Query 032871
Match_columns 131
No_of_seqs 106 out of 437
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 06:58:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032871.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032871hhsearch_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 9.7E-50 2.1E-54 280.7 16.2 127 1-131 1-150 (150)
2 smart00392 PROF Profilin. Bind 100.0 2.7E-47 5.9E-52 265.3 16.0 127 1-131 1-129 (129)
3 cd00148 PROF Profilin binds ac 100.0 4.2E-47 9.2E-52 263.7 16.2 125 2-131 1-127 (127)
4 KOG1755 Profilin [Cytoskeleton 100.0 1.2E-43 2.6E-48 242.9 14.4 127 1-131 1-128 (128)
5 PF00235 Profilin: Profilin; 100.0 4.4E-42 9.6E-47 236.0 11.9 121 2-126 1-121 (121)
6 COG2018 Uncharacterized distan 89.4 2.1 4.5E-05 29.4 6.3 90 18-117 17-106 (119)
7 PF13734 Inhibitor_I69: Spi pr 84.1 2.6 5.6E-05 27.8 4.3 81 37-128 3-91 (96)
8 PF03259 Robl_LC7: Roadblock/L 83.5 0.72 1.6E-05 28.9 1.5 64 19-84 14-77 (91)
9 PF08923 MAPKK1_Int: Mitogen-a 78.4 13 0.00028 25.4 6.4 111 3-128 3-114 (119)
10 PF02911 Formyl_trans_C: Formy 65.0 33 0.00071 21.7 6.3 37 38-78 10-46 (100)
11 COG0223 Fmt Methionyl-tRNA for 59.0 54 0.0012 26.1 6.9 66 38-109 213-278 (307)
12 TIGR00460 fmt methionyl-tRNA f 53.8 93 0.002 24.5 7.5 37 38-78 212-248 (313)
13 COG3382 Solo B3/4 domain (OB-f 53.4 41 0.00089 25.7 5.2 37 93-129 179-215 (229)
14 PRK00394 transcription factor; 51.6 38 0.00082 24.7 4.7 39 89-131 46-84 (179)
15 PF10144 SMP_2: Bacterial viru 49.9 23 0.0005 26.6 3.4 26 10-38 80-105 (210)
16 PF08513 LisH: LisH; InterPro 46.9 15 0.00033 18.2 1.4 10 122-131 7-16 (27)
17 PRK06988 putative formyltransf 46.0 1.2E+02 0.0026 23.9 7.1 38 38-78 211-248 (312)
18 COG2139 RPL21A Ribosomal prote 43.4 38 0.00083 22.4 3.2 24 87-110 57-80 (98)
19 PHA02610 uvsY.-2 hypothetical 43.0 40 0.00087 19.7 2.9 24 99-122 13-36 (53)
20 cd04516 TBP_eukaryotes eukaryo 41.5 80 0.0017 22.9 5.0 36 92-131 50-85 (174)
21 PF02770 Acyl-CoA_dh_M: Acyl-C 41.4 22 0.00047 20.1 1.7 17 62-78 24-40 (52)
22 PRK00005 fmt methionyl-tRNA fo 39.9 1.8E+02 0.0039 22.7 7.5 37 38-78 212-248 (309)
23 PLN00062 TATA-box-binding prot 39.6 95 0.002 22.7 5.2 37 91-131 49-85 (179)
24 PF02789 Peptidase_M17_N: Cyto 39.5 73 0.0016 20.8 4.3 34 97-130 52-86 (126)
25 PF12965 DUF3854: Domain of un 39.0 75 0.0016 21.8 4.4 34 98-131 68-103 (130)
26 smart00667 LisH Lissencephaly 39.0 19 0.00042 17.6 1.1 12 120-131 8-19 (34)
27 cd04518 TBP_archaea archaeal T 38.8 86 0.0019 22.7 4.9 38 90-131 48-85 (174)
28 KOG0141 Isovaleryl-CoA dehydro 38.7 47 0.001 27.0 3.6 44 62-105 183-228 (421)
29 PRK11246 hypothetical protein; 38.2 67 0.0015 24.4 4.3 27 10-39 80-106 (218)
30 COG3377 Uncharacterized conser 37.9 1.1E+02 0.0025 20.0 4.7 32 62-93 4-36 (95)
31 PRK13604 luxD acyl transferase 36.2 94 0.002 24.7 5.0 53 74-131 13-65 (307)
32 COG1157 FliI Flagellar biosynt 36.1 36 0.00079 28.4 2.8 33 99-131 220-253 (441)
33 PF08479 POTRA_2: POTRA domain 35.8 41 0.00089 20.4 2.4 22 110-131 31-52 (76)
34 cd00652 TBP_TLF TATA box bindi 35.6 1.1E+02 0.0023 22.2 4.9 38 90-131 48-85 (174)
35 PF02021 UPF0102: Uncharacteri 35.5 62 0.0014 20.8 3.4 66 62-130 12-79 (93)
36 TIGR02764 spore_ybaN_pdaB poly 35.5 79 0.0017 22.5 4.3 21 111-131 162-182 (191)
37 PF09176 Mpt_N: Methylene-tetr 33.8 24 0.00052 22.6 1.1 31 41-71 20-53 (81)
38 PF05176 ATP-synt_10: ATP10 pr 33.7 45 0.00098 25.7 2.8 34 19-55 216-250 (252)
39 cd00861 ProRS_anticodon_short 32.8 90 0.0019 19.1 3.8 19 113-131 14-32 (94)
40 PF04312 DUF460: Protein of un 31.9 1.3E+02 0.0027 21.3 4.6 39 12-52 35-73 (138)
41 cd01132 F1_ATPase_alpha F1 ATP 31.6 64 0.0014 25.3 3.4 33 99-131 128-161 (274)
42 PF07244 Surf_Ag_VNR: Surface 31.3 58 0.0013 19.2 2.6 22 110-131 32-53 (78)
43 PF07494 Reg_prop: Two compone 31.1 67 0.0015 15.1 2.5 16 23-38 9-24 (24)
44 COG1832 Predicted CoA-binding 30.8 77 0.0017 22.4 3.3 30 96-131 15-44 (140)
45 cd00862 ProRS_anticodon_zinc P 29.6 1.1E+02 0.0024 22.4 4.3 34 98-131 11-44 (202)
46 PF11513 TA0956: Thermoplasma 29.5 1.7E+02 0.0037 19.3 4.6 38 91-131 66-104 (110)
47 PF14584 DUF4446: Protein of u 29.2 91 0.002 22.1 3.6 29 24-53 116-150 (151)
48 PHA02119 hypothetical protein 28.5 40 0.00086 21.1 1.4 12 120-131 57-68 (87)
49 PF01509 TruB_N: TruB family p 28.0 89 0.0019 22.0 3.4 43 29-72 60-105 (149)
50 COG4725 IME4 Transcriptional a 27.7 90 0.0019 22.9 3.3 58 65-124 98-156 (198)
51 PF00352 TBP: Transcription fa 27.5 1.6E+02 0.0035 18.3 5.9 36 91-130 51-86 (86)
52 cd01134 V_A-ATPase_A V/A-type 27.1 67 0.0015 26.3 2.9 33 99-131 221-254 (369)
53 cd04517 TLF TBP-like factors ( 27.1 1.6E+02 0.0034 21.3 4.6 37 91-131 49-85 (174)
54 cd00320 cpn10 Chaperonin 10 Kd 27.0 47 0.001 21.5 1.6 17 62-78 71-87 (93)
55 PF08356 EF_assoc_2: EF hand a 26.9 54 0.0012 21.3 1.9 30 41-70 3-34 (89)
56 PF07799 DUF1643: Protein of u 26.5 1E+02 0.0022 20.9 3.4 34 98-131 13-46 (136)
57 PRK00364 groES co-chaperonin G 25.9 52 0.0011 21.4 1.7 17 62-78 72-88 (95)
58 TIGR01752 flav_long flavodoxin 25.8 1.4E+02 0.003 20.9 4.1 35 97-131 78-112 (167)
59 PRK05922 type III secretion sy 25.2 83 0.0018 26.3 3.2 34 98-131 213-247 (434)
60 PF10886 DUF2685: Protein of u 25.0 1.2E+02 0.0026 17.9 3.0 24 99-122 13-36 (54)
61 COG4443 Uncharacterized protei 24.9 56 0.0012 20.1 1.6 18 38-56 54-71 (72)
62 PRK08125 bifunctional UDP-gluc 24.8 4.6E+02 0.01 22.7 8.0 38 38-78 209-246 (660)
63 TIGR01664 DNA-3'-Pase DNA 3'-p 24.6 41 0.00088 23.8 1.1 18 20-37 12-29 (166)
64 KOG2500 Uncharacterized conser 24.5 1.1E+02 0.0025 23.4 3.5 33 49-81 67-99 (253)
65 PTZ00414 10 kDa heat shock pro 24.4 80 0.0017 20.9 2.4 18 61-78 75-92 (100)
66 PF14553 YqbF: YqbF, hypotheti 24.4 71 0.0015 17.9 1.8 14 118-131 21-34 (43)
67 PF06918 DUF1280: Protein of u 24.2 1.6E+02 0.0034 22.3 4.3 30 99-128 191-220 (224)
68 PF03665 UPF0172: Uncharacteri 23.9 69 0.0015 23.7 2.3 22 47-69 12-33 (196)
69 PRK02821 hypothetical protein; 23.7 1.6E+02 0.0035 18.4 3.6 44 47-90 6-52 (77)
70 PRK14533 groES co-chaperonin G 23.6 67 0.0014 20.8 1.9 18 61-78 66-83 (91)
71 PRK00468 hypothetical protein; 22.8 2E+02 0.0044 17.8 4.0 44 47-90 5-51 (75)
72 PF13989 YejG: YejG-like prote 22.7 1.7E+02 0.0036 19.6 3.6 50 47-97 55-104 (106)
73 PRK12359 flavodoxin FldB; Prov 22.0 1.7E+02 0.0036 21.1 3.9 35 96-130 78-112 (172)
74 TIGR01043 ATP_syn_A_arch ATP s 21.9 1E+02 0.0022 26.9 3.1 32 100-131 287-319 (578)
75 PF10653 Phage-A118_gp45: Prot 21.8 74 0.0016 18.7 1.6 14 115-128 38-51 (62)
76 COG1660 Predicted P-loop-conta 21.7 2.1E+02 0.0045 22.7 4.5 35 95-130 238-272 (286)
77 PRK11835 hypothetical protein; 21.7 2E+02 0.0044 19.5 3.9 51 47-98 58-108 (114)
78 PHA02754 hypothetical protein; 21.6 1.3E+02 0.0029 18.0 2.7 19 60-78 27-45 (67)
79 TIGR01626 ytfJ_HI0045 conserve 21.6 1.2E+02 0.0026 22.2 3.1 34 20-55 146-180 (184)
80 PF13856 Gifsy-2: ATP-binding 21.4 1.2E+02 0.0026 19.3 2.8 20 59-78 66-85 (95)
81 PF00166 Cpn10: Chaperonin 10 21.3 86 0.0019 20.1 2.1 17 62-78 71-87 (93)
82 PF08127 Propeptide_C1: Peptid 21.2 54 0.0012 18.0 1.0 28 30-57 13-40 (41)
83 PF11389 Porin_OmpL1: Leptospi 20.9 1.8E+02 0.0039 22.4 4.0 47 53-102 30-79 (267)
84 PRK06936 type III secretion sy 20.6 1E+02 0.0022 25.8 2.8 32 100-131 220-252 (439)
85 cd01133 F1-ATPase_beta F1 ATP 20.5 1E+02 0.0022 24.1 2.6 33 99-131 129-163 (274)
86 PF13098 Thioredoxin_2: Thiore 20.3 1.2E+02 0.0027 19.1 2.7 27 23-51 86-112 (112)
87 PF05952 ComX: Bacillus compet 20.2 86 0.0019 18.7 1.7 18 41-58 28-45 (57)
88 PRK04192 V-type ATP synthase s 20.1 1.1E+02 0.0024 26.7 3.0 32 100-131 292-324 (586)
No 1
>PTZ00316 profilin; Provisional
Probab=100.00 E-value=9.7e-50 Score=280.65 Aligned_cols=127 Identities=35% Similarity=0.638 Sum_probs=121.7
Q ss_pred CChHHHhhhhcccccccCccceEEEEcc-CCCeEEecCCCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeCC
Q 032871 1 MSWQAYVDDHLLCEIEGNHLSAAAIIGH-DGSVWAQSENFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEP 79 (131)
Q Consensus 1 MSW~~yv~~~Lv~~~sg~~~~~aaI~g~-dG~~wA~s~~f~~i~~~E~~~l~~~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 032871 80 ---GAVIRGKKGPGGVTIKKTSAALIIGIYDE-------------------PMTPGQCNMIVERLGDYLIDQGL 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 57999999999999999999998
No 2
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=100.00 E-value=2.7e-47 Score=265.31 Aligned_cols=127 Identities=54% Similarity=0.872 Sum_probs=123.0
Q ss_pred CChHHHhhhhcccccccCccceEEEEccCCCeEEecCC--CCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeC
Q 032871 1 MSWQAYVDDHLLCEIEGNHLSAAAIIGHDGSVWAQSEN--FPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 1 MSW~~yv~~~Lv~~~sg~~~~~aaI~g~dG~~wA~s~~--f~~i~~~E~~~l~~~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 7457999999999999999888899999999999999999
Q ss_pred CCceEEEEcCCCcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 79 PGAVIRGKKGPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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=4.2e-47 Score=263.75 Aligned_cols=125 Identities=56% Similarity=0.979 Sum_probs=122.3
Q ss_pred ChHHHhhhhcccccccCccceEEEEccC-CCeEEecCC-CCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeCC
Q 032871 2 SWQAYVDDHLLCEIEGNHLSAAAIIGHD-GSVWAQSEN-FPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEP 79 (131)
Q Consensus 2 SW~~yv~~~Lv~~~sg~~~~~aaI~g~d-G~~wA~s~~-f~~i~~~E~~~l~~~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 99999999999999999889999999999999999999
Q ss_pred CceEEEEcCCCcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 80 GAVIRGKKGPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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=1.2e-43 Score=242.95 Aligned_cols=127 Identities=63% Similarity=1.082 Sum_probs=123.5
Q ss_pred CChHHHhhhhcccccccCccceEEEEccCC-CeEEecCCCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeCC
Q 032871 1 MSWQAYVDDHLLCEIEGNHLSAAAIIGHDG-SVWAQSENFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEP 79 (131)
Q Consensus 1 MSW~~yv~~~Lv~~~sg~~~~~aaI~g~dG-~~wA~s~~f~~i~~~E~~~l~~~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 032871 80 GAVIRGKKGPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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=4.4e-42 Score=235.97 Aligned_cols=121 Identities=50% Similarity=0.983 Sum_probs=116.9
Q ss_pred ChHHHhhhhcccccccCccceEEEEccCCCeEEecCCCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeCCCc
Q 032871 2 SWQAYVDDHLLCEIEGNHLSAAAIIGHDGSVWAQSENFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGA 81 (131)
Q Consensus 2 SW~~yv~~~Lv~~~sg~~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~l~~~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 899999999999999999999889999999999999999888899999999999999998 89
Q ss_pred eEEEEcCCCcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHH
Q 032871 82 VIRGKKGPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYL 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=89.44 E-value=2.1 Score=29.44 Aligned_cols=90 Identities=18% Similarity=0.213 Sum_probs=55.5
Q ss_pred CccceEEEEccCCCeEEecCCCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeCCCceEEEEcCCCcEEEEec
Q 032871 18 NHLSAAAIIGHDGSVWAQSENFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKT 97 (131)
Q Consensus 18 ~~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d~~~~i~~kk~~~G~~i~kt 97 (131)
+.+..++|.+.||-+-++...+ +...+-+.++....-...+....-|--+...++.++.++++.+.-.-|..++
T Consensus 17 ~gv~ga~Ivs~DGL~ia~~~p~-~~d~e~vaA~~a~~~g~~er~~~~l~~g~leqi~I~g~~g~i~l~~~g~~~i----- 90 (119)
T COG2018 17 PGVRGALVVSKDGLPIAAELPG-NVDAEIVAAMAATALGLAERAADELGGGELEQIMIEGKKGKILLYDAGDDAI----- 90 (119)
T ss_pred cCceEEEEEccCCceEeecCCC-cccHHHHHHHHHHHHHHhHHHHHHhCCCCceEEEEeccccEEEEEEcCCceE-----
Confidence 3799999999999999987777 7776777777655432222334556666777888887733443323344444
Q ss_pred CCEEEEEEeCCCCCcchHHH
Q 032871 98 SAALIIGIYDEPMTPGQCNM 117 (131)
Q Consensus 98 ~~~ivI~~~~~~~~~~~~~~ 117 (131)
++..-+...+-|...-
T Consensus 91 ----l~~~a~~~~nLGli~~ 106 (119)
T COG2018 91 ----LVVLADEGTNLGLIRM 106 (119)
T ss_pred ----EEEEcCCCCcchhhhh
Confidence 3444445555554433
No 7
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=84.08 E-value=2.6 Score=27.80 Aligned_cols=81 Identities=21% Similarity=0.224 Sum_probs=38.3
Q ss_pred CCCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEe--CC-C--ceEEEEcCCCcEEEEecCC--EEEEEEeCCC
Q 032871 37 ENFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQG--EP-G--AVIRGKKGPGGVTIKKTSA--ALIIGIYDEP 109 (131)
Q Consensus 37 ~~f~~i~~~E~~~l~~~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 578 88999999999988432211 111122221 11 1 125545 777888887665 4489998888
Q ss_pred CC-cchHHHHHHHHHHHHHh
Q 032871 110 MT-PGQCNMIVERLGDYLID 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 53 223 2344556666654
No 8
>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=83.45 E-value=0.72 Score=28.86 Aligned_cols=64 Identities=17% Similarity=0.193 Sum_probs=35.9
Q ss_pred ccceEEEEccCCCeEEecCCCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeCCCceEE
Q 032871 19 HLSAAAIIGHDGSVWAQSENFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIR 84 (131)
Q Consensus 19 ~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d~~~~i~ 84 (131)
.+..+.|++.||.+-++ .++....++.+..+...+-........-+..+..+++.++.+ +..++
T Consensus 14 gv~~~~l~~~dG~~i~~-~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~-~~~i~ 77 (91)
T PF03259_consen 14 GVRGAVLVDKDGLVIAS-SGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETE-KGEII 77 (91)
T ss_dssp TEEEEEEEETTSEEEEE-TSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEES-SEEEE
T ss_pred CeeEEEEEcCCCCEEEE-ecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEEC-CCEEE
Confidence 89999999999999888 333233444444443332111001112222567778888887 44333
No 9
>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=78.36 E-value=13 Score=25.39 Aligned_cols=111 Identities=18% Similarity=0.177 Sum_probs=63.3
Q ss_pred hHHHhhhhcccccccCccceEEEEccCCCeEEecCCCCCCCHHHH-HHHHHhcCCCCCCCccceEEcCeEEEEEEeCCCc
Q 032871 3 WQAYVDDHLLCEIEGNHLSAAAIIGHDGSVWAQSENFPQLKPEEI-TGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGA 81 (131)
Q Consensus 3 W~~yv~~~Lv~~~sg~~~~~aaI~g~dG~~wA~s~~f~~i~~~E~-~~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d~~~ 81 (131)
-+.++. .|+. .-+.+....|.|+||-+.+....= .....++ ..++..|.- ..-+.+-+.+++.|+++...+ +.
T Consensus 3 l~~~L~-~ll~--~v~Gl~~I~itDrDGvpi~~v~~~-~~~~~~~~~~~~~tf~~-a~~Q~~KL~lG~nk~ii~~Y~-~~ 76 (119)
T PF08923_consen 3 LKRFLQ-KLLS--RVDGLQAIVITDRDGVPIAKVSSD-SAPESAMRPSLLSTFAM-AIDQASKLGLGKNKSIIAYYD-SY 76 (119)
T ss_dssp HHHHHH-HHGG--GSTTEEEEEEEETTS-EEEEEE-T-TS-GGGGSHHHHCCHHH-HHHHHTTSSS-SEEEEEEEES-SE
T ss_pred HHHHHH-HHHh--ccCCeEEEEEECCCCcEEEEecCC-CCcchhhhhHHHHHHHH-HhhcccccCCCCceEEEEEeC-CE
Confidence 366776 5665 323688889999999766652111 1112222 233333321 001355678899999999999 55
Q ss_pred eEEEEcCCCcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHh
Q 032871 82 VIRGKKGPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLID 128 (131)
Q Consensus 82 ~i~~kk~~~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~ 128 (131)
.+.-.. + ...+|..+...+.+-|....--++|+++|.+
T Consensus 77 qvv~~~--------~-~pl~it~ias~~aN~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 77 QVVQFN--------K-LPLYITFIASSNANTGLILSLEEELAPILNE 114 (119)
T ss_dssp EEEEEE--------E-TTEEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred EEEEEe--------C-CCeEEEEEecCCCCHHHHHHhHHHHHHHHHH
Confidence 443222 2 3356666667777888777777777777754
No 10
>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=64.95 E-value=33 Score=21.68 Aligned_cols=37 Identities=19% Similarity=0.370 Sum_probs=28.2
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeC
Q 032871 38 NFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~l~~~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 57 779999999999997 42 233456799999999874
No 11
>COG0223 Fmt Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]
Probab=59.04 E-value=54 Score=26.11 Aligned_cols=66 Identities=15% Similarity=0.212 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeCCCceEEEEcCCCcEEEEecCCEEEEEEeCCC
Q 032871 38 NFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKTSAALIIGIYDEP 109 (131)
Q Consensus 38 ~f~~i~~~E~~~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~ 109 (131)
+| +-+..++-..+.+|.. .+.-=..++|+++.+.+++-.+.-.. ++-|-++...++.++|+..++.
T Consensus 213 dw-~~~a~~i~n~IRa~~P---~Pga~~~~~~~~iki~~a~~~~~~~~--~~pG~i~~~~~~~l~Va~~~g~ 278 (307)
T COG0223 213 DW-SKPAAQILNKIRAFNP---WPGAWTELGGKRIKIWEARVLEGASN--GKPGEILAADKKGLLVACGDGA 278 (307)
T ss_pred CC-ccCHHHHHHHHhccCC---CCceEEEECCeEEEEEEEEEcccccc--CCCcceEEecCCcEEEEeCCce
Confidence 47 6678888899999883 34667788999999998762111111 5667777777777888774444
No 12
>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=53.81 E-value=93 Score=24.47 Aligned_cols=37 Identities=16% Similarity=0.337 Sum_probs=28.2
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeC
Q 032871 38 NFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~l~~~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 47 668899999999997 3 2333457899999998764
No 13
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=53.44 E-value=41 Score=25.68 Aligned_cols=37 Identities=16% Similarity=0.090 Sum_probs=32.9
Q ss_pred EEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhC
Q 032871 93 TIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQ 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 3457888999999999999999999999999999863
No 14
>PRK00394 transcription factor; Reviewed
Probab=51.62 E-value=38 Score=24.68 Aligned_cols=39 Identities=13% Similarity=0.096 Sum_probs=29.9
Q ss_pred CCcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 89 PGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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 344667777777776544 446999999999999999986
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=49.92 E-value=23 Score=26.58 Aligned_cols=26 Identities=31% Similarity=0.341 Sum_probs=22.0
Q ss_pred hcccccccCccceEEEEccCCCeEEecCC
Q 032871 10 HLLCEIEGNHLSAAAIIGHDGSVWAQSEN 38 (131)
Q Consensus 10 ~Lv~~~sg~~~~~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 54 99999999999999999864
No 16
>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=46.93 E-value=15 Score=18.18 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=8.0
Q ss_pred HHHHHHhCCC
Q 032871 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 17
>PRK06988 putative formyltransferase; Provisional
Probab=46.01 E-value=1.2e+02 Score=23.87 Aligned_cols=38 Identities=16% Similarity=0.380 Sum_probs=28.8
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeC
Q 032871 38 NFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~l~~~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 47 56789999999999654 2233357899999999865
No 18
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=43.44 E-value=38 Score=22.40 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=21.6
Q ss_pred cCCCcEEEEecCCEEEEEEeCCCC
Q 032871 87 KGPGGVTIKKTSAALIIGIYDEPM 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 578999999999999999998764
No 19
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=42.98 E-value=40 Score=19.72 Aligned_cols=24 Identities=38% Similarity=0.685 Sum_probs=18.6
Q ss_pred CEEEEEEeCCCCCcchHHHHHHHH
Q 032871 99 AALIIGIYDEPMTPGQCNMIVERL 122 (131)
Q Consensus 99 ~~ivI~~~~~~~~~~~~~~~v~~l 122 (131)
+++.|-.-.++++||.|...++.+
T Consensus 13 ~al~v~T~~Gpvh~g~C~~y~~e~ 36 (53)
T PHA02610 13 KALVVETEKGPVHPGPCYNYVEEL 36 (53)
T ss_pred hceEEecCCCCCCChhHHHHHHhc
Confidence 366666667788999999888765
No 20
>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=41.53 E-value=80 Score=22.90 Aligned_cols=36 Identities=8% Similarity=0.189 Sum_probs=27.4
Q ss_pred EEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 92 VTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 92 ~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~gy 131 (131)
+.|..+.+.++-|-. ...++..+++++++.|++.||
T Consensus 50 ~lIF~SGKiviTGak----s~e~a~~a~~~i~~~L~~~g~ 85 (174)
T cd04516 50 ALIFSSGKMVCTGAK----SEDDSKLAARKYARIIQKLGF 85 (174)
T ss_pred EEEECCCeEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 556666666665433 457899999999999999986
No 21
>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=41.37 E-value=22 Score=20.14 Aligned_cols=17 Identities=29% Similarity=0.395 Sum_probs=14.8
Q ss_pred ccceEEcCeEEEEEEeC
Q 032871 62 PTGLYLGGTKYMVIQGE 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 22
>PRK00005 fmt methionyl-tRNA formyltransferase; Reviewed
Probab=39.90 E-value=1.8e+02 Score=22.71 Aligned_cols=37 Identities=19% Similarity=0.395 Sum_probs=27.1
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeC
Q 032871 38 NFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~l~~~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 46 557889999999995 3 2233346899999998864
No 23
>PLN00062 TATA-box-binding protein; Provisional
Probab=39.57 E-value=95 Score=22.66 Aligned_cols=37 Identities=8% Similarity=0.156 Sum_probs=27.8
Q ss_pred cEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 91 GVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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~~~~~~~L~~lg~ 85 (179)
T PLN00062 49 TALIFASGKMVCTGAK----SEHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred EEEEECCCeEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 3566666766665433 457899999999999999886
No 24
>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=39.48 E-value=73 Score=20.78 Aligned_cols=34 Identities=12% Similarity=0.109 Sum_probs=29.0
Q ss_pred cCCEEEEEEeCCC-CCcchHHHHHHHHHHHHHhCC
Q 032871 97 TSAALIIGIYDEP-MTPGQCNMIVERLGDYLIDQG 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 4668899999987 589999999999999998754
No 25
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=39.01 E-value=75 Score=21.82 Aligned_cols=34 Identities=21% Similarity=0.328 Sum_probs=25.5
Q ss_pred CCEEEEEEeCCCC--CcchHHHHHHHHHHHHHhCCC
Q 032871 98 SAALIIGIYDEPM--TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 98 ~~~ivI~~~~~~~--~~~~~~~~v~~la~yL~~~gy 131 (131)
..-|+|++-.+.. .-.+.+.++.++++.|++.|+
T Consensus 68 gr~v~iaFD~D~~~~Tn~~V~~a~~~l~~~L~~~G~ 103 (130)
T PF12965_consen 68 GREVYIAFDADTKPKTNKNVRRAIKRLGKLLKEAGC 103 (130)
T ss_pred CceEEEEecCCCccchhHHHHHHHHHHHHHHHHCCC
Confidence 4566776666533 347899999999999999884
No 26
>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=38.98 E-value=19 Score=17.65 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=9.9
Q ss_pred HHHHHHHHhCCC
Q 032871 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 27
>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=38.81 E-value=86 Score=22.72 Aligned_cols=38 Identities=16% Similarity=0.147 Sum_probs=28.5
Q ss_pred CcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 90 GGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 90 ~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~gy 131 (131)
.-+.|..+.+.++.|. -...++..+++++++.|++.||
T Consensus 48 ~t~lIF~SGKiv~tGa----ks~~~a~~a~~~~~~~L~~~g~ 85 (174)
T cd04518 48 IAALIFRSGKMVCTGA----KSVEDLHRAVKEIIKKLKDYGI 85 (174)
T ss_pred EEEEEECCCeEEEEcc----CCHHHHHHHHHHHHHHHHhcCC
Confidence 3455666666666543 3567899999999999999986
No 28
>KOG0141 consensus Isovaleryl-CoA dehydrogenase [Amino acid transport and metabolism; Lipid transport and metabolism]
Probab=38.70 E-value=47 Score=26.98 Aligned_cols=44 Identities=20% Similarity=0.325 Sum_probs=30.6
Q ss_pred ccceEEcCeEEEEEEeCCCce--EEEEcCCCcEEEEecCCEEEEEE
Q 032871 62 PTGLYLGGTKYMVIQGEPGAV--IRGKKGPGGVTIKKTSAALIIGI 105 (131)
Q Consensus 62 ~~Gi~~~g~Ky~v~r~d~~~~--i~~kk~~~G~~i~kt~~~ivI~~ 105 (131)
.+...+||.|+.++...+.++ +|+|.+.+++--.+--+++||=.
T Consensus 183 g~~yiLNGsK~witNG~~advliVyAkTd~~a~~~~hGIt~FiVEk 228 (421)
T KOG0141|consen 183 GDDYILNGSKFWITNGPDADVLIVYAKTDHSAVPPSHGITAFIVEK 228 (421)
T ss_pred CCcEEecCcEEEEecCCCCcEEEEEEecCCCCCCCcCceEEEEEcC
Confidence 578899999999999763343 88887777555444455566543
No 29
>PRK11246 hypothetical protein; Provisional
Probab=38.15 E-value=67 Score=24.37 Aligned_cols=27 Identities=22% Similarity=0.292 Sum_probs=23.0
Q ss_pred hcccccccCccceEEEEccCCCeEEecCCC
Q 032871 10 HLLCEIEGNHLSAAAIIGHDGSVWAQSENF 39 (131)
Q Consensus 10 ~Lv~~~sg~~~~~aaI~g~dG~~wA~s~~f 39 (131)
+|.. +. .|-+|.|++.||...|++.+.
T Consensus 80 ~La~--d~-~VlDAsIY~~~G~llA~S~~~ 106 (218)
T PRK11246 80 QLTD--ES-RILDASVYDEQGDLIARSGES 106 (218)
T ss_pred HHhc--CC-ceeeEEEECCCCCEEEecCCC
Confidence 5666 54 999999999999999998765
No 30
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=37.88 E-value=1.1e+02 Score=19.99 Aligned_cols=32 Identities=16% Similarity=0.263 Sum_probs=21.7
Q ss_pred ccceEEcCeEEEEEEeCCCce-EEEEcCCCcEE
Q 032871 62 PTGLYLGGTKYMVIQGEPGAV-IRGKKGPGGVT 93 (131)
Q Consensus 62 ~~Gi~~~g~Ky~v~r~d~~~~-i~~kk~~~G~~ 93 (131)
-+-|.++|++|..++.+=++. +..-++..|.+
T Consensus 4 i~~i~i~gk~~l~~~~~L~napll~~~~ekgy~ 36 (95)
T COG3377 4 IEPIDIEGKKFLGLKVDLPNAPLLALKGEKGYA 36 (95)
T ss_pred eeeEeeCCeEEEEEEecCCCCcEEEEEccccEE
Confidence 356889999999999885443 44455555543
No 31
>PRK13604 luxD acyl transferase; Provisional
Probab=36.18 E-value=94 Score=24.71 Aligned_cols=53 Identities=23% Similarity=0.152 Sum_probs=29.2
Q ss_pred EEEeCCCceEEEEcCCCcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 74 VIQGEPGAVIRGKKGPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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 45555355566553211101122234667766555421 238899999999997
No 32
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=36.06 E-value=36 Score=28.43 Aligned_cols=33 Identities=18% Similarity=0.411 Sum_probs=22.4
Q ss_pred CEEEEEEeCCC-CCcchHHHHHHHHHHHHHhCCC
Q 032871 99 AALIIGIYDEP-MTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 99 ~~ivI~~~~~~-~~~~~~~~~v~~la~yL~~~gy 131 (131)
+.+|++.-|++ ...-++......+|+|++++|.
T Consensus 220 sViVvATSD~s~l~R~~aa~~At~IAEyFRDqG~ 253 (441)
T COG1157 220 SVVVVATSDESALMRLKAAFTATTIAEYFRDQGK 253 (441)
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHHHhCCC
Confidence 34455555554 2455677778889999999983
No 33
>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=35.77 E-value=41 Score=20.40 Aligned_cols=22 Identities=18% Similarity=0.439 Sum_probs=17.7
Q ss_pred CCcchHHHHHHHHHHHHHhCCC
Q 032871 110 MTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 110 ~~~~~~~~~v~~la~yL~~~gy 131 (131)
......+..+..+.+++++.||
T Consensus 31 l~~~~l~~~~~~l~~~y~~~GY 52 (76)
T PF08479_consen 31 LTLADLQQLADALTNYYREKGY 52 (76)
T ss_dssp B-HHHHHHHHHHHHHHHHHTT-
T ss_pred cCHHHHHHHHHHHHHHHHHcCc
Confidence 4567788999999999999998
No 34
>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=35.61 E-value=1.1e+02 Score=22.15 Aligned_cols=38 Identities=13% Similarity=0.211 Sum_probs=28.7
Q ss_pred CcEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 90 GGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 90 ~G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~gy 131 (131)
.-+.|..+.+.++.|.. ...++..+++++++.|++.||
T Consensus 48 ~t~lIf~sGKivitGak----s~~~~~~a~~~~~~~L~~~g~ 85 (174)
T cd00652 48 TTALIFSSGKMVITGAK----SEEDAKLAARKYARILQKLGF 85 (174)
T ss_pred EEEEEECCCEEEEEecC----CHHHHHHHHHHHHHHHHHcCC
Confidence 34566677766665543 457899999999999999886
No 35
>PF02021 UPF0102: Uncharacterised protein family UPF0102; InterPro: IPR003509 The proteins in this entry are functionally uncharacterised.; PDB: 3FOV_A.
Probab=35.50 E-value=62 Score=20.79 Aligned_cols=66 Identities=20% Similarity=0.240 Sum_probs=32.1
Q ss_pred ccceEEcCeEEEEEEeCCCce-EEEEcCCCc-EEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCC
Q 032871 62 PTGLYLGGTKYMVIQGEPGAV-IRGKKGPGG-VTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQG 130 (131)
Q Consensus 62 ~~Gi~~~g~Ky~v~r~d~~~~-i~~kk~~~G-~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~g 130 (131)
..|.++=...|.+-..| . |.++++..- ++-+||.+.--.+.-.+.+++.+...-......||.+.+
T Consensus 12 ~~G~~IL~rN~r~~~GE---IDiIa~~~~~lvfVEVK~R~~~~~~~~~~~v~~~K~~ri~~~A~~yL~~~~ 79 (93)
T PF02021_consen 12 RKGYRILERNWRCRRGE---IDIIARDGDTLVFVEVKTRSSSSFGSPEEAVDPRKQRRIRRAAEYYLAENP 79 (93)
T ss_dssp HTT-EEEEEEEEETTEE---EEEEEEETTEEEEEEEEE--------------HHHHHHHHHHHHHHHHH-G
T ss_pred HCCCEEeeeeecCCCCc---EeEEEEEcccEEEEEEEEeecccccCHHHHChHHHHHHHHHHHHHHHHHCC
Confidence 45777777777773332 3 666775554 455788877665555566677777666666667776653
No 36
>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=35.48 E-value=79 Score=22.51 Aligned_cols=21 Identities=14% Similarity=0.145 Sum_probs=17.6
Q ss_pred CcchHHHHHHHHHHHHHhCCC
Q 032871 111 TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 111 ~~~~~~~~v~~la~yL~~~gy 131 (131)
......+++..+.++|++.||
T Consensus 162 ~~~~t~~~l~~~i~~l~~~Gy 182 (191)
T TIGR02764 162 SAKQTVKALPTIIKKLKEKGY 182 (191)
T ss_pred CcHhHHHHHHHHHHHHHHCCC
Confidence 345567889999999999998
No 37
>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=33.78 E-value=24 Score=22.56 Aligned_cols=31 Identities=32% Similarity=0.828 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHh--c-CCCCCCCccceEEcCeE
Q 032871 41 QLKPEEITGIMND--F-NEPGTLAPTGLYLGGTK 71 (131)
Q Consensus 41 ~i~~~E~~~l~~~--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 6799999999853 5 56777789999999863
No 38
>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=33.67 E-value=45 Score=25.66 Aligned_cols=34 Identities=21% Similarity=0.369 Sum_probs=25.0
Q ss_pred ccceEEEEccCCC-eEEecCCCCCCCHHHHHHHHHhcC
Q 032871 19 HLSAAAIIGHDGS-VWAQSENFPQLKPEEITGIMNDFN 55 (131)
Q Consensus 19 ~~~~aaI~g~dG~-~wA~s~~f~~i~~~E~~~l~~~f~ 55 (131)
.+--.-++|.+|. .||.+. . -+++|+..|.++.+
T Consensus 216 ~~GYvyLVD~~grIRWagsG-~--At~~E~~~L~k~~~ 250 (252)
T PF05176_consen 216 YVGYVYLVDPNGRIRWAGSG-P--ATPEELESLWKCVK 250 (252)
T ss_pred CcCeEEEECCCCeEEeCccC-C--CCHHHHHHHHHHHh
Confidence 4445667788885 599764 3 48999999988653
No 39
>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=32.76 E-value=90 Score=19.13 Aligned_cols=19 Identities=21% Similarity=0.181 Sum_probs=16.0
Q ss_pred chHHHHHHHHHHHHHhCCC
Q 032871 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 40
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=31.93 E-value=1.3e+02 Score=21.25 Aligned_cols=39 Identities=15% Similarity=0.215 Sum_probs=22.7
Q ss_pred ccccccCccceEEEEccCCCeEEecCCCCCCCHHHHHHHHH
Q 032871 12 LCEIEGNHLSAAAIIGHDGSVWAQSENFPQLKPEEITGIMN 52 (131)
Q Consensus 12 v~~~sg~~~~~aaI~g~dG~~wA~s~~f~~i~~~E~~~l~~ 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 343345 778899999999865532211 234455444444
No 41
>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=31.65 E-value=64 Score=25.26 Aligned_cols=33 Identities=15% Similarity=0.313 Sum_probs=22.7
Q ss_pred CEEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032871 99 AALIIGIYDEPM-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 356666666643 333456667889999999885
No 42
>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=31.26 E-value=58 Score=19.22 Aligned_cols=22 Identities=36% Similarity=0.637 Sum_probs=19.6
Q ss_pred CCcchHHHHHHHHHHHHHhCCC
Q 032871 110 MTPGQCNMIVERLGDYLIDQGL 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 4788899999999999999997
No 43
>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=31.14 E-value=67 Score=15.13 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=11.0
Q ss_pred EEEEccCCCeEEecCC
Q 032871 23 AAIIGHDGSVWAQSEN 38 (131)
Q Consensus 23 aaI~g~dG~~wA~s~~ 38 (131)
+-..+.+|.+|..+.+
T Consensus 9 ~i~~D~~G~lWigT~~ 24 (24)
T PF07494_consen 9 SIYEDSDGNLWIGTYN 24 (24)
T ss_dssp EEEE-TTSCEEEEETS
T ss_pred EEEEcCCcCEEEEeCC
Confidence 4556679999987653
No 44
>COG1832 Predicted CoA-binding protein [General function prediction only]
Probab=30.85 E-value=77 Score=22.39 Aligned_cols=30 Identities=27% Similarity=0.573 Sum_probs=22.9
Q ss_pred ecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 96 KTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 96 kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~gy 131 (131)
++|+-.|||..+.+..++ ..+++||.++||
T Consensus 15 ~~K~IAvVG~S~~P~r~s------y~V~kyL~~~GY 44 (140)
T COG1832 15 SAKTIAVVGASDKPDRPS------YRVAKYLQQKGY 44 (140)
T ss_pred hCceEEEEecCCCCCccH------HHHHHHHHHCCC
Confidence 456667888887776554 578899999998
No 45
>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=29.65 E-value=1.1e+02 Score=22.37 Aligned_cols=34 Identities=15% Similarity=0.137 Sum_probs=24.8
Q ss_pred CCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 98 SAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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 3567777765533445688899999999999885
No 46
>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=29.46 E-value=1.7e+02 Score=19.31 Aligned_cols=38 Identities=13% Similarity=0.204 Sum_probs=22.8
Q ss_pred cEEEEecC-CEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 91 GVTIKKTS-AALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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 55554444 4555544432 23458889999999999997
No 47
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=29.18 E-value=91 Score=22.13 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=19.2
Q ss_pred EEEccCCC-eEEec-----CCCCCCCHHHHHHHHHh
Q 032871 24 AIIGHDGS-VWAQS-----ENFPQLKPEEITGIMND 53 (131)
Q Consensus 24 aI~g~dG~-~wA~s-----~~f~~i~~~E~~~l~~~ 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 34455553 67762 224 7899999998765
No 48
>PHA02119 hypothetical protein
Probab=28.47 E-value=40 Score=21.07 Aligned_cols=12 Identities=33% Similarity=0.556 Sum_probs=9.1
Q ss_pred HHHHHHHHhCCC
Q 032871 120 ERLGDYLIDQGL 131 (131)
Q Consensus 120 ~~la~yL~~~gy 131 (131)
..+.|||++.||
T Consensus 57 ~divdylr~lgy 68 (87)
T PHA02119 57 KDIVDYLRSLGY 68 (87)
T ss_pred HHHHHHHHHccc
Confidence 346788888887
No 49
>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=27.95 E-value=89 Score=22.01 Aligned_cols=43 Identities=12% Similarity=0.234 Sum_probs=28.1
Q ss_pred CCCeEEecCCCCCCCHHHHHHHHHhcCCC---CCCCccceEEcCeEE
Q 032871 29 DGSVWAQSENFPQLKPEEITGIMNDFNEP---GTLAPTGLYLGGTKY 72 (131)
Q Consensus 29 dG~~wA~s~~f~~i~~~E~~~l~~~f~~~---~~~~~~Gi~~~g~Ky 72 (131)
+|.+....+-. .++.+++..++.-|... ..-.-+.+.++|++-
T Consensus 60 ~G~v~~~~~~~-~it~e~l~~~l~~f~G~~~Q~pP~ySAvki~G~ra 105 (149)
T PF01509_consen 60 EGEVTETKPYD-HITEEDLEKVLAKFQGEIEQVPPMYSAVKINGKRA 105 (149)
T ss_dssp TSSEEEE---T-T--HHHHHHHHHHTSEEEEES-SSSSSSECTTCEH
T ss_pred eeeEEEeeccc-cCCHHHHHHHHHhCcCCEeeeCchheeEcCCCccH
Confidence 57888875444 89999999999988631 122468888888875
No 50
>COG4725 IME4 Transcriptional activator, adenine-specific DNA methyltransferase [Signal transduction mechanisms / Transcription]
Probab=27.71 E-value=90 Score=22.91 Aligned_cols=58 Identities=22% Similarity=0.286 Sum_probs=42.3
Q ss_pred eEEcCeEEEEEEeCCCceEEEEcCCCcEEEEecCCEEEEEEeCCCC-CcchHHHHHHHHHH
Q 032871 65 LYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKTSAALIIGIYDEPM-TPGQCNMIVERLGD 124 (131)
Q Consensus 65 i~~~g~Ky~v~r~d~~~~i~~kk~~~G~~i~kt~~~ivI~~~~~~~-~~~~~~~~v~~la~ 124 (131)
++++ +-+- +|...+.+..|.+|+---+-+.+...+|+.+.-+.. .|......+|+||-
T Consensus 98 v~~G-tGhw-lr~S~Eh~~vg~~GNpK~~~~~~~i~li~S~~RE~SRKP~E~y~i~ErL~~ 156 (198)
T COG4725 98 VRMG-TGHW-LRTSGEHVFVGTLGNPKQSHVPPTISLIVSMTRETSRKPDELYGIAERLAG 156 (198)
T ss_pred EEee-ccee-ecCCCcEEEEEecCCchhhcCCCceEEEEccchhhccCCHHHHHHHHHhCC
Confidence 3443 4443 344446788888887766667777789999988876 79999999999874
No 51
>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=27.54 E-value=1.6e+02 Score=18.35 Aligned_cols=36 Identities=19% Similarity=0.246 Sum_probs=27.7
Q ss_pred cEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCC
Q 032871 91 GVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQG 130 (131)
Q Consensus 91 G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~g 130 (131)
-+.|..|.+.+|.|.- +..++..+++++.+.|.+.|
T Consensus 51 t~~IF~sGki~itGak----s~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 51 TVLIFSSGKIVITGAK----SEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp EEEEETTSEEEEEEES----SHHHHHHHHHHHHHHHHHTT
T ss_pred EEEEEcCCEEEEEecC----CHHHHHHHHHHHHHHHHHcC
Confidence 3566677777776643 57899999999999999875
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=27.12 E-value=67 Score=26.30 Aligned_cols=33 Identities=18% Similarity=0.283 Sum_probs=21.0
Q ss_pred CEEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032871 99 AALIIGIYDEPM-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 99 ~~ivI~~~~~~~-~~~~~~~~v~~la~yL~~~gy 131 (131)
+.+|++..+++. ....+..+.-.+|+|++++||
T Consensus 221 tvlV~nts~~p~~~R~~s~yta~tiAEYfrd~G~ 254 (369)
T cd01134 221 TVLIANTSNMPVAAREASIYTGITIAEYFRDMGY 254 (369)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 345555555552 233345555669999999986
No 53
>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=27.08 E-value=1.6e+02 Score=21.29 Aligned_cols=37 Identities=14% Similarity=0.213 Sum_probs=27.1
Q ss_pred cEEEEecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 91 GVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 91 G~~i~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~gy 131 (131)
-+-|..+.+.++.|. -...++..+++++++.|++.||
T Consensus 49 t~lIF~sGKiviTGa----ks~~~~~~a~~~~~~~l~~~g~ 85 (174)
T cd04517 49 TASVWSSGKITITGA----TSEEEAKQAARRAARLLQKLGF 85 (174)
T ss_pred EEEEECCCeEEEEcc----CCHHHHHHHHHHHHHHHHHcCC
Confidence 345566666665443 3567899999999999999886
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=26.99 E-value=47 Score=21.48 Aligned_cols=17 Identities=24% Similarity=0.569 Sum_probs=15.3
Q ss_pred ccceEEcCeEEEEEEeC
Q 032871 62 PTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 62 ~~Gi~~~g~Ky~v~r~d 78 (131)
.+-+.++|++|+++|.+
T Consensus 71 g~~v~~~~~~y~i~~~~ 87 (93)
T cd00320 71 GTEVKLDGEEYLILRES 87 (93)
T ss_pred ceEEEECCEEEEEEEHH
Confidence 66799999999999987
No 55
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=26.92 E-value=54 Score=21.26 Aligned_cols=30 Identities=30% Similarity=0.550 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHhcCC--CCCCCccceEEcCe
Q 032871 41 QLKPEEITGIMNDFNE--PGTLAPTGLYLGGT 70 (131)
Q Consensus 41 ~i~~~E~~~l~~~f~~--~~~~~~~Gi~~~g~ 70 (131)
.++++|+..+...+.. |.....+||++.|-
T Consensus 3 pL~~~el~~ik~~v~~~~~~gv~~~GiT~~GF 34 (89)
T PF08356_consen 3 PLQPQELEDIKKVVRENIPDGVNDNGITLDGF 34 (89)
T ss_pred CCCHHHHHHHHHHHHHHCCCCcCCCccchhhH
Confidence 5789999998887743 34456788888774
No 56
>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=26.52 E-value=1e+02 Score=20.88 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=23.0
Q ss_pred CCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 98 SAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 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 4578888888776665555566666666666676
No 57
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=25.94 E-value=52 Score=21.36 Aligned_cols=17 Identities=18% Similarity=0.546 Sum_probs=15.1
Q ss_pred ccceEEcCeEEEEEEeC
Q 032871 62 PTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 62 ~~Gi~~~g~Ky~v~r~d 78 (131)
..-+.++|++|+++|.+
T Consensus 72 g~ev~~~~~~y~iv~~~ 88 (95)
T PRK00364 72 GTEVKIDGEEYLILRES 88 (95)
T ss_pred CeEEEECCEEEEEEEHH
Confidence 55789999999999987
No 58
>TIGR01752 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli.
Probab=25.81 E-value=1.4e+02 Score=20.95 Aligned_cols=35 Identities=14% Similarity=0.059 Sum_probs=22.4
Q ss_pred cCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 032871 97 TSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 97 t~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~gy 131 (131)
.++..|+|.++....+..-..++..+.+.|.+.|+
T Consensus 78 gk~v~~fg~g~~~~y~~~f~~a~~~l~~~l~~~G~ 112 (167)
T TIGR01752 78 GKTVALFGLGDQEGYSETFCDGMGILYDKIKARGA 112 (167)
T ss_pred CCEEEEEecCCCCcccHHHHHHHHHHHHHHHHcCC
Confidence 35566777665444455556667777788877663
No 59
>PRK05922 type III secretion system ATPase; Validated
Probab=25.24 E-value=83 Score=26.28 Aligned_cols=34 Identities=21% Similarity=0.212 Sum_probs=24.3
Q ss_pred CCEEEEEEeCCC-CCcchHHHHHHHHHHHHHhCCC
Q 032871 98 SAALIIGIYDEP-MTPGQCNMIVERLGDYLIDQGL 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 345666666664 3455677778889999999885
No 60
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=25.04 E-value=1.2e+02 Score=17.86 Aligned_cols=24 Identities=33% Similarity=0.678 Sum_probs=18.1
Q ss_pred CEEEEEEeCCCCCcchHHHHHHHH
Q 032871 99 AALIIGIYDEPMTPGQCNMIVERL 122 (131)
Q Consensus 99 ~~ivI~~~~~~~~~~~~~~~v~~l 122 (131)
.+.+|-.-.+.++|+.|...++.+
T Consensus 13 ~a~~v~T~~G~VH~g~C~~y~~e~ 36 (54)
T PF10886_consen 13 DALVVETESGPVHPGVCAQYLEEL 36 (54)
T ss_pred cceEEEcCCCccCcHHHHHHHHhc
Confidence 355666666778999999888876
No 61
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.89 E-value=56 Score=20.14 Aligned_cols=18 Identities=22% Similarity=0.353 Sum_probs=15.4
Q ss_pred CCCCCCHHHHHHHHHhcCC
Q 032871 38 NFPQLKPEEITGIMNDFNE 56 (131)
Q Consensus 38 ~f~~i~~~E~~~l~~~f~~ 56 (131)
|. +++.+|++.|.++|+.
T Consensus 54 Gi-TLt~eE~~~l~d~l~~ 71 (72)
T COG4443 54 GI-TLTNEEFKALKDLLNS 71 (72)
T ss_pred ce-eecHHHHHHHHHHHhc
Confidence 46 8899999999998864
No 62
>PRK08125 bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated
Probab=24.82 E-value=4.6e+02 Score=22.72 Aligned_cols=38 Identities=13% Similarity=0.322 Sum_probs=28.7
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCCccceEEcCeEEEEEEeC
Q 032871 38 NFPQLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 38 ~f~~i~~~E~~~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d 78 (131)
+| +-+.+++..++.+|.+|- +..=.+++|+++.+.+++
T Consensus 209 dw-~~~a~~i~~~iRa~~~p~--pga~~~~~g~~~~i~~a~ 246 (660)
T PRK08125 209 DW-HKPASTLHNLVRAVTDPW--PGAFSYVGEQKFTVWSSR 246 (660)
T ss_pred CC-CCCHHHHHHHHhhcCCCC--CceEEEECCEEEEEEEEE
Confidence 47 668899999999998652 222346899999998865
No 63
>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=24.58 E-value=41 Score=23.84 Aligned_cols=18 Identities=22% Similarity=0.270 Sum_probs=14.7
Q ss_pred cceEEEEccCCCeEEecC
Q 032871 20 LSAAAIIGHDGSVWAQSE 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 378899999999998543
No 64
>KOG2500 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.53 E-value=1.1e+02 Score=23.44 Aligned_cols=33 Identities=18% Similarity=0.154 Sum_probs=21.3
Q ss_pred HHHHhcCCCCCCCccceEEcCeEEEEEEeCCCc
Q 032871 49 GIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGA 81 (131)
Q Consensus 49 ~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d~~~ 81 (131)
-++.+|-|......---.+..-+|||+|.++++
T Consensus 67 LfA~c~id~~~~~avEav~DSSRYFViRv~dgn 99 (253)
T KOG2500|consen 67 LFAQCPIDEGPGNAVEAVSDSSRYFVIRVEDGN 99 (253)
T ss_pred hhhhCcccCCCCccceeecccceEEEEEEeCCC
Confidence 345555554444444456778899999998543
No 65
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=24.40 E-value=80 Score=20.91 Aligned_cols=18 Identities=6% Similarity=0.364 Sum_probs=15.5
Q ss_pred CccceEEcCeEEEEEEeC
Q 032871 61 APTGLYLGGTKYMVIQGE 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 356799999999999987
No 66
>PF14553 YqbF: YqbF, hypothetical protein domain; PDB: 2HJQ_A.
Probab=24.37 E-value=71 Score=17.93 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=9.8
Q ss_pred HHHHHHHHHHhCCC
Q 032871 118 IVERLGDYLIDQGL 131 (131)
Q Consensus 118 ~v~~la~yL~~~gy 131 (131)
...++++||.++++
T Consensus 21 V~kk~y~YL~~ne~ 34 (43)
T PF14553_consen 21 VSKKIYNYLNDNEF 34 (43)
T ss_dssp E-HHHHHHHHHSTT
T ss_pred hhHHHHHHHhcCCc
Confidence 34678899988764
No 67
>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=24.19 E-value=1.6e+02 Score=22.35 Aligned_cols=30 Identities=13% Similarity=0.214 Sum_probs=26.6
Q ss_pred CEEEEEEeCCCCCcchHHHHHHHHHHHHHh
Q 032871 99 AALIIGIYDEPMTPGQCNMIVERLGDYLID 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 478999999999999999999998888764
No 68
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=23.94 E-value=69 Score=23.66 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=16.4
Q ss_pred HHHHHHhcCCCCCCCccceEEcC
Q 032871 47 ITGIMNDFNEPGTLAPTGLYLGG 69 (131)
Q Consensus 47 ~~~l~~~f~~~~~~~~~Gi~~~g 69 (131)
.+-++.+++-|. ..-+|+-++-
T Consensus 12 ~K~~LHaaKyP~-~aVnGvLlg~ 33 (196)
T PF03665_consen 12 AKMILHAAKYPH-CAVNGVLLGK 33 (196)
T ss_pred HHHHHHhccCCC-CceeeEEEec
Confidence 466778888875 4578888876
No 69
>PRK02821 hypothetical protein; Provisional
Probab=23.68 E-value=1.6e+02 Score=18.41 Aligned_cols=44 Identities=9% Similarity=0.234 Sum_probs=25.5
Q ss_pred HHHHHHhc-CCCCCCCccceEEcCeEEEEEEeCCCc--eEEEEcCCC
Q 032871 47 ITGIMNDF-NEPGTLAPTGLYLGGTKYMVIQGEPGA--VIRGKKGPG 90 (131)
Q Consensus 47 ~~~l~~~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 45566666 456655444444445555666765433 488888763
No 70
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=23.58 E-value=67 Score=20.83 Aligned_cols=18 Identities=22% Similarity=0.418 Sum_probs=15.6
Q ss_pred CccceEEcCeEEEEEEeC
Q 032871 61 APTGLYLGGTKYMVIQGE 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 356799999999999987
No 71
>PRK00468 hypothetical protein; Provisional
Probab=22.79 E-value=2e+02 Score=17.84 Aligned_cols=44 Identities=14% Similarity=0.240 Sum_probs=22.8
Q ss_pred HHHHHHhc-CCCCCCCccceEEcCeEEEEEEeCCCc--eEEEEcCCC
Q 032871 47 ITGIMNDF-NEPGTLAPTGLYLGGTKYMVIQGEPGA--VIRGKKGPG 90 (131)
Q Consensus 47 ~~~l~~~f-~~~~~~~~~Gi~~~g~Ky~v~r~d~~~--~i~~kk~~~ 90 (131)
+..|+..| ++|..+.-+-..-++.-.+.++.++++ -++||+|..
T Consensus 5 v~~iv~~LVd~Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~ 51 (75)
T PRK00468 5 VETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRI 51 (75)
T ss_pred HHHHHHHhcCCCCeEEEEEEeCCCeEEEEEEEChhhCcceecCCChh
Confidence 45666666 456655444332223333345555333 488887754
No 72
>PF13989 YejG: YejG-like protein
Probab=22.74 E-value=1.7e+02 Score=19.63 Aligned_cols=50 Identities=12% Similarity=0.131 Sum_probs=33.3
Q ss_pred HHHHHHhcCCCCCCCccceEEcCeEEEEEEeCCCceEEEEcCCCcEEEEec
Q 032871 47 ITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKT 97 (131)
Q Consensus 47 ~~~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d~~~~i~~kk~~~G~~i~kt 97 (131)
++.|...+.+- .+...=+...|+.|.+++.+++.....+-..-|+.|+.+
T Consensus 55 m~~L~~sL~ei-qv~~~vvE~eGepCLFv~~~DEsa~~CrLKn~GVAIAE~ 104 (106)
T PF13989_consen 55 MQQLSQSLAEI-QVDCAVVEWEGEPCLFVHREDESAAMCRLKNFGVAIAEP 104 (106)
T ss_pred HHHHHHHHHHh-cccceEEEecCCceEEEecccchhhheeeccCceEEecc
Confidence 45555666663 355777889999999999883333444555667777644
No 73
>PRK12359 flavodoxin FldB; Provisional
Probab=22.00 E-value=1.7e+02 Score=21.10 Aligned_cols=35 Identities=17% Similarity=0.065 Sum_probs=26.1
Q ss_pred ecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCC
Q 032871 96 KTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQG 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 34566677777655567777888999999998766
No 74
>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=21.94 E-value=1e+02 Score=26.86 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=18.9
Q ss_pred EEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032871 100 ALIIGIYDEPM-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 100 ~ivI~~~~~~~-~~~~~~~~v~~la~yL~~~gy 131 (131)
.+|++.-+.+. ....+.-+.-.+|+|++++||
T Consensus 287 vlVanTSn~p~~aR~~s~ytg~TiAEYfRD~G~ 319 (578)
T TIGR01043 287 VLIANTSNMPVAAREASIYTGITIAEYFRDMGY 319 (578)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 44444444443 223344445569999999997
No 75
>PF10653 Phage-A118_gp45: Protein gp45 of Bacteriophage A118; InterPro: IPR018915 The proteins in this entry represents Gp45 in Listeria phage A118 (Bacteriophage A118) and related proteins; Gp45 is thought to have a function in the phage tail-fibre system.
Probab=21.77 E-value=74 Score=18.67 Aligned_cols=14 Identities=21% Similarity=0.430 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHh
Q 032871 115 CNMIVERLGDYLID 128 (131)
Q Consensus 115 ~~~~v~~la~yL~~ 128 (131)
....+++++||+.+
T Consensus 38 ietgcekm~dyiee 51 (62)
T PF10653_consen 38 IETGCEKMTDYIEE 51 (62)
T ss_pred hhhhhHHHHHHHHH
Confidence 34568899999766
No 76
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=21.69 E-value=2.1e+02 Score=22.66 Aligned_cols=35 Identities=29% Similarity=0.298 Sum_probs=25.9
Q ss_pred EecCCEEEEEEeCCCCCcchHHHHHHHHHHHHHhCC
Q 032871 95 KKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQG 130 (131)
Q Consensus 95 ~kt~~~ivI~~~~~~~~~~~~~~~v~~la~yL~~~g 130 (131)
.-.++++.||.+.-+-+... ...+|+||+||++.|
T Consensus 238 ~egks~lTIaIGCTGGqHRS-V~iae~La~~l~~~~ 272 (286)
T COG1660 238 KEGKSYLTIAIGCTGGQHRS-VYIAEQLAEYLRARG 272 (286)
T ss_pred hcCCeEEEEEEccCCCccch-HHHHHHHHHHHHhcc
Confidence 34577899998876654443 456899999999865
No 77
>PRK11835 hypothetical protein; Provisional
Probab=21.66 E-value=2e+02 Score=19.50 Aligned_cols=51 Identities=10% Similarity=0.120 Sum_probs=35.3
Q ss_pred HHHHHHhcCCCCCCCccceEEcCeEEEEEEeCCCceEEEEcCCCcEEEEecC
Q 032871 47 ITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKTS 98 (131)
Q Consensus 47 ~~~l~~~f~~~~~~~~~Gi~~~g~Ky~v~r~d~~~~i~~kk~~~G~~i~kt~ 98 (131)
++.|..++.+- .+...=+...|+.|.+++.+++.....+-..-|+.|+.+-
T Consensus 58 m~~L~~sL~ei-qv~~~ivEweGepCLFv~~~DE~aa~CrLKn~GVAIAE~~ 108 (114)
T PRK11835 58 MQKLSQALSDI-QVPCSVLECEGEPCLFVNRQDESAATCRLKNFGVAIAEPF 108 (114)
T ss_pred HHHHHHHHHhh-cccceEEEecCCceEEEecccchhhheeeccCcEEEeccc
Confidence 45666666663 3557788899999999998833345556667788776654
No 78
>PHA02754 hypothetical protein; Provisional
Probab=21.61 E-value=1.3e+02 Score=18.05 Aligned_cols=19 Identities=26% Similarity=0.634 Sum_probs=14.2
Q ss_pred CCccceEEcCeEEEEEEeC
Q 032871 60 LAPTGLYLGGTKYMVIQGE 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 4577999888887766655
No 79
>TIGR01626 ytfJ_HI0045 conserved hypothetical protein YtfJ-family, TIGR01626. This model represents sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ.
Probab=21.60 E-value=1.2e+02 Score=22.22 Aligned_cols=34 Identities=21% Similarity=0.268 Sum_probs=25.9
Q ss_pred cceE-EEEccCCCeEEecCCCCCCCHHHHHHHHHhcC
Q 032871 20 LSAA-AIIGHDGSVWAQSENFPQLKPEEITGIMNDFN 55 (131)
Q Consensus 20 ~~~a-aI~g~dG~~wA~s~~f~~i~~~E~~~l~~~f~ 55 (131)
+-.. -|+|.+|.+.....|. ++++|+..++..++
T Consensus 146 ~P~T~fVIDk~GkVv~~~~G~--l~~ee~e~~~~li~ 180 (184)
T TIGR01626 146 EDSAIIVLDKTGKVKFVKEGA--LSDSDIQTVISLVN 180 (184)
T ss_pred CCceEEEECCCCcEEEEEeCC--CCHHHHHHHHHHHH
Confidence 4345 6999999988877776 68999887776654
No 80
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=21.40 E-value=1.2e+02 Score=19.35 Aligned_cols=20 Identities=15% Similarity=0.217 Sum_probs=15.4
Q ss_pred CCCccceEEcCeEEEEEEeC
Q 032871 59 TLAPTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 59 ~~~~~Gi~~~g~Ky~v~r~d 78 (131)
+.+..-++++|++|.|.+..
T Consensus 66 P~~gd~v~~dG~~y~V~~~~ 85 (95)
T PF13856_consen 66 PRRGDRVVIDGESYTVTRFQ 85 (95)
T ss_dssp --TT-EEEETTEEEEEEEEE
T ss_pred CCCCCEEEECCeEEEEeEEe
Confidence 34678899999999999975
No 81
>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=21.33 E-value=86 Score=20.08 Aligned_cols=17 Identities=24% Similarity=0.624 Sum_probs=15.3
Q ss_pred ccceEEcCeEEEEEEeC
Q 032871 62 PTGLYLGGTKYMVIQGE 78 (131)
Q Consensus 62 ~~Gi~~~g~Ky~v~r~d 78 (131)
..-+.++|++|+++|.+
T Consensus 71 g~~v~~~~~~~~~~~~~ 87 (93)
T PF00166_consen 71 GTEVKFDGEKYLIVRED 87 (93)
T ss_dssp SEEEEETTEEEEEEEGG
T ss_pred ceEEEECCEEEEEEEHH
Confidence 56889999999999987
No 82
>PF08127 Propeptide_C1: Peptidase family C1 propeptide; InterPro: IPR012599 This domain is found at the N-terminal of cathepsin B and cathepsin B-like peptidases that belong to MEROPS peptidase subfamily C1A. Cathepsin B are lysosomal cysteine proteinases belonging to the papain superfamily and are unique in their ability to act as both an endo- and an exopeptidases. They are synthesized as inactive zymogens. Activation of the peptidases occurs with the removal of the propeptide [, ]. ; GO: 0004197 cysteine-type endopeptidase activity, 0050790 regulation of catalytic activity; PDB: 1MIR_A 1PBH_A 2PBH_A 3PBH_A.
Probab=21.21 E-value=54 Score=18.00 Aligned_cols=28 Identities=21% Similarity=0.501 Sum_probs=16.2
Q ss_pred CCeEEecCCCCCCCHHHHHHHHHhcCCC
Q 032871 30 GSVWAQSENFPQLKPEEITGIMNDFNEP 57 (131)
Q Consensus 30 G~~wA~s~~f~~i~~~E~~~l~~~f~~~ 57 (131)
...|-+..+|...+.+.++.|+....++
T Consensus 13 ~~tWkAG~NF~~~~~~~ik~LlGv~~~~ 40 (41)
T PF08127_consen 13 NTTWKAGRNFENTSIEYIKRLLGVLPDP 40 (41)
T ss_dssp T-SEEE----SSB-HHHHHHCS-B-TTS
T ss_pred CCcccCCCCCCCCCHHHHHHHcCCCCCC
Confidence 5689888889888999999988876654
No 83
>PF11389 Porin_OmpL1: Leptospira porin protein OmpL1; InterPro: IPR021058 OmpL1 is a member of the outer membrane (OM) proteins in the mammalian pathogen Leptospira, related proteins are restricted to the Spirochaetes. Specifically, it is a porin [].
Probab=20.90 E-value=1.8e+02 Score=22.42 Aligned_cols=47 Identities=21% Similarity=0.135 Sum_probs=28.2
Q ss_pred hcCCCCCCCcc--ceEEcCeEEEEEEeCCCceEEEEcCCCcEEEEe-cCCEEE
Q 032871 53 DFNEPGTLAPT--GLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKK-TSAALI 102 (131)
Q Consensus 53 ~f~~~~~~~~~--Gi~~~g~Ky~v~r~d~~~~i~~kk~~~G~~i~k-t~~~iv 102 (131)
+|.+|.+...+ .+-+..+|-+ -.| ++.+...+..+|++-.| |+.+.+
T Consensus 30 ~~~~~~k~~~~~~~~gv~~r~aI--~aE-NrLitL~~tt~g~I~a~~tngaM~ 79 (267)
T PF11389_consen 30 CVQNPYKPAGEGNYTGVLPRKAI--IAE-NRLITLDRTTGGLINAKSTNGAMT 79 (267)
T ss_pred cccCCCCcCCcCcceeecccccc--ccc-ceEEEEecccCceeeeeeccCcee
Confidence 44555544333 3334444432 245 67788888888988888 776653
No 84
>PRK06936 type III secretion system ATPase; Provisional
Probab=20.60 E-value=1e+02 Score=25.84 Aligned_cols=32 Identities=22% Similarity=0.535 Sum_probs=19.4
Q ss_pred EEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032871 100 ALIIGIYDEPM-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 100 ~ivI~~~~~~~-~~~~~~~~v~~la~yL~~~gy 131 (131)
.+|++.-+++. ..-.+..+.-.+|+|++++|+
T Consensus 220 vvv~atsd~p~~~R~~a~~~a~tiAEyfrd~G~ 252 (439)
T PRK06936 220 VLVVATSDRPSMERAKAGFVATSIAEYFRDQGK 252 (439)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 44555544431 223455556679999999885
No 85
>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=20.46 E-value=1e+02 Score=24.12 Aligned_cols=33 Identities=24% Similarity=0.476 Sum_probs=20.9
Q ss_pred CEEEEEEeCCCC-CcchHHHHHHHHHHHHHhC-CC
Q 032871 99 AALIIGIYDEPM-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 345555555542 3344556667799999987 74
No 86
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=20.34 E-value=1.2e+02 Score=19.05 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=18.7
Q ss_pred EEEEccCCCeEEecCCCCCCCHHHHHHHH
Q 032871 23 AAIIGHDGSVWAQSENFPQLKPEEITGIM 51 (131)
Q Consensus 23 aaI~g~dG~~wA~s~~f~~i~~~E~~~l~ 51 (131)
-.+++.||.+...-.|+ ++++|+..++
T Consensus 86 ~~~~d~~G~~v~~~~G~--~~~~~l~~~L 112 (112)
T PF13098_consen 86 IVFLDKDGKIVYRIPGY--LSPEELLKML 112 (112)
T ss_dssp EEECTTTSCEEEEEESS----HHHHHHHH
T ss_pred EEEEcCCCCEEEEecCC--CCHHHHHhhC
Confidence 45566689887777788 6899988764
No 87
>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=20.24 E-value=86 Score=18.66 Aligned_cols=18 Identities=17% Similarity=0.433 Sum_probs=15.4
Q ss_pred CCCHHHHHHHHHhcCCCC
Q 032871 41 QLKPEEITGIMNDFNEPG 58 (131)
Q Consensus 41 ~i~~~E~~~l~~~f~~~~ 58 (131)
.+++.|...|+++|++..
T Consensus 28 Gv~~~e~~aIi~~F~~~~ 45 (57)
T PF05952_consen 28 GVDKDEQKAIIDAFKDEE 45 (57)
T ss_pred cCCHHHHHHHHHHHcccc
Confidence 568999999999998753
No 88
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=20.07 E-value=1.1e+02 Score=26.65 Aligned_cols=32 Identities=19% Similarity=0.265 Sum_probs=19.4
Q ss_pred EEEEEEeCCCC-CcchHHHHHHHHHHHHHhCCC
Q 032871 100 ALIIGIYDEPM-TPGQCNMIVERLGDYLIDQGL 131 (131)
Q Consensus 100 ~ivI~~~~~~~-~~~~~~~~v~~la~yL~~~gy 131 (131)
.+|++.-+.+. ....+.-..-.+|+|++++||
T Consensus 292 vlVanTSn~Pv~aR~~s~ytgiTiAEYfRd~G~ 324 (586)
T PRK04192 292 VLIANTSNMPVAAREASIYTGITIAEYYRDMGY 324 (586)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence 44444444443 233344455669999999997
Done!