Query 037546
Match_columns 66
No_of_seqs 107 out of 154
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 13:21:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037546hhsearch_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 7.7E-42 1.7E-46 212.1 7.1 66 1-66 1-69 (69)
2 cd04457 S1_S28E S1_S28E: S28E, 100.0 1.3E-40 2.9E-45 202.3 6.9 60 7-66 1-60 (60)
3 PRK04007 rps28e 30S ribosomal 100.0 7.8E-39 1.7E-43 199.3 7.8 61 6-66 6-68 (70)
4 PTZ00085 40S ribosomal protein 100.0 9.5E-39 2.1E-43 200.2 7.6 61 6-66 10-73 (73)
5 KOG3502 40S ribosomal protein 100.0 5.1E-40 1.1E-44 202.6 0.2 65 1-66 1-66 (66)
6 COG2053 RPS28A Ribosomal prote 100.0 3E-35 6.6E-40 182.7 6.2 61 6-66 5-67 (69)
7 KOG0187 40S ribosomal protein 71.9 2.8 6E-05 29.2 1.7 20 43-63 62-81 (134)
8 TIGR00008 infA translation ini 70.5 22 0.00047 21.8 5.5 42 7-57 7-55 (68)
9 cd05793 S1_IF1A S1_IF1A: Trans 60.1 37 0.00081 20.7 5.1 45 7-60 2-52 (77)
10 COG0361 InfA Translation initi 58.8 43 0.00092 21.0 5.5 45 6-59 8-59 (75)
11 TIGR03635 S17_bact 30S ribosom 53.3 18 0.00039 22.0 2.7 23 36-58 38-60 (71)
12 PF11213 DUF3006: Protein of u 53.0 12 0.00026 22.2 1.9 13 43-55 30-42 (71)
13 cd03701 IF2_IF5B_II IF2_IF5B_I 51.6 13 0.00027 23.2 1.9 25 41-65 65-89 (95)
14 PF00833 Ribosomal_S17e: Ribos 50.6 4.1 8.9E-05 27.7 -0.5 20 43-63 62-81 (121)
15 PLN00208 translation initiatio 49.3 71 0.0015 22.3 5.4 42 6-56 33-80 (145)
16 PF13533 Biotin_lipoyl_2: Biot 48.9 12 0.00027 20.6 1.4 17 46-62 23-39 (50)
17 PRK12442 translation initiatio 48.0 74 0.0016 20.5 5.9 42 6-56 8-56 (87)
18 CHL00142 rps17 ribosomal prote 46.1 24 0.00051 22.3 2.5 24 36-59 40-63 (84)
19 PF07892 DUF1667: Protein of u 46.0 11 0.00025 23.8 1.0 13 42-54 56-68 (82)
20 PTZ00329 eukaryotic translatio 45.8 87 0.0019 22.1 5.5 43 6-57 33-81 (155)
21 PTZ00154 40S ribosomal protein 45.5 11 0.00024 26.2 1.0 23 40-63 59-81 (134)
22 PRK05610 rpsQ 30S ribosomal pr 45.4 28 0.00061 21.8 2.8 22 37-58 44-65 (84)
23 PF11584 Toxin_ToxA: Proteinac 45.2 23 0.00051 23.8 2.5 43 14-56 28-87 (118)
24 TIGR00074 hypC_hupF hydrogenas 44.8 53 0.0011 20.3 3.9 40 7-55 5-44 (76)
25 PF14801 GCD14_N: tRNA methylt 44.3 15 0.00032 22.1 1.3 15 44-58 3-17 (54)
26 PF00018 SH3_1: SH3 domain; I 44.0 14 0.0003 19.7 1.0 14 46-59 15-28 (48)
27 cd03440 hot_dog The hotdog fol 43.9 20 0.00043 17.9 1.6 15 42-56 53-67 (100)
28 cd03702 IF2_mtIF2_II This fami 43.8 18 0.0004 22.8 1.8 23 43-65 67-89 (95)
29 cd03451 FkbR2 FkbR2 is a Strep 42.9 18 0.00039 22.5 1.6 15 41-55 86-100 (146)
30 PRK13692 (3R)-hydroxyacyl-ACP 41.9 19 0.0004 24.2 1.6 14 42-55 92-105 (159)
31 COG1096 Predicted RNA-binding 40.2 67 0.0014 23.4 4.3 43 6-54 67-126 (188)
32 cd03708 GTPBP_III Domain III o 40.0 76 0.0016 18.4 4.9 27 7-33 34-60 (87)
33 COG0186 RpsQ Ribosomal protein 39.6 18 0.00039 23.3 1.2 12 47-58 56-67 (87)
34 TIGR03028 EpsE polysaccharide 39.6 29 0.00063 24.4 2.4 13 46-58 225-237 (239)
35 COG1607 Acyl-CoA hydrolase [Li 39.4 36 0.00077 23.7 2.8 27 21-56 53-79 (157)
36 CHL00036 ycf4 photosystem I as 39.2 44 0.00094 24.3 3.3 43 23-65 124-173 (184)
37 PF12791 RsgI_N: Anti-sigma fa 38.1 72 0.0016 17.6 4.1 31 30-60 9-39 (56)
38 PRK10694 acyl-CoA esterase; Pr 37.6 24 0.00053 23.1 1.7 14 42-55 63-76 (133)
39 PRK02542 photosystem I assembl 36.2 51 0.0011 24.0 3.3 43 23-65 128-177 (188)
40 PF11095 Gemin7: Gem-associate 35.4 92 0.002 19.7 4.0 31 25-55 35-76 (80)
41 cd03452 MaoC_C MaoC_C The C-t 33.6 32 0.00068 22.1 1.7 14 42-55 84-97 (142)
42 PRK04424 fatty acid biosynthes 33.6 30 0.00065 23.7 1.7 14 42-55 134-147 (185)
43 PRK10413 hydrogenase 2 accesso 33.5 1.2E+02 0.0027 18.9 4.9 41 7-55 5-51 (82)
44 PRK07217 replication factor A; 31.3 2.3E+02 0.0049 22.0 6.2 49 6-57 86-138 (311)
45 PF02392 Ycf4: Ycf4; InterPro 31.2 67 0.0014 23.2 3.1 43 23-65 121-170 (180)
46 cd03455 SAV4209 SAV4209 is a S 30.9 36 0.00078 20.9 1.6 14 42-55 75-88 (123)
47 TIGR03000 plancto_dom_1 Planct 30.8 1E+02 0.0023 19.3 3.6 30 25-55 44-73 (75)
48 smart00652 eIF1a eukaryotic tr 29.6 1.4E+02 0.0031 18.4 5.4 45 6-59 6-56 (83)
49 cd03446 MaoC_like MoaC_like 29.4 42 0.00091 20.7 1.7 14 42-55 86-99 (140)
50 PF12961 DUF3850: Domain of Un 29.2 44 0.00095 20.8 1.7 21 40-60 22-42 (72)
51 PF04149 DUF397: Domain of unk 28.7 1.2E+02 0.0026 17.4 3.6 38 19-62 12-49 (56)
52 PF01176 eIF-1a: Translation i 28.5 1.3E+02 0.0027 17.4 3.7 43 7-58 5-53 (65)
53 cd04456 S1_IF1A_like S1_IF1A_l 28.4 1.5E+02 0.0032 18.2 5.6 44 7-59 2-51 (78)
54 cd00174 SH3 Src homology 3 dom 28.3 42 0.0009 16.7 1.3 13 46-58 17-29 (54)
55 cd04091 mtEFG1_II_like mtEFG1_ 27.5 34 0.00074 19.9 1.0 22 38-59 17-38 (81)
56 cd03449 R_hydratase (R)-hydrat 27.3 49 0.0011 19.7 1.7 14 42-55 78-91 (128)
57 smart00326 SH3 Src homology 3 27.1 45 0.00097 16.7 1.3 13 47-59 21-33 (58)
58 cd03441 R_hydratase_like (R)-h 26.7 50 0.0011 19.5 1.6 14 43-56 77-90 (127)
59 cd01288 FabZ FabZ is a 17kD be 26.6 50 0.0011 19.9 1.7 13 43-55 84-96 (131)
60 cd03691 BipA_TypA_II BipA_TypA 26.2 1.4E+02 0.003 17.2 4.0 21 38-58 18-38 (86)
61 PF14604 SH3_9: Variant SH3 do 25.7 41 0.00089 18.3 1.0 13 46-58 14-26 (49)
62 cd03447 FAS_MaoC FAS_MaoC, the 25.4 51 0.0011 21.0 1.6 14 42-55 76-89 (126)
63 COG3365 Uncharacterized protei 25.0 41 0.00089 23.0 1.1 25 39-63 22-49 (118)
64 cd03453 SAV4209_like SAV4209_l 25.0 56 0.0012 20.2 1.7 15 42-56 76-90 (127)
65 PRK00006 fabZ (3R)-hydroxymyri 24.5 55 0.0012 20.7 1.6 14 43-56 98-111 (147)
66 COG4136 ABC-type uncharacteriz 24.4 71 0.0015 23.6 2.3 25 33-57 11-35 (213)
67 PRK06386 replication factor A; 24.3 3.3E+02 0.0072 21.3 6.1 48 7-57 122-174 (358)
68 TIGR00523 eIF-1A eukaryotic/ar 24.3 2E+02 0.0044 18.4 5.6 41 6-55 20-66 (99)
69 PF00278 Orn_DAP_Arg_deC: Pyri 24.2 80 0.0017 19.0 2.2 24 34-57 68-93 (116)
70 CHL00010 infA translation init 24.1 1.7E+02 0.0038 17.6 6.0 41 7-56 9-56 (78)
71 PF05550 Peptidase_C53: Pestiv 24.0 89 0.0019 22.5 2.7 26 6-31 109-135 (168)
72 PRK08572 rps17p 30S ribosomal 23.7 89 0.0019 20.7 2.5 14 45-58 76-89 (108)
73 PRK13691 (3R)-hydroxyacyl-ACP 23.3 59 0.0013 22.0 1.7 14 43-56 93-106 (166)
74 cd03703 aeIF5B_II aeIF5B_II: T 23.3 2.1E+02 0.0045 18.9 4.2 25 40-65 80-104 (110)
75 KOG2716 Polymerase delta-inter 22.8 28 0.00061 25.7 -0.0 18 47-65 64-81 (230)
76 PF08402 TOBE_2: TOBE domain; 22.6 1.4E+02 0.003 15.9 3.8 36 21-56 28-66 (75)
77 PF07653 SH3_2: Variant SH3 do 22.5 39 0.00084 18.4 0.5 10 47-56 18-27 (55)
78 PTZ00241 40S ribosomal protein 22.2 52 0.0011 23.3 1.2 13 46-58 116-128 (158)
79 PF00190 Cupin_1: Cupin; Inte 22.1 1.9E+02 0.0041 18.4 3.8 26 28-55 66-96 (144)
80 PF03061 4HBT: Thioesterase su 22.1 81 0.0018 16.9 1.8 14 42-55 39-52 (79)
81 cd03450 NodN NodN (nodulation 21.9 60 0.0013 21.5 1.5 14 42-55 93-106 (149)
82 PRK13259 regulatory protein Sp 21.9 1.6E+02 0.0035 19.1 3.4 10 24-33 3-12 (94)
83 PF08817 YukD: WXG100 protein 21.4 57 0.0012 19.2 1.1 11 46-56 69-79 (79)
84 TIGR01750 fabZ beta-hydroxyacy 21.3 71 0.0015 20.0 1.6 14 42-55 93-106 (140)
85 PRK08402 replication factor A; 21.3 3.9E+02 0.0085 20.6 6.3 49 6-56 76-137 (355)
86 PF00366 Ribosomal_S17: Riboso 21.0 57 0.0012 19.5 1.1 19 40-58 37-55 (69)
87 COG0298 HypC Hydrogenase matur 21.0 2.4E+02 0.0053 18.1 4.4 38 7-55 5-47 (82)
88 cd00493 FabA_FabZ FabA/Z, beta 20.9 77 0.0017 18.9 1.7 14 43-56 85-98 (131)
89 PLN00212 glutelin; Provisional 20.6 1.2E+02 0.0027 24.6 3.2 26 27-55 380-405 (493)
90 cd03454 YdeM YdeM is a Bacillu 20.2 79 0.0017 19.6 1.7 15 41-55 83-97 (140)
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=7.7e-42 Score=212.06 Aligned_cols=66 Identities=79% Similarity=1.085 Sum_probs=51.7
Q ss_pred CCCC--CCeeEEEEEeccccCCcCcEEEEEEEEecCCC-cEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546 1 MDTG--GPKKATVIKVIGRTGSRGQVTQVRVQFMDDTK-RQITRNVKGPVRVGDILTLLESEREARRLR 66 (66)
Q Consensus 1 md~~--~~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~-r~i~RnVkGPVr~GDil~LlEsErEarrlr 66 (66)
||+. .+++|+|+||||||||+|+||||||+||++++ |+|+||||||||+||||+|+||||||||||
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 7763 29999999999999999999999999999766 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=202.32 Aligned_cols=60 Identities=80% Similarity=1.139 Sum_probs=58.6
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr 66 (66)
++|+|+||+|||||+|+||||||+||+|++|+|+||||||||+||||+|+|||||||+||
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=7.8e-39 Score=199.33 Aligned_cols=61 Identities=61% Similarity=0.902 Sum_probs=58.8
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecC--CCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDD--TKRQITRNVKGPVRVGDILTLLESEREARRLR 66 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d--~~r~i~RnVkGPVr~GDil~LlEsErEarrlr 66 (66)
.++|+|+||||||||+|++|||||+||++ .+|+|+||||||||+||||+|+|||||||+|+
T Consensus 6 ~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~~~R~i~RNVkGPVR~GDIl~L~EteREAr~l~ 68 (70)
T PRK04007 6 GTPAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETEREARKLG 68 (70)
T ss_pred CceEEEEEEeccccccccEEEEEEEEecCCCcCcEEEEeccCCcccCcEEEEhhhhhHHHhhc
Confidence 78999999999999999999999999994 59999999999999999999999999999985
No 4
>PTZ00085 40S ribosomal protein S28; Provisional
Probab=100.00 E-value=9.5e-39 Score=200.20 Aligned_cols=61 Identities=74% Similarity=1.087 Sum_probs=59.0
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCC---CcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDT---KRQITRNVKGPVRVGDILTLLESEREARRLR 66 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~---~r~i~RnVkGPVr~GDil~LlEsErEarrlr 66 (66)
+++|+|+||||||||+|+||||||+||+++ +|+|+||||||||+||||+|+|||||||+||
T Consensus 10 ~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~d~~r~i~RNVkGPVr~GDIl~L~EteREAr~lr 73 (73)
T PTZ00085 10 PKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLMETEREARRLR 73 (73)
T ss_pred ceeEEEEEEeccccCcccEEEEEEEEccCCcccCcEEEEeccCCcccCcEEeehhhhhhhhhcC
Confidence 899999999999999999999999999955 6999999999999999999999999999997
No 5
>KOG3502 consensus 40S ribosomal protein S28 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.1e-40 Score=202.63 Aligned_cols=65 Identities=77% Similarity=1.040 Sum_probs=61.6
Q ss_pred CCCC-CCeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546 1 MDTG-GPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66 (66)
Q Consensus 1 md~~-~~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr 66 (66)
||+. .+++|+|+||||||||+|+|||||||||+ .+|+|+||||||||+||||.|+||||||||||
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 7872 28999999999999999999999999998 79999999999999999999999999999997
No 6
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-35 Score=182.71 Aligned_cols=61 Identities=69% Similarity=1.027 Sum_probs=59.0
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEec--CCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARRLR 66 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~--d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr 66 (66)
.++|+|++||||||++|++|||+|+||+ |++|+|+||||||||+||||+|+|||||||+|+
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 4779999999999999999999999999 999999999999999999999999999999985
No 7
>KOG0187 consensus 40S ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=71.89 E-value=2.8 Score=29.21 Aligned_cols=20 Identities=60% Similarity=0.835 Sum_probs=17.3
Q ss_pred ecCccccCcEEEeehhHHHHh
Q 037546 43 VKGPVRVGDILTLLESEREAR 63 (66)
Q Consensus 43 VkGPVr~GDil~LlEsErEar 63 (66)
-||||| |=-+-|.|.|||-|
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=70.50 E-value=22 Score=21.77 Aligned_cols=42 Identities=17% Similarity=0.307 Sum_probs=31.7
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccc-------cCcEEEeeh
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVR-------VGDILTLLE 57 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr-------~GDil~LlE 57 (66)
..+.|++.|+ -+..+|++. .+..++-.+.|-.| +||.+.+.=
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 346677763 47889999999755 799987653
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=60.14 E-value=37 Score=20.74 Aligned_cols=45 Identities=18% Similarity=0.324 Sum_probs=30.3
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc------cccCcEEEeehhHH
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP------VRVGDILTLLESER 60 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP------Vr~GDil~LlEsEr 60 (66)
..|+|++.+| -...+|++. .+..++-.+.|- +++||++.+..++.
T Consensus 2 ~~g~V~~~~g-------~~~~~V~~~--~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~ 52 (77)
T cd05793 2 EYGQVEKMLG-------NGRLEVRCF--DGKKRLCRIRGKMRKRVWINEGDIVLVAPWDF 52 (77)
T ss_pred EEEEEEEEcC-------CCEEEEEEC--CCCEEEEEEchhhcccEEEcCCCEEEEEeccc
Confidence 4689999998 334555543 356666667776 56899988866554
No 10
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=58.76 E-value=43 Score=20.99 Aligned_cols=45 Identities=20% Similarity=0.298 Sum_probs=31.9
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCcc-------ccCcEEEeehhH
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPV-------RVGDILTLLESE 59 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPV-------r~GDil~LlEsE 59 (66)
...+.|++.|| -+.++|++. .+...+--+.|-. ++||++.+.=++
T Consensus 8 e~~g~V~e~L~-------~~~f~v~~e--dg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~ 59 (75)
T COG0361 8 EMEGTVIEMLP-------NGRFRVELE--NGHERLAHISGKMRKNRIRILPGDVVLVELSP 59 (75)
T ss_pred EEEEEEEEecC-------CCEEEEEec--CCcEEEEEccCcchheeEEeCCCCEEEEEecc
Confidence 46799999998 457777764 3666666666664 569999876443
No 11
>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=53.35 E-value=18 Score=22.05 Aligned_cols=23 Identities=22% Similarity=0.537 Sum_probs=17.3
Q ss_pred CcEEEeeecCccccCcEEEeehh
Q 037546 36 KRQITRNVKGPVRVGDILTLLES 58 (66)
Q Consensus 36 ~r~i~RnVkGPVr~GDil~LlEs 58 (66)
.++....-.-..++||++.+.||
T Consensus 38 kk~~aHD~~~~~k~GD~V~I~ec 60 (71)
T TIGR03635 38 KKYHAHDENNECKVGDVVRIIET 60 (71)
T ss_pred EEEEEECCCCCCCCCCEEEEEEc
Confidence 34555555557899999999997
No 12
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=52.95 E-value=12 Score=22.22 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=10.5
Q ss_pred ecCccccCcEEEe
Q 037546 43 VKGPVRVGDILTL 55 (66)
Q Consensus 43 VkGPVr~GDil~L 55 (66)
.-..+++||+|.+
T Consensus 30 LP~~~keGDvl~i 42 (71)
T PF11213_consen 30 LPEGAKEGDVLEI 42 (71)
T ss_pred CCCCCCcccEEEE
Confidence 4467999999977
No 13
>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=51.61 E-value=13 Score=23.20 Aligned_cols=25 Identities=28% Similarity=0.452 Sum_probs=21.0
Q ss_pred eeecCccccCcEEEeehhHHHHhhc
Q 037546 41 RNVKGPVRVGDILTLLESEREARRL 65 (66)
Q Consensus 41 RnVkGPVr~GDil~LlEsErEarrl 65 (66)
=-.++....||.+...++|.+|+++
T Consensus 65 ~g~~~~p~aGd~~~~~~~e~~a~~~ 89 (95)
T cd03701 65 LGLKDVPKAGDGVLVVASEKEAKEI 89 (95)
T ss_pred eeecCCccCCCEEEEeCCCHHHHHh
Confidence 3456677899999999999999875
No 14
>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=50.61 E-value=4.1 Score=27.71 Aligned_cols=20 Identities=55% Similarity=0.827 Sum_probs=17.2
Q ss_pred ecCccccCcEEEeehhHHHHh
Q 037546 43 VKGPVRVGDILTLLESEREAR 63 (66)
Q Consensus 43 VkGPVr~GDil~LlEsErEar 63 (66)
-+|||| |=-+.|.|.|||.|
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 15
>PLN00208 translation initiation factor (eIF); Provisional
Probab=49.34 E-value=71 Score=22.25 Aligned_cols=42 Identities=19% Similarity=0.389 Sum_probs=28.3
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc------cccCcEEEee
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP------VRVGDILTLL 56 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP------Vr~GDil~Ll 56 (66)
..+|+|++.+| -..++|++.+ +...+--+.|- |++||+|.+.
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 57899999998 3355555543 55666666665 6688888764
No 16
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=48.86 E-value=12 Score=20.60 Aligned_cols=17 Identities=35% Similarity=0.554 Sum_probs=14.1
Q ss_pred ccccCcEEEeehhHHHH
Q 037546 46 PVRVGDILTLLESEREA 62 (66)
Q Consensus 46 PVr~GDil~LlEsErEa 62 (66)
.|+.||+|.-+++....
T Consensus 23 ~VkkGd~L~~ld~~~~~ 39 (50)
T PF13533_consen 23 QVKKGDVLLVLDSPDLQ 39 (50)
T ss_pred EEcCCCEEEEECcHHHH
Confidence 58999999999987653
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=47.98 E-value=74 Score=20.54 Aligned_cols=42 Identities=24% Similarity=0.335 Sum_probs=30.8
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccc-------cCcEEEee
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVR-------VGDILTLL 56 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr-------~GDil~Ll 56 (66)
...+.|+++|+ =+..+|++ +++..++-.++|=+| +||.+.+.
T Consensus 8 e~~G~V~e~Lp-------~~~frV~L--enG~~vla~isGKmR~~rIrIl~GD~V~VE 56 (87)
T PRK12442 8 ELDGIVDEVLP-------DSRFRVTL--ENGVEVGAYASGRMRKHRIRILAGDRVTLE 56 (87)
T ss_pred EEEEEEEEECC-------CCEEEEEe--CCCCEEEEEeccceeeeeEEecCCCEEEEE
Confidence 45688888887 23566766 357888889999865 58888764
No 18
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=46.13 E-value=24 Score=22.32 Aligned_cols=24 Identities=17% Similarity=0.387 Sum_probs=17.3
Q ss_pred CcEEEeeecCccccCcEEEeehhH
Q 037546 36 KRQITRNVKGPVRVGDILTLLESE 59 (66)
Q Consensus 36 ~r~i~RnVkGPVr~GDil~LlEsE 59 (66)
.++....-..-+++||++.+.||=
T Consensus 40 kk~~aHDe~n~~~~GD~V~I~e~R 63 (84)
T CHL00142 40 KKYLVHDEENECNIGDQVLIEETR 63 (84)
T ss_pred EEEEEeCCCCCCCCCCEEEEEEcC
Confidence 344555555568999999999873
No 19
>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=45.96 E-value=11 Score=23.82 Aligned_cols=13 Identities=46% Similarity=1.076 Sum_probs=6.5
Q ss_pred eecCccccCcEEE
Q 037546 42 NVKGPVRVGDILT 54 (66)
Q Consensus 42 nVkGPVr~GDil~ 54 (66)
.|+-||+.||||.
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 20
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=45.81 E-value=87 Score=22.06 Aligned_cols=43 Identities=16% Similarity=0.362 Sum_probs=28.9
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc------cccCcEEEeeh
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP------VRVGDILTLLE 57 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP------Vr~GDil~LlE 57 (66)
..+|.|++.|| -..++|++. .+...+-.+.|- |++||+|.+.-
T Consensus 33 q~~g~V~~~LG-------n~~f~V~c~--dG~~rLa~I~GKmRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 33 QEYAQVLRMLG-------NGRLEAYCF--DGVKRLCHIRGKMRKRVWINIGDIILVSL 81 (155)
T ss_pred cEEEEEEEEcC-------CCEEEEEEC--CCCEEEEEeeccceeeEEecCCCEEEEec
Confidence 47899999998 234455543 356666666665 66899888743
No 21
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=45.54 E-value=11 Score=26.24 Aligned_cols=23 Identities=61% Similarity=0.772 Sum_probs=18.9
Q ss_pred EeeecCccccCcEEEeehhHHHHh
Q 037546 40 TRNVKGPVRVGDILTLLESEREAR 63 (66)
Q Consensus 40 ~RnVkGPVr~GDil~LlEsErEar 63 (66)
-|--+|||| |=-+-|.|.|||-|
T Consensus 59 kri~~gpvr-gis~klqeeererr 81 (134)
T PTZ00154 59 KRIQKGPVR-GISLKLQEEERERR 81 (134)
T ss_pred hhhccCCcc-ccceehhHHHHHHh
Confidence 345689998 88899999999955
No 22
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=45.35 E-value=28 Score=21.83 Aligned_cols=22 Identities=14% Similarity=0.510 Sum_probs=16.1
Q ss_pred cEEEeeecCccccCcEEEeehh
Q 037546 37 RQITRNVKGPVRVGDILTLLES 58 (66)
Q Consensus 37 r~i~RnVkGPVr~GDil~LlEs 58 (66)
++....-.-.+++||++.+.||
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 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=45.21 E-value=23 Score=23.79 Aligned_cols=43 Identities=33% Similarity=0.546 Sum_probs=30.8
Q ss_pred eccccCCcCcEE---------------EEEEEEec--CCCcEEEeeecCccccCcEEEee
Q 037546 14 VIGRTGSRGQVT---------------QVRVQFMD--DTKRQITRNVKGPVRVGDILTLL 56 (66)
Q Consensus 14 VlGRtGs~G~~t---------------qVrve~l~--d~~r~i~RnVkGPVr~GDil~Ll 56 (66)
+|||.|+-|... .|||.+-. -.+|.|+-.+.-.|--||+-.|.
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 46777764 55688999999999999998764
No 24
>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=44.83 E-value=53 Score=20.27 Aligned_cols=40 Identities=25% Similarity=0.427 Sum_probs=22.1
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEe
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTL 55 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~L 55 (66)
-|++|+++-|.+ -.|++-.- .|.+-=..-+++.+||.+.+
T Consensus 5 iP~~V~~i~~~~--------A~v~~~G~-~~~v~l~lv~~~~vGD~VLV 44 (76)
T TIGR00074 5 IPGQVVEIDENI--------ALVEFCGI-KRDVSLDLVGEVKVGDYVLV 44 (76)
T ss_pred cceEEEEEcCCE--------EEEEcCCe-EEEEEEEeeCCCCCCCEEEE
Confidence 478999986621 34444321 12111112267899998764
No 25
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=44.30 E-value=15 Score=22.07 Aligned_cols=15 Identities=40% Similarity=0.851 Sum_probs=8.6
Q ss_pred cCccccCcEEEeehh
Q 037546 44 KGPVRVGDILTLLES 58 (66)
Q Consensus 44 kGPVr~GDil~LlEs 58 (66)
.||.++||-+.|.+.
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 599999999999764
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=44.04 E-value=14 Score=19.70 Aligned_cols=14 Identities=36% Similarity=0.695 Sum_probs=10.5
Q ss_pred ccccCcEEEeehhH
Q 037546 46 PVRVGDILTLLESE 59 (66)
Q Consensus 46 PVr~GDil~LlEsE 59 (66)
++++||+|.+++..
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
>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=43.89 E-value=20 Score=17.95 Aligned_cols=15 Identities=47% Similarity=0.609 Sum_probs=11.7
Q ss_pred eecCccccCcEEEee
Q 037546 42 NVKGPVRVGDILTLL 56 (66)
Q Consensus 42 nVkGPVr~GDil~Ll 56 (66)
+.++|++.||.+.+.
T Consensus 53 ~~~~~~~~g~~v~~~ 67 (100)
T cd03440 53 RFLRPVRPGDTLTVE 67 (100)
T ss_pred EEecCCCCCCEEEEE
Confidence 557899999988763
No 28
>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=43.82 E-value=18 Score=22.77 Aligned_cols=23 Identities=39% Similarity=0.683 Sum_probs=18.6
Q ss_pred ecCccccCcEEEeehhHHHHhhc
Q 037546 43 VKGPVRVGDILTLLESEREARRL 65 (66)
Q Consensus 43 VkGPVr~GDil~LlEsErEarrl 65 (66)
.++.--.||.+.-.++|.+|+++
T Consensus 67 ~~~~P~aGd~~~~~~se~~Ak~~ 89 (95)
T cd03702 67 LKGVPQAGDKFLVVESEKEAKEI 89 (95)
T ss_pred CCCCCCCCCEEEEeCCHHHHHHH
Confidence 34444679999999999999986
No 29
>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=42.93 E-value=18 Score=22.52 Aligned_cols=15 Identities=33% Similarity=0.350 Sum_probs=12.1
Q ss_pred eeecCccccCcEEEe
Q 037546 41 RNVKGPVRVGDILTL 55 (66)
Q Consensus 41 RnVkGPVr~GDil~L 55 (66)
=+...||+.||.|++
T Consensus 86 ~~f~~pv~~GDtl~~ 100 (146)
T cd03451 86 VRFPAPVFHGDTLYA 100 (146)
T ss_pred EEecCCCCCCCEEEE
Confidence 356799999999974
No 30
>PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional
Probab=41.93 E-value=19 Score=24.18 Aligned_cols=14 Identities=29% Similarity=0.468 Sum_probs=11.7
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+...||+.||.|+.
T Consensus 92 ~f~~PV~~GDtL~~ 105 (159)
T PRK13692 92 KFEKPIVAGDKLYC 105 (159)
T ss_pred EEeCCccCCCEEEE
Confidence 47799999999953
No 31
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=40.15 E-value=67 Score=23.37 Aligned_cols=43 Identities=23% Similarity=0.317 Sum_probs=28.8
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCC-----------------cEEEeeecCccccCcEEE
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTK-----------------RQITRNVKGPVRVGDILT 54 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~-----------------r~i~RnVkGPVr~GDil~ 54 (66)
+.+|+|+.+ +++..+|++-..++.. -...++++.-++.||||-
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 456666655 3466777777666533 234678889999999984
No 32
>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=39.98 E-value=76 Score=18.38 Aligned_cols=27 Identities=19% Similarity=0.303 Sum_probs=23.3
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEec
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMD 33 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~ 33 (66)
..|++.++.++.=..|+...|+++|+.
T Consensus 34 ~~~~i~~i~~~~l~~g~~~~v~i~f~~ 60 (87)
T cd03708 34 QTARIVSIDKDVLRTGDRALVRFRFLY 60 (87)
T ss_pred EEEEEEeccHhhccCCCeEEEEEEECC
Confidence 478999999888889999999999864
No 33
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=39.64 E-value=18 Score=23.34 Aligned_cols=12 Identities=42% Similarity=0.828 Sum_probs=11.0
Q ss_pred cccCcEEEeehh
Q 037546 47 VRVGDILTLLES 58 (66)
Q Consensus 47 Vr~GDil~LlEs 58 (66)
+++||++.+.||
T Consensus 56 ~k~GD~V~I~Et 67 (87)
T COG0186 56 AKVGDIVRIAET 67 (87)
T ss_pred CCCCCEEEEEEc
Confidence 689999999997
No 34
>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=39.61 E-value=29 Score=24.44 Aligned_cols=13 Identities=31% Similarity=0.386 Sum_probs=11.5
Q ss_pred ccccCcEEEeehh
Q 037546 46 PVRVGDILTLLES 58 (66)
Q Consensus 46 PVr~GDil~LlEs 58 (66)
+++.||+|..-||
T Consensus 225 ~l~~gDii~V~~s 237 (239)
T TIGR03028 225 LVQPDDVIYVRES 237 (239)
T ss_pred ccCCCCEEEEeCc
Confidence 5999999999886
No 35
>COG1607 Acyl-CoA hydrolase [Lipid metabolism]
Probab=39.45 E-value=36 Score=23.70 Aligned_cols=27 Identities=48% Similarity=0.685 Sum_probs=19.2
Q ss_pred cCcEEEEEEEEecCCCcEEEeeecCccccCcEEEee
Q 037546 21 RGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLL 56 (66)
Q Consensus 21 ~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~Ll 56 (66)
+|.|--+.|+.++. +=||+.||+|++.
T Consensus 53 ~~~vVTasvd~v~F---------~~Pv~vGd~v~~~ 79 (157)
T COG1607 53 GGRVVTASVDSVDF---------KKPVRVGDIVCLY 79 (157)
T ss_pred CCeEEEEEeceEEE---------ccccccCcEEEEE
Confidence 45666666666543 4599999999874
No 36
>CHL00036 ycf4 photosystem I assembly protein Ycf4
Probab=39.18 E-value=44 Score=24.26 Aligned_cols=43 Identities=30% Similarity=0.564 Sum_probs=36.4
Q ss_pred cEEEEEEEEec--CCCcEEEeeecCc-----cccCcEEEeehhHHHHhhc
Q 037546 23 QVTQVRVQFMD--DTKRQITRNVKGP-----VRVGDILTLLESEREARRL 65 (66)
Q Consensus 23 ~~tqVrve~l~--d~~r~i~RnVkGP-----Vr~GDil~LlEsErEarrl 65 (66)
.+..+|+++-+ +|.|.|-=.+||- -|.||-++|.|-|.+|-.|
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 8889998889985 4789999999999998665
No 37
>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=38.05 E-value=72 Score=17.56 Aligned_cols=31 Identities=16% Similarity=0.135 Sum_probs=23.4
Q ss_pred EEecCCCcEEEeeecCccccCcEEEeehhHH
Q 037546 30 QFMDDTKRQITRNVKGPVRVGDILTLLESER 60 (66)
Q Consensus 30 e~l~d~~r~i~RnVkGPVr~GDil~LlEsEr 60 (66)
=+|.+.|..+-=.-+++...||.+.+.|.+.
T Consensus 9 iVlT~dGeF~~ik~~~~~~vG~eI~~~~~~~ 39 (56)
T PF12791_consen 9 IVLTPDGEFIKIKRKPGMEVGQEIEFDEKDI 39 (56)
T ss_pred EEEcCCCcEEEEeCCCCCcccCEEEEechhh
Confidence 3566667776666677799999999988763
No 38
>PRK10694 acyl-CoA esterase; Provisional
Probab=37.63 E-value=24 Score=23.07 Aligned_cols=14 Identities=36% Similarity=0.608 Sum_probs=11.2
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+-.-|++.||+|.+
T Consensus 63 ~F~~Pv~~Gd~l~~ 76 (133)
T PRK10694 63 TFLRPVAVGDVVCC 76 (133)
T ss_pred EECCCcccCcEEEE
Confidence 44679999999965
No 39
>PRK02542 photosystem I assembly protein Ycf4; Provisional
Probab=36.23 E-value=51 Score=23.99 Aligned_cols=43 Identities=30% Similarity=0.537 Sum_probs=35.8
Q ss_pred cEEEEEEEEec--CCCcEEEeeecCc-----cccCcEEEeehhHHHHhhc
Q 037546 23 QVTQVRVQFMD--DTKRQITRNVKGP-----VRVGDILTLLESEREARRL 65 (66)
Q Consensus 23 ~~tqVrve~l~--d~~r~i~RnVkGP-----Vr~GDil~LlEsErEarrl 65 (66)
.+..+|+++-+ +|.|.|-=.+||- -|.||-++|.|-|.+|-.|
T Consensus 128 dIqsIrveikeGlnprr~iyL~~kg~~~IPLTrig~pl~l~eiE~qAaeL 177 (188)
T PRK02542 128 DIQAVKVEIREGLNPRRRLYLRLKGRRDIPLTRVGQPLPLAELENQGAEL 177 (188)
T ss_pred HeEEEEEEEecCcCCccEEEEEEcCCCcCCcccCCCCCCHHHHHHHHHHH
Confidence 46778888877 8889888888884 3689999999999998765
No 40
>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=35.38 E-value=92 Score=19.67 Aligned_cols=31 Identities=26% Similarity=0.499 Sum_probs=22.0
Q ss_pred EEEEEEEec---CCCcEEEeeecCc--------cccCcEEEe
Q 037546 25 TQVRVQFMD---DTKRQITRNVKGP--------VRVGDILTL 55 (66)
Q Consensus 25 tqVrve~l~---d~~r~i~RnVkGP--------Vr~GDil~L 55 (66)
|+|.-+|-. |....++.|-+.| +|-+||+.+
T Consensus 35 t~V~a~F~a~d~~~~~f~Vs~L~TPlGv~~eAlLR~~DVi~~ 76 (80)
T PF11095_consen 35 TTVSARFGACDIDVSNFQVSNLQTPLGVQPEALLRCSDVISI 76 (80)
T ss_dssp -EEEEEEEEE-TTS-EEEEEEEETTTTEEEEEEEEGGGEEEE
T ss_pred eEEEEEEEEecCchheEEhhhcCCCcccChhheeecCCEEEE
Confidence 346556653 6678899999999 578888875
No 41
>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=33.62 E-value=32 Score=22.05 Aligned_cols=14 Identities=29% Similarity=0.482 Sum_probs=11.5
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+.+.||+.||.|+.
T Consensus 84 rf~~PV~~GDtl~~ 97 (142)
T cd03452 84 RFLEPVYPGDTIQV 97 (142)
T ss_pred EECCCCCCCCEEEE
Confidence 46789999998864
No 42
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=33.58 E-value=30 Score=23.74 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=11.6
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+-+.||++||.|.+
T Consensus 134 rF~kPV~pGD~L~~ 147 (185)
T PRK04424 134 RFKRPVKLGERVVA 147 (185)
T ss_pred EEccCCCCCCEEEE
Confidence 35689999999986
No 43
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=33.50 E-value=1.2e+02 Score=18.91 Aligned_cols=41 Identities=12% Similarity=0.126 Sum_probs=23.7
Q ss_pred eeEEEEEeccc------cCCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEe
Q 037546 7 KKATVIKVIGR------TGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTL 55 (66)
Q Consensus 7 ~~A~V~kVlGR------tGs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~L 55 (66)
-|++|+++-|. ....|...+|.+.++.+. +-++.+||.+.+
T Consensus 5 iP~kVi~i~~~~~~~A~vd~~Gv~r~V~l~Lv~~~--------~~~~~vGDyVLV 51 (82)
T PRK10413 5 VPGQVLAVGEDIHQLAQVEVCGIKRDVNIALICEG--------NPADLLGQWVLV 51 (82)
T ss_pred cceEEEEECCCCCcEEEEEcCCeEEEEEeeeeccC--------CcccccCCEEEE
Confidence 47899998664 233344555555555321 124677888754
No 44
>PRK07217 replication factor A; Reviewed
Probab=31.28 E-value=2.3e+02 Score=22.02 Aligned_cols=49 Identities=16% Similarity=0.153 Sum_probs=35.8
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeec----CccccCcEEEeeh
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVK----GPVRVGDILTLLE 57 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVk----GPVr~GDil~LlE 57 (66)
.-.|+|+++-.+. .+.+.|+-+ +=|++|++-.=.|+ +.+.+||++.+..
T Consensus 86 sV~aKVl~l~e~~--~~si~qvGl-lgDETG~IkfT~W~~s~~~~leeGd~~rI~n 138 (311)
T PRK07217 86 DVTAKVVQLWEPS--SDSIAQVGL-LGDETGTIKFTKWAKSDLPELEEGKSYLLKN 138 (311)
T ss_pred EEEEEEEEecCCC--CCceEEEEE-EEcCCceEEEEEccCCCCCcccCCCEEEEEe
Confidence 3468898887655 467888774 44678887666666 4599999998754
No 45
>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=31.24 E-value=67 Score=23.17 Aligned_cols=43 Identities=35% Similarity=0.621 Sum_probs=35.3
Q ss_pred cEEEEEEEEec--CCCcEEEeeecC----c-cccCcEEEeehhHHHHhhc
Q 037546 23 QVTQVRVQFMD--DTKRQITRNVKG----P-VRVGDILTLLESEREARRL 65 (66)
Q Consensus 23 ~~tqVrve~l~--d~~r~i~RnVkG----P-Vr~GDil~LlEsErEarrl 65 (66)
.+..+|+++-+ +|+|.|-=.+|| | -|.||-++|.|-|.+|-.|
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 688999888888 4 3779999999999998665
No 46
>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=30.90 E-value=36 Score=20.94 Aligned_cols=14 Identities=29% Similarity=0.612 Sum_probs=11.9
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+..+||..||.|++
T Consensus 75 rf~~pv~~Gdtl~~ 88 (123)
T cd03455 75 RLGAPLYAGDTLRF 88 (123)
T ss_pred EeeccccCCCEEEE
Confidence 56789999999875
No 47
>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=30.77 E-value=1e+02 Score=19.33 Aligned_cols=30 Identities=33% Similarity=0.443 Sum_probs=23.8
Q ss_pred EEEEEEEecCCCcEEEeeecCccccCcEEEe
Q 037546 25 TQVRVQFMDDTKRQITRNVKGPVRVGDILTL 55 (66)
Q Consensus 25 tqVrve~l~d~~r~i~RnVkGPVr~GDil~L 55 (66)
.+|++++.-| |+.+.+-=+=+||-||...|
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 68888888889999998876
No 48
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=29.55 E-value=1.4e+02 Score=18.39 Aligned_cols=45 Identities=22% Similarity=0.367 Sum_probs=28.2
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc------cccCcEEEeehhH
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP------VRVGDILTLLESE 59 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP------Vr~GDil~LlEsE 59 (66)
...|+|++.+| -...+|++- .+..++-.+.|= ++.||++.+..++
T Consensus 6 q~~g~V~~~lG-------~~~~~V~~~--dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~ 56 (83)
T smart00652 6 QEIAQVVKMLG-------NGRLEVMCA--DGKERLARIPGKMRKKVWIRRGDIVLVDPWD 56 (83)
T ss_pred cEEEEEEEEcC-------CCEEEEEEC--CCCEEEEEEchhhcccEEEcCCCEEEEEecC
Confidence 46899999998 234444442 344555445554 6688888876543
No 49
>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=29.36 E-value=42 Score=20.70 Aligned_cols=14 Identities=29% Similarity=0.517 Sum_probs=11.5
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+...||+.||.|..
T Consensus 86 ~f~~pv~~GD~l~~ 99 (140)
T cd03446 86 RFLNPVFIGDTIRA 99 (140)
T ss_pred EEcCCCCCCCEEEE
Confidence 36789999998865
No 50
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=29.17 E-value=44 Score=20.79 Aligned_cols=21 Identities=38% Similarity=0.491 Sum_probs=15.4
Q ss_pred EeeecCccccCcEEEeehhHH
Q 037546 40 TRNVKGPVRVGDILTLLESER 60 (66)
Q Consensus 40 ~RnVkGPVr~GDil~LlEsEr 60 (66)
+|.=--.-..||+|.|.|...
T Consensus 22 iRkNDRdf~VGD~L~L~E~~~ 42 (72)
T PF12961_consen 22 IRKNDRDFQVGDILVLREWDN 42 (72)
T ss_pred EEecCCCCCCCCEEEEEEecC
Confidence 444445677899999999763
No 51
>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=28.69 E-value=1.2e+02 Score=17.35 Aligned_cols=38 Identities=29% Similarity=0.424 Sum_probs=28.0
Q ss_pred CCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEeehhHHHH
Q 037546 19 GSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREA 62 (66)
Q Consensus 19 Gs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~LlEsErEa 62 (66)
|..|.|-+|. +. ++...+|+-|-| .|=+|.+-..|-.|
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 32 335999999998 68889888777654
No 52
>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=28.49 E-value=1.3e+02 Score=17.43 Aligned_cols=43 Identities=19% Similarity=0.300 Sum_probs=26.1
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc------cccCcEEEeehh
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP------VRVGDILTLLES 58 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP------Vr~GDil~LlEs 58 (66)
..|+|++.+| -..++|++.| +..++-.+.|= ++.||.+...-+
T Consensus 5 ~~~~V~~~lG-------~~~~~V~~~d--g~~~l~~i~gK~r~~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 5 VIGRVTEMLG-------NNLFEVECED--GEERLARIPGKFRKRIWIKRGDFVLVEPS 53 (65)
T ss_dssp EEEEEEEEES-------SSEEEEEETT--SEEEEEEE-HHHHTCC---TTEEEEEEES
T ss_pred EEEEEEEECC-------CCEEEEEeCC--CCEEEEEeccceeeeEecCCCCEEEEEec
Confidence 5799999998 2345666543 55555555553 788998866543
No 53
>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=28.36 E-value=1.5e+02 Score=18.16 Aligned_cols=44 Identities=18% Similarity=0.344 Sum_probs=27.7
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc------cccCcEEEeehhH
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP------VRVGDILTLLESE 59 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP------Vr~GDil~LlEsE 59 (66)
.+|+|++.+| -...+|+.. .+...+-.+.|- +++||++.+.-++
T Consensus 2 ~i~~V~~~lG-------~~~~~V~~~--dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~ 51 (78)
T cd04456 2 QIVRVLRMLG-------NNRHEVECA--DGQRRLVSIPGKLRKNIWIKRGDFLIVDPIE 51 (78)
T ss_pred eEEEEEEECC-------CCEEEEEEC--CCCEEEEEEchhhccCEEEcCCCEEEEEecc
Confidence 4789999988 234455543 355555556554 6688988775443
No 54
>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=28.26 E-value=42 Score=16.74 Aligned_cols=13 Identities=38% Similarity=0.744 Sum_probs=10.7
Q ss_pred ccccCcEEEeehh
Q 037546 46 PVRVGDILTLLES 58 (66)
Q Consensus 46 PVr~GDil~LlEs 58 (66)
+++.||++.+++.
T Consensus 17 ~~~~Gd~v~v~~~ 29 (54)
T cd00174 17 SFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCEEEEEEc
Confidence 3678999999876
No 55
>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=27.46 E-value=34 Score=19.94 Aligned_cols=22 Identities=18% Similarity=0.324 Sum_probs=16.7
Q ss_pred EEEeeecCccccCcEEEeehhH
Q 037546 38 QITRNVKGPVRVGDILTLLESE 59 (66)
Q Consensus 38 ~i~RnVkGPVr~GDil~LlEsE 59 (66)
.+.|-..|-++.||.|....+.
T Consensus 17 ~~~Rv~sG~lk~gd~v~~~~~~ 38 (81)
T cd04091 17 TYMRIYQGKLKKGDTIYNVRTG 38 (81)
T ss_pred EEEEEecCEEcCCCEEEEcCCC
Confidence 4778888888888888776543
No 56
>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=27.30 E-value=49 Score=19.71 Aligned_cols=14 Identities=36% Similarity=0.525 Sum_probs=11.9
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+.+.||..||.|.+
T Consensus 78 ~f~~Pv~~gd~l~~ 91 (128)
T cd03449 78 RFLRPVFIGDTVTA 91 (128)
T ss_pred EECCCccCCCEEEE
Confidence 67899999998875
No 57
>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=27.14 E-value=45 Score=16.73 Aligned_cols=13 Identities=46% Similarity=0.805 Sum_probs=10.6
Q ss_pred cccCcEEEeehhH
Q 037546 47 VRVGDILTLLESE 59 (66)
Q Consensus 47 Vr~GDil~LlEsE 59 (66)
++.||++.+.+..
T Consensus 21 ~~~Gd~v~v~~~~ 33 (58)
T smart00326 21 FKKGDIITVLEKS 33 (58)
T ss_pred CCCCCEEEEEEcC
Confidence 6889999998763
No 58
>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=26.65 E-value=50 Score=19.49 Aligned_cols=14 Identities=36% Similarity=0.430 Sum_probs=11.6
Q ss_pred ecCccccCcEEEee
Q 037546 43 VKGPVRVGDILTLL 56 (66)
Q Consensus 43 VkGPVr~GDil~Ll 56 (66)
...||..||.|++.
T Consensus 77 f~~Pv~~Gd~l~~~ 90 (127)
T cd03441 77 FLAPVFPGDTLRVE 90 (127)
T ss_pred EeCCcCCCCEEEEE
Confidence 46899999999864
No 59
>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=26.60 E-value=50 Score=19.89 Aligned_cols=13 Identities=46% Similarity=0.659 Sum_probs=11.0
Q ss_pred ecCccccCcEEEe
Q 037546 43 VKGPVRVGDILTL 55 (66)
Q Consensus 43 VkGPVr~GDil~L 55 (66)
.++||+.||.|.+
T Consensus 84 f~~pv~pgd~l~i 96 (131)
T cd01288 84 FRKPVVPGDQLIL 96 (131)
T ss_pred EccccCCCCEEEE
Confidence 5699999999865
No 60
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=26.19 E-value=1.4e+02 Score=17.23 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=17.3
Q ss_pred EEEeeecCccccCcEEEeehh
Q 037546 38 QITRNVKGPVRVGDILTLLES 58 (66)
Q Consensus 38 ~i~RnVkGPVr~GDil~LlEs 58 (66)
.+.|-..|-++.||.|.....
T Consensus 18 ~~~Rv~sG~l~~g~~v~~~~~ 38 (86)
T cd03691 18 AIGRIFRGTVKVGQQVAVVKR 38 (86)
T ss_pred EEEEEEeCEEcCCCEEEEEcC
Confidence 478999999999999976654
No 61
>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=25.68 E-value=41 Score=18.30 Aligned_cols=13 Identities=38% Similarity=0.787 Sum_probs=9.7
Q ss_pred ccccCcEEEeehh
Q 037546 46 PVRVGDILTLLES 58 (66)
Q Consensus 46 PVr~GDil~LlEs 58 (66)
.++.||+|.+++.
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 62
>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=25.43 E-value=51 Score=20.99 Aligned_cols=14 Identities=29% Similarity=0.263 Sum_probs=11.8
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+..+||..||.|.+
T Consensus 76 rf~~PV~~gdtl~~ 89 (126)
T cd03447 76 SFVGMVLPNDELEV 89 (126)
T ss_pred EEcccCcCCCEEEE
Confidence 36799999999886
No 63
>COG3365 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.00 E-value=41 Score=23.01 Aligned_cols=25 Identities=44% Similarity=0.553 Sum_probs=16.1
Q ss_pred EEeeecCccccCcEEEee---hhHHHHh
Q 037546 39 ITRNVKGPVRVGDILTLL---ESEREAR 63 (66)
Q Consensus 39 i~RnVkGPVr~GDil~Ll---EsErEar 63 (66)
-+|-+---||+||||.|. .-|.||+
T Consensus 22 kvr~Iid~vr~G~IlVLE~gL~P~eeak 49 (118)
T COG3365 22 KVRYIIDKVREGDILVLEGGLTPEEEAK 49 (118)
T ss_pred HHHHHHHhccCCcEEEEeCCCChHHHHH
Confidence 345555668899999984 3344554
No 64
>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=24.96 E-value=56 Score=20.24 Aligned_cols=15 Identities=40% Similarity=0.426 Sum_probs=12.4
Q ss_pred eecCccccCcEEEee
Q 037546 42 NVKGPVRVGDILTLL 56 (66)
Q Consensus 42 nVkGPVr~GDil~Ll 56 (66)
...+||..||.|++.
T Consensus 76 rf~~Pv~~Gdtl~~~ 90 (127)
T cd03453 76 RFTKPVPVPDTLTCT 90 (127)
T ss_pred EECCcCcCCCEEEEE
Confidence 567999999998863
No 65
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=24.48 E-value=55 Score=20.73 Aligned_cols=14 Identities=50% Similarity=0.560 Sum_probs=11.1
Q ss_pred ecCccccCcEEEee
Q 037546 43 VKGPVRVGDILTLL 56 (66)
Q Consensus 43 VkGPVr~GDil~Ll 56 (66)
...||+.||.|.+.
T Consensus 98 F~~pv~pGd~l~i~ 111 (147)
T PRK00006 98 FKRPVVPGDQLILE 111 (147)
T ss_pred EccccCCCCEEEEE
Confidence 45899999998753
No 66
>COG4136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=24.39 E-value=71 Score=23.65 Aligned_cols=25 Identities=24% Similarity=0.272 Sum_probs=22.1
Q ss_pred cCCCcEEEeeecCccccCcEEEeeh
Q 037546 33 DDTKRQITRNVKGPVRVGDILTLLE 57 (66)
Q Consensus 33 ~d~~r~i~RnVkGPVr~GDil~LlE 57 (66)
.-+++.+.-|+.=.|-+|||++|+-
T Consensus 11 ~l~g~cLLa~~n~Tia~GeivtlMG 35 (213)
T COG4136 11 RLPGSCLLANVNFTIAKGEIVTLMG 35 (213)
T ss_pred cCCCceEEEeeeEEecCCcEEEEEC
Confidence 3578999999999999999999973
No 67
>PRK06386 replication factor A; Reviewed
Probab=24.34 E-value=3.3e+02 Score=21.27 Aligned_cols=48 Identities=15% Similarity=0.223 Sum_probs=30.4
Q ss_pred eeEEEEEecc----ccCCcCcEEEEEEEEe-cCCCcEEEeeecCccccCcEEEeeh
Q 037546 7 KKATVIKVIG----RTGSRGQVTQVRVQFM-DDTKRQITRNVKGPVRVGDILTLLE 57 (66)
Q Consensus 7 ~~A~V~kVlG----RtGs~G~~tqVrve~l-~d~~r~i~RnVkGPVr~GDil~LlE 57 (66)
..|+|+++-- +.|+.| .|+.=++ |++++.=+=.+.-++.+||++.+..
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 4578877633 334334 4444444 4677775555655899999998764
No 68
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=24.27 E-value=2e+02 Score=18.41 Aligned_cols=41 Identities=17% Similarity=0.393 Sum_probs=26.6
Q ss_pred CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc------cccCcEEEe
Q 037546 6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP------VRVGDILTL 55 (66)
Q Consensus 6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP------Vr~GDil~L 55 (66)
...|+|++.+| +.. .+|++. .+..++-.+.|= +++||++.+
T Consensus 20 e~~g~V~~~lG-----~~~--~~V~~~--dG~~~la~i~GK~Rk~iwI~~GD~VlV 66 (99)
T TIGR00523 20 EILGVIEQMLG-----AGR--VKVRCL--DGKTRLGRIPGKLKKRIWIREGDVVIV 66 (99)
T ss_pred EEEEEEEEEcC-----CCE--EEEEeC--CCCEEEEEEchhhcccEEecCCCEEEE
Confidence 46899999998 233 344432 356666666665 567888776
No 69
>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=24.20 E-value=80 Score=18.97 Aligned_cols=24 Identities=38% Similarity=0.545 Sum_probs=18.2
Q ss_pred CCCcEEEeeecCc--cccCcEEEeeh
Q 037546 34 DTKRQITRNVKGP--VRVGDILTLLE 57 (66)
Q Consensus 34 d~~r~i~RnVkGP--Vr~GDil~LlE 57 (66)
++.-.|.+++.-| +++||.|.+..
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 5556788888887 99999998865
No 70
>CHL00010 infA translation initiation factor 1
Probab=24.12 E-value=1.7e+02 Score=17.60 Aligned_cols=41 Identities=17% Similarity=0.266 Sum_probs=24.6
Q ss_pred eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCc-------cccCcEEEee
Q 037546 7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGP-------VRVGDILTLL 56 (66)
Q Consensus 7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGP-------Vr~GDil~Ll 56 (66)
..+.|++++| +..--| ++ +.+..+....+|= +.+||++.+.
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 4588888885 122223 32 2355666666664 4469999886
No 71
>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=24.02 E-value=89 Score=22.50 Aligned_cols=26 Identities=38% Similarity=0.557 Sum_probs=21.9
Q ss_pred CeeEEEEEeccc-cCCcCcEEEEEEEE
Q 037546 6 PKKATVIKVIGR-TGSRGQVTQVRVQF 31 (66)
Q Consensus 6 ~~~A~V~kVlGR-tGs~G~~tqVrve~ 31 (66)
.+..+|+|-+|| |||-|....+-|=+
T Consensus 109 ~~~CEvTkriGRvTGSDgkLYHiyvC~ 135 (168)
T PF05550_consen 109 TQMCEVTKRIGRVTGSDGKLYHIYVCI 135 (168)
T ss_pred cceEeecceEEEEECCCCCEEEEEEec
Confidence 567899999999 89999998877654
No 72
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=23.71 E-value=89 Score=20.73 Aligned_cols=14 Identities=29% Similarity=0.415 Sum_probs=12.1
Q ss_pred CccccCcEEEeehh
Q 037546 45 GPVRVGDILTLLES 58 (66)
Q Consensus 45 GPVr~GDil~LlEs 58 (66)
-.+++||++.+.||
T Consensus 76 n~~kvGD~V~I~E~ 89 (108)
T PRK08572 76 IDAKVGDKVKIAEC 89 (108)
T ss_pred CCCCCCCEEEEEEc
Confidence 35899999999987
No 73
>PRK13691 (3R)-hydroxyacyl-ACP dehydratase subunit HadC; Provisional
Probab=23.30 E-value=59 Score=22.00 Aligned_cols=14 Identities=36% Similarity=0.354 Sum_probs=11.8
Q ss_pred ecCccccCcEEEee
Q 037546 43 VKGPVRVGDILTLL 56 (66)
Q Consensus 43 VkGPVr~GDil~Ll 56 (66)
...||+.||.|+..
T Consensus 93 f~rPV~~GDtL~~~ 106 (166)
T PRK13691 93 FHKPVLAGDKLWAR 106 (166)
T ss_pred EeCCcCCCCEEEEE
Confidence 67899999999753
No 74
>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=23.29 E-value=2.1e+02 Score=18.85 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=19.0
Q ss_pred EeeecCccccCcEEEeehhHHHHhhc
Q 037546 40 TRNVKGPVRVGDILTLLESEREARRL 65 (66)
Q Consensus 40 ~RnVkGPVr~GDil~LlEsErEarrl 65 (66)
..+..+. -.||.+..-++|.||+.+
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 75
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=22.79 E-value=28 Score=25.69 Aligned_cols=18 Identities=50% Similarity=0.687 Sum_probs=15.0
Q ss_pred cccCcEEEeehhHHHHhhc
Q 037546 47 VRVGDILTLLESEREARRL 65 (66)
Q Consensus 47 Vr~GDil~LlEsErEarrl 65 (66)
.|.||+. |-|+|+|.+.|
T Consensus 64 mRdGdv~-LPe~~kel~El 81 (230)
T KOG2716|consen 64 MRDGDVD-LPESEKELKEL 81 (230)
T ss_pred hhccccc-CccchHHHHHH
Confidence 6889998 99999996654
No 76
>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=22.60 E-value=1.4e+02 Score=15.92 Aligned_cols=36 Identities=19% Similarity=0.232 Sum_probs=20.4
Q ss_pred cCcEEEEEEEEecCCCcEEEeeecC---ccccCcEEEee
Q 037546 21 RGQVTQVRVQFMDDTKRQITRNVKG---PVRVGDILTLL 56 (66)
Q Consensus 21 ~G~~tqVrve~l~d~~r~i~RnVkG---PVr~GDil~Ll 56 (66)
.|.-+.+.+++-+.....+...... +...||-+.|.
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 4567777777644433334444433 68899988764
No 77
>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=22.52 E-value=39 Score=18.38 Aligned_cols=10 Identities=30% Similarity=0.800 Sum_probs=8.1
Q ss_pred cccCcEEEee
Q 037546 47 VRVGDILTLL 56 (66)
Q Consensus 47 Vr~GDil~Ll 56 (66)
+..||+|.++
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 78
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=22.15 E-value=52 Score=23.33 Aligned_cols=13 Identities=31% Similarity=0.509 Sum_probs=11.6
Q ss_pred ccccCcEEEeehh
Q 037546 46 PVRVGDILTLLES 58 (66)
Q Consensus 46 PVr~GDil~LlEs 58 (66)
.+.+||++.+.||
T Consensus 116 ~~kvGD~V~I~Ec 128 (158)
T PTZ00241 116 DVKEGDIVVVGQC 128 (158)
T ss_pred CCCCCCEEEEEEc
Confidence 3899999999987
No 79
>PF00190 Cupin_1: Cupin; InterPro: IPR006045 This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. ; GO: 0045735 nutrient reservoir activity; PDB: 2E9Q_A 2EVX_A 1OD5_A 1UCX_A 1UD1_C 1FXZ_C 3KGL_C 3KSC_D 1UIJ_F 1IPK_B ....
Probab=22.11 E-value=1.9e+02 Score=18.37 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=17.4
Q ss_pred EEEEecCCC-----cEEEeeecCccccCcEEEe
Q 037546 28 RVQFMDDTK-----RQITRNVKGPVRVGDILTL 55 (66)
Q Consensus 28 rve~l~d~~-----r~i~RnVkGPVr~GDil~L 55 (66)
++.++.+.+ +....++ .+++||++.+
T Consensus 66 ~~~~v~~~~~~~~~~~~~~~v--~l~~Gdv~~v 96 (144)
T PF00190_consen 66 RVGVVGPGGPQEEFRDFSQKV--RLKAGDVFVV 96 (144)
T ss_dssp EEEEEETTCSSSEEEEEEEEE--EEETTEEEEE
T ss_pred EEEEEecCCccccceeeecee--eeecccceee
Confidence 445554333 4566667 8999999875
No 80
>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=22.09 E-value=81 Score=16.94 Aligned_cols=14 Identities=43% Similarity=0.700 Sum_probs=9.4
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
+-..|++.||.|..
T Consensus 39 ~f~~p~~~gd~l~~ 52 (79)
T PF03061_consen 39 DFLRPVRPGDTLRV 52 (79)
T ss_dssp EESS-BBTTSEEEE
T ss_pred EEccccCCCeEEEE
Confidence 45678889987764
No 81
>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=21.90 E-value=60 Score=21.48 Aligned_cols=14 Identities=29% Similarity=0.375 Sum_probs=11.8
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
...+||..||.|+.
T Consensus 93 rF~~PV~~GDtl~~ 106 (149)
T cd03450 93 RFPAPVPVGSRVRG 106 (149)
T ss_pred EeCcceeCCcEEEE
Confidence 36799999999875
No 82
>PRK13259 regulatory protein SpoVG; Reviewed
Probab=21.86 E-value=1.6e+02 Score=19.05 Aligned_cols=10 Identities=40% Similarity=0.624 Sum_probs=5.6
Q ss_pred EEEEEEEEec
Q 037546 24 VTQVRVQFMD 33 (66)
Q Consensus 24 ~tqVrve~l~ 33 (66)
+|.||+.-++
T Consensus 3 ITdVri~~~~ 12 (94)
T PRK13259 3 VTDVRLRKVN 12 (94)
T ss_pred EEEEEEEEeC
Confidence 5555555554
No 83
>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=21.43 E-value=57 Score=19.18 Aligned_cols=11 Identities=55% Similarity=0.721 Sum_probs=5.5
Q ss_pred ccccCcEEEee
Q 037546 46 PVRVGDILTLL 56 (66)
Q Consensus 46 PVr~GDil~Ll 56 (66)
+|+-||+|.|+
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 84
>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=21.34 E-value=71 Score=19.96 Aligned_cols=14 Identities=43% Similarity=0.634 Sum_probs=11.3
Q ss_pred eecCccccCcEEEe
Q 037546 42 NVKGPVRVGDILTL 55 (66)
Q Consensus 42 nVkGPVr~GDil~L 55 (66)
...+||+.||.|++
T Consensus 93 kF~~~v~pGd~l~i 106 (140)
T TIGR01750 93 KFRRPVVPGDQLIL 106 (140)
T ss_pred EECCccCCCCEEEE
Confidence 45699999999875
No 85
>PRK08402 replication factor A; Reviewed
Probab=21.30 E-value=3.9e+02 Score=20.65 Aligned_cols=49 Identities=27% Similarity=0.416 Sum_probs=30.2
Q ss_pred CeeEEEEEecc-cc-----CCcCcEEEEEEEEecCCCcEEEeeec-------CccccCcEEEee
Q 037546 6 PKKATVIKVIG-RT-----GSRGQVTQVRVQFMDDTKRQITRNVK-------GPVRVGDILTLL 56 (66)
Q Consensus 6 ~~~A~V~kVlG-Rt-----Gs~G~~tqVrve~l~d~~r~i~RnVk-------GPVr~GDil~Ll 56 (66)
.-.|+|+.+-+ |+ |+.|.+.. +.+-|+++++-+=-+. ..+.+||++.+.
T Consensus 76 ~v~~rVl~~~~~r~f~rrdG~~~~V~~--i~l~DeTG~ir~TlW~~~a~~~~~~l~~Gdvi~I~ 137 (355)
T PRK08402 76 NIVGRVLRKYPPREYTKKDGSTGRVAS--LIIYDDTGRARVVLWDAKVAKYYNKINVGDVIKVI 137 (355)
T ss_pred eEEEEEEEccCCceeeccCCCcceEEE--EEEEcCCCeEEEEEechhhhhhcccCCCCCEEEEE
Confidence 34688888754 53 66554443 5556877766332121 349999999875
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=21.02 E-value=57 Score=19.50 Aligned_cols=19 Identities=21% Similarity=0.375 Sum_probs=12.6
Q ss_pred EeeecCccccCcEEEeehh
Q 037546 40 TRNVKGPVRVGDILTLLES 58 (66)
Q Consensus 40 ~RnVkGPVr~GDil~LlEs 58 (66)
..+-..-.+.||++.+.||
T Consensus 37 aHD~~~~~~vGD~V~I~e~ 55 (69)
T PF00366_consen 37 AHDENNICKVGDKVRIREC 55 (69)
T ss_dssp EE-TTSSSTTTSEEEEEEE
T ss_pred EeCCccCCCCCCEEEEEee
Confidence 3333344567999999887
No 87
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.95 E-value=2.4e+02 Score=18.12 Aligned_cols=38 Identities=16% Similarity=0.366 Sum_probs=24.9
Q ss_pred eeEEEEEeccccC-----CcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEe
Q 037546 7 KKATVIKVIGRTG-----SRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTL 55 (66)
Q Consensus 7 ~~A~V~kVlGRtG-----s~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~L 55 (66)
-|++|++|-+-.+ .-|-..+|+..+++. +++.||.+.+
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 4677888876433 234556677777653 8889997753
No 88
>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=20.89 E-value=77 Score=18.93 Aligned_cols=14 Identities=57% Similarity=0.828 Sum_probs=10.8
Q ss_pred ecCccccCcEEEee
Q 037546 43 VKGPVRVGDILTLL 56 (66)
Q Consensus 43 VkGPVr~GDil~Ll 56 (66)
..+||..||.|.+.
T Consensus 85 f~~~v~pgd~l~i~ 98 (131)
T cd00493 85 FRGPVLPGDTLTLE 98 (131)
T ss_pred ECCCcCCCCEEEEE
Confidence 45899999977653
No 89
>PLN00212 glutelin; Provisional
Probab=20.64 E-value=1.2e+02 Score=24.59 Aligned_cols=26 Identities=27% Similarity=0.608 Sum_probs=20.1
Q ss_pred EEEEEecCCCcEEEeeecCccccCcEEEe
Q 037546 27 VRVQFMDDTKRQITRNVKGPVRVGDILTL 55 (66)
Q Consensus 27 Vrve~l~d~~r~i~RnVkGPVr~GDil~L 55 (66)
.+|+|.++.+... ..+-|++||++.+
T Consensus 380 g~vqvV~~~g~~v---f~~~L~~GdvfVV 405 (493)
T PLN00212 380 ARVQVVSNNGKTV---FNGVLRPGQLLII 405 (493)
T ss_pred eEEEEEcCCCCEE---EEEEEcCCCEEEE
Confidence 5778887666544 7788999999875
No 90
>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=20.24 E-value=79 Score=19.64 Aligned_cols=15 Identities=40% Similarity=0.574 Sum_probs=11.8
Q ss_pred eeecCccccCcEEEe
Q 037546 41 RNVKGPVRVGDILTL 55 (66)
Q Consensus 41 RnVkGPVr~GDil~L 55 (66)
-....||..||.|+.
T Consensus 83 ~~f~~pv~~Gd~l~~ 97 (140)
T cd03454 83 LRWPRPVRPGDTLSV 97 (140)
T ss_pred eEeCCCCCCCCEEEE
Confidence 356789999998865
Done!