Query 033115
Match_columns 127
No_of_seqs 105 out of 408
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 09:59:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033115.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033115hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00148 PROF Profilin binds ac 100.0 7.1E-40 1.5E-44 231.3 15.6 113 13-127 13-127 (127)
2 PTZ00316 profilin; Provisional 100.0 6.9E-40 1.5E-44 235.7 15.4 114 13-127 14-150 (150)
3 smart00392 PROF Profilin. Bind 100.0 7.7E-39 1.7E-43 226.3 15.2 114 13-127 14-129 (129)
4 PF00235 Profilin: Profilin; 100.0 1.7E-35 3.6E-40 206.0 11.1 108 14-122 14-121 (121)
5 KOG1755 Profilin [Cytoskeleton 100.0 1.6E-34 3.5E-39 202.5 13.1 112 15-127 16-128 (128)
6 COG2018 Uncharacterized distan 80.8 17 0.00036 25.5 8.6 94 16-119 19-112 (119)
7 PF13734 Inhibitor_I69: Spi pr 74.8 17 0.00037 24.4 6.1 81 33-124 3-91 (96)
8 PF04312 DUF460: Protein of un 68.2 22 0.00047 25.6 5.7 44 8-52 33-77 (138)
9 PF07494 Reg_prop: Two compone 64.3 13 0.00028 18.2 2.9 22 13-34 3-24 (24)
10 PF03259 Robl_LC7: Roadblock/L 59.9 5.1 0.00011 25.2 1.1 63 17-81 16-78 (91)
11 PF09176 Mpt_N: Methylene-tetr 51.9 7.3 0.00016 25.5 0.9 31 37-67 20-53 (81)
12 COG0223 Fmt Methionyl-tRNA for 49.1 96 0.0021 25.1 7.0 65 34-104 213-277 (307)
13 COG2139 RPL21A Ribosomal prote 48.3 28 0.0006 23.6 3.2 24 83-106 57-80 (98)
14 PRK02821 hypothetical protein; 47.2 40 0.00086 21.7 3.7 45 42-86 5-52 (77)
15 PRK00468 hypothetical protein; 46.6 50 0.0011 21.0 4.1 45 42-86 4-51 (75)
16 PF07454 SpoIIP: Stage II spor 45.8 80 0.0017 25.0 6.0 89 8-123 177-267 (268)
17 PF01509 TruB_N: TruB family p 45.7 29 0.00064 24.9 3.3 44 24-68 59-105 (149)
18 PF08513 LisH: LisH; InterPro 45.1 17 0.00036 18.5 1.4 10 118-127 7-16 (27)
19 COG2433 Uncharacterized conser 43.6 69 0.0015 28.5 5.7 45 8-53 245-290 (652)
20 TIGR00460 fmt methionyl-tRNA f 42.0 1.8E+02 0.0038 23.2 7.7 37 34-74 212-248 (313)
21 COG3382 Solo B3/4 domain (OB-f 39.9 87 0.0019 24.4 5.2 43 83-125 173-215 (229)
22 PHA02610 uvsY.-2 hypothetical 38.5 50 0.0011 19.8 2.9 24 95-118 13-36 (53)
23 PF08923 MAPKK1_Int: Mitogen-a 37.5 1.4E+02 0.003 20.6 5.8 93 17-124 18-114 (119)
24 PF14584 DUF4446: Protein of u 37.3 55 0.0012 23.7 3.6 28 21-49 117-150 (151)
25 smart00667 LisH Lissencephaly 37.2 21 0.00047 17.8 1.1 13 115-127 7-19 (34)
26 TIGR02867 spore_II_P stage II 36.1 1.7E+02 0.0037 22.0 6.3 89 9-124 100-193 (196)
27 PRK00394 transcription factor; 35.6 1E+02 0.0022 22.8 4.9 40 84-127 45-84 (179)
28 PF08479 POTRA_2: POTRA domain 34.9 41 0.0009 20.7 2.4 22 106-127 31-52 (76)
29 PRK06988 putative formyltransf 34.8 2.3E+02 0.0049 22.6 7.2 38 34-74 211-248 (312)
30 COG1837 Predicted RNA-binding 34.2 1.1E+02 0.0024 19.6 4.3 44 43-86 5-51 (76)
31 PF12965 DUF3854: Domain of un 32.9 91 0.002 21.8 4.1 34 94-127 68-103 (130)
32 PRK01064 hypothetical protein; 32.2 1.4E+02 0.003 19.1 4.6 45 42-86 4-51 (78)
33 cd05126 Mth938 Mth938 domain. 31.4 79 0.0017 21.7 3.5 41 9-49 9-57 (117)
34 PF08127 Propeptide_C1: Peptid 31.3 31 0.00066 19.5 1.2 28 26-53 13-40 (41)
35 PF02911 Formyl_trans_C: Formy 31.0 1.4E+02 0.0031 18.9 8.2 37 34-74 10-46 (100)
36 COG3377 Uncharacterized conser 30.9 1.6E+02 0.0034 19.8 4.7 20 58-77 4-23 (95)
37 COG2896 MoaA Molybdenum cofact 29.7 45 0.00098 27.2 2.4 44 7-52 12-57 (322)
38 PF07799 DUF1643: Protein of u 29.0 90 0.002 21.5 3.5 34 94-127 13-46 (136)
39 PF07244 Surf_Ag_VNR: Surface 28.9 65 0.0014 19.3 2.5 22 106-127 32-53 (78)
40 COG1832 Predicted CoA-binding 28.4 87 0.0019 22.6 3.4 31 91-127 14-44 (140)
41 TIGR02764 spore_ybaN_pdaB poly 28.3 1.2E+02 0.0026 21.8 4.2 20 108-127 163-182 (191)
42 COG1660 Predicted P-loop-conta 27.8 1.2E+02 0.0025 24.5 4.3 33 92-126 239-272 (286)
43 PF02770 Acyl-CoA_dh_M: Acyl-C 27.6 48 0.001 19.0 1.7 17 58-74 24-40 (52)
44 cd04516 TBP_eukaryotes eukaryo 27.4 1.8E+02 0.0039 21.4 5.1 36 88-127 50-85 (174)
45 cd00861 ProRS_anticodon_short 26.8 1.3E+02 0.0028 18.7 3.7 30 95-127 3-32 (94)
46 PF14553 YqbF: YqbF, hypotheti 26.7 59 0.0013 18.7 1.8 14 114-127 21-34 (43)
47 PF05952 ComX: Bacillus compet 26.4 68 0.0015 19.5 2.2 19 37-55 28-46 (57)
48 PLN00062 TATA-box-binding prot 26.4 2E+02 0.0044 21.2 5.2 38 86-127 48-85 (179)
49 cd04517 TLF TBP-like factors ( 26.1 1.8E+02 0.004 21.3 4.9 39 85-127 47-85 (174)
50 cd04518 TBP_archaea archaeal T 26.0 1.5E+02 0.0032 21.8 4.4 39 85-127 47-85 (174)
51 PF10886 DUF2685: Protein of u 25.3 1.1E+02 0.0024 18.4 2.9 25 95-119 13-37 (54)
52 PF08356 EF_assoc_2: EF hand a 24.9 60 0.0013 21.5 1.9 30 37-66 3-34 (89)
53 PTZ00414 10 kDa heat shock pro 24.9 76 0.0017 21.4 2.4 19 56-74 74-92 (100)
54 cd00862 ProRS_anticodon_zinc P 24.7 1.5E+02 0.0032 22.0 4.3 34 94-127 11-44 (202)
55 cd00320 cpn10 Chaperonin 10 Kd 24.6 68 0.0015 21.1 2.1 18 57-74 70-87 (93)
56 PF02866 Ldh_1_C: lactate/mala 24.2 1.2E+02 0.0025 21.7 3.5 30 19-50 131-160 (174)
57 PF03668 ATP_bind_2: P-loop AT 23.1 1.7E+02 0.0037 23.5 4.5 34 92-127 238-272 (284)
58 PF02789 Peptidase_M17_N: Cyto 22.8 2.1E+02 0.0045 18.7 4.4 34 93-126 52-86 (126)
59 PRK00364 groES co-chaperonin G 22.7 79 0.0017 20.9 2.2 17 58-74 72-88 (95)
60 KOG0141 Isovaleryl-CoA dehydro 22.7 1.2E+02 0.0026 25.2 3.6 43 58-100 183-227 (421)
61 cd01132 F1_ATPase_alpha F1 ATP 22.7 1.2E+02 0.0026 24.1 3.5 34 94-127 127-161 (274)
62 PF14080 DUF4261: Domain of un 22.5 1.7E+02 0.0036 18.3 3.6 23 104-126 18-40 (77)
63 TIGR01752 flav_long flavodoxin 22.2 1.8E+02 0.0039 20.6 4.1 35 93-127 78-112 (167)
64 PRK14533 groES co-chaperonin G 22.0 91 0.002 20.6 2.3 18 57-74 66-83 (91)
65 cd00652 TBP_TLF TATA box bindi 21.8 2.3E+02 0.0049 20.7 4.7 39 85-127 47-85 (174)
66 COG1157 FliI Flagellar biosynt 21.8 95 0.0021 26.5 2.9 34 94-127 219-253 (441)
67 PF09695 YtfJ_HI0045: Bacteria 21.4 2.1E+02 0.0046 21.0 4.3 34 15-51 122-158 (160)
68 PF14620 YPEB: YpeB sporulatio 21.0 4.7E+02 0.01 21.5 7.8 82 36-127 205-299 (361)
69 PRK00005 fmt methionyl-tRNA fo 20.8 4.3E+02 0.0092 20.9 7.7 37 34-74 212-248 (309)
70 PF00166 Cpn10: Chaperonin 10 20.5 92 0.002 20.3 2.1 17 58-74 71-87 (93)
71 KOG3619 Adenylate/guanylate cy 20.4 76 0.0017 29.4 2.2 45 6-50 759-817 (867)
72 cd01134 V_A-ATPase_A V/A-type 20.3 1.1E+02 0.0023 25.6 2.9 34 94-127 220-254 (369)
73 PF05176 ATP-synt_10: ATP10 pr 20.1 1.4E+02 0.003 23.3 3.4 33 15-50 214-249 (252)
74 PF11429 Colicin_D: Colicin D; 20.1 73 0.0016 21.3 1.6 30 8-41 52-81 (92)
No 1
>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=7.1e-40 Score=231.25 Aligned_cols=113 Identities=45% Similarity=0.705 Sum_probs=109.4
Q ss_pred CCCCceEEEEcCC-CCEEEecCC-CCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCCCcEEE
Q 033115 13 SQLPLSSATTAAF-GPRVKTSLR-FFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTI 90 (127)
Q Consensus 13 ~~~~~~aAI~g~d-G~vWA~s~~-f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~~G~~i 90 (127)
+++...|||+|+| |++||+|++ | +++|+|+++|+++|+||+.++.+||+|+|+||+++|+| ++++++|++++|+++
T Consensus 13 ~g~~~~aAI~g~d~g~vwA~s~~~f-~~t~~E~~~i~~~f~d~~~~~~~Gi~l~G~KY~~l~~d-~~~i~~kk~~~Gi~i 90 (127)
T cd00148 13 TGKVDSAAIVGHDDGSVWAASAGGF-NLTPEEVGTLVAGFKDPDGVFSTGLTLGGQKYMVIRAD-DRSIYGKKGAGGVVI 90 (127)
T ss_pred cCCcCEEEEEecCCCCeEEecCCCC-ccCHHHHHHHHHHccCccccccCCEEECCeEEEEEecC-ccEEEeeeCCCeEEE
Confidence 4577889999998 999999999 9 99999999999999999999999999999999999999 899999999999999
Q ss_pred EeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 91 KKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 91 ~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+||+|++|||+|+++++|++|+++|++|||||+++||
T Consensus 91 ~kT~~~ivi~~y~e~~~~g~~~~~v~~ladYL~~~gy 127 (127)
T cd00148 91 VKTKQALVIGMYEEGVQPGQANKVVEKLADYLRSQGY 127 (127)
T ss_pred EECCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999999999999999999998
No 2
>PTZ00316 profilin; Provisional
Probab=100.00 E-value=6.9e-40 Score=235.74 Aligned_cols=114 Identities=25% Similarity=0.382 Sum_probs=107.1
Q ss_pred CCCCceEEEEcC-CCCEEEecCCCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCC---CcEEEeecCCCcE
Q 033115 13 SQLPLSSATTAA-FGPRVKTSLRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEP---GAVIRGKKGPGGV 88 (127)
Q Consensus 13 ~~~~~~aAI~g~-dG~vWA~s~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~---~~~i~~kkg~~G~ 88 (127)
++....|||+|+ ||++||+|++| +++|+|+++|+++|+||+.+..+||+|+|+||+++|.+. ++++|+||+++|+
T Consensus 14 sg~v~kAAIiG~~DGsvWA~S~gF-~lspeE~~~I~~~F~d~~~l~~~Gi~l~G~KY~~lr~~~d~d~~~i~gKKg~~G~ 92 (150)
T PTZ00316 14 SGNMHSAAIVGLADGSYWAYGGSY-IPQPEEVAHILKCLGNFSLVQSSGVTIYGVKFFGLQSGTEGDMKYIFFKKGAAGG 92 (150)
T ss_pred cCCcceEEEEecCCCCEeecCCCC-ccCHHHHHHHHHHhcCCccccCCCEEEcceEEEEEEeccCCCcceEEEecCCCeE
Confidence 456777999997 99999999999 999999999999999999999999999999999999832 4789999999999
Q ss_pred EEEeCCcEEEEEEeCC-------------------CCCcchHHHHHHHHHHHHHhCCC
Q 033115 89 TIKKTSAALIIGIYDE-------------------PMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 89 ~i~KT~~aiVIg~y~~-------------------~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+++||+|++|||+|++ +++|++|+.+||+|||||+++||
T Consensus 93 ~i~kT~qaiiI~~y~~~~~~~~~~~~~~~~~~~~~~~~pg~~~~~Ve~LadYL~~~gy 150 (150)
T PTZ00316 93 CIYTSKQTAIIAVYGNPGDTSSLQQDLEKNEAHAVAVNPADCNTTVKRIAEYLISLDY 150 (150)
T ss_pred EEEEcCCEEEEEEeCCcccccccccccccccccccccCHHHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999 57999999999999999999998
No 3
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=100.00 E-value=7.7e-39 Score=226.34 Aligned_cols=114 Identities=45% Similarity=0.638 Sum_probs=109.0
Q ss_pred CCCCceEEEEcCCCCEEEecCC--CCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCCCcEEE
Q 033115 13 SQLPLSSATTAAFGPRVKTSLR--FFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTI 90 (127)
Q Consensus 13 ~~~~~~aAI~g~dG~vWA~s~~--f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~~G~~i 90 (127)
++....|||+++||++||+|++ |+.++|+|+++|++.|+||+.++.+||+|+|+||+++|+| ++.+++||+++|+++
T Consensus 14 ~g~~~~AaI~g~dGsvWA~s~g~~f~~~~~~E~~~i~~~f~~~~~~~~~Gi~l~G~Ky~~~~~d-~~~i~~kk~~~Gv~i 92 (129)
T smart00392 14 SGCVDAAAIGGKDGSVWAASAGGNFQKITPEEIAAIAALFNSLAAVFSNGLTLGGQKYMVIRAD-DRSIMGKKGAGGVVI 92 (129)
T ss_pred cCCCcEEEEEeCCCCeeeccCCCCCCcCCHHHHHHHHHHccCcchhccCCeEECCeEEEEEEec-CcEEEeecCCceEEE
Confidence 3567789999999999999999 8568999999999999999889999999999999999999 899999999999999
Q ss_pred EeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 91 KKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 91 ~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+||+|+||||+|+++++|++|+++|++|||||+++||
T Consensus 93 ~kT~~aivI~~y~e~~~~g~~~~~v~~ladYL~~~Gy 129 (129)
T smart00392 93 VKTKQALIIGMYKEGVQPGQANKTVEKLADYLRSSGY 129 (129)
T ss_pred EECCCEEEEEECCCCCChHHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999999999999999999998
No 4
>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=1.7e-35 Score=206.01 Aligned_cols=108 Identities=41% Similarity=0.724 Sum_probs=103.4
Q ss_pred CCCceEEEEcCCCCEEEecCCCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCCCcEEEEeC
Q 033115 14 QLPLSSATTAAFGPRVKTSLRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKT 93 (127)
Q Consensus 14 ~~~~~aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~~G~~i~KT 93 (127)
+....|||++.||++||++++|++++|+|++.|+++|++|+.++.+||+|+|+||+++|.| ++++++|++++|++++||
T Consensus 14 ~~~~~aaI~~~dG~vwA~s~~f~~~~~~E~~~i~~~f~~~~~~~~~gi~l~G~kY~~~~~d-~~~i~~k~~~~G~~i~kt 92 (121)
T PF00235_consen 14 GNITKAAIIGSDGSVWASSPGFSNISPEEAKAIIKAFNNPSKFPSNGITLGGKKYIVLRAD-DNSIYGKKGKGGIIIVKT 92 (121)
T ss_dssp SSESEEEEEETTSSEEEEETTGGGCSHHHHHHHHHHHHSSSHHHHH-EEETTEEEEEEEEE-TTEEEEEETTEEEEEEEC
T ss_pred CcEeEEEEEcCCCCEEEecCCCCCCCHHHHHHHHHHhcCchhcccCCeEEcCcEeEEEecC-CceEEeeCCCCcEEEEEC
Confidence 4577899999999999999999999999999999999999888899999999999999999 899999999999999999
Q ss_pred CcEEEEEEeCCCCCcchHHHHHHHHHHHH
Q 033115 94 SAALIIGIYDEPMTPGQCNMIVERLGDYL 122 (127)
Q Consensus 94 ~~aiVIg~y~~~~~~g~~~~~ve~lAdyL 122 (127)
++++|||+|+++++|++|+++|++|||||
T Consensus 93 ~~~ivIg~y~~~~~~~~~~~~v~~lA~yL 121 (121)
T PF00235_consen 93 KQAIVIGMYDESIQPGNCNKAVEKLADYL 121 (121)
T ss_dssp SSEEEEEEEETTSTHHHHHHHHHHHHHHH
T ss_pred CCEEEEEEeCCCCCHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999998
No 5
>KOG1755 consensus Profilin [Cytoskeleton]
Probab=100.00 E-value=1.6e-34 Score=202.48 Aligned_cols=112 Identities=52% Similarity=0.825 Sum_probs=107.4
Q ss_pred CCceEEEEcCCC-CEEEecCCCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCCCcEEEEeC
Q 033115 15 LPLSSATTAAFG-PRVKTSLRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKT 93 (127)
Q Consensus 15 ~~~~aAI~g~dG-~vWA~s~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~~G~~i~KT 93 (127)
....|||++.|| ++||.|++| +++|+|...+++.|+||+.+..+|++|+|+||+++|.|.+..+++|++.+|+++.||
T Consensus 16 ~v~~AAIvg~~~~SVWA~S~~f-~~~~~e~~~~v~~F~d~~~~~~~Gl~L~Gqkylv~~ge~~~~~~gk~~~~gv~i~kT 94 (128)
T KOG1755|consen 16 HVTRAAIVGYDGGSVWAASAGF-NVKPSEIPAIVAGFKDPGGLAGTGLTLGGQKYLVVRGEEGRVIRGKEGTGGVTIKKT 94 (128)
T ss_pred ccceeeEEecCCCeeEEecCCC-cccHHHHHHHHhcccCcccccccceeecccEEEEEecccceEEecccCCCcEEEEEc
Confidence 455699999954 999999999 999999999999999999999999999999999999997788999999999999999
Q ss_pred CcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 94 SAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 94 ~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
.+++|+++|+++++|++|+++||.|||||+++||
T Consensus 95 ~~~li~~~y~e~v~~g~~~k~ve~LadYL~~~gy 128 (128)
T KOG1755|consen 95 GQALIFSIYKEGVQPGQCNKVVESLADYLRESGY 128 (128)
T ss_pred ceEEEEEEcCCCCCHHHHHHHHHHHHHHHHhcCC
Confidence 9999999999999999999999999999999998
No 6
>COG2018 Uncharacterized distant relative of homeotic protein bithoraxoid [General function prediction only]
Probab=80.76 E-value=17 Score=25.50 Aligned_cols=94 Identities=17% Similarity=0.176 Sum_probs=54.0
Q ss_pred CceEEEEcCCCCEEEecCCCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCCCcEEEEeCCc
Q 033115 16 PLSSATTAAFGPRVKTSLRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKTSA 95 (127)
Q Consensus 16 ~~~aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~~G~~i~KT~~ 95 (127)
-.+++|.+.||-+-+++..+ +...+=+.+++...-.-......-|--+...++.++.+++..+.-.-|..
T Consensus 19 v~ga~Ivs~DGL~ia~~~p~-~~d~e~vaA~~a~~~g~~er~~~~l~~g~leqi~I~g~~g~i~l~~~g~~--------- 88 (119)
T COG2018 19 VRGALVVSKDGLPIAAELPG-NVDAEIVAAMAATALGLAERAADELGGGELEQIMIEGKKGKILLYDAGDD--------- 88 (119)
T ss_pred ceEEEEEccCCceEeecCCC-cccHHHHHHHHHHHHHHhHHHHHHhCCCCceEEEEeccccEEEEEEcCCc---------
Confidence 35688999999999988777 76666666666543222222344555667788888877222222233334
Q ss_pred EEEEEEeCCCCCcchHHHHHHHHH
Q 033115 96 ALIIGIYDEPMTPGQCNMIVERLG 119 (127)
Q Consensus 96 aiVIg~y~~~~~~g~~~~~ve~lA 119 (127)
++++..-+...+-|...--..+.|
T Consensus 89 ~il~~~a~~~~nLGli~~e~k~aa 112 (119)
T COG2018 89 AILVVLADEGTNLGLIRMEMKRAA 112 (119)
T ss_pred eEEEEEcCCCCcchhhhhHHHHHH
Confidence 444444455555555443333333
No 7
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=74.84 E-value=17 Score=24.35 Aligned_cols=81 Identities=16% Similarity=0.143 Sum_probs=37.9
Q ss_pred CCCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEe-----CCCcEEEeecCCCcEEEEe--CCcEEEEEEeCCC
Q 033115 33 LRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQG-----EPGAVIRGKKGPGGVTIKK--TSAALIIGIYDEP 105 (127)
Q Consensus 33 ~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~-----d~~~~i~~kkg~~G~~i~K--T~~aiVIg~y~~~ 105 (127)
.+| .-|++|...|+..|-....- ....+-++. +.+-.|+-. +..|++|+- ....=|+|+-+++
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 88999999999998322111 111122221 111234555 567877765 4557788998886
Q ss_pred CC-cchHHHHHHHHHHHHHh
Q 033115 106 MT-PGQCNMIVERLGDYLID 124 (127)
Q Consensus 106 ~~-~g~~~~~ve~lAdyL~~ 124 (127)
.- ..+. +.-.-|+.|+.+
T Consensus 73 ~fd~~~~-n~~~~l~~y~~~ 91 (96)
T PF13734_consen 73 SFDTNNA-NVRPGLQAYLEQ 91 (96)
T ss_dssp ----T-H-HHHHHHHHHHHH
T ss_pred CcCccch-hHHHHHHHHHHH
Confidence 43 3332 355556666654
No 8
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=68.22 E-value=22 Score=25.57 Aligned_cols=44 Identities=14% Similarity=0.101 Sum_probs=30.3
Q ss_pred EEEeeC-CCCceEEEEcCCCCEEEecCCCCCCCHHHHHHHHHhcCC
Q 033115 8 LRVTIS-QLPLSSATTAAFGPRVKTSLRFFLLKPEEITGIMNDFNE 52 (127)
Q Consensus 8 ~~~~~~-~~~~~aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f~~ 52 (127)
|-|+++ +-..+-||+++||.+....+.= +++..|+-.++..+..
T Consensus 33 lIVGiDPG~ttgiAildL~G~~l~l~S~R-~~~~~evi~~I~~~G~ 77 (138)
T PF04312_consen 33 LIVGIDPGTTTGIAILDLDGELLDLKSSR-NMSRSEVIEWISEYGK 77 (138)
T ss_pred EEEEECCCceeEEEEEecCCcEEEEEeec-CCCHHHHHHHHHHcCC
Confidence 558888 6777899999999887764433 4466666666555443
No 9
>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=64.31 E-value=13 Score=18.22 Aligned_cols=22 Identities=9% Similarity=-0.099 Sum_probs=14.9
Q ss_pred CCCCceEEEEcCCCCEEEecCC
Q 033115 13 SQLPLSSATTAAFGPRVKTSLR 34 (127)
Q Consensus 13 ~~~~~~aAI~g~dG~vWA~s~~ 34 (127)
+++...+-..+.+|.+|..|.+
T Consensus 3 ~~n~I~~i~~D~~G~lWigT~~ 24 (24)
T PF07494_consen 3 PNNNIYSIYEDSDGNLWIGTYN 24 (24)
T ss_dssp SSSCEEEEEE-TTSCEEEEETS
T ss_pred CCCeEEEEEEcCCcCEEEEeCC
Confidence 4455556677889999987753
No 10
>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=59.89 E-value=5.1 Score=25.15 Aligned_cols=63 Identities=11% Similarity=-0.019 Sum_probs=32.7
Q ss_pred ceEEEEcCCCCEEEecCCCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEe
Q 033115 17 LSSATTAAFGPRVKTSLRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRG 81 (127)
Q Consensus 17 ~~aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~ 81 (127)
.++.|++.||-+-++ .++....++.+.++...+-.-......-+..+.-+++.++.+ +..++-
T Consensus 16 ~~~~l~~~dG~~i~~-~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~-~~~i~i 78 (91)
T PF03259_consen 16 RGAVLVDKDGLVIAS-SGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETE-KGEIII 78 (91)
T ss_dssp EEEEEEETTSEEEEE-TSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEES-SEEEEE
T ss_pred eEEEEEcCCCCEEEE-ecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEEC-CCEEEE
Confidence 357789999999998 344222334444333332110000112222567788888888 444433
No 11
>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=51.91 E-value=7.3 Score=25.49 Aligned_cols=31 Identities=32% Similarity=0.791 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHh--c-CCCCCcCccceEEcCEE
Q 033115 37 LLKPEEITGIMND--F-NEPGTLAPTGLYLGGTK 67 (127)
Q Consensus 37 ~l~~~E~~~i~~~--f-~~~~~~~~~Gi~l~G~K 67 (127)
+++++|+..|+.. | +.|+.+..+||.+||..
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 6799999999954 6 57788889999999963
No 12
>COG0223 Fmt Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]
Probab=49.12 E-value=96 Score=25.09 Aligned_cols=65 Identities=17% Similarity=0.230 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCCCcEEEEeCCcEEEEEEeCC
Q 033115 34 RFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKKTSAALIIGIYDE 104 (127)
Q Consensus 34 ~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~~G~~i~KT~~aiVIg~y~~ 104 (127)
+| +-+..++...+.+|+ | ....=..++|+++.+.+++..+.-+. ++-|-++...+..++|+..++
T Consensus 213 dw-~~~a~~i~n~IRa~~-P--~Pga~~~~~~~~iki~~a~~~~~~~~--~~pG~i~~~~~~~l~Va~~~g 277 (307)
T COG0223 213 DW-SKPAAQILNKIRAFN-P--WPGAWTELGGKRIKIWEARVLEGASN--GKPGEILAADKKGLLVACGDG 277 (307)
T ss_pred CC-ccCHHHHHHHHhccC-C--CCceEEEECCeEEEEEEEEEcccccc--CCCcceEEecCCcEEEEeCCc
Confidence 57 667888889999987 3 34556788999999888763222111 566777777778888888444
No 13
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=48.32 E-value=28 Score=23.57 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=21.9
Q ss_pred cCCCcEEEEeCCcEEEEEEeCCCC
Q 033115 83 KGPGGVTIKKTSAALIIGIYDEPM 106 (127)
Q Consensus 83 kg~~G~~i~KT~~aiVIg~y~~~~ 106 (127)
+|+.|.++.++..|++|.+++++.
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 789999999999999999998753
No 14
>PRK02821 hypothetical protein; Provisional
Probab=47.21 E-value=40 Score=21.69 Aligned_cols=45 Identities=9% Similarity=0.235 Sum_probs=30.1
Q ss_pred HHHHHHHhc-CCCCCcCccceEEcCEEEEEEEeCCC--cEEEeecCCC
Q 033115 42 EITGIMNDF-NEPGTLAPTGLYLGGTKYMVIQGEPG--AVIRGKKGPG 86 (127)
Q Consensus 42 E~~~i~~~f-~~~~~~~~~Gi~l~G~KY~~~r~d~~--~~i~~kkg~~ 86 (127)
=+..|++.+ ++|+.+.-+-..-.+...+.++.+++ .-+.||+|+.
T Consensus 5 lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~ 52 (77)
T PRK02821 5 AVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRT 52 (77)
T ss_pred HHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCch
Confidence 355677777 67877666655555666677777644 3588988864
No 15
>PRK00468 hypothetical protein; Provisional
Probab=46.63 E-value=50 Score=21.04 Aligned_cols=45 Identities=13% Similarity=0.220 Sum_probs=27.3
Q ss_pred HHHHHHHhc-CCCCCcCccceEEcCEEEEEEEeCCC--cEEEeecCCC
Q 033115 42 EITGIMNDF-NEPGTLAPTGLYLGGTKYMVIQGEPG--AVIRGKKGPG 86 (127)
Q Consensus 42 E~~~i~~~f-~~~~~~~~~Gi~l~G~KY~~~r~d~~--~~i~~kkg~~ 86 (127)
=+..|+..| ++|+.+.-+-..-++.-.+.++.+++ .-++||+|+.
T Consensus 4 Lv~~iv~~LVd~Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~ 51 (75)
T PRK00468 4 LVETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRI 51 (75)
T ss_pred HHHHHHHHhcCCCCeEEEEEEeCCCeEEEEEEEChhhCcceecCCChh
Confidence 355677777 67877665544333444455666644 3588888864
No 16
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=45.81 E-value=80 Score=24.99 Aligned_cols=89 Identities=12% Similarity=0.085 Sum_probs=57.9
Q ss_pred EEEeeCCCCce--EEEEcCCCCEEEecCCCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCC
Q 033115 8 LRVTISQLPLS--SATTAAFGPRVKTSLRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGP 85 (127)
Q Consensus 8 ~~~~~~~~~~~--aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~ 85 (127)
..+++++++.+ --|+|.+ .|+| .-+-+-...|.+.++..-+....||.+.+-+|- -|
T Consensus 177 ~t~~InG~~~Aki~fVvG~~------np~~-~~N~~fA~~l~~~~~~~yPGl~rgI~~k~~~YN---Qd----------- 235 (268)
T PF07454_consen 177 TTTTINGKNYAKIMFVVGRD------NPNW-EKNLAFAKQLHAKLEKKYPGLSRGIFVKDGRYN---QD----------- 235 (268)
T ss_pred ceEEECCEEeeEEEEEEcCC------CCCH-HHHHHHHHHHHHHHHhHCCCccceeeecCceeC---Cc-----------
Confidence 45667777666 3366666 5555 333333444444443222345778888876332 23
Q ss_pred CcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHH
Q 033115 86 GGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLI 123 (127)
Q Consensus 86 ~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~ 123 (127)
.++.+++|=+....-+..++..+++-||+-|.
T Consensus 236 ------Ls~~slLiEiG~~~Nt~eEa~~s~~~lA~vi~ 267 (268)
T PF07454_consen 236 ------LSPNSLLIEIGGVDNTLEEAKRSAEYLADVIA 267 (268)
T ss_pred ------CCCCeEEEEeCCCCCCHHHHHHHHHHHHHHhc
Confidence 45778899888888889999999999999875
No 17
>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=45.68 E-value=29 Score=24.91 Aligned_cols=44 Identities=11% Similarity=0.141 Sum_probs=28.5
Q ss_pred CCCCEEEecCCCCCCCHHHHHHHHHhcCCC---CCcCccceEEcCEEE
Q 033115 24 AFGPRVKTSLRFFLLKPEEITGIMNDFNEP---GTLAPTGLYLGGTKY 68 (127)
Q Consensus 24 ~dG~vWA~s~~f~~l~~~E~~~i~~~f~~~---~~~~~~Gi~l~G~KY 68 (127)
.+|.+...++-. .++.+++...+..|... ..-.-+.+.++|++-
T Consensus 59 ~~G~v~~~~~~~-~it~e~l~~~l~~f~G~~~Q~pP~ySAvki~G~ra 105 (149)
T PF01509_consen 59 IEGEVTETKPYD-HITEEDLEKVLAKFQGEIEQVPPMYSAVKINGKRA 105 (149)
T ss_dssp TTSSEEEE---T-T--HHHHHHHHHHTSEEEEES-SSSSSSECTTCEH
T ss_pred eeeeEEEeeccc-cCCHHHHHHHHHhCcCCEeeeCchheeEcCCCccH
Confidence 358999986555 88999999999999621 122367888888764
No 18
>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=45.10 E-value=17 Score=18.49 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=7.9
Q ss_pred HHHHHHhCCC
Q 033115 118 LGDYLIDQGL 127 (127)
Q Consensus 118 lAdyL~~~Gy 127 (127)
+-|||.++||
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 19
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=43.58 E-value=69 Score=28.51 Aligned_cols=45 Identities=18% Similarity=0.223 Sum_probs=32.3
Q ss_pred EEEeeC-CCCceEEEEcCCCCEEEecCCCCCCCHHHHHHHHHhcCCC
Q 033115 8 LRVTIS-QLPLSSATTAAFGPRVKTSLRFFLLKPEEITGIMNDFNEP 53 (127)
Q Consensus 8 ~~~~~~-~~~~~aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f~~~ 53 (127)
|-|+++ +-+.+-|++++||.+....+.= ++++.|+-.++.....|
T Consensus 245 lIVGIDPGiTtgiAvldldGevl~~~S~r-~~~~~eVve~I~~lG~P 290 (652)
T COG2433 245 LIVGIDPGITTGIAVLDLDGEVLDLESRR-GIDRSEVVEFISELGKP 290 (652)
T ss_pred eEEEeCCCceeeEEEEecCCcEEeeeccc-cCCHHHHHHHHHHcCCc
Confidence 568888 6777899999999888764433 44677777766665544
No 20
>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=42.01 E-value=1.8e+02 Score=23.18 Aligned_cols=37 Identities=16% Similarity=0.282 Sum_probs=28.0
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeC
Q 033115 34 RFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 34 ~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d 74 (127)
+| +-+.+++..++++|. | ....-..++|+++.+.++.
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 57 678899999999996 4 2233457899999988754
No 21
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=39.89 E-value=87 Score=24.38 Aligned_cols=43 Identities=14% Similarity=0.067 Sum_probs=35.6
Q ss_pred cCCCcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhC
Q 033115 83 KGPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQ 125 (127)
Q Consensus 83 kg~~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~ 125 (127)
.+..-.+=-.|+.+++|+..-+++.-....++.+.|+++|...
T Consensus 173 ds~rT~vt~~Tk~~l~I~e~vp~~~~~~l~~a~~~l~~~l~~~ 215 (229)
T COG3382 173 DSVRTMVTESTKNVLLIAEGVPGVEVEDLVEALDSLADLLEKL 215 (229)
T ss_pred cceeeehhhccceEEEEEecCCCccHHHHHHHHHHHHHHHHHh
Confidence 3444444567999999999999999999999999999999863
No 22
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=38.50 E-value=50 Score=19.82 Aligned_cols=24 Identities=38% Similarity=0.685 Sum_probs=18.9
Q ss_pred cEEEEEEeCCCCCcchHHHHHHHH
Q 033115 95 AALIIGIYDEPMTPGQCNMIVERL 118 (127)
Q Consensus 95 ~aiVIg~y~~~~~~g~~~~~ve~l 118 (127)
.++.|-.-.++++||.|..-++.+
T Consensus 13 ~al~v~T~~Gpvh~g~C~~y~~e~ 36 (53)
T PHA02610 13 KALVVETEKGPVHPGPCYNYVEEL 36 (53)
T ss_pred hceEEecCCCCCCChhHHHHHHhc
Confidence 366666677789999999888776
No 23
>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=37.46 E-value=1.4e+02 Score=20.65 Aligned_cols=93 Identities=14% Similarity=0.080 Sum_probs=53.1
Q ss_pred ceEEEEcCCCCEEEecC--CCC--CCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCCcEEEeecCCCcEEEEe
Q 033115 17 LSSATTAAFGPRVKTSL--RFF--LLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPGAVIRGKKGPGGVTIKK 92 (127)
Q Consensus 17 ~~aAI~g~dG~vWA~s~--~f~--~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~~~i~~kkg~~G~~i~K 92 (127)
.+..|.+.||-+-++.. +-+ .+.|.=...+.-+. + +.+-+.+|+.|+++...| +..+.-. -
T Consensus 18 ~~I~itDrDGvpi~~v~~~~~~~~~~~~~~~~tf~~a~-~----Q~~KL~lG~nk~ii~~Y~-~~qvv~~---------~ 82 (119)
T PF08923_consen 18 QAIVITDRDGVPIAKVSSDSAPESAMRPSLLSTFAMAI-D----QASKLGLGKNKSIIAYYD-SYQVVQF---------N 82 (119)
T ss_dssp EEEEEEETTS-EEEEEE-TTS-GGGGSHHHHCCHHHHH-H----HHTTSSS-SEEEEEEEES-SEEEEEE---------E
T ss_pred EEEEEECCCCcEEEEecCCCCcchhhhhHHHHHHHHHh-h----cccccCCCCceEEEEEeC-CEEEEEE---------e
Confidence 34568888998777632 221 22222222222221 1 244578999999999999 4443222 2
Q ss_pred CCcEEEEEEeCCCCCcchHHHHHHHHHHHHHh
Q 033115 93 TSAALIIGIYDEPMTPGQCNMIVERLGDYLID 124 (127)
Q Consensus 93 T~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~ 124 (127)
....+|.-+...+.+-|....-=++|+.+|.+
T Consensus 83 ~~pl~it~ias~~aN~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 83 KLPLYITFIASSNANTGLILSLEEELAPILNE 114 (119)
T ss_dssp ETTEEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred CCCeEEEEEecCCCCHHHHHHhHHHHHHHHHH
Confidence 33466666667667778777777777777754
No 24
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=37.31 E-value=55 Score=23.66 Aligned_cols=28 Identities=11% Similarity=0.046 Sum_probs=18.8
Q ss_pred EEcCCC-CEEEec-----CCCCCCCHHHHHHHHHh
Q 033115 21 TTAAFG-PRVKTS-----LRFFLLKPEEITGIMND 49 (127)
Q Consensus 21 I~g~dG-~vWA~s-----~~f~~l~~~E~~~i~~~ 49 (127)
|.+.|+ .+||+. +.. .|+|||..+|..+
T Consensus 117 I~~Re~s~~YaK~I~~G~S~~-~LS~EE~eal~~A 150 (151)
T PF14584_consen 117 IHSREESRTYAKPIVNGQSSY-PLSEEEKEALEKA 150 (151)
T ss_pred eecCCCcEEEEEEecCCcccc-cCCHHHHHHHHHh
Confidence 444554 556652 235 7899999998775
No 25
>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=37.19 E-value=21 Score=17.81 Aligned_cols=13 Identities=23% Similarity=0.480 Sum_probs=10.3
Q ss_pred HHHHHHHHHhCCC
Q 033115 115 VERLGDYLIDQGL 127 (127)
Q Consensus 115 ve~lAdyL~~~Gy 127 (127)
..-+.+||..+||
T Consensus 7 ~~lI~~yL~~~g~ 19 (34)
T smart00667 7 NRLILEYLLRNGY 19 (34)
T ss_pred HHHHHHHHHHcCH
Confidence 3457999999987
No 26
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=36.15 E-value=1.7e+02 Score=21.98 Aligned_cols=89 Identities=10% Similarity=0.102 Sum_probs=53.2
Q ss_pred EEeeCCCCce--EEEEcCCCCEEEecCCCCCCCHHHHHHHHHhcCCCCCcCccceEEcC---EEEEEEEeCCCcEEEeec
Q 033115 9 RVTISQLPLS--SATTAAFGPRVKTSLRFFLLKPEEITGIMNDFNEPGTLAPTGLYLGG---TKYMVIQGEPGAVIRGKK 83 (127)
Q Consensus 9 ~~~~~~~~~~--aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G---~KY~~~r~d~~~~i~~kk 83 (127)
.+++++++.+ --++|.+ .|+| .-+.+-...|.+.++..-+....|+.+.+ -.|- -|
T Consensus 100 t~~inG~~~Aki~fVvG~~------np~~-~~N~~fA~~l~~~~~~~yPgl~rgi~~k~~~~~~YN---Qd--------- 160 (196)
T TIGR02867 100 TVNINGESVAKVMFVIGKN------NPHF-EKNLQLANKLHAKLEKKYPGLSRGIFYKDYGNGVYN---QD--------- 160 (196)
T ss_pred eEEECCEEEEEEEEEEcCC------CCCH-HHHHHHHHHHHHHHHhhCCCcccceEEccCCCCccc---cc---------
Confidence 3445555444 2244443 3555 43444444555555432234477888843 2222 33
Q ss_pred CCCcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHh
Q 033115 84 GPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLID 124 (127)
Q Consensus 84 g~~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~ 124 (127)
.++.+++|=+.....+-.++...++-||+-|.+
T Consensus 161 --------l~~~alLiEiG~~~Nt~eEa~~s~~~lA~~i~~ 193 (196)
T TIGR02867 161 --------LSPNAILIEVGGVDNTLEEAKRSADYLAEAIAE 193 (196)
T ss_pred --------CCCCeEEEEECCCCCcHHHHHHHHHHHHHHHHH
Confidence 457789998888877888899999999887764
No 27
>PRK00394 transcription factor; Reviewed
Probab=35.62 E-value=1e+02 Score=22.77 Aligned_cols=40 Identities=13% Similarity=0.072 Sum_probs=31.0
Q ss_pred CCCcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 84 GPGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 84 g~~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
.+.-+.+..+.+.++.|... ..++..+++++++.|++.||
T Consensus 45 Pk~t~lIf~sGKiv~tGa~S----~~~a~~a~~~~~~~l~~~g~ 84 (179)
T PRK00394 45 PKIAALIFRSGKVVCTGAKS----VEDLHEAVKIIIKKLKELGI 84 (179)
T ss_pred CceEEEEEcCCcEEEEccCC----HHHHHHHHHHHHHHHHHcCC
Confidence 34556677777777776654 46899999999999999886
No 28
>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=34.88 E-value=41 Score=20.73 Aligned_cols=22 Identities=18% Similarity=0.439 Sum_probs=17.8
Q ss_pred CCcchHHHHHHHHHHHHHhCCC
Q 033115 106 MTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 106 ~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
++....+..+..+.++++++||
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 29
>PRK06988 putative formyltransferase; Provisional
Probab=34.76 E-value=2.3e+02 Score=22.59 Aligned_cols=38 Identities=16% Similarity=0.303 Sum_probs=28.8
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeC
Q 033115 34 RFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 34 ~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d 74 (127)
+| +-+.+|+..++++|.+|- ...=.+++|+++.+.+++
T Consensus 211 dw-~~~a~~I~~~iRA~~~p~--pga~~~~~g~~v~i~~a~ 248 (312)
T PRK06988 211 DW-SKPAAQVYNLIRAVAPPY--PGAFTDLGGTRFVVARAR 248 (312)
T ss_pred CC-CCCHHHHHHHhccCCCCC--CeeEEEECCEEEEEEEEE
Confidence 57 668899999999996552 223357899999998865
No 30
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=34.19 E-value=1.1e+02 Score=19.64 Aligned_cols=44 Identities=16% Similarity=0.197 Sum_probs=30.2
Q ss_pred HHHHHHhc-CCCCCcCccceEEcCEEEEEEEeCCC--cEEEeecCCC
Q 033115 43 ITGIMNDF-NEPGTLAPTGLYLGGTKYMVIQGEPG--AVIRGKKGPG 86 (127)
Q Consensus 43 ~~~i~~~f-~~~~~~~~~Gi~l~G~KY~~~r~d~~--~~i~~kkg~~ 86 (127)
+..+++.| ++|..+.-.-.......-+-++.+++ ..+.||+|..
T Consensus 5 v~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRt 51 (76)
T COG1837 5 VEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRT 51 (76)
T ss_pred HHHHHHHhcCCccceEEEEEecCCeEEEEEEECcccccceecCCChh
Confidence 45667776 67887766655556666677777644 4588998864
No 31
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=32.90 E-value=91 Score=21.78 Aligned_cols=34 Identities=21% Similarity=0.328 Sum_probs=25.6
Q ss_pred CcEEEEEEeCCCC--CcchHHHHHHHHHHHHHhCCC
Q 033115 94 SAALIIGIYDEPM--TPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 94 ~~aiVIg~y~~~~--~~g~~~~~ve~lAdyL~~~Gy 127 (127)
..-++|+.-.+.. +-.+.+.++.+|++.|.+.|+
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 4567777666633 337799999999999999874
No 32
>PRK01064 hypothetical protein; Provisional
Probab=32.17 E-value=1.4e+02 Score=19.13 Aligned_cols=45 Identities=16% Similarity=0.129 Sum_probs=25.0
Q ss_pred HHHHHHHhc-CCCCCcCccceEEcCEEEEEEEeCCC--cEEEeecCCC
Q 033115 42 EITGIMNDF-NEPGTLAPTGLYLGGTKYMVIQGEPG--AVIRGKKGPG 86 (127)
Q Consensus 42 E~~~i~~~f-~~~~~~~~~Gi~l~G~KY~~~r~d~~--~~i~~kkg~~ 86 (127)
=+..|++.| ++|+.+.-.-..-++.-.+-++.+++ ..+.||+|..
T Consensus 4 Lv~~iv~~LVd~Pe~V~V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~ 51 (78)
T PRK01064 4 FLAYIVKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRT 51 (78)
T ss_pred HHHHHHHHhcCCCCeEEEEEEeCCCEEEEEEEECcccceEEECCCCcc
Confidence 355677777 67876654433223444444555533 3577777754
No 33
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=31.41 E-value=79 Score=21.71 Aligned_cols=41 Identities=17% Similarity=0.251 Sum_probs=28.8
Q ss_pred EEeeCCCCce-EEEEcCCCCE-EE--ecC----CCCCCCHHHHHHHHHh
Q 033115 9 RVTISQLPLS-SATTAAFGPR-VK--TSL----RFFLLKPEEITGIMND 49 (127)
Q Consensus 9 ~~~~~~~~~~-aAI~g~dG~v-WA--~s~----~f~~l~~~E~~~i~~~ 49 (127)
+|.++++... ..|+..+|.+ |. ..+ .|+.++++++..+++.
T Consensus 9 ~i~i~g~~y~~~viv~p~~~~~w~~~~~s~~~~~~~~l~~~~l~~ll~~ 57 (117)
T cd05126 9 SITVGGETYEHDIVVYPDGSRARRWKELSKKTGTSHGLQPEELEELLEE 57 (117)
T ss_pred EEEECCEEEcCCEEEeCCccccccccccccccCCcccCCHHHHHHHHhc
Confidence 4667766554 5677778755 54 332 7778899999999873
No 34
>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=31.31 E-value=31 Score=19.47 Aligned_cols=28 Identities=18% Similarity=0.178 Sum_probs=16.6
Q ss_pred CCEEEecCCCCCCCHHHHHHHHHhcCCC
Q 033115 26 GPRVKTSLRFFLLKPEEITGIMNDFNEP 53 (127)
Q Consensus 26 G~vWA~s~~f~~l~~~E~~~i~~~f~~~ 53 (127)
.+.|-+..+|++.+.+.++.++....+|
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 5789999999889999999988876554
No 35
>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=30.97 E-value=1.4e+02 Score=18.85 Aligned_cols=37 Identities=19% Similarity=0.312 Sum_probs=27.7
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeC
Q 033115 34 RFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 34 ~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d 74 (127)
+| +-+.+|+..++.+|. |-. ..=..++|++..+.+++
T Consensus 10 dw-~~~A~~I~~~vRal~-p~p--ga~~~~~~~~i~i~~~~ 46 (100)
T PF02911_consen 10 DW-NQSAEEIYNLVRALN-PYP--GAFTTFNGKRIKILKAE 46 (100)
T ss_dssp -T-TSBHHHHHHHHHHTT-TTT---EEEEETTEEEEEEEEE
T ss_pred CC-CCCHHHHHHHHhCCC-CCC--CEEEeeCCeEEEEEeee
Confidence 57 789999999999997 422 33356799999888874
No 36
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=30.90 E-value=1.6e+02 Score=19.79 Aligned_cols=20 Identities=10% Similarity=0.197 Sum_probs=16.1
Q ss_pred ccceEEcCEEEEEEEeCCCc
Q 033115 58 PTGLYLGGTKYMVIQGEPGA 77 (127)
Q Consensus 58 ~~Gi~l~G~KY~~~r~d~~~ 77 (127)
-+-|.++|++|..++.|-++
T Consensus 4 i~~i~i~gk~~l~~~~~L~n 23 (95)
T COG3377 4 IEPIDIEGKKFLGLKVDLPN 23 (95)
T ss_pred eeeEeeCCeEEEEEEecCCC
Confidence 34589999999999998554
No 37
>COG2896 MoaA Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]
Probab=29.69 E-value=45 Score=27.17 Aligned_cols=44 Identities=25% Similarity=0.247 Sum_probs=32.5
Q ss_pred EEEEeeCCCCceEEEEcC-CC-CEEEecCCCCCCCHHHHHHHHHhcCC
Q 033115 7 KLRVTISQLPLSSATTAA-FG-PRVKTSLRFFLLKPEEITGIMNDFNE 52 (127)
Q Consensus 7 ~~~~~~~~~~~~aAI~g~-dG-~vWA~s~~f~~l~~~E~~~i~~~f~~ 52 (127)
.||+++.|.|+--+++=+ +| ..|--..+ -+++||+..+++.|..
T Consensus 12 ~LRiSvTdrCNfrC~YCm~eg~~~~~~~~~--~Ls~eei~~~~~~~~~ 57 (322)
T COG2896 12 YLRISVTDRCNFRCTYCMPEGPLAFLPKEE--LLSLEEIRRLVRAFAE 57 (322)
T ss_pred eEEEEEecCcCCcccccCCCCCcccCcccc--cCCHHHHHHHHHHHHH
Confidence 689999999999776554 77 44433222 4699999999999844
No 38
>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=28.99 E-value=90 Score=21.45 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=25.3
Q ss_pred CcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 94 SAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 94 ~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+.+++|++++...++...=.++.++-.+....||
T Consensus 13 ~~~~~I~lNPS~A~~~~~D~T~~~~~~~a~~~gy 46 (136)
T PF07799_consen 13 PPLLFIGLNPSTADAEKDDPTIRRCINFARRWGY 46 (136)
T ss_pred CEEEEEEeCCCCCCCcCCCHHHHHHHHHHhhcCC
Confidence 5688999999877766666667777777777776
No 39
>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=28.86 E-value=65 Score=19.27 Aligned_cols=22 Identities=36% Similarity=0.637 Sum_probs=19.3
Q ss_pred CCcchHHHHHHHHHHHHHhCCC
Q 033115 106 MTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 106 ~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
.++....+..++|.+++.+.||
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 4577889999999999999997
No 40
>COG1832 Predicted CoA-binding protein [General function prediction only]
Probab=28.36 E-value=87 Score=22.55 Aligned_cols=31 Identities=29% Similarity=0.589 Sum_probs=23.4
Q ss_pred EeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 91 KKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 91 ~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
.+.|+--|||..+.+.-++ ...++||.++||
T Consensus 14 ~~~K~IAvVG~S~~P~r~s------y~V~kyL~~~GY 44 (140)
T COG1832 14 KSAKTIAVVGASDKPDRPS------YRVAKYLQQKGY 44 (140)
T ss_pred HhCceEEEEecCCCCCccH------HHHHHHHHHCCC
Confidence 3567778888888765543 567899999998
No 41
>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=28.32 E-value=1.2e+02 Score=21.83 Aligned_cols=20 Identities=15% Similarity=0.127 Sum_probs=17.0
Q ss_pred cchHHHHHHHHHHHHHhCCC
Q 033115 108 PGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 108 ~g~~~~~ve~lAdyL~~~Gy 127 (127)
..+..+++..+.++|+++||
T Consensus 163 ~~~t~~~l~~~i~~l~~~Gy 182 (191)
T TIGR02764 163 AKQTVKALPTIIKKLKEKGY 182 (191)
T ss_pred cHhHHHHHHHHHHHHHHCCC
Confidence 34567889999999999998
No 42
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=27.80 E-value=1.2e+02 Score=24.46 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=24.0
Q ss_pred eCCcEEEEEEeCC-CCCcchHHHHHHHHHHHHHhCC
Q 033115 92 KTSAALIIGIYDE-PMTPGQCNMIVERLGDYLIDQG 126 (127)
Q Consensus 92 KT~~aiVIg~y~~-~~~~g~~~~~ve~lAdyL~~~G 126 (127)
-.++.+.||..-- +++ .....+|+||+||++.|
T Consensus 239 egks~lTIaIGCTGGqH--RSV~iae~La~~l~~~~ 272 (286)
T COG1660 239 EGKSYLTIAIGCTGGQH--RSVYIAEQLAEYLRARG 272 (286)
T ss_pred cCCeEEEEEEccCCCcc--chHHHHHHHHHHHHhcc
Confidence 3467888888663 233 36678899999999875
No 43
>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=27.61 E-value=48 Score=19.02 Aligned_cols=17 Identities=29% Similarity=0.395 Sum_probs=14.6
Q ss_pred ccceEEcCEEEEEEEeC
Q 033115 58 PTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 58 ~~Gi~l~G~KY~~~r~d 74 (127)
..|+.|+|+|+++....
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 57899999999998764
No 44
>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=27.38 E-value=1.8e+02 Score=21.37 Aligned_cols=36 Identities=8% Similarity=0.180 Sum_probs=27.2
Q ss_pred EEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 88 VTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 88 ~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+.+..+.+.++-|... ..++..+++++++.|++.||
T Consensus 50 ~lIF~SGKiviTGaks----~e~a~~a~~~i~~~L~~~g~ 85 (174)
T cd04516 50 ALIFSSGKMVCTGAKS----EDDSKLAARKYARIIQKLGF 85 (174)
T ss_pred EEEECCCeEEEEecCC----HHHHHHHHHHHHHHHHHcCC
Confidence 5566666666665543 46899999999999999886
No 45
>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=26.75 E-value=1.3e+02 Score=18.65 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=20.2
Q ss_pred cEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 95 AALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 95 ~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
|.+|+-..+. + ........++|+.|+++|+
T Consensus 3 qv~i~p~~~~--~-~~~~~~a~~la~~Lr~~g~ 32 (94)
T cd00861 3 DVVIIPMNMK--D-EVQQELAEKLYAELQAAGV 32 (94)
T ss_pred EEEEEEcCCC--c-HHHHHHHHHHHHHHHHCCC
Confidence 3444444433 1 4567788999999999886
No 46
>PF14553 YqbF: YqbF, hypothetical protein domain; PDB: 2HJQ_A.
Probab=26.71 E-value=59 Score=18.70 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=10.2
Q ss_pred HHHHHHHHHHhCCC
Q 033115 114 IVERLGDYLIDQGL 127 (127)
Q Consensus 114 ~ve~lAdyL~~~Gy 127 (127)
..+++++||.++++
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 45788999998864
No 47
>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=26.41 E-value=68 Score=19.54 Aligned_cols=19 Identities=16% Similarity=0.377 Sum_probs=15.8
Q ss_pred CCCHHHHHHHHHhcCCCCC
Q 033115 37 LLKPEEITGIMNDFNEPGT 55 (127)
Q Consensus 37 ~l~~~E~~~i~~~f~~~~~ 55 (127)
.++++|.++|+++|++...
T Consensus 28 Gv~~~e~~aIi~~F~~~~~ 46 (57)
T PF05952_consen 28 GVDKDEQKAIIDAFKDEES 46 (57)
T ss_pred cCCHHHHHHHHHHHccccc
Confidence 5689999999999987543
No 48
>PLN00062 TATA-box-binding protein; Provisional
Probab=26.40 E-value=2e+02 Score=21.24 Aligned_cols=38 Identities=8% Similarity=0.134 Sum_probs=28.0
Q ss_pred CcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 86 GGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 86 ~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
.-+.+..+.+.++-|.-. ..++..++.++++.|.+.||
T Consensus 48 ~t~lIF~SGKiviTGaks----~e~a~~a~~~~~~~L~~lg~ 85 (179)
T PLN00062 48 TTALIFASGKMVCTGAKS----EHDSKLAARKYARIIQKLGF 85 (179)
T ss_pred EEEEEECCCeEEEEecCC----HHHHHHHHHHHHHHHHHcCC
Confidence 345566666666665443 46899999999999999886
No 49
>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=26.08 E-value=1.8e+02 Score=21.28 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=27.6
Q ss_pred CCcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 85 PGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 85 ~~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+.-+-+..+.+.++.|.- +..++..+++++++.|++.||
T Consensus 47 k~t~lIF~sGKiviTGak----s~~~~~~a~~~~~~~l~~~g~ 85 (174)
T cd04517 47 RATASVWSSGKITITGAT----SEEEAKQAARRAARLLQKLGF 85 (174)
T ss_pred cEEEEEECCCeEEEEccC----CHHHHHHHHHHHHHHHHHcCC
Confidence 334455566666655543 357899999999999999875
No 50
>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=26.04 E-value=1.5e+02 Score=21.82 Aligned_cols=39 Identities=15% Similarity=0.132 Sum_probs=29.0
Q ss_pred CCcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 85 PGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 85 ~~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+.-+.+..+.+.++.|.- +..++..+++++++.|++.||
T Consensus 47 k~t~lIF~SGKiv~tGak----s~~~a~~a~~~~~~~L~~~g~ 85 (174)
T cd04518 47 KIAALIFRSGKMVCTGAK----SVEDLHRAVKEIIKKLKDYGI 85 (174)
T ss_pred cEEEEEECCCeEEEEccC----CHHHHHHHHHHHHHHHHhcCC
Confidence 445566666666666553 357899999999999999885
No 51
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=25.30 E-value=1.1e+02 Score=18.43 Aligned_cols=25 Identities=32% Similarity=0.630 Sum_probs=19.5
Q ss_pred cEEEEEEeCCCCCcchHHHHHHHHH
Q 033115 95 AALIIGIYDEPMTPGQCNMIVERLG 119 (127)
Q Consensus 95 ~aiVIg~y~~~~~~g~~~~~ve~lA 119 (127)
.+.+|-.-.++++||.|...++.+.
T Consensus 13 ~a~~v~T~~G~VH~g~C~~y~~e~~ 37 (54)
T PF10886_consen 13 DALVVETESGPVHPGVCAQYLEELP 37 (54)
T ss_pred cceEEEcCCCccCcHHHHHHHHhcc
Confidence 3666666777899999999888773
No 52
>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=24.92 E-value=60 Score=21.48 Aligned_cols=30 Identities=27% Similarity=0.457 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHHhcC--CCCCcCccceEEcCE
Q 033115 37 LLKPEEITGIMNDFN--EPGTLAPTGLYLGGT 66 (127)
Q Consensus 37 ~l~~~E~~~i~~~f~--~~~~~~~~Gi~l~G~ 66 (127)
.++++|+..+.+... -|......||++.|-
T Consensus 3 pL~~~el~~ik~~v~~~~~~gv~~~GiT~~GF 34 (89)
T PF08356_consen 3 PLQPQELEDIKKVVRENIPDGVNDNGITLDGF 34 (89)
T ss_pred CCCHHHHHHHHHHHHHHCCCCcCCCccchhhH
Confidence 578999998888763 344566778887773
No 53
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=24.88 E-value=76 Score=21.44 Aligned_cols=19 Identities=5% Similarity=0.380 Sum_probs=15.8
Q ss_pred cCccceEEcCEEEEEEEeC
Q 033115 56 LAPTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 56 ~~~~Gi~l~G~KY~~~r~d 74 (127)
...+-+.++|++|+++|.+
T Consensus 74 y~Gtevk~dg~ey~i~~e~ 92 (100)
T PTZ00414 74 FGGSSVKVEGEEFFLYNED 92 (100)
T ss_pred CCCcEEEECCEEEEEEEhH
Confidence 3356699999999999987
No 54
>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=24.71 E-value=1.5e+02 Score=22.02 Aligned_cols=34 Identities=15% Similarity=0.137 Sum_probs=24.7
Q ss_pred CcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 94 SAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 94 ~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
.|.+||-..............+.++++.|+++|+
T Consensus 11 ~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Gi 44 (202)
T cd00862 11 IQVVIVPIGIKDEKREEVLEAADELAERLKAAGI 44 (202)
T ss_pred ceEEEEEecCCccchHHHHHHHHHHHHHHHHCCC
Confidence 4677777765533334578889999999998874
No 55
>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=24.58 E-value=68 Score=21.08 Aligned_cols=18 Identities=28% Similarity=0.582 Sum_probs=15.5
Q ss_pred CccceEEcCEEEEEEEeC
Q 033115 57 APTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 57 ~~~Gi~l~G~KY~~~r~d 74 (127)
..+-+.++|++|+++|.+
T Consensus 70 ~g~~v~~~~~~y~i~~~~ 87 (93)
T cd00320 70 AGTEVKLDGEEYLILRES 87 (93)
T ss_pred CceEEEECCEEEEEEEHH
Confidence 366799999999999987
No 56
>PF02866 Ldh_1_C: lactate/malate dehydrogenase, alpha/beta C-terminal domain Prosite entry for lactate dehydrogenase Prosite entry for malate dehydrogenase; InterPro: IPR022383 L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis []. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate []. The enzyme participates in the citric acid cycle. This entry represents the C-terminal, and is thought to be an is an unusual alpha+beta fold.; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 4MDH_B 5MDH_A 1GV0_A 1GUZ_D 2EWD_B 2FRM_D 2FNZ_B 2FN7_B 2FM3_A 1LTH_T ....
Probab=24.23 E-value=1.2e+02 Score=21.75 Aligned_cols=30 Identities=17% Similarity=0.069 Sum_probs=23.2
Q ss_pred EEEEcCCCCEEEecCCCCCCCHHHHHHHHHhc
Q 033115 19 SATTAAFGPRVKTSLRFFLLKPEEITGIMNDF 50 (127)
Q Consensus 19 aAI~g~dG~vWA~s~~f~~l~~~E~~~i~~~f 50 (127)
=+++|.+| +|..-+.+ +|+++|.+.|.+..
T Consensus 131 P~~ig~~G-v~~i~~~~-~L~~~E~~~l~~sa 160 (174)
T PF02866_consen 131 PVVIGKNG-VEKIVEDL-PLSEEEQEKLKESA 160 (174)
T ss_dssp EEEEETTE-EEEEECSB-SSTHHHHHHHHHHH
T ss_pred eEEEcCCe-eEEEeCCC-CCCHHHHHHHHHHH
Confidence 45788876 67776668 89999999887653
No 57
>PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This entry represents UPF0042 nucleotide-binding proteins. This is a family of putative P-loop ATPases [], as they contain an ATP-binding site and display ATPase and GTPase activities.; GO: 0005524 ATP binding
Probab=23.10 E-value=1.7e+02 Score=23.47 Aligned_cols=34 Identities=26% Similarity=0.293 Sum_probs=25.1
Q ss_pred eCCcEEEEEEeCC-CCCcchHHHHHHHHHHHHHhCCC
Q 033115 92 KTSAALIIGIYDE-PMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 92 KT~~aiVIg~y~~-~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
..++.+.||..-- +.+ .....+|.||++|++.||
T Consensus 238 egk~~ltIaiGCTGG~H--RSV~iae~La~~L~~~~~ 272 (284)
T PF03668_consen 238 EGKSYLTIAIGCTGGQH--RSVAIAERLAERLREKGY 272 (284)
T ss_pred cCCceEEEEEEcCCCcC--cHHHHHHHHHHHHHhcCC
Confidence 3466788887663 333 367789999999999885
No 58
>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=22.76 E-value=2.1e+02 Score=18.74 Aligned_cols=34 Identities=12% Similarity=0.109 Sum_probs=28.7
Q ss_pred CCcEEEEEEeCCC-CCcchHHHHHHHHHHHHHhCC
Q 033115 93 TSAALIIGIYDEP-MTPGQCNMIVERLGDYLIDQG 126 (127)
Q Consensus 93 T~~aiVIg~y~~~-~~~g~~~~~ve~lAdyL~~~G 126 (127)
.++.++||..+.. .++....++...+++.|.+.+
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 4778999999885 678999999999999998754
No 59
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=22.74 E-value=79 Score=20.86 Aligned_cols=17 Identities=18% Similarity=0.546 Sum_probs=14.9
Q ss_pred ccceEEcCEEEEEEEeC
Q 033115 58 PTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 58 ~~Gi~l~G~KY~~~r~d 74 (127)
..-+.++|++|+++|.+
T Consensus 72 g~ev~~~~~~y~iv~~~ 88 (95)
T PRK00364 72 GTEVKIDGEEYLILRES 88 (95)
T ss_pred CeEEEECCEEEEEEEHH
Confidence 55789999999999987
No 60
>KOG0141 consensus Isovaleryl-CoA dehydrogenase [Amino acid transport and metabolism; Lipid transport and metabolism]
Probab=22.73 E-value=1.2e+02 Score=25.18 Aligned_cols=43 Identities=19% Similarity=0.346 Sum_probs=29.1
Q ss_pred ccceEEcCEEEEEEEeCCCc--EEEeecCCCcEEEEeCCcEEEEE
Q 033115 58 PTGLYLGGTKYMVIQGEPGA--VIRGKKGPGGVTIKKTSAALIIG 100 (127)
Q Consensus 58 ~~Gi~l~G~KY~~~r~d~~~--~i~~kkg~~G~~i~KT~~aiVIg 100 (127)
.+...+||.|+.+++..+.+ .+|+|.+..++--.+--+++||=
T Consensus 183 g~~yiLNGsK~witNG~~advliVyAkTd~~a~~~~hGIt~FiVE 227 (421)
T KOG0141|consen 183 GDDYILNGSKFWITNGPDADVLIVYAKTDHSAVPPSHGITAFIVE 227 (421)
T ss_pred CCcEEecCcEEEEecCCCCcEEEEEEecCCCCCCCcCceEEEEEc
Confidence 57889999999999875333 47888766654444444556653
No 61
>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=22.70 E-value=1.2e+02 Score=24.15 Aligned_cols=34 Identities=15% Similarity=0.299 Sum_probs=23.3
Q ss_pred CcEEEEEEeCCCCC-cchHHHHHHHHHHHHHhCCC
Q 033115 94 SAALIIGIYDEPMT-PGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 94 ~~aiVIg~y~~~~~-~g~~~~~ve~lAdyL~~~Gy 127 (127)
++.+|++..+++.- .-.+..+.-.+|+|++++|+
T Consensus 127 ~tvvv~~t~d~~~~~r~~a~~~a~aiAE~fr~~G~ 161 (274)
T cd01132 127 YTIVVAATASDPAPLQYLAPYTGCAMGEYFMDNGK 161 (274)
T ss_pred eeEEEEeCCCCchhHHHHHHHHHHHHHHHHHHCCC
Confidence 34677777776432 33456677889999999885
No 62
>PF14080 DUF4261: Domain of unknown function (DUF4261)
Probab=22.53 E-value=1.7e+02 Score=18.28 Aligned_cols=23 Identities=13% Similarity=0.458 Sum_probs=20.4
Q ss_pred CCCCcchHHHHHHHHHHHHHhCC
Q 033115 104 EPMTPGQCNMIVERLGDYLIDQG 126 (127)
Q Consensus 104 ~~~~~g~~~~~ve~lAdyL~~~G 126 (127)
...+|.........+|.||.++|
T Consensus 18 ~~~~p~ev~~~l~~ia~Yil~~~ 40 (77)
T PF14080_consen 18 SDLDPEEVYNFLYNIAYYILENG 40 (77)
T ss_pred CCCCHHHHHHHHHHHHHHHHcCC
Confidence 56789999999999999999876
No 63
>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=22.16 E-value=1.8e+02 Score=20.65 Aligned_cols=35 Identities=14% Similarity=0.059 Sum_probs=23.9
Q ss_pred CCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 93 TSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 93 T~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
.++..++|.++....+..-..++..|.+.|.+.|.
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 46677888776443455566777888888887763
No 64
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=21.96 E-value=91 Score=20.58 Aligned_cols=18 Identities=22% Similarity=0.418 Sum_probs=15.4
Q ss_pred CccceEEcCEEEEEEEeC
Q 033115 57 APTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 57 ~~~Gi~l~G~KY~~~r~d 74 (127)
..+-+.++|++|+++|.+
T Consensus 66 ~g~ev~~~~~~y~iv~e~ 83 (91)
T PRK14533 66 AGTEIKIDDEDYIIIDVN 83 (91)
T ss_pred CCeEEEECCEEEEEEEhH
Confidence 356799999999999987
No 65
>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=21.80 E-value=2.3e+02 Score=20.75 Aligned_cols=39 Identities=13% Similarity=0.192 Sum_probs=29.3
Q ss_pred CCcEEEEeCCcEEEEEEeCCCCCcchHHHHHHHHHHHHHhCCC
Q 033115 85 PGGVTIKKTSAALIIGIYDEPMTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 85 ~~G~~i~KT~~aiVIg~y~~~~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
+.-+.+..+.+.++.|... ..++..+++++++.|++.||
T Consensus 47 ~~t~lIf~sGKivitGaks----~~~~~~a~~~~~~~L~~~g~ 85 (174)
T cd00652 47 KTTALIFSSGKMVITGAKS----EEDAKLAARKYARILQKLGF 85 (174)
T ss_pred cEEEEEECCCEEEEEecCC----HHHHHHHHHHHHHHHHHcCC
Confidence 4456666666666666544 46899999999999999885
No 66
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=21.80 E-value=95 Score=26.48 Aligned_cols=34 Identities=18% Similarity=0.397 Sum_probs=23.5
Q ss_pred CcEEEEEEeCCC-CCcchHHHHHHHHHHHHHhCCC
Q 033115 94 SAALIIGIYDEP-MTPGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 94 ~~aiVIg~y~~~-~~~g~~~~~ve~lAdyL~~~Gy 127 (127)
++.+|++.-|++ +.--++......+|+|.+++|.
T Consensus 219 rsViVvATSD~s~l~R~~aa~~At~IAEyFRDqG~ 253 (441)
T COG1157 219 RSVVVVATSDESALMRLKAAFTATTIAEYFRDQGK 253 (441)
T ss_pred ceEEEEECCCCCHHHHHHHHHHHHHHHHHHHhCCC
Confidence 445555555554 2345677788889999999983
No 67
>PF09695 YtfJ_HI0045: Bacterial protein of unknown function (YtfJ_HI0045); InterPro: IPR006513 These are sequences from gammaproteobacteria that are related to the Escherichia coli protein, YtfJ.
Probab=21.40 E-value=2.1e+02 Score=21.05 Aligned_cols=34 Identities=18% Similarity=0.167 Sum_probs=22.7
Q ss_pred CCceEE--EEcCCC-CEEEecCCCCCCCHHHHHHHHHhcC
Q 033115 15 LPLSSA--TTAAFG-PRVKTSLRFFLLKPEEITGIMNDFN 51 (127)
Q Consensus 15 ~~~~aA--I~g~dG-~vWA~s~~f~~l~~~E~~~i~~~f~ 51 (127)
++++.| +++.+| -.|++...+ +|+|++.++..++
T Consensus 122 ~~~~SaiiVlDK~G~V~F~k~G~L---s~~Ev~qVi~Ll~ 158 (160)
T PF09695_consen 122 QEESSAIIVLDKQGKVQFVKEGAL---SPAEVQQVIALLK 158 (160)
T ss_pred CCCCceEEEEcCCccEEEEECCCC---CHHHHHHHHHHHh
Confidence 344444 444567 456665555 9999999998764
No 68
>PF14620 YPEB: YpeB sporulation
Probab=21.02 E-value=4.7e+02 Score=21.46 Aligned_cols=82 Identities=11% Similarity=0.121 Sum_probs=44.7
Q ss_pred CCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeCCC----c--EEEee--cCCCc-EEEEeCCc-EEEEEEeCC-
Q 033115 36 FLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGEPG----A--VIRGK--KGPGG-VTIKKTSA-ALIIGIYDE- 104 (127)
Q Consensus 36 ~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d~~----~--~i~~k--kg~~G-~~i~KT~~-aiVIg~y~~- 104 (127)
+.++++|+..+++-|-+... .. ++.+..+.. . ++.-. +...+ +.+--|++ .-||-+.+.
T Consensus 205 ~~Is~eeA~~iak~fl~~~~--~~--------~~~~~~~~~~~~~~~Ys~~~~~~~~~~~~~~~dVtkkGG~vi~~~~~R 274 (361)
T PF14620_consen 205 KEISKEEAKQIAKKFLGKPK--NS--------SIKVTKNGKGGNIPSYSFSVSDKGRNNNRIYMDVTKKGGHVIWFLNSR 274 (361)
T ss_pred CCcCHHHHHHHHHHHhCCCC--cc--------ceEeeccCCCCCCceEEEEEecCCCCCceEEEEEEcCCCEEEEEECCC
Confidence 47899999999998843211 11 111111101 1 12211 22233 55555555 444555444
Q ss_pred CCC--cchHHHHHHHHHHHHHhCCC
Q 033115 105 PMT--PGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 105 ~~~--~g~~~~~ve~lAdyL~~~Gy 127 (127)
++. .=...+|.++-.+||.+.||
T Consensus 275 ~v~~~kis~~eA~~~A~~fL~~~g~ 299 (361)
T PF14620_consen 275 PVGKPKISLEEAKNKAEEFLKKHGY 299 (361)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHhCC
Confidence 332 23478888888999999987
No 69
>PRK00005 fmt methionyl-tRNA formyltransferase; Reviewed
Probab=20.81 E-value=4.3e+02 Score=20.87 Aligned_cols=37 Identities=19% Similarity=0.322 Sum_probs=27.0
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCcCccceEEcCEEEEEEEeC
Q 033115 34 RFFLLKPEEITGIMNDFNEPGTLAPTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 34 ~f~~l~~~E~~~i~~~f~~~~~~~~~Gi~l~G~KY~~~r~d 74 (127)
+| +-+.+|+..++++|. |- ...=..++|+++.+.+++
T Consensus 212 dw-~~~a~~I~~~iRA~~-p~--pga~~~~~g~~v~i~~a~ 248 (309)
T PRK00005 212 DW-SKPAAELENHIRGFN-PW--PGAWTELDGQRLKILEAE 248 (309)
T ss_pred cC-CCCHHHHHHHHhcCC-CC--CceEEEECCEEEEEEEEE
Confidence 57 557889999999984 31 122356899999998864
No 70
>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=20.47 E-value=92 Score=20.29 Aligned_cols=17 Identities=24% Similarity=0.624 Sum_probs=15.1
Q ss_pred ccceEEcCEEEEEEEeC
Q 033115 58 PTGLYLGGTKYMVIQGE 74 (127)
Q Consensus 58 ~~Gi~l~G~KY~~~r~d 74 (127)
..-+.++|++|+++|.+
T Consensus 71 g~~v~~~~~~~~~~~~~ 87 (93)
T PF00166_consen 71 GTEVKFDGEKYLIVRED 87 (93)
T ss_dssp SEEEEETTEEEEEEEGG
T ss_pred ceEEEECCEEEEEEEHH
Confidence 56789999999999987
No 71
>KOG3619 consensus Adenylate/guanylate cyclase [Energy production and conversion]
Probab=20.42 E-value=76 Score=29.38 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=32.7
Q ss_pred EEEEEeeCCCCceEEEEcCCC---CEEEecCCC---------C-C-CCHHHHHHHHHhc
Q 033115 6 VKLRVTISQLPLSSATTAAFG---PRVKTSLRF---------F-L-LKPEEITGIMNDF 50 (127)
Q Consensus 6 ~~~~~~~~~~~~~aAI~g~dG---~vWA~s~~f---------~-~-l~~~E~~~i~~~f 50 (127)
..|||+++..|.-|.++|.+. .+|+.+=+. + . --+||...+...+
T Consensus 759 F~LrIGin~GpvvAGVIGArKPqYDIWGNTVNvASRMdSTGv~g~IQVTEEt~~iL~~~ 817 (867)
T KOG3619|consen 759 FELRIGINHGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPGRIQVTEETANILQGL 817 (867)
T ss_pred ceeeeceeccceeeeEecCCCCCccccccchhhhhcccccCCCCeEEecHHHHHHHhcC
Confidence 369999999999999999976 899864322 0 1 1367777777654
No 72
>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=20.29 E-value=1.1e+02 Score=25.56 Aligned_cols=34 Identities=18% Similarity=0.273 Sum_probs=22.0
Q ss_pred CcEEEEEEeCCCCC-cchHHHHHHHHHHHHHhCCC
Q 033115 94 SAALIIGIYDEPMT-PGQCNMIVERLGDYLIDQGL 127 (127)
Q Consensus 94 ~~aiVIg~y~~~~~-~g~~~~~ve~lAdyL~~~Gy 127 (127)
++.+|++..+++.- .-.+..+.-.+|+|++++||
T Consensus 220 rtvlV~nts~~p~~~R~~s~yta~tiAEYfrd~G~ 254 (369)
T cd01134 220 RTVLIANTSNMPVAAREASIYTGITIAEYFRDMGY 254 (369)
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 44566666665432 23355566679999999986
No 73
>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=20.09 E-value=1.4e+02 Score=23.33 Aligned_cols=33 Identities=18% Similarity=0.072 Sum_probs=23.5
Q ss_pred CCceEE--EEcCCC-CEEEecCCCCCCCHHHHHHHHHhc
Q 033115 15 LPLSSA--TTAAFG-PRVKTSLRFFLLKPEEITGIMNDF 50 (127)
Q Consensus 15 ~~~~aA--I~g~dG-~vWA~s~~f~~l~~~E~~~i~~~f 50 (127)
++..|- +++.+| -.||.++.- +|+|+..|.++.
T Consensus 214 N~~~GYvyLVD~~grIRWagsG~A---t~~E~~~L~k~~ 249 (252)
T PF05176_consen 214 NSYVGYVYLVDPNGRIRWAGSGPA---TPEELESLWKCV 249 (252)
T ss_pred CCCcCeEEEECCCCeEEeCccCCC---CHHHHHHHHHHH
Confidence 344444 555666 779987655 899999998864
No 74
>PF11429 Colicin_D: Colicin D; InterPro: IPR024440 Colicin D is a bacteriocin that kills target cells by cleaving tRNA(Arg). This entry represents a domain found in the C terminus of colicin D, which is responsible for its catalytic activity []. The domain is also found in some S-type pyocins, which are also bacteriocins.; GO: 0004540 ribonuclease activity; PDB: 1TFO_A 1V74_A 1TFK_A.
Probab=20.08 E-value=73 Score=21.28 Aligned_cols=30 Identities=17% Similarity=0.087 Sum_probs=18.9
Q ss_pred EEEeeCCCCceEEEEcCCCCEEEecCCCCCCCHH
Q 033115 8 LRVTISQLPLSSATTAAFGPRVKTSLRFFLLKPE 41 (127)
Q Consensus 8 ~~~~~~~~~~~aAI~g~dG~vWA~s~~f~~l~~~ 41 (127)
..|..+..+.-++|++.||.-| .+| .|+|.
T Consensus 52 skV~~N~~T~~~Vi~d~~G~Fv---sgw-kl~p~ 81 (92)
T PF11429_consen 52 SKVYFNPKTNNVVIIDKDGNFV---SGW-KLSPG 81 (92)
T ss_dssp -EEEEETTTTEEEEE-TTS-EE---EEE-E--TT
T ss_pred cEEEEeCCCCeEEEEcCCCCEE---EEE-ecccc
Confidence 3566677777899999999877 477 77654
Done!