Query 035463
Match_columns 65
No_of_seqs 110 out of 156
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:08:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035463.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035463hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01200 Ribosomal_S28e: Ribos 100.0 1.2E-41 2.6E-46 210.7 7.3 65 1-65 1-69 (69)
2 cd04457 S1_S28E S1_S28E: S28E, 100.0 1.3E-40 2.8E-45 201.9 6.7 60 6-65 1-60 (60)
3 PRK04007 rps28e 30S ribosomal 100.0 3.3E-39 7.3E-44 200.5 7.4 63 3-65 4-68 (70)
4 PTZ00085 40S ribosomal protein 100.0 3.5E-39 7.5E-44 201.7 7.5 63 3-65 8-73 (73)
5 KOG3502 40S ribosomal protein 100.0 4.2E-40 9.2E-45 202.5 0.3 64 1-65 1-66 (66)
6 COG2053 RPS28A Ribosomal prote 100.0 2.9E-35 6.3E-40 182.4 6.1 61 5-65 5-67 (69)
7 KOG0187 40S ribosomal protein 71.3 2.9 6.3E-05 29.0 1.7 20 42-62 62-81 (134)
8 TIGR00008 infA translation ini 61.9 34 0.00074 20.9 5.5 42 6-56 7-55 (68)
9 cd05793 S1_IF1A S1_IF1A: Trans 55.2 46 0.001 20.3 4.8 45 6-59 2-52 (77)
10 PF11213 DUF3006: Protein of u 54.1 11 0.00025 22.3 1.9 13 42-54 30-42 (71)
11 cd03701 IF2_IF5B_II IF2_IF5B_I 52.3 12 0.00027 23.2 1.9 25 40-64 65-89 (95)
12 TIGR03635 S17_bact 30S ribosom 51.8 18 0.0004 21.9 2.6 23 35-57 38-60 (71)
13 PF00833 Ribosomal_S17e: Ribos 51.7 4.5 9.8E-05 27.4 -0.2 20 42-62 62-81 (121)
14 PLN00208 translation initiatio 50.4 69 0.0015 22.2 5.5 42 5-55 33-80 (145)
15 COG0361 InfA Translation initi 50.1 61 0.0013 20.2 5.6 45 5-58 8-59 (75)
16 TIGR00074 hypC_hupF hydrogenas 49.9 47 0.001 20.4 4.2 40 6-54 5-44 (76)
17 PF13533 Biotin_lipoyl_2: Biot 48.6 12 0.00026 20.6 1.3 17 45-61 23-39 (50)
18 PF01176 eIF-1a: Translation i 48.2 16 0.00036 21.2 1.9 44 5-57 4-53 (65)
19 PTZ00329 eukaryotic translatio 47.0 80 0.0017 22.2 5.5 43 5-56 33-81 (155)
20 PF07892 DUF1667: Protein of u 45.8 12 0.00026 23.7 1.1 13 41-53 56-68 (82)
21 cd03440 hot_dog The hotdog fol 45.5 19 0.0004 18.0 1.7 15 41-55 53-67 (100)
22 PTZ00154 40S ribosomal protein 45.0 11 0.00024 26.1 1.0 24 38-62 58-81 (134)
23 PF11584 Toxin_ToxA: Proteinac 44.8 25 0.00054 23.6 2.6 43 13-55 28-87 (118)
24 cd03451 FkbR2 FkbR2 is a Strep 44.4 17 0.00036 22.6 1.6 15 40-54 86-100 (146)
25 cd03702 IF2_mtIF2_II This fami 44.1 17 0.00038 22.8 1.7 23 42-64 67-89 (95)
26 PF00018 SH3_1: SH3 domain; I 43.9 14 0.0003 19.6 1.0 14 45-58 15-28 (48)
27 PF14801 GCD14_N: tRNA methylt 43.5 15 0.00032 22.0 1.2 15 43-57 3-17 (54)
28 PRK13692 (3R)-hydroxyacyl-ACP 43.3 17 0.00038 24.3 1.7 14 41-54 92-105 (159)
29 CHL00142 rps17 ribosomal prote 43.2 26 0.00056 22.1 2.3 23 36-58 41-63 (84)
30 CHL00036 ycf4 photosystem I as 42.4 38 0.00082 24.5 3.4 43 22-64 124-173 (184)
31 PRK05610 rpsQ 30S ribosomal pr 42.4 31 0.00067 21.6 2.6 22 36-57 44-65 (84)
32 PRK12442 translation initiatio 40.4 1E+02 0.0022 19.9 5.3 42 5-55 8-56 (87)
33 COG0186 RpsQ Ribosomal protein 39.4 18 0.00039 23.3 1.2 12 46-57 56-67 (87)
34 PRK02542 photosystem I assembl 39.2 45 0.00097 24.2 3.3 43 22-64 128-177 (188)
35 TIGR03028 EpsE polysaccharide 39.2 31 0.00066 24.3 2.4 13 45-57 225-237 (239)
36 PRK10694 acyl-CoA esterase; Pr 38.0 24 0.00051 23.0 1.6 14 41-54 63-76 (133)
37 PRK10413 hydrogenase 2 accesso 36.9 1.1E+02 0.0023 19.2 4.8 41 6-54 5-51 (82)
38 COG1096 Predicted RNA-binding 36.5 83 0.0018 22.8 4.3 43 5-53 67-126 (188)
39 cd03708 GTPBP_III Domain III o 35.7 90 0.002 18.0 3.8 28 6-33 34-61 (87)
40 PF02392 Ycf4: Ycf4; InterPro 35.3 58 0.0013 23.4 3.4 43 22-64 121-170 (180)
41 PRK04424 fatty acid biosynthes 35.0 28 0.0006 23.8 1.7 14 41-54 134-147 (185)
42 cd03452 MaoC_C MaoC_C The C-t 34.7 30 0.00064 22.1 1.7 14 41-54 84-97 (142)
43 COG1607 Acyl-CoA hydrolase [Li 34.7 22 0.00047 24.7 1.1 27 20-55 53-79 (157)
44 cd04456 S1_IF1A_like S1_IF1A_l 33.9 1.1E+02 0.0025 18.6 5.3 44 6-58 2-51 (78)
45 TIGR03000 plancto_dom_1 Planct 32.9 89 0.0019 19.6 3.6 30 24-54 44-73 (75)
46 PF11095 Gemin7: Gem-associate 32.4 1.1E+02 0.0023 19.3 3.9 30 25-54 36-76 (80)
47 cd03455 SAV4209 SAV4209 is a S 32.4 33 0.00071 21.0 1.6 15 40-54 74-88 (123)
48 PRK07217 replication factor A; 31.3 2.2E+02 0.0047 22.1 6.1 48 6-56 87-138 (311)
49 PF04149 DUF397: Domain of unk 30.9 1E+02 0.0022 17.6 3.4 38 18-61 12-49 (56)
50 cd03446 MaoC_like MoaC_like 30.8 38 0.00083 20.8 1.7 14 41-54 86-99 (140)
51 CHL00010 infA translation init 29.3 1.3E+02 0.0029 18.0 5.3 41 6-55 9-56 (78)
52 PF12791 RsgI_N: Anti-sigma fa 29.1 1.1E+02 0.0023 16.8 3.9 30 30-59 10-39 (56)
53 cd03449 R_hydratase (R)-hydrat 28.5 45 0.00098 19.8 1.7 15 40-54 77-91 (128)
54 cd03441 R_hydratase_like (R)-h 28.3 45 0.00099 19.6 1.6 14 42-55 77-90 (127)
55 cd00174 SH3 Src homology 3 dom 28.3 41 0.00089 16.7 1.3 13 45-57 17-29 (54)
56 PF12961 DUF3850: Domain of Un 27.7 49 0.0011 20.5 1.7 22 38-59 21-42 (72)
57 cd01288 FabZ FabZ is a 17kD be 27.6 47 0.001 20.0 1.6 13 42-54 84-96 (131)
58 cd04091 mtEFG1_II_like mtEFG1_ 27.2 35 0.00077 19.8 1.0 22 37-58 17-38 (81)
59 smart00326 SH3 Src homology 3 27.0 45 0.00097 16.7 1.3 13 46-58 21-33 (58)
60 cd03447 FAS_MaoC FAS_MaoC, the 26.8 47 0.001 21.1 1.6 14 41-54 76-89 (126)
61 cd03453 SAV4209_like SAV4209_l 26.4 51 0.0011 20.4 1.7 15 41-55 76-90 (127)
62 PRK00006 fabZ (3R)-hydroxymyri 25.9 50 0.0011 20.9 1.6 14 41-54 97-110 (147)
63 PF05550 Peptidase_C53: Pestiv 25.4 82 0.0018 22.6 2.7 26 5-30 109-135 (168)
64 PRK06386 replication factor A; 25.3 3.2E+02 0.007 21.3 6.1 48 6-56 122-174 (358)
65 PF14604 SH3_9: Variant SH3 do 25.1 43 0.00093 18.2 1.0 13 45-57 14-26 (49)
66 cd03703 aeIF5B_II aeIF5B_II: T 24.8 1.9E+02 0.0042 19.0 4.2 25 39-64 80-104 (110)
67 COG0298 HypC Hydrogenase matur 24.8 2E+02 0.0043 18.5 4.4 38 6-54 5-47 (82)
68 PF08402 TOBE_2: TOBE domain; 24.7 1.2E+02 0.0027 16.1 4.2 36 20-55 28-66 (75)
69 COG3365 Uncharacterized protei 24.5 42 0.00092 22.9 1.1 18 38-55 22-39 (118)
70 PRK13691 (3R)-hydroxyacyl-ACP 24.4 55 0.0012 22.1 1.7 13 42-54 93-105 (166)
71 KOG2716 Polymerase delta-inter 23.4 27 0.00059 25.7 0.0 18 46-64 64-81 (230)
72 PF00278 Orn_DAP_Arg_deC: Pyri 23.1 87 0.0019 18.7 2.2 24 33-56 68-93 (116)
73 PF03061 4HBT: Thioesterase su 23.0 76 0.0016 17.0 1.8 15 40-54 38-52 (79)
74 cd03450 NodN NodN (nodulation 22.9 56 0.0012 21.6 1.4 14 41-54 93-106 (149)
75 PF08817 YukD: WXG100 protein 22.8 50 0.0011 19.4 1.1 11 45-55 69-79 (79)
76 PF07653 SH3_2: Variant SH3 do 22.7 40 0.00087 18.3 0.6 10 46-55 18-27 (55)
77 TIGR01750 fabZ beta-hydroxyacy 22.7 64 0.0014 20.1 1.6 14 41-54 93-106 (140)
78 PF01455 HupF_HypC: HupF/HypC 22.6 83 0.0018 18.7 2.0 42 6-54 5-46 (68)
79 smart00652 eIF1a eukaryotic tr 22.5 2E+02 0.0043 17.7 5.7 45 5-58 6-56 (83)
80 cd00493 FabA_FabZ FabA/Z, beta 22.2 70 0.0015 19.1 1.7 14 42-55 85-98 (131)
81 PTZ00241 40S ribosomal protein 22.2 51 0.0011 23.3 1.2 12 46-57 117-128 (158)
82 cd03454 YdeM YdeM is a Bacillu 21.4 72 0.0016 19.8 1.7 15 40-54 83-97 (140)
83 PRK08572 rps17p 30S ribosomal 21.2 95 0.0021 20.5 2.3 14 44-57 76-89 (108)
84 PF10442 FIST_C: FIST C domain 21.2 1.1E+02 0.0025 18.8 2.5 24 35-60 47-70 (136)
85 COG4136 ABC-type uncharacteriz 20.9 1E+02 0.0022 22.8 2.5 25 32-56 11-35 (213)
86 PF00366 Ribosomal_S17: Riboso 20.7 57 0.0012 19.5 1.0 20 38-57 36-55 (69)
87 TIGR00413 rlpA rare lipoprotei 20.3 1.8E+02 0.0039 21.3 3.8 35 24-58 37-72 (208)
88 PRK11536 6-N-hydroxylaminopuri 20.1 58 0.0013 23.6 1.2 16 43-58 151-166 (223)
89 PRK10409 hydrogenase assembly 20.1 2.5E+02 0.0054 17.9 4.2 41 6-54 5-50 (90)
No 1
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=100.00 E-value=1.2e-41 Score=210.70 Aligned_cols=65 Identities=80% Similarity=1.147 Sum_probs=52.0
Q ss_pred CCc---cceeEEEEEEccccCCcccEEEEEEEEcCCCC-ceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463 1 MDS---QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQN-RFIMRNVKGPVREGDILTLLESEREARRLR 65 (65)
Q Consensus 1 md~---~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~-r~i~RnVkGPVr~GDil~LlEserEarrlr 65 (65)
||+ ++++|+|+||||||||+|+||||||+||++++ |+|+||||||||+||||+|+||||||||||
T Consensus 1 m~~~~~~~~~A~V~kVlgRtGs~G~~tQVrv~~l~~~~gR~i~RNVkGPVr~GDil~LlEtEREArrlr 69 (69)
T PF01200_consen 1 MDTSVQPIKLARVIKVLGRTGSRGQVTQVRVEFLDGDKGRSIIRNVKGPVREGDILTLLETEREARRLR 69 (69)
T ss_dssp --S---SSEEEEEEEEECCCTSSSSEEEEEEEESSSSSS-EEEEEECSTTSTT-EEEESSSS-------
T ss_pred CCcccCCceeEEEEEEcccccCcccEEEEEEEEecCCcceEEeecccCCcccCcEEEEeehhhhhhhcC
Confidence 664 68999999999999999999999999999876 999999999999999999999999999997
No 2
>cd04457 S1_S28E S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.
Probab=100.00 E-value=1.3e-40 Score=201.89 Aligned_cols=60 Identities=78% Similarity=1.161 Sum_probs=58.7
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR 65 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~LlEserEarrlr 65 (65)
++|+|+||+|||||+|+||||||+||+|++|+|+||||||||+||||+|+|||||||+||
T Consensus 1 ~~A~V~kvlGRtG~~G~~tQVrv~~l~d~~r~i~RNVKGPVr~GDIl~L~EteREArrlr 60 (60)
T cd04457 1 KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60 (60)
T ss_pred CceEEEEEeccccCcCcEEEEEEEEeeCCCcEEEEeccCCcccCcEEeehhhhhhhhhcC
Confidence 479999999999999999999999999999999999999999999999999999999996
No 3
>PRK04007 rps28e 30S ribosomal protein S28e; Validated
Probab=100.00 E-value=3.3e-39 Score=200.47 Aligned_cols=63 Identities=54% Similarity=0.843 Sum_probs=59.9
Q ss_pred ccceeEEEEEEccccCCcccEEEEEEEEcCCC--CceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463 3 SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ--NRFIMRNVKGPVREGDILTLLESEREARRLR 65 (65)
Q Consensus 3 ~~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~--~r~i~RnVkGPVr~GDil~LlEserEarrlr 65 (65)
...++|+|+||||||||+|++|||||+||+++ +|+|+||||||||+||||+|+|||||||+|+
T Consensus 4 ~~~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~~~R~i~RNVkGPVR~GDIl~L~EteREAr~l~ 68 (70)
T PRK04007 4 EEGTPAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETEREARKLG 68 (70)
T ss_pred ccCceEEEEEEeccccccccEEEEEEEEecCCCcCcEEEEeccCCcccCcEEEEhhhhhHHHhhc
Confidence 45789999999999999999999999999955 9999999999999999999999999999985
No 4
>PTZ00085 40S ribosomal protein S28; Provisional
Probab=100.00 E-value=3.5e-39 Score=201.69 Aligned_cols=63 Identities=68% Similarity=1.038 Sum_probs=60.4
Q ss_pred ccceeEEEEEEccccCCcccEEEEEEEEcCCC---CceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463 3 SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ---NRFIMRNVKGPVREGDILTLLESEREARRLR 65 (65)
Q Consensus 3 ~~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~---~r~i~RnVkGPVr~GDil~LlEserEarrlr 65 (65)
.++++|+|+||||||||+|+||||||+||+++ +|+|+||||||||+||||+|+|||||||+||
T Consensus 8 ~~~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~d~~r~i~RNVkGPVr~GDIl~L~EteREAr~lr 73 (73)
T PTZ00085 8 EQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLMETEREARRLR 73 (73)
T ss_pred cCceeEEEEEEeccccCcccEEEEEEEEccCCcccCcEEEEeccCCcccCcEEeehhhhhhhhhcC
Confidence 47899999999999999999999999999965 6999999999999999999999999999997
No 5
>KOG3502 consensus 40S ribosomal protein S28 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.2e-40 Score=202.50 Aligned_cols=64 Identities=80% Similarity=1.111 Sum_probs=61.9
Q ss_pred CCc--cceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463 1 MDS--QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR 65 (65)
Q Consensus 1 md~--~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~LlEserEarrlr 65 (65)
||+ |+++|+|+||||||||+|+|||||||||+ .+|+|+||||||||+||||.|+||||||||||
T Consensus 1 m~~~~~~~larVtkVlGRTgsqGq~tqvrvef~~-~~RsIirnVKgPvr~gdil~lleserEarrlr 66 (66)
T KOG3502|consen 1 MDSKQPIKLARVTKVLGRTGSQGQCTQVRVEFMD-TSRSIIRNVKGPVREGDILTLLESEREARRLR 66 (66)
T ss_pred CCccchhhHhhhhhhhcccCCCCcEEEEEEEecc-ccHHHHHhccCCccccchhhhhhchhhHhhcC
Confidence 787 79999999999999999999999999998 68999999999999999999999999999997
No 6
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-35 Score=182.38 Aligned_cols=61 Identities=66% Similarity=1.002 Sum_probs=59.0
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcC--CCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR 65 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~--~~~r~i~RnVkGPVr~GDil~LlEserEarrlr 65 (65)
.++|+|++||||||++|++|||+|+||+ |++|+|+||||||||+||||+|+|||||||+|+
T Consensus 5 ~~~aeVi~vlgRTG~~GevtQVk~ril~grdkgRiitRNV~GPVrvgDIl~L~EteREAr~l~ 67 (69)
T COG2053 5 ATPAEVIEVLGRTGMTGEVTQVKVRILEGRDKGRIITRNVKGPVRVGDILMLLETEREARRLR 67 (69)
T ss_pred ccchheeeeecccCccCcEEEEEEEEeecCCcCcEEeeeccCCcccccEEeehhhhhhhhhhc
Confidence 5679999999999999999999999999 899999999999999999999999999999985
No 7
>KOG0187 consensus 40S ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=71.32 E-value=2.9 Score=29.03 Aligned_cols=20 Identities=60% Similarity=0.835 Sum_probs=17.3
Q ss_pred ecCccccCcEEeeehhHHHHh
Q 035463 42 VKGPVREGDILTLLESEREAR 62 (65)
Q Consensus 42 VkGPVr~GDil~LlEserEar 62 (65)
-+|||| |=-+-|.|.|||-|
T Consensus 62 qkGpvR-GISiKLQEEERErr 81 (134)
T KOG0187|consen 62 QKGPVR-GISIKLQEEERERR 81 (134)
T ss_pred HcCCcc-ceeEeecHHHHHhh
Confidence 489998 88899999999965
No 8
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=61.94 E-value=34 Score=20.87 Aligned_cols=42 Identities=17% Similarity=0.293 Sum_probs=31.2
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccc-------cCcEEeeeh
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVR-------EGDILTLLE 56 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr-------~GDil~LlE 56 (65)
..+.|++.|+ -+..+|++. .+..++-.+.|-.| +||.+.+.=
T Consensus 7 ~~G~V~e~L~-------~~~f~V~l~--ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~ 55 (68)
T TIGR00008 7 MEGKVTESLP-------NAMFRVELE--NGHEVLAHISGKIRMHYIRILPGDKVKVEL 55 (68)
T ss_pred EEEEEEEECC-------CCEEEEEEC--CCCEEEEEecCcchhccEEECCCCEEEEEE
Confidence 4688899988 446777764 36888888888755 799987643
No 9
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=55.16 E-value=46 Score=20.27 Aligned_cols=45 Identities=22% Similarity=0.411 Sum_probs=29.7
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCc------cccCcEEeeehhHH
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGP------VREGDILTLLESER 59 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGP------Vr~GDil~LlEser 59 (65)
..|+|++.+| -...+|++.+ +..++-.+.|- +++||.+.+..++.
T Consensus 2 ~~g~V~~~~g-------~~~~~V~~~~--g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~ 52 (77)
T cd05793 2 EYGQVEKMLG-------NGRLEVRCFD--GKKRLCRIRGKMRKRVWINEGDIVLVAPWDF 52 (77)
T ss_pred EEEEEEEEcC-------CCEEEEEECC--CCEEEEEEchhhcccEEEcCCCEEEEEeccc
Confidence 3689999998 3445555533 45555666665 56899988866554
No 10
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=54.07 E-value=11 Score=22.27 Aligned_cols=13 Identities=31% Similarity=0.675 Sum_probs=10.4
Q ss_pred ecCccccCcEEee
Q 035463 42 VKGPVREGDILTL 54 (65)
Q Consensus 42 VkGPVr~GDil~L 54 (65)
.-..+++||+|.+
T Consensus 30 LP~~~keGDvl~i 42 (71)
T PF11213_consen 30 LPEGAKEGDVLEI 42 (71)
T ss_pred CCCCCCcccEEEE
Confidence 3467999999977
No 11
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=52.33 E-value=12 Score=23.20 Aligned_cols=25 Identities=28% Similarity=0.450 Sum_probs=21.1
Q ss_pred eeecCccccCcEEeeehhHHHHhhc
Q 035463 40 RNVKGPVREGDILTLLESEREARRL 64 (65)
Q Consensus 40 RnVkGPVr~GDil~LlEserEarrl 64 (65)
=-.++....||.+...++|.+|+++
T Consensus 65 ~g~~~~p~aGd~~~~~~~e~~a~~~ 89 (95)
T cd03701 65 LGLKDVPKAGDGVLVVASEKEAKEI 89 (95)
T ss_pred eeecCCccCCCEEEEeCCCHHHHHh
Confidence 3456777899999999999999875
No 12
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=51.78 E-value=18 Score=21.93 Aligned_cols=23 Identities=13% Similarity=0.505 Sum_probs=17.3
Q ss_pred CceEEeeecCccccCcEEeeehh
Q 035463 35 NRFIMRNVKGPVREGDILTLLES 57 (65)
Q Consensus 35 ~r~i~RnVkGPVr~GDil~LlEs 57 (65)
.++....-.-..++||++.+.||
T Consensus 38 kk~~aHD~~~~~k~GD~V~I~ec 60 (71)
T TIGR03635 38 KKYHAHDENNECKVGDVVRIIET 60 (71)
T ss_pred EEEEEECCCCCCCCCCEEEEEEc
Confidence 34555555556899999999997
No 13
>PF00833 Ribosomal_S17e: Ribosomal S17; InterPro: IPR001210 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped in this family of ribosomal proteins, S17e. They include, vertebrate, Drosophila and Neurospora crassa (crp-3) S17's as well as yeast S17a (RP51A) and S17b (RP51B) and archaebacterial S17e [, , ].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1RQ6_A 2XZM_V 2XZN_V 3IZ6_Q 3IZB_Q 3O30_K 3O2Z_K 3U5G_R 3U5C_R.
Probab=51.66 E-value=4.5 Score=27.42 Aligned_cols=20 Identities=55% Similarity=0.827 Sum_probs=17.3
Q ss_pred ecCccccCcEEeeehhHHHHh
Q 035463 42 VKGPVREGDILTLLESEREAR 62 (65)
Q Consensus 42 VkGPVr~GDil~LlEserEar 62 (65)
-+|||| |=-+.|.|.|||.|
T Consensus 62 q~g~vr-gis~klqEeErerr 81 (121)
T PF00833_consen 62 QRGPVR-GISIKLQEEERERR 81 (121)
T ss_dssp TSSSST-TCSSCCCCHHHHCC
T ss_pred Hhcccc-ccchhhhHHHHHhh
Confidence 489998 88899999999964
No 14
>PLN00208 translation initiation factor (eIF); Provisional
Probab=50.39 E-value=69 Score=22.23 Aligned_cols=42 Identities=19% Similarity=0.358 Sum_probs=27.6
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCc------cccCcEEeee
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGP------VREGDILTLL 55 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGP------Vr~GDil~Ll 55 (65)
..+|+|++.+| -..++|++.+ +...+--+.|- |++||+|.+.
T Consensus 33 q~~g~V~~~lG-------n~~~~V~c~d--G~~rLa~IpGKmRKrIWI~~GD~VlVe 80 (145)
T PLN00208 33 QEYAQVLRMLG-------NGRCEALCID--GTKRLCHIRGKMRKKVWIAAGDIILVG 80 (145)
T ss_pred cEEEEEEEEcC-------CCEEEEEECC--CCEEEEEEeccceeeEEecCCCEEEEE
Confidence 46899999998 3355555544 44555555554 6688888763
No 15
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=50.13 E-value=61 Score=20.22 Aligned_cols=45 Identities=16% Similarity=0.274 Sum_probs=30.9
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCc-------cccCcEEeeehhH
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGP-------VREGDILTLLESE 58 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGP-------Vr~GDil~LlEse 58 (65)
.-.|.|++.|| -+.++|++.+ +...+--+.|- +++||++.+.=++
T Consensus 8 e~~g~V~e~L~-------~~~f~v~~ed--g~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~ 59 (75)
T COG0361 8 EMEGTVIEMLP-------NGRFRVELEN--GHERLAHISGKMRKNRIRILPGDVVLVELSP 59 (75)
T ss_pred EEEEEEEEecC-------CCEEEEEecC--CcEEEEEccCcchheeEEeCCCCEEEEEecc
Confidence 45789999998 4677787644 45555555555 4569999876444
No 16
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=49.91 E-value=47 Score=20.45 Aligned_cols=40 Identities=23% Similarity=0.283 Sum_probs=22.6
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEee
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTL 54 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~L 54 (65)
-|++|+++-|.+ -.|++-.-. |.+-=..-+++.+||.+.+
T Consensus 5 iP~~V~~i~~~~--------A~v~~~G~~-~~v~l~lv~~~~vGD~VLV 44 (76)
T TIGR00074 5 IPGQVVEIDENI--------ALVEFCGIK-RDVSLDLVGEVKVGDYVLV 44 (76)
T ss_pred cceEEEEEcCCE--------EEEEcCCeE-EEEEEEeeCCCCCCCEEEE
Confidence 478999986621 344543321 2221122268899998764
No 17
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=48.63 E-value=12 Score=20.58 Aligned_cols=17 Identities=35% Similarity=0.610 Sum_probs=14.1
Q ss_pred ccccCcEEeeehhHHHH
Q 035463 45 PVREGDILTLLESEREA 61 (65)
Q Consensus 45 PVr~GDil~LlEserEa 61 (65)
.|+.||+|.-+++....
T Consensus 23 ~VkkGd~L~~ld~~~~~ 39 (50)
T PF13533_consen 23 QVKKGDVLLVLDSPDLQ 39 (50)
T ss_pred EEcCCCEEEEECcHHHH
Confidence 58999999999987653
No 18
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=48.19 E-value=16 Score=21.17 Aligned_cols=44 Identities=18% Similarity=0.238 Sum_probs=25.9
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecC------ccccCcEEeeehh
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKG------PVREGDILTLLES 57 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkG------PVr~GDil~LlEs 57 (65)
...|+|++.+| -..++|++.+ +..++-.+.| -++.||.+...-+
T Consensus 4 e~~~~V~~~lG-------~~~~~V~~~d--g~~~l~~i~gK~r~~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 4 EVIGRVTEMLG-------NNLFEVECED--GEERLARIPGKFRKRIWIKRGDFVLVEPS 53 (65)
T ss_dssp EEEEEEEEEES-------SSEEEEEETT--SEEEEEEE-HHHHTCC---TTEEEEEEES
T ss_pred EEEEEEEEECC-------CCEEEEEeCC--CCEEEEEeccceeeeEecCCCCEEEEEec
Confidence 35799999998 3356666644 4444444444 3788999866544
No 19
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=46.98 E-value=80 Score=22.18 Aligned_cols=43 Identities=19% Similarity=0.326 Sum_probs=28.1
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCc------cccCcEEeeeh
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGP------VREGDILTLLE 56 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGP------Vr~GDil~LlE 56 (65)
..+|.|++.+| -..++|++.+ +...+-.+.|= |++||+|.+.-
T Consensus 33 q~~g~V~~~LG-------n~~f~V~c~d--G~~rLa~I~GKmRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 33 QEYAQVLRMLG-------NGRLEAYCFD--GVKRLCHIRGKMRKRVWINIGDIILVSL 81 (155)
T ss_pred cEEEEEEEEcC-------CCEEEEEECC--CCEEEEEeeccceeeEEecCCCEEEEec
Confidence 46899999998 3345555433 45555555554 66899888743
No 20
>PF07892 DUF1667: Protein of unknown function (DUF1667); InterPro: IPR012460 Hypothetical archaeal and bacterial proteins make up this family. A few proteins are annotated as being potential metal-binding proteins, and in fact the members of this family have four highly conserved cysteine residues, but no further literature evidence was found in this regard. ; PDB: 2JOV_A.
Probab=45.81 E-value=12 Score=23.66 Aligned_cols=13 Identities=46% Similarity=0.928 Sum_probs=6.5
Q ss_pred eecCccccCcEEe
Q 035463 41 NVKGPVREGDILT 53 (65)
Q Consensus 41 nVkGPVr~GDil~ 53 (65)
.|+-||+.||||.
T Consensus 56 ~v~aPV~~GdVi~ 68 (82)
T PF07892_consen 56 EVKAPVKIGDVIV 68 (82)
T ss_dssp EE-----SSEEEE
T ss_pred EEcCCccCCCEEE
Confidence 5789999999985
No 21
>cd03440 hot_dog The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold. These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis.
Probab=45.53 E-value=19 Score=18.02 Aligned_cols=15 Identities=47% Similarity=0.638 Sum_probs=11.9
Q ss_pred eecCccccCcEEeee
Q 035463 41 NVKGPVREGDILTLL 55 (65)
Q Consensus 41 nVkGPVr~GDil~Ll 55 (65)
+..+|++.||.+.+.
T Consensus 53 ~~~~~~~~g~~v~~~ 67 (100)
T cd03440 53 RFLRPVRPGDTLTVE 67 (100)
T ss_pred EEecCCCCCCEEEEE
Confidence 567899999988763
No 22
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=45.04 E-value=11 Score=26.10 Aligned_cols=24 Identities=58% Similarity=0.754 Sum_probs=19.3
Q ss_pred EEeeecCccccCcEEeeehhHHHHh
Q 035463 38 IMRNVKGPVREGDILTLLESEREAR 62 (65)
Q Consensus 38 i~RnVkGPVr~GDil~LlEserEar 62 (65)
+-|--+|||| |=-+-|.|.|||-|
T Consensus 58 mkri~~gpvr-gis~klqeeererr 81 (134)
T PTZ00154 58 MKRIQKGPVR-GISLKLQEEERERR 81 (134)
T ss_pred HhhhccCCcc-ccceehhHHHHHHh
Confidence 3345689998 88899999999954
No 23
>PF11584 Toxin_ToxA: Proteinaceous host-selective toxin ToxA; InterPro: IPR021635 ToxA is produced by particular Pyrenophora triticirepentis races and is a proteinaceous host-selective toxin. It is necessary and sufficient to cause cell death in sensitive wheat cultivars [].ToxA adopts a single-domain, beta-sandwich fold which has novel topology. The protein is directly involved in recognition events required for ToxA action. It is thought to be distantly related to FnIII proteins, gaining entry to the host via an integrin-like receptor []. ; PDB: 1ZLE_C 1ZLD_A.
Probab=44.80 E-value=25 Score=23.60 Aligned_cols=43 Identities=33% Similarity=0.617 Sum_probs=30.6
Q ss_pred EccccCCcccEE---------------EEEEEEcC--CCCceEEeeecCccccCcEEeee
Q 035463 13 VMGRTGSRGQVT---------------QVRVKFLD--DQNRFIMRNVKGPVREGDILTLL 55 (65)
Q Consensus 13 VlGRtGs~G~~t---------------qVrve~l~--~~~r~i~RnVkGPVr~GDil~Ll 55 (65)
+|||.|+-|... .|||.+-. -.+|.|+-.+.-.|--||+-.|.
T Consensus 28 ilgrpgaigswelnnfitiglnrvnadtvrvnirntgrtnrliitqwdntvtrgdvyelf 87 (118)
T PF11584_consen 28 ILGRPGAIGSWELNNFITIGLNRVNADTVRVNIRNTGRTNRLIITQWDNTVTRGDVYELF 87 (118)
T ss_dssp HTS-TT-EEEEE-SSSEEEEEEEESSSEEEEEEEESSS-EEEEEEEEEEETTTEEEEEEE
T ss_pred EecCCCccceEEecceEEEeecccccceEEEEeccCCccceEEEEeecCceecccHHhhh
Confidence 589999888642 46777654 45688999999999999998764
No 24
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown.
Probab=44.39 E-value=17 Score=22.61 Aligned_cols=15 Identities=33% Similarity=0.403 Sum_probs=12.2
Q ss_pred eeecCccccCcEEee
Q 035463 40 RNVKGPVREGDILTL 54 (65)
Q Consensus 40 RnVkGPVr~GDil~L 54 (65)
=+...||+.||.|++
T Consensus 86 ~~f~~pv~~GDtl~~ 100 (146)
T cd03451 86 VRFPAPVFHGDTLYA 100 (146)
T ss_pred EEecCCCCCCCEEEE
Confidence 456799999999974
No 25
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=44.08 E-value=17 Score=22.83 Aligned_cols=23 Identities=39% Similarity=0.681 Sum_probs=18.8
Q ss_pred ecCccccCcEEeeehhHHHHhhc
Q 035463 42 VKGPVREGDILTLLESEREARRL 64 (65)
Q Consensus 42 VkGPVr~GDil~LlEserEarrl 64 (65)
.++.--.||.+.-.++|.+|+++
T Consensus 67 ~~~~P~aGd~~~~~~se~~Ak~~ 89 (95)
T cd03702 67 LKGVPQAGDKFLVVESEKEAKEI 89 (95)
T ss_pred CCCCCCCCCEEEEeCCHHHHHHH
Confidence 34444779999999999999986
No 26
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=43.91 E-value=14 Score=19.64 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=10.5
Q ss_pred ccccCcEEeeehhH
Q 035463 45 PVREGDILTLLESE 58 (65)
Q Consensus 45 PVr~GDil~LlEse 58 (65)
++++||+|.+++..
T Consensus 15 s~~~Gd~i~v~~~~ 28 (48)
T PF00018_consen 15 SFKKGDIIEVLEKS 28 (48)
T ss_dssp EB-TTEEEEEEEES
T ss_pred eEECCCEEEEEEec
Confidence 47899999998853
No 27
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=43.47 E-value=15 Score=21.98 Aligned_cols=15 Identities=40% Similarity=0.849 Sum_probs=8.6
Q ss_pred cCccccCcEEeeehh
Q 035463 43 KGPVREGDILTLLES 57 (65)
Q Consensus 43 kGPVr~GDil~LlEs 57 (65)
.||.++||-+.|.+.
T Consensus 3 ~Gpf~~GdrVQlTD~ 17 (54)
T PF14801_consen 3 RGPFRAGDRVQLTDP 17 (54)
T ss_dssp --S--TT-EEEEEET
T ss_pred cCCCCCCCEEEEccC
Confidence 599999999998764
No 28
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=43.26 E-value=17 Score=24.26 Aligned_cols=14 Identities=29% Similarity=0.465 Sum_probs=11.7
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
+...||+.||.|+.
T Consensus 92 ~f~~PV~~GDtL~~ 105 (159)
T PRK13692 92 KFEKPIVAGDKLYC 105 (159)
T ss_pred EEeCCccCCCEEEE
Confidence 57799999999953
No 29
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=43.18 E-value=26 Score=22.09 Aligned_cols=23 Identities=13% Similarity=0.395 Sum_probs=16.7
Q ss_pred ceEEeeecCccccCcEEeeehhH
Q 035463 36 RFIMRNVKGPVREGDILTLLESE 58 (65)
Q Consensus 36 r~i~RnVkGPVr~GDil~LlEse 58 (65)
++....-..-.++||++.+.||=
T Consensus 41 k~~aHDe~n~~~~GD~V~I~e~R 63 (84)
T CHL00142 41 KYLVHDEENECNIGDQVLIEETR 63 (84)
T ss_pred EEEEeCCCCCCCCCCEEEEEEcC
Confidence 44445545568999999999873
No 30
>CHL00036 ycf4 photosystem I assembly protein Ycf4
Probab=42.43 E-value=38 Score=24.50 Aligned_cols=43 Identities=30% Similarity=0.559 Sum_probs=36.4
Q ss_pred cEEEEEEEEcC--CCCceEEeeecCc-----cccCcEEeeehhHHHHhhc
Q 035463 22 QVTQVRVKFLD--DQNRFIMRNVKGP-----VREGDILTLLESEREARRL 64 (65)
Q Consensus 22 ~~tqVrve~l~--~~~r~i~RnVkGP-----Vr~GDil~LlEserEarrl 64 (65)
.+..+|+++-+ +|.|.|-=.+||- -|.||-++|.|-|.+|-.|
T Consensus 124 dI~sIrieikeGlnprr~iyL~~kg~~~IPLTrig~pl~l~eiE~qAaeL 173 (184)
T CHL00036 124 DIQSIRIEVKEGLNPRRVLYLEIKGQRDIPLTRTGEPLTLREIEQKAAEL 173 (184)
T ss_pred HeEEEEEEEecCcCcccEEEEEEcCCCcCCcccCCCCCCHHHHHHHHHHH
Confidence 56778888877 7889998889985 4789999999999998765
No 31
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=42.43 E-value=31 Score=21.59 Aligned_cols=22 Identities=14% Similarity=0.505 Sum_probs=16.0
Q ss_pred ceEEeeecCccccCcEEeeehh
Q 035463 36 RFIMRNVKGPVREGDILTLLES 57 (65)
Q Consensus 36 r~i~RnVkGPVr~GDil~LlEs 57 (65)
++....-.--+++||++.+.||
T Consensus 44 k~~aHD~~n~~k~GD~V~I~e~ 65 (84)
T PRK05610 44 KYHAHDENNEAKIGDVVRIMET 65 (84)
T ss_pred EEEEECCCCCCCCCCEEEEEEc
Confidence 4444444446899999999997
No 32
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=40.43 E-value=1e+02 Score=19.89 Aligned_cols=42 Identities=24% Similarity=0.260 Sum_probs=29.9
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccc-------cCcEEeee
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVR-------EGDILTLL 55 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr-------~GDil~Ll 55 (65)
...+.|+++|+ =+..+|++- .+..++-.++|=+| +||.+.+.
T Consensus 8 e~~G~V~e~Lp-------~~~frV~Le--nG~~vla~isGKmR~~rIrIl~GD~V~VE 56 (87)
T PRK12442 8 ELDGIVDEVLP-------DSRFRVTLE--NGVEVGAYASGRMRKHRIRILAGDRVTLE 56 (87)
T ss_pred EEEEEEEEECC-------CCEEEEEeC--CCCEEEEEeccceeeeeEEecCCCEEEEE
Confidence 35688888887 235677763 46888888888765 58888764
No 33
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=39.37 E-value=18 Score=23.28 Aligned_cols=12 Identities=33% Similarity=0.681 Sum_probs=11.0
Q ss_pred cccCcEEeeehh
Q 035463 46 VREGDILTLLES 57 (65)
Q Consensus 46 Vr~GDil~LlEs 57 (65)
+++||++.+.||
T Consensus 56 ~k~GD~V~I~Et 67 (87)
T COG0186 56 AKVGDIVRIAET 67 (87)
T ss_pred CCCCCEEEEEEc
Confidence 689999999997
No 34
>PRK02542 photosystem I assembly protein Ycf4; Provisional
Probab=39.20 E-value=45 Score=24.22 Aligned_cols=43 Identities=28% Similarity=0.444 Sum_probs=35.8
Q ss_pred cEEEEEEEEcC--CCCceEEeeecCc-----cccCcEEeeehhHHHHhhc
Q 035463 22 QVTQVRVKFLD--DQNRFIMRNVKGP-----VREGDILTLLESEREARRL 64 (65)
Q Consensus 22 ~~tqVrve~l~--~~~r~i~RnVkGP-----Vr~GDil~LlEserEarrl 64 (65)
.+..+|+++-+ +|.|.|-=.+||- -|.||-++|.|-|.+|-.|
T Consensus 128 dIqsIrveikeGlnprr~iyL~~kg~~~IPLTrig~pl~l~eiE~qAaeL 177 (188)
T PRK02542 128 DIQAVKVEIREGLNPRRRLYLRLKGRRDIPLTRVGQPLPLAELENQGAEL 177 (188)
T ss_pred HeEEEEEEEecCcCCccEEEEEEcCCCcCCcccCCCCCCHHHHHHHHHHH
Confidence 56778888877 7889888888884 3689999999999998765
No 35
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=39.17 E-value=31 Score=24.26 Aligned_cols=13 Identities=31% Similarity=0.419 Sum_probs=11.5
Q ss_pred ccccCcEEeeehh
Q 035463 45 PVREGDILTLLES 57 (65)
Q Consensus 45 PVr~GDil~LlEs 57 (65)
+++.||+|..-||
T Consensus 225 ~l~~gDii~V~~s 237 (239)
T TIGR03028 225 LVQPDDVIYVRES 237 (239)
T ss_pred ccCCCCEEEEeCc
Confidence 5999999999876
No 36
>PRK10694 acyl-CoA esterase; Provisional
Probab=37.95 E-value=24 Score=23.05 Aligned_cols=14 Identities=29% Similarity=0.482 Sum_probs=11.2
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
+-.-|++.||+|.+
T Consensus 63 ~F~~Pv~~Gd~l~~ 76 (133)
T PRK10694 63 TFLRPVAVGDVVCC 76 (133)
T ss_pred EECCCcccCcEEEE
Confidence 45679999999965
No 37
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=36.92 E-value=1.1e+02 Score=19.16 Aligned_cols=41 Identities=12% Similarity=0.055 Sum_probs=23.0
Q ss_pred eeEEEEEEccc------cCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEee
Q 035463 6 KHAVVVKVMGR------TGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTL 54 (65)
Q Consensus 6 ~~A~V~kVlGR------tGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~L 54 (65)
-|++|+++-|. ....|...+|.+.++.+ .+-++.+||.+.+
T Consensus 5 iP~kVi~i~~~~~~~A~vd~~Gv~r~V~l~Lv~~--------~~~~~~vGDyVLV 51 (82)
T PRK10413 5 VPGQVLAVGEDIHQLAQVEVCGIKRDVNIALICE--------GNPADLLGQWVLV 51 (82)
T ss_pred cceEEEEECCCCCcEEEEEcCCeEEEEEeeeecc--------CCcccccCCEEEE
Confidence 47899998664 22334444454444432 1124677888754
No 38
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.53 E-value=83 Score=22.83 Aligned_cols=43 Identities=26% Similarity=0.302 Sum_probs=27.6
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcCCCC-----------------ceEEeeecCccccCcEEe
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQN-----------------RFIMRNVKGPVREGDILT 53 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~-----------------r~i~RnVkGPVr~GDil~ 53 (65)
+.+|+|+.+ +++..+|++-..++.. -....+++.-++.||||-
T Consensus 67 iV~grV~~v------~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivr 126 (188)
T COG1096 67 IVYGRVTDV------REQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVR 126 (188)
T ss_pred EEEEEEeec------cceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEE
Confidence 345666554 3456666666666522 234678889999999984
No 39
>cd03708 GTPBP_III Domain III of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=35.73 E-value=90 Score=18.00 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=23.8
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCC
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDD 33 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~ 33 (65)
..|++.++.++.=+.|+...|+++|+..
T Consensus 34 ~~~~i~~i~~~~l~~g~~~~v~i~f~~~ 61 (87)
T cd03708 34 QTARIVSIDKDVLRTGDRALVRFRFLYH 61 (87)
T ss_pred EEEEEEeccHhhccCCCeEEEEEEECCC
Confidence 4789999988888899999999998653
No 40
>PF02392 Ycf4: Ycf4; InterPro: IPR003359 Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. It consists of 11 subunits, ~100 chlorophyll a molecules, 2 phylloquinones, and 3 Fe4S4-clusters. The three dimensional structure of the PSI complex has been resolved at 2.5 A [], which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA (IPR005137 from INTERPRO) [], Ycf3 [, ], and Ycf4 []. Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. These gene products are therefore involved either in the stabilisation or in the assembly of the PSI complex. However, their exact roles remain unknown. The BtpA protein appears to act at the level of PSI stabilisation []. It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane [, ]. Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain []. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids []. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners []. Ycf3 contains a number of tetratrico peptide repeats (TPR, IPR001440 from INTERPRO); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions. ; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009579 thylakoid, 0016021 integral to membrane
Probab=35.34 E-value=58 Score=23.41 Aligned_cols=43 Identities=35% Similarity=0.572 Sum_probs=35.4
Q ss_pred cEEEEEEEEcC--CCCceEEeeecC----c-cccCcEEeeehhHHHHhhc
Q 035463 22 QVTQVRVKFLD--DQNRFIMRNVKG----P-VREGDILTLLESEREARRL 64 (65)
Q Consensus 22 ~~tqVrve~l~--~~~r~i~RnVkG----P-Vr~GDil~LlEserEarrl 64 (65)
.+..+|+++-+ +|+|.|-=.+|| | -|.||-+.|.|-|.+|-.|
T Consensus 121 dI~sIrv~i~eg~nprr~lyl~~k~~~~IPLTrig~~~~l~eiE~~aaeL 170 (180)
T PF02392_consen 121 DIQSIRVEIKEGFNPRRVLYLRTKGQRDIPLTRIGEPLTLSEIEEKAAEL 170 (180)
T ss_pred HeEEEEEEEccCCCCcceEEEEecCCcccCCccCCCCCCHHHHHHHHHHH
Confidence 46778888877 588999888898 4 3779999999999998765
No 41
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=34.95 E-value=28 Score=23.83 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=11.7
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
+-+.||++||.|.+
T Consensus 134 rF~kPV~pGD~L~~ 147 (185)
T PRK04424 134 RFKRPVKLGERVVA 147 (185)
T ss_pred EEccCCCCCCEEEE
Confidence 45789999999976
No 42
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=34.72 E-value=30 Score=22.11 Aligned_cols=14 Identities=29% Similarity=0.513 Sum_probs=11.6
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
+...||+.||.|+.
T Consensus 84 rf~~PV~~GDtl~~ 97 (142)
T cd03452 84 RFLEPVYPGDTIQV 97 (142)
T ss_pred EECCCCCCCCEEEE
Confidence 46789999998864
No 43
>COG1607 Acyl-CoA hydrolase [Lipid metabolism]
Probab=34.72 E-value=22 Score=24.69 Aligned_cols=27 Identities=44% Similarity=0.674 Sum_probs=18.2
Q ss_pred cccEEEEEEEEcCCCCceEEeeecCccccCcEEeee
Q 035463 20 RGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLL 55 (65)
Q Consensus 20 ~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~Ll 55 (65)
+|.|--+.|..++ .+=||+.||+|++.
T Consensus 53 ~~~vVTasvd~v~---------F~~Pv~vGd~v~~~ 79 (157)
T COG1607 53 GGRVVTASVDSVD---------FKKPVRVGDIVCLY 79 (157)
T ss_pred CCeEEEEEeceEE---------EccccccCcEEEEE
Confidence 4555555555543 34599999999874
No 44
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=33.87 E-value=1.1e+02 Score=18.61 Aligned_cols=44 Identities=20% Similarity=0.375 Sum_probs=27.0
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCc------cccCcEEeeehhH
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGP------VREGDILTLLESE 58 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGP------Vr~GDil~LlEse 58 (65)
.+|+|++.+| -...+|+..| +...+-.+.|- |++||++.+.-++
T Consensus 2 ~i~~V~~~lG-------~~~~~V~~~d--g~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~ 51 (78)
T cd04456 2 QIVRVLRMLG-------NNRHEVECAD--GQRRLVSIPGKLRKNIWIKRGDFLIVDPIE 51 (78)
T ss_pred eEEEEEEECC-------CCEEEEEECC--CCEEEEEEchhhccCEEEcCCCEEEEEecc
Confidence 4689999988 2345555533 44444455554 6688888775443
No 45
>TIGR03000 plancto_dom_1 Planctomycetes uncharacterized domain TIGR03000. Domains described by this model are found, so far, only in the Planctomycetes (Pirellula sp. strain 1 and Gemmata obscuriglobus), in up to six proteins per genome, and may be duplicated within a protein. The function is unknown.
Probab=32.95 E-value=89 Score=19.58 Aligned_cols=30 Identities=30% Similarity=0.440 Sum_probs=23.6
Q ss_pred EEEEEEEcCCCCceEEeeecCccccCcEEee
Q 035463 24 TQVRVKFLDDQNRFIMRNVKGPVREGDILTL 54 (65)
Q Consensus 24 tqVrve~l~~~~r~i~RnVkGPVr~GDil~L 54 (65)
.+|++++.-| |+.+.+-=+=+||-||...|
T Consensus 44 Y~v~a~~~~d-G~~~t~~~~V~vrAGd~~~v 73 (75)
T TIGR03000 44 YTVTAEYDRD-GRILTRTRTVVVRAGDTVTV 73 (75)
T ss_pred EEEEEEEecC-CcEEEEEEEEEEcCCceEEe
Confidence 4677777655 68888888888999998876
No 46
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=32.44 E-value=1.1e+02 Score=19.32 Aligned_cols=30 Identities=27% Similarity=0.574 Sum_probs=21.6
Q ss_pred EEEEEEcC---CCCceEEeeecCc--------cccCcEEee
Q 035463 25 QVRVKFLD---DQNRFIMRNVKGP--------VREGDILTL 54 (65)
Q Consensus 25 qVrve~l~---~~~r~i~RnVkGP--------Vr~GDil~L 54 (65)
+|.-+|-. |....++.|.+.| +|-+||+.+
T Consensus 36 ~V~a~F~a~d~~~~~f~Vs~L~TPlGv~~eAlLR~~DVi~~ 76 (80)
T PF11095_consen 36 TVSARFGACDIDVSNFQVSNLQTPLGVQPEALLRCSDVISI 76 (80)
T ss_dssp EEEEEEEEE-TTS-EEEEEEEETTTTEEEEEEEEGGGEEEE
T ss_pred EEEEEEEEecCchheEEhhhcCCCcccChhheeecCCEEEE
Confidence 45555543 5678899999999 577888875
No 47
>cd03455 SAV4209 SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The alpha- and gamma-proteobacterial members of this CD have, in addition to a hot dog fold, an N-terminal extension.
Probab=32.36 E-value=33 Score=21.05 Aligned_cols=15 Identities=27% Similarity=0.499 Sum_probs=12.3
Q ss_pred eeecCccccCcEEee
Q 035463 40 RNVKGPVREGDILTL 54 (65)
Q Consensus 40 RnVkGPVr~GDil~L 54 (65)
=+..+||..||.|++
T Consensus 74 ~rf~~pv~~Gdtl~~ 88 (123)
T cd03455 74 FRLGAPLYAGDTLRF 88 (123)
T ss_pred EEeeccccCCCEEEE
Confidence 356799999999875
No 48
>PRK07217 replication factor A; Reviewed
Probab=31.34 E-value=2.2e+02 Score=22.07 Aligned_cols=48 Identities=19% Similarity=0.225 Sum_probs=34.6
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeec----CccccCcEEeeeh
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVK----GPVREGDILTLLE 56 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVk----GPVr~GDil~LlE 56 (65)
-.|+|+++-.+. .+.+.|+-+ +=|+++++-.=.|+ +.+.+||++.+..
T Consensus 87 V~aKVl~l~e~~--~~si~qvGl-lgDETG~IkfT~W~~s~~~~leeGd~~rI~n 138 (311)
T PRK07217 87 VTAKVVQLWEPS--SDSIAQVGL-LGDETGTIKFTKWAKSDLPELEEGKSYLLKN 138 (311)
T ss_pred EEEEEEEecCCC--CCceEEEEE-EEcCCceEEEEEccCCCCCcccCCCEEEEEe
Confidence 358888887655 467888774 44567887666666 4599999998754
No 49
>PF04149 DUF397: Domain of unknown function (DUF397); InterPro: IPR007278 The function of this family is unknown. It has been suggested that some members of this family are regulators of transcription.
Probab=30.93 E-value=1e+02 Score=17.63 Aligned_cols=38 Identities=32% Similarity=0.522 Sum_probs=28.1
Q ss_pred CCcccEEEEEEEEcCCCCceEEeeecCccccCcEEeeehhHHHH
Q 035463 18 GSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREA 61 (65)
Q Consensus 18 Gs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~LlEserEa 61 (65)
|..|.|.+|. +. ++...+|+-|-| .|=+|..-..|-.|
T Consensus 12 ~~~~~CVEva--~~--~~~v~vRDSk~p--~~~~L~~t~~eW~a 49 (56)
T PF04149_consen 12 GGGGNCVEVA--RL--PGGVAVRDSKDP--DGPVLTFTPAEWAA 49 (56)
T ss_pred CCCCCcEEEE--ee--cceEEEecCCCC--CCCEEEeCHHHHHH
Confidence 5667776665 22 445999999998 68888888777654
No 50
>cd03446 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=30.81 E-value=38 Score=20.81 Aligned_cols=14 Identities=29% Similarity=0.380 Sum_probs=11.6
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
+...||+.||.|..
T Consensus 86 ~f~~pv~~GD~l~~ 99 (140)
T cd03446 86 RFLNPVFIGDTIRA 99 (140)
T ss_pred EEcCCCCCCCEEEE
Confidence 36799999998865
No 51
>CHL00010 infA translation initiation factor 1
Probab=29.35 E-value=1.3e+02 Score=18.05 Aligned_cols=41 Identities=15% Similarity=0.314 Sum_probs=24.0
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCc-------cccCcEEeee
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGP-------VREGDILTLL 55 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGP-------Vr~GDil~Ll 55 (65)
..+.|++++| +..--| ++ +.+..+....+|= +.+||++.+.
T Consensus 9 ~~G~Vik~lg-----~~~y~V--~~--~~g~~~~c~~rGklr~~~i~~~vGD~V~ve 56 (78)
T CHL00010 9 MEGLVTESLP-----NGMFRV--RL--DNGCQVLGYISGKIRRNSIRILPGDRVKVE 56 (78)
T ss_pred EEEEEEEEcC-----CCEEEE--Ee--CCCCEEEEEeccceecCCcccCCCCEEEEE
Confidence 3588888885 122223 32 2245555556664 4469999886
No 52
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=29.13 E-value=1.1e+02 Score=16.81 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=22.1
Q ss_pred EcCCCCceEEeeecCccccCcEEeeehhHH
Q 035463 30 FLDDQNRFIMRNVKGPVREGDILTLLESER 59 (65)
Q Consensus 30 ~l~~~~r~i~RnVkGPVr~GDil~LlEser 59 (65)
+|.+.|..+-=.-+++...||.+.+.|.+.
T Consensus 10 VlT~dGeF~~ik~~~~~~vG~eI~~~~~~~ 39 (56)
T PF12791_consen 10 VLTPDGEFIKIKRKPGMEVGQEIEFDEKDI 39 (56)
T ss_pred EEcCCCcEEEEeCCCCCcccCEEEEechhh
Confidence 455556666556677799999999988763
No 53
>cd03449 R_hydratase (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase II, and beta-hydroxydecanoyl-ACP dehydratase, MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit. The active site lies within a substrate-binding tunnel formed by the (R)-hydratase homodimer. A subset of the bacterial (R)-hydratases contain a C-terminal phosphotransacetylase (PTA) domain.
Probab=28.51 E-value=45 Score=19.81 Aligned_cols=15 Identities=33% Similarity=0.313 Sum_probs=12.3
Q ss_pred eeecCccccCcEEee
Q 035463 40 RNVKGPVREGDILTL 54 (65)
Q Consensus 40 RnVkGPVr~GDil~L 54 (65)
-+.+.||..||.|.+
T Consensus 77 ~~f~~Pv~~gd~l~~ 91 (128)
T cd03449 77 LRFLRPVFIGDTVTA 91 (128)
T ss_pred EEECCCccCCCEEEE
Confidence 367899999998875
No 54
>cd03441 R_hydratase_like (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold. The active site lies within a substrate-binding tunnel formed by the homodimer. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit.
Probab=28.33 E-value=45 Score=19.63 Aligned_cols=14 Identities=36% Similarity=0.460 Sum_probs=11.7
Q ss_pred ecCccccCcEEeee
Q 035463 42 VKGPVREGDILTLL 55 (65)
Q Consensus 42 VkGPVr~GDil~Ll 55 (65)
...||..||.|++.
T Consensus 77 f~~Pv~~Gd~l~~~ 90 (127)
T cd03441 77 FLAPVFPGDTLRVE 90 (127)
T ss_pred EeCCcCCCCEEEEE
Confidence 56899999999864
No 55
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=28.31 E-value=41 Score=16.72 Aligned_cols=13 Identities=38% Similarity=0.818 Sum_probs=10.7
Q ss_pred ccccCcEEeeehh
Q 035463 45 PVREGDILTLLES 57 (65)
Q Consensus 45 PVr~GDil~LlEs 57 (65)
+++.||++.+++.
T Consensus 17 ~~~~Gd~v~v~~~ 29 (54)
T cd00174 17 SFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCEEEEEEc
Confidence 3678999999876
No 56
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=27.73 E-value=49 Score=20.52 Aligned_cols=22 Identities=32% Similarity=0.395 Sum_probs=15.9
Q ss_pred EEeeecCccccCcEEeeehhHH
Q 035463 38 IMRNVKGPVREGDILTLLESER 59 (65)
Q Consensus 38 i~RnVkGPVr~GDil~LlEser 59 (65)
=+|.=--.-..||+|.|.|...
T Consensus 21 EiRkNDRdf~VGD~L~L~E~~~ 42 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLREWDN 42 (72)
T ss_pred EEEecCCCCCCCCEEEEEEecC
Confidence 3444455678899999999763
No 57
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=27.61 E-value=47 Score=19.96 Aligned_cols=13 Identities=46% Similarity=0.692 Sum_probs=11.0
Q ss_pred ecCccccCcEEee
Q 035463 42 VKGPVREGDILTL 54 (65)
Q Consensus 42 VkGPVr~GDil~L 54 (65)
.++||+.||.|.+
T Consensus 84 f~~pv~pgd~l~i 96 (131)
T cd01288 84 FRKPVVPGDQLIL 96 (131)
T ss_pred EccccCCCCEEEE
Confidence 5799999999865
No 58
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=27.23 E-value=35 Score=19.81 Aligned_cols=22 Identities=23% Similarity=0.409 Sum_probs=16.8
Q ss_pred eEEeeecCccccCcEEeeehhH
Q 035463 37 FIMRNVKGPVREGDILTLLESE 58 (65)
Q Consensus 37 ~i~RnVkGPVr~GDil~LlEse 58 (65)
.+.|-..|-++.||.|....+.
T Consensus 17 ~~~Rv~sG~lk~gd~v~~~~~~ 38 (81)
T cd04091 17 TYMRIYQGKLKKGDTIYNVRTG 38 (81)
T ss_pred EEEEEecCEEcCCCEEEEcCCC
Confidence 4778888888888888766543
No 59
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=27.05 E-value=45 Score=16.69 Aligned_cols=13 Identities=46% Similarity=0.879 Sum_probs=10.6
Q ss_pred cccCcEEeeehhH
Q 035463 46 VREGDILTLLESE 58 (65)
Q Consensus 46 Vr~GDil~LlEse 58 (65)
++.||++.+.+..
T Consensus 21 ~~~Gd~v~v~~~~ 33 (58)
T smart00326 21 FKKGDIITVLEKS 33 (58)
T ss_pred CCCCCEEEEEEcC
Confidence 6789999998763
No 60
>cd03447 FAS_MaoC FAS_MaoC, the MaoC-like hot dog fold of the fatty acid synthase, beta subunit. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and 17-beta-hydroxysteriod dehydrogenase (HSD).
Probab=26.84 E-value=47 Score=21.11 Aligned_cols=14 Identities=29% Similarity=0.294 Sum_probs=12.0
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
+..+||..||.|.+
T Consensus 76 rf~~PV~~gdtl~~ 89 (126)
T cd03447 76 SFVGMVLPNDELEV 89 (126)
T ss_pred EEcccCcCCCEEEE
Confidence 46799999999886
No 61
>cd03453 SAV4209_like SAV4209_like. Similar in sequence to the Streptomyces avermitilis SAV4209 protein, with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=26.42 E-value=51 Score=20.38 Aligned_cols=15 Identities=33% Similarity=0.308 Sum_probs=12.5
Q ss_pred eecCccccCcEEeee
Q 035463 41 NVKGPVREGDILTLL 55 (65)
Q Consensus 41 nVkGPVr~GDil~Ll 55 (65)
...+||..||.|++.
T Consensus 76 rf~~Pv~~Gdtl~~~ 90 (127)
T cd03453 76 RFTKPVPVPDTLTCT 90 (127)
T ss_pred EECCcCcCCCEEEEE
Confidence 567999999998863
No 62
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=25.90 E-value=50 Score=20.85 Aligned_cols=14 Identities=50% Similarity=0.665 Sum_probs=11.1
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
....||+.||.|.+
T Consensus 97 kF~~pv~pGd~l~i 110 (147)
T PRK00006 97 RFKRPVVPGDQLIL 110 (147)
T ss_pred EEccccCCCCEEEE
Confidence 34589999999875
No 63
>PF05550 Peptidase_C53: Pestivirus Npro endopeptidase C53; InterPro: IPR008751 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C53 (clan C-). The active site residues occur in the order E, H, C in the sequence which is unlike that in any other family. They are unique to pestiviruses. The N-terminal cysteine peptidase (Npro) encoded by the bovine viral diarrhoea virus genome is responsible for the self-cleavage that releases the N terminus of the core protein. This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core [, , , ].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=25.38 E-value=82 Score=22.61 Aligned_cols=26 Identities=35% Similarity=0.510 Sum_probs=21.9
Q ss_pred ceeEEEEEEccc-cCCcccEEEEEEEE
Q 035463 5 IKHAVVVKVMGR-TGSRGQVTQVRVKF 30 (65)
Q Consensus 5 ~~~A~V~kVlGR-tGs~G~~tqVrve~ 30 (65)
.+..+|+|-+|| |||-|..-.+-|=+
T Consensus 109 ~~~CEvTkriGRvTGSDgkLYHiyvC~ 135 (168)
T PF05550_consen 109 TQMCEVTKRIGRVTGSDGKLYHIYVCI 135 (168)
T ss_pred cceEeecceEEEEECCCCCEEEEEEec
Confidence 567899999999 89999998877654
No 64
>PRK06386 replication factor A; Reviewed
Probab=25.32 E-value=3.2e+02 Score=21.28 Aligned_cols=48 Identities=10% Similarity=0.256 Sum_probs=30.0
Q ss_pred eeEEEEEEcc----ccCCcccEEEEEEEEcC-CCCceEEeeecCccccCcEEeeeh
Q 035463 6 KHAVVVKVMG----RTGSRGQVTQVRVKFLD-DQNRFIMRNVKGPVREGDILTLLE 56 (65)
Q Consensus 6 ~~A~V~kVlG----RtGs~G~~tqVrve~l~-~~~r~i~RnVkGPVr~GDil~LlE 56 (65)
-.|+|+++-- +.|+.| .|+.=++. ++++.=+=.+.-++.+||++.+..
T Consensus 122 V~akVle~~e~e~~~~g~~~---~v~sg~lgDeTGrIr~TlW~~~l~eGd~v~i~n 174 (358)
T PRK06386 122 VIGKITGITKKEYDSDGTSK---IVYQGYIEDDTARVRISSFGKPLEDNRFVRIEN 174 (358)
T ss_pred EEEEEEEccCceEecCCCcc---EEEEEEEEcCCCeEEEEEccccccCCCEEEEee
Confidence 3577777633 334434 44444444 567775555655899999998764
No 65
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=25.06 E-value=43 Score=18.19 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=9.6
Q ss_pred ccccCcEEeeehh
Q 035463 45 PVREGDILTLLES 57 (65)
Q Consensus 45 PVr~GDil~LlEs 57 (65)
.++.||+|.+++.
T Consensus 14 s~~~Gd~i~v~~~ 26 (49)
T PF14604_consen 14 SFKKGDVITVLEK 26 (49)
T ss_dssp EB-TTEEEEEEEE
T ss_pred eEcCCCEEEEEEe
Confidence 3678999999865
No 66
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=24.83 E-value=1.9e+02 Score=18.97 Aligned_cols=25 Identities=20% Similarity=0.291 Sum_probs=19.1
Q ss_pred EeeecCccccCcEEeeehhHHHHhhc
Q 035463 39 MRNVKGPVREGDILTLLESEREARRL 64 (65)
Q Consensus 39 ~RnVkGPVr~GDil~LlEserEarrl 64 (65)
..+..+. -.||.+..-++|.||+.+
T Consensus 80 ~~gL~~v-~aG~~~~vv~~e~~a~~~ 104 (110)
T cd03703 80 APDLEKA-IAGSPLLVVGPEDEIEEL 104 (110)
T ss_pred eCCCccc-cCCCEEEEECCHHHHHHH
Confidence 3344444 679999999999999875
No 67
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.82 E-value=2e+02 Score=18.49 Aligned_cols=38 Identities=16% Similarity=0.310 Sum_probs=24.5
Q ss_pred eeEEEEEEccccC-----CcccEEEEEEEEcCCCCceEEeeecCccccCcEEee
Q 035463 6 KHAVVVKVMGRTG-----SRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTL 54 (65)
Q Consensus 6 ~~A~V~kVlGRtG-----s~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~L 54 (65)
-|++|++|-+-.+ .-|-..+|+..+++. +++.||-+.+
T Consensus 5 iPgqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~-----------~v~~GdyVLV 47 (82)
T COG0298 5 IPGQIVEIDDNNHLAIVDVGGVKREVNLDLVGE-----------EVKVGDYVLV 47 (82)
T ss_pred cccEEEEEeCCCceEEEEeccEeEEEEeeeecC-----------ccccCCEEEE
Confidence 3677888876433 234556677776653 7888997643
No 68
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the domain. ; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=24.66 E-value=1.2e+02 Score=16.08 Aligned_cols=36 Identities=19% Similarity=0.263 Sum_probs=21.2
Q ss_pred cccEEEEEEEEcCCCCceEEeeecC---ccccCcEEeee
Q 035463 20 RGQVTQVRVKFLDDQNRFIMRNVKG---PVREGDILTLL 55 (65)
Q Consensus 20 ~G~~tqVrve~l~~~~r~i~RnVkG---PVr~GDil~Ll 55 (65)
.|.-+.+.+++-+.+...+...... +...||-+.|.
T Consensus 28 ~G~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~G~~v~l~ 66 (75)
T PF08402_consen 28 LGSETRYTVRLEGGEELVVRVPNSQRDSPLEPGDEVRLS 66 (75)
T ss_dssp ESSEEEEEEEETTSSEEEEEEESSG-TTT--TTSEEEEE
T ss_pred CCCEEEEEEEECCCCEEEEEecCccccCCCCCCCEEEEE
Confidence 4567777777655444344444444 78899988764
No 69
>COG3365 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.51 E-value=42 Score=22.89 Aligned_cols=18 Identities=50% Similarity=0.658 Sum_probs=13.0
Q ss_pred EEeeecCccccCcEEeee
Q 035463 38 IMRNVKGPVREGDILTLL 55 (65)
Q Consensus 38 i~RnVkGPVr~GDil~Ll 55 (65)
-+|-+---||+||||.|.
T Consensus 22 kvr~Iid~vr~G~IlVLE 39 (118)
T COG3365 22 KVRYIIDKVREGDILVLE 39 (118)
T ss_pred HHHHHHHhccCCcEEEEe
Confidence 345555667899999884
No 70
>PRK13691 (3R)-hydroxyacyl-ACP dehydratase subunit HadC; Provisional
Probab=24.38 E-value=55 Score=22.09 Aligned_cols=13 Identities=38% Similarity=0.435 Sum_probs=11.4
Q ss_pred ecCccccCcEEee
Q 035463 42 VKGPVREGDILTL 54 (65)
Q Consensus 42 VkGPVr~GDil~L 54 (65)
...||+.||.|+.
T Consensus 93 f~rPV~~GDtL~~ 105 (166)
T PRK13691 93 FHKPVLAGDKLWA 105 (166)
T ss_pred EeCCcCCCCEEEE
Confidence 6799999999875
No 71
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=23.40 E-value=27 Score=25.68 Aligned_cols=18 Identities=50% Similarity=0.791 Sum_probs=15.0
Q ss_pred cccCcEEeeehhHHHHhhc
Q 035463 46 VREGDILTLLESEREARRL 64 (65)
Q Consensus 46 Vr~GDil~LlEserEarrl 64 (65)
.|.||+. |-|+|+|-+.|
T Consensus 64 mRdGdv~-LPe~~kel~El 81 (230)
T KOG2716|consen 64 MRDGDVD-LPESEKELKEL 81 (230)
T ss_pred hhccccc-CccchHHHHHH
Confidence 5889998 99999986654
No 72
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=23.10 E-value=87 Score=18.73 Aligned_cols=24 Identities=33% Similarity=0.479 Sum_probs=17.8
Q ss_pred CCCceEEeeecCc--cccCcEEeeeh
Q 035463 33 DQNRFIMRNVKGP--VREGDILTLLE 56 (65)
Q Consensus 33 ~~~r~i~RnVkGP--Vr~GDil~LlE 56 (65)
++.-.|.+++.-| ++.||.|.+..
T Consensus 68 ~~~D~i~~~~~lP~~l~~GD~l~f~~ 93 (116)
T PF00278_consen 68 DSGDVIARDVMLPKELEVGDWLVFEN 93 (116)
T ss_dssp STTSEEEEEEEEESTTTTT-EEEESS
T ss_pred CCCceEeeeccCCCCCCCCCEEEEec
Confidence 4556777888887 99999998765
No 73
>PF03061 4HBT: Thioesterase superfamily; InterPro: IPR006683 This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (3.1.2.23 from EC) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. ; PDB: 3F5O_F 2F0X_D 2H4U_C 2PRX_A 2OV9_D 1YLI_B 3BJK_F 1IXL_A 3DKZ_B 2EIS_B ....
Probab=23.00 E-value=76 Score=17.00 Aligned_cols=15 Identities=40% Similarity=0.629 Sum_probs=9.8
Q ss_pred eeecCccccCcEEee
Q 035463 40 RNVKGPVREGDILTL 54 (65)
Q Consensus 40 RnVkGPVr~GDil~L 54 (65)
=+-..|++.||.|..
T Consensus 38 i~f~~p~~~gd~l~~ 52 (79)
T PF03061_consen 38 IDFLRPVRPGDTLRV 52 (79)
T ss_dssp EEESS-BBTTSEEEE
T ss_pred EEEccccCCCeEEEE
Confidence 345678888987764
No 74
>cd03450 NodN NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division. The nodulation gene products, including NodN, are involved in producing the Nod factors, however the role played by NodN is unclear.
Probab=22.85 E-value=56 Score=21.57 Aligned_cols=14 Identities=21% Similarity=0.249 Sum_probs=11.8
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
...+||..||.|+.
T Consensus 93 rF~~PV~~GDtl~~ 106 (149)
T cd03450 93 RFPAPVPVGSRVRG 106 (149)
T ss_pred EeCcceeCCcEEEE
Confidence 46799999999875
No 75
>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.
Probab=22.78 E-value=50 Score=19.35 Aligned_cols=11 Identities=55% Similarity=0.890 Sum_probs=5.5
Q ss_pred ccccCcEEeee
Q 035463 45 PVREGDILTLL 55 (65)
Q Consensus 45 PVr~GDil~Ll 55 (65)
+|+-||+|.|+
T Consensus 69 gV~dGd~L~L~ 79 (79)
T PF08817_consen 69 GVRDGDVLVLR 79 (79)
T ss_dssp T--TT-EEEE-
T ss_pred CCCCCCEEEeC
Confidence 47888888874
No 76
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=22.72 E-value=40 Score=18.26 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=8.1
Q ss_pred cccCcEEeee
Q 035463 46 VREGDILTLL 55 (65)
Q Consensus 46 Vr~GDil~Ll 55 (65)
+..||+|.++
T Consensus 18 ~~~Gd~i~v~ 27 (55)
T PF07653_consen 18 FKKGDVIEVL 27 (55)
T ss_dssp B-TTEEEEEE
T ss_pred EecCCEEEEE
Confidence 6789999998
No 77
>TIGR01750 fabZ beta-hydroxyacyl-[acyl carrier protein] dehydratase FabZ. This enzyme, FabZ, shows overlapping substrate specificity with FabA with regard to chain length in fatty acid biosynthesis. FabZ works preferentially on shorter chains and is often designated (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase, although its actual specificity is broader. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains.
Probab=22.71 E-value=64 Score=20.11 Aligned_cols=14 Identities=43% Similarity=0.665 Sum_probs=11.4
Q ss_pred eecCccccCcEEee
Q 035463 41 NVKGPVREGDILTL 54 (65)
Q Consensus 41 nVkGPVr~GDil~L 54 (65)
...+||+.||.|++
T Consensus 93 kF~~~v~pGd~l~i 106 (140)
T TIGR01750 93 KFRRPVVPGDQLIL 106 (140)
T ss_pred EECCccCCCCEEEE
Confidence 45699999999875
No 78
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=22.59 E-value=83 Score=18.75 Aligned_cols=42 Identities=24% Similarity=0.226 Sum_probs=19.0
Q ss_pred eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEee
Q 035463 6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTL 54 (65)
Q Consensus 6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~L 54 (65)
-|++|+++- -.|..+ .|++-. ..|.+-=..-+++.+||.+..
T Consensus 5 iP~~Vv~v~-~~~~~A-----~v~~~G-~~~~V~~~lv~~v~~Gd~VLV 46 (68)
T PF01455_consen 5 IPGRVVEVD-EDGGMA-----VVDFGG-VRREVSLALVPDVKVGDYVLV 46 (68)
T ss_dssp EEEEEEEEE-TTTTEE-----EEEETT-EEEEEEGTTCTSB-TT-EEEE
T ss_pred ccEEEEEEe-CCCCEE-----EEEcCC-cEEEEEEEEeCCCCCCCEEEE
Confidence 478899982 012221 234321 122232233466888887753
No 79
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=22.50 E-value=2e+02 Score=17.67 Aligned_cols=45 Identities=27% Similarity=0.391 Sum_probs=27.4
Q ss_pred ceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCc------cccCcEEeeehhH
Q 035463 5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGP------VREGDILTLLESE 58 (65)
Q Consensus 5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGP------Vr~GDil~LlEse 58 (65)
...|+|++.+| -...+|++-+ +..++-.+.|= ++.||++.+..++
T Consensus 6 q~~g~V~~~lG-------~~~~~V~~~d--G~~~la~ipgK~Rk~iwI~~GD~VlVe~~~ 56 (83)
T smart00652 6 QEIAQVVKMLG-------NGRLEVMCAD--GKERLARIPGKMRKKVWIRRGDIVLVDPWD 56 (83)
T ss_pred cEEEEEEEEcC-------CCEEEEEECC--CCEEEEEEchhhcccEEEcCCCEEEEEecC
Confidence 46799999998 3344555433 33444444443 6788888876543
No 80
>cd00493 FabA_FabZ FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ. FabA is bifunctional and catalyzes an additional isomerization reaction of trans-2-acyl-ACP to cis-3-acyl-ACP, an essential reaction to unsaturated fatty acid synthesis. FabZ is the primary dehydratase that participates in the elongation cycles of saturated as well as unsaturated fatty acid biosynthesis, whereas FabA is more active in the dehydration of beta-hydroxydecanoyl-ACP. The FabA structure is homodimeric with two independent active sites located at the dimer interface.
Probab=22.16 E-value=70 Score=19.06 Aligned_cols=14 Identities=57% Similarity=0.859 Sum_probs=10.8
Q ss_pred ecCccccCcEEeee
Q 035463 42 VKGPVREGDILTLL 55 (65)
Q Consensus 42 VkGPVr~GDil~Ll 55 (65)
..+||..||.|.+.
T Consensus 85 f~~~v~pgd~l~i~ 98 (131)
T cd00493 85 FRGPVLPGDTLTLE 98 (131)
T ss_pred ECCCcCCCCEEEEE
Confidence 45899999977653
No 81
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=22.15 E-value=51 Score=23.29 Aligned_cols=12 Identities=42% Similarity=0.722 Sum_probs=11.2
Q ss_pred cccCcEEeeehh
Q 035463 46 VREGDILTLLES 57 (65)
Q Consensus 46 Vr~GDil~LlEs 57 (65)
+.+||++.+.||
T Consensus 117 ~kvGD~V~I~Ec 128 (158)
T PTZ00241 117 VKEGDIVVVGQC 128 (158)
T ss_pred CCCCCEEEEEEc
Confidence 899999999987
No 82
>cd03454 YdeM YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=21.42 E-value=72 Score=19.76 Aligned_cols=15 Identities=40% Similarity=0.603 Sum_probs=11.9
Q ss_pred eeecCccccCcEEee
Q 035463 40 RNVKGPVREGDILTL 54 (65)
Q Consensus 40 RnVkGPVr~GDil~L 54 (65)
-....||..||.|+.
T Consensus 83 ~~f~~pv~~Gd~l~~ 97 (140)
T cd03454 83 LRWPRPVRPGDTLSV 97 (140)
T ss_pred eEeCCCCCCCCEEEE
Confidence 456789999998865
No 83
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=21.19 E-value=95 Score=20.53 Aligned_cols=14 Identities=21% Similarity=0.290 Sum_probs=12.1
Q ss_pred CccccCcEEeeehh
Q 035463 44 GPVREGDILTLLES 57 (65)
Q Consensus 44 GPVr~GDil~LlEs 57 (65)
-.+.+||++.+.||
T Consensus 76 n~~kvGD~V~I~E~ 89 (108)
T PRK08572 76 IDAKVGDKVKIAEC 89 (108)
T ss_pred CCCCCCCEEEEEEc
Confidence 35899999999997
No 84
>PF10442 FIST_C: FIST C domain; InterPro: IPR019494 This entry represents a novel sensory domain, designated FIST C (short for F-box and intracellular signal transduction, C-terminal), which is present in signal transduction proteins from bacteria, archaea and eukaryotes. The chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [].
Probab=21.16 E-value=1.1e+02 Score=18.80 Aligned_cols=24 Identities=29% Similarity=0.498 Sum_probs=18.9
Q ss_pred CceEEeeecCccccCcEEeeehhHHH
Q 035463 35 NRFIMRNVKGPVREGDILTLLESERE 60 (65)
Q Consensus 35 ~r~i~RnVkGPVr~GDil~LlEserE 60 (65)
..+| ..-++|.+|+.|.|++...+
T Consensus 47 ~gsl--~~~~~v~eG~~v~l~~~~~~ 70 (136)
T PF10442_consen 47 DGSL--TFAGDVPEGSEVQLMEGDPE 70 (136)
T ss_pred CCEE--EEeeecCCCCEEEEEcCCHH
Confidence 5566 56689999999999876655
No 85
>COG4136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=20.94 E-value=1e+02 Score=22.83 Aligned_cols=25 Identities=24% Similarity=0.402 Sum_probs=21.9
Q ss_pred CCCCceEEeeecCccccCcEEeeeh
Q 035463 32 DDQNRFIMRNVKGPVREGDILTLLE 56 (65)
Q Consensus 32 ~~~~r~i~RnVkGPVr~GDil~LlE 56 (65)
.-+++-+.-|+.=.|-+|||++|+-
T Consensus 11 ~l~g~cLLa~~n~Tia~GeivtlMG 35 (213)
T COG4136 11 RLPGSCLLANVNFTIAKGEIVTLMG 35 (213)
T ss_pred cCCCceEEEeeeEEecCCcEEEEEC
Confidence 3578899999999999999999973
No 86
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=20.69 E-value=57 Score=19.48 Aligned_cols=20 Identities=15% Similarity=0.288 Sum_probs=12.9
Q ss_pred EEeeecCccccCcEEeeehh
Q 035463 38 IMRNVKGPVREGDILTLLES 57 (65)
Q Consensus 38 i~RnVkGPVr~GDil~LlEs 57 (65)
+..+-..-.+.||++.+.||
T Consensus 36 ~aHD~~~~~~vGD~V~I~e~ 55 (69)
T PF00366_consen 36 MAHDENNICKVGDKVRIREC 55 (69)
T ss_dssp EEE-TTSSSTTTSEEEEEEE
T ss_pred EEeCCccCCCCCCEEEEEee
Confidence 33333344567999999987
No 87
>TIGR00413 rlpA rare lipoprotein A. This is a family of prokaryotic proteins with unknown function. Lipoprotein annotation based on the presence of consensus lipoprotein signal sequence. Included in this family is the E. coli putative lipoprotein rlpA.
Probab=20.33 E-value=1.8e+02 Score=21.35 Aligned_cols=35 Identities=31% Similarity=0.529 Sum_probs=24.1
Q ss_pred EEEEEEEcCCCCceEEe-eecCccccCcEEeeehhH
Q 035463 24 TQVRVKFLDDQNRFIMR-NVKGPVREGDILTLLESE 58 (65)
Q Consensus 24 tqVrve~l~~~~r~i~R-nVkGPVr~GDil~LlEse 58 (65)
|.|+|.-+++....++| |=.||-..|-||.|...-
T Consensus 37 T~V~VtNl~ngrsviVrVnDRGPf~~gRiIDLS~aA 72 (208)
T TIGR00413 37 TYVKVTNLHNNRSVIVRINDRGPFSDDRIIDLSHAA 72 (208)
T ss_pred CEEEEEECCCCCEEEEEEeCCCCCCCCCEEECCHHH
Confidence 67777777643333333 668999999999986543
No 88
>PRK11536 6-N-hydroxylaminopurine resistance protein; Provisional
Probab=20.11 E-value=58 Score=23.64 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=13.9
Q ss_pred cCccccCcEEeeehhH
Q 035463 43 KGPVREGDILTLLESE 58 (65)
Q Consensus 43 kGPVr~GDil~LlEse 58 (65)
-|.|+.||.|.|+|.-
T Consensus 151 ~G~V~~GD~v~l~~r~ 166 (223)
T PRK11536 151 PGKVSADAPLELVSRV 166 (223)
T ss_pred CcEEcCCCEEEEEeCC
Confidence 4899999999999864
No 89
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=20.10 E-value=2.5e+02 Score=17.88 Aligned_cols=41 Identities=12% Similarity=0.193 Sum_probs=22.3
Q ss_pred eeEEEEEEccc---cCCcccEEEEEEEEcCCCCceEEeeecC--ccccCcEEee
Q 035463 6 KHAVVVKVMGR---TGSRGQVTQVRVKFLDDQNRFIMRNVKG--PVREGDILTL 54 (65)
Q Consensus 6 ~~A~V~kVlGR---tGs~G~~tqVrve~l~~~~r~i~RnVkG--PVr~GDil~L 54 (65)
-|++|+++-|- ....|...+|...+++ ...+ ++..||.+.+
T Consensus 5 iP~kVv~i~~~~A~vd~~Gv~reV~l~Lv~--------~~~~~~~~~vGDyVLV 50 (90)
T PRK10409 5 VPGQIRTIDGNQAKVDVCGIQRDVDLTLVG--------SCDENGQPRVGQWVLV 50 (90)
T ss_pred cceEEEEEcCCeEEEEcCCeEEEEEEeeec--------ccCCCCccCCCCEEEE
Confidence 47899998652 2223333344443332 2222 5888998764
Done!