Query 037036
Match_columns 87
No_of_seqs 110 out of 723
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 07:57:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0093 RplN Ribosomal protein 100.0 5.9E-41 1.3E-45 227.6 9.1 86 1-87 27-112 (122)
2 CHL00057 rpl14 ribosomal prote 100.0 6.3E-39 1.4E-43 218.7 9.5 86 1-87 27-112 (122)
3 PRK05483 rplN 50S ribosomal pr 100.0 7.9E-39 1.7E-43 218.2 9.9 86 1-87 27-112 (122)
4 TIGR01067 rplN_bact ribosomal 100.0 2E-38 4.3E-43 216.1 10.0 86 1-87 27-112 (122)
5 PTZ00320 ribosomal protein L14 100.0 2.1E-37 4.6E-42 222.7 9.5 85 2-87 84-178 (188)
6 PTZ00054 60S ribosomal protein 100.0 2.4E-36 5.1E-41 210.0 9.5 78 5-87 52-129 (139)
7 TIGR03673 rpl14p_arch 50S ribo 100.0 2.6E-36 5.6E-41 208.1 9.4 78 5-87 44-121 (131)
8 PRK08571 rpl14p 50S ribosomal 100.0 4.2E-36 9.1E-41 207.2 9.5 78 5-87 45-122 (132)
9 PF00238 Ribosomal_L14: Riboso 100.0 5.4E-36 1.2E-40 203.8 7.0 85 2-87 28-112 (122)
10 KOG0901 60S ribosomal protein 99.9 7.7E-24 1.7E-28 148.0 7.1 80 5-86 53-134 (145)
11 KOG3441 Mitochondrial ribosoma 99.5 4.1E-14 8.9E-19 97.9 5.9 65 4-82 66-130 (149)
12 PF08447 PAS_3: PAS fold; Int 67.7 9.5 0.00021 22.2 3.3 30 41-70 57-86 (91)
13 PF00575 S1: S1 RNA binding do 66.1 18 0.0004 20.9 4.3 33 26-63 1-33 (74)
14 PF10382 DUF2439: Protein of u 55.9 25 0.00055 22.0 3.8 29 47-75 20-49 (83)
15 PF03864 Phage_cap_E: Phage ma 44.1 74 0.0016 23.5 5.3 47 32-80 232-281 (329)
16 TIGR01024 rplS_bact ribosomal 43.1 55 0.0012 22.1 4.1 31 8-41 20-50 (113)
17 KOG2449 Methylmalonate semiald 41.1 51 0.0011 23.6 3.8 55 11-66 64-121 (157)
18 PF00659 POLO_box: POLO box du 39.7 68 0.0015 18.7 3.8 23 45-67 10-33 (68)
19 PF11429 Colicin_D: Colicin D; 38.3 54 0.0012 21.5 3.4 28 44-71 46-75 (92)
20 COG1443 Idi Isopentenyldiphosp 38.2 21 0.00045 26.3 1.5 14 58-71 5-18 (185)
21 PF01245 Ribosomal_L19: Riboso 37.3 66 0.0014 21.5 3.8 32 8-42 20-51 (113)
22 PF04773 FecR: FecR protein; 36.6 82 0.0018 18.8 3.9 29 42-70 11-39 (98)
23 PF07481 DUF1521: Domain of Un 35.4 78 0.0017 23.0 4.1 35 42-76 10-45 (171)
24 PRK05338 rplS 50S ribosomal pr 34.0 99 0.0021 20.9 4.2 31 8-41 20-50 (116)
25 CHL00084 rpl19 ribosomal prote 33.4 98 0.0021 21.0 4.1 31 8-41 24-54 (117)
26 KOG0149 Predicted RNA-binding 32.8 47 0.001 25.5 2.7 29 30-58 37-65 (247)
27 PRK06299 rpsA 30S ribosomal pr 31.9 1.9E+02 0.0041 23.6 6.3 51 8-64 420-490 (565)
28 PF07039 DUF1325: SGF29 tudor- 31.6 61 0.0013 22.0 2.9 25 32-58 88-112 (130)
29 PRK13149 H/ACA RNA-protein com 31.4 47 0.001 20.4 2.1 26 51-79 23-50 (73)
30 PF04170 NlpE: NlpE N-terminal 31.2 68 0.0015 20.0 2.9 22 48-69 62-83 (87)
31 COG0824 FcbC Predicted thioest 31.1 1.6E+02 0.0035 19.5 5.4 16 5-21 68-83 (137)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 31.1 1.2E+02 0.0026 18.0 4.3 33 26-63 11-43 (83)
33 cd04454 S1_Rrp4_like S1_Rrp4_l 30.3 1.2E+02 0.0027 17.9 3.9 15 8-23 5-19 (82)
34 PF12791 RsgI_N: Anti-sigma fa 29.9 52 0.0011 18.6 2.1 21 54-74 3-23 (56)
35 COG2063 FlgH Flagellar basal b 29.6 39 0.00084 25.6 1.8 19 4-23 69-87 (230)
36 TIGR03711 acc_sec_asp3 accesso 29.2 51 0.0011 23.0 2.2 27 48-74 15-41 (135)
37 PF01217 Clat_adaptor_s: Clath 28.0 49 0.0011 21.9 2.0 25 57-81 3-27 (141)
38 COG4959 TraF Type IV secretory 27.9 68 0.0015 23.3 2.7 37 43-80 122-159 (173)
39 PF13426 PAS_9: PAS domain; PD 27.6 1.2E+02 0.0027 17.1 4.0 29 43-71 67-95 (104)
40 smart00316 S1 Ribosomal protei 27.6 1.1E+02 0.0024 16.5 4.3 29 29-62 2-30 (72)
41 PF12508 DUF3714: Protein of u 27.3 73 0.0016 23.4 2.9 44 29-75 51-94 (200)
42 KOG0936 Clathrin adaptor compl 26.7 63 0.0014 23.5 2.4 25 58-82 4-28 (182)
43 PF05325 DUF730: Protein of un 26.6 63 0.0014 21.8 2.3 43 39-81 6-51 (122)
44 CHL00142 rps17 ribosomal prote 25.4 85 0.0019 20.0 2.6 22 6-30 50-71 (84)
45 cd07581 nitrilase_3 Uncharacte 24.9 91 0.002 22.0 3.0 16 57-72 92-107 (255)
46 PF02107 FlgH: Flagellar L-rin 24.4 55 0.0012 23.2 1.8 17 4-21 22-38 (179)
47 PF07661 MORN_2: MORN repeat v 24.3 65 0.0014 14.3 1.5 15 47-61 1-15 (22)
48 cd04452 S1_IF2_alpha S1_IF2_al 24.2 1.5E+02 0.0032 16.9 3.4 24 28-56 2-25 (76)
49 TIGR00399 metG_C_term methiony 24.0 67 0.0014 21.9 2.1 28 46-73 106-136 (137)
50 PRK07252 hypothetical protein; 23.4 2.2E+02 0.0048 18.8 4.5 29 28-61 2-30 (120)
51 TIGR03422 mito_frataxin fratax 23.3 57 0.0012 21.2 1.5 40 44-83 31-75 (97)
52 TIGR00717 rpsA ribosomal prote 23.2 3.7E+02 0.0081 21.5 6.5 50 7-62 318-387 (516)
53 cd04472 S1_PNPase S1_PNPase: P 22.9 1.5E+02 0.0032 16.3 4.2 29 30-63 1-29 (68)
54 PF08696 Dna2: DNA replication 22.8 3E+02 0.0065 19.8 7.8 61 11-77 9-69 (209)
55 PRK00249 flgH flagellar basal 22.4 62 0.0013 24.0 1.8 17 4-21 61-77 (222)
56 COG3269 Predicted RNA-binding 22.2 68 0.0015 20.2 1.6 18 7-25 46-63 (73)
57 PRK12700 flgH flagellar basal 22.0 66 0.0014 24.1 1.8 17 4-21 68-84 (230)
58 PF08206 OB_RNB: Ribonuclease 21.8 78 0.0017 18.2 1.8 10 11-20 35-44 (58)
59 PRK12698 flgH flagellar basal 21.7 69 0.0015 23.8 1.9 17 4-21 61-77 (224)
60 PF13098 Thioredoxin_2: Thiore 21.4 1.1E+02 0.0025 18.5 2.6 23 56-79 83-105 (112)
61 PF01491 Frataxin_Cyay: Fratax 20.8 42 0.00091 22.0 0.5 40 44-83 34-78 (109)
62 cd02799 tRNA_bind_EMAP-II_like 20.6 1.3E+02 0.0028 19.1 2.8 29 46-74 73-105 (105)
63 PRK12699 flgH flagellar basal 20.1 75 0.0016 24.1 1.8 18 4-22 85-102 (246)
No 1
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.9e-41 Score=227.63 Aligned_cols=86 Identities=31% Similarity=0.494 Sum_probs=83.9
Q ss_pred CCCcceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhh
Q 037036 1 ASNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPE 80 (87)
Q Consensus 1 g~~~~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~e 80 (87)
|++|+||.+ ||+|++|||++.|...+||||+++||||||+++++|+||++|+|||||+||+|++++|+||||||||++|
T Consensus 27 g~~r~~A~v-GD~ivvsVKka~P~~~vKkg~V~~AViVRtkk~~rR~DGs~i~FddNA~Viin~~g~P~GtrI~GPVaRE 105 (122)
T COG0093 27 GSRRRYAGV-GDIIVVSVKKAIPRGMVKKGDVVKAVVVRTKKEVRRPDGSYIKFDDNAAVIINPDGEPRGTRIFGPVARE 105 (122)
T ss_pred cccccccCC-CCEEEEEEeeccCCcceeccceEEEEEEEeCCceEcCCCCEEEeCCceEEEECCCCCcccceEecchhHH
Confidence 577889999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCC
Q 037036 81 IDKVEFY 87 (87)
Q Consensus 81 lr~kk~~ 87 (87)
||+++|+
T Consensus 106 lr~~~~~ 112 (122)
T COG0093 106 LRERGFM 112 (122)
T ss_pred HHhcCCc
Confidence 9999985
No 2
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=6.3e-39 Score=218.73 Aligned_cols=86 Identities=44% Similarity=0.733 Sum_probs=83.2
Q ss_pred CCCcceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhh
Q 037036 1 ASNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPE 80 (87)
Q Consensus 1 g~~~~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~e 80 (87)
|+++++|++ ||+|+||||++.|+++++|||+++|||||||++++|+||++++|||||+||||++++|+||||+||||+|
T Consensus 27 ~~~~~~a~v-GD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~~~~r~dG~~i~F~~Na~VLin~~~~p~GTrI~Gpv~~e 105 (122)
T CHL00057 27 ASNRKYAHI-GDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCKELKRDNGMIIRFDDNAAVVIDQEGNPKGTRVFGPIARE 105 (122)
T ss_pred CCCCccccC-CCEEEEEEEeccCCCceecCCEEEEEEEEeccccCcCCCcEEEcCCceEEEECCCCCEeEeEEEccchHH
Confidence 357789999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCC
Q 037036 81 IDKVEFY 87 (87)
Q Consensus 81 lr~kk~~ 87 (87)
||+++|+
T Consensus 106 lr~k~~~ 112 (122)
T CHL00057 106 LREKNFT 112 (122)
T ss_pred HhhcCCe
Confidence 9999985
No 3
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=7.9e-39 Score=218.18 Aligned_cols=86 Identities=31% Similarity=0.502 Sum_probs=83.1
Q ss_pred CCCcceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhh
Q 037036 1 ASNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPE 80 (87)
Q Consensus 1 g~~~~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~e 80 (87)
|+++++|++ ||+|+||||++.|+++++|||+++|||||||++++|.||++++|||||+||||++++|+|||||||||+|
T Consensus 27 ~~~~~~a~i-GD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~dNavVLin~~~~p~GTrI~Gpv~~e 105 (122)
T PRK05483 27 GSKRRYASI-GDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKKGVRRPDGSYIRFDDNAAVLLNNDGEPRGTRIFGPVARE 105 (122)
T ss_pred CCCCCcccc-CCEEEEEEEEcCCCCcccCCCEeeEEEEEeccceecCCCCEEEcCCCEEEEECCCCCEeEeEEeccchHH
Confidence 357789999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCC
Q 037036 81 IDKVEFY 87 (87)
Q Consensus 81 lr~kk~~ 87 (87)
||+++|+
T Consensus 106 lr~~~~~ 112 (122)
T PRK05483 106 LRDKKFM 112 (122)
T ss_pred HhhcCCc
Confidence 9998885
No 4
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=100.00 E-value=2e-38 Score=216.14 Aligned_cols=86 Identities=34% Similarity=0.516 Sum_probs=83.0
Q ss_pred CCCcceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhh
Q 037036 1 ASNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPE 80 (87)
Q Consensus 1 g~~~~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~e 80 (87)
++++++|.+ ||+|+||||++.|++++++||+++|||||||++++|.||++++|||||+||+|++++|+||||+||||+|
T Consensus 27 ~~~~~~a~i-GD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~~Na~VLin~~~~p~GTrI~Gpv~~e 105 (122)
T TIGR01067 27 GSRRRYATV-GDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKKGVRRKDGSYIRFDDNACVLINKNKEPRGTRIFGPVARE 105 (122)
T ss_pred CCCCCcccc-CCEEEEEEEEcCCCCccccccEEEEEEEEeecceEeCCCCEEECCCceEEEECCCCCEeeeEEEccchHH
Confidence 356789999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCC
Q 037036 81 IDKVEFY 87 (87)
Q Consensus 81 lr~kk~~ 87 (87)
||+++|+
T Consensus 106 lr~~~~~ 112 (122)
T TIGR01067 106 LRDKGFM 112 (122)
T ss_pred HhhcCCc
Confidence 9999885
No 5
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=2.1e-37 Score=222.66 Aligned_cols=85 Identities=13% Similarity=0.301 Sum_probs=82.4
Q ss_pred CCcceeeecCCE----EEEEEEccCC------CCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeee
Q 037036 2 SNRRYAHILRNV----FVVVIKKAIP------KMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGN 71 (87)
Q Consensus 2 ~~~~~a~i~GD~----I~vsVkk~~~------~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~Gt 71 (87)
+++++|+| ||+ |+||||++.| ++++|||||++|||||||++++|+||++++||||||||||++++|+||
T Consensus 84 ~~rr~A~I-GDi~~~~IvVsVKka~P~~~~~~~~kVKKG~V~kAVIVRTKK~irR~DGs~IrFDdNAaVLIN~qgePlGT 162 (188)
T PTZ00320 84 TAERFAHC-RVFPAVAHRVSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRRQTNTRMSGLQTNFDRNTCILMNDQRVPLGT 162 (188)
T ss_pred cCCCceee-ccccCceEEEEEeecccCccccccCceecCCEEEEEEEEECcccCCCCCCEEEeCCcEEEEECCCCCEeee
Confidence 46799999 999 9999999999 789999999999999999999999999999999999999999999999
Q ss_pred EEeccchhhhhcccCC
Q 037036 72 SSFWCGRPEIDKVEFY 87 (87)
Q Consensus 72 RI~Gpv~~elr~kk~~ 87 (87)
||||||++|||+++|+
T Consensus 163 RIfGPVaRELR~k~f~ 178 (188)
T PTZ00320 163 RVMYCAGRHVNHKYHL 178 (188)
T ss_pred EEecchhHHHhhcCCc
Confidence 9999999999999985
No 6
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=2.4e-36 Score=209.97 Aligned_cols=78 Identities=18% Similarity=0.287 Sum_probs=74.8
Q ss_pred ceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhhhhcc
Q 037036 5 RYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPEIDKV 84 (87)
Q Consensus 5 ~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~elr~k 84 (87)
++|.+ ||+|+||||++.| +++||+++|||||||++++|+||++++|||||+||||++++|+|||||||||+|| ++
T Consensus 52 ~~a~i-GD~IvvsVKk~~p---~~kg~V~kAVIVRtKk~~rR~dGs~i~F~dNA~VLin~~~~p~GTRI~GpV~rEl-~~ 126 (139)
T PTZ00054 52 PSASL-GDMVLATVKKGKP---ELRKKVLNAVIIRQRKAWRRKDGVFIYFEDNAGVIVNPKGEMKGSAITGPVAKEC-AD 126 (139)
T ss_pred ccccc-CCEEEEEEEECCC---cccCCEeeEEEEEECcceEcCCCcEEEeCCcEEEEECCCCCEeeeEEeCchhHHH-Hh
Confidence 58999 9999999999999 6799999999999999999999999999999999999999999999999999999 66
Q ss_pred cCC
Q 037036 85 EFY 87 (87)
Q Consensus 85 k~~ 87 (87)
+|+
T Consensus 127 ~~~ 129 (139)
T PTZ00054 127 LWP 129 (139)
T ss_pred Ccc
Confidence 774
No 7
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=100.00 E-value=2.6e-36 Score=208.07 Aligned_cols=78 Identities=19% Similarity=0.282 Sum_probs=74.8
Q ss_pred ceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhhhhcc
Q 037036 5 RYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPEIDKV 84 (87)
Q Consensus 5 ~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~elr~k 84 (87)
++|.+ ||+|+||||++.| +++||+++|||||||++++|+||++++|||||+||||++++|+|||||||||+|| ++
T Consensus 44 ~~a~i-GD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs~i~FddNa~VLin~~~~P~GTRI~GpV~rEl-~~ 118 (131)
T TIGR03673 44 PCAGV-GDMVVVSVKKGTP---EMRKQVFKAVVVRQRKEYRRPDGTRVKFEDNAVVIVTPDGEPKGTEIKGPVAREA-AE 118 (131)
T ss_pred Ccccc-CCEEEEEEEECCc---cccCCEeEEEEEEeCcceecCCCcEEEeCCcEEEEECCCCCEeeeEEEccchHHH-Hh
Confidence 67999 9999999999999 6799999999999999999999999999999999999999999999999999999 66
Q ss_pred cCC
Q 037036 85 EFY 87 (87)
Q Consensus 85 k~~ 87 (87)
+|+
T Consensus 119 ~~~ 121 (131)
T TIGR03673 119 RWP 121 (131)
T ss_pred Ccc
Confidence 775
No 8
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=4.2e-36 Score=207.25 Aligned_cols=78 Identities=18% Similarity=0.253 Sum_probs=74.5
Q ss_pred ceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhhhhcc
Q 037036 5 RYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPEIDKV 84 (87)
Q Consensus 5 ~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~elr~k 84 (87)
++|.+ ||+|+||||++.| +++||+++|||||||++++|+||++++|||||+||||++++|+|||||||||+|| ++
T Consensus 45 ~~a~i-GD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs~i~F~dNa~VLin~~~~p~GTRI~GpV~~El-~~ 119 (132)
T PRK08571 45 PKAGV-GDMVVVSVKKGTP---EMRKQVLRAVVVRQRKEYRRPDGTRVKFEDNAAVIVTPEGTPKGTEIKGPVAREA-AE 119 (132)
T ss_pred Ccccc-CCEEEEEEEECCC---cccCCEeEEEEEEeccceEcCCCcEEEeCCcEEEEECCCCCEeeeEEeccchHHH-hh
Confidence 57999 9999999999999 6799999999999999999999999999999999999999999999999999999 66
Q ss_pred cCC
Q 037036 85 EFY 87 (87)
Q Consensus 85 k~~ 87 (87)
+|+
T Consensus 120 ~~~ 122 (132)
T PRK08571 120 RWP 122 (132)
T ss_pred CCc
Confidence 774
No 9
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=100.00 E-value=5.4e-36 Score=203.76 Aligned_cols=85 Identities=29% Similarity=0.483 Sum_probs=80.4
Q ss_pred CCcceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhhh
Q 037036 2 SNRRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPEI 81 (87)
Q Consensus 2 ~~~~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~el 81 (87)
+++++|++ ||+|+||||++.|+.+++|||+++|||||||++++|.||++++|||||+||+|++++|+||||+||||+||
T Consensus 28 ~~~~~a~v-GD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~~~~r~dg~~i~F~~Na~VLln~~~~p~GtrI~Gpv~~el 106 (122)
T PF00238_consen 28 KRRKYASV-GDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKKPIRRKDGSFIKFDDNAVVLLNKKGNPLGTRIFGPVPREL 106 (122)
T ss_dssp TTTSEE-T-TSEEEEEEEEE-SSSSSTTTEEEEEEEEECSSEEETTTSEEEEESSEEEEEEETTSSBSSSSBCSEEEHHH
T ss_pred cCcccccc-ceEEEEEEeecccCccccccceEEEEEEEEeEEEEEeCCcEEEeCCccEEEEcCCCCEeeeEEEeeehHHh
Confidence 46789999 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccCC
Q 037036 82 DKVEFY 87 (87)
Q Consensus 82 r~kk~~ 87 (87)
|+++|+
T Consensus 107 r~~~~~ 112 (122)
T PF00238_consen 107 RKKKFP 112 (122)
T ss_dssp HHTTSH
T ss_pred hHcCCc
Confidence 998884
No 10
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=7.7e-24 Score=147.99 Aligned_cols=80 Identities=20% Similarity=0.334 Sum_probs=76.9
Q ss_pred ceeeecCCEEEEEEEc--cCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhhhh
Q 037036 5 RYAHILRNVFVVVIKK--AIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPEID 82 (87)
Q Consensus 5 ~~a~i~GD~I~vsVkk--~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~elr 82 (87)
.+|.+ ||+++++||+ ..|..++|.|+++.|+|||++++..|.||+++.|+|||+|++|+.++|.||+|+|||++|++
T Consensus 53 ~~A~~-GD~vva~vKka~~~Pe~r~k~g~~~~avvVr~~k~~~r~dgs~~~f~dnA~v~~~~~~e~~gs~i~G~v~~e~~ 131 (145)
T KOG0901|consen 53 PAAGV-GDMVVATVKKAHGKPELRKKVGEVLPAVVVRQKKSKRRKDGSIAYFEDNAGVIVNNKGEPKGSAITGPVGKELA 131 (145)
T ss_pred cCCCc-CCEEEEEEecccCCCccCcEecccceeeEEeeccccccCCCcEEEEcCceEEEEcccCccccceeccccChhHh
Confidence 37899 9999999999 79999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccC
Q 037036 83 KVEF 86 (87)
Q Consensus 83 ~kk~ 86 (87)
. .|
T Consensus 132 ~-~~ 134 (145)
T KOG0901|consen 132 D-LW 134 (145)
T ss_pred h-hh
Confidence 7 54
No 11
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=99.50 E-value=4.1e-14 Score=97.90 Aligned_cols=65 Identities=14% Similarity=0.196 Sum_probs=57.4
Q ss_pred cceeeecCCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccchhhhh
Q 037036 4 RRYAHILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCGRPEID 82 (87)
Q Consensus 4 ~~~a~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv~~elr 82 (87)
+..+.+ ||.|+|+| |||..+|+||..+.. ++.|. .+||+|.+|||+++|+|+||||.-|||..||
T Consensus 66 rgvg~~-GDkiLvAI----------kGQmkKa~vVGh~~~--~k~~~-P~fDsNniVLiddnGnPlGtRI~~PIPT~Lr 130 (149)
T KOG3441|consen 66 RGVGEL-GDKILVAI----------KGQMKKAYVVGHVHY--RKHGV-PVFDSNNIVLIDDNGNPLGTRITAPIPTKLR 130 (149)
T ss_pred cccccc-ccEEEEEE----------ecceeeeEEEEeecc--CCCCC-cccCCCcEEEECCCCCcccceEeccCcHHHH
Confidence 446788 99999999 799999999997654 44454 6999999999999999999999999999998
No 12
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=67.68 E-value=9.5 Score=22.22 Aligned_cols=30 Identities=13% Similarity=0.083 Sum_probs=24.9
Q ss_pred eeceecCCCeeEEecCceEEEECCCCCeee
Q 037036 41 CTNLRRDNGIIIAYDDSTTAVIHQKEKFEG 70 (87)
Q Consensus 41 k~~~~r~dG~~i~F~~Na~VLl~~~~~p~G 70 (87)
-..++++||.+.-+...+.++-+++|+|..
T Consensus 57 e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~ 86 (91)
T PF08447_consen 57 EYRIRRKDGEYRWIEVRGRPIFDENGKPIR 86 (91)
T ss_dssp EEEEEGTTSTEEEEEEEEEEEETTTS-EEE
T ss_pred EEEEECCCCCEEEEEEEEEEEECCCCCEEE
Confidence 344778999999999999999999999863
No 13
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=66.07 E-value=18 Score=20.91 Aligned_cols=33 Identities=15% Similarity=0.290 Sum_probs=24.1
Q ss_pred CccccCeeEEEEEeeeeceecCCCeeEEecCceEEEEC
Q 037036 26 PLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIH 63 (87)
Q Consensus 26 kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~ 63 (87)
|.+.|+++.|.|.+-. .+|.++.+.++.-.++-
T Consensus 1 k~~~G~iv~g~V~~v~-----~~g~~V~l~~~~~g~ip 33 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVE-----DFGVFVDLGNGIEGFIP 33 (74)
T ss_dssp -SSTTSEEEEEEEEEE-----TTEEEEEESTSSEEEEE
T ss_pred CCCCCCEEEEEEEEEE-----CCEEEEEECCcEEEEEE
Confidence 4577999999998744 37889999866666554
No 14
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=55.89 E-value=25 Score=22.03 Aligned_cols=29 Identities=7% Similarity=0.122 Sum_probs=22.1
Q ss_pred CCCeeEEe-cCceEEEECCCCCeeeeEEec
Q 037036 47 DNGIIIAY-DDSTTAVIHQKEKFEGNSSFW 75 (87)
Q Consensus 47 ~dG~~i~F-~~Na~VLl~~~~~p~GtRI~G 75 (87)
.||....+ ..|-+.|.|.++..+|+.+.-
T Consensus 20 ~DG~l~~~~~~~kv~Lyde~~~~i~~~~~~ 49 (83)
T PF10382_consen 20 HDGFLKYHSFNKKVMLYDEDGNLIGSDFLK 49 (83)
T ss_pred ECCEEEEEeCCCEEEEEcCCCCEEeEEEEe
Confidence 48875333 267799999999999998753
No 15
>PF03864 Phage_cap_E: Phage major capsid protein E; InterPro: IPR005564 This entry is represented by Bacteriophage lambda, GpE. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Major capsid protein E plays a role in the stabilisation of the condensed form of the DNA molecule in phage heads [].; PDB: 3BQW_A.
Probab=44.11 E-value=74 Score=23.48 Aligned_cols=47 Identities=11% Similarity=0.108 Sum_probs=20.6
Q ss_pred eeEEEEEeeee-ceecC-CCeeE-EecCceEEEECCCCCeeeeEEeccchhh
Q 037036 32 VFTTLIVCTCT-NLRRD-NGIII-AYDDSTTAVIHQKEKFEGNSSFWCGRPE 80 (87)
Q Consensus 32 v~~AvIVrtk~-~~~r~-dG~~i-~F~~Na~VLl~~~~~p~GtRI~Gpv~~e 80 (87)
.+.++++..-- .+... ||... .+.+|.++++-. ..+|...+||++.+
T Consensus 232 ~~~g~~i~~y~~~y~~~~~G~~~~~i~~~~~~~~p~--~~~g~~~~g~~~~~ 281 (329)
T PF03864_consen 232 TFGGVLIVVYDGTYIDYDDGTSKRFIPDDKVVLLPD--GGLGKTYYGPTDEE 281 (329)
T ss_dssp EEEEEEEEEE--EEE-T-T--EEESS-TTEEEEE-T--T---EEEE------
T ss_pred EEccEEEEEEccEEEecCCCceeeecCCCeEEEEcc--ccCceEEEEecccc
Confidence 34454433332 23333 67655 478999999988 78999999999944
No 16
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=43.13 E-value=55 Score=22.10 Aligned_cols=31 Identities=16% Similarity=0.172 Sum_probs=22.8
Q ss_pred eecCCEEEEEEEccCCCCCccccCeeEEEEEeee
Q 037036 8 HILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTC 41 (87)
Q Consensus 8 ~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk 41 (87)
.+ ||+|.|.++-.. +.=++-|.+.++|+..+
T Consensus 20 ~~-GD~v~V~~~i~e--g~k~R~q~f~GvvI~~~ 50 (113)
T TIGR01024 20 RV-GDTVRVHVKIVE--GKKERIQVFEGVVIARR 50 (113)
T ss_pred CC-CCEEEEEEEEcc--CCceEcccEEEEEEEEe
Confidence 45 999999987543 22336788999999876
No 17
>KOG2449 consensus Methylmalonate semialdehyde dehydrogenase [Amino acid transport and metabolism; Carbohydrate transport and metabolism]
Probab=41.09 E-value=51 Score=23.62 Aligned_cols=55 Identities=22% Similarity=0.288 Sum_probs=39.4
Q ss_pred CCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecC---ceEEEECCCC
Q 037036 11 RNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDD---STTAVIHQKE 66 (87)
Q Consensus 11 GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~---Na~VLl~~~~ 66 (87)
|.++...|-...|++..-+-||+..|.||..... ..|++.|.|++ |++.++..++
T Consensus 64 ~~f~~~tiLsvtP~ms~ykeeI~gpVlv~l~~~t-ldd~I~Iin~nPygn~t~i~Tsn~ 121 (157)
T KOG2449|consen 64 GNFVGPTILSVTPNMSCYKEEIFGPVLVRLETET-LDDAIFIINNNPYGNGTAIFTSNG 121 (157)
T ss_pred CCcccceEEEecCCcceeHhhhhcceEEEEeecC-CCceeEEEecCCCCceeEEEecCc
Confidence 3444444444689999999999999999976543 56788888875 6666666543
No 18
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=39.73 E-value=68 Score=18.72 Aligned_cols=23 Identities=22% Similarity=0.469 Sum_probs=17.9
Q ss_pred ecCCCe-eEEecCceEEEECCCCC
Q 037036 45 RRDNGI-IIAYDDSTTAVIHQKEK 67 (87)
Q Consensus 45 ~r~dG~-~i~F~~Na~VLl~~~~~ 67 (87)
+..||. .+.|+|.+=+++.+.+.
T Consensus 10 ~LSng~vqv~FnD~tkivl~~~~~ 33 (68)
T PF00659_consen 10 QLSNGTVQVNFNDHTKIVLSPDGR 33 (68)
T ss_dssp EETTSEEEEEETTS-EEEEETTCC
T ss_pred EEeCCCEEEEEeCCCEEEECCCCC
Confidence 567885 58899999999988765
No 19
>PF11429 Colicin_D: Colicin D; InterPro: IPR024440 Colicin D is a bacteriocin that kills target cells by cleaving tRNA(Arg). This entry represents a domain found in the C terminus of colicin D, which is responsible for its catalytic activity []. The domain is also found in some S-type pyocins, which are also bacteriocins.; GO: 0004540 ribonuclease activity; PDB: 1TFO_A 1V74_A 1TFK_A.
Probab=38.32 E-value=54 Score=21.46 Aligned_cols=28 Identities=14% Similarity=0.322 Sum_probs=19.3
Q ss_pred eecCCCeeEEe--cCceEEEECCCCCeeee
Q 037036 44 LRRDNGIIIAY--DDSTTAVIHQKEKFEGN 71 (87)
Q Consensus 44 ~~r~dG~~i~F--~~Na~VLl~~~~~p~Gt 71 (87)
+++..++.+.| ..|-+|+++.+|+.+.-
T Consensus 46 Yr~~~~skV~~N~~T~~~Vi~d~~G~Fvsg 75 (92)
T PF11429_consen 46 YRRVKDSKVYFNPKTNNVVIIDKDGNFVSG 75 (92)
T ss_dssp ETTSTT-EEEEETTTTEEEEE-TTS-EEEE
T ss_pred eecCCCcEEEEeCCCCeEEEEcCCCCEEEE
Confidence 34455899999 77889999999998843
No 20
>COG1443 Idi Isopentenyldiphosphate isomerase [Lipid metabolism]
Probab=38.19 E-value=21 Score=26.27 Aligned_cols=14 Identities=7% Similarity=0.254 Sum_probs=12.6
Q ss_pred eEEEECCCCCeeee
Q 037036 58 TTAVIHQKEKFEGN 71 (87)
Q Consensus 58 a~VLl~~~~~p~Gt 71 (87)
-|||+|.+++|.|+
T Consensus 5 ~vill~~~d~~~G~ 18 (185)
T COG1443 5 DVILLNDDDVPTGT 18 (185)
T ss_pred eEEEECCCCCcccc
Confidence 48899999999997
No 21
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=37.34 E-value=66 Score=21.51 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=23.6
Q ss_pred eecCCEEEEEEEccCCCCCccccCeeEEEEEeeee
Q 037036 8 HILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCT 42 (87)
Q Consensus 8 ~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~ 42 (87)
.+ ||+|.|.++....+ =.+-+.+.++++.-+.
T Consensus 20 ~~-GD~v~V~~~i~e~~--k~r~q~f~GvvIa~~~ 51 (113)
T PF01245_consen 20 RV-GDTVRVTYKISEGN--KERIQVFEGVVIARRR 51 (113)
T ss_dssp SS-SSEEEEEEEEESSS--SEEEEEEEEEEEEEEB
T ss_pred CC-CCEEEEEEEEecCC--CceeEEEEEEEEEEEC
Confidence 45 99999999765322 1356899999998765
No 22
>PF04773 FecR: FecR protein; InterPro: IPR006860 FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.
Probab=36.63 E-value=82 Score=18.80 Aligned_cols=29 Identities=7% Similarity=0.158 Sum_probs=20.0
Q ss_pred eceecCCCeeEEecCceEEEECCCCCeee
Q 037036 42 TNLRRDNGIIIAYDDSTTAVIHQKEKFEG 70 (87)
Q Consensus 42 ~~~~r~dG~~i~F~~Na~VLl~~~~~p~G 70 (87)
..+.-.||+.+.++.|+.+..........
T Consensus 11 ~~i~l~dgs~v~l~~~s~~~~~~~~~~~~ 39 (98)
T PF04773_consen 11 AEIALSDGSRVRLGPNSRVSVDRDSGSEP 39 (98)
T ss_pred EEEEECCCCEEEECCCcEEEEEcccCCCc
Confidence 34566889999999999885555444433
No 23
>PF07481 DUF1521: Domain of Unknown Function (DUF1521); InterPro: IPR011086 This domain of unknown function is found in a limited set of Bradyrhizobium proteins. There appears to be a periodic -DG- motif in the domain.
Probab=35.38 E-value=78 Score=23.00 Aligned_cols=35 Identities=14% Similarity=0.147 Sum_probs=26.7
Q ss_pred eceecCCCeeEEecCc-eEEEECCCCCeeeeEEecc
Q 037036 42 TNLRRDNGIIIAYDDS-TTAVIHQKEKFEGNSSFWC 76 (87)
Q Consensus 42 ~~~~r~dG~~i~F~~N-a~VLl~~~~~p~GtRI~Gp 76 (87)
..+...|+..|.++++ +.++|.++....=|||.|=
T Consensus 10 ati~lgd~Y~I~~~e~ds~~~itnk~tG~~TriwGD 45 (171)
T PF07481_consen 10 ATIDLGDGYTIEANEKDSEWTITNKQTGETTRIWGD 45 (171)
T ss_pred eEEecCCceEEEecCCcceEEEecCCCCcEeEEeCC
Confidence 3456689999999994 6777777767777888873
No 24
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=34.04 E-value=99 Score=20.94 Aligned_cols=31 Identities=13% Similarity=0.097 Sum_probs=21.7
Q ss_pred eecCCEEEEEEEccCCCCCccccCeeEEEEEeee
Q 037036 8 HILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTC 41 (87)
Q Consensus 8 ~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk 41 (87)
.+ ||+|.|.++-... .=++-|.+.++|+..+
T Consensus 20 ~~-GD~V~V~~~i~eg--~k~R~q~f~GvvI~~~ 50 (116)
T PRK05338 20 RP-GDTVRVHVKVVEG--NKERIQAFEGVVIARR 50 (116)
T ss_pred CC-CCEEEEEEEEccC--CceEeccEEEEEEEEe
Confidence 45 9999998864322 1124678999999876
No 25
>CHL00084 rpl19 ribosomal protein L19
Probab=33.37 E-value=98 Score=21.01 Aligned_cols=31 Identities=6% Similarity=0.053 Sum_probs=21.7
Q ss_pred eecCCEEEEEEEccCCCCCccccCeeEEEEEeee
Q 037036 8 HILRNVFVVVIKKAIPKMPLEVSDVFTTLIVCTC 41 (87)
Q Consensus 8 ~i~GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk 41 (87)
.+ ||+|.|.++-...+ =++-|.+.++|+..+
T Consensus 24 ~~-GDtV~V~~~i~eg~--k~R~q~F~GvvI~~r 54 (117)
T CHL00084 24 RV-GDTVKVGVLIQEGN--KERVQFYEGTVIAKK 54 (117)
T ss_pred CC-CCEEEEEEEEecCC--eeEeceEEEEEEEEe
Confidence 46 99999998543321 135678999999865
No 26
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=32.80 E-value=47 Score=25.46 Aligned_cols=29 Identities=7% Similarity=0.234 Sum_probs=23.9
Q ss_pred cCeeEEEEEeeeeceecCCCeeEEecCce
Q 037036 30 SDVFTTLIVCTCTNLRRDNGIIIAYDDST 58 (87)
Q Consensus 30 g~v~~AvIVrtk~~~~r~dG~~i~F~~Na 58 (87)
|||..|+||..|..-+.+---++.|.|-.
T Consensus 37 GeI~eavvitd~~t~rskGyGfVTf~d~~ 65 (247)
T KOG0149|consen 37 GEIVEAVVITDKNTGRSKGYGFVTFRDAE 65 (247)
T ss_pred CceEEEEEEeccCCccccceeeEEeecHH
Confidence 99999999999887776666689998743
No 27
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=31.85 E-value=1.9e+02 Score=23.58 Aligned_cols=51 Identities=12% Similarity=0.143 Sum_probs=37.2
Q ss_pred eecCCEEEEEEEccCCC--------------------CCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECC
Q 037036 8 HILRNVFVVVIKKAIPK--------------------MPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQ 64 (87)
Q Consensus 8 ~i~GD~I~vsVkk~~~~--------------------~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~ 64 (87)
.+ ||.|.+.|....+. ..++.|+++.+.|++... .|.++.++++-..++..
T Consensus 420 ~~-Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~~v~~-----~G~fV~l~~gi~g~i~~ 490 (565)
T PRK06299 420 KK-GDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKD-----KGAFVELEDGVEGLIRA 490 (565)
T ss_pred CC-CCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEEEEec-----CceEEecCCCcEEEEEH
Confidence 56 99998887665431 135789999999988653 48999998776666653
No 28
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=31.55 E-value=61 Score=21.99 Aligned_cols=25 Identities=8% Similarity=0.352 Sum_probs=16.1
Q ss_pred eeEEEEEeeeeceecCCCeeEEecCce
Q 037036 32 VFTTLIVCTCTNLRRDNGIIIAYDDST 58 (87)
Q Consensus 32 v~~AvIVrtk~~~~r~dG~~i~F~~Na 58 (87)
-++|+|+.+.. ...+...++|+|+.
T Consensus 88 FY~A~V~~~p~--~~~~~y~l~Fedd~ 112 (130)
T PF07039_consen 88 FYPATVVSPPK--KKSGEYKLKFEDDE 112 (130)
T ss_dssp EEEEEEEEE-S--STTS-EEEEECTTT
T ss_pred EEEEEEEeCCC--CCCCcEEEEEeCCC
Confidence 35677888733 45556779999864
No 29
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=31.42 E-value=47 Score=20.37 Aligned_cols=26 Identities=19% Similarity=0.065 Sum_probs=18.8
Q ss_pred eEEecCceEEEECCCCCeeee--EEeccchh
Q 037036 51 IIAYDDSTTAVIHQKEKFEGN--SSFWCGRP 79 (87)
Q Consensus 51 ~i~F~~Na~VLl~~~~~p~Gt--RI~Gpv~~ 79 (87)
..+| |+. +.+++.+.+|. .|||||..
T Consensus 23 ~P~~--n~~-V~~~~~~~IGkV~dIfGPV~~ 50 (73)
T PRK13149 23 QPPI--GSV-VYDKKLKKIGKVVDVFGPVKE 50 (73)
T ss_pred CCCC--CCE-eECCCCCEeEEEEEEECCCCC
Confidence 3455 443 48888899997 68999864
No 30
>PF04170 NlpE: NlpE N-terminal domain; InterPro: IPR007298 This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway []. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. NlpE from Escherichia coli and Salmonella typhi is also known to confer copper tolerance in copper-sensitive strains of E. coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [].; PDB: 3LHN_A 2Z4I_B 2Z4H_A.
Probab=31.17 E-value=68 Score=19.97 Aligned_cols=22 Identities=5% Similarity=0.046 Sum_probs=14.9
Q ss_pred CCeeEEecCceEEEECCCCCee
Q 037036 48 NGIIIAYDDSTTAVIHQKEKFE 69 (87)
Q Consensus 48 dG~~i~F~~Na~VLl~~~~~p~ 69 (87)
+..+.+-++|...+||.+|+|+
T Consensus 62 ~~~~f~v~~~~L~~Ld~~G~~i 83 (87)
T PF04170_consen 62 DKRYFKVGENSLEMLDQDGNPI 83 (87)
T ss_dssp TCEEEEEETTEEEEE-TTS-B-
T ss_pred CEEEEEECCCEEEEECCCCCcC
Confidence 3456677899999999988764
No 31
>COG0824 FcbC Predicted thioesterase [General function prediction only]
Probab=31.09 E-value=1.6e+02 Score=19.51 Aligned_cols=16 Identities=25% Similarity=0.331 Sum_probs=10.4
Q ss_pred ceeeecCCEEEEEEEcc
Q 037036 5 RYAHILRNVFVVVIKKA 21 (87)
Q Consensus 5 ~~a~i~GD~I~vsVkk~ 21 (87)
+.+.. ||.+.|...-.
T Consensus 68 ~p~~~-~d~l~v~~~v~ 83 (137)
T COG0824 68 RPARL-GDVLTVRTRVE 83 (137)
T ss_pred CCccC-CCEEEEEEEEE
Confidence 45666 77777776544
No 32
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=31.08 E-value=1.2e+02 Score=18.02 Aligned_cols=33 Identities=12% Similarity=0.157 Sum_probs=24.2
Q ss_pred CccccCeeEEEEEeeeeceecCCCeeEEecCceEEEEC
Q 037036 26 PLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIH 63 (87)
Q Consensus 26 kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~ 63 (87)
.++.|+++.|.|.+.. ..|.++.+.++.-.++.
T Consensus 11 ~~~~G~i~~g~V~~v~-----~~G~fv~l~~~~~g~v~ 43 (83)
T cd04461 11 DLKPGMVVHGYVRNIT-----PYGVFVEFLGGLTGLAP 43 (83)
T ss_pred hCCCCCEEEEEEEEEe-----eceEEEEcCCCCEEEEE
Confidence 3678889988888755 46888888776666654
No 33
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=30.29 E-value=1.2e+02 Score=17.92 Aligned_cols=15 Identities=0% Similarity=0.288 Sum_probs=10.9
Q ss_pred eecCCEEEEEEEccCC
Q 037036 8 HILRNVFVVVIKKAIP 23 (87)
Q Consensus 8 ~i~GD~I~vsVkk~~~ 23 (87)
.. ||+|.+.|.+...
T Consensus 5 ~~-GdiV~G~V~~v~~ 19 (82)
T cd04454 5 DV-GDIVIGIVTEVNS 19 (82)
T ss_pred CC-CCEEEEEEEEEcC
Confidence 55 8888888876644
No 34
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=29.92 E-value=52 Score=18.56 Aligned_cols=21 Identities=10% Similarity=0.033 Sum_probs=14.6
Q ss_pred ecCceEEEECCCCCeeeeEEe
Q 037036 54 YDDSTTAVIHQKEKFEGNSSF 74 (87)
Q Consensus 54 F~~Na~VLl~~~~~p~GtRI~ 74 (87)
-++|-+++++++|+.+=-+..
T Consensus 3 i~~~~aiVlT~dGeF~~ik~~ 23 (56)
T PF12791_consen 3 IKKKYAIVLTPDGEFIKIKRK 23 (56)
T ss_pred CcCCEEEEEcCCCcEEEEeCC
Confidence 367888999998886544333
No 35
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=29.62 E-value=39 Score=25.57 Aligned_cols=19 Identities=21% Similarity=0.555 Sum_probs=15.2
Q ss_pred cceeeecCCEEEEEEEccCC
Q 037036 4 RRYAHILRNVFVVVIKKAIP 23 (87)
Q Consensus 4 ~~~a~i~GD~I~vsVkk~~~ 23 (87)
+|...| ||+|.|.|++-..
T Consensus 69 ~RA~~v-GDilTV~i~E~~~ 87 (230)
T COG2063 69 RRASNV-GDILTIVIQENTS 87 (230)
T ss_pred cccccC-CCEEEEEEEeccc
Confidence 566788 9999999987543
No 36
>TIGR03711 acc_sec_asp3 accessory Sec system protein Asp3. This protein is designated Asp3 because, along with SecY2, SecA2, and other proteins it is part of the accessory Sec system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown.
Probab=29.21 E-value=51 Score=22.96 Aligned_cols=27 Identities=7% Similarity=0.113 Sum_probs=22.9
Q ss_pred CCeeEEecCceEEEECCCCCeeeeEEe
Q 037036 48 NGIIIAYDDSTTAVIHQKEKFEGNSSF 74 (87)
Q Consensus 48 dG~~i~F~~Na~VLl~~~~~p~GtRI~ 74 (87)
=|+.|+|.++.-|...+..-|-||.|.
T Consensus 15 YGs~i~f~~~~~V~feN~lMpsG~~I~ 41 (135)
T TIGR03711 15 YGTTVKFLSDNEVYFENPLMPSGETIH 41 (135)
T ss_pred cccEEEEccCCcEEEeccCCCCCCEEE
Confidence 389999988888888888889999875
No 37
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=27.96 E-value=49 Score=21.88 Aligned_cols=25 Identities=8% Similarity=-0.049 Sum_probs=21.4
Q ss_pred ceEEEECCCCCeeeeEEeccchhhh
Q 037036 57 STTAVIHQKEKFEGNSSFWCGRPEI 81 (87)
Q Consensus 57 Na~VLl~~~~~p~GtRI~Gpv~~el 81 (87)
+|+.++|.+|+++=.|-+.+++.+-
T Consensus 3 ~~i~i~n~~G~~i~~k~y~~~~~~~ 27 (141)
T PF01217_consen 3 KAILILNSQGKRILSKYYRDVSEEE 27 (141)
T ss_dssp EEEEEEETTSEEEEEEESSTSTSHH
T ss_pred EEEEEEcCCCCEEEehhcCCccHHH
Confidence 4789999999999999998887544
No 38
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=27.90 E-value=68 Score=23.33 Aligned_cols=37 Identities=14% Similarity=-0.021 Sum_probs=24.8
Q ss_pred ceecCCCeeEEecCceEEEEC-CCCCeeeeEEeccchhh
Q 037036 43 NLRRDNGIIIAYDDSTTAVIH-QKEKFEGNSSFWCGRPE 80 (87)
Q Consensus 43 ~~~r~dG~~i~F~~Na~VLl~-~~~~p~GtRI~Gpv~~e 80 (87)
.+.+-+|+.. -...-..|++ +.....-+|-|||||.|
T Consensus 122 ~lp~~~gcR~-l~~~el~lL~~~~~~SfDsRYfGpipas 159 (173)
T COG4959 122 ALPRWQGCRY-LAPSELLLLTDRSSTSFDSRYFGPIPAS 159 (173)
T ss_pred cCCcccCCce-ecCCeEEEEeccCCcccccceecccCHH
Confidence 3455566654 4444455555 45668999999999986
No 39
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=27.60 E-value=1.2e+02 Score=17.09 Aligned_cols=29 Identities=21% Similarity=0.333 Sum_probs=24.4
Q ss_pred ceecCCCeeEEecCceEEEECCCCCeeee
Q 037036 43 NLRRDNGIIIAYDDSTTAVIHQKEKFEGN 71 (87)
Q Consensus 43 ~~~r~dG~~i~F~~Na~VLl~~~~~p~Gt 71 (87)
...+.||..+-+.=++..+.+.++++.|-
T Consensus 67 ~~~~~~g~~~~~~~~~~~i~~~~g~~~~~ 95 (104)
T PF13426_consen 67 RLRRKDGETFWVEVSASPIRDEDGEITGI 95 (104)
T ss_dssp EEEETTSEEEEEEEEEEEEEETTSSEEEE
T ss_pred EEEcCCCCEEEEEEEEEEEECCCCCEEEE
Confidence 35688999999999999999999887764
No 40
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=27.58 E-value=1.1e+02 Score=16.48 Aligned_cols=29 Identities=17% Similarity=0.278 Sum_probs=17.0
Q ss_pred ccCeeEEEEEeeeeceecCCCeeEEecCceEEEE
Q 037036 29 VSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVI 62 (87)
Q Consensus 29 kg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl 62 (87)
.|+++.|.|++... +|.++.++.+.-.++
T Consensus 2 ~G~~v~g~V~~v~~-----~g~~v~i~~~~~g~l 30 (72)
T smart00316 2 VGDVVEGTVTEITP-----FGAFVDLGNGVEGLI 30 (72)
T ss_pred CCCEEEEEEEEEEc-----cEEEEEeCCCCEEEE
Confidence 46777777776543 466666664433333
No 41
>PF12508 DUF3714: Protein of unknown function (DUF3714) ; InterPro: IPR022187 Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=27.29 E-value=73 Score=23.37 Aligned_cols=44 Identities=9% Similarity=-0.063 Sum_probs=33.2
Q ss_pred ccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEec
Q 037036 29 VSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFW 75 (87)
Q Consensus 29 kg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~G 75 (87)
...-.+|+|=++- .-.||+.+++.=---+.++...-|.||.++|
T Consensus 51 ~~n~I~A~V~~~q---tv~~Gs~vrlRLle~i~i~g~~IPkgt~l~G 94 (200)
T PF12508_consen 51 EKNTIRAVVDGTQ---TVVDGSRVRLRLLEDIQIGGILIPKGTYLYG 94 (200)
T ss_pred CCCeEEEEEecce---EEeCCCEEEEEEcCceEECCEEeCCCCEEEE
Confidence 4567888888874 3467888777655555667788899999999
No 42
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.69 E-value=63 Score=23.49 Aligned_cols=25 Identities=12% Similarity=-0.063 Sum_probs=22.1
Q ss_pred eEEEECCCCCeeeeEEeccchhhhh
Q 037036 58 TTAVIHQKEKFEGNSSFWCGRPEID 82 (87)
Q Consensus 58 a~VLl~~~~~p~GtRI~Gpv~~elr 82 (87)
|+.+.|++|.|.=++..-|+|.|..
T Consensus 4 AvlifNn~gkPRL~KFY~p~~~~~Q 28 (182)
T KOG0936|consen 4 AVLIFNNKGKPRLVKFYTPVDEEKQ 28 (182)
T ss_pred EEEEecCCCCcceeeecCcCChHHH
Confidence 7888999999999999999997643
No 43
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=26.61 E-value=63 Score=21.84 Aligned_cols=43 Identities=23% Similarity=0.274 Sum_probs=32.1
Q ss_pred eeee--ceecCCCeeEEecCceEEEECCCCCeeeeEE-eccchhhh
Q 037036 39 CTCT--NLRRDNGIIIAYDDSTTAVIHQKEKFEGNSS-FWCGRPEI 81 (87)
Q Consensus 39 rtk~--~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI-~Gpv~~el 81 (87)
|+++ ..+|..|..|.+|-||.|++-....|+-|.- +-..|+|+
T Consensus 6 r~rygenrrrdkgv~ie~dcnakvvvats~dpvts~klyfscpyei 51 (122)
T PF05325_consen 6 RMRYGENRRRDKGVPIECDCNAKVVVATSRDPVTSGKLYFSCPYEI 51 (122)
T ss_pred eeecccccccCCCcceeccCCceEEEEeccCCcccceeeecCcccc
Confidence 4444 3467789999999999999998888887753 34555555
No 44
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=25.41 E-value=85 Score=20.01 Aligned_cols=22 Identities=9% Similarity=0.099 Sum_probs=15.7
Q ss_pred eeeecCCEEEEEEEccCCCCCcccc
Q 037036 6 YAHILRNVFVVVIKKAIPKMPLEVS 30 (87)
Q Consensus 6 ~a~i~GD~I~vsVkk~~~~~kvkkg 30 (87)
.+.+ ||+|.+ .+.+|-++-|.-
T Consensus 50 ~~~~-GD~V~I--~e~RPlSKtK~~ 71 (84)
T CHL00142 50 ECNI-GDQVLI--EETRPLSKTKRW 71 (84)
T ss_pred CCCC-CCEEEE--EEcCCCCCcEEE
Confidence 3677 998765 488898866553
No 45
>cd07581 nitrilase_3 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer.
Probab=24.92 E-value=91 Score=22.03 Aligned_cols=16 Identities=13% Similarity=0.059 Sum_probs=13.7
Q ss_pred ceEEEECCCCCeeeeE
Q 037036 57 STTAVIHQKEKFEGNS 72 (87)
Q Consensus 57 Na~VLl~~~~~p~GtR 72 (87)
|++++++++|+.+|..
T Consensus 92 Ns~~~i~~~G~i~~~y 107 (255)
T cd07581 92 NTLVVVGPDGEIIAVY 107 (255)
T ss_pred EeEEEECCCCcEEEEE
Confidence 8999999999887765
No 46
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=24.42 E-value=55 Score=23.23 Aligned_cols=17 Identities=24% Similarity=0.520 Sum_probs=13.4
Q ss_pred cceeeecCCEEEEEEEcc
Q 037036 4 RRYAHILRNVFVVVIKKA 21 (87)
Q Consensus 4 ~~~a~i~GD~I~vsVkk~ 21 (87)
+|.-.+ ||+|.|.|.+.
T Consensus 22 ~rA~~V-GDiiTV~v~E~ 38 (179)
T PF02107_consen 22 RRARRV-GDIITVVVSEN 38 (179)
T ss_pred ccccCC-CCEEEEEEEEc
Confidence 345577 99999999875
No 47
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=24.30 E-value=65 Score=14.29 Aligned_cols=15 Identities=13% Similarity=0.016 Sum_probs=11.4
Q ss_pred CCCeeEEecCceEEE
Q 037036 47 DNGIIIAYDDSTTAV 61 (87)
Q Consensus 47 ~dG~~i~F~~Na~VL 61 (87)
.||.+..|.+|.-+.
T Consensus 1 ~~G~~~~yy~nG~l~ 15 (22)
T PF07661_consen 1 LDGEWKFYYENGKLK 15 (22)
T ss_pred CcceEEEEeCCCCEE
Confidence 478888888887664
No 48
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=24.24 E-value=1.5e+02 Score=16.92 Aligned_cols=24 Identities=13% Similarity=0.242 Sum_probs=17.6
Q ss_pred cccCeeEEEEEeeeeceecCCCeeEEecC
Q 037036 28 EVSDVFTTLIVCTCTNLRRDNGIIIAYDD 56 (87)
Q Consensus 28 kkg~v~~AvIVrtk~~~~r~dG~~i~F~~ 56 (87)
+.|+++.|.|++.. ..|.++.+++
T Consensus 2 ~~G~~~~g~V~~v~-----~~g~~v~l~~ 25 (76)
T cd04452 2 EEGELVVVTVKSIA-----DMGAYVSLLE 25 (76)
T ss_pred CCCCEEEEEEEEEE-----ccEEEEEEcC
Confidence 46888888888764 3677777764
No 49
>TIGR00399 metG_C_term methionyl-tRNA synthetase C-terminal region/beta chain. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (E. coli, B. subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. Proteins hit by this model should called methionyl-tRNA synthetase beta chain if and only if the model metG hits a separate protein not also hit by this model.
Probab=24.01 E-value=67 Score=21.91 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=20.2
Q ss_pred cCCCeeEEecCc--eEEEECCC-CCeeeeEE
Q 037036 46 RDNGIIIAYDDS--TTAVIHQK-EKFEGNSS 73 (87)
Q Consensus 46 r~dG~~i~F~~N--a~VLl~~~-~~p~GtRI 73 (87)
..+||...++++ .++|+... ..|.|+||
T Consensus 106 ~S~GMlls~~~~~~~~~l~~~~~~~~~G~~i 136 (137)
T TIGR00399 106 KSEGMILAAEDDGKVLFLLSPDQEAIAGERI 136 (137)
T ss_pred EeccEEEEEecCCCeEEEecCCCCCCCcCCc
Confidence 567888777654 47777754 56999987
No 50
>PRK07252 hypothetical protein; Provisional
Probab=23.36 E-value=2.2e+02 Score=18.84 Aligned_cols=29 Identities=21% Similarity=0.333 Sum_probs=16.4
Q ss_pred cccCeeEEEEEeeeeceecCCCeeEEecCceEEE
Q 037036 28 EVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAV 61 (87)
Q Consensus 28 kkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VL 61 (87)
+.|+++.|.|+... ..|.++.+++....|
T Consensus 2 kvG~iv~G~V~~V~-----~~G~fVei~~~~~Gl 30 (120)
T PRK07252 2 KIGDKLKGTITGIK-----PYGAFVALENGTTGL 30 (120)
T ss_pred CCCCEEEEEEEEEe-----CcEEEEEECCCCEEE
Confidence 34667777776653 356666665443333
No 51
>TIGR03422 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately.
Probab=23.30 E-value=57 Score=21.18 Aligned_cols=40 Identities=13% Similarity=0.120 Sum_probs=27.8
Q ss_pred eecCCCe-eEEecCceEEEECCCCC----eeeeEEeccchhhhhc
Q 037036 44 LRRDNGI-IIAYDDSTTAVIHQKEK----FEGNSSFWCGRPEIDK 83 (87)
Q Consensus 44 ~~r~dG~-~i~F~~Na~VLl~~~~~----p~GtRI~Gpv~~elr~ 83 (87)
.-..+|. .|.|++.+.++||+|-- =+.+.+.||--....+
T Consensus 31 ~e~~~gVLti~~~~~~~~VINkQ~p~~QIWlsSp~sGp~hfd~~~ 75 (97)
T TIGR03422 31 VEYSSGVLTLELPSVGTYVINKQPPNKQIWLSSPVSGPKRYDYVN 75 (97)
T ss_pred cccCCCEEEEEECCCCEEEEeCCChhhHHheecCCCCCcceeecC
Confidence 3456775 69999999999998732 4567777775544433
No 52
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=23.18 E-value=3.7e+02 Score=21.47 Aligned_cols=50 Identities=20% Similarity=0.189 Sum_probs=35.2
Q ss_pred eeecCCEEEEEEEccCCCC--------------------CccccCeeEEEEEeeeeceecCCCeeEEecCceEEEE
Q 037036 7 AHILRNVFVVVIKKAIPKM--------------------PLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVI 62 (87)
Q Consensus 7 a~i~GD~I~vsVkk~~~~~--------------------kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl 62 (87)
-.+ ||.|.|.|....+.. .++.|+++.|.|... ...|.++.++++.-.++
T Consensus 318 ~~v-G~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v-----~~~G~fV~l~~~v~glv 387 (516)
T TIGR00717 318 VKK-GDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKI-----TDFGAFVELEGGIDGLI 387 (516)
T ss_pred ccC-CCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEE-----ecceEEEECCCCCEEEE
Confidence 457 999999987665521 256799999999874 34577777776555555
No 53
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=22.88 E-value=1.5e+02 Score=16.31 Aligned_cols=29 Identities=10% Similarity=0.225 Sum_probs=19.8
Q ss_pred cCeeEEEEEeeeeceecCCCeeEEecCceEEEEC
Q 037036 30 SDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIH 63 (87)
Q Consensus 30 g~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~ 63 (87)
|+++.|.|..... .|.++.++++.--++.
T Consensus 1 g~~~~g~V~~v~~-----~G~~v~l~~~~~g~l~ 29 (68)
T cd04472 1 GKIYEGKVVKIKD-----FGAFVEILPGKDGLVH 29 (68)
T ss_pred CCEEEEEEEEEEE-----eEEEEEeCCCCEEEEE
Confidence 5678888887663 6788887765555544
No 54
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=22.81 E-value=3e+02 Score=19.82 Aligned_cols=61 Identities=15% Similarity=0.138 Sum_probs=42.0
Q ss_pred CCEEEEEEEccCCCCCccccCeeEEEEEeeeeceecCCCeeEEecCceEEEECCCCCeeeeEEeccc
Q 037036 11 RNVFVVVIKKAIPKMPLEVSDVFTTLIVCTCTNLRRDNGIIIAYDDSTTAVIHQKEKFEGNSSFWCG 77 (87)
Q Consensus 11 GD~I~vsVkk~~~~~kvkkg~v~~AvIVrtk~~~~r~dG~~i~F~~Na~VLl~~~~~p~GtRI~Gpv 77 (87)
|+...|..+..-....++.|+++.-+- ....++.++-=++++.++++++-..-||.|-+-+
T Consensus 9 ~~~~~v~L~~~W~~t~v~~Gd~I~ii~------~~~~~~~~~v~~~~~~lIl~PD~LiS~T~Va~s~ 69 (209)
T PF08696_consen 9 GETRTVILRDEWCETPVSPGDIIHIIG------EFDDDDPCIVDNDSNLLILHPDILISATSVASSF 69 (209)
T ss_pred CCeEEEEEeCCcccCCCcCCCEEEEEE------EeCCCCCEEEeCCCCEEEEcCCceecceeeeccc
Confidence 555556666555567788999987665 2233344555556669999999999999997654
No 55
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=22.41 E-value=62 Score=23.97 Aligned_cols=17 Identities=24% Similarity=0.573 Sum_probs=14.1
Q ss_pred cceeeecCCEEEEEEEcc
Q 037036 4 RRYAHILRNVFVVVIKKA 21 (87)
Q Consensus 4 ~~~a~i~GD~I~vsVkk~ 21 (87)
+|...| ||+|.|.|.+.
T Consensus 61 ~rA~~V-GDivTV~i~E~ 77 (222)
T PRK00249 61 RRARNV-GDILTVVLQEN 77 (222)
T ss_pred cccccC-CCeEEEEEEEe
Confidence 566788 99999999864
No 56
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=22.17 E-value=68 Score=20.22 Aligned_cols=18 Identities=28% Similarity=0.383 Sum_probs=14.1
Q ss_pred eeecCCEEEEEEEccCCCC
Q 037036 7 AHILRNVFVVVIKKAIPKM 25 (87)
Q Consensus 7 a~i~GD~I~vsVkk~~~~~ 25 (87)
|.. ||.+.+.|++..|+.
T Consensus 46 a~~-Gd~V~vkI~~v~~~~ 63 (73)
T COG3269 46 AEV-GDEVKVKITKVKPNF 63 (73)
T ss_pred CCC-CCeeeEEEEEeeccc
Confidence 455 999999998887763
No 57
>PRK12700 flgH flagellar basal body L-ring protein; Reviewed
Probab=21.96 E-value=66 Score=24.07 Aligned_cols=17 Identities=18% Similarity=0.505 Sum_probs=13.9
Q ss_pred cceeeecCCEEEEEEEcc
Q 037036 4 RRYAHILRNVFVVVIKKA 21 (87)
Q Consensus 4 ~~~a~i~GD~I~vsVkk~ 21 (87)
+|...| ||+|.|.|.+.
T Consensus 68 ~RA~~V-GDivTV~i~E~ 84 (230)
T PRK12700 68 RRPRNV-GDIVTIVLEEK 84 (230)
T ss_pred cccccC-CCEEEEEEEEe
Confidence 456678 99999999875
No 58
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=21.80 E-value=78 Score=18.16 Aligned_cols=10 Identities=20% Similarity=0.212 Sum_probs=6.6
Q ss_pred CCEEEEEEEc
Q 037036 11 RNVFVVVIKK 20 (87)
Q Consensus 11 GD~I~vsVkk 20 (87)
||.|+|.+-.
T Consensus 35 gD~V~v~i~~ 44 (58)
T PF08206_consen 35 GDKVLVRITP 44 (58)
T ss_dssp T-EEEEEEEE
T ss_pred CCEEEEEEec
Confidence 7777777755
No 59
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=21.67 E-value=69 Score=23.84 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=14.0
Q ss_pred cceeeecCCEEEEEEEcc
Q 037036 4 RRYAHILRNVFVVVIKKA 21 (87)
Q Consensus 4 ~~~a~i~GD~I~vsVkk~ 21 (87)
+|...| ||+|.|.|.+-
T Consensus 61 ~rA~~V-GDivTV~i~E~ 77 (224)
T PRK12698 61 IKAHKV-GDIITVVLKES 77 (224)
T ss_pred cccccC-CCeEEEEEEEe
Confidence 466688 99999999875
No 60
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=21.44 E-value=1.1e+02 Score=18.52 Aligned_cols=23 Identities=13% Similarity=0.010 Sum_probs=15.7
Q ss_pred CceEEEECCCCCeeeeEEeccchh
Q 037036 56 DSTTAVIHQKEKFEGNSSFWCGRP 79 (87)
Q Consensus 56 ~Na~VLl~~~~~p~GtRI~Gpv~~ 79 (87)
--+.+++|++|+.+ -++.|-++.
T Consensus 83 tPt~~~~d~~G~~v-~~~~G~~~~ 105 (112)
T PF13098_consen 83 TPTIVFLDKDGKIV-YRIPGYLSP 105 (112)
T ss_dssp SSEEEECTTTSCEE-EEEESS--H
T ss_pred cCEEEEEcCCCCEE-EEecCCCCH
Confidence 34678888888877 458888875
No 61
>PF01491 Frataxin_Cyay: Frataxin-like domain; InterPro: IPR002908 The eukaryotic proteins in this entry include frataxin, the protein that is mutated in Friedreich's ataxia [], and related sequences. Friedreich's ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [, , ]. The bacterial proteins in this entry are iron-sulphur cluster (FeS) metabolism CyaY proteins hmologous to eukaryotic frataxin. Partial Phylogenetic Profiling [] suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species [, ]. ; PDB: 1EW4_A 2P1X_A 1SOY_A 2EFF_A 3T3T_B 3S4M_A 3T3K_A 3S5D_A 1LY7_A 3T3X_B ....
Probab=20.84 E-value=42 Score=21.98 Aligned_cols=40 Identities=18% Similarity=0.228 Sum_probs=27.5
Q ss_pred eecCCCe-eEEecCceEEEECCCCC----eeeeEEeccchhhhhc
Q 037036 44 LRRDNGI-IIAYDDSTTAVIHQKEK----FEGNSSFWCGRPEIDK 83 (87)
Q Consensus 44 ~~r~dG~-~i~F~~Na~VLl~~~~~----p~GtRI~Gpv~~elr~ 83 (87)
+.+.+|. .|.|++.+.++||+|-- =+.+.|.||--.+...
T Consensus 34 ~e~~~gVLti~~~~~~~~VINkQ~p~~QIWlsSpisG~~hf~~~~ 78 (109)
T PF01491_consen 34 VERSGGVLTIEFPDGGQYVINKQPPNRQIWLSSPISGPFHFDYDD 78 (109)
T ss_dssp EEEETTEEEEEETTSEEEEEEEECCCTEEEEEETTTEEEEEEEES
T ss_pred EEccCCEEEEEECCCCEEEEeCCCHHHHHHHhcccCCceEEEEcC
Confidence 3455675 68999999999997632 5667777776554443
No 62
>cd02799 tRNA_bind_EMAP-II_like tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.
Probab=20.61 E-value=1.3e+02 Score=19.06 Aligned_cols=29 Identities=7% Similarity=0.292 Sum_probs=17.6
Q ss_pred cCCCeeEEecC---ceEEEEC-CCCCeeeeEEe
Q 037036 46 RDNGIIIAYDD---STTAVIH-QKEKFEGNSSF 74 (87)
Q Consensus 46 r~dG~~i~F~~---Na~VLl~-~~~~p~GtRI~ 74 (87)
...|+.+.+++ +...|+. +...|.|+||+
T Consensus 73 ~S~GMll~~~~~~~~~~~~~~~~~~~~~G~~i~ 105 (105)
T cd02799 73 KSQGMVLCASNADHEKVELLEPPEGAKPGERVT 105 (105)
T ss_pred eeceEEEEeccCCCCcEEEEECCCCCCCCCEeC
Confidence 45677645433 3454444 55679999985
No 63
>PRK12699 flgH flagellar basal body L-ring protein; Reviewed
Probab=20.11 E-value=75 Score=24.10 Aligned_cols=18 Identities=22% Similarity=0.484 Sum_probs=14.3
Q ss_pred cceeeecCCEEEEEEEccC
Q 037036 4 RRYAHILRNVFVVVIKKAI 22 (87)
Q Consensus 4 ~~~a~i~GD~I~vsVkk~~ 22 (87)
+|...| ||+|.|.|.+-.
T Consensus 85 ~RA~~V-GDiiTV~i~E~t 102 (246)
T PRK12699 85 RRARQI-GDTIIVLLNEKT 102 (246)
T ss_pred cccccC-CCEEEEEEEEec
Confidence 456678 999999998753
Done!