eA~kkA~K~lkKN~rEIkRL~~ 51 (109)
T PHA02571 17 EELLSELQARNEAEAEKKAAKILKKNRREIKRLKK 51 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 34444444556677888999999999999998864
No 32
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=46.47 E-value=28 Score=24.39 Aligned_cols=53 Identities=19% Similarity=0.282 Sum_probs=34.8
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHH
Q 033676 31 RNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFR 87 (114)
Q Consensus 31 ~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~ 87 (114)
..++|++. .+.++++|+..|+.-.+.+.++|..-..-.+.+.+....++++-.
T Consensus 77 ~~~~s~~~----r~~~~~~l~~~~~~f~~~Va~~R~~~~~~v~~~~~~~~~~~~~A~ 129 (154)
T PF01343_consen 77 RDPMSEEE----RENLQELLDELYDQFVNDVAEGRGLSPDDVEEIADGGVFTAQQAL 129 (154)
T ss_dssp TSS--HHH----HHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHH
T ss_pred CCCCCHHH----HHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHhhccccHHHHH
Confidence 34556554 567888999999999999999996433334445555666666543
No 33
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=43.94 E-value=1.2e+02 Score=21.88 Aligned_cols=38 Identities=11% Similarity=0.153 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 033676 38 LAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVL 75 (114)
Q Consensus 38 t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~L 75 (114)
.......++.+|+.++-..+.+++.+-...-+..++..
T Consensus 11 il~~A~~ea~~il~~A~~~a~~i~~~a~~~a~~~~~~i 48 (198)
T PRK03963 11 INREAEQKIEYILEEAQKEAEKIKEEARKRAESKAEWI 48 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555555555555555555554444444433333
No 34
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=43.87 E-value=76 Score=29.17 Aligned_cols=51 Identities=10% Similarity=0.156 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccCCC
Q 033676 44 AAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVEIP 97 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~~~ 97 (114)
..|++||..-.++=.+.|.+-...|+++++.+ .+|+++++-.|.+.++..|
T Consensus 396 ~~I~~ii~~Ee~~f~~tl~~G~~~~~~~~~~~---~~l~g~~~f~LYDt~G~P~ 446 (900)
T PRK13902 396 DYILDIVDLEEEKYRETLERGKRIVERLAKKK---EEIPLDDLIELYDSHGIPP 446 (900)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCHHHHhhhhhcCCCCH
Confidence 46888888888888889999999999888876 7899999999998876543
No 35
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=43.31 E-value=65 Score=22.90 Aligned_cols=48 Identities=17% Similarity=0.228 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHH---HHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 42 IDAAVKRLSDRAYEIALSQIRNNRE---AIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 42 iD~eV~~il~~~y~~a~~iL~~nr~---~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
+=....+-.++.|+++++.|.+|.. .+..|++++ -++-+.|..++..-
T Consensus 20 iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~t----gVs~~~I~~~IreG 70 (137)
T TIGR03826 20 VCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEET----GVSEKLILKFIREG 70 (137)
T ss_pred cCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH----CcCHHHHHHHHHcC
Confidence 3445666778899999999999988 788888877 78888898888543
No 36
>PRK01584 alanyl-tRNA synthetase; Provisional
Probab=42.41 E-value=75 Score=27.90 Aligned_cols=53 Identities=13% Similarity=0.158 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccC
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVE 95 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~ 95 (114)
...|+++|+.-.++=.+.|..=...|+++.+.|.++.+|+|++.-.|.+.++-
T Consensus 350 ~~~I~~ii~~EE~~F~~tl~~G~~~l~~~i~~~~~~~~~~g~~af~LydTyGf 402 (594)
T PRK01584 350 KDFIKEELNKEEEKFFKTLRKGEQEFIKLIPNLGSSKIIPGDIAFKLYDTYGF 402 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccCHHHHHhhhccCCC
Confidence 35688899999999999999999999999988865678999999999887754
No 37
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=41.39 E-value=87 Score=26.38 Aligned_cols=35 Identities=14% Similarity=0.210 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHH---HHHhHHHHHHHHHHHHHH
Q 033676 44 AAVKRLSDRAYEIALSQ---IRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~i---L~~nr~~L~~la~~Lle~ 78 (114)
.+.+.-+.+.+.+|+.+ |...+..|.+++++++++
T Consensus 292 ~e~~~ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~ 329 (455)
T PRK05932 292 DEDKQFLREKLQEAKWLIKSLEQRKETLLKVARCIVEQ 329 (455)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 68888999999999999 778899999999999875
No 38
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=40.93 E-value=85 Score=26.19 Aligned_cols=36 Identities=17% Similarity=0.223 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHH---HHHhHHHHHHHHHHHHHH
Q 033676 43 DAAVKRLSDRAYEIALSQ---IRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~i---L~~nr~~L~~la~~Lle~ 78 (114)
+.+++.-+++.+++|+.+ |...+..|.++++++++.
T Consensus 266 ~~~~~~ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~ 304 (429)
T TIGR02395 266 KEAAAQYLKQKLKEARWLIKALEQREETLLKVAEAIVEH 304 (429)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457888999999999998 778899999999999875
No 39
>TIGR00344 alaS alanine--tRNA ligase. The model describes alanine--tRNA ligase. This enzyme catalyzes the reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala + pyrophosphate + AMP).
Probab=40.33 E-value=97 Score=28.27 Aligned_cols=51 Identities=12% Similarity=0.198 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccC
Q 033676 44 AAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVE 95 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~ 95 (114)
..|+++|..-+++=.+.|..-...|+++.+.+ .+.+|+|++.-.|.+.++-
T Consensus 347 ~~i~~ii~~Ee~~f~~tl~~G~~~l~~~~~~~-~~~~i~g~~af~LydTyGf 397 (851)
T TIGR00344 347 EFVEQILELEEERFAKTLERGLRLFEKLLKKL-GKKELDGEDAFKLYDTYGF 397 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCccCHHHHHHHHHccCC
Confidence 45899999999999999999999999999887 6678999999988877753
No 40
>PF05527 DUF758: Domain of unknown function (DUF758) ; InterPro: IPR008477 This is a family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.; PDB: 3F4M_A.
Probab=40.11 E-value=1.4e+02 Score=22.40 Aligned_cols=50 Identities=24% Similarity=0.345 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH----------HHHHHHhcCCHHHHHHH
Q 033676 39 AADIDAAVKRLSDRAYEIALSQIRNNREAIDKIV----------EVLLEKETMSGDEFRAI 89 (114)
Q Consensus 39 ~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la----------~~Lle~EtL~g~e~~~l 89 (114)
.--||++..+++++.|.-++..-. |+..-+++. ..|..++.++.+|+..+
T Consensus 28 k~fIddtsselLD~ly~l~K~~t~-~kkeA~ki~KniIKi~vKigvl~rn~qf~~eEl~~~ 87 (186)
T PF05527_consen 28 KMFIDDTSSELLDELYRLLKEYTG-NKKEAEKIIKNIIKIVVKIGVLYRNNQFSDEELALA 87 (186)
T ss_dssp -----HHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHH
T ss_pred HHhcCchHHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHHHHhheeeecCCCCHHHHHHH
Confidence 345677777777777776665442 333334443 34667899999998754
No 41
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=39.98 E-value=1.3e+02 Score=21.20 Aligned_cols=44 Identities=30% Similarity=0.303 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHH------HHHHHHHHHHHhHHHHHHHHHHHHHHhcC
Q 033676 38 LAADIDAAVKRLSDR------AYEIALSQIRNNREAIDKIVEVLLEKETM 81 (114)
Q Consensus 38 t~~~iD~eV~~il~~------~y~~a~~iL~~nr~~L~~la~~Lle~EtL 81 (114)
.+..+-.+|-.-|.. ..+.+++++.+|.+.|+++|+.-+..+-.
T Consensus 21 lKl~VRD~Vl~~l~~~~~~~~~~~ea~~~i~~~~~~Ie~~A~~~l~~~G~ 70 (130)
T PF09551_consen 21 LKLKVRDAVLEYLSPWLSQAKSKEEAREVIRENLPEIEQIAEEVLAEEGY 70 (130)
T ss_pred HHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhHHHHHHHHHHHHHHhCC
Confidence 444444444444443 35688999999999999999998877654
No 42
>COG4453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.62 E-value=1e+02 Score=20.69 Aligned_cols=47 Identities=21% Similarity=0.292 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 35 SEKLAADIDAAV--------KRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 35 Se~t~~~iD~eV--------~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
+++..+.||... .-+|+.+|+.|+++|.+++-. .|+.++.+.++.--
T Consensus 18 ~~d~~~Li~~AAai~g~s~tdFvl~aA~~~A~~vi~~~~~~------------~L~e~~~~~fl~~L 72 (95)
T COG4453 18 TPDQRDLIDRAAAIEGKSLTDFVLSAALEAAEDVIEDQRRF------------ILDEEDYRRFLAAL 72 (95)
T ss_pred CHHHHHHHHHHHHHHCCcHHHHHHHHHHHHHHHHHHhhHHH------------hCCHHHHHHHHHHh
Confidence 344455555543 457999999999999998844 46777777766443
No 43
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=38.01 E-value=1.4e+02 Score=21.51 Aligned_cols=19 Identities=11% Similarity=0.202 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 033676 40 ADIDAAVKRLSDRAYEIAL 58 (114)
Q Consensus 40 ~~iD~eV~~il~~~y~~a~ 58 (114)
.....++.+|++++..+|.
T Consensus 24 ~~A~~~a~~i~~~a~~~a~ 42 (198)
T PRK03963 24 EEAQKEAEKIKEEARKRAE 42 (198)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3334444445544444444
No 44
>PF07011 DUF1313: Protein of unknown function (DUF1313); InterPro: IPR009741 This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.
Probab=37.66 E-value=57 Score=21.61 Aligned_cols=31 Identities=23% Similarity=0.209 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 033676 42 IDAAVKRLSDRAYEIALSQIRNNREAIDKIV 72 (114)
Q Consensus 42 iD~eV~~il~~~y~~a~~iL~~nr~~L~~la 72 (114)
.|.+|-..+...+..+..||..||-++..|-
T Consensus 3 ~d~~~~~tf~~sF~qVQ~iLDqNR~LI~eIN 33 (87)
T PF07011_consen 3 GDGKVWQTFQKSFVQVQSILDQNRLLINEIN 33 (87)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhHHHHHHHh
Confidence 4667777888888888888888888877664
No 45
>KOG2751 consensus Beclin-like protein [Signal transduction mechanisms]
Probab=37.63 E-value=95 Score=26.36 Aligned_cols=56 Identities=18% Similarity=0.324 Sum_probs=41.5
Q ss_pred cchhhHHHHHHHHHHHHHHHH--HHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHH
Q 033676 31 RNSMSEKLAADIDAAVKRLSD--RAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFR 87 (114)
Q Consensus 31 ~~~~Se~t~~~iD~eV~~il~--~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~ 87 (114)
-..+++.+.+.+|.|+.-..+ +.|++..++|..+.... ...+.+.++|-+..++-+
T Consensus 137 C~eC~d~l~~~ld~e~~~~~~e~~~Y~~~l~~Le~~~~~~-~~~~~~~e~~~l~~eE~~ 194 (447)
T KOG2751|consen 137 CEECMDVLLNKLDKEVEDAEDEVDTYKACLQRLEQQNQDV-SEEDLLKELKNLKEEEER 194 (447)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccc-chHHHHHHHHHHHHHHHH
Confidence 356788899999998887765 46888888888877665 666667777776666654
No 46
>PF04368 DUF507: Protein of unknown function (DUF507); InterPro: IPR007463 This entry represents a bacterial protein of unknown function.
Probab=36.83 E-value=1.1e+02 Score=22.72 Aligned_cols=42 Identities=10% Similarity=0.027 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh
Q 033676 38 LAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKE 79 (114)
Q Consensus 38 t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~E 79 (114)
....||++++.||++..+.-...--+.+..+..+-+.|-++.
T Consensus 48 ~E~~Lde~areiLe~~~~eie~~~id~r~mF~~iKkkLA~e~ 89 (183)
T PF04368_consen 48 KEEALDEEAREILEENEDEIEFMGIDYRQMFWMIKKKLAKER 89 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHc
Confidence 456788888888888777754444455555555555555544
No 47
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=36.80 E-value=73 Score=20.12 Aligned_cols=26 Identities=35% Similarity=0.385 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHh
Q 033676 65 REAIDKIVEVLLEKETMSGDEFRAIL 90 (114)
Q Consensus 65 r~~L~~la~~Lle~EtL~g~e~~~ll 90 (114)
+..+.+|...=-++..||.++|...|
T Consensus 6 ~~~i~~Li~~gK~~G~lT~~eI~~~L 31 (82)
T PF03979_consen 6 EEAIKKLIEKGKKKGYLTYDEINDAL 31 (82)
T ss_dssp HHHHHHHHHHHHHHSS-BHHHHHHH-
T ss_pred HHHHHHHHHHHhhcCcCCHHHHHHHc
Confidence 33333333333344444444444443
No 48
>KOG0188 consensus Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=36.38 E-value=69 Score=29.25 Aligned_cols=51 Identities=16% Similarity=0.232 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhccc
Q 033676 44 AAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFV 94 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~ 94 (114)
..|..|+++-...=.+.|.+-|..+++.+..|=...||.|+....|...|+
T Consensus 355 ~~v~diineEE~~F~ktl~rg~~~f~r~~~~~~~s~tipGd~~w~LydTyG 405 (895)
T KOG0188|consen 355 QHVIDIINEEEAQFLKTLDRGRKLFDRVARELGSSKTIPGDVAWRLYDTYG 405 (895)
T ss_pred HHHHHHhcHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchHHHHHHHhhcC
Confidence 457788888888889999999999999999999999999999999987765
No 49
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=36.23 E-value=1.6e+02 Score=21.07 Aligned_cols=48 Identities=6% Similarity=0.034 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHH
Q 033676 39 AADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEF 86 (114)
Q Consensus 39 ~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~ 86 (114)
+..+-.+.+.++.++...+.+|+.+-+..-+.+.+..+++=.-..+.+
T Consensus 72 a~~~~~e~e~~L~~Ar~eA~~Ii~~A~~eAe~~~~~ii~~A~~ea~~~ 119 (167)
T PRK08475 72 SKEKKEDALKKLEEAKEKAELIVETAKKEAYILTQKIEKQTKDDIENL 119 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455667777788888888888888888877777777766544444333
No 50
>PRK02292 V-type ATP synthase subunit E; Provisional
Probab=35.78 E-value=1.7e+02 Score=21.06 Aligned_cols=38 Identities=13% Similarity=0.197 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 033676 37 KLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEV 74 (114)
Q Consensus 37 ~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~ 74 (114)
+.....+.++..|+.++...|.++..+-....++.+..
T Consensus 20 ~I~~ea~~~~~~i~~ea~~~a~~i~~~~~~~a~~e~~~ 57 (188)
T PRK02292 20 EIRAEADEEAEEIIAEAEADAEEILEDREAEAEREIEQ 57 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555555555555554444444444433
No 51
>PF10398 DUF2443: Protein of unknown function (DUF2443); InterPro: IPR019469 This entry represents a small group of highly conserved proteins from bacteria, in particular Helicobacter species. The structure is a bundle of alpha helices. The function is not known. ; PDB: 1ZKE_F.
Probab=35.77 E-value=69 Score=20.72 Aligned_cols=32 Identities=25% Similarity=0.482 Sum_probs=20.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 033676 32 NSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVL 75 (114)
Q Consensus 32 ~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~L 75 (114)
...+...-.+||+||.+ |+++.++|.++...+
T Consensus 45 e~l~~~~~~QideeV~~------------LKe~IdaLNK~KkE~ 76 (79)
T PF10398_consen 45 EHLNMAFLAQIDEEVEK------------LKEHIDALNKIKKEL 76 (79)
T ss_dssp TTS-HHHHHHHHHHHHH------------HHHHHHHHHHHHGGG
T ss_pred ccccHHHHHHHHHHHHH------------HHHHHHHHHHHHHHH
Confidence 44555667888988875 456677777765544
No 52
>PF07369 DUF1488: Protein of unknown function (DUF1488); InterPro: IPR009962 This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown.; PDB: 2GPI_A.
Probab=35.18 E-value=77 Score=19.78 Aligned_cols=25 Identities=28% Similarity=0.324 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 54 YEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 54 y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
-.........||..++.+|+.|++.
T Consensus 48 ~~~~l~~F~~~R~~Ie~~Ae~~i~~ 72 (83)
T PF07369_consen 48 EEDLLAAFDRHRFDIEEAAERLIEQ 72 (83)
T ss_dssp HHHHHHHHHHTHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHCHHHHHHHHHHHHHh
Confidence 4556778889999999999999987
No 53
>PF04757 Pex2_Pex12: Pex2 / Pex12 amino terminal region; InterPro: IPR006845 This region is the N-terminal part of a number of peroxisomal biogenesis proteins, including Pex2, Pex10 and Pex12, which contain two predicted transmembrane segments. The majority of these proteins have a C-terminal ring finger domain IPR001841 from INTERPRO.; GO: 0007031 peroxisome organization, 0005778 peroxisomal membrane
Probab=35.18 E-value=90 Score=22.84 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH---------HhHHHHHHHHHHHHHHhcCC
Q 033676 43 DAAVKRLSDRAYEIALSQIR---------NNREAIDKIVEVLLEKETMS 82 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~---------~nr~~L~~la~~Lle~EtL~ 82 (114)
|+|+..++..+...+.+.+. .+.+.+..+.+.|++.=++-
T Consensus 1 d~~l~~~L~~~l~~i~~~l~~~~~~~~~~~~~~Ei~~ll~~l~~~~tl~ 49 (229)
T PF04757_consen 1 DEELESLLKPALSYILQYLAQPRGPRRLLRYFDEIFLLLKLLYESLTLL 49 (229)
T ss_pred ChHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45555666666666666555 79999999999999987775
No 54
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=34.62 E-value=1.5e+02 Score=20.44 Aligned_cols=24 Identities=13% Similarity=0.094 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHH
Q 033676 45 AVKRLSDRAYEIALSQIRNNREAI 68 (114)
Q Consensus 45 eV~~il~~~y~~a~~iL~~nr~~L 68 (114)
....||..++.+|.+|+.+-+...
T Consensus 14 ~A~~il~~A~~~a~~i~~~A~~~~ 37 (166)
T TIGR02499 14 QAQAILAAARQRAEAILADAEEEA 37 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444433
No 55
>PRK14135 recX recombination regulator RecX; Provisional
Probab=34.21 E-value=2.1e+02 Score=21.67 Aligned_cols=59 Identities=12% Similarity=0.198 Sum_probs=43.1
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 31 RNSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 31 ~~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
+..++++.-+.|-.+ .....+++.|..+|......-..|.+.|.++ -++.+.|..++..
T Consensus 39 g~~l~~~~~~~i~~~--~~~~~a~~~Al~~L~~r~~s~~el~~kL~~k-g~~~~~Ie~vl~~ 97 (263)
T PRK14135 39 GKELDEEDLEEIQYA--DQVSKGKNLALYYLSYQMRTEKEVRDYLKKH-EISEEIISEVIDK 97 (263)
T ss_pred CCcCCHHHHHHHHHH--HHHHHHHHHHHHHhhhccccHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence 456666655555443 5677899999999998877778888888877 4577888777653
No 56
>PF06428 Sec2p: GDP/GTP exchange factor Sec2p; InterPro: IPR009449 In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion []. It catalyzes the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. Binds the Rab GTPase YPT32, but does not have exhange activity on YPT32 [, , ].; PDB: 2EQB_C 2E7S_K 2OCY_A.
Probab=34.05 E-value=1.5e+02 Score=19.93 Aligned_cols=44 Identities=25% Similarity=0.372 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHHHh
Q 033676 36 EKLAADIDAAVKRLSDRAYEIALSQIRNNR-------EAIDKIVEVLLEKE 79 (114)
Q Consensus 36 e~t~~~iD~eV~~il~~~y~~a~~iL~~nr-------~~L~~la~~Lle~E 79 (114)
+.....|+.|+..|-...++.|-++...-| .....+...|-+.+
T Consensus 14 e~~~~~ie~ElEeLTasLFeEAN~MVa~ar~e~~~~e~k~~~le~~l~e~~ 64 (100)
T PF06428_consen 14 EQEKEQIESELEELTASLFEEANKMVADARRERAALEEKNEQLEKQLKEKE 64 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788999999999999999999998877 44444555554444
No 57
>PF09687 PRESAN: Plasmodium RESA N-terminal; InterPro: IPR019111 The short, four-helical domain first identified in the Plasmodium export proteins PHISTa and PHISTc [] has been extended to become this six-helical PRESAC domain identified in the P. falciparum-specific RESA-type (Ring-infected erythrocyte surface antigen) proteins in association with the DnaJ domain. Overall, at least 67 proteins have been detected in P. falciparum with complete copies of the PRESAC domain. No versions of this domain were detected in other apicomplexan genera, suggesting that the domain was 'invented' after the divergence of the lineage leading to the genus Plasmodium undergoing a dramatic proliferation only in P. falciparum. A secondary structure-prediction derived from the multiple alignment of the PRESAC family reveals that it is composed of an all-helical fold with six conserved helical segments. There is some evidence it might localise to membranes [].
Probab=33.70 E-value=1.4e+02 Score=19.42 Aligned_cols=51 Identities=22% Similarity=0.308 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
+....++...|+.....-|..........-..++.+++++..+|..++...
T Consensus 64 ~~~~~k~W~~c~~~i~~~l~~~e~~~~~~f~~~~~~~~~~~~ef~~fi~~~ 114 (129)
T PF09687_consen 64 EEYKKKIWKECYEEITKELKKMEKFYNKNFYDLLKKGICSRDEFKNFINSC 114 (129)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence 355578888999999999999999999999999999999999999988643
No 58
>PRK06718 precorrin-2 dehydrogenase; Reviewed
Probab=33.50 E-value=1.1e+02 Score=22.51 Aligned_cols=38 Identities=29% Similarity=0.397 Sum_probs=31.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 033676 33 SMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDK 70 (114)
Q Consensus 33 ~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~ 70 (114)
--|+..+..|-+++.+++...|..-.+++.+-|+.+..
T Consensus 127 G~sP~la~~lr~~ie~~~~~~~~~~~~~~~~~R~~~k~ 164 (202)
T PRK06718 127 GASPKLAKKIRDELEALYDESYESYIDFLYECRQKIKE 164 (202)
T ss_pred CCChHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHHHH
Confidence 34788899999999999999999888888888877654
No 59
>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=33.29 E-value=77 Score=29.18 Aligned_cols=54 Identities=11% Similarity=0.141 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccCC
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVEI 96 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~~ 96 (114)
..-|.++|+.-.++=.+.|..=...|+++++.|-+..+|+|++.-+|.+.|+-.
T Consensus 348 ~~~I~~vl~~EEe~F~~TL~~G~~l~~~~~~~~~~~~~l~ge~afkLYDTyGfP 401 (879)
T COG0013 348 EDFIKEVLKLEEERFAKTLERGLKLLEKELAKLKKSKTLDGEDAFKLYDTYGFP 401 (879)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCccChHHheeehhcCCCC
Confidence 445778888888888888999999999999988888999999999999888644
No 60
>TIGR03683 A-tRNA_syn_arch alanyl-tRNA synthetase. This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases.
Probab=31.85 E-value=1.5e+02 Score=27.37 Aligned_cols=51 Identities=12% Similarity=0.203 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccCCC
Q 033676 44 AAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVEIP 97 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~~~ 97 (114)
..|++||+.-.++=.+.|..-...|+++++. +.+|+++++-.|.+.++..|
T Consensus 400 ~~I~~ii~~Ee~~f~~Tl~~G~~~~~~~~~~---~~~i~g~~~f~LyDTyGfP~ 450 (902)
T TIGR03683 400 DYILDILDLEEEKYRETLERGRRIVERLLKT---KKEIPLDDLIELYDSHGIPP 450 (902)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---CCcCCHHHHHHHHHccCCCH
Confidence 3488888888888888999888888888874 56899999999998876443
No 61
>TIGR02837 spore_II_R stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage II sporulation protein R.
Probab=31.42 E-value=2.2e+02 Score=21.08 Aligned_cols=31 Identities=29% Similarity=0.335 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHhcCCH
Q 033676 53 AYEIALSQIRNNREAIDKIVEVLLEKETMSG 83 (114)
Q Consensus 53 ~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g 83 (114)
..+.|++++.+|.+.++.+|+.-+.++-.+.
T Consensus 77 s~~ea~~~i~~~l~~Ie~~a~~~l~~~G~~y 107 (168)
T TIGR02837 77 SLEEARRVIRENLPEIERIAESVIKAEGADY 107 (168)
T ss_pred CHHHHHHHHHHhhHHHHHHHHHHHHHhCCCC
Confidence 3578899999999999999999988875543
No 62
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=31.28 E-value=1.2e+02 Score=22.52 Aligned_cols=39 Identities=15% Similarity=0.091 Sum_probs=32.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 033676 33 SMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKI 71 (114)
Q Consensus 33 ~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~l 71 (114)
--|+..+..|-+++.+++...|..-.+++.+-|..+...
T Consensus 127 G~sP~la~~lr~~ie~~l~~~~~~~~~~~~~~R~~~k~~ 165 (205)
T TIGR01470 127 GAAPVLARLLRERIETLLPPSLGDLATLAATWRDAVKKR 165 (205)
T ss_pred CCCcHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHhh
Confidence 456788999999999999999999888888888877643
No 63
>PF10849 DUF2654: Protein of unknown function (DUF2654); InterPro: IPR022558 This entry is represented by Bacteriophage T4, a-gt.4; it is a family of uncharacterised viral proteins.
Probab=30.32 E-value=60 Score=20.66 Aligned_cols=21 Identities=10% Similarity=0.295 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHh
Q 033676 68 IDKIVEVLLEKETMSGDEFRAIL 90 (114)
Q Consensus 68 L~~la~~Lle~EtL~g~e~~~ll 90 (114)
+.+|-+.+-+ .++.+.++.++
T Consensus 39 I~KLR~i~kQ--p~~~~~i~~mW 59 (70)
T PF10849_consen 39 IKKLRDIYKQ--PYNDELIETMW 59 (70)
T ss_pred HHHHHHHHcC--CCcHHHHHHHH
Confidence 4444444433 55555555544
No 64
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=29.53 E-value=1e+02 Score=22.66 Aligned_cols=52 Identities=12% Similarity=0.200 Sum_probs=36.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHH
Q 033676 33 SMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRA 88 (114)
Q Consensus 33 ~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ 88 (114)
++|++. .+.++++++..|+.-.+.+.++|..-..-.+.+++..+.++++-.+
T Consensus 134 ~~s~~~----~e~~~~~l~~~~~~f~~~va~~R~~~~~~~~~~~~~~~~~~~~A~~ 185 (207)
T TIGR00706 134 ELTPEE----RDILQNLVNESYEQFVQVVAKGRNLPVEDVKKFADGRVFTGRQALK 185 (207)
T ss_pred CCCHHH----HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhcCCcccHHHHHH
Confidence 355544 5566678899999989999998885545455667777777776554
No 65
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=29.43 E-value=1.4e+02 Score=21.17 Aligned_cols=46 Identities=13% Similarity=0.268 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHH----HHHHHhcCCHHHHHHHhhccc
Q 033676 49 LSDRAYEIALSQIRNNREAIDKIVE----VLLEKETMSGDEFRAILSEFV 94 (114)
Q Consensus 49 il~~~y~~a~~iL~~nr~~L~~la~----~Lle~EtL~g~e~~~ll~~~~ 94 (114)
+|+..+.|-.+-|...++.|-...+ .|+.-|.++.+|+.++-..+.
T Consensus 59 LIQn~q~Rd~~al~~KLdeLi~~~~~a~n~li~iE~l~~~el~~~~~~~~ 108 (132)
T PF04120_consen 59 LIQNTQNRDTKALQAKLDELIRAVKEARNELIDIEDLTEEELEEIRKRYE 108 (132)
T ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCcccCCHHHHHHHHHHHH
Confidence 3455555555555555555555444 789999999999998876554
No 66
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=28.66 E-value=99 Score=19.50 Aligned_cols=19 Identities=21% Similarity=0.146 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHhHH
Q 033676 48 RLSDRAYEIALSQIRNNRE 66 (114)
Q Consensus 48 ~il~~~y~~a~~iL~~nr~ 66 (114)
-+++.++++|.++|.+|.-
T Consensus 28 Fi~~aa~~~A~~~i~~~~~ 46 (80)
T PF08681_consen 28 FILSAALEAAEEVIEEHER 46 (80)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhcce
Confidence 3566777777777777754
No 67
>PRK09173 F0F1 ATP synthase subunit B; Validated
Probab=28.39 E-value=2.1e+02 Score=19.99 Aligned_cols=39 Identities=8% Similarity=0.008 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 40 ADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 40 ~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
.....+...|++++...+..++.+-+...+..++.+++.
T Consensus 64 ~~A~~ea~~ii~~A~~~a~~~~~~a~~~a~~~~~~~~~~ 102 (159)
T PRK09173 64 KEAEKEAADIVAAAEREAEALTAEAKRKTEEYVARRNKL 102 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455677777888888888877777777777776665543
No 68
>cd00211 PTS_IIA_fru PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=28.37 E-value=1.2e+02 Score=19.81 Aligned_cols=28 Identities=21% Similarity=0.430 Sum_probs=13.3
Q ss_pred hHHHHHHHHHHHHHHhcCCHHHHHHHhh
Q 033676 64 NREAIDKIVEVLLEKETMSGDEFRAILS 91 (114)
Q Consensus 64 nr~~L~~la~~Lle~EtL~g~e~~~ll~ 91 (114)
..++++.+++.|.+..-++.+-+..++.
T Consensus 15 ~~~~l~~~~~~l~~~~~~~~~~~~~l~~ 42 (136)
T cd00211 15 KEEAIEELAQLLVAAGYVEEEYIEALLE 42 (136)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3445555555555555444334444443
No 69
>cd07215 Pat17_PNPLA8_PNPLA9_like2 Patatin-like phospholipase of bacteria. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum.
Probab=27.36 E-value=62 Score=25.55 Aligned_cols=34 Identities=21% Similarity=0.389 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 033676 42 IDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVL 75 (114)
Q Consensus 42 iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~L 75 (114)
+|..-.+-++...+.+.+++.+|++.++++++.|
T Consensus 296 lD~a~~~~i~~L~~~~~~~~~~~~~~i~~~~~~~ 329 (329)
T cd07215 296 MDDASPENLEKLREVGQALAEDHKDQLDEIVDRL 329 (329)
T ss_pred cccCCHHHHHHHHHHHHHHHHHhHHHHHHHHHhC
Confidence 4444444455555556666666666666665543
No 70
>PHA00743 helix-turn-helix protein
Probab=27.20 E-value=1e+02 Score=18.35 Aligned_cols=39 Identities=21% Similarity=0.353 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhc
Q 033676 41 DIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKET 80 (114)
Q Consensus 41 ~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~Et 80 (114)
.+|.+||+++.--.+--.+++..|.+. +++-.+|.--..
T Consensus 3 eLD~~iReLLs~iheIKID~i~~~~~k-~kvekAl~Ls~~ 41 (51)
T PHA00743 3 ELDEDVRELLSIIHEIKIDIITQSYDK-EKIEKAIFLSQK 41 (51)
T ss_pred hhHHHHHHHHHHHHHHhhhhhcccCCH-HHHHHHHHHHHH
Confidence 579999999999999888888888544 455555544333
No 71
>KOG0450 consensus 2-oxoglutarate dehydrogenase, E1 subunit [Carbohydrate transport and metabolism]
Probab=27.03 E-value=65 Score=29.45 Aligned_cols=36 Identities=28% Similarity=0.452 Sum_probs=31.6
Q ss_pred HHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 58 LSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 58 ~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
.+-|++|...|+.-++.||...|++.+||.+....+
T Consensus 526 Yk~I~k~~~~l~~Y~ekLl~egtvs~~evd~~~~k~ 561 (1017)
T KOG0450|consen 526 YKQIRKHKPVLQKYAEKLLSEGTVSQQEVDEEIKKY 561 (1017)
T ss_pred HHHHHcCCcHHHHHHHHHHhcCcccHHHHHHHHHHH
Confidence 456789999999999999999999999999877554
No 72
>PRK09098 type III secretion system protein HrpB; Validated
Probab=26.93 E-value=2.9e+02 Score=21.07 Aligned_cols=27 Identities=22% Similarity=0.198 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 033676 40 ADIDAAVKRLSDRAYEIALSQIRNNRE 66 (114)
Q Consensus 40 ~~iD~eV~~il~~~y~~a~~iL~~nr~ 66 (114)
..-..+..+||+++..+|.+|+.+-+.
T Consensus 46 a~Ar~~A~~Il~~A~~~A~~I~~~A~~ 72 (233)
T PRK09098 46 AAARARAERIVAEARAQAEAILEAARR 72 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333445555555555555555554433
No 73
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=26.62 E-value=1.6e+02 Score=21.77 Aligned_cols=51 Identities=20% Similarity=0.239 Sum_probs=35.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHH
Q 033676 33 SMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFR 87 (114)
Q Consensus 33 ~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~ 87 (114)
++|++. .+..+.+++..|+.-.+.+.++|..-...++.+.+....++++-.
T Consensus 152 ~~s~~~----r~~~~~~l~~~~~~f~~~Va~~R~~~~~~~~~~~~~~~~~~~~A~ 202 (222)
T cd07018 152 DMSPEA----REQTQALLDSLWDQYLADVAASRGLSPDALEALIDLGGDSAEEAL 202 (222)
T ss_pred cCCHHH----HHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCCcHHHHHH
Confidence 455544 556678888899999999999987555555556656666666543
No 74
>PF08838 DUF1811: Protein of unknown function (DUF1811); InterPro: IPR014938 This entry consists uncharacterised bacterial proteins. Some of the proteins are annotated as being transcriptional regulators (see Q4MQL7 from SWISSPROT, Q65MA2 from SWISSPROT). The structure of one of the proteins has revealed a beta-barrel like structure with helix-turn-helix like motif. ; PDB: 2YXY_A 1SF9_A.
Probab=26.51 E-value=83 Score=21.43 Aligned_cols=28 Identities=21% Similarity=0.281 Sum_probs=20.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033676 32 NSMSEKLAADIDAAVKRLSDRAYEIALSQ 60 (114)
Q Consensus 32 ~~~Se~t~~~iD~eV~~il~~~y~~a~~i 60 (114)
+.||+-|.+++..||..+-..+ .+|.++
T Consensus 2 krySeMs~~EL~~Ei~~L~eka-rKAEq~ 29 (102)
T PF08838_consen 2 KRYSEMSEEELRQEIARLKEKA-RKAEQL 29 (102)
T ss_dssp HHHHC--HHHHHHHHHHHHHHH-HHHHHC
T ss_pred cchhhcCHHHHHHHHHHHHHHH-HHHHHc
Confidence 4688889999999999988777 555554
No 75
>PF03909 BSD: BSD domain ; InterPro: IPR005607 The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PDOC50097 from PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown []. Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain []. Some proteins known to contain one or two BSD domains are listed below: Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1). Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2. Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination. Drosophila synapse-associated protein SAP47. Mammalian SYAP1. Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.; PDB: 1X3A_A 1PFJ_A 2RNR_B 2DII_A.
Probab=26.32 E-value=1.1e+02 Score=18.15 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHH
Q 033676 53 AYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAI 89 (114)
Q Consensus 53 ~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~l 89 (114)
..+.+..||..+.. |.++-..|+ -..|+.++|.+.
T Consensus 13 ~~e~i~~lL~~~p~-l~~~~~~lV-P~~~~e~~FW~r 47 (62)
T PF03909_consen 13 QTEEIKKLLEEDPN-LRKLYNELV-PSKMSEEEFWKR 47 (62)
T ss_dssp HHHHHHHHHHH-HH-HHHHHHHCC-TTTS-HHHHHHH
T ss_pred CHHHHHHHHHhCHH-HHHHHHHhC-CCCCCHHHHHHH
Confidence 35566678877776 788888888 788999998864
No 76
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=26.14 E-value=1.7e+02 Score=20.13 Aligned_cols=30 Identities=20% Similarity=0.488 Sum_probs=17.8
Q ss_pred HhHHHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 63 NNREAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 63 ~nr~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
.-.+.+.+|++.|+++-.|+.++=++++.+
T Consensus 21 ~~~ek~~klvDelVkkGeln~eEak~~vdd 50 (108)
T COG3937 21 ETAEKVQKLVDELVKKGELNAEEAKRFVDD 50 (108)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 334455666666666666666666655543
No 77
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.09 E-value=1.4e+02 Score=20.24 Aligned_cols=40 Identities=25% Similarity=0.180 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHH-----HHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 39 AADIDAAVKRLSDRA-----YEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 39 ~~~iD~eV~~il~~~-----y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
+..+|-...-+++.. -+.+++.++++|..+++||.-|-.+
T Consensus 55 a~~ll~~~ivllkel~~~Aeseeake~irq~rq~~EklAg~lTkk 99 (103)
T COG4847 55 ANLLLLYLIVLLKELAVIAESEEAKESIRQVRQEVEKLAGDLTKK 99 (103)
T ss_pred HHHHHHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555556665544 3678899999999999999887554
No 78
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=25.92 E-value=1.1e+02 Score=19.04 Aligned_cols=15 Identities=13% Similarity=0.381 Sum_probs=11.2
Q ss_pred HHHHHhHHHHHHHHH
Q 033676 59 SQIRNNREAIDKIVE 73 (114)
Q Consensus 59 ~iL~~nr~~L~~la~ 73 (114)
+++.+|+++|+.||+
T Consensus 60 ~~~~~y~~~l~~La~ 74 (74)
T TIGR02609 60 RAMSKYDEALKELAD 74 (74)
T ss_pred HHHHHHHHHHHHHhC
Confidence 466788888888874
No 79
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=25.51 E-value=2.1e+02 Score=19.87 Aligned_cols=28 Identities=18% Similarity=0.133 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 51 DRAYEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 51 ~~~y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
..+++.|..+|...-..-..|.+.|.++
T Consensus 11 ~~a~~~al~~L~~r~~s~~el~~kL~~k 38 (157)
T PRK00117 11 ASARARALRLLARREHSRAELRRKLAAK 38 (157)
T ss_pred HHHHHHHHHHHccchhHHHHHHHHHHhc
Confidence 3444444444444444444444444433
No 80
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=25.35 E-value=2.7e+02 Score=20.28 Aligned_cols=36 Identities=14% Similarity=0.083 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 033676 40 ADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVL 75 (114)
Q Consensus 40 ~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~L 75 (114)
+..+.++..|+.++-..|.+|+.+-+...+.+.+.-
T Consensus 12 ~ea~~~a~~I~~eA~~~aeei~~ea~~~a~~~~~~~ 47 (185)
T PRK01194 12 KSREEKKKEINDEYSKRIEKLEKECDSKIQSIKEYY 47 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555555555555555555555555554433
No 81
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=25.29 E-value=1.6e+02 Score=17.69 Aligned_cols=27 Identities=22% Similarity=0.485 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 66 EAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 66 ~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
.-++.+.+.|+++..|+.+|...+...
T Consensus 13 ~~~~~il~~L~~~~vlt~~e~~~i~~~ 39 (80)
T cd01671 13 LDVEDVLDHLLSDGVLTEEEYEKIRSE 39 (80)
T ss_pred ccHHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 456778888999999999998887654
No 82
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) 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 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (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. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=25.21 E-value=2.3e+02 Score=19.31 Aligned_cols=45 Identities=11% Similarity=0.260 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
++-+..+++-+|..+.++|.+-...-+. -.+.||+.+||+-.+..
T Consensus 21 ~~v~~~Lle~~~ry~~~il~dA~~~a~h-----A~r~tV~~eDV~lAi~~ 65 (117)
T cd07979 21 PRVINQLLEFAYRYTTDVLDDAKVYSEH-----AGKANIDADDVKLAIQS 65 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----cCCCCCCHHHHHHHHHH
Confidence 4557778888888888888775543322 24699999999966543
No 83
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=24.91 E-value=80 Score=17.56 Aligned_cols=21 Identities=10% Similarity=0.200 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHhHHHHHHHHH
Q 033676 53 AYEIALSQIRNNREAIDKIVE 73 (114)
Q Consensus 53 ~y~~a~~iL~~nr~~L~~la~ 73 (114)
.++++..+|..|-+.++....
T Consensus 24 v~~~v~~Ll~~hpdLl~~F~~ 44 (47)
T PF02671_consen 24 VIEEVSELLRGHPDLLEEFNR 44 (47)
T ss_dssp HHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHccCHHHHHHHHh
Confidence 667788888888888876544
No 84
>PF11401 Tetrabrachion: Tetrabrachion; InterPro: IPR021535 Tetrabrachion forms a parallel right-handed coiled coil structure with hydrophobic interactions and salt bridges forming a thermostable tetrameric structure. It contains large hydrophobic cavities. No function is known for this family of proteins []. ; PDB: 1FE6_C 1YBK_A.
Probab=24.59 E-value=1.5e+02 Score=17.03 Aligned_cols=36 Identities=22% Similarity=0.271 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 033676 37 KLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIV 72 (114)
Q Consensus 37 ~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la 72 (114)
+|++.|---..-|+++.|+--+++++-.-+.|+-+.
T Consensus 4 etaddivyrltviiddryeslknlitlradrlemii 39 (49)
T PF11401_consen 4 ETADDIVYRLTVIIDDRYESLKNLITLRADRLEMII 39 (49)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccceeEEEEEEEccHHHHHHHHHhhhHhhhhhhh
Confidence 456666666677899999999999988887777553
No 85
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.54 E-value=1.7e+02 Score=18.80 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 033676 44 AAVKRLSDRAYEIALSQIRNNREAIDKIVEVLL 76 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Ll 76 (114)
.+|+.+++..-....++|.+++..|+.=.+.|.
T Consensus 61 ~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~~l~ 93 (96)
T cd04768 61 AEIKELLDTEMEELTAMLLEKKQAIQQKIDRLQ 93 (96)
T ss_pred HHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677766555777778777777776555553
No 86
>PRK01558 V-type ATP synthase subunit E; Provisional
Probab=24.52 E-value=2.9e+02 Score=20.31 Aligned_cols=26 Identities=12% Similarity=0.054 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhH
Q 033676 40 ADIDAAVKRLSDRAYEIALSQIRNNR 65 (114)
Q Consensus 40 ~~iD~eV~~il~~~y~~a~~iL~~nr 65 (114)
..-..+..+|++++..+|.+|+.+-+
T Consensus 29 ~eA~~eAe~Ii~eA~~eAe~i~~kAe 54 (198)
T PRK01558 29 LEAKEEAEEIIAKAEEEAKELKAKAE 54 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33345555555555555555554433
No 87
>PF01023 S_100: S-100/ICaBP type calcium binding domain; InterPro: IPR013787 The calcium-binding domain found in S100 and CaBP-9k proteins is a subfamily of the EF-hand calcium-binding domain []. S100s are small dimeric acidic calcium and zinc-binding proteins abundant in the brain, with S100B playing an important role in modulating the proliferation and differentiation of neurons and glia cells []. S100 proteins have two different types of calcium-binding sites: a low affinity one with a special structure, and a 'normal' EF-hand type high-affinity site. Calbindin-D9k (CaBP-9k) also belong to this family of proteins, but it does not form dimers. CaBP-9k is a cytosolic protein expressed in a variety of tissues. Although its precise function is unknown, it appears to be under the control of the steroid hormones oestrogen and progesterone in the female reproductive system []. In the intestine, CaBP-9k may be involved in calcium absorption by mediating intracellular diffusion []. This entry represents a subdomain of the calcium-binding domain found in S100, CaBP-9k, and related proteins.; PDB: 2RGI_A 4DUQ_B 2KAY_B 2KAX_A 2CNP_A 1CNP_A 1A03_A 1JWD_B 2JTT_A 1XK4_B ....
Probab=24.51 E-value=38 Score=19.23 Aligned_cols=17 Identities=29% Similarity=0.552 Sum_probs=13.6
Q ss_pred HHhcCCHHHHHHHhhcc
Q 033676 77 EKETMSGDEFRAILSEF 93 (114)
Q Consensus 77 e~EtL~g~e~~~ll~~~ 93 (114)
.+.||+..||+.++...
T Consensus 21 d~~~Lsk~Elk~Ll~~E 37 (44)
T PF01023_consen 21 DKDTLSKKELKELLEKE 37 (44)
T ss_dssp STTSEEHHHHHHHHHHH
T ss_pred CCCeEcHHHHHHHHHHH
Confidence 46789999999998764
No 88
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=24.49 E-value=55 Score=20.55 Aligned_cols=44 Identities=16% Similarity=0.220 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHH-HHHHHHhcCCHHHHHHHhhcc
Q 033676 46 VKRLSDRAYEIALSQIRNNREAIDKIV-EVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 46 V~~il~~~y~~a~~iL~~nr~~L~~la-~~Lle~EtL~g~e~~~ll~~~ 93 (114)
+.++|.++-.+|.+ ++.+..+.|. +.-+ ...|+.++++.+++..
T Consensus 23 Ah~lv~~~a~~a~~---~~~~l~e~l~~d~~i-~~~ls~~el~~l~dp~ 67 (81)
T PF10397_consen 23 AHELVQEAAMEAWE---NGRDLREVLLADPEI-AAYLSEEELEELFDPE 67 (81)
T ss_dssp HHHHHHHHHHHHHH---TTS-HHHHHCTTHHH-HTTSHHHHHHHHT-GG
T ss_pred HHHHHHHHHHHHHH---HCCCHHHHHHCCHHH-HhHCCHHHHHhhcCHH
Confidence 33444444333333 4445444444 2222 2567799999999764
No 89
>PRK05562 precorrin-2 dehydrogenase; Provisional
Probab=24.49 E-value=3.2e+02 Score=20.80 Aligned_cols=37 Identities=22% Similarity=0.224 Sum_probs=30.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 033676 33 SMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDK 70 (114)
Q Consensus 33 ~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~ 70 (114)
--|+..+..|-+++.+++ ..|..-.+++..-|..+..
T Consensus 143 G~sP~lar~lR~~ie~~l-~~~~~l~~~l~~~R~~vk~ 179 (223)
T PRK05562 143 GGSPKTSVFIGEKVKNFL-KKYDDFIEYVTKIRNKAKK 179 (223)
T ss_pred CcCcHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHh
Confidence 347788899999999999 6699888888888887765
No 90
>PTZ00015 histone H4; Provisional
Probab=24.34 E-value=2.3e+02 Score=19.13 Aligned_cols=49 Identities=18% Similarity=0.169 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH---HHhcCCHHHHHHHhhccc
Q 033676 46 VKRLSDRAYEIALSQIRNNREAIDKIVEVLL---EKETMSGDEFRAILSEFV 94 (114)
Q Consensus 46 V~~il~~~y~~a~~iL~~nr~~L~~la~~Ll---e~EtL~g~e~~~ll~~~~ 94 (114)
|.+|-..+|+..+.+|+..-..+-+=|-.+. .+.|++.+||.-.+....
T Consensus 45 vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g 96 (102)
T PTZ00015 45 VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQG 96 (102)
T ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcC
Confidence 4455566677777777666555444444444 468999999987775543
No 91
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=24.23 E-value=1.1e+02 Score=23.19 Aligned_cols=28 Identities=25% Similarity=0.542 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 033676 51 DRAYEIALSQIRNNREAIDKIVEVLLEK 78 (114)
Q Consensus 51 ~~~y~~a~~iL~~nr~~L~~la~~Lle~ 78 (114)
+.|..-|..+|+.++..++.+|++|.+-
T Consensus 23 KsA~R~AfhLL~~~~~~~~~la~al~~a 50 (198)
T COG0353 23 KSAQRLAFHLLQRDREDVERLAKALLEA 50 (198)
T ss_pred hHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence 3566678999999999999999999863
No 92
>PF00676 E1_dh: Dehydrogenase E1 component; InterPro: IPR001017 This entry includes a number of dehydrogenases all of which use thiamine pyrophosphate as a cofactor and are members of a multienzyme complex. Pyruvate dehydrogenase (1.2.4.1 from EC), a component of the multienzyme pyruvate dehydrogenase complex; 2-oxoglutarate dehydrogenase (1.2.4.2 from EC), a component of the multienzyme 2-oxoglutarate dehydrogenase which contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3); and 2-oxoisovalerate dehydrogenase (1.2.4.4 from EC), a component of the multienzyme branched-chain alpha-keto dehydrogenase complex all belong to this family.; GO: 0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 0008152 metabolic process; PDB: 1X7Y_A 1V1M_A 1X7W_A 1OLU_A 2J9F_A 2BEW_A 1V11_A 2BFE_A 1U5B_A 2BEU_A ....
Probab=24.07 E-value=1.4e+02 Score=23.48 Aligned_cols=28 Identities=25% Similarity=0.295 Sum_probs=21.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 033676 32 NSMSEKLAADIDAAVKRLSDRAYEIALS 59 (114)
Q Consensus 32 ~~~Se~t~~~iD~eV~~il~~~y~~a~~ 59 (114)
.-++++-.+.|+.|+++.|++++++|++
T Consensus 266 g~~t~~~~~~i~~e~~~~v~~a~~~a~~ 293 (300)
T PF00676_consen 266 GVLTEEELDAIEAEIKAEVEEAVEFAEA 293 (300)
T ss_dssp TSS-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3567777888899999999998888864
No 93
>PRK01005 V-type ATP synthase subunit E; Provisional
Probab=23.92 E-value=3.2e+02 Score=20.55 Aligned_cols=19 Identities=37% Similarity=0.319 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHHhH
Q 033676 47 KRLSDRAYEIALSQIRNNR 65 (114)
Q Consensus 47 ~~il~~~y~~a~~iL~~nr 65 (114)
..|++++...+..++..-+
T Consensus 41 e~Ii~eA~~EAe~ii~~A~ 59 (207)
T PRK01005 41 KRIIAEAQEEAEKIIRSAE 59 (207)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444433
No 94
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=23.85 E-value=4e+02 Score=21.70 Aligned_cols=52 Identities=13% Similarity=0.192 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhH-------------HHHHHHHHHHHHHhcCCHHHHHHHhh
Q 033676 38 LAADIDAAVKRLSDRAYEIALSQIRNNR-------------EAIDKIVEVLLEKETMSGDEFRAILS 91 (114)
Q Consensus 38 t~~~iD~eV~~il~~~y~~a~~iL~~nr-------------~~L~~la~~Lle~EtL~g~e~~~ll~ 91 (114)
.-+.||.++-++|.+..+-+.+|-.-.+ +.|+++.+. ....++.+.++.++.
T Consensus 12 ~ID~ID~eIl~LL~~R~~~~~~I~~~K~~~g~pi~dp~RE~~vl~~~~~~--~~g~l~~~~i~~If~ 76 (360)
T PRK12595 12 EIDEINLQLLELLSKRGELVQEIGEEKTKQGTKRYDPVREREMLDMIAEN--NEGPFEDSTIQHLFK 76 (360)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHh--ccCCCCHHHHHHHHH
Confidence 3578999999999999999998876554 355666552 234578888877763
No 95
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=23.76 E-value=1.9e+02 Score=19.76 Aligned_cols=32 Identities=31% Similarity=0.507 Sum_probs=20.6
Q ss_pred HHHhHHHHHHHHHHHHHH--hcCCHHHHHHHhhc
Q 033676 61 IRNNREAIDKIVEVLLEK--ETMSGDEFRAILSE 92 (114)
Q Consensus 61 L~~nr~~L~~la~~Lle~--EtL~g~e~~~ll~~ 92 (114)
+++++++.+++++.=+++ |.|+.+|..+++.+
T Consensus 68 ~k~Ye~a~~~~~~~~lqkRle~l~~eE~~~L~~e 101 (104)
T PF11460_consen 68 RKDYEEAVDQLTNEELQKRLEELSPEELEALQAE 101 (104)
T ss_pred HHHHHHHHHHHhHHHHHHHHHhCCHHHHHHHHHH
Confidence 445666665555554443 67888888888754
No 96
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=23.63 E-value=1.8e+02 Score=18.76 Aligned_cols=47 Identities=23% Similarity=0.243 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
.+-|+.+|..+.++- ..+++..-.+...|.+...++.+.|..-+...
T Consensus 35 ~~vv~~~i~~~le~~----~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~ 81 (113)
T smart00544 35 HEVVKVLLTCALEEK----RTYREMYSVLLSRLCQANVISTKQFEKGFWRL 81 (113)
T ss_pred HHHHHHHHHHHHcCC----ccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHH
Confidence 456667777777761 36889999999999999999999999876543
No 97
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=23.35 E-value=3e+02 Score=20.09 Aligned_cols=56 Identities=21% Similarity=0.327 Sum_probs=32.1
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhh
Q 033676 32 NSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILS 91 (114)
Q Consensus 32 ~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~ 91 (114)
.+.+++....+-+.++++.+. ++.-|+.-|.....-...+.+.+.++.|+.+.+..
T Consensus 94 P~lT~E~RkelvK~~k~~~E~----aKv~iRniRr~~~~~iKk~~k~~~iseD~~k~~~~ 149 (176)
T TIGR00496 94 PPLTEERRKELVKHAKKIAEQ----AKVAVRNVRRDANDKVKKLEKDKEISEDEERRLQE 149 (176)
T ss_pred CCCCHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhhcCCCChhHHHHHHH
Confidence 356666655555555555554 55555554444444444555667788877776543
No 98
>PF11553 DUF3231: Protein of unknown function (DUF3231); InterPro: IPR021617 This bacterial family of proteins has no known function. ; PDB: 2RBD_B.
Probab=23.29 E-value=2e+02 Score=20.21 Aligned_cols=24 Identities=17% Similarity=0.344 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 033676 42 IDAAVKRLSDRAYEIALSQIRNNREAID 69 (114)
Q Consensus 42 iD~eV~~il~~~y~~a~~iL~~nr~~L~ 69 (114)
=|.+++.+++.+.+ +..+|.+.|+
T Consensus 44 ~D~dik~~l~~~~~----~~~~~i~~l~ 67 (166)
T PF11553_consen 44 EDKDIKKLLKKGLD----LSQKQIEQLE 67 (166)
T ss_dssp --HHHHHHHHHHHH----HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH----HHHHHHHHHH
Confidence 37788887776543 4444444443
No 99
>PHA02734 coat protein; Provisional
Probab=23.15 E-value=1e+02 Score=21.95 Aligned_cols=41 Identities=20% Similarity=0.217 Sum_probs=33.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 033676 33 SMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVE 73 (114)
Q Consensus 33 ~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~ 73 (114)
+-|....-.|-..|+.-++..|++++.+|..-+.....++.
T Consensus 92 pns~~~p~~i~~qv~a~~ealyqqakafl~a~~~~~~~~~k 132 (149)
T PHA02734 92 PNSQAIPGEIAAQVKAKLEALYQQAKAFLAAPAAAAREAAK 132 (149)
T ss_pred CcCCCCCHHHHHHHHhcHHHHHHHHHHHHhChHHHHHHHHh
Confidence 34555667788899999999999999999988887776654
No 100
>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei
Probab=23.01 E-value=1.1e+02 Score=20.19 Aligned_cols=25 Identities=12% Similarity=0.227 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 68 IDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 68 L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
...+.+.|++++.+|.++...|-..
T Consensus 21 ~~~v~d~ll~~~ilT~~d~e~I~aa 45 (88)
T cd08819 21 TRDVCDKCLEQGLLTEEDRNRIEAA 45 (88)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHh
Confidence 5678999999999999999999873
No 101
>COG2315 MmcQ Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.62 E-value=90 Score=21.64 Aligned_cols=24 Identities=13% Similarity=0.398 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHH
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNRE 66 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~ 66 (114)
|+|+..+|+++|+-|+.-|.+...
T Consensus 89 ~e~l~~li~~Sy~Lv~~~Lpk~~r 112 (118)
T COG2315 89 DEELYDLIEQSYQLVKAGLPKKKR 112 (118)
T ss_pred HHHHHHHHHHHHHHHHhhCChhhh
Confidence 789999999999999987766543
No 102
>PRK09665 PTS system galactitol-specific transporter subunit IIA; Provisional
Probab=22.58 E-value=1.2e+02 Score=21.12 Aligned_cols=32 Identities=19% Similarity=0.239 Sum_probs=22.8
Q ss_pred HhHHHHHHHHHHHHHHhcCCHHHHHHHhhccc
Q 033676 63 NNREAIDKIVEVLLEKETMSGDEFRAILSEFV 94 (114)
Q Consensus 63 ~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~ 94 (114)
...++|+.+++.|.++..++.+-+.+++....
T Consensus 14 skee~i~~l~~~L~~~g~v~~~~~~~v~~RE~ 45 (150)
T PRK09665 14 DRSEALTHIGNEMLAKGVVHDTYPQALIAREA 45 (150)
T ss_pred CHHHHHHHHHHHHHHcCCchHHHHHHHHHHHH
Confidence 45678888999999888887555555554443
No 103
>cd08787 CARD_NOD2_1_CARD15 Caspase activation and recruitment domain of NOD2, repeat 1. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 1. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are pr
Probab=22.51 E-value=98 Score=20.42 Aligned_cols=24 Identities=21% Similarity=0.548 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHH
Q 033676 66 EAIDKIVEVLLEKETMSGDEFRAI 89 (114)
Q Consensus 66 ~~L~~la~~Lle~EtL~g~e~~~l 89 (114)
+-++.+-+.|+..|.|+.+|...+
T Consensus 19 e~~esvLD~LLs~evlswEDYe~~ 42 (87)
T cd08787 19 EPFESVLDWLLSQEVLSWEDYEGF 42 (87)
T ss_pred ccHHHHHHHHHHHhHhhHHHHhhh
Confidence 347888999999999999998865
No 104
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=22.20 E-value=1e+02 Score=18.47 Aligned_cols=25 Identities=24% Similarity=0.399 Sum_probs=15.4
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 69 DKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 69 ~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
..+-+.|.+.+.|+.+|.+.++...
T Consensus 3 ~~~l~~l~~g~~Ls~~e~~~~~~~i 27 (66)
T PF02885_consen 3 KEILKKLRDGEDLSREEAKAAFDAI 27 (66)
T ss_dssp HHHHHHHHTT----HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 4455667778999999999888654
No 105
>PRK00252 alaS alanyl-tRNA synthetase; Reviewed
Probab=22.16 E-value=2.5e+02 Score=25.67 Aligned_cols=53 Identities=9% Similarity=0.157 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccCC
Q 033676 44 AAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVEI 96 (114)
Q Consensus 44 ~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~~ 96 (114)
..|++||+.-.++=.+.|..-...|+++.+.+-...+|+|++.-.|.+.++-.
T Consensus 340 ~~i~~ii~~Ee~~f~~tl~~G~~~~~~~~~~~~~~~~l~g~~~f~LydtyGfP 392 (865)
T PRK00252 340 DLIEKVLKAEEERFLKTLERGLKLLEEALAKLKAGKVLSGEDAFKLYDTYGFP 392 (865)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCccCHHHHHHHHhccCCC
Confidence 45889999999999999999999999888764322479999999888777543
No 106
>PLN00035 histone H4; Provisional
Probab=22.09 E-value=2.6e+02 Score=18.93 Aligned_cols=49 Identities=18% Similarity=0.131 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH---HHhcCCHHHHHHHhhccc
Q 033676 46 VKRLSDRAYEIALSQIRNNREAIDKIVEVLL---EKETMSGDEFRAILSEFV 94 (114)
Q Consensus 46 V~~il~~~y~~a~~iL~~nr~~L~~la~~Ll---e~EtL~g~e~~~ll~~~~ 94 (114)
|.+|-..+|+...+.|+..-..+-+=+-.+. .+.|++.+||.-.+....
T Consensus 44 vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 44 VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcC
Confidence 4455566677777777665554444443443 458999999988776543
No 107
>PF11815 DUF3336: Domain of unknown function (DUF3336); InterPro: IPR021771 This family of proteins is characterised by an N-terminal domain that is found adjacent to the patatin/phospholipase A2-related domain (see PF01734 from PFAM). The family of proteins, which contain these two domains, have been characterised in Saccharomyces cerevisiae (Baker's yeast) as a bifunctional enzyme with triacylglycerol lipase and lysophosphatidic acid acyltransferase or lysophosphatidylethanolamine acyltransferase activity. They are generally involved in triacylglycerol mobilisation and localized to lipid particles [, ].
Probab=21.96 E-value=2.1e+02 Score=20.09 Aligned_cols=45 Identities=20% Similarity=0.241 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcc
Q 033676 49 LSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEF 93 (114)
Q Consensus 49 il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~ 93 (114)
+-..+|--+|.++.++.+.+..--+.|.+...++.++-..++...
T Consensus 98 LY~~s~~GTK~lIe~Yi~ev~~~L~~l~~~~~~~~~~kl~ff~~~ 142 (145)
T PF11815_consen 98 LYSHSYSGTKRLIEEYIDEVVRCLEYLAESPELSDEEKLSFFQET 142 (145)
T ss_pred HHHHccccchHHHHHHHHHHHHHHHHHHhCcCCCHHHHHHHHHHH
Confidence 444556668999999999999988999998999999888777543
No 108
>PF01991 vATP-synt_E: ATP synthase (E/31 kDa) subunit; InterPro: IPR002842 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 V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit E from the V1 and A1 complexes of V- and A-ATPases, respectively. Subunit E appears to form a tight interaction with subunit G in the F0 complex, which together may act as stators to prevent certain subunits from rotating with the central rotary element, much in the same way as the F0 complex subunit B does in F-ATPases []. In addition to its key role in stator structure, subunit E appears to have a role in mediating interactions with putative regulatory subunits []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 3LG8_A 2KK7_A 4DT0_A 2DM9_A 2DMA_A 3V6I_A 3K5B_A 3J0J_L 2KZ9_A.
Probab=21.82 E-value=3e+02 Score=19.42 Aligned_cols=13 Identities=15% Similarity=0.217 Sum_probs=4.9
Q ss_pred HHHHHHHHHHHHH
Q 033676 44 AAVKRLSDRAYEI 56 (114)
Q Consensus 44 ~eV~~il~~~y~~ 56 (114)
+++..+++++.++
T Consensus 19 ~e~~~i~~~~~~~ 31 (198)
T PF01991_consen 19 EEAEKILEEAEEE 31 (198)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 109
>PRK06397 V-type ATP synthase subunit H; Validated
Probab=21.78 E-value=2.7e+02 Score=19.01 Aligned_cols=35 Identities=14% Similarity=0.121 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 033676 40 ADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEV 74 (114)
Q Consensus 40 ~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~ 74 (114)
..+|+||..+.+.+.+..++.=..+...+.+-.+.
T Consensus 20 ~S~dkEI~~~k~eqe~~iKEa~~k~ee~~~kteeE 54 (111)
T PRK06397 20 ESIDKEIANIKNEQENEIKEAKSKYEEKAKKTEEE 54 (111)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence 34577777777777766666665555555444433
No 110
>COG2180 NarJ Nitrate reductase delta subunit [Energy production and conversion]
Probab=21.64 E-value=2.1e+02 Score=21.31 Aligned_cols=45 Identities=22% Similarity=0.244 Sum_probs=38.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhcccCCCCc
Q 033676 55 EIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSEFVEIPSE 99 (114)
Q Consensus 55 ~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~~~~~~~~ 99 (114)
+.++..|.+++..+..++.+|-++.+.=..=|.+++.-...++..
T Consensus 126 ~~a~~~L~~~~~~~~~l~~~Lee~~spYa~~~~aL~~~~~~~~~~ 170 (179)
T COG2180 126 EAARRLLSDIRPILAELAKRLEERDSPYAYLFDALLKLLDEILES 170 (179)
T ss_pred HHHHHHHHHhccHHHHHHHHHHhcCCcHHHHHHHHHHHhcccccc
Confidence 688889999999999999999999999999999888665555444
No 111
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=21.37 E-value=48 Score=21.23 Aligned_cols=14 Identities=21% Similarity=0.577 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHH
Q 033676 40 ADIDAAVKRLSDRA 53 (114)
Q Consensus 40 ~~iD~eV~~il~~~ 53 (114)
+.||++|++|++.|
T Consensus 1 ~~ld~~V~~iv~~C 14 (73)
T PF02187_consen 1 NKLDDEVRRIVNQC 14 (73)
T ss_dssp -HHHHHHHHHHTS-
T ss_pred CcHHHHHHHHHhcC
Confidence 35788888888765
No 112
>PRK10250 hypothetical protein; Provisional
Probab=20.88 E-value=1.1e+02 Score=20.74 Aligned_cols=24 Identities=8% Similarity=0.379 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHH
Q 033676 43 DAAVKRLSDRAYEIALSQIRNNRE 66 (114)
Q Consensus 43 D~eV~~il~~~y~~a~~iL~~nr~ 66 (114)
+.+++.+|+.+|+.+..=|.+...
T Consensus 93 ~~~l~~lI~~Sy~lv~~~l~Kk~~ 116 (122)
T PRK10250 93 EALLRDLINDSWNLVVDGLAKRDQ 116 (122)
T ss_pred HHHHHHHHHHHHHHHHhhCCHHHH
Confidence 889999999999999877765543
No 113
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=20.86 E-value=3.8e+02 Score=20.37 Aligned_cols=42 Identities=12% Similarity=0.270 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 48 RLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 48 ~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
.|+...-+...+.|.+.++.|+.+.+.|-+. +.+.|.+++..
T Consensus 228 ~i~~~N~~~i~~~l~~~~~~l~~~~~~l~~~---d~~~l~~~~~~ 269 (279)
T PRK07417 228 MMAEYNRAALLRSLASYRQSLDQLEELIEQE---NWSALEQKLEQ 269 (279)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHcC---CHHHHHHHHHH
Confidence 3444444445666777777777777777544 56778877754
No 114
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=20.29 E-value=2.2e+02 Score=17.33 Aligned_cols=47 Identities=17% Similarity=0.263 Sum_probs=28.6
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHh
Q 033676 32 NSMSEKLAADIDAAVKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAIL 90 (114)
Q Consensus 32 ~~~Se~t~~~iD~eV~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll 90 (114)
+..|+.....+-..+...+.+--+.|.++..-- ++.||+.+||...+
T Consensus 18 ~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~ha------------kRktlt~~DI~~Al 64 (65)
T smart00803 18 GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHS------------KRTTLTTSDIDSAL 64 (65)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh------------CCCeecHHHHHHHh
Confidence 356666666666665555555555555554433 55789998887544
No 115
>PRK06545 prephenate dehydrogenase; Validated
Probab=20.17 E-value=3.6e+02 Score=21.50 Aligned_cols=44 Identities=11% Similarity=0.206 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCHHHHHHHhhc
Q 033676 46 VKRLSDRAYEIALSQIRNNREAIDKIVEVLLEKETMSGDEFRAILSE 92 (114)
Q Consensus 46 V~~il~~~y~~a~~iL~~nr~~L~~la~~Lle~EtL~g~e~~~ll~~ 92 (114)
-+.|+...-..+.+.|.+.++.|+.+.+.|-.+ +.+++.+++..
T Consensus 228 w~di~~~N~~~~~~~l~~~~~~l~~~~~~l~~~---d~~~l~~~~~~ 271 (359)
T PRK06545 228 WRDILESNAEALLDALDEWIEDLDRARDALESG---DAEAIAELFDA 271 (359)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcC---CHHHHHHHHHH
Confidence 455666666777788888888888888888665 56778887754
No 116
>TIGR01791 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase.
Probab=20.14 E-value=2.3e+02 Score=17.57 Aligned_cols=52 Identities=13% Similarity=0.196 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHH-------------HHHHHHHHHHHHhcCCHHHHHHHhh
Q 033676 39 AADIDAAVKRLSDRAYEIALSQIRNNRE-------------AIDKIVEVLLEKETMSGDEFRAILS 91 (114)
Q Consensus 39 ~~~iD~eV~~il~~~y~~a~~iL~~nr~-------------~L~~la~~Lle~EtL~g~e~~~ll~ 91 (114)
-+.||.++-.++.....-+.++-.-... .++++.+..-+ .-++.+.++.++.
T Consensus 8 Id~iD~~i~~Ll~~R~~l~~~i~~~K~~~g~~i~d~~RE~~v~~~~~~~~~~-~~l~~~~i~~if~ 72 (83)
T TIGR01791 8 IEEIDKSILDLIEKRIKIARKIGEIKHNNGLPITDEEREERVIERLRNTARN-LGLDVLKLKEIFE 72 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHh-cCCCHHHHHHHHH
Confidence 4788999999999999988888554443 35566554433 5688888777764
No 117
>COG4029 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.06 E-value=2.3e+02 Score=20.25 Aligned_cols=16 Identities=50% Similarity=0.706 Sum_probs=13.7
Q ss_pred HHhcCCHHHHHHHhhc
Q 033676 77 EKETMSGDEFRAILSE 92 (114)
Q Consensus 77 e~EtL~g~e~~~ll~~ 92 (114)
++|.|.-++|+.|+..
T Consensus 123 ~k~ki~vde~rki~Ek 138 (142)
T COG4029 123 EKEKIPVDEFRKIAEK 138 (142)
T ss_pred hccCCCHHHHHHHHHH
Confidence 7899999999998754
No 118
>PRK02292 V-type ATP synthase subunit E; Provisional
Probab=20.03 E-value=3.4e+02 Score=19.40 Aligned_cols=31 Identities=19% Similarity=0.177 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 033676 41 DIDAAVKRLSDRAYEIALSQIRNNREAIDKI 71 (114)
Q Consensus 41 ~iD~eV~~il~~~y~~a~~iL~~nr~~L~~l 71 (114)
.-..++.+|+.++-..+..|+.+-+...+.+
T Consensus 13 ~a~~e~~~I~~ea~~~~~~i~~ea~~~a~~i 43 (188)
T PRK02292 13 EARARASEIRAEADEEAEEIIAEAEADAEEI 43 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455555555555555555544444444
Done!