Query psy8483
Match_columns 161
No_of_seqs 110 out of 1056
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 20:02:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8483.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8483hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00225 60S ribosomal protein 100.0 7.8E-50 1.7E-54 324.4 16.7 158 2-161 1-158 (214)
2 PTZ00029 60S ribosomal protein 100.0 4.9E-48 1.1E-52 314.2 16.5 160 2-161 1-160 (216)
3 PRK04203 rpl1P 50S ribosomal p 100.0 1.8E-46 3.8E-51 304.8 16.7 155 5-161 2-158 (215)
4 COG0081 RplA Ribosomal protein 100.0 1E-45 2.3E-50 300.6 14.4 147 5-161 18-168 (228)
5 CHL00129 rpl1 ribosomal protei 100.0 1.2E-43 2.5E-48 290.8 15.2 142 9-161 21-166 (229)
6 PRK05424 rplA 50S ribosomal pr 100.0 3.2E-42 6.9E-47 282.5 14.8 142 9-161 21-166 (230)
7 TIGR01169 rplA_bact ribosomal 100.0 8.8E-42 1.9E-46 279.4 15.0 142 9-161 20-165 (227)
8 TIGR01170 rplA_mito ribosomal 100.0 7.4E-38 1.6E-42 239.9 14.2 135 9-154 2-141 (141)
9 cd00403 Ribosomal_L1 Ribosomal 100.0 5.3E-34 1.1E-38 228.7 14.8 149 11-161 2-152 (208)
10 KOG1570|consensus 100.0 1.5E-34 3.2E-39 231.5 8.8 161 1-161 1-162 (218)
11 PF00687 Ribosomal_L1: Ribosom 100.0 1.1E-28 2.5E-33 198.9 11.3 138 23-160 15-165 (220)
12 KOG1569|consensus 99.8 3.7E-18 8E-23 143.7 10.8 105 47-158 133-244 (323)
13 KOG1685|consensus 99.5 3.7E-14 8E-19 121.8 5.9 131 26-160 50-202 (343)
14 PF13003 MRL1: Ribosomal prote 92.0 0.4 8.6E-06 36.6 5.1 56 9-68 71-133 (133)
15 PRK02228 V-type ATP synthase s 81.2 5.6 0.00012 28.5 5.6 84 63-153 1-95 (100)
16 PRK01189 V-type ATP synthase s 80.6 7.6 0.00016 28.2 6.2 82 64-152 4-97 (104)
17 PTZ00029 60S ribosomal protein 76.7 1.1 2.4E-05 36.5 0.9 27 123-150 118-145 (216)
18 PRK01395 V-type ATP synthase s 76.5 6.1 0.00013 28.6 4.6 68 63-138 4-75 (104)
19 PTZ00225 60S ribosomal protein 65.7 3.8 8.1E-05 33.5 1.6 30 122-152 115-145 (214)
20 PRK03957 V-type ATP synthase s 61.6 49 0.0011 23.5 6.7 56 64-125 2-63 (100)
21 TIGR00853 pts-lac PTS system, 60.6 24 0.00051 24.9 4.8 64 62-137 3-79 (95)
22 PF01990 ATP-synt_F: ATP synth 57.5 21 0.00045 24.9 4.0 57 65-127 1-63 (95)
23 PRK09590 celB cellobiose phosp 57.0 48 0.001 23.9 6.0 80 64-152 3-101 (104)
24 cd05564 PTS_IIB_chitobiose_lic 46.2 78 0.0017 22.1 5.5 67 73-151 19-94 (96)
25 COG1436 NtpG Archaeal/vacuolar 43.0 23 0.0005 25.8 2.4 59 63-127 3-67 (104)
26 KOG0780|consensus 38.8 26 0.00056 31.9 2.5 79 30-115 101-192 (483)
27 cd05565 PTS_IIB_lactose PTS_II 38.8 1.1E+02 0.0025 21.8 5.5 59 64-133 2-73 (99)
28 COG1568 Predicted methyltransf 29.8 1.1E+02 0.0025 26.7 4.9 76 53-128 142-244 (354)
29 PF05991 NYN_YacP: YacP-like N 29.0 73 0.0016 24.6 3.4 33 62-94 94-127 (166)
30 KOG1588|consensus 28.9 22 0.00048 30.1 0.5 11 124-134 109-119 (259)
31 PRK13958 N-(5'-phosphoribosyl) 28.9 23 0.00049 28.5 0.5 26 63-88 3-28 (207)
32 COG0135 TrpF Phosphoribosylant 24.4 30 0.00065 28.2 0.4 26 62-87 3-28 (208)
33 PF10740 DUF2529: Protein of u 23.6 18 0.00038 28.9 -1.0 74 46-125 60-146 (172)
34 COG1440 CelA Phosphotransferas 23.4 1.7E+02 0.0037 21.4 4.2 63 64-138 3-78 (102)
35 PRK01222 N-(5'-phosphoribosyl) 22.6 32 0.00069 27.7 0.3 27 62-88 4-30 (210)
36 PF04208 MtrA: Tetrahydrometha 22.5 83 0.0018 25.2 2.6 98 47-157 9-128 (176)
37 PF03946 Ribosomal_L11_N: Ribo 22.1 8.8 0.00019 25.2 -2.5 31 124-156 17-47 (60)
38 PRK06063 DNA polymerase III su 21.8 1.5E+02 0.0031 25.4 4.2 21 73-93 284-304 (313)
39 PF01861 DUF43: Protein of unk 21.5 94 0.002 26.1 2.8 57 61-117 44-123 (243)
40 PLN02363 phosphoribosylanthran 21.4 41 0.0009 28.1 0.7 26 62-87 48-73 (256)
41 COG2257 Uncharacterized homolo 21.3 2E+02 0.0044 20.6 4.1 46 49-94 7-58 (92)
42 KOG3666|consensus 21.0 25 0.00055 34.2 -0.7 75 65-155 665-740 (1141)
43 COG0161 BioA Adenosylmethionin 20.6 50 0.0011 30.1 1.1 39 98-137 239-279 (449)
44 PRK10499 PTS system N,N'-diace 20.4 2.6E+02 0.0056 20.0 4.7 50 63-122 4-66 (106)
45 PRK00536 speE spermidine synth 20.2 58 0.0013 27.4 1.4 76 61-136 72-169 (262)
No 1
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=7.8e-50 Score=324.40 Aligned_cols=158 Identities=52% Similarity=0.861 Sum_probs=152.9
Q ss_pred CCcCChHHHHHHHHHHHhcccccccccceEEEEEEEEeecCCCCCcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCC
Q psy8483 2 QSKVSRDTLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQKDKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAAN 81 (161)
Q Consensus 2 ~s~~~~~~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag 81 (161)
||+++++++.+||+.+++. .++++|+|||||+|+||||||++++++||+|.||||+|++.+||||++++++++|+++|
T Consensus 1 m~k~~~~~i~~Av~~~lk~--~~~~kF~Etvdl~v~Lk~iDp~kd~~irg~v~LPhg~gk~~kV~v~~~~~~~~~Ak~aG 78 (214)
T PTZ00225 1 MSKIPPQTLSEAIQAVLKV--DKERKFKESIDLQVNLKNYDPQKDKRFSGSLKLPNVCRPRMTVCLLCDLVHEDIAKKEG 78 (214)
T ss_pred CCcCCHHHHHHHHHHHHHh--cccCCCCceEEEEEeccCcCCCcCcccceeEECCCCCCCCcEEEEECChHHHHHHHHCC
Confidence 6889999999999998865 48999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCCccHHHHHHHHhccceeeecC
Q psy8483 82 VPFMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQESMTQKIDEVKGTIKFQMKK 161 (161)
Q Consensus 82 ~~vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~~dl~~~i~~~~~~v~~r~kk 161 (161)
|+++|.+||+++.++++++|+|+.+||+|||++++||+|||+||+.|||+||||+|.++++|+.+.|++++++++||+++
T Consensus 79 ad~v~~e~l~~l~k~~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~k 158 (214)
T PTZ00225 79 VPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLKK 158 (214)
T ss_pred CCEECHHHHHHHHhccHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999985
No 2
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=4.9e-48 Score=314.21 Aligned_cols=160 Identities=61% Similarity=1.041 Sum_probs=154.2
Q ss_pred CCcCChHHHHHHHHHHHhcccccccccceEEEEEEEEeecCCCCCcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCC
Q psy8483 2 QSKVSRDTLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQKDKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAAN 81 (161)
Q Consensus 2 ~s~~~~~~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag 81 (161)
||+++++++++||++++++.+.++++|+||||++|+||||||++++++||+|.||||+|++.+|||||+++.+++|+++|
T Consensus 1 m~~~~~~~~~~av~~~~~~~~~~~~~f~esv~~~i~Lk~id~~~~~~ir~~v~LP~~~gk~~~v~V~a~~~~~~~Ak~aG 80 (216)
T PTZ00029 1 MSKLSSEALRKAIAEILEGSEEKKRKFVETVELQIGLKDYDTQKDKRFSGSVKLPNVPKPNLKVCVLGDAVHCDEAKKLG 80 (216)
T ss_pred CCcCCHHHHHHHHHHHHhhccccccCCceEEEEEEEcCCCCCCcCcccceeEecCCCCCCCcEEEEECCcHHHHHHHHcC
Confidence 68889999999999999865579999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCCccHHHHHHHHhccceeeecC
Q psy8483 82 VPFMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQESMTQKIDEVKGTIKFQMKK 161 (161)
Q Consensus 82 ~~vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~~dl~~~i~~~~~~v~~r~kk 161 (161)
|++||.+||++++++++..|+|+.+||+|||++++||.||++||+.|+|+||||.|++.+.|+.+.|++++++++||++|
T Consensus 81 a~vvg~edL~~~~k~~k~~kkl~~~fD~flA~~~im~~l~riLGp~l~p~~K~P~~v~~~~d~~~~i~~~k~~v~~r~~k 160 (216)
T PTZ00029 81 LDFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIPRLLGPGLNKAGKFPTLITHNDDIEDKINELKSSVKFQLKK 160 (216)
T ss_pred CCEecHHHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCcccCccCHHHHHHHHHheEEEEECC
Confidence 99999999999999999999999999999999999999999999999999999999998999999999999999999875
No 3
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=1.8e-46 Score=304.80 Aligned_cols=155 Identities=30% Similarity=0.499 Sum_probs=148.7
Q ss_pred CChHHHHHHHHHHHhcccccccccceEEEEEEEEeecCCCC-CcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCCCC
Q psy8483 5 VSRDTLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQK-DKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAANVP 83 (161)
Q Consensus 5 ~~~~~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk-~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag~~ 83 (161)
+++|++.|||+.+++. .++++|+|||||+|+|||||+++ ++++||+|.|||+++++.+|||||+++++++|+++||+
T Consensus 2 ~~~~~~~eai~~~k~~--~~~~kf~esvel~v~Lk~id~~k~~~~irg~i~LP~~~~k~~~V~vf~~~~~~~~Ak~aGa~ 79 (215)
T PRK04203 2 MDREKIEEAVKEALEE--APKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAKGELALQAKEAGAD 79 (215)
T ss_pred CcHHHHHHHHHHHHHh--cccCCCCceEEEEEEecCCCCCccCceeeEEEECCCCCCCCcEEEEEcChHhHHHHHHcCCC
Confidence 5889999999999984 48999999999999999999999 99999999999999999999999999999999999999
Q ss_pred -CCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCCccHHHHHHHHhccceeeecC
Q psy8483 84 -FMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQESMTQKIDEVKGTIKFQMKK 161 (161)
Q Consensus 84 -vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~~dl~~~i~~~~~~v~~r~kk 161 (161)
++|.|+|+++.++++++|+|+.+||+|||++++||.|+++||++||||||||+|++++.|+.+.|++++++++||+++
T Consensus 80 ~v~~~e~L~~i~~~~k~~rkl~~~fD~~lA~~~im~~l~k~LGk~lgprgkmP~p~~~t~di~~~i~~~~~~~~~r~~k 158 (215)
T PRK04203 80 YVITREELEELGGDKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGPRGKMPTPLPPNADIKPLVERLKNTVRIRTKD 158 (215)
T ss_pred EEeCHHHHHHHhcChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCcCCCCCHHHHHHHHhhceEEEeCC
Confidence 899999999998899999999999999999999999999999999999999999999889999999999999999875
No 4
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-45 Score=300.62 Aligned_cols=147 Identities=30% Similarity=0.497 Sum_probs=137.4
Q ss_pred CChHHHHHHHHHHHhcccccccccceEEEEEEEEeecCCCC-CcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCCCC
Q psy8483 5 VSRDTLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQK-DKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAANVP 83 (161)
Q Consensus 5 ~~~~~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk-~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag~~ 83 (161)
.....+.+||+.+++. .+++|+||||++|+| +|||++ ||++||+|.|||++|++.|||||++++.+++|++|||+
T Consensus 18 ~~~~~i~eai~~~ke~---~~~kF~etVevav~L-~vD~~k~dq~vrg~VvLP~g~gk~vrV~Vfa~g~~~~~A~~AGad 93 (228)
T COG0081 18 NKLYSLEEAVKLLKET---SKRKFDETVEVAVNL-KVDPRKPDQRVRGSVVLPNGTGKTVRVAVFADGEKAEEAKAAGAD 93 (228)
T ss_pred hhhhhHHHHHHHHHhc---cccCcceEEEEEEEc-ccCCCCcccccceeEECCCCCCCccEEEEEcChHhHHHHHHcCCC
Confidence 4567899999999987 779999999999999 599988 99999999999999999999999999999999999999
Q ss_pred CCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCC--CccHHHHHHHHhc-cceeeec
Q psy8483 84 FMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSH--QESMTQKIDEVKG-TIKFQMK 160 (161)
Q Consensus 84 vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~--~~dl~~~i~~~~~-~v~~r~k 160 (161)
+||.|||.+..++++ +.+||+|||+|++||.+++ ||++||||||||+|+++ |.|+.++|+++++ +++||++
T Consensus 94 ~Vg~edl~e~ik~~r-----~~~fD~~IAtpdmM~~v~~-LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~v~~R~d 167 (228)
T COG0081 94 YVGGEDLIELIKNGR-----AKDFDVFIATPDMMPLVGK-LGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRAD 167 (228)
T ss_pred EecHHHHHHHHhCcc-----hhcCCEEEECchHHHHHHH-HhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCcEEEEEC
Confidence 999999998887764 5899999999999999965 99999999999999995 7999999999999 8999987
Q ss_pred C
Q psy8483 161 K 161 (161)
Q Consensus 161 k 161 (161)
+
T Consensus 168 k 168 (228)
T COG0081 168 K 168 (228)
T ss_pred C
Confidence 5
No 5
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=100.00 E-value=1.2e-43 Score=290.76 Aligned_cols=142 Identities=23% Similarity=0.404 Sum_probs=133.3
Q ss_pred HHHHHHHHHHhcccccccccceEEEEEEEEeecCCCC-CcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCCCCCCCH
Q psy8483 9 TLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQK-DKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAANVPFMDV 87 (161)
Q Consensus 9 ~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk-~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag~~vvg~ 87 (161)
.+.|||+.+++. +.++|+||||++|+| |||+++ ++++||+|.|||+++++.+|||||+++++++|+++||+++|.
T Consensus 21 ~l~eAi~~~k~~---~~~kF~esvel~i~L-~id~kk~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~eAk~aGad~vg~ 96 (229)
T CHL00129 21 SPEEAINLLKET---ATAKFIETAEAHISL-NIDPKYADQQLRTTVTLPKGTGKTIRIAVLTNEEKITEAKNAGADIVGS 96 (229)
T ss_pred CHHHHHHHHHHh---CcCCCCccEEEEEEE-CCCCCCCCCceeeEEECCCCCCCCcEEEEECChHhHHHHHHcCCCEeCH
Confidence 578999999975 889999999999999 999998 999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCC--ccHHHHHHHHhc-cceeeecC
Q psy8483 88 EALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQ--ESMTQKIDEVKG-TIKFQMKK 161 (161)
Q Consensus 88 ~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~--~dl~~~i~~~~~-~v~~r~kk 161 (161)
+||++. +++++.+||+|||++++||+|++ ||++||||||||+|+++| +|+.+.|+++++ +++||++|
T Consensus 97 edLi~~------ik~~~~~fd~~iAt~d~m~~l~k-LgriLGprGlMP~pk~gTvt~di~~~V~~~k~G~v~~r~dk 166 (229)
T CHL00129 97 DDLIEE------ITKGNLDFDLLIATPDMMPKLAK-LGRVLGPRGLMPSPKSGTVTTDLASAINEFKKGKLEYRADK 166 (229)
T ss_pred HHHHHH------HHcCcccCCEEEECHHHHHHHHH-hcCcccccCCCCCCCCCCccccHHHHHHHHhcCcEEEEecC
Confidence 999863 34577999999999999999999 999999999999999986 999999999998 79999875
No 6
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=100.00 E-value=3.2e-42 Score=282.49 Aligned_cols=142 Identities=25% Similarity=0.415 Sum_probs=132.7
Q ss_pred HHHHHHHHHHhcccccccccceEEEEEEEEeecCCCC-CcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCCCCCCCH
Q psy8483 9 TLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQK-DKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAANVPFMDV 87 (161)
Q Consensus 9 ~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk-~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag~~vvg~ 87 (161)
.+.+|++.+++. +.++|+||||++|+| +||+++ ++++||+|.|||+.+++.+|||||+++++++|+++||++||.
T Consensus 21 ~l~eAi~~lk~~---~~~kF~esvel~v~L-~id~kK~~~~irg~v~LP~~~gk~~kI~Vfa~~~~~~~Ak~aGa~~vg~ 96 (230)
T PRK05424 21 SLEEAIALVKET---ATAKFDETVDVAVNL-GVDPRKADQQVRGAVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADIVGG 96 (230)
T ss_pred CHHHHHHHHHhh---ccCCCCCcEEEEEEe-CCCCCCCCCeeeEEEECCCCCCCCcEEEEECChHhHHHHHHcCCCEeCH
Confidence 588999999985 889999999999999 999999 999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCC--ccHHHHHHHHhc-cceeeecC
Q psy8483 88 EALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQ--ESMTQKIDEVKG-TIKFQMKK 161 (161)
Q Consensus 88 ~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~--~dl~~~i~~~~~-~v~~r~kk 161 (161)
+||++..++ +| .+||+|||++++||+|++ ||++||||||||+|+++| +|+.+.|+++++ +++||++|
T Consensus 97 eeLi~~ik~-----~~-~~fd~~iat~~~m~~l~~-Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g~v~~r~~k 166 (230)
T PRK05424 97 EDLIEKIKG-----GW-LDFDVVIATPDMMGKVGK-LGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVDK 166 (230)
T ss_pred HHHHHHHhc-----CC-CcCCEEEECHHHHHHHHH-hccccccccCCCCCCCCCcchhHHHHHHHHhcCcEEEEecC
Confidence 999976643 35 489999999999999999 999999999999999986 999999999998 69999875
No 7
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=100.00 E-value=8.8e-42 Score=279.39 Aligned_cols=142 Identities=25% Similarity=0.426 Sum_probs=132.9
Q ss_pred HHHHHHHHHHhcccccccccceEEEEEEEEeecCCCC-CcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCCCCCCCH
Q psy8483 9 TLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQK-DKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAANVPFMDV 87 (161)
Q Consensus 9 ~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk-~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag~~vvg~ 87 (161)
.+.||++.+++. +.++|+||||++|+| ++|+++ +++++|+|.|||+.+++.+|||||+++++++|+++||++||.
T Consensus 20 ~l~eAi~~lk~~---~~~~f~esvel~i~L-~id~kK~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~~Ak~aGa~~vg~ 95 (227)
T TIGR01169 20 SLDEAIALLKET---ATAKFDETVEVAIRL-GIDPRKSDQQVRGTVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADYVGS 95 (227)
T ss_pred CHHHHHHHHHhh---ccCCCCCCEEEEEEE-CcCCCcCCCeeeEEEECCCCCCCCcEEEEEcCchhHHHHHHcCCCEeCH
Confidence 588999999975 889999999999999 999999 999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCC--ccHHHHHHHHhc-cceeeecC
Q psy8483 88 EALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQ--ESMTQKIDEVKG-TIKFQMKK 161 (161)
Q Consensus 88 ~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~--~dl~~~i~~~~~-~v~~r~kk 161 (161)
+||++. +++++.+||+|||++++||+|+. ||++||||||||+|+++| +|+.+.|+++++ +++||++|
T Consensus 96 ~eLi~~------ik~~~~~fd~~iat~~~m~~l~~-Lg~iLGPrGlMP~~k~gtv~~di~~~I~~~k~g~v~~r~~k 165 (227)
T TIGR01169 96 DDLIEK------IKKGWLDFDVVIATPDMMRVVGK-LGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRADK 165 (227)
T ss_pred HHHHHH------HHcCCccCCEEEECHHHHHHHHH-hccccccccCCCCCCCCCccccHHHHHHHHHcCcEEEEeCC
Confidence 999864 34567999999999999999995 999999999999999996 999999999998 69999875
No 8
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1.
Probab=100.00 E-value=7.4e-38 Score=239.86 Aligned_cols=135 Identities=17% Similarity=0.247 Sum_probs=117.6
Q ss_pred HHHHHHHHHHhcccccccccceEEEEEEEEeecCCCCCcceeeeEEcCCCCCCCcEEEEecCccc-HHHHHHCCCCCCCH
Q psy8483 9 TLYECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQKDKRFSGTVKLKHIPRPKMQVCILGDQQH-CDEAKAANVPFMDV 87 (161)
Q Consensus 9 ~~~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk~~~i~~~v~LP~~~~k~~kI~V~~~~~~-~~~ak~ag~~vvg~ 87 (161)
.+.+|++.+++..... .+|+||||++|+| ++|+++ .++||+|.|||+.+++.+|||||++++ +++|+++||+++|.
T Consensus 2 ~i~eA~~~lk~~~~~~-~~~~etvel~i~L-~~~~~~-~~irg~v~LP~~~~k~~kV~Vf~~~~~~~~~Ak~aGa~~vg~ 78 (141)
T TIGR01170 2 KVIKAFVYLKTKSISM-YVPKQSVNLDIGL-LMELGK-ESVQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGG 78 (141)
T ss_pred CHHHHHHHHHHhcccC-CCCCceEEEEEEE-CCCCCC-CCceEEEECCCCCCCCCEEEEECCChHHHHHHHHcCCCEeCH
Confidence 3689999998862222 3999999999999 777654 559999999999999999999999987 67899999999999
Q ss_pred HHHH-HhhhcHHHHHhhhhh-cCEEEEehhhHhhhhhhhccccccCCCCCCccCCC--ccHHHHHHHHhcc
Q psy8483 88 EALK-KLNKNKKLVKKLAKK-YDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQ--ESMTQKIDEVKGT 154 (161)
Q Consensus 88 ~eL~-~~~~~~k~~kkl~~~-~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~--~dl~~~i~~~~~~ 154 (161)
+||+ ++.+++ .+ ||+|||++++||.|+ .||++||||||||+|+++| +|+.++|++++++
T Consensus 79 edLi~~i~~g~-------~~~fd~~iA~~~~m~~l~-~Lg~iLGprGlMP~~k~gTv~~di~~~I~~~k~G 141 (141)
T TIGR01170 79 DDLIKKIEDGE-------IKPFDYLIAHPDIVPELA-QLRRLLGPKGLMPSPKRGTVGDNLLSMIETFKKG 141 (141)
T ss_pred HHHHHHHhcCC-------cccccEEEECHHHHHHHH-HhhcccccCcCCCCCCCCCcccCHHHHHHHHhCc
Confidence 9996 554332 45 999999999999999 5999999999999999997 9999999999875
No 9
>cd00403 Ribosomal_L1 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.
Probab=100.00 E-value=5.3e-34 Score=228.68 Aligned_cols=149 Identities=37% Similarity=0.570 Sum_probs=137.9
Q ss_pred HHHHHHHHhcccccccccceEEEEEEEEeecCCCCCcceeeeEEcCCCCCCCcEEEEecCcccHHHHHHCCCCCCCHHHH
Q psy8483 11 YECVNGVLNNAKVNKKRFLQTVELQIGLKNYDPQKDKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKAANVPFMDVEAL 90 (161)
Q Consensus 11 ~~av~~~~~~~~~~~~~F~esv~l~v~lk~id~kk~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ag~~vvg~~eL 90 (161)
.+|++.+++... ..+.|.|+|+|+|+|+.++.+.++++++.|.|||+.+++.+||||++++++++|+++|++++|.++|
T Consensus 2 ~~Ai~~l~~~~~-~~~~~~~~v~l~i~l~~~~~~~~~~~~~~i~LPh~~~~~~~i~v~~~d~~~~~a~~~~a~vig~~~L 80 (208)
T cd00403 2 EEAIKALKKTSV-KKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQAKEAKAAGADVVGGEDL 80 (208)
T ss_pred HHHHHHHHHhcc-ccCCCCceEEEEEEeCCCCCccccccceeEECCCCCCCCeEEEEEcChHhHHHHHHcCCCEEcHHHH
Confidence 588999888621 5889999999999999887556889999999999999999999999999999999999999999999
Q ss_pred HHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCC--CccHHHHHHHHhccceeeecC
Q psy8483 91 KKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSH--QESMTQKIDEVKGTIKFQMKK 161 (161)
Q Consensus 91 ~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~--~~dl~~~i~~~~~~v~~r~kk 161 (161)
++.++.++.+ +|+.+||+|||++++|+.+++.||+.|||||+||+++.+ ++|+.+.|+++++++.|++++
T Consensus 81 ~~~~~~~~~~-~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~~~t~~~~l~~~i~~~~~~~~~~~~~ 152 (208)
T cd00403 81 KKKIKNGEAK-KLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTEDLAKAIEEAKSSVEFRLDK 152 (208)
T ss_pred HHHhhcchhh-hhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCCCCCCcccHHHHHHHHHhCeEEEECC
Confidence 9988888887 999999999999999999999999999999999999998 689999999999999999864
No 10
>KOG1570|consensus
Probab=100.00 E-value=1.5e-34 Score=231.54 Aligned_cols=161 Identities=69% Similarity=1.091 Sum_probs=156.0
Q ss_pred CCCcCChHHHHHHHHHHHhcc-cccccccceEEEEEEEEeecCCCCCcceeeeEEcCCCCCCCcEEEEecCcccHHHHHH
Q psy8483 1 MQSKVSRDTLYECVNGVLNNA-KVNKKRFLQTVELQIGLKNYDPQKDKRFSGTVKLKHIPRPKMQVCILGDQQHCDEAKA 79 (161)
Q Consensus 1 ~~s~~~~~~~~~av~~~~~~~-~~~~~~F~esv~l~v~lk~id~kk~~~i~~~v~LP~~~~k~~kI~V~~~~~~~~~ak~ 79 (161)
|||.++++++.+||..++..+ +.+.++|.|||++|++||||||.+|.|+.+++.|||.+++..++|||+|..++.+|++
T Consensus 1 M~sk~~~~~l~~~v~~i~~~~~~~k~~~~~~tielQi~Lk~ydp~Kdkr~s~~~~l~~~~~p~~k~cv~gd~~h~~~ak~ 80 (218)
T KOG1570|consen 1 MSSKVEEEALREAVAEILLRSKEFKNRNFVETIELQINLKNYDPQKDKRFSGSVKLPHAPRPKMKVCVIGDQQHCDEAKA 80 (218)
T ss_pred CCcchhHHHHHHHHHHHHhccccccCccceeeeeeeecccccChhHhCcccceEecCCCCCccceeeeechHHHHHHhhc
Confidence 899999999999999999876 4588999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCCccHHHHHHHHhccceeee
Q psy8483 80 ANVPFMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQESMTQKIDEVKGTIKFQM 159 (161)
Q Consensus 80 ag~~vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~~dl~~~i~~~~~~v~~r~ 159 (161)
.|.+.+..|+|++.+++++..+++++.||+|||.++++.+|+++|||.|...|++|.++...+|+-+.+++++++++|++
T Consensus 81 ~~~p~m~~d~lkklnk~Kklvkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~l~~~d~l~akv~evk~t~k~q~ 160 (218)
T KOG1570|consen 81 IDLPAMDIDALKKLNKNKKLVKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSLLVHGDSLYAKVEEVKSTIKFQM 160 (218)
T ss_pred CCCCCcCHHHHhcCcccchHHHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCccccchHHHHHHHHHHHhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q psy8483 160 KK 161 (161)
Q Consensus 160 kk 161 (161)
||
T Consensus 161 kk 162 (218)
T KOG1570|consen 161 KK 162 (218)
T ss_pred Hh
Confidence 86
No 11
>PF00687 Ribosomal_L1: Ribosomal protein L1p/L10e family; InterPro: IPR002143 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 L1 is the largest protein from the large ribosomal subunit. The L1 protein contains two domains: 2-layer alpha/beta domain and a 3-layer alpha/beta domain (interrupts the first domain). In Escherichia coli, L1 is known to bind to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L1. Algal and plant chloroplast L1. Cyanelle L1. Archaebacterial L1. Vertebrate L10A. Yeast SSM1. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3QOY_A 3BBO_D 1VSA_A 1VSP_A 2NOQ_G 3IZS_A 1S1I_A 3O5H_A 3O58_A 2WRL_C ....
Probab=99.96 E-value=1.1e-28 Score=198.93 Aligned_cols=138 Identities=32% Similarity=0.493 Sum_probs=124.0
Q ss_pred ccccccceEEEEEEEEeecCCCCCcce-eeeEEcCCCCC-CCcEEEEecCcccHHH---------HHHCCCCCCCHHHHH
Q psy8483 23 VNKKRFLQTVELQIGLKNYDPQKDKRF-SGTVKLKHIPR-PKMQVCILGDQQHCDE---------AKAANVPFMDVEALK 91 (161)
Q Consensus 23 ~~~~~F~esv~l~v~lk~id~kk~~~i-~~~v~LP~~~~-k~~kI~V~~~~~~~~~---------ak~ag~~vvg~~eL~ 91 (161)
....+|.++|+|+|+++.++.+.++++ ++.|.|||+++ ++.+||||+++.+.+. +.++|+.++|.++|.
T Consensus 15 ~~~~~~~~~v~l~i~~~~~~~~~~~~~~~~~i~LPh~~~~~~~~vcli~~d~~~~~~~~~~~~~~~~~~~~~vi~~~~L~ 94 (220)
T PF00687_consen 15 NEDDNFDESVYLQITLKKIPKKKDKSFKPGRIPLPHPLYIKNSKVCLIVKDPQKKAKEKEKLEEKAVEAGAKVIGGEELK 94 (220)
T ss_dssp CCCSSSSTEEEEEEEESSSTTSSCTST-EEEEEBSTSSS-SSSBEEEEESCHHHHHH-------HHHHTTCSEEECHHHH
T ss_pred cccCCCCcEEEEEEEeCcCCCccccccccceeeecCCCCCCccEEEEEecCcchhhhhhhhhhhhhhhcccceecHHHHH
Confidence 367889999999999999877777777 99999999998 8999999997665443 467899999999999
Q ss_pred HhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhcccc-ccCCCCCCccCC-CccHHHHHHHHhccceeeec
Q psy8483 92 KLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGL-NKAGKFPGLLSH-QESMTQKIDEVKGTIKFQMK 160 (161)
Q Consensus 92 ~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~L-gprgkmP~p~~~-~~dl~~~i~~~~~~v~~r~k 160 (161)
+.++.+++.|+|+.+||+|||++++||.|++.||++| ||+|+||+|+.. .+|+.+.|+++.+++.++.+
T Consensus 95 ~~~~~~~~~r~l~~~~d~flad~~i~~~l~~~Lgk~~~~~k~k~P~~v~~~~~~l~~~i~~~~~~~~~~~~ 165 (220)
T PF00687_consen 95 KKYKTIEAKRKLAKSYDFFLADPRIMPKLPKLLGKIFYGKKGKMPIPVTLSKEDLKEQIEKALNSTKFRLS 165 (220)
T ss_dssp HHHCHHHHCHHHHHCSSEEEEEGGGHHHHHHHTHHHH-CCTTTSCEEBSSHTSCHHHHHHHHHTEEEEEET
T ss_pred HHHHHHHHHHHHHhhcCEEEECHHHHHHHHHhhhhheecccCCcceEEeccchhHHHHHHHHHCCEEEEee
Confidence 8887788889999999999999999999999999999 999999999887 48999999999999888875
No 12
>KOG1569|consensus
Probab=99.76 E-value=3.7e-18 Score=143.65 Aligned_cols=105 Identities=22% Similarity=0.362 Sum_probs=88.8
Q ss_pred cceeeeEEcCCCCC--CCcEEEEecCc-ccHHHHHHCCCCCCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhh
Q psy8483 47 KRFSGTVKLKHIPR--PKMQVCILGDQ-QHCDEAKAANVPFMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRL 123 (161)
Q Consensus 47 ~~i~~~v~LP~~~~--k~~kI~V~~~~-~~~~~ak~ag~~vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~ 123 (161)
..+.+.+..|||.+ ...+|+||+.+ ...++|+++||+++|+.||++..++++ +..+||+++|+|+|||.|.+
T Consensus 133 ~~~~~~v~vP~Pf~~ge~r~IavFtn~~~kveeArEaGA~l~GG~dLIkkI~~Ge----i~~Dyd~~vA~Pdim~~l~~- 207 (323)
T KOG1569|consen 133 APLQGSVTVPHPFAHGEIRKIAVFTNDASKVEEAREAGAALAGGTDLIKKIKSGE----IVADYDFYVAHPDIMPELNR- 207 (323)
T ss_pred CCCceeEeccccCCCCceEEEEEecCChHHHHHHHhccccccccHHHHHHhhcCe----EEEeeceeeecchHHHHHHH-
Confidence 34556677777765 46679999987 678899999999999999986555554 56779999999999999999
Q ss_pred hccccccCCCCCCccCC--CccHHHHHHHHhcc--ceee
Q psy8483 124 LGPGLNKAGKFPGLLSH--QESMTQKIDEVKGT--IKFQ 158 (161)
Q Consensus 124 LG~~LgprgkmP~p~~~--~~dl~~~i~~~~~~--v~~r 158 (161)
|+++|||| ||+|+.+ +.||.++|++++++ +.|+
T Consensus 208 Lr~iL~~r--~Pn~k~gtvg~nipemieeFk~G~~i~~d 244 (323)
T KOG1569|consen 208 LRKILGPR--FPNPKRGTVGRNIPEMIEEFKNGHEIKFD 244 (323)
T ss_pred HHHHhccc--CCCcccCccccchHHHHHHhhCCcccccc
Confidence 99999999 9999988 58999999999999 5554
No 13
>KOG1685|consensus
Probab=99.48 E-value=3.7e-14 Score=121.78 Aligned_cols=131 Identities=24% Similarity=0.377 Sum_probs=101.6
Q ss_pred cccceEEEEEEEEeecCCCCCcceeeeEEcCCCC----C--CCcEEEEecCcccH---------HHHHHCCCC----CCC
Q psy8483 26 KRFLQTVELQIGLKNYDPQKDKRFSGTVKLKHIP----R--PKMQVCILGDQQHC---------DEAKAANVP----FMD 86 (161)
Q Consensus 26 ~~F~esv~l~v~lk~id~kk~~~i~~~v~LP~~~----~--k~~kI~V~~~~~~~---------~~ak~ag~~----vvg 86 (161)
.++...++++.++ + ......+-.|++||.. - +...||+|.++.+. +...++|++ ||+
T Consensus 50 ~k~~~~~~~~k~~-~---~~~~~n~~~IP~k~~~~~~~~~~~~~~vcLIvkD~~~~~~t~~~~~d~l~~~gi~~itkVI~ 125 (343)
T KOG1685|consen 50 LKNVYKVVLQKNT-P---QKVGTNKLKIPLKHLLKKLLLKHDDTDVCLIVKDLQQSYLTEEDAEDLLESEGIKSITKVIS 125 (343)
T ss_pred hhhhHHHHHHHhc-c---cccccccccccCcchhcccccCCCCCceEEEecCchhccccHHHHHHHHHHcCCccceeeee
Confidence 3444556666555 2 1211222234455543 2 36689999976422 345678988 899
Q ss_pred HHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCCC-cc--HHHHHHHHhccceeeec
Q psy8483 87 VEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSHQ-ES--MTQKIDEVKGTIKFQMK 160 (161)
Q Consensus 87 ~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~~-~d--l~~~i~~~~~~v~~r~k 160 (161)
..+|+..++.+++.++|+.+||+|||+.+++|+||++||+.|+.+.+.|.|+... .+ +...|+++..++.|+++
T Consensus 126 ~~~LK~~yksyeaKr~L~~sfDlflaD~RV~~~LP~llGK~f~q~kk~Pv~i~l~k~~~~l~~qi~~a~~~t~~~~~ 202 (343)
T KOG1685|consen 126 LSKLKRDYKSYEAKRKLLSSFDLFLADDRVIPLLPKLLGKEFYQKKKVPVSIRLSKKNELLKQQIENACGSTYFRLR 202 (343)
T ss_pred hHHHHHHHHHHHHHHHHHhhccEEEEcchhHhHHHHHhhhhhcccccCceEEEecccchHHHHHHHHHhhhheeecc
Confidence 9999999999999999999999999999999999999999999999999999763 34 89999999999999976
No 14
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=91.99 E-value=0.4 Score=36.62 Aligned_cols=56 Identities=16% Similarity=0.210 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhcccccccccc---eEEEEEEEEeecCC-CC--CcceeeeEEcCCCCCCCc-EEEEe
Q psy8483 9 TLYECVNGVLNNAKVNKKRFL---QTVELQIGLKNYDP-QK--DKRFSGTVKLKHIPRPKM-QVCIL 68 (161)
Q Consensus 9 ~~~~av~~~~~~~~~~~~~F~---esv~l~v~lk~id~-kk--~~~i~~~v~LP~~~~k~~-kI~V~ 68 (161)
.+++|+..++.. ..-+|+ |-|++-++| +.-+ ++ --++.+.|.|||+.-.+. +|+||
T Consensus 71 eve~Ai~mLKkf---Q~lDfT~pkQ~VYldL~L-dm~l~KKkkVePF~s~i~lPypF~~eiNKv~VF 133 (133)
T PF13003_consen 71 EVEKAIDMLKKF---QILDFTSPKQPVYLDLTL-DMKLEKKKKVEPFASVILLPYPFTSEINKVLVF 133 (133)
T ss_pred HHHHHHHHHHhc---ccccCCCCCCcEEEeeee-hhhhccccccCCCccceecccccccccceeeeC
Confidence 688999999876 556664 788888888 4434 22 446789999999975543 78886
No 15
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=81.23 E-value=5.6 Score=28.49 Aligned_cols=84 Identities=15% Similarity=0.320 Sum_probs=55.7
Q ss_pred cEEEEecCcccHHHHHHCCCC--C-CCH-HHHHHhhhcHHHHHhh--hhhcCEEEEehhhHhhhhhhhccccccCCCCCC
Q psy8483 63 MQVCILGDQQHCDEAKAANVP--F-MDV-EALKKLNKNKKLVKKL--AKKYDAFLASDALIKQIPRLLGPGLNKAGKFPG 136 (161)
Q Consensus 63 ~kI~V~~~~~~~~~ak~ag~~--v-vg~-~eL~~~~~~~k~~kkl--~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~ 136 (161)
.||+|++|.+...--+-+|+. + +.. +|+.+.. +++ ..+|..++.+.++...++..+-+. -.....|.
T Consensus 1 mkIaVIGD~dtv~GFrLaGi~~~~~~~~~ee~~~~l------~~l~~~~d~gII~Ite~~~~~i~e~i~~~-~~~~~~P~ 73 (100)
T PRK02228 1 MEIAVIGSPEFTTGFRLAGIRKVYEVPDDEKLDEAV------EEVLEDDDVGILVMHDDDLEKLPRRLRRT-LEESVEPT 73 (100)
T ss_pred CEEEEEeCHHHHHHHHHcCCceEEeeCCHHHHHHHH------HHHhhCCCEEEEEEehhHhHhhHHHHHHH-HhcCCCCE
Confidence 379999998888888999997 2 344 4555433 223 356999999999999998755443 34455665
Q ss_pred cc--CC---CccHHHHHHHHhc
Q psy8483 137 LL--SH---QESMTQKIDEVKG 153 (161)
Q Consensus 137 p~--~~---~~dl~~~i~~~~~ 153 (161)
.+ |+ ++.+.+.|+++-+
T Consensus 74 ii~IP~~~~~~~i~~~v~raIG 95 (100)
T PRK02228 74 VVTLGGGGGSGGLREKIKRAIG 95 (100)
T ss_pred EEEECCCccchHHHHHHHHHhC
Confidence 44 32 3356666666543
No 16
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=80.57 E-value=7.6 Score=28.21 Aligned_cols=82 Identities=11% Similarity=0.137 Sum_probs=54.2
Q ss_pred EEEEecCcccHHHHHHCCCC---CCC-HHHHHHhhhcHHHHHhhh-hhcCEEEEehhhHhhhhhhhccccccCCCCCCcc
Q psy8483 64 QVCILGDQQHCDEAKAANVP---FMD-VEALKKLNKNKKLVKKLA-KKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLL 138 (161)
Q Consensus 64 kI~V~~~~~~~~~ak~ag~~---vvg-~~eL~~~~~~~k~~kkl~-~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~ 138 (161)
||||++|.+...--+-+|++ .+. .++..++. +.++ .+|-.++.|+++...+++-+=.-+. ....|..+
T Consensus 4 kIaVvGd~DtilGFrlaGi~~v~~~~~~e~~~~~~------~~l~~~~~gII~iTE~~a~~i~~~~i~~~~-~~~~P~II 76 (104)
T PRK01189 4 CITVIGERDVVLGFRLLGIGDTIEAEGKDLVKKFL------EIFNNPKCKYIFVSESTKNMFDKNTLRSLE-SSSKPLVV 76 (104)
T ss_pred eEEEEcCHHHHHHHHHcCCceEEEcCCHHHHHHHH------HHHhcCCeEEEEEEHHHHhhCCHHHHHHHh-ccCCCeEE
Confidence 79999999888888999996 233 33343332 2344 3499999999999999831223344 67777665
Q ss_pred ----CCC---ccHHHHHHHHh
Q psy8483 139 ----SHQ---ESMTQKIDEVK 152 (161)
Q Consensus 139 ----~~~---~dl~~~i~~~~ 152 (161)
+++ +.+..+|+++.
T Consensus 77 ~Ipipg~~~~~~i~~~ik~ai 97 (104)
T PRK01189 77 FIPLPGISEEESIEEMAKRIL 97 (104)
T ss_pred EEeCCCCccchhHHHHHHHHh
Confidence 232 35777776654
No 17
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=76.73 E-value=1.1 Score=36.51 Aligned_cols=27 Identities=11% Similarity=-0.026 Sum_probs=19.7
Q ss_pred hhccccccCCCCCCccCCCc-cHHHHHHH
Q psy8483 123 LLGPGLNKAGKFPGLLSHQE-SMTQKIDE 150 (161)
Q Consensus 123 ~LG~~LgprgkmP~p~~~~~-dl~~~i~~ 150 (161)
.||++||| |+||+++.|+. .+.+-+..
T Consensus 118 ~l~riLGp-~l~p~~K~P~~v~~~~d~~~ 145 (216)
T PTZ00029 118 QIPRLLGP-GLNKAGKFPTLITHNDDIED 145 (216)
T ss_pred HHHHHhcc-ccccCCCCCCcccCccCHHH
Confidence 37999999 99999998863 33433433
No 18
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=76.55 E-value=6.1 Score=28.65 Aligned_cols=68 Identities=16% Similarity=0.325 Sum_probs=51.0
Q ss_pred cEEEEecCcccHHHHHHCCCC---CCCHHHHHHhhhcHHHHHhh-hhhcCEEEEehhhHhhhhhhhccccccCCCCCCcc
Q psy8483 63 MQVCILGDQQHCDEAKAANVP---FMDVEALKKLNKNKKLVKKL-AKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLL 138 (161)
Q Consensus 63 ~kI~V~~~~~~~~~ak~ag~~---vvg~~eL~~~~~~~k~~kkl-~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~ 138 (161)
.||+|++|.+...--+-+|++ +.+.+++.+... ++ ..+|-.++.++++...++..+-+. ....+|..+
T Consensus 4 ~kIaVIGD~dtv~GFrLaGi~~~~v~~~ee~~~~i~------~l~~~d~gII~Ite~~a~~i~~~i~~~--~~~~~P~Il 75 (104)
T PRK01395 4 YKIGVVGDKDSILPFKALGIDVFPVIDEQEAINTLR------KLAMEDYGIIYITEQIAADIPETIERY--DNQVLPAII 75 (104)
T ss_pred eeEEEEECHHHHHHHHHcCCeeEEecChHHHHHHHH------HHhcCCcEEEEEcHHHHHHhHHHHHHh--cCCCCCEEE
Confidence 489999998888888889998 556677665432 23 356999999999999999877554 356777654
No 19
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=65.66 E-value=3.8 Score=33.51 Aligned_cols=30 Identities=3% Similarity=-0.209 Sum_probs=21.4
Q ss_pred hhhccccccCCCCCCccCCC-ccHHHHHHHHh
Q psy8483 122 RLLGPGLNKAGKFPGLLSHQ-ESMTQKIDEVK 152 (161)
Q Consensus 122 k~LG~~LgprgkmP~p~~~~-~dl~~~i~~~~ 152 (161)
+.||++|||++. |+++.|+ -++..-+..+.
T Consensus 115 ~~lgk~LGp~~~-p~gK~P~~~~~~~dl~~~i 145 (214)
T PTZ00225 115 KTVPRLVGPHMH-RMGKFPTVCSPSESLPDKV 145 (214)
T ss_pred HhhhhhcCCCCC-cCCCCCcccCCccCHHHHH
Confidence 348999999997 9999886 23444454443
No 20
>PRK03957 V-type ATP synthase subunit F; Provisional
Probab=61.63 E-value=49 Score=23.55 Aligned_cols=56 Identities=16% Similarity=0.332 Sum_probs=41.8
Q ss_pred EEEEecCcccHHHHHHCCCC---CCC-HHHHHHhhhcHHHHHhhh--hhcCEEEEehhhHhhhhhhhc
Q psy8483 64 QVCILGDQQHCDEAKAANVP---FMD-VEALKKLNKNKKLVKKLA--KKYDAFLASDALIKQIPRLLG 125 (161)
Q Consensus 64 kI~V~~~~~~~~~ak~ag~~---vvg-~~eL~~~~~~~k~~kkl~--~~~d~fiA~~~~m~~l~k~LG 125 (161)
||+|++|.+...--+-+|+. ++. .+|+.+.. +++. .+|-.++.+.++...+...+-
T Consensus 2 kIaVIgD~dtv~GFrLaGi~~~~~v~~~ee~~~~l------~~l~~~~d~gII~ite~~~~~i~~~i~ 63 (100)
T PRK03957 2 KIAVVGDRDTVTGFRLAGLTEVYEVKNPEEAKNAI------KELVENDEIGIIIITERIAEEIRDLIS 63 (100)
T ss_pred EEEEEeCHHHHHHHHHcCCCceEEeCCHHHHHHHH------HHHhhCCCeEEEEEcHHHHHHHHHHHh
Confidence 79999998888778889995 333 45665443 2344 569999999999999977554
No 21
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=60.64 E-value=24 Score=24.93 Aligned_cols=64 Identities=19% Similarity=0.203 Sum_probs=41.5
Q ss_pred CcEEEEecCc---------ccHHHHHHCCCC----CCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhcccc
Q psy8483 62 KMQVCILGDQ---------QHCDEAKAANVP----FMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGL 128 (161)
Q Consensus 62 ~~kI~V~~~~---------~~~~~ak~ag~~----vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~L 128 (161)
..+|+++|.. ...+.+++.|.+ ..+..++.+. ..+||+++.+|.+--.+.. +-..+
T Consensus 3 ~~~ILl~C~~G~sSS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~~----------~~~~Dvill~pqi~~~~~~-i~~~~ 71 (95)
T TIGR00853 3 ETNILLLCAAGMSTSLLVNKMNKAAEEYGVPVKIAAGSYGAAGEK----------LDDADVVLLAPQVAYMLPD-LKKET 71 (95)
T ss_pred ccEEEEECCCchhHHHHHHHHHHHHHHCCCcEEEEEecHHHHHhh----------cCCCCEEEECchHHHHHHH-HHHHh
Confidence 4578888864 234557888988 3455555432 2579999999999887776 44444
Q ss_pred ccCCCCCCc
Q psy8483 129 NKAGKFPGL 137 (161)
Q Consensus 129 gprgkmP~p 137 (161)
.+.| .|..
T Consensus 72 ~~~~-ipv~ 79 (95)
T TIGR00853 72 DKKG-IPVE 79 (95)
T ss_pred hhcC-CCEE
Confidence 4444 3433
No 22
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=57.53 E-value=21 Score=24.90 Aligned_cols=57 Identities=19% Similarity=0.288 Sum_probs=43.3
Q ss_pred EEEecCcccHHHHHHCCCC--C-C-CHHHHHHhhhcHHHHHhhh--hhcCEEEEehhhHhhhhhhhccc
Q psy8483 65 VCILGDQQHCDEAKAANVP--F-M-DVEALKKLNKNKKLVKKLA--KKYDAFLASDALIKQIPRLLGPG 127 (161)
Q Consensus 65 I~V~~~~~~~~~ak~ag~~--v-v-g~~eL~~~~~~~k~~kkl~--~~~d~fiA~~~~m~~l~k~LG~~ 127 (161)
|+|+++.+...--+-+|++ + . +.+++.+..+ ++. .+|-.+|-+.+++..++..+-..
T Consensus 1 IavIGd~~~v~gFrLaGv~~~~~~~~~ee~~~~l~------~l~~~~~~gIIii~e~~~~~~~~~l~~~ 63 (95)
T PF01990_consen 1 IAVIGDRDTVLGFRLAGVEGVYVNTDPEEAEEALK------ELLKDEDVGIIIITEDLAEKIRDELDEY 63 (95)
T ss_dssp EEEEE-HHHHHHHHHTTSEEEEESHSHHHHHHHHH------HHHHHTTEEEEEEEHHHHTTHHHHHHHH
T ss_pred CEEEeCHHHHHHHHHcCCCCccCCCCHHHHHHHHH------HHhcCCCccEEEeeHHHHHHHHHHHHHH
Confidence 7899998888888889999 3 4 7777775542 243 57999999999999999866444
No 23
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=56.99 E-value=48 Score=23.92 Aligned_cols=80 Identities=14% Similarity=0.096 Sum_probs=48.7
Q ss_pred EEEEecCc---------ccHHHHHHCCCCC----CCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhcccccc
Q psy8483 64 QVCILGDQ---------QHCDEAKAANVPF----MDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNK 130 (161)
Q Consensus 64 kI~V~~~~---------~~~~~ak~ag~~v----vg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~Lgp 130 (161)
+|+++|.+ ...+.|++.|.++ .+..++.+... ..+||+++..|.+-=.+.. +-....+
T Consensus 3 kILlvCg~G~STSlla~k~k~~~~e~gi~~~i~a~~~~e~~~~~~--------~~~~DvIll~PQi~~~~~~-i~~~~~~ 73 (104)
T PRK09590 3 KALIICAAGMSSSMMAKKTTEYLKEQGKDIEVDAITATEGEKAIA--------AAEYDLYLVSPQTKMYFKQ-FEEAGAK 73 (104)
T ss_pred EEEEECCCchHHHHHHHHHHHHHHHCCCceEEEEecHHHHHHhhc--------cCCCCEEEEChHHHHHHHH-HHHHhhh
Confidence 68888853 2345678888883 66766654321 1469999999998777776 5556555
Q ss_pred CCCCCCccCC---C---ccHHHHHHHHh
Q psy8483 131 AGKFPGLLSH---Q---ESMTQKIDEVK 152 (161)
Q Consensus 131 rgkmP~p~~~---~---~dl~~~i~~~~ 152 (161)
.|.-...+++ + -|+...++.+.
T Consensus 74 ~~ipv~~I~~~~Y~~~~~~~~~~~~~~~ 101 (104)
T PRK09590 74 VGKPVVQIPPQAYIPIPMGIEKMAKLIL 101 (104)
T ss_pred cCCCEEEeCHHHcCCCccCHHHHHHHHH
Confidence 5543322222 1 35555555544
No 24
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=46.17 E-value=78 Score=22.13 Aligned_cols=67 Identities=7% Similarity=0.034 Sum_probs=39.3
Q ss_pred cHHHHHHCCCC----CCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccC-----CCcc
Q psy8483 73 HCDEAKAANVP----FMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLS-----HQES 143 (161)
Q Consensus 73 ~~~~ak~ag~~----vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~-----~~~d 143 (161)
..+.+++.|.+ ..+..++.+. ..+||+++.+|.+--.+.+ +-....+. -.|.... +.-|
T Consensus 19 i~~~~~~~~~~~~v~~~~~~~~~~~----------~~~~Diil~~Pqv~~~~~~-i~~~~~~~-~~pv~~I~~~~Y~~~d 86 (96)
T cd05564 19 MKKAAEKRGIDAEIEAVPESELEEY----------IDDADVVLLGPQVRYMLDE-VKKKAAEY-GIPVAVIDMMDYGMMN 86 (96)
T ss_pred HHHHHHHCCCceEEEEecHHHHHHh----------cCCCCEEEEChhHHHHHHH-HHHHhccC-CCcEEEcChHhcccCC
Confidence 34557788887 3444444321 3679999999999888877 33333332 2333332 2346
Q ss_pred HHHHHHHH
Q psy8483 144 MTQKIDEV 151 (161)
Q Consensus 144 l~~~i~~~ 151 (161)
-.+.++.+
T Consensus 87 g~~il~~~ 94 (96)
T cd05564 87 GEKVLKQA 94 (96)
T ss_pred HHHHHHHH
Confidence 56665544
No 25
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=42.97 E-value=23 Score=25.82 Aligned_cols=59 Identities=22% Similarity=0.327 Sum_probs=42.5
Q ss_pred cEEEEecCcccHHHHHHCCCC---CCCHHH--HHHhhhcHHHHHhhhh-hcCEEEEehhhHhhhhhhhccc
Q psy8483 63 MQVCILGDQQHCDEAKAANVP---FMDVEA--LKKLNKNKKLVKKLAK-KYDAFLASDALIKQIPRLLGPG 127 (161)
Q Consensus 63 ~kI~V~~~~~~~~~ak~ag~~---vvg~~e--L~~~~~~~k~~kkl~~-~~d~fiA~~~~m~~l~k~LG~~ 127 (161)
.+|||++|.+...--+=+|+. +++.++ +.+... .++. +|+.++-+.+++..+...+-+.
T Consensus 3 ~~I~VIGd~dtvtGFrLaGv~~~~v~~~~~~~~~~~~~------~l~~~~~~iIiite~~a~~i~~~i~~~ 67 (104)
T COG1436 3 MKIAVIGDRDTVTGFRLAGVRVVYVADDEEDELRAALR------VLAEDDVGIILITEDLAEKIREEIRRI 67 (104)
T ss_pred eEEEEEEccchhhceeeecceeEEEecChhHHHHHHHH------hhccCCceEEEEeHHHHhhhHHHHHHH
Confidence 589999999887777778888 255543 444432 2333 5999999999999999855444
No 26
>KOG0780|consensus
Probab=38.85 E-value=26 Score=31.88 Aligned_cols=79 Identities=20% Similarity=0.326 Sum_probs=45.4
Q ss_pred eEEEEEEEEeecCCCCCcceeeeEEcCCCC-CCCcEEEEecCc--------ccHHHHHHCCCCCCCH-HHHH--HhhhcH
Q psy8483 30 QTVELQIGLKNYDPQKDKRFSGTVKLKHIP-RPKMQVCILGDQ--------QHCDEAKAANVPFMDV-EALK--KLNKNK 97 (161)
Q Consensus 30 esv~l~v~lk~id~kk~~~i~~~v~LP~~~-~k~~kI~V~~~~--------~~~~~ak~ag~~vvg~-~eL~--~~~~~~ 97 (161)
-||-+-|.|-|.. |-. ..-+|-|-. ++..|+|++|-+ +....|.+++++++|. .|.. ++..
T Consensus 101 psVimfVGLqG~G--KTT---tc~KlA~y~kkkG~K~~LvcaDTFRagAfDQLkqnA~k~~iP~ygsyte~dpv~ia~-- 173 (483)
T KOG0780|consen 101 PSVIMFVGLQGSG--KTT---TCTKLAYYYKKKGYKVALVCADTFRAGAFDQLKQNATKARVPFYGSYTEADPVKIAS-- 173 (483)
T ss_pred CcEEEEEeccCCC--cce---eHHHHHHHHHhcCCceeEEeecccccchHHHHHHHhHhhCCeeEecccccchHHHHH--
Confidence 5888888886643 111 112333332 356789999853 3345588999996664 3332 3321
Q ss_pred HHHHhhh-hhcCEEEEehh
Q psy8483 98 KLVKKLA-KKYDAFLASDA 115 (161)
Q Consensus 98 k~~kkl~-~~~d~fiA~~~ 115 (161)
+-.+++. ..||++|.+.+
T Consensus 174 egv~~fKke~fdvIIvDTS 192 (483)
T KOG0780|consen 174 EGVDRFKKENFDVIIVDTS 192 (483)
T ss_pred HHHHHHHhcCCcEEEEeCC
Confidence 1122232 45999999863
No 27
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=38.79 E-value=1.1e+02 Score=21.80 Aligned_cols=59 Identities=17% Similarity=0.207 Sum_probs=39.2
Q ss_pred EEEEecCc---------ccHHHHHHCCCCC----CCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhcccccc
Q psy8483 64 QVCILGDQ---------QHCDEAKAANVPF----MDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNK 130 (161)
Q Consensus 64 kI~V~~~~---------~~~~~ak~ag~~v----vg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~Lgp 130 (161)
+|+|+|.+ ...+.|++.|.++ .+..++... ..+||+++.+|.+-=.+.. +-....+
T Consensus 2 ~Ill~C~~GaSSs~la~km~~~a~~~gi~~~i~a~~~~e~~~~----------~~~~Dvill~PQv~~~~~~-i~~~~~~ 70 (99)
T cd05565 2 NVLVLCAGGGTSGLLANALNKGAKERGVPLEAAAGAYGSHYDM----------IPDYDLVILAPQMASYYDE-LKKDTDR 70 (99)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHHHh----------ccCCCEEEEcChHHHHHHH-HHHHhhh
Confidence 57788753 2445688899982 445554432 3679999999988777776 5556665
Q ss_pred CCC
Q psy8483 131 AGK 133 (161)
Q Consensus 131 rgk 133 (161)
.|.
T Consensus 71 ~~i 73 (99)
T cd05565 71 LGI 73 (99)
T ss_pred cCC
Confidence 543
No 28
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=29.76 E-value=1.1e+02 Score=26.66 Aligned_cols=76 Identities=26% Similarity=0.460 Sum_probs=40.5
Q ss_pred EEcCCCCCC--CcEEEEecCcccHHHHHH-CCCC----CCCHHH-HHHhhhc------HH------------HHHhhhhh
Q psy8483 53 VKLKHIPRP--KMQVCILGDQQHCDEAKA-ANVP----FMDVEA-LKKLNKN------KK------------LVKKLAKK 106 (161)
Q Consensus 53 v~LP~~~~k--~~kI~V~~~~~~~~~ak~-ag~~----vvg~~e-L~~~~~~------~k------------~~kkl~~~ 106 (161)
|.|=|..|. ..+|.|.+|++.--.|-. .|-+ ||.++| |+++... .+ .-..+...
T Consensus 142 v~lm~~RGDL~gK~I~vvGDDDLtsia~aLt~mpk~iaVvDIDERli~fi~k~aee~g~~~ie~~~~Dlr~plpe~~~~k 221 (354)
T COG1568 142 VALMYSRGDLEGKEIFVVGDDDLTSIALALTGMPKRIAVVDIDERLIKFIEKVAEELGYNNIEAFVFDLRNPLPEDLKRK 221 (354)
T ss_pred eeeeccccCcCCCeEEEEcCchhhHHHHHhcCCCceEEEEechHHHHHHHHHHHHHhCccchhheeehhcccChHHHHhh
Confidence 455555542 445777777665444333 1322 666666 4444211 00 00124466
Q ss_pred cCEEEEehh-hHhhhhhhhcccc
Q psy8483 107 YDAFLASDA-LIKQIPRLLGPGL 128 (161)
Q Consensus 107 ~d~fiA~~~-~m~~l~k~LG~~L 128 (161)
||.|+.+|- -++.+.-.|||..
T Consensus 222 FDvfiTDPpeTi~alk~FlgRGI 244 (354)
T COG1568 222 FDVFITDPPETIKALKLFLGRGI 244 (354)
T ss_pred CCeeecCchhhHHHHHHHHhccH
Confidence 999999874 4555555666654
No 29
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=29.02 E-value=73 Score=24.63 Aligned_cols=33 Identities=12% Similarity=0.095 Sum_probs=25.1
Q ss_pred CcEEEEecCcc-cHHHHHHCCCCCCCHHHHHHhh
Q psy8483 62 KMQVCILGDQQ-HCDEAKAANVPFMDVEALKKLN 94 (161)
Q Consensus 62 ~~kI~V~~~~~-~~~~ak~ag~~vvg~~eL~~~~ 94 (161)
...|+|++++. ....|...||..++.++|....
T Consensus 94 ~~~v~VVTSD~~iq~~~~~~GA~~iss~ef~~~l 127 (166)
T PF05991_consen 94 PRQVTVVTSDREIQRAARGRGAKRISSEEFLREL 127 (166)
T ss_pred CCeEEEEeCCHHHHHHHhhCCCEEEcHHHHHHHH
Confidence 46899998654 3445788999999999988443
No 30
>KOG1588|consensus
Probab=28.89 E-value=22 Score=30.09 Aligned_cols=11 Identities=27% Similarity=0.329 Sum_probs=9.3
Q ss_pred hccccccCCCC
Q psy8483 124 LGPGLNKAGKF 134 (161)
Q Consensus 124 LG~~Lgprgkm 134 (161)
.||+|||||..
T Consensus 109 VGRILGPrGnS 119 (259)
T KOG1588|consen 109 VGRILGPRGNS 119 (259)
T ss_pred ccccccCCcch
Confidence 69999999853
No 31
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=28.87 E-value=23 Score=28.53 Aligned_cols=26 Identities=8% Similarity=0.163 Sum_probs=22.6
Q ss_pred cEEEEecCcccHHHHHHCCCCCCCHH
Q psy8483 63 MQVCILGDQQHCDEAKAANVPFMDVE 88 (161)
Q Consensus 63 ~kI~V~~~~~~~~~ak~ag~~vvg~~ 88 (161)
.|||=+.+.+.++.|.++|++++|.-
T Consensus 3 vKICGit~~eda~~~~~~GaD~iGfI 28 (207)
T PRK13958 3 LKFCGFTTIKDVTAASQLPIDAIGFI 28 (207)
T ss_pred EEEcCCCcHHHHHHHHHcCCCEEEEe
Confidence 68999999888999999999977763
No 32
>COG0135 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=24.45 E-value=30 Score=28.23 Aligned_cols=26 Identities=19% Similarity=0.413 Sum_probs=22.4
Q ss_pred CcEEEEecCcccHHHHHHCCCCCCCH
Q psy8483 62 KMQVCILGDQQHCDEAKAANVPFMDV 87 (161)
Q Consensus 62 ~~kI~V~~~~~~~~~ak~ag~~vvg~ 87 (161)
..|||=++..+.++.|.++|++++|.
T Consensus 3 ~vKICGlt~~eda~~a~~~gad~iG~ 28 (208)
T COG0135 3 KVKICGLTRLEDAKAAAKAGADYIGF 28 (208)
T ss_pred ceEECCCCCHHHHHHHHHcCCCEEEE
Confidence 46899999988899999999997664
No 33
>PF10740 DUF2529: Protein of unknown function (DUF2529); InterPro: IPR019676 This entry represents a protein family conserved in the Bacillales. Their function is not known. ; PDB: 3JX9_A.
Probab=23.60 E-value=18 Score=28.89 Aligned_cols=74 Identities=14% Similarity=0.177 Sum_probs=32.9
Q ss_pred CcceeeeEEcCC-C-----CCCCcEEEEecCcc-------cHHHHHHCCCCCCCHHHHHHhhhcHHHHHhhhhhcCEEEE
Q psy8483 46 DKRFSGTVKLKH-I-----PRPKMQVCILGDQQ-------HCDEAKAANVPFMDVEALKKLNKNKKLVKKLAKKYDAFLA 112 (161)
Q Consensus 46 ~~~i~~~v~LP~-~-----~~k~~kI~V~~~~~-------~~~~ak~ag~~vvg~~eL~~~~~~~k~~kkl~~~~d~fiA 112 (161)
.-+++..-.||. . .-...||++|+... .+++..+.|+++|+.....+.. -.|..-.|+||.
T Consensus 60 ~E~l~~~k~l~~~~~~~~~lt~~DRVllfs~~~~~~e~~~~a~~L~~~gi~~v~Vs~~~~~~------~~l~~~~~~~Id 133 (172)
T PF10740_consen 60 AEPLPSAKRLSEDLENFDELTETDRVLLFSPFSTDEEAVALAKQLIEQGIPFVGVSPNKPDE------EDLEDLADVHID 133 (172)
T ss_dssp TT--TTEEE--TT--------TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEE-SS---------TTGGG-SSS-EE
T ss_pred CCCCchhhcCcccccccccccccceEEEEeCCCCCHHHHHHHHHHHHCCCCEEEEEecCCCC------Cchhhhhhheee
Confidence 345666777772 2 33456999999531 2345677899987777332221 126555889998
Q ss_pred ehhhHhhhhhhhc
Q psy8483 113 SDALIKQIPRLLG 125 (161)
Q Consensus 113 ~~~~m~~l~k~LG 125 (161)
..--+|.||.==|
T Consensus 134 l~~~~~LvP~EdG 146 (172)
T PF10740_consen 134 LKLPKPLVPTEDG 146 (172)
T ss_dssp ----S-SEE-TTS
T ss_pred cccCCCcccCCCC
Confidence 7777777765333
No 34
>COG1440 CelA Phosphotransferase system cellobiose-specific component IIB [Carbohydrate transport and metabolism]
Probab=23.38 E-value=1.7e+02 Score=21.37 Aligned_cols=63 Identities=11% Similarity=0.132 Sum_probs=43.6
Q ss_pred EEEEecCc---------ccHHHHHHCCCC----CCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhcccccc
Q psy8483 64 QVCILGDQ---------QHCDEAKAANVP----FMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNK 130 (161)
Q Consensus 64 kI~V~~~~---------~~~~~ak~ag~~----vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~Lgp 130 (161)
+|.++|.. ...+.|++.|.+ -++..++.+-. .++|++|--|.+-=+++. +-+.+.+
T Consensus 3 ~IlLvC~aGmSTSlLV~Km~~aA~~kg~~~~I~A~s~~e~~~~~----------~~~DvvLlGPQv~y~~~~-~~~~~~~ 71 (102)
T COG1440 3 KILLVCAAGMSTSLLVTKMKKAAESKGKDVTIEAYSETELSEYI----------DNADVVLLGPQVRYMLKQ-LKEAAEE 71 (102)
T ss_pred eEEEEecCCCcHHHHHHHHHHHHHhCCCceEEEEechhHHHHhh----------hcCCEEEEChHHHHHHHH-HHHHhcc
Confidence 67788753 234557777777 46777665432 479999999998777776 6788888
Q ss_pred CCCCCCcc
Q psy8483 131 AGKFPGLL 138 (161)
Q Consensus 131 rgkmP~p~ 138 (161)
+| .|.-+
T Consensus 72 ~g-iPV~v 78 (102)
T COG1440 72 KG-IPVEV 78 (102)
T ss_pred cC-CCeEE
Confidence 88 45444
No 35
>PRK01222 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=22.60 E-value=32 Score=27.68 Aligned_cols=27 Identities=7% Similarity=0.271 Sum_probs=23.0
Q ss_pred CcEEEEecCcccHHHHHHCCCCCCCHH
Q psy8483 62 KMQVCILGDQQHCDEAKAANVPFMDVE 88 (161)
Q Consensus 62 ~~kI~V~~~~~~~~~ak~ag~~vvg~~ 88 (161)
..|||=+.+.+.++.|.++|++++|.-
T Consensus 4 ~vKICGi~~~eda~~~~~~Gad~iGfI 30 (210)
T PRK01222 4 RVKICGITTPEDAEAAAELGADAIGFV 30 (210)
T ss_pred eEEECCCCcHHHHHHHHHcCCCEEEEc
Confidence 378999998888999999999987773
No 36
>PF04208 MtrA: Tetrahydromethanopterin S-methyltransferase, subunit A ; InterPro: IPR013340 This domain is mostly found in N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A (MtrA) in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. 5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the N-terminal region of what appears to be a fusion of the MtrA and MtrF proteins [, ]. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism. ; GO: 0008168 methyltransferase activity, 0030269 tetrahydromethanopterin S-methyltransferase activity
Probab=22.50 E-value=83 Score=25.19 Aligned_cols=98 Identities=11% Similarity=0.192 Sum_probs=53.7
Q ss_pred cceeeeEEcCCCCCCCcEEEEecCccc-HHHHHHCCCCC--------CCHHHHH-HhhhcHHHHHhhhhhcCEEEEehhh
Q psy8483 47 KRFSGTVKLKHIPRPKMQVCILGDQQH-CDEAKAANVPF--------MDVEALK-KLNKNKKLVKKLAKKYDAFLASDAL 116 (161)
Q Consensus 47 ~~i~~~v~LP~~~~k~~kI~V~~~~~~-~~~ak~ag~~v--------vg~~eL~-~~~~~~k~~kkl~~~~d~fiA~~~~ 116 (161)
+.++|.+.+=++ +..|+|.+=+.+ ....-++|+.+ +|.|.++ ....|+. ..| +++|-.++
T Consensus 9 P~~~GdY~vGdp---~S~VAV~TL~S~~~~~~l~~gaAI~G~~~TENlGIEKvI~NvisNpn------IRf-lilcG~Ev 78 (176)
T PF04208_consen 9 PPVKGDYVVGDP---ESPVAVCTLGSHLLQAPLDAGAAIAGPCKTENLGIEKVIANVISNPN------IRF-LILCGSEV 78 (176)
T ss_pred CCCCcceEECCC---CCCEEEEECccccchhhhhcCceeeecccccccCHHHHHHHHhcCCC------ceE-EEEecCcc
Confidence 445666665332 334555542222 23334456553 5667766 4445542 223 34443333
Q ss_pred --------Hhhhhhh----hccccccCCCCCCccCCCccHHHHHHHHhcccee
Q psy8483 117 --------IKQIPRL----LGPGLNKAGKFPGLLSHQESMTQKIDEVKGTIKF 157 (161)
Q Consensus 117 --------m~~l~k~----LG~~LgprgkmP~p~~~~~dl~~~i~~~~~~v~~ 157 (161)
+-.|.+. =|++.|-.|..|+.-+.+ ...|++|+++|.+
T Consensus 79 ~GH~~Gqsl~aLh~NGid~~grIiGa~GaiPfleNi~---~~aV~rFq~qVel 128 (176)
T PF04208_consen 79 KGHLTGQSLLALHENGIDEDGRIIGAKGAIPFLENIP---REAVERFQQQVEL 128 (176)
T ss_pred CCCcchHHHHHHHHcCCCCCCCCccCCCCcchhhcCC---HHHHHHHHHheEE
Confidence 2333331 378999999999876544 3588999888764
No 37
>PF03946 Ribosomal_L11_N: Ribosomal protein L11, N-terminal domain; InterPro: IPR020784 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; PDB: 2ZJQ_F 2ZJP_F 3CF5_F 2WRJ_K 2WH4_K 2WRL_K 3FIN_L 2X9U_K 3I8I_L 2XUX_K ....
Probab=22.12 E-value=8.8 Score=25.23 Aligned_cols=31 Identities=23% Similarity=0.267 Sum_probs=16.7
Q ss_pred hccccccCCCCCCccCCCccHHHHHHHHhccce
Q psy8483 124 LGPGLNKAGKFPGLLSHQESMTQKIDEVKGTIK 156 (161)
Q Consensus 124 LG~~LgprgkmP~p~~~~~dl~~~i~~~~~~v~ 156 (161)
||+.|||.|.-+.- ..+|+-+.-++++.+++
T Consensus 17 lgp~LG~~Gin~~~--f~k~fN~~T~~~k~G~~ 47 (60)
T PF03946_consen 17 LGPALGPLGINIKK--FCKDFNKATKDYKPGIP 47 (60)
T ss_dssp STHHHHTTTS-HHH--HHHHHHHHTTTCTTSSE
T ss_pred cCcccccCCCCHHH--HHHHHHHHHhcccCCCE
Confidence 89999999975421 13344444444443333
No 38
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=21.84 E-value=1.5e+02 Score=25.41 Aligned_cols=21 Identities=29% Similarity=0.390 Sum_probs=11.1
Q ss_pred cHHHHHHCCCCCCCHHHHHHh
Q psy8483 73 HCDEAKAANVPFMDVEALKKL 93 (161)
Q Consensus 73 ~~~~ak~ag~~vvg~~eL~~~ 93 (161)
...+|++.|+++++.+++.++
T Consensus 284 K~~kA~~~gi~ii~e~~f~~l 304 (313)
T PRK06063 284 KGYHARQLGVPVLDEAAFLEL 304 (313)
T ss_pred HHHHHHHcCCccccHHHHHHH
Confidence 344555555555555555443
No 39
>PF01861 DUF43: Protein of unknown function DUF43; InterPro: IPR002723 This family of prokaryotic proteins have not been characterised. All the members are 350-400 amino acids long.; PDB: 2QM3_A.
Probab=21.46 E-value=94 Score=26.10 Aligned_cols=57 Identities=19% Similarity=0.320 Sum_probs=25.3
Q ss_pred CCcEEEEecCcccHHHHHH-----CCCCCCCHHH-HHHhhhcHHH-----------------HHhhhhhcCEEEEehhhH
Q psy8483 61 PKMQVCILGDQQHCDEAKA-----ANVPFMDVEA-LKKLNKNKKL-----------------VKKLAKKYDAFLASDALI 117 (161)
Q Consensus 61 k~~kI~V~~~~~~~~~ak~-----ag~~vvg~~e-L~~~~~~~k~-----------------~kkl~~~~d~fiA~~~~m 117 (161)
...+|.+++|++....|-. +.+.|+..|| |.++....-. =..+...||.|+++|---
T Consensus 44 ~gk~il~lGDDDLtSlA~al~~~~~~I~VvDiDeRll~fI~~~a~~~gl~i~~~~~DlR~~LP~~~~~~fD~f~TDPPyT 123 (243)
T PF01861_consen 44 EGKRILFLGDDDLTSLALALTGLPKRITVVDIDERLLDFINRVAEEEGLPIEAVHYDLRDPLPEELRGKFDVFFTDPPYT 123 (243)
T ss_dssp TT-EEEEES-TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EEEE---TTS---TTTSS-BSEEEE---SS
T ss_pred cCCEEEEEcCCcHHHHHHHhhCCCCeEEEEEcCHHHHHHHHHHHHHcCCceEEEEecccccCCHHHhcCCCEEEeCCCCC
Confidence 4557888887775544332 1233677766 4444321100 023567799999998543
No 40
>PLN02363 phosphoribosylanthranilate isomerase
Probab=21.41 E-value=41 Score=28.11 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=23.1
Q ss_pred CcEEEEecCcccHHHHHHCCCCCCCH
Q psy8483 62 KMQVCILGDQQHCDEAKAANVPFMDV 87 (161)
Q Consensus 62 ~~kI~V~~~~~~~~~ak~ag~~vvg~ 87 (161)
..|||=+.+.+.+..|.++|++++|.
T Consensus 48 ~VKICGit~~eda~~a~~~GaD~iGf 73 (256)
T PLN02363 48 LVKMCGITSARDAAMAVEAGADFIGM 73 (256)
T ss_pred eEEECCCCcHHHHHHHHHcCCCEEEE
Confidence 57999999988899999999997776
No 41
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=21.31 E-value=2e+02 Score=20.64 Aligned_cols=46 Identities=22% Similarity=0.196 Sum_probs=30.6
Q ss_pred eeeeEEcCCCCCC--CcEEEEecCcccH----HHHHHCCCCCCCHHHHHHhh
Q psy8483 49 FSGTVKLKHIPRP--KMQVCILGDQQHC----DEAKAANVPFMDVEALKKLN 94 (161)
Q Consensus 49 i~~~v~LP~~~~k--~~kI~V~~~~~~~----~~ak~ag~~vvg~~eL~~~~ 94 (161)
.|..+.|-+..++ -.+|..-++|+.+ +.|+++|+++....+|.++.
T Consensus 7 ~r~AvAl~Yd~~~~~AP~vvA~G~G~iAe~II~~Ake~~Vpi~edp~Lv~~L 58 (92)
T COG2257 7 IRKAVALAYDEGKDKAPKVVASGKGEIAEKIIEKAKEHGVPIQEDPLLVELL 58 (92)
T ss_pred cchheeeeeccCCCCCCEEEeecchHHHHHHHHHHHHcCCCcccCHHHHHHH
Confidence 3445666666543 3455555566544 46999999999988888664
No 42
>KOG3666|consensus
Probab=21.00 E-value=25 Score=34.22 Aligned_cols=75 Identities=19% Similarity=0.197 Sum_probs=41.7
Q ss_pred EEEecCcccHHHHHHCCCCCCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhhhhccccccCCCCCCccCC-Ccc
Q psy8483 65 VCILGDQQHCDEAKAANVPFMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKAGKFPGLLSH-QES 143 (161)
Q Consensus 65 I~V~~~~~~~~~ak~ag~~vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~LgprgkmP~p~~~-~~d 143 (161)
|++|+.|-.-.+-.-.|+--+...+|-+..-.++..+.+++.| .+|-+|.|||| |+-.-+ -..
T Consensus 665 IA~ft~GIlmMktTlVG~IEidPKqLLEdGirkeLvk~ia~a~---------------~~Glif~p~~k-ps~l~~kL~~ 728 (1141)
T KOG3666|consen 665 IAIFTEGILMMKTTLVGIIEVDPKQLLEDGIRKELVKRVAFAL---------------HRGLIFNPRAK-PSELMPKLKE 728 (1141)
T ss_pred HHHHHHHHHHHHHhheeEEeeCHHHHHHHHHHHHHHHHHHHHH---------------hcccccCCCCC-cHHHHHHHHH
Confidence 5555555333333334555556666554332333334443322 36999999999 765533 245
Q ss_pred HHHHHHHHhccc
Q psy8483 144 MTQKIDEVKGTI 155 (161)
Q Consensus 144 l~~~i~~~~~~v 155 (161)
+...|+.+|+|-
T Consensus 729 l~~tIEg~RrSF 740 (1141)
T KOG3666|consen 729 LGATIEGFRRSF 740 (1141)
T ss_pred HHHHHHHHHhhH
Confidence 667777777763
No 43
>COG0161 BioA Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism]
Probab=20.55 E-value=50 Score=30.13 Aligned_cols=39 Identities=26% Similarity=0.452 Sum_probs=31.3
Q ss_pred HHHHhhhhhcCEEEEehhhHhhhhhhhccccccC--CCCCCc
Q psy8483 98 KLVKKLAKKYDAFLASDALIKQIPRLLGPGLNKA--GKFPGL 137 (161)
Q Consensus 98 k~~kkl~~~~d~fiA~~~~m~~l~k~LG~~Lgpr--gkmP~p 137 (161)
+..|++|..||..+-.+++|-=.|| .|+.|+-- |-.|..
T Consensus 239 ~~vr~iC~ky~ILlI~DEV~tGFGR-TG~~FA~e~~gi~PDi 279 (449)
T COG0161 239 KRVREICDKYGILLIADEVATGFGR-TGKMFACEHAGIVPDI 279 (449)
T ss_pred HHHHHHHHHcCcEEEeecceeCCCc-CchhhhhhhcCCCCCe
Confidence 3567899999999999999999999 79988752 444444
No 44
>PRK10499 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIB; Provisional
Probab=20.36 E-value=2.6e+02 Score=19.95 Aligned_cols=50 Identities=12% Similarity=0.204 Sum_probs=33.7
Q ss_pred cEEEEecCc---------ccHHHHHHCCCC----CCCHHHHHHhhhcHHHHHhhhhhcCEEEEehhhHhhhhh
Q psy8483 63 MQVCILGDQ---------QHCDEAKAANVP----FMDVEALKKLNKNKKLVKKLAKKYDAFLASDALIKQIPR 122 (161)
Q Consensus 63 ~kI~V~~~~---------~~~~~ak~ag~~----vvg~~eL~~~~~~~k~~kkl~~~~d~fiA~~~~m~~l~k 122 (161)
.+|+++|.. ...+++++.|++ .++.+.... . ..+||++|..|++--.+..
T Consensus 4 kkIllvC~~G~sTSll~~km~~~~~~~gi~~~V~A~~~~~~~~-~---------~~~~DviLl~Pqi~~~~~~ 66 (106)
T PRK10499 4 KHIYLFCSAGMSTSLLVSKMRAQAEKYEVPVIIEAFPETLAGE-K---------GQNADVVLLGPQIAYMLPE 66 (106)
T ss_pred CEEEEECCCCccHHHHHHHHHHHHHHCCCCEEEEEeecchhhc-c---------ccCCCEEEECHHHHHHHHH
Confidence 478888863 234457778887 233333322 1 2579999999999988876
No 45
>PRK00536 speE spermidine synthase; Provisional
Probab=20.23 E-value=58 Score=27.38 Aligned_cols=76 Identities=18% Similarity=0.149 Sum_probs=42.5
Q ss_pred CCcEEEEecCcc--cHHHHHHCC--CCCCCHHH-HHHhhhc-----------HH-----HHHhh-hhhcCEEEEehhhHh
Q psy8483 61 PKMQVCILGDQQ--HCDEAKAAN--VPFMDVEA-LKKLNKN-----------KK-----LVKKL-AKKYDAFLASDALIK 118 (161)
Q Consensus 61 k~~kI~V~~~~~--~~~~ak~ag--~~vvg~~e-L~~~~~~-----------~k-----~~kkl-~~~~d~fiA~~~~m~ 118 (161)
.+.+|+|++.|+ .+.|.-+.. ++.|.+|+ +.+..+. ++ ..++- ...||++|.+..-=+
T Consensus 72 ~pk~VLIiGGGDGg~~REvLkh~~~v~mVeID~~Vv~~~k~~lP~~~~~~~DpRv~l~~~~~~~~~~~fDVIIvDs~~~~ 151 (262)
T PRK00536 72 ELKEVLIVDGFDLELAHQLFKYDTHVDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIICLQEPDI 151 (262)
T ss_pred CCCeEEEEcCCchHHHHHHHCcCCeeEEEECCHHHHHHHHHHCHHHHHhhcCCCEEEeehhhhccCCcCCEEEEcCCCCh
Confidence 466899998655 344444443 44555544 3333221 00 11111 256999999843333
Q ss_pred hhhhhhccccccCCCCCC
Q psy8483 119 QIPRLLGPGLNKAGKFPG 136 (161)
Q Consensus 119 ~l~k~LG~~LgprgkmP~ 136 (161)
.--+.+-+.|.|.|.|=.
T Consensus 152 ~fy~~~~~~L~~~Gi~v~ 169 (262)
T PRK00536 152 HKIDGLKRMLKEDGVFIS 169 (262)
T ss_pred HHHHHHHHhcCCCcEEEE
Confidence 333457788999988743
Done!