Query 032890
Match_columns 131
No_of_seqs 104 out of 432
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 07:12:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032890.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032890hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00316 profilin; Provisional 100.0 2.2E-49 4.7E-54 278.6 16.1 127 1-131 1-150 (150)
2 smart00392 PROF Profilin. Bind 100.0 2.5E-47 5.5E-52 265.2 15.8 127 1-131 1-129 (129)
3 cd00148 PROF Profilin binds ac 100.0 4.6E-47 9.9E-52 263.3 16.0 125 2-131 1-127 (127)
4 KOG1755 Profilin [Cytoskeleton 100.0 1.1E-43 2.5E-48 242.8 14.2 127 1-131 1-128 (128)
5 PF00235 Profilin: Profilin; 100.0 3.6E-42 7.8E-47 236.2 12.1 121 2-126 1-121 (121)
6 COG2018 Uncharacterized distan 89.3 5.3 0.00012 27.4 9.1 95 19-123 18-116 (119)
7 PF03259 Robl_LC7: Roadblock/L 84.4 0.69 1.5E-05 28.9 1.7 59 19-78 14-72 (91)
8 PF08923 MAPKK1_Int: Mitogen-a 78.9 15 0.00033 25.0 6.8 108 3-128 3-114 (119)
9 PF13734 Inhibitor_I69: Spi pr 75.2 12 0.00026 24.6 5.3 81 37-128 3-91 (96)
10 PHA02610 uvsY.-2 hypothetical 65.1 10 0.00022 22.1 2.9 31 92-122 4-36 (53)
11 COG0223 Fmt Methionyl-tRNA for 59.1 53 0.0012 26.1 6.9 65 38-108 213-277 (307)
12 PRK00394 transcription factor; 52.1 38 0.00081 24.7 4.7 39 89-131 46-84 (179)
13 TIGR00460 fmt methionyl-tRNA f 50.8 1.1E+02 0.0024 24.0 7.5 37 38-78 212-248 (313)
14 COG3382 Solo B3/4 domain (OB-f 49.1 53 0.0012 25.1 5.2 37 93-129 179-215 (229)
15 PF10144 SMP_2: Bacterial viru 47.7 25 0.00053 26.4 3.2 26 10-38 80-105 (210)
16 PF10886 DUF2685: Protein of u 47.0 28 0.00061 20.5 2.7 32 92-123 4-37 (54)
17 PF12965 DUF3854: Domain of un 45.7 50 0.0011 22.7 4.3 35 97-131 67-103 (130)
18 cd04516 TBP_eukaryotes eukaryo 43.9 72 0.0016 23.1 5.1 37 91-131 49-85 (174)
19 PF08513 LisH: LisH; InterPro 43.4 18 0.0004 17.9 1.4 10 122-131 7-16 (27)
20 PHA02102 hypothetical protein 43.4 27 0.0006 21.3 2.4 16 21-36 55-70 (72)
21 COG3377 Uncharacterized conser 42.5 86 0.0019 20.5 4.7 33 62-94 4-37 (95)
22 PF02911 Formyl_trans_C: Formy 42.5 85 0.0018 19.7 8.2 37 38-78 10-46 (100)
23 PRK11246 hypothetical protein; 41.9 52 0.0011 24.9 4.2 32 10-46 80-111 (218)
24 PLN00062 TATA-box-binding prot 41.2 88 0.0019 22.8 5.2 38 90-131 48-85 (179)
25 cd04518 TBP_archaea archaeal T 41.0 77 0.0017 22.9 4.9 39 89-131 47-85 (174)
26 PRK06988 putative formyltransf 40.3 1.6E+02 0.0034 23.2 7.0 38 38-78 211-248 (312)
27 cd00652 TBP_TLF TATA box bindi 38.3 93 0.002 22.4 5.0 39 89-131 47-85 (174)
28 smart00667 LisH Lissencephaly 38.3 20 0.00043 17.6 1.1 12 120-131 8-19 (34)
29 COG2139 RPL21A Ribosomal prote 37.2 55 0.0012 21.7 3.2 24 87-110 57-80 (98)
30 PF11513 TA0956: Thermoplasma 36.3 1.2E+02 0.0026 20.0 4.7 38 91-131 66-104 (110)
31 PF02770 Acyl-CoA_dh_M: Acyl-C 36.1 31 0.00066 19.5 1.8 17 62-78 24-40 (52)
32 TIGR02764 spore_ybaN_pdaB poly 35.9 75 0.0016 22.6 4.2 29 102-131 154-182 (191)
33 PF05176 ATP-synt_10: ATP10 pr 35.7 43 0.00093 25.7 3.0 34 19-55 216-250 (252)
34 COG4725 IME4 Transcriptional a 35.2 55 0.0012 24.0 3.3 54 70-124 102-156 (198)
35 PF02789 Peptidase_M17_N: Cyto 35.0 93 0.002 20.2 4.3 34 97-130 52-86 (126)
36 cd01132 F1_ATPase_alpha F1 ATP 34.3 57 0.0012 25.5 3.5 33 99-131 128-161 (274)
37 COG1832 Predicted CoA-binding 34.2 62 0.0013 22.8 3.3 31 95-131 14-44 (140)
38 PRK06901 aspartate-semialdehyd 33.6 2.4E+02 0.0052 22.7 6.9 87 27-131 228-322 (322)
39 COG1157 FliI Flagellar biosynt 33.6 45 0.00097 27.9 2.9 34 98-131 218-253 (441)
40 PF09176 Mpt_N: Methylene-tetr 32.6 17 0.00038 23.2 0.3 31 41-71 20-53 (81)
41 cd04517 TLF TBP-like factors ( 32.3 1.2E+02 0.0025 22.0 4.7 38 90-131 48-85 (174)
42 PF08479 POTRA_2: POTRA domain 32.3 50 0.0011 20.0 2.4 21 111-131 32-52 (76)
43 cd00861 ProRS_anticodon_short 31.9 95 0.0021 19.0 3.8 19 113-131 14-32 (94)
44 PF04312 DUF460: Protein of un 31.7 1.3E+02 0.0028 21.2 4.6 39 12-52 35-73 (138)
45 PRK00005 fmt methionyl-tRNA fo 31.6 2.5E+02 0.0054 21.9 7.5 37 38-78 212-248 (309)
46 PHA02754 hypothetical protein; 31.6 87 0.0019 18.8 3.2 19 60-78 27-45 (67)
47 PRK13604 luxD acyl transferase 30.8 1.3E+02 0.0027 24.0 5.0 53 74-131 13-65 (307)
48 PF01509 TruB_N: TruB family p 30.7 81 0.0018 22.2 3.5 44 29-73 60-106 (149)
49 PF07244 Surf_Ag_VNR: Surface 29.9 64 0.0014 19.0 2.6 22 110-131 32-53 (78)
50 cd00862 ProRS_anticodon_zinc P 29.1 1.2E+02 0.0025 22.3 4.3 34 98-131 11-44 (202)
51 PF14584 DUF4446: Protein of u 28.9 1E+02 0.0023 21.8 3.9 29 24-53 116-150 (151)
52 cd01134 V_A-ATPase_A V/A-type 28.9 60 0.0013 26.5 2.9 32 100-131 222-254 (369)
53 PTZ00414 10 kDa heat shock pro 28.5 62 0.0013 21.4 2.5 18 61-78 75-92 (100)
54 cd00320 cpn10 Chaperonin 10 Kd 27.2 58 0.0013 21.0 2.1 18 61-78 70-87 (93)
55 PF07799 DUF1643: Protein of u 27.0 1E+02 0.0023 20.8 3.5 34 98-131 13-46 (136)
56 PRK05922 type III secretion sy 25.8 80 0.0017 26.4 3.2 34 98-131 213-247 (434)
57 PRK00364 groES co-chaperonin G 25.8 66 0.0014 20.9 2.2 18 61-78 71-88 (95)
58 PF00352 TBP: Transcription fa 25.5 1.8E+02 0.0038 18.1 5.9 37 90-130 50-86 (86)
59 PRK14533 groES co-chaperonin G 25.5 73 0.0016 20.6 2.3 18 61-78 66-83 (91)
60 PF07494 Reg_prop: Two compone 25.1 90 0.002 14.6 2.5 15 23-37 9-23 (24)
61 PF06918 DUF1280: Protein of u 24.8 1.5E+02 0.0032 22.4 4.2 30 99-128 191-220 (224)
62 PF00166 Cpn10: Chaperonin 10 23.8 73 0.0016 20.4 2.1 18 61-78 70-87 (93)
63 COG1660 Predicted P-loop-conta 23.8 1.7E+02 0.0038 23.0 4.5 35 95-130 238-272 (286)
64 PHA02119 hypothetical protein 23.7 51 0.0011 20.6 1.3 11 121-131 58-68 (87)
65 cd01133 F1-ATPase_beta F1 ATP 23.5 85 0.0019 24.5 2.8 33 99-131 129-163 (274)
66 TIGR01043 ATP_syn_A_arch ATP s 23.3 90 0.002 27.1 3.1 17 115-131 303-319 (578)
67 PF14553 YqbF: YqbF, hypotheti 23.1 77 0.0017 17.8 1.8 13 119-131 22-34 (43)
68 PF03665 UPF0172: Uncharacteri 22.3 83 0.0018 23.2 2.4 23 46-69 11-33 (196)
69 cd01136 ATPase_flagellum-secre 22.3 86 0.0019 25.1 2.7 32 100-131 127-159 (326)
70 KOG4107 MP1 adaptor interactin 22.2 56 0.0012 22.0 1.3 97 16-128 16-117 (125)
71 COG4831 Roadblock/LC7 domain [ 22.0 2.5E+02 0.0054 18.6 7.0 29 7-39 5-33 (109)
72 TIGR03496 FliI_clade1 flagella 21.9 92 0.002 25.7 2.8 18 114-131 210-227 (411)
73 PRK06936 type III secretion sy 21.5 94 0.002 26.0 2.8 18 114-131 235-252 (439)
74 PRK04192 V-type ATP synthase s 21.4 1E+02 0.0022 26.9 3.0 33 99-131 290-324 (586)
75 PRK02821 hypothetical protein; 21.3 2E+02 0.0043 18.0 3.7 44 47-90 6-52 (77)
76 PF05952 ComX: Bacillus compet 21.2 1.2E+02 0.0025 18.1 2.4 18 41-58 28-45 (57)
77 COG3726 AhpA Uncharacterized m 21.2 45 0.00098 24.9 0.8 30 6-39 77-106 (214)
78 PRK02983 lysS lysyl-tRNA synth 21.1 3.8E+02 0.0082 25.3 6.8 58 72-131 256-313 (1094)
79 PRK08972 fliI flagellum-specif 20.7 1E+02 0.0022 25.9 2.8 18 114-131 235-252 (444)
80 PRK12359 flavodoxin FldB; Prov 20.5 1.8E+02 0.004 20.8 3.9 35 96-130 78-112 (172)
81 TIGR01664 DNA-3'-Pase DNA 3'-p 20.3 63 0.0014 22.8 1.4 18 20-37 12-29 (166)
82 TIGR03497 FliI_clade2 flagella 20.2 1.1E+02 0.0024 25.2 3.0 33 99-131 194-227 (413)
83 TIGR03498 FliI_clade3 flagella 20.1 1.1E+02 0.0024 25.4 2.9 32 100-131 198-230 (418)
No 1
>PTZ00316 profilin; Provisional
Probab=100.00 E-value=2.2e-49 Score=278.58 Aligned_cols=127 Identities=37% Similarity=0.644 Sum_probs=121.5
Q ss_pred CChHHHhhccccccccccccceeEEEcC-CCCeEEecCCCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeCC
Q 032890 1 MSWQTYVDDHLMCDIDGHHLTSAAIVGH-DGSVWAQSSNFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGEP 79 (131)
Q Consensus 1 MSW~~yv~~~L~~~~~g~~~~~aaI~g~-dG~~wA~s~~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d~ 79 (131)
||||+|||++|++ +| ++++|||+|+ ||++||+|++| +++|+|++.|+++|+||+.+..+||+++|+||+++|.++
T Consensus 1 MSWQaYVD~~L~g--sg-~v~kAAIiG~~DGsvWA~S~gF-~lspeE~~~I~~~F~d~~~l~~~Gi~l~G~KY~~lr~~~ 76 (150)
T PTZ00316 1 MSWQAYVDDSLIG--SG-NMHSAAIVGLADGSYWAYGGSY-IPQPEEVAHILKCLGNFSLVQSSGVTIYGVKFFGLQSGT 76 (150)
T ss_pred CCHHHHHHhhhhc--cC-CcceEEEEecCCCCEeecCCCC-ccCHHHHHHHHHHhcCCccccCCCEEEcceEEEEEEecc
Confidence 9999999999999 99 9999999998 99999999999 999999999999999999999999999999999999732
Q ss_pred ---CceEEEEcCCCcEEEEecCcEEEEEEeCC-------------------CCCcchHHHHHHHHHHHHHhCCC
Q 032890 80 ---GAVIRGKKGSGGVTVKKTGQALIFGIYDE-------------------PLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 80 ---~~~i~~kk~~~G~~i~kt~~~ivI~~~~~-------------------~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
++++|+||+++|+|++||+|++|||+|++ +++|++|+.+||+|||||+++||
T Consensus 77 d~d~~~i~gKKg~~G~~i~kT~qaiiI~~y~~~~~~~~~~~~~~~~~~~~~~~~pg~~~~~Ve~LadYL~~~gy 150 (150)
T PTZ00316 77 EGDMKYIFFKKGAAGGCIYTSKQTAIIAVYGNPGDTSSLQQDLEKNEAHAVAVNPADCNTTVKRIAEYLISLDY 150 (150)
T ss_pred CCCcceEEEecCCCeEEEEEcCCEEEEEEeCCcccccccccccccccccccccCHHHHHHHHHHHHHHHHHcCC
Confidence 47899999999999999999999999999 47999999999999999999998
No 2
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=100.00 E-value=2.5e-47 Score=265.20 Aligned_cols=127 Identities=53% Similarity=0.868 Sum_probs=122.9
Q ss_pred CChHHHhhccccccccccccceeEEEcCCCCeEEecCC--CCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeC
Q 032890 1 MSWQTYVDDHLMCDIDGHHLTSAAIVGHDGSVWAQSSN--FPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 1 MSW~~yv~~~L~~~~~g~~~~~aaI~g~dG~~wA~s~~--f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d 78 (131)
||||+|||++|++ +| ++++|||++.||++||++++ |..++|+|++.|++.|+||+.++.+||+|+|+||+++|.|
T Consensus 1 MsWq~yvd~~l~~--~g-~~~~AaI~g~dGsvWA~s~g~~f~~~~~~E~~~i~~~f~~~~~~~~~Gi~l~G~Ky~~~~~d 77 (129)
T smart00392 1 MSWQAYVDNLLVG--SG-CVDAAAIGGKDGSVWAASAGGNFQKITPEEIAAIAALFNSLAAVFSNGLTLGGQKYMVIRAD 77 (129)
T ss_pred CChHHHHHHHhhc--cC-CCcEEEEEeCCCCeeeccCCCCCCcCCHHHHHHHHHHccCcchhccCCeEECCeEEEEEEec
Confidence 9999999988999 88 99999999999999999999 7557999999999999999888899999999999999999
Q ss_pred CCceEEEEcCCCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 79 PGAVIRGKKGSGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 79 ~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
++.+++||++.|++++||+++||||+|+++++|++|+++|++|||||+++||
T Consensus 78 -~~~i~~kk~~~Gv~i~kT~~aivI~~y~e~~~~g~~~~~v~~ladYL~~~Gy 129 (129)
T smart00392 78 -DRSIMGKKGAGGVVIVKTKQALIIGMYKEGVQPGQANKTVEKLADYLRSSGY 129 (129)
T ss_pred -CcEEEeecCCceEEEEECCCEEEEEECCCCCChHHHHHHHHHHHHHHHHcCC
Confidence 8999999999999999999999999999999999999999999999999998
No 3
>cd00148 PROF Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway.
Probab=100.00 E-value=4.6e-47 Score=263.33 Aligned_cols=125 Identities=54% Similarity=0.986 Sum_probs=122.2
Q ss_pred ChHHHhhccccccccccccceeEEEcCC-CCeEEecCC-CCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeCC
Q 032890 2 SWQTYVDDHLMCDIDGHHLTSAAIVGHD-GSVWAQSSN-FPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGEP 79 (131)
Q Consensus 2 SW~~yv~~~L~~~~~g~~~~~aaI~g~d-G~~wA~s~~-f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d~ 79 (131)
|||+|||++|++ +| +|++|||+|+| |++||++++ | +++|+|+++|+++|+||+.++.+||+|+|+||+++|.|
T Consensus 1 sWq~yvd~~L~~--~g-~~~~aAI~g~d~g~vwA~s~~~f-~~t~~E~~~i~~~f~d~~~~~~~Gi~l~G~KY~~l~~d- 75 (127)
T cd00148 1 SWQAYVDDNLLG--TG-KVDSAAIVGHDDGSVWAASAGGF-NLTPEEVGTLVAGFKDPDGVFSTGLTLGGQKYMVIRAD- 75 (127)
T ss_pred ChHHHHHHHHhh--cC-CcCEEEEEecCCCCeEEecCCCC-ccCHHHHHHHHHHccCccccccCCEEECCeEEEEEecC-
Confidence 899999999999 98 99999999997 999999999 9 99999999999999999888999999999999999999
Q ss_pred CceEEEEcCCCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 80 GAVIRGKKGSGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 80 ~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
++++++|++++|++++||+++||||+|+++++|++|+++|++|||||+++||
T Consensus 76 ~~~i~~kk~~~Gi~i~kT~~~ivi~~y~e~~~~g~~~~~v~~ladYL~~~gy 127 (127)
T cd00148 76 DRSIYGKKGAGGVVIVKTKQALVIGMYEEGVQPGQANKVVEKLADYLRSQGY 127 (127)
T ss_pred ccEEEeeeCCCeEEEEECCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 8999999999999999999999999999999999999999999999999998
No 4
>KOG1755 consensus Profilin [Cytoskeleton]
Probab=100.00 E-value=1.1e-43 Score=242.81 Aligned_cols=127 Identities=65% Similarity=1.133 Sum_probs=123.4
Q ss_pred CChHHHhhccccccccccccceeEEEcCCC-CeEEecCCCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeCC
Q 032890 1 MSWQTYVDDHLMCDIDGHHLTSAAIVGHDG-SVWAQSSNFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGEP 79 (131)
Q Consensus 1 MSW~~yv~~~L~~~~~g~~~~~aaI~g~dG-~~wA~s~~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d~ 79 (131)
||||+|||++|++ ++ +|++|||++.|| ++||+|++| +++|+|+..++..|+|++.+..+|++|+|+||+++|.|+
T Consensus 1 ~~Wq~Yvd~~l~~--~~-~v~~AAIvg~~~~SVWA~S~~f-~~~~~e~~~~v~~F~d~~~~~~~Gl~L~Gqkylv~~ge~ 76 (128)
T KOG1755|consen 1 MSWQAYVDDHLLG--TG-HVTRAAIVGYDGGSVWAASAGF-NVKPSEIPAIVAGFKDPGGLAGTGLTLGGQKYLVVRGEE 76 (128)
T ss_pred CCHHHHHHHhhcc--cc-ccceeeEEecCCCeeEEecCCC-cccHHHHHHHHhcccCcccccccceeecccEEEEEeccc
Confidence 8999999999999 88 999999999955 999999999 999999999999999999999999999999999999997
Q ss_pred CceEEEEcCCCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 80 GAVIRGKKGSGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 80 ~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
+..+++|++.+||+++||.+++|+++|+++++|++|+++||.|||||+++||
T Consensus 77 ~~~~~gk~~~~gv~i~kT~~~li~~~y~e~v~~g~~~k~ve~LadYL~~~gy 128 (128)
T KOG1755|consen 77 GRVIRGKEGTGGVTIKKTGQALIFSIYKEGVQPGQCNKVVESLADYLRESGY 128 (128)
T ss_pred ceEEecccCCCcEEEEEcceEEEEEEcCCCCCHHHHHHHHHHHHHHHHhcCC
Confidence 7889999999999999999999999999999999999999999999999998
No 5
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=100.00 E-value=3.6e-42 Score=236.21 Aligned_cols=121 Identities=50% Similarity=0.986 Sum_probs=116.8
Q ss_pred ChHHHhhccccccccccccceeEEEcCCCCeEEecCCCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeCCCc
Q 032890 2 SWQTYVDDHLMCDIDGHHLTSAAIVGHDGSVWAQSSNFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGEPGA 81 (131)
Q Consensus 2 SW~~yv~~~L~~~~~g~~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d~~~ 81 (131)
|||+||+++|++ ++ ++++|||+|.||++||++++|++++|+|++.|+++|++|+.++.+||+|+|+||+++|.| ++
T Consensus 1 sW~~~i~~~L~~--~~-~~~~aaI~~~dG~vwA~s~~f~~~~~~E~~~i~~~f~~~~~~~~~gi~l~G~kY~~~~~d-~~ 76 (121)
T PF00235_consen 1 SWQDYIDEQLIG--TG-NITKAAIIGSDGSVWASSPGFSNISPEEAKAIIKAFNNPSKFPSNGITLGGKKYIVLRAD-DN 76 (121)
T ss_dssp THHHHHHTHHHT--TS-SESEEEEEETTSSEEEEETTGGGCSHHHHHHHHHHHHSSSHHHHH-EEETTEEEEEEEEE-TT
T ss_pred ChhHHHHHHhcc--cC-cEeEEEEEcCCCCEEEecCCCCCCCHHHHHHHHHHhcCchhcccCCeEEcCcEeEEEecC-Cc
Confidence 899999999999 88 899999999999999999999899999999999999999888899999999999999999 88
Q ss_pred eEEEEcCCCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHH
Q 032890 82 VIRGKKGSGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYL 126 (131)
Q Consensus 82 ~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL 126 (131)
++++|++++|++++||++++|||+|+++++|++|+++|++|||||
T Consensus 77 ~i~~k~~~~G~~i~kt~~~ivIg~y~~~~~~~~~~~~v~~lA~yL 121 (121)
T PF00235_consen 77 SIYGKKGKGGIIIVKTKQAIVIGMYDESIQPGNCNKAVEKLADYL 121 (121)
T ss_dssp EEEEEETTEEEEEEECSSEEEEEEEETTSTHHHHHHHHHHHHHHH
T ss_pred eEEeeCCCCcEEEEECCCEEEEEEeCCCCCHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999998
No 6
>COG2018 Uncharacterized distant relative of homeotic protein bithoraxoid [General function prediction only]
Probab=89.34 E-value=5.3 Score=27.40 Aligned_cols=95 Identities=21% Similarity=0.235 Sum_probs=54.7
Q ss_pred ccceeEEEcCCCCeEEecCCCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeCCCceEEEEcCCCcEEEEecC
Q 032890 19 HLTSAAIVGHDGSVWAQSSNFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGEPGAVIRGKKGSGGVTVKKTG 98 (131)
Q Consensus 19 ~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d~~~~i~~kk~~~G~~i~kt~ 98 (131)
.+..++|++.||-+-++.-.+ +...+-+.++....-........-+-.+...++.++.+++..+.-.-|..
T Consensus 18 gv~ga~Ivs~DGL~ia~~~p~-~~d~e~vaA~~a~~~g~~er~~~~l~~g~leqi~I~g~~g~i~l~~~g~~-------- 88 (119)
T COG2018 18 GVRGALVVSKDGLPIAAELPG-NVDAEIVAAMAATALGLAERAADELGGGELEQIMIEGKKGKILLYDAGDD-------- 88 (119)
T ss_pred CceEEEEEccCCceEeecCCC-cccHHHHHHHHHHHHHHhHHHHHHhCCCCceEEEEeccccEEEEEEcCCc--------
Confidence 799999999999999987566 66655556655543222222344556667777777777333322222333
Q ss_pred cEEEEEEeCCCCCcch----HHHHHHHHH
Q 032890 99 QALIFGIYDEPLTPGQ----CNMIVERLG 123 (131)
Q Consensus 99 ~~ivI~~~~~~~~~~~----~~~~v~~lA 123 (131)
++++..-+...+-|. ...++++++
T Consensus 89 -~il~~~a~~~~nLGli~~e~k~aa~~i~ 116 (119)
T COG2018 89 -AILVVLADEGTNLGLIRMEMKRAAEKIA 116 (119)
T ss_pred -eEEEEEcCCCCcchhhhhHHHHHHHHHh
Confidence 444444455555444 444444444
No 7
>PF03259 Robl_LC7: Roadblock/LC7 domain; InterPro: IPR004942 This family includes proteins that are about 100 amino acids long and have been shown to be related []. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions []. This family also includes Golgi-associated MP1 adapter protein (Q9Y2Q5 from SWISSPROT) and MglB from Myxococcus xanthus (Q50883 from SWISSPROT), a protein involved in gliding motility []. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.; PDB: 2B95_B 1Z09_A 2E8J_B 2HZ5_B 3KYE_A 2ZL1_B 1SKO_B 3CPT_B 1VEU_B 1VET_B ....
Probab=84.36 E-value=0.69 Score=28.94 Aligned_cols=59 Identities=24% Similarity=0.261 Sum_probs=33.3
Q ss_pred ccceeEEEcCCCCeEEecCCCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeC
Q 032890 19 HLTSAAIVGHDGSVWAQSSNFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 19 ~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d 78 (131)
.+..+.|++.||-+-++ .++....++.+..+...+-.-......-+..+.-+++.++.+
T Consensus 14 gv~~~~l~~~dG~~i~~-~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~ 72 (91)
T PF03259_consen 14 GVRGAVLVDKDGLVIAS-SGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETE 72 (91)
T ss_dssp TEEEEEEEETTSEEEEE-TSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEES
T ss_pred CeeEEEEEcCCCCEEEE-ecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEEC
Confidence 79999999999999887 333233344444333332110000112222567777888887
No 8
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=78.88 E-value=15 Score=25.01 Aligned_cols=108 Identities=17% Similarity=0.207 Sum_probs=63.6
Q ss_pred hHHHhhccccccccccccceeEEEcCCCCeEEec--CCCC--CCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeC
Q 032890 3 WQTYVDDHLMCDIDGHHLTSAAIVGHDGSVWAQS--SNFP--QFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 3 W~~yv~~~L~~~~~g~~~~~aaI~g~dG~~wA~s--~~f~--~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d 78 (131)
-+.|+. .|+. .-+.+....|.|.||-+.+.. +.-+ .+.|.-+.++.-+.+ +.+-+.+|+.|+++...|
T Consensus 3 l~~~L~-~ll~--~v~Gl~~I~itDrDGvpi~~v~~~~~~~~~~~~~~~~tf~~a~~-----Q~~KL~lG~nk~ii~~Y~ 74 (119)
T PF08923_consen 3 LKRFLQ-KLLS--RVDGLQAIVITDRDGVPIAKVSSDSAPESAMRPSLLSTFAMAID-----QASKLGLGKNKSIIAYYD 74 (119)
T ss_dssp HHHHHH-HHGG--GSTTEEEEEEEETTS-EEEEEE-TTS-GGGGSHHHHCCHHHHHH-----HHTTSSS-SEEEEEEEES
T ss_pred HHHHHH-HHHh--ccCCeEEEEEECCCCcEEEEecCCCCcchhhhhHHHHHHHHHhh-----cccccCCCCceEEEEEeC
Confidence 366776 5665 323688888889999766652 2211 233443333333322 355678999999999999
Q ss_pred CCceEEEEcCCCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHh
Q 032890 79 PGAVIRGKKGSGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLID 128 (131)
Q Consensus 79 ~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~ 128 (131)
+..+.-.. ....+|..+.....+-|....--++|+++|.+
T Consensus 75 -~~qvv~~~---------~~pl~it~ias~~aN~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 75 -SYQVVQFN---------KLPLYITFIASSNANTGLILSLEEELAPILNE 114 (119)
T ss_dssp -SEEEEEEE---------ETTEEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred -CEEEEEEe---------CCCeEEEEEecCCCCHHHHHHhHHHHHHHHHH
Confidence 54433121 23466666666667777777777777776654
No 9
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=75.18 E-value=12 Score=24.62 Aligned_cols=81 Identities=20% Similarity=0.229 Sum_probs=38.0
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEe--CC-C--ceEEEEcCCCcEEEEecC--cEEEEEEeCCC
Q 032890 37 SNFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQG--EP-G--AVIRGKKGSGGVTVKKTG--QALIFGIYDEP 109 (131)
Q Consensus 37 ~~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~--d~-~--~~i~~kk~~~G~~i~kt~--~~ivI~~~~~~ 109 (131)
.+| ..+++|+..|+..|-....- ....+-++. .+ + -.|+-. +++|++|+--. ..=|+|+-+++
T Consensus 3 ~~f-~rt~~eA~~IA~~F~~~~~~--------~k~~~~~~~~s~~~~~~~YI~N~-~~~GFVIVSgDdr~~~ILaYS~~G 72 (96)
T PF13734_consen 3 ENF-QRTEKEALQIAKTFVQKNGQ--------SKTKLRTRSTSTPSDTPYYIFND-NNKGFVIVSGDDRMGPILAYSDEG 72 (96)
T ss_dssp ----B--HHHHHHHHHHHHH----------------EE----TTT-SSSEEEEEE-TTS-EEEEESBTTS-SEEEEESSS
T ss_pred ccc-ccCHHHHHHHHHHHHHhccc--------ccceeEecccCCCCCCcEEEEEc-CCCEEEEEECCCCccceeEEcCCC
Confidence 478 88999999999988432111 111122221 11 1 235555 67788888764 46688888887
Q ss_pred C-CcchHHHHHHHHHHHHHh
Q 032890 110 L-TPGQCNMIVERLGDYLID 128 (131)
Q Consensus 110 ~-~~~~~~~~v~~lA~yL~~ 128 (131)
. ...+ .+.-.-|+.|+.+
T Consensus 73 ~fd~~~-~n~~~~l~~y~~~ 91 (96)
T PF13734_consen 73 SFDTNN-ANVRPGLQAYLEQ 91 (96)
T ss_dssp ----T--HHHHHHHHHHHHH
T ss_pred CcCccc-hhHHHHHHHHHHH
Confidence 5 3333 2344556666554
No 10
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=65.10 E-value=10 Score=22.14 Aligned_cols=31 Identities=35% Similarity=0.545 Sum_probs=23.0
Q ss_pred EEEEecC--cEEEEEEeCCCCCcchHHHHHHHH
Q 032890 92 VTVKKTG--QALIFGIYDEPLTPGQCNMIVERL 122 (131)
Q Consensus 92 ~~i~kt~--~~ivI~~~~~~~~~~~~~~~v~~l 122 (131)
++++|++ +++.|-.-.++.+||.|...++.+
T Consensus 4 CvvCK~Pi~~al~v~T~~Gpvh~g~C~~y~~e~ 36 (53)
T PHA02610 4 CVVCKQPIEKALVVETEKGPVHPGPCYNYVEEL 36 (53)
T ss_pred eeeeCCchhhceEEecCCCCCCChhHHHHHHhc
Confidence 3455554 577777777788999999888775
No 11
>COG0223 Fmt Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]
Probab=59.11 E-value=53 Score=26.11 Aligned_cols=65 Identities=15% Similarity=0.246 Sum_probs=43.8
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeCCCceEEEEcCCCcEEEEecCcEEEEEEeCC
Q 032890 38 NFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGEPGAVIRGKKGSGGVTVKKTGQALIFGIYDE 108 (131)
Q Consensus 38 ~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~ 108 (131)
+| +-+..++...+++|. | .+.--..++|+++.+.+++-.+.-.. ++-|-++...++.++|+..++
T Consensus 213 dw-~~~a~~i~n~IRa~~-P--~Pga~~~~~~~~iki~~a~~~~~~~~--~~pG~i~~~~~~~l~Va~~~g 277 (307)
T COG0223 213 DW-SKPAAQILNKIRAFN-P--WPGAWTELGGKRIKIWEARVLEGASN--GKPGEILAADKKGLLVACGDG 277 (307)
T ss_pred CC-ccCHHHHHHHHhccC-C--CCceEEEECCeEEEEEEEEEcccccc--CCCcceEEecCCcEEEEeCCc
Confidence 36 556778888888887 3 45667889999999998862111110 556767777777777777433
No 12
>PRK00394 transcription factor; Reviewed
Probab=52.08 E-value=38 Score=24.69 Aligned_cols=39 Identities=13% Similarity=0.150 Sum_probs=30.2
Q ss_pred CCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 89 SGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 89 ~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
+.-+.|..+.+.++.|.. ...++..+++++++.|++.||
T Consensus 46 k~t~lIf~sGKiv~tGa~----S~~~a~~a~~~~~~~l~~~g~ 84 (179)
T PRK00394 46 KIAALIFRSGKVVCTGAK----SVEDLHEAVKIIIKKLKELGI 84 (179)
T ss_pred ceEEEEEcCCcEEEEccC----CHHHHHHHHHHHHHHHHHcCC
Confidence 445677777777775544 446899999999999999886
No 13
>TIGR00460 fmt methionyl-tRNA formyltransferase. The top-scoring characterized proteins other than methionyl-tRNA formyltransferase (fmt) itself are formyltetrahydrofolate dehydrogenases. The mitochondrial methionyl-tRNA formyltransferases are so divergent that, in a multiple alignment of bacterial fmt, mitochondrial fmt, and formyltetrahydrofolate dehydrogenases, the mitochondrial fmt appears the most different. However, because both bacterial and mitochondrial fmt are included in the seed alignment, all credible fmt sequences score higher than any non-fmt sequence. This enzyme modifies Met on initiator tRNA to f-Met.
Probab=50.82 E-value=1.1e+02 Score=24.03 Aligned_cols=37 Identities=14% Similarity=0.333 Sum_probs=27.6
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeC
Q 032890 38 NFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d 78 (131)
+| +-+.+++..++++|. | ...--..++|+++.+.++.
T Consensus 212 dw-~~~a~~I~~~iRA~~-p--~pga~~~~~g~~i~i~~a~ 248 (313)
T TIGR00460 212 DW-NQSAEELLNKIRALN-P--WPTAWLTFEGKNIKIHKAK 248 (313)
T ss_pred Cc-cCCHHHHHHHHhccC-C--CCceEEEECCEEEEEEEEE
Confidence 36 567889999999996 3 2333467899999998754
No 14
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=49.13 E-value=53 Score=25.07 Aligned_cols=37 Identities=14% Similarity=0.068 Sum_probs=32.5
Q ss_pred EEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhC
Q 032890 93 TVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQ 129 (131)
Q Consensus 93 ~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~ 129 (131)
+=..|+++++|+..-+++......++.+.+++.|.+.
T Consensus 179 vt~~Tk~~l~I~e~vp~~~~~~l~~a~~~l~~~l~~~ 215 (229)
T COG3382 179 VTESTKNVLLIAEGVPGVEVEDLVEALDSLADLLEKL 215 (229)
T ss_pred hhhccceEEEEEecCCCccHHHHHHHHHHHHHHHHHh
Confidence 3356889999999999999999999999999999863
No 15
>PF10144 SMP_2: Bacterial virulence factor haemolysin; InterPro: IPR019305 This entry represents a group of bacterial proteins that are membrane proteins that effect the expression of haemolysin under anaerobic conditions [].
Probab=47.73 E-value=25 Score=26.40 Aligned_cols=26 Identities=35% Similarity=0.404 Sum_probs=21.9
Q ss_pred cccccccccccceeEEEcCCCCeEEecCC
Q 032890 10 HLMCDIDGHHLTSAAIVGHDGSVWAQSSN 38 (131)
Q Consensus 10 ~L~~~~~g~~~~~aaI~g~dG~~wA~s~~ 38 (131)
+|.. +- .|-+|+|++.+|...|.|.+
T Consensus 80 ~L~~--d~-~VldAsIYd~~G~lLA~S~~ 105 (210)
T PF10144_consen 80 QLAK--DP-FVLDASIYDADGVLLAQSGE 105 (210)
T ss_pred HHhc--CC-eEeEEEEECCCCCEEEEcCC
Confidence 5665 43 99999999999999999865
No 16
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=46.99 E-value=28 Score=20.51 Aligned_cols=32 Identities=31% Similarity=0.499 Sum_probs=22.5
Q ss_pred EEEEecC--cEEEEEEeCCCCCcchHHHHHHHHH
Q 032890 92 VTVKKTG--QALIFGIYDEPLTPGQCNMIVERLG 123 (131)
Q Consensus 92 ~~i~kt~--~~ivI~~~~~~~~~~~~~~~v~~lA 123 (131)
++++|++ .+.+|-.-.+.++||.|...++.+.
T Consensus 4 CvVCKqpi~~a~~v~T~~G~VH~g~C~~y~~e~~ 37 (54)
T PF10886_consen 4 CVVCKQPIDDALVVETESGPVHPGVCAQYLEELP 37 (54)
T ss_pred eeeeCCccCcceEEEcCCCccCcHHHHHHHHhcc
Confidence 3455654 5666666666789999998888763
No 17
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=45.66 E-value=50 Score=22.70 Aligned_cols=35 Identities=17% Similarity=0.340 Sum_probs=26.9
Q ss_pred cCcEEEEEEeCCCCC--cchHHHHHHHHHHHHHhCCC
Q 032890 97 TGQALIFGIYDEPLT--PGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 97 t~~~ivI~~~~~~~~--~~~~~~~v~~lA~yL~~~gy 131 (131)
..+-|+|++-.+... -.+.+.++.++++.|.+.|.
T Consensus 67 ~gr~v~iaFD~D~~~~Tn~~V~~a~~~l~~~L~~~G~ 103 (130)
T PF12965_consen 67 PGREVYIAFDADTKPKTNKNVRRAIKRLGKLLKEAGC 103 (130)
T ss_pred CCceEEEEecCCCccchhHHHHHHHHHHHHHHHHCCC
Confidence 356777777776443 36799999999999999874
No 18
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=43.88 E-value=72 Score=23.12 Aligned_cols=37 Identities=8% Similarity=0.224 Sum_probs=27.8
Q ss_pred cEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 91 GVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 91 G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
-+.|..+.+.++-|.. ...++..++.++++.|++.||
T Consensus 49 t~lIF~SGKiviTGak----s~e~a~~a~~~i~~~L~~~g~ 85 (174)
T cd04516 49 TALIFSSGKMVCTGAK----SEDDSKLAARKYARIIQKLGF 85 (174)
T ss_pred EEEEECCCeEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 3566667776665433 457899999999999999886
No 19
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=43.44 E-value=18 Score=17.85 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=7.9
Q ss_pred HHHHHHhCCC
Q 032890 122 LGDYLIDQGL 131 (131)
Q Consensus 122 lA~yL~~~gy 131 (131)
+.+||.++||
T Consensus 7 I~~YL~~~Gy 16 (27)
T PF08513_consen 7 IYDYLVENGY 16 (27)
T ss_dssp HHHHHHHCT-
T ss_pred HHHHHHHCCc
Confidence 5799999997
No 20
>PHA02102 hypothetical protein
Probab=43.39 E-value=27 Score=21.31 Aligned_cols=16 Identities=44% Similarity=0.700 Sum_probs=11.9
Q ss_pred ceeEEEcCCCCeEEec
Q 032890 21 TSAAIVGHDGSVWAQS 36 (131)
Q Consensus 21 ~~aaI~g~dG~~wA~s 36 (131)
..+-.+..||++|-.|
T Consensus 55 ~eaF~~~SDGsvWm~S 70 (72)
T PHA02102 55 GEAFVARSDGSVWMPS 70 (72)
T ss_pred cceeeeccCCcEeccC
Confidence 5566666799999765
No 21
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=42.53 E-value=86 Score=20.52 Aligned_cols=33 Identities=15% Similarity=0.311 Sum_probs=22.0
Q ss_pred ccceEEcCeEEEEEEeCCCce-EEEEcCCCcEEE
Q 032890 62 PTGLHLGGTKYMVIQGEPGAV-IRGKKGSGGVTV 94 (131)
Q Consensus 62 ~~gi~~~g~KY~v~r~d~~~~-i~~kk~~~G~~i 94 (131)
-+-|.++|.+|..++.|=.+. +..-++..|.++
T Consensus 4 i~~i~i~gk~~l~~~~~L~napll~~~~ekgy~m 37 (95)
T COG3377 4 IEPIDIEGKKFLGLKVDLPNAPLLALKGEKGYAM 37 (95)
T ss_pred eeeEeeCCeEEEEEEecCCCCcEEEEEccccEEE
Confidence 356899999999999984432 444555555443
No 22
>PF02911 Formyl_trans_C: Formyl transferase, C-terminal domain; InterPro: IPR005793 Methionyl-tRNA formyltransferase (2.1.2.9 from EC) transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. This family also includes formyltetrahydrofolate dehydrogenases, which produce formate from formyl-tetrahydrofolate. These enzymes contain an N-terminal domain in common with other formyl transferase enzymes (IPR002376 from INTERPRO). The C-terminal domain has an open beta-barrel fold [].; GO: 0016742 hydroxymethyl-, formyl- and related transferase activity, 0009058 biosynthetic process; PDB: 3RFO_D 1Z7E_C 2BLN_A 1YRW_A 1FMT_A 2FMT_B 3Q0I_A 3R8X_A 3TQQ_A 2BW0_A ....
Probab=42.51 E-value=85 Score=19.66 Aligned_cols=37 Identities=16% Similarity=0.362 Sum_probs=28.0
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeC
Q 032890 38 NFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d 78 (131)
+| +-+.+|+..++++|. |- ..--..++|++..+.+++
T Consensus 10 dw-~~~A~~I~~~vRal~-p~--pga~~~~~~~~i~i~~~~ 46 (100)
T PF02911_consen 10 DW-NQSAEEIYNLVRALN-PY--PGAFTTFNGKRIKILKAE 46 (100)
T ss_dssp -T-TSBHHHHHHHHHHTT-TT--T-EEEEETTEEEEEEEEE
T ss_pred CC-CCCHHHHHHHHhCCC-CC--CCEEEeeCCeEEEEEeee
Confidence 47 778999999999997 42 234456799999999874
No 23
>PRK11246 hypothetical protein; Provisional
Probab=41.93 E-value=52 Score=24.92 Aligned_cols=32 Identities=16% Similarity=0.292 Sum_probs=25.0
Q ss_pred cccccccccccceeEEEcCCCCeEEecCCCCCCCHHH
Q 032890 10 HLMCDIDGHHLTSAAIVGHDGSVWAQSSNFPQFKPEE 46 (131)
Q Consensus 10 ~L~~~~~g~~~~~aaI~g~dG~~wA~s~~f~~i~~~E 46 (131)
+|.. +. .|-+|.|++.||...|++.+. ++-.|
T Consensus 80 ~La~--d~-~VlDAsIY~~~G~llA~S~~~--~~~re 111 (218)
T PRK11246 80 QLTD--ES-RILDASVYDEQGDLIARSGES--VNVRD 111 (218)
T ss_pred HHhc--CC-ceeeEEEECCCCCEEEecCCC--ccHHH
Confidence 5665 54 899999999999999998765 44434
No 24
>PLN00062 TATA-box-binding protein; Provisional
Probab=41.16 E-value=88 Score=22.79 Aligned_cols=38 Identities=8% Similarity=0.191 Sum_probs=28.4
Q ss_pred CcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 90 GGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 90 ~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
.-+.|..+.+.++-|.- ...++..++.++++.|++.||
T Consensus 48 ~t~lIF~SGKiviTGak----s~e~a~~a~~~~~~~L~~lg~ 85 (179)
T PLN00062 48 TTALIFASGKMVCTGAK----SEHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred EEEEEECCCeEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 34666677777665432 457899999999999999886
No 25
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=41.02 E-value=77 Score=22.94 Aligned_cols=39 Identities=15% Similarity=0.186 Sum_probs=29.1
Q ss_pred CCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 89 SGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 89 ~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
+.-+.|..+.+.++.|. ....++..+++++++.|++.||
T Consensus 47 k~t~lIF~SGKiv~tGa----ks~~~a~~a~~~~~~~L~~~g~ 85 (174)
T cd04518 47 KIAALIFRSGKMVCTGA----KSVEDLHRAVKEIIKKLKDYGI 85 (174)
T ss_pred cEEEEEECCCeEEEEcc----CCHHHHHHHHHHHHHHHHhcCC
Confidence 34466667777666543 3567899999999999999885
No 26
>PRK06988 putative formyltransferase; Provisional
Probab=40.34 E-value=1.6e+02 Score=23.16 Aligned_cols=38 Identities=16% Similarity=0.412 Sum_probs=28.2
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeC
Q 032890 38 NFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d 78 (131)
+| +-+..|+..++++|.+| ...--..++|+|+.+.+++
T Consensus 211 dw-~~~a~~I~~~iRA~~~p--~pga~~~~~g~~v~i~~a~ 248 (312)
T PRK06988 211 DW-SKPAAQVYNLIRAVAPP--YPGAFTDLGGTRFVVARAR 248 (312)
T ss_pred CC-CCCHHHHHHHhccCCCC--CCeeEEEECCEEEEEEEEE
Confidence 36 55788999999999644 2233357899999999865
No 27
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=38.31 E-value=93 Score=22.44 Aligned_cols=39 Identities=13% Similarity=0.254 Sum_probs=29.3
Q ss_pred CCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 89 SGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 89 ~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
+.-+.|..+.+.++.|.. ...++..+++++++.|++.||
T Consensus 47 ~~t~lIf~sGKivitGak----s~~~~~~a~~~~~~~L~~~g~ 85 (174)
T cd00652 47 KTTALIFSSGKMVITGAK----SEEDAKLAARKYARILQKLGF 85 (174)
T ss_pred cEEEEEECCCEEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 344666777777775543 457899999999999999885
No 28
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=38.28 E-value=20 Score=17.57 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=9.8
Q ss_pred HHHHHHHHhCCC
Q 032890 120 ERLGDYLIDQGL 131 (131)
Q Consensus 120 ~~lA~yL~~~gy 131 (131)
.-+.+||..+||
T Consensus 8 ~lI~~yL~~~g~ 19 (34)
T smart00667 8 RLILEYLLRNGY 19 (34)
T ss_pred HHHHHHHHHcCH
Confidence 348999999987
No 29
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=37.24 E-value=55 Score=21.65 Aligned_cols=24 Identities=29% Similarity=0.468 Sum_probs=21.5
Q ss_pred cCCCcEEEEecCcEEEEEEeCCCC
Q 032890 87 KGSGGVTVKKTGQALIFGIYDEPL 110 (131)
Q Consensus 87 k~~~G~~i~kt~~~ivI~~~~~~~ 110 (131)
.|..|.++-++..+++|.+++++.
T Consensus 57 ~G~TG~Vvg~~g~ay~V~v~~G~k 80 (98)
T COG2139 57 QGKTGTVVGVRGRAYKVEVYDGNK 80 (98)
T ss_pred cCcceEEEeccCCEEEEEEecCCc
Confidence 578899999999999999998764
No 30
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=36.26 E-value=1.2e+02 Score=20.01 Aligned_cols=38 Identities=16% Similarity=0.184 Sum_probs=22.5
Q ss_pred cEEEEec-CcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 91 GVTVKKT-GQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 91 G~~i~kt-~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
|+++... |+.+=|.+.+- -.+..+.++..++-.++.||
T Consensus 66 GFvviN~dKK~mSvsFsdi---deNmK~~i~ei~kkykd~Gy 104 (110)
T PF11513_consen 66 GFVVINKDKKMMSVSFSDI---DENMKNSIEEIVKKYKDSGY 104 (110)
T ss_dssp EEEEEETTTTEEEEEE-S-----CCHHHHHHHHHHHHHCCS-
T ss_pred EEEEEecCCeEEEEEecch---hHHHHHHHHHHHHHhhcCCc
Confidence 4444444 44444444432 23458899999999999997
No 31
>PF02770 Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle domain; InterPro: IPR006091 Acyl-CoA dehydrogenases (1.3.99.3 from EC) are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [] prefers branched-chain substrates. The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents the middle beta-barrel domain found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO; 1.3.3.6 from EC) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [].; GO: 0003995 acyl-CoA dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 3MDD_B 1UDY_C 3MDE_B 2UXW_A 3B96_A 1SIQ_A 1SIR_A 2R0N_A 2R0M_A 2D29_B ....
Probab=36.07 E-value=31 Score=19.48 Aligned_cols=17 Identities=29% Similarity=0.378 Sum_probs=14.8
Q ss_pred ccceEEcCeEEEEEEeC
Q 032890 62 PTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 62 ~~gi~~~g~KY~v~r~d 78 (131)
..|+.|+|+|+++....
T Consensus 24 ~~~~~L~G~K~~v~~~~ 40 (52)
T PF02770_consen 24 GDGYVLNGEKRFVSNAP 40 (52)
T ss_dssp TTEEEEEEEEEEEETTT
T ss_pred cceEEEeeEEEEECCcC
Confidence 57899999999999765
No 32
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=35.88 E-value=75 Score=22.59 Aligned_cols=29 Identities=14% Similarity=0.072 Sum_probs=20.7
Q ss_pred EEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 102 IFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 102 vI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
||-+++. .......+++..+-++|+++||
T Consensus 154 Iil~Hd~-~~~~~t~~~l~~~i~~l~~~Gy 182 (191)
T TIGR02764 154 IILLHAS-DSAKQTVKALPTIIKKLKEKGY 182 (191)
T ss_pred EEEEeCC-CCcHhHHHHHHHHHHHHHHCCC
Confidence 3335542 2344567889999999999998
No 33
>PF05176 ATP-synt_10: ATP10 protein; InterPro: IPR007849 This entry represents the ATPase assembly factor ATP10 found in mitochondria, which is essential for the assembly of the mitochondrial F1-F0 complex. A yeast nuclear gene (ATP10) encodes a product that is essential for the assembly of a functional mitochondrial ATPase complex. Mutations in ATP10 induce a loss of rutamycin sensitivity in the mitochondrial ATPase, but do not affect the respiratory enzymes. ATP10 has an Mr of 30,293 and its primary structure is not related to any known subunit of the yeast or mammalian mitochondrial ATPase complexes. ATP10 is associated with the mitochondrial membrane. It is suggested that the ATP10 product is not a subunit of the ATPase complex but rather a protein required for the assembly of the F0 sector of the complex [].; GO: 0033615 mitochondrial proton-transporting ATP synthase complex assembly, 0005743 mitochondrial inner membrane
Probab=35.71 E-value=43 Score=25.75 Aligned_cols=34 Identities=26% Similarity=0.396 Sum_probs=25.1
Q ss_pred ccceeEEEcCCCC-eEEecCCCCCCCHHHHHHHHHHcC
Q 032890 19 HLTSAAIVGHDGS-VWAQSSNFPQFKPEEIAAIMKDFE 55 (131)
Q Consensus 19 ~~~~aaI~g~dG~-~wA~s~~f~~i~~~E~~~i~~~f~ 55 (131)
.+--.-++|.+|. -||.+ |. -+|+|+..|.++.+
T Consensus 216 ~~GYvyLVD~~grIRWags-G~--At~~E~~~L~k~~~ 250 (252)
T PF05176_consen 216 YVGYVYLVDPNGRIRWAGS-GP--ATPEELESLWKCVK 250 (252)
T ss_pred CcCeEEEECCCCeEEeCcc-CC--CCHHHHHHHHHHHh
Confidence 4445567888885 59976 43 48999999998754
No 34
>COG4725 IME4 Transcriptional activator, adenine-specific DNA methyltransferase [Signal transduction mechanisms / Transcription]
Probab=35.23 E-value=55 Score=23.96 Aligned_cols=54 Identities=22% Similarity=0.215 Sum_probs=40.5
Q ss_pred eEEEEEEeCCCceEEEEcCCCcEEEEecCcEEEEEEeCCCC-CcchHHHHHHHHHH
Q 032890 70 TKYMVIQGEPGAVIRGKKGSGGVTVKKTGQALIFGIYDEPL-TPGQCNMIVERLGD 124 (131)
Q Consensus 70 ~KY~v~r~d~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~-~~~~~~~~v~~lA~ 124 (131)
+-|- +|..+++++.|.+|+-=-+-+.+...+|+.+.-+.. .|.+....+|+||-
T Consensus 102 tGhw-lr~S~Eh~~vg~~GNpK~~~~~~~i~li~S~~RE~SRKP~E~y~i~ErL~~ 156 (198)
T COG4725 102 TGHW-LRTSGEHVFVGTLGNPKQSHVPPTISLIVSMTRETSRKPDELYGIAERLAG 156 (198)
T ss_pred ccee-ecCCCcEEEEEecCCchhhcCCCceEEEEccchhhccCCHHHHHHHHHhCC
Confidence 4443 445547888899887666666777779999988875 68899999999874
No 35
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=35.04 E-value=93 Score=20.24 Aligned_cols=34 Identities=15% Similarity=0.100 Sum_probs=28.8
Q ss_pred cCcEEEEEEeCCC-CCcchHHHHHHHHHHHHHhCC
Q 032890 97 TGQALIFGIYDEP-LTPGQCNMIVERLGDYLIDQG 130 (131)
Q Consensus 97 t~~~ivI~~~~~~-~~~~~~~~~v~~lA~yL~~~g 130 (131)
.++.++||..+.. ..+...+++...+++.|.+.+
T Consensus 52 ~~~v~lvGlG~~~~~~~~~~r~a~~~~~~~l~~~~ 86 (126)
T PF02789_consen 52 AKRVLLVGLGKKEKLTAESLRKAGAAAARALKKLK 86 (126)
T ss_dssp CSEEEEEEEESCTGBCHHHHHHHHHHHHHHHHHTT
T ss_pred ccEEEEEECCCcCcCCHHHHHHHHHHHHHHHhhCC
Confidence 4678899999886 588999999999999998754
No 36
>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.
Probab=34.26 E-value=57 Score=25.52 Aligned_cols=33 Identities=15% Similarity=0.286 Sum_probs=21.8
Q ss_pred cEEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032890 99 QALIFGIYDEPL-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 99 ~~ivI~~~~~~~-~~~~~~~~v~~lA~yL~~~gy 131 (131)
+.+|++..+++. ..-.+....-.+|||++++|+
T Consensus 128 tvvv~~t~d~~~~~r~~a~~~a~aiAE~fr~~G~ 161 (274)
T cd01132 128 TIVVAATASDPAPLQYLAPYTGCAMGEYFMDNGK 161 (274)
T ss_pred eEEEEeCCCCchhHHHHHHHHHHHHHHHHHHCCC
Confidence 356666655543 233456667889999999885
No 37
>COG1832 Predicted CoA-binding protein [General function prediction only]
Probab=34.24 E-value=62 Score=22.82 Aligned_cols=31 Identities=29% Similarity=0.527 Sum_probs=23.4
Q ss_pred EecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 95 KKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 95 ~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
.+.|+--|||..+.+..++ ..+++||.++||
T Consensus 14 ~~~K~IAvVG~S~~P~r~s------y~V~kyL~~~GY 44 (140)
T COG1832 14 KSAKTIAVVGASDKPDRPS------YRVAKYLQQKGY 44 (140)
T ss_pred HhCceEEEEecCCCCCccH------HHHHHHHHHCCC
Confidence 3466777788877766554 578999999998
No 38
>PRK06901 aspartate-semialdehyde dehydrogenase; Provisional
Probab=33.64 E-value=2.4e+02 Score=22.67 Aligned_cols=87 Identities=15% Similarity=0.072 Sum_probs=51.5
Q ss_pred cCCCCeEEecCCCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEE------eCCCc--eEEEEcCCCcEEEEecC
Q 032890 27 GHDGSVWAQSSNFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQ------GEPGA--VIRGKKGSGGVTVKKTG 98 (131)
Q Consensus 27 g~dG~~wA~s~~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r------~d~~~--~i~~kk~~~G~~i~kt~ 98 (131)
|+.-++|...+. .++.+|+..++.. ..|+.+-..+|-.-- ..+|. ...+|-.. ..
T Consensus 228 GHs~sV~ve~e~--~~~~e~~~~~l~~--------~~gv~l~d~~yPtPi~~~~~~~g~d~vvv~Vgrir~-------~~ 290 (322)
T PRK06901 228 GLAQMVTALSEY--ELDIESQLAEWQQ--------NNLLRYHEEKLITPVLNGENENGEESVKLHISQLSA-------VE 290 (322)
T ss_pred cEEEEEEEEECC--CCCHHHHHHHHHh--------CCCcEEeCCCCCCCcccccccCCCCCccEEEEcccc-------CC
Confidence 334478888755 5789999988873 234555444443221 12233 33333211 23
Q ss_pred cEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 99 QALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 99 ~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
+.+-+=...|...-|-+.++|. +|++|.++||
T Consensus 291 ~~l~lwvvaDNlRkGAA~NAVq-IaE~l~~~~~ 322 (322)
T PRK06901 291 NGVQFWSVADEQRFNLAFLAVK-LLELIYQQGY 322 (322)
T ss_pred CEEEEEEEechHHHHHHHHHHH-HHHHHHHccC
Confidence 4444455566677777777764 8999999998
No 39
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=33.63 E-value=45 Score=27.87 Aligned_cols=34 Identities=12% Similarity=0.245 Sum_probs=21.6
Q ss_pred CcEEEEEEeCC-CC-CcchHHHHHHHHHHHHHhCCC
Q 032890 98 GQALIFGIYDE-PL-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 98 ~~~ivI~~~~~-~~-~~~~~~~~v~~lA~yL~~~gy 131 (131)
++++||+-..+ +. ..-++......+|+|.+++|.
T Consensus 218 ~rsViVvATSD~s~l~R~~aa~~At~IAEyFRDqG~ 253 (441)
T COG1157 218 KRSVVVVATSDESALMRLKAAFTATTIAEYFRDQGK 253 (441)
T ss_pred cceEEEEECCCCCHHHHHHHHHHHHHHHHHHHhCCC
Confidence 34444444444 32 345677778889999999984
No 40
>PF09176 Mpt_N: Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; InterPro: IPR015259 Prokaryotic methylene-tetrahydromethanopterin dehydrogenase catalyses the dehydrogenation of methylene-tetrahydromethanopterin during growth on one-carbon compounds such as methanol. It can also catalyse the reversible dehydrogenation of methylene-tetrahydrofolate, though at much lower efficiency []. The pterin domain of this protein is composed of two alpha-beta segments found at the N- and C-terminal ends of the polypeptide respectivly. This entry represents the N-terminal segment of the pterin domain, with a core comprising three alpha/beta/alpha layers in which each sheet contains four strands. ; PDB: 1LUA_A 1LU9_C.
Probab=32.61 E-value=17 Score=23.16 Aligned_cols=31 Identities=26% Similarity=0.608 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHH--Hc-CCCCCCCccceEEcCeE
Q 032890 41 QFKPEEIAAIMK--DF-EEPGSLAPTGLHLGGTK 71 (131)
Q Consensus 41 ~i~~~E~~~i~~--~f-~~~~~~~~~gi~~~g~K 71 (131)
+++++|+..|+. .| +.|..+..+||.++|..
T Consensus 20 ~V~~~~V~~LvqdaIFsR~P~~~~~TaiFIGG~d 53 (81)
T PF09176_consen 20 GVTPDEVRGLVQDAIFSRGPKDLKRTAIFIGGRD 53 (81)
T ss_dssp S--TTTHHHHHHHHHSSS-GGGGGGEEEEEE-S-
T ss_pred CcCHHHhhhhhcceeEccCCcCCceeEEEECCcc
Confidence 678999999885 44 45667889999999863
No 41
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=32.32 E-value=1.2e+02 Score=21.96 Aligned_cols=38 Identities=18% Similarity=0.265 Sum_probs=27.8
Q ss_pred CcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 90 GGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 90 ~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
.-+.|..+.+.++.|. ....++.++++++++.|++.||
T Consensus 48 ~t~lIF~sGKiviTGa----ks~~~~~~a~~~~~~~l~~~g~ 85 (174)
T cd04517 48 ATASVWSSGKITITGA----TSEEEAKQAARRAARLLQKLGF 85 (174)
T ss_pred EEEEEECCCeEEEEcc----CCHHHHHHHHHHHHHHHHHcCC
Confidence 3455666666666443 3567899999999999999875
No 42
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=32.30 E-value=50 Score=20.00 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=17.1
Q ss_pred CcchHHHHHHHHHHHHHhCCC
Q 032890 111 TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 111 ~~~~~~~~v~~lA~yL~~~gy 131 (131)
.....+..+..+.+++++.||
T Consensus 32 ~~~~l~~~~~~l~~~y~~~GY 52 (76)
T PF08479_consen 32 TLADLQQLADALTNYYREKGY 52 (76)
T ss_dssp -HHHHHHHHHHHHHHHHHTT-
T ss_pred CHHHHHHHHHHHHHHHHHcCc
Confidence 456788999999999999998
No 43
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=31.93 E-value=95 Score=19.00 Aligned_cols=19 Identities=21% Similarity=0.181 Sum_probs=15.9
Q ss_pred chHHHHHHHHHHHHHhCCC
Q 032890 113 GQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 113 ~~~~~~v~~lA~yL~~~gy 131 (131)
......+.++|+.|+++|+
T Consensus 14 ~~~~~~a~~la~~Lr~~g~ 32 (94)
T cd00861 14 EVQQELAEKLYAELQAAGV 32 (94)
T ss_pred HHHHHHHHHHHHHHHHCCC
Confidence 4577788999999999886
No 44
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=31.75 E-value=1.3e+02 Score=21.18 Aligned_cols=39 Identities=21% Similarity=0.206 Sum_probs=23.1
Q ss_pred cccccccccceeEEEcCCCCeEEecCCCCCCCHHHHHHHHH
Q 032890 12 MCDIDGHHLTSAAIVGHDGSVWAQSSNFPQFKPEEIAAIMK 52 (131)
Q Consensus 12 ~~~~~g~~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~i~~ 52 (131)
+|...| .....||+++||.+....+.= +++..|+-.++.
T Consensus 35 VGiDPG-~ttgiAildL~G~~l~l~S~R-~~~~~evi~~I~ 73 (138)
T PF04312_consen 35 VGIDPG-TTTGIAILDLDGELLDLKSSR-NMSRSEVIEWIS 73 (138)
T ss_pred EEECCC-ceeEEEEEecCCcEEEEEeec-CCCHHHHHHHHH
Confidence 343346 778899999999865542221 334555444444
No 45
>PRK00005 fmt methionyl-tRNA formyltransferase; Reviewed
Probab=31.60 E-value=2.5e+02 Score=21.89 Aligned_cols=37 Identities=16% Similarity=0.402 Sum_probs=26.6
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeC
Q 032890 38 NFPQFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d 78 (131)
+| +-+.+|+..+++++. | ...--..++|+++.+.+++
T Consensus 212 dw-~~~a~~I~~~iRA~~-p--~pga~~~~~g~~v~i~~a~ 248 (309)
T PRK00005 212 DW-SKPAAELENHIRGFN-P--WPGAWTELDGQRLKILEAE 248 (309)
T ss_pred cC-CCCHHHHHHHHhcCC-C--CCceEEEECCEEEEEEEEE
Confidence 36 447789999999985 3 1223356899999998864
No 46
>PHA02754 hypothetical protein; Provisional
Probab=31.55 E-value=87 Score=18.83 Aligned_cols=19 Identities=21% Similarity=0.459 Sum_probs=14.3
Q ss_pred CCccceEEcCeEEEEEEeC
Q 032890 60 LAPTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 60 ~~~~gi~~~g~KY~v~r~d 78 (131)
+.+.|+++...|-+.++.|
T Consensus 27 LSe~GiYi~RIkai~~SGd 45 (67)
T PHA02754 27 LSEAGIYIDRIKAITTSGD 45 (67)
T ss_pred HhhCceEEEEEEEEEecCC
Confidence 5678999988877666655
No 47
>PRK13604 luxD acyl transferase; Provisional
Probab=30.84 E-value=1.3e+02 Score=23.98 Aligned_cols=53 Identities=21% Similarity=0.140 Sum_probs=28.1
Q ss_pred EEEeCCCceEEEEcCCCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 74 VIQGEPGAVIRGKKGSGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 74 v~r~d~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
+++.+++..|+|.-....--..+.+..+||++.-.... ....++|+||.++||
T Consensus 13 ~~~~~dG~~L~Gwl~~P~~~~~~~~~~vIi~HGf~~~~-----~~~~~~A~~La~~G~ 65 (307)
T PRK13604 13 VICLENGQSIRVWETLPKENSPKKNNTILIASGFARRM-----DHFAGLAEYLSSNGF 65 (307)
T ss_pred eEEcCCCCEEEEEEEcCcccCCCCCCEEEEeCCCCCCh-----HHHHHHHHHHHHCCC
Confidence 45554355565542111000112234666665544321 238889999999997
No 48
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=30.69 E-value=81 Score=22.21 Aligned_cols=44 Identities=11% Similarity=0.256 Sum_probs=28.3
Q ss_pred CCCeEEecCCCCCCCHHHHHHHHHHcCCC---CCCCccceEEcCeEEE
Q 032890 29 DGSVWAQSSNFPQFKPEEIAAIMKDFEEP---GSLAPTGLHLGGTKYM 73 (131)
Q Consensus 29 dG~~wA~s~~f~~i~~~E~~~i~~~f~~~---~~~~~~gi~~~g~KY~ 73 (131)
+|.+..+.+-. .++.+++...+..|... ..-.-+.+.++|++-.
T Consensus 60 ~G~v~~~~~~~-~it~e~l~~~l~~f~G~~~Q~pP~ySAvki~G~raY 106 (149)
T PF01509_consen 60 EGEVTETKPYD-HITEEDLEKVLAKFQGEIEQVPPMYSAVKINGKRAY 106 (149)
T ss_dssp TSSEEEE---T-T--HHHHHHHHHHTSEEEEES-SSSSSSECTTCEHH
T ss_pred eeeEEEeeccc-cCCHHHHHHHHHhCcCCEeeeCchheeEcCCCccHH
Confidence 67888885444 88999999999988631 1124678888888753
No 49
>PF07244 Surf_Ag_VNR: Surface antigen variable number repeat; InterPro: IPR010827 This motif is found primarily in bacterial surface antigens, normally as variable number repeats at the N terminus. The C terminus of these proteins is normally represented by IPR000184 from INTERPRO. There may also be a relationship to haemolysin activator HlyB (IPR005565 from INTERPRO). The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.; GO: 0019867 outer membrane; PDB: 2X8X_X 3MC8_A 3OG5_A 3MC9_B 2QCZ_B 3EFC_A 3Q6B_A 2QDF_A 2V9H_A.
Probab=29.87 E-value=64 Score=19.02 Aligned_cols=22 Identities=36% Similarity=0.643 Sum_probs=19.4
Q ss_pred CCcchHHHHHHHHHHHHHhCCC
Q 032890 110 LTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 110 ~~~~~~~~~v~~lA~yL~~~gy 131 (131)
.++....+...+|.+++.+.||
T Consensus 32 ~~~~~i~~~~~~l~~~y~~~Gy 53 (78)
T PF07244_consen 32 FNPEKIEEDIERLQDYYKDKGY 53 (78)
T ss_dssp ECHHHHHHHHHHHHHHHHTTSC
T ss_pred eCHHHHHHHHHHHHHHHHHcCC
Confidence 3678889999999999999997
No 50
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=29.10 E-value=1.2e+02 Score=22.28 Aligned_cols=34 Identities=18% Similarity=0.102 Sum_probs=24.5
Q ss_pred CcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 98 GQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 98 ~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
.+.+||-+.............+.++++.|+++|+
T Consensus 11 ~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Gi 44 (202)
T cd00862 11 IQVVIVPIGIKDEKREEVLEAADELAERLKAAGI 44 (202)
T ss_pred ceEEEEEecCCccchHHHHHHHHHHHHHHHHCCC
Confidence 3566777765533445578899999999998874
No 51
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=28.92 E-value=1e+02 Score=21.79 Aligned_cols=29 Identities=24% Similarity=0.416 Sum_probs=19.5
Q ss_pred EEEcCCCC-eEEec--C---CCCCCCHHHHHHHHHH
Q 032890 24 AIVGHDGS-VWAQS--S---NFPQFKPEEIAAIMKD 53 (131)
Q Consensus 24 aI~g~dG~-~wA~s--~---~f~~i~~~E~~~i~~~ 53 (131)
+|.|.+++ +||+. . .. .++|+|..+|-.+
T Consensus 116 sI~~Re~s~~YaK~I~~G~S~~-~LS~EE~eal~~A 150 (151)
T PF14584_consen 116 SIHSREESRTYAKPIVNGQSSY-PLSEEEKEALEKA 150 (151)
T ss_pred eeecCCCcEEEEEEecCCcccc-cCCHHHHHHHHHh
Confidence 45555664 67753 1 24 7899999998765
No 52
>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.
Probab=28.90 E-value=60 Score=26.54 Aligned_cols=32 Identities=19% Similarity=0.272 Sum_probs=19.3
Q ss_pred EEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032890 100 ALIFGIYDEPL-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 100 ~ivI~~~~~~~-~~~~~~~~v~~lA~yL~~~gy 131 (131)
.+|++.-+++. ..-.+....-.+|||++++||
T Consensus 222 vlV~nts~~p~~~R~~s~yta~tiAEYfrd~G~ 254 (369)
T cd01134 222 VLIANTSNMPVAAREASIYTGITIAEYFRDMGY 254 (369)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 44444444442 222344555669999999996
No 53
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=28.55 E-value=62 Score=21.43 Aligned_cols=18 Identities=6% Similarity=0.414 Sum_probs=15.5
Q ss_pred CccceEEcCeEEEEEEeC
Q 032890 61 APTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 61 ~~~gi~~~g~KY~v~r~d 78 (131)
..+-+.++|++|+++|.+
T Consensus 75 ~Gtevk~dg~ey~i~~e~ 92 (100)
T PTZ00414 75 GGSSVKVEGEEFFLYNED 92 (100)
T ss_pred CCcEEEECCEEEEEEEhH
Confidence 356699999999999987
No 54
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=27.17 E-value=58 Score=20.99 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=15.6
Q ss_pred CccceEEcCeEEEEEEeC
Q 032890 61 APTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 61 ~~~gi~~~g~KY~v~r~d 78 (131)
...-+.++|++|+++|.+
T Consensus 70 ~g~~v~~~~~~y~i~~~~ 87 (93)
T cd00320 70 AGTEVKLDGEEYLILRES 87 (93)
T ss_pred CceEEEECCEEEEEEEHH
Confidence 366799999999999987
No 55
>PF07799 DUF1643: Protein of unknown function (DUF1643); InterPro: IPR012441 This entry is represented by Bacteriophage D3, Orf41.6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The members of this family are all sequences found within hypothetical proteins expressed by various bacteria, archaea and phage. The region concerned is approximately 150 residues long.
Probab=27.04 E-value=1e+02 Score=20.81 Aligned_cols=34 Identities=12% Similarity=0.158 Sum_probs=21.2
Q ss_pred CcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 98 GQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 98 ~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
+.+++|++.+....+...=..+.++-.+.+..||
T Consensus 13 ~~~~~I~lNPS~A~~~~~D~T~~~~~~~a~~~gy 46 (136)
T PF07799_consen 13 PPLLFIGLNPSTADAEKDDPTIRRCINFARRWGY 46 (136)
T ss_pred CEEEEEEeCCCCCCCcCCCHHHHHHHHHHhhcCC
Confidence 4678888888776555444444455555555565
No 56
>PRK05922 type III secretion system ATPase; Validated
Probab=25.83 E-value=80 Score=26.37 Aligned_cols=34 Identities=21% Similarity=0.195 Sum_probs=23.1
Q ss_pred CcEEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032890 98 GQALIFGIYDEPL-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 98 ~~~ivI~~~~~~~-~~~~~~~~v~~lA~yL~~~gy 131 (131)
++.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 213 rTVlv~atsd~~~~~r~~a~~~a~tiAEyfrd~G~ 247 (434)
T PRK05922 213 RTIIIASPAHETAPTKVIAGRAAMTIAEYFRDQGH 247 (434)
T ss_pred ceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3455555555543 344577778889999999985
No 57
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=25.81 E-value=66 Score=20.86 Aligned_cols=18 Identities=22% Similarity=0.610 Sum_probs=15.3
Q ss_pred CccceEEcCeEEEEEEeC
Q 032890 61 APTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 61 ~~~gi~~~g~KY~v~r~d 78 (131)
...-+.++|++|+++|.+
T Consensus 71 ~g~ev~~~~~~y~iv~~~ 88 (95)
T PRK00364 71 AGTEVKIDGEEYLILRES 88 (95)
T ss_pred CCeEEEECCEEEEEEEHH
Confidence 355789999999999987
No 58
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=25.48 E-value=1.8e+02 Score=18.14 Aligned_cols=37 Identities=19% Similarity=0.294 Sum_probs=28.6
Q ss_pred CcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCC
Q 032890 90 GGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQG 130 (131)
Q Consensus 90 ~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~g 130 (131)
.-+.|..|.+.+|.|.- ....+.+++.++.+.|.+.|
T Consensus 50 ~t~~IF~sGki~itGak----s~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 50 ATVLIFSSGKIVITGAK----SEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp EEEEEETTSEEEEEEES----SHHHHHHHHHHHHHHHHHTT
T ss_pred EEEEEEcCCEEEEEecC----CHHHHHHHHHHHHHHHHHcC
Confidence 34667777777776653 56889999999999998865
No 59
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=25.45 E-value=73 Score=20.62 Aligned_cols=18 Identities=22% Similarity=0.468 Sum_probs=15.5
Q ss_pred CccceEEcCeEEEEEEeC
Q 032890 61 APTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 61 ~~~gi~~~g~KY~v~r~d 78 (131)
..+-+.++|++|+++|.+
T Consensus 66 ~g~ev~~~~~~y~iv~e~ 83 (91)
T PRK14533 66 AGTEIKIDDEDYIIIDVN 83 (91)
T ss_pred CCeEEEECCEEEEEEEhH
Confidence 456799999999999986
No 60
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=25.11 E-value=90 Score=14.64 Aligned_cols=15 Identities=20% Similarity=0.525 Sum_probs=10.4
Q ss_pred eEEEcCCCCeEEecC
Q 032890 23 AAIVGHDGSVWAQSS 37 (131)
Q Consensus 23 aaI~g~dG~~wA~s~ 37 (131)
+...+.+|.+|..+.
T Consensus 9 ~i~~D~~G~lWigT~ 23 (24)
T PF07494_consen 9 SIYEDSDGNLWIGTY 23 (24)
T ss_dssp EEEE-TTSCEEEEET
T ss_pred EEEEcCCcCEEEEeC
Confidence 455567999998764
No 61
>PF06918 DUF1280: Protein of unknown function (DUF1280); InterPro: IPR009689 This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans.
Probab=24.77 E-value=1.5e+02 Score=22.44 Aligned_cols=30 Identities=13% Similarity=0.205 Sum_probs=26.8
Q ss_pred cEEEEEEeCCCCCcchHHHHHHHHHHHHHh
Q 032890 99 QALIFGIYDEPLTPGQCNMIVERLGDYLID 128 (131)
Q Consensus 99 ~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~ 128 (131)
..+++|+|+++....+..+.+..+.+.|..
T Consensus 191 ~~~~~~~~~g~D~~~~l~~~~~~v~~qln~ 220 (224)
T PF06918_consen 191 NLLLLGLYEGDDNYENLKKYLGPVFEQLNN 220 (224)
T ss_pred cEEEEEEEcCCCCHHHHHHHHHHHHHHHhc
Confidence 589999999999999999999999888865
No 62
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=23.83 E-value=73 Score=20.39 Aligned_cols=18 Identities=28% Similarity=0.684 Sum_probs=15.6
Q ss_pred CccceEEcCeEEEEEEeC
Q 032890 61 APTGLHLGGTKYMVIQGE 78 (131)
Q Consensus 61 ~~~gi~~~g~KY~v~r~d 78 (131)
...-+.++|++|+++|.+
T Consensus 70 ~g~~v~~~~~~~~~~~~~ 87 (93)
T PF00166_consen 70 AGTEVKFDGEKYLIVRED 87 (93)
T ss_dssp TSEEEEETTEEEEEEEGG
T ss_pred CceEEEECCEEEEEEEHH
Confidence 356789999999999987
No 63
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=23.79 E-value=1.7e+02 Score=23.02 Aligned_cols=35 Identities=26% Similarity=0.240 Sum_probs=25.7
Q ss_pred EecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCC
Q 032890 95 KKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQG 130 (131)
Q Consensus 95 ~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~g 130 (131)
...++.+.||.+--+.+.. ....+|+||+||++.|
T Consensus 238 ~egks~lTIaIGCTGGqHR-SV~iae~La~~l~~~~ 272 (286)
T COG1660 238 KEGKSYLTIAIGCTGGQHR-SVYIAEQLAEYLRARG 272 (286)
T ss_pred hcCCeEEEEEEccCCCccc-hHHHHHHHHHHHHhcc
Confidence 3457889999877655443 3456799999999875
No 64
>PHA02119 hypothetical protein
Probab=23.69 E-value=51 Score=20.57 Aligned_cols=11 Identities=36% Similarity=0.570 Sum_probs=8.2
Q ss_pred HHHHHHHhCCC
Q 032890 121 RLGDYLIDQGL 131 (131)
Q Consensus 121 ~lA~yL~~~gy 131 (131)
.+.|||++.||
T Consensus 58 divdylr~lgy 68 (87)
T PHA02119 58 DIVDYLRSLGY 68 (87)
T ss_pred HHHHHHHHccc
Confidence 46788888887
No 65
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=23.51 E-value=85 Score=24.50 Aligned_cols=33 Identities=24% Similarity=0.529 Sum_probs=19.8
Q ss_pred cEEEEEEeCCCC-CcchHHHHHHHHHHHHHhC-CC
Q 032890 99 QALIFGIYDEPL-TPGQCNMIVERLGDYLIDQ-GL 131 (131)
Q Consensus 99 ~~ivI~~~~~~~-~~~~~~~~v~~lA~yL~~~-gy 131 (131)
+.+|++..+++. ..-.+..+.-.+|||++++ |+
T Consensus 129 tvvv~~t~d~~~~~r~~~~~~a~~~AEyfr~~~g~ 163 (274)
T cd01133 129 TALVYGQMNEPPGARARVALTGLTMAEYFRDEEGQ 163 (274)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 344444444432 2334556667799999987 74
No 66
>TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.
Probab=23.30 E-value=90 Score=27.11 Aligned_cols=17 Identities=18% Similarity=0.276 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHhCCC
Q 032890 115 CNMIVERLGDYLIDQGL 131 (131)
Q Consensus 115 ~~~~v~~lA~yL~~~gy 131 (131)
+.-..-.+|||++++||
T Consensus 303 s~ytg~TiAEYfRD~G~ 319 (578)
T TIGR01043 303 SIYTGITIAEYFRDMGY 319 (578)
T ss_pred HHHHHHHHHHHHHHCCC
Confidence 44444569999999997
No 67
>PF14553 YqbF: YqbF, hypothetical protein domain; PDB: 2HJQ_A.
Probab=23.11 E-value=77 Score=17.76 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=9.4
Q ss_pred HHHHHHHHHhCCC
Q 032890 119 VERLGDYLIDQGL 131 (131)
Q Consensus 119 v~~lA~yL~~~gy 131 (131)
..++++||.++++
T Consensus 22 ~kk~y~YL~~ne~ 34 (43)
T PF14553_consen 22 SKKIYNYLNDNEF 34 (43)
T ss_dssp -HHHHHHHHHSTT
T ss_pred hHHHHHHHhcCCc
Confidence 4578899988764
No 68
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=22.30 E-value=83 Score=23.22 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=16.4
Q ss_pred HHHHHHHHcCCCCCCCccceEEcC
Q 032890 46 EIAAIMKDFEEPGSLAPTGLHLGG 69 (131)
Q Consensus 46 E~~~i~~~f~~~~~~~~~gi~~~g 69 (131)
=.+-++.+++.|.. .-+|+-++-
T Consensus 11 Y~K~~LHaaKyP~~-aVnGvLlg~ 33 (196)
T PF03665_consen 11 YAKMILHAAKYPHC-AVNGVLLGK 33 (196)
T ss_pred HHHHHHHhccCCCC-ceeeEEEec
Confidence 34667788888753 578888875
No 69
>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
Probab=22.29 E-value=86 Score=25.07 Aligned_cols=32 Identities=19% Similarity=0.310 Sum_probs=20.4
Q ss_pred EEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032890 100 ALIFGIYDEPL-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 100 ~ivI~~~~~~~-~~~~~~~~v~~lA~yL~~~gy 131 (131)
.+|++..+++. ..-.+....-.+|+|++++|+
T Consensus 127 vvv~~t~d~~~~~r~~~~~~a~~~AEyfr~~g~ 159 (326)
T cd01136 127 VVVVATSDESPLLRVKAAYTATAIAEYFRDQGK 159 (326)
T ss_pred EEEEcCCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 45555555532 333456667779999999884
No 70
>KOG4107 consensus MP1 adaptor interacting protein P14 [Signal transduction mechanisms]
Probab=22.15 E-value=56 Score=22.02 Aligned_cols=97 Identities=16% Similarity=0.350 Sum_probs=59.2
Q ss_pred cccccceeEEEcCCCCeEEecCCCC----CCCHHHHHHHHHHcCCCCCCCccceEEcCeEEEEEEeCCCceEEEEcCCCc
Q 032890 16 DGHHLTSAAIVGHDGSVWAQSSNFP----QFKPEEIAAIMKDFEEPGSLAPTGLHLGGTKYMVIQGEPGAVIRGKKGSGG 91 (131)
Q Consensus 16 ~g~~~~~aaI~g~dG~~wA~s~~f~----~i~~~E~~~i~~~f~~~~~~~~~gi~~~g~KY~v~r~d~~~~i~~kk~~~G 91 (131)
+| .++.--+++.+|.+.|-+ |+. +++..-+..+-.+++.+. ...|.=+.-||.++..+ +..
T Consensus 16 Tg-GV~~tlLln~EG~LLAYs-GygdkdarvtaAiasniWAAyer~g---n~af~e~~Lkf~lldce-nG~--------- 80 (125)
T KOG4107|consen 16 TG-GVDGTLLLNKEGLLLAYS-GYGDKDARVTAAIASNIWAAYERRG---NQAFNEDDLKFTLLDCE-NGV--------- 80 (125)
T ss_pred cC-CccceEEEcCCCcEEEec-ccCcchhHHHHHHHHHHHHHHHHhc---cccccccCceeeeeeec-CCe---------
Confidence 56 789999999999999976 331 344444555555554321 23345556677777777 221
Q ss_pred EEEEecCcEEEEEEeCC-CCCcchHHHHHHHHHHHHHh
Q 032890 92 VTVKKTGQALIFGIYDE-PLTPGQCNMIVERLGDYLID 128 (131)
Q Consensus 92 ~~i~kt~~~ivI~~~~~-~~~~~~~~~~v~~lA~yL~~ 128 (131)
+-+..-.+ ++.++|.+ +..-|........||.||.+
T Consensus 81 vaiT~VA~-~LLc~yAk~tvglGmlkaKa~tLa~YLE~ 117 (125)
T KOG4107|consen 81 VAITLVAR-MLLCVYAKKTVGLGMLKAKAHTLAAYLEQ 117 (125)
T ss_pred eeHHHHHH-HHHHHhhhcccchHHHHHHHHHHHHHHHh
Confidence 11111122 34445544 45678888889999999875
No 71
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=21.98 E-value=2.5e+02 Score=18.65 Aligned_cols=29 Identities=17% Similarity=0.233 Sum_probs=21.2
Q ss_pred hhccccccccccccceeEEEcCCCCeEEecCCC
Q 032890 7 VDDHLMCDIDGHHLTSAAIVGHDGSVWAQSSNF 39 (131)
Q Consensus 7 v~~~L~~~~~g~~~~~aaI~g~dG~~wA~s~~f 39 (131)
+| .|+. -. .+-.|.+++.||.+.+-..+.
T Consensus 5 Ld-eLlq--i~-Gv~AAGefs~DGkLv~Ykgdm 33 (109)
T COG4831 5 LD-ELLQ--IK-GVMAAGEFSPDGKLVEYKGDM 33 (109)
T ss_pred HH-HHhC--cc-ceeEeceeCCCCceEEeeCCC
Confidence 44 4665 33 578899999999998876554
No 72
>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=21.90 E-value=92 Score=25.71 Aligned_cols=18 Identities=22% Similarity=0.506 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHHHHhCCC
Q 032890 114 QCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 114 ~~~~~v~~lA~yL~~~gy 131 (131)
.+..+.-.+|+|++++|+
T Consensus 210 ~a~~~a~tiAEyfr~~G~ 227 (411)
T TIGR03496 210 RAAFYATAIAEYFRDQGK 227 (411)
T ss_pred HHHHHHHHHHHHHHHCCC
Confidence 466666778999999885
No 73
>PRK06936 type III secretion system ATPase; Provisional
Probab=21.45 E-value=94 Score=25.99 Aligned_cols=18 Identities=22% Similarity=0.597 Sum_probs=13.5
Q ss_pred hHHHHHHHHHHHHHhCCC
Q 032890 114 QCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 114 ~~~~~v~~lA~yL~~~gy 131 (131)
.+....-.+|||++++|+
T Consensus 235 ~a~~~a~tiAEyfrd~G~ 252 (439)
T PRK06936 235 KAGFVATSIAEYFRDQGK 252 (439)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 345555669999999985
No 74
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=21.44 E-value=1e+02 Score=26.89 Aligned_cols=33 Identities=12% Similarity=0.254 Sum_probs=19.2
Q ss_pred cEEEEEEeCC-CCC-cchHHHHHHHHHHHHHhCCC
Q 032890 99 QALIFGIYDE-PLT-PGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 99 ~~ivI~~~~~-~~~-~~~~~~~v~~lA~yL~~~gy 131 (131)
+.++|+-..+ +.- ...+....-.+|+|++++||
T Consensus 290 RTvlVanTSn~Pv~aR~~s~ytgiTiAEYfRd~G~ 324 (586)
T PRK04192 290 RTVLIANTSNMPVAAREASIYTGITIAEYYRDMGY 324 (586)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 4444444443 322 22344455569999999997
No 75
>PRK02821 hypothetical protein; Provisional
Probab=21.35 E-value=2e+02 Score=18.02 Aligned_cols=44 Identities=9% Similarity=0.289 Sum_probs=24.8
Q ss_pred HHHHHHHc-CCCCCCCccceEEcCeEEEEEEeCCC--ceEEEEcCCC
Q 032890 47 IAAIMKDF-EEPGSLAPTGLHLGGTKYMVIQGEPG--AVIRGKKGSG 90 (131)
Q Consensus 47 ~~~i~~~f-~~~~~~~~~gi~~~g~KY~v~r~d~~--~~i~~kk~~~ 90 (131)
+..|++.| ++|..+.-+-..-.+...+-++.+++ ..+.||+|..
T Consensus 6 v~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~ 52 (77)
T PRK02821 6 VEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRT 52 (77)
T ss_pred HHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCch
Confidence 45666666 45655544434444445556666533 3588888753
No 76
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=21.25 E-value=1.2e+02 Score=18.06 Aligned_cols=18 Identities=22% Similarity=0.403 Sum_probs=15.3
Q ss_pred CCCHHHHHHHHHHcCCCC
Q 032890 41 QFKPEEIAAIMKDFEEPG 58 (131)
Q Consensus 41 ~i~~~E~~~i~~~f~~~~ 58 (131)
.+++.|...++++|++..
T Consensus 28 Gv~~~e~~aIi~~F~~~~ 45 (57)
T PF05952_consen 28 GVDKDEQKAIIDAFKDEE 45 (57)
T ss_pred cCCHHHHHHHHHHHcccc
Confidence 578999999999998653
No 77
>COG3726 AhpA Uncharacterized membrane protein affecting hemolysin expression [General function prediction only]
Probab=21.15 E-value=45 Score=24.95 Aligned_cols=30 Identities=20% Similarity=0.349 Sum_probs=23.7
Q ss_pred HhhccccccccccccceeEEEcCCCCeEEecCCC
Q 032890 6 YVDDHLMCDIDGHHLTSAAIVGHDGSVWAQSSNF 39 (131)
Q Consensus 6 yv~~~L~~~~~g~~~~~aaI~g~dG~~wA~s~~f 39 (131)
.+| +|.. +. .+-+|+|++.||.+.|.++.|
T Consensus 77 lln-ql~k--~~-~VldAsIY~~~g~LlA~ag~~ 106 (214)
T COG3726 77 LLN-QLTK--ES-LVLDASIYDEDGDLLARAGSS 106 (214)
T ss_pred HHH-HHhh--cc-eeeeceeecccchhHHhcccc
Confidence 344 5665 44 899999999999999988665
No 78
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=21.14 E-value=3.8e+02 Score=25.25 Aligned_cols=58 Identities=9% Similarity=0.070 Sum_probs=39.4
Q ss_pred EEEEEeCCCceEEEEcCCCcEEEEecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032890 72 YMVIQGEPGAVIRGKKGSGGVTVKKTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 72 Y~v~r~d~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~gy 131 (131)
|+.++.| ...++ -.++.+++.++...-+.|++++.=-.+..-..++..+.++-+..|+
T Consensus 256 ~la~~~D-k~~~f-s~~g~a~i~Yrv~~~~~i~~GDPvG~~e~~~~~i~~F~~~a~~~g~ 313 (1094)
T PRK02983 256 YFATRRD-KSVVF-APSGRAAITYRVEVGVCLASGDPVGDPEAWPQAIDAWLALARTYGW 313 (1094)
T ss_pred eeeecCC-ceEEE-CCCCCEEEEEEEECCEEEEECCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 4455555 33334 3345677777777666666766555788889999999999888774
No 79
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=20.67 E-value=1e+02 Score=25.93 Aligned_cols=18 Identities=28% Similarity=0.488 Sum_probs=13.8
Q ss_pred hHHHHHHHHHHHHHhCCC
Q 032890 114 QCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 114 ~~~~~v~~lA~yL~~~gy 131 (131)
.+..+.-.+|||++++|+
T Consensus 235 ~a~~~A~tiAEyfrd~G~ 252 (444)
T PRK08972 235 KGCETATTIAEYFRDQGL 252 (444)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 355566669999999885
No 80
>PRK12359 flavodoxin FldB; Provisional
Probab=20.50 E-value=1.8e+02 Score=20.82 Aligned_cols=35 Identities=17% Similarity=0.090 Sum_probs=25.5
Q ss_pred ecCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCC
Q 032890 96 KTGQALIFGIYDEPLTPGQCNMIVERLGDYLIDQG 130 (131)
Q Consensus 96 kt~~~ivI~~~~~~~~~~~~~~~v~~lA~yL~~~g 130 (131)
+-|+..|.|.++....+..-..++..|.+.|.+.|
T Consensus 78 ~gK~vAlFG~Gd~~~y~~~f~~a~~~l~~~l~~~G 112 (172)
T PRK12359 78 EGKIVALYGMGDQLGYGEWFLDALGMLHDKLAPKG 112 (172)
T ss_pred CCCEEEEEeCCCCccchHHHHHHHHHHHHHHHhCC
Confidence 34567777776654456677888899999998765
No 81
>TIGR01664 DNA-3'-Pase DNA 3'-phosphatase. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region.
Probab=20.33 E-value=63 Score=22.81 Aligned_cols=18 Identities=22% Similarity=0.287 Sum_probs=14.7
Q ss_pred cceeEEEcCCCCeEEecC
Q 032890 20 LTSAAIVGHDGSVWAQSS 37 (131)
Q Consensus 20 ~~~aaI~g~dG~~wA~s~ 37 (131)
..+.++++.||.+|...+
T Consensus 12 ~~k~~~~D~Dgtl~~~~~ 29 (166)
T TIGR01664 12 QSKVAAFDLDGTLITTRS 29 (166)
T ss_pred cCcEEEEeCCCceEecCC
Confidence 378899999999998643
No 82
>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=20.19 E-value=1.1e+02 Score=25.24 Aligned_cols=33 Identities=18% Similarity=0.381 Sum_probs=20.6
Q ss_pred cEEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032890 99 QALIFGIYDEPL-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 99 ~~ivI~~~~~~~-~~~~~~~~v~~lA~yL~~~gy 131 (131)
+.+|++.-+++. ..-.+..+.-.+|||++++|+
T Consensus 194 ~v~v~~tsd~~~~~r~~~~~~a~tiAEyfr~~G~ 227 (413)
T TIGR03497 194 SVVVVATSDQPALMRLKAAFTATAIAEYFRDQGK 227 (413)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 345555555432 223455667789999999885
No 83
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=20.07 E-value=1.1e+02 Score=25.37 Aligned_cols=32 Identities=22% Similarity=0.353 Sum_probs=19.1
Q ss_pred EEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032890 100 ALIFGIYDEPL-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 100 ~ivI~~~~~~~-~~~~~~~~v~~lA~yL~~~gy 131 (131)
.+|++.-+++. ..-.+....-.+|+|++++|+
T Consensus 198 vvv~atsd~~~~~r~~a~~~a~~iAEyfrd~G~ 230 (418)
T TIGR03498 198 VVVVATSDESPLMRRQAAYTATAIAEYFRDQGK 230 (418)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 34444444432 223355567779999999885
Done!