Query 031803
Match_columns 152
No_of_seqs 103 out of 1021
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 05:34:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031803.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031803hhsearch_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 4.9E-45 1.1E-49 292.9 15.1 145 1-148 1-145 (214)
2 PTZ00029 60S ribosomal protein 100.0 2.2E-44 4.7E-49 289.5 14.3 145 1-146 1-145 (216)
3 PRK04203 rpl1P 50S ribosomal p 100.0 3.5E-38 7.5E-43 253.2 14.5 142 4-148 2-145 (215)
4 COG0081 RplA Ribosomal protein 100.0 2.8E-38 6.1E-43 254.3 12.1 134 5-146 16-152 (228)
5 CHL00129 rpl1 ribosomal protei 100.0 3.3E-37 7.1E-42 249.8 11.6 128 13-148 22-152 (229)
6 PRK05424 rplA 50S ribosomal pr 100.0 8.6E-36 1.9E-40 241.6 12.7 128 13-148 22-152 (230)
7 TIGR01169 rplA_bact ribosomal 100.0 3.1E-35 6.7E-40 238.0 12.8 128 13-148 21-151 (227)
8 TIGR01170 rplA_mito ribosomal 100.0 2.6E-34 5.7E-39 217.8 13.0 127 13-148 3-135 (141)
9 KOG1570 60S ribosomal protein 100.0 4E-30 8.7E-35 203.8 8.0 145 1-145 2-146 (218)
10 cd00403 Ribosomal_L1 Ribosomal 100.0 3.1E-28 6.7E-33 193.0 12.9 134 10-146 2-137 (208)
11 PF00687 Ribosomal_L1: Ribosom 99.9 1E-23 2.3E-28 168.0 7.5 123 24-146 16-151 (220)
12 KOG1569 50S ribosomal protein 99.8 2.8E-20 6E-25 154.7 9.3 128 13-149 92-233 (323)
13 KOG1685 Uncharacterized conser 98.5 6.5E-08 1.4E-12 82.6 4.0 109 27-139 51-178 (343)
14 PF13003 MRL1: Ribosomal prote 96.9 0.0024 5.3E-08 48.0 5.3 59 8-68 68-133 (133)
15 TIGR01170 rplA_mito ribosomal 96.7 0.001 2.2E-08 50.6 2.0 24 117-140 106-130 (141)
16 CHL00129 rpl1 ribosomal protei 96.2 0.0025 5.4E-08 52.0 2.0 105 8-140 21-147 (229)
17 COG0081 RplA Ribosomal protein 96.2 0.0031 6.8E-08 51.5 2.4 110 2-140 16-149 (228)
18 TIGR01169 rplA_bact ribosomal 95.9 0.0044 9.6E-08 50.4 1.9 24 117-140 122-146 (227)
19 PRK05424 rplA 50S ribosomal pr 95.9 0.0041 8.9E-08 50.7 1.6 24 117-140 123-147 (230)
20 PRK04203 rpl1P 50S ribosomal p 88.3 0.33 7.2E-06 39.1 2.1 21 117-137 117-139 (215)
21 TIGR00853 pts-lac PTS system, 76.1 11 0.00023 26.4 5.7 51 61-121 2-65 (95)
22 PRK09590 celB cellobiose phosp 66.9 18 0.00038 25.9 5.1 48 64-119 3-63 (104)
23 cd00403 Ribosomal_L1 Ribosomal 62.6 6 0.00013 31.0 2.2 26 115-140 108-134 (208)
24 PRK01395 V-type ATP synthase s 58.5 33 0.00071 24.5 5.3 55 63-123 4-62 (104)
25 cd05565 PTS_IIB_lactose PTS_II 55.7 30 0.00064 24.6 4.6 46 64-119 2-60 (99)
26 cd05564 PTS_IIB_chitobiose_lic 51.0 49 0.0011 22.9 5.1 48 64-121 1-61 (96)
27 PRK13958 N-(5'-phosphoribosyl) 47.3 11 0.00024 30.0 1.4 26 63-88 3-28 (207)
28 COG0135 TrpF Phosphoribosylant 45.0 12 0.00027 30.1 1.4 26 62-87 3-28 (208)
29 PRK01222 N-(5'-phosphoribosyl) 40.4 15 0.00033 29.2 1.3 26 63-88 5-30 (210)
30 COG2257 Uncharacterized homolo 39.8 80 0.0017 22.4 4.6 46 49-94 7-58 (92)
31 PRK10499 PTS system N,N'-diace 39.7 76 0.0017 22.5 4.7 51 63-123 4-67 (106)
32 PF00697 PRAI: N-(5'phosphorib 38.6 20 0.00044 28.0 1.7 26 63-88 1-26 (197)
33 KOG1198 Zinc-binding oxidoredu 37.1 54 0.0012 28.2 4.2 46 62-112 183-231 (347)
34 PF05991 NYN_YacP: YacP-like N 36.8 53 0.0012 25.1 3.7 86 6-94 21-127 (166)
35 PLN02363 phosphoribosylanthran 36.5 20 0.00043 29.7 1.3 28 61-88 47-74 (256)
36 PF01990 ATP-synt_F: ATP synth 35.3 1.1E+02 0.0024 20.9 4.9 51 65-121 1-57 (95)
37 PTZ00469 60S ribosomal subunit 35.1 1.3E+02 0.0028 24.0 5.7 73 61-141 95-170 (187)
38 PRK02228 V-type ATP synthase s 34.1 1.4E+02 0.003 20.9 5.3 53 63-121 1-59 (100)
39 cd00405 PRAI Phosphoribosylant 32.2 27 0.00058 27.1 1.4 27 63-89 1-27 (203)
40 PF10820 DUF2543: Protein of u 30.9 36 0.00079 23.2 1.7 26 72-97 53-78 (81)
41 PF04481 DUF561: Protein of un 29.6 72 0.0016 26.4 3.5 51 65-118 64-130 (242)
42 PRK03957 V-type ATP synthase s 29.2 2E+02 0.0044 20.1 5.9 52 64-121 2-59 (100)
43 PF02302 PTS_IIB: PTS system, 28.9 17 0.00037 24.1 -0.2 21 105-125 46-67 (90)
44 PRK00536 speE spermidine synth 28.6 91 0.002 25.9 4.0 72 60-131 71-169 (262)
45 PF01262 AlaDh_PNT_C: Alanine 26.4 24 0.00053 26.6 0.3 37 53-90 12-52 (168)
46 PRK01189 V-type ATP synthase s 26.1 2.4E+02 0.0053 20.0 5.5 67 64-138 4-76 (104)
47 PRK06063 DNA polymerase III su 25.2 1.1E+02 0.0025 25.7 4.1 20 73-92 284-303 (313)
48 COG1436 NtpG Archaeal/vacuolar 24.8 83 0.0018 22.6 2.8 55 63-123 3-63 (104)
49 TIGR02922 conserved hypothetic 24.8 48 0.001 22.0 1.4 25 48-72 30-54 (67)
50 PF13241 NAD_binding_7: Putati 24.1 21 0.00045 24.9 -0.5 54 61-114 6-68 (103)
51 KOG2697 Histidinol dehydrogena 23.6 49 0.0011 28.9 1.6 19 116-134 206-226 (446)
52 PF04413 Glycos_transf_N: 3-De 23.0 1.6E+02 0.0036 22.7 4.4 68 52-119 76-162 (186)
53 COG5583 Uncharacterized small 22.0 2.2E+02 0.0047 18.2 3.9 24 7-37 8-31 (54)
54 PF09558 DUF2375: Protein of u 21.9 58 0.0012 21.9 1.4 24 49-72 33-56 (71)
55 COG1568 Predicted methyltransf 21.9 3.4E+02 0.0073 23.6 6.2 75 53-127 142-243 (354)
56 TIGR03884 sel_bind_Methan sele 21.8 51 0.0011 22.5 1.1 14 73-86 34-48 (74)
57 PRK09427 bifunctional indole-3 21.7 45 0.00098 29.9 1.1 28 61-88 257-284 (454)
58 PF01861 DUF43: Protein of unk 21.0 1E+02 0.0022 25.6 3.0 57 61-117 44-123 (243)
No 1
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=4.9e-45 Score=292.89 Aligned_cols=145 Identities=52% Similarity=0.826 Sum_probs=138.3
Q ss_pred CCcccHHHHHHHHHHHHHhhhhhccCCCceeEEEEEEecccCCCCCCceeeeEEccCCCCCCcEEEEecCchhHHHHHHc
Q 031803 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKI 80 (152)
Q Consensus 1 ~~~~~~~~l~~av~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~a 80 (152)
||||+++.+.+||+.++++. ++++|+||||++|+|||+|+++++++||+|.|||+++++.+|||||+++++++|+++
T Consensus 1 m~k~~~~~i~~Av~~~lk~~---~~~kF~Etvdl~v~Lk~iDp~kd~~irg~v~LPhg~gk~~kV~v~~~~~~~~~Ak~a 77 (214)
T PTZ00225 1 MSKIPPQTLSEAIQAVLKVD---KERKFKESIDLQVNLKNYDPQKDKRFSGSLKLPNVCRPRMTVCLLCDLVHEDIAKKE 77 (214)
T ss_pred CCcCCHHHHHHHHHHHHHhc---ccCCCCceEEEEEeccCcCCCcCcccceeEECCCCCCCCcEEEEECChHHHHHHHHC
Confidence 89999999999999988654 778999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCCCCCccccc
Q 031803 81 GLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCYSPRIPGVQ 148 (152)
Q Consensus 81 Ga~~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~~~~~~~~~ 148 (152)
||+++|.+||.+++++++.+|||+.+||+|||||++||.|+|+|||.|+|++|||+++++++|+.+.+
T Consensus 78 Gad~v~~e~l~~l~k~~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~~~~~~dl~~~i 145 (214)
T PTZ00225 78 GVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTVCSPSESLPDKV 145 (214)
T ss_pred CCCEECHHHHHHHHhccHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCcccCCccCHHHHH
Confidence 99999999999999999999999999999999999999999999998889999999999999987543
No 2
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=2.2e-44 Score=289.45 Aligned_cols=145 Identities=68% Similarity=1.045 Sum_probs=138.8
Q ss_pred CCcccHHHHHHHHHHHHHhhhhhccCCCceeEEEEEEecccCCCCCCceeeeEEccCCCCCCcEEEEecCchhHHHHHHc
Q 031803 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKI 80 (152)
Q Consensus 1 ~~~~~~~~l~~av~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~a 80 (152)
||+++++.|++||+++++|.+. ++++|+||||++|+|||+|+++++++||+|.|||++|++.+|||||+++.+++|+++
T Consensus 1 m~~~~~~~~~~av~~~~~~~~~-~~~~f~esv~~~i~Lk~id~~~~~~ir~~v~LP~~~gk~~~v~V~a~~~~~~~Ak~a 79 (216)
T PTZ00029 1 MSKLSSEALRKAIAEILEGSEE-KKRKFVETVELQIGLKDYDTQKDKRFSGSVKLPNVPKPNLKVCVLGDAVHCDEAKKL 79 (216)
T ss_pred CCcCCHHHHHHHHHHHHhhccc-cccCCceEEEEEEEcCCCCCCcCcccceeEecCCCCCCCcEEEEECCcHHHHHHHHc
Confidence 8999999999999999987544 889999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCCCCCccc
Q 031803 81 GLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCYSPRIPG 146 (152)
Q Consensus 81 Ga~~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~~~~~~~ 146 (152)
||++||.+||+++.++++..|+++.+||+||||+++||.|+|+|||+|||++|+|++++.++|+.+
T Consensus 80 Ga~vvg~edL~~~~k~~k~~kkl~~~fD~flA~~~im~~l~riLGp~l~p~~K~P~~v~~~~d~~~ 145 (216)
T PTZ00029 80 GLDFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIPRLLGPGLNKAGKFPTLITHNDDIED 145 (216)
T ss_pred CCCEecHHHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCcccCccCHHH
Confidence 999999999999999999999999999999999999999999999999999999999988888774
No 3
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=3.5e-38 Score=253.23 Aligned_cols=142 Identities=30% Similarity=0.467 Sum_probs=129.3
Q ss_pred ccHHHHHHHHHHHHHhhhhhccCCCceeEEEEEEecccCCCC-CCceeeeEEccCCCCCCcEEEEecCchhHHHHHHcCC
Q 031803 4 LQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGL 82 (152)
Q Consensus 4 ~~~~~l~~av~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~-~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~aGa 82 (152)
+++|.+.+||+.+++.. ++++|+||||++|+|||+|+++ ++++||+|.|||+++++.+|||||+++.+++|+++||
T Consensus 2 ~~~~~~~eai~~~k~~~---~~~kf~esvel~v~Lk~id~~k~~~~irg~i~LP~~~~k~~~V~vf~~~~~~~~Ak~aGa 78 (215)
T PRK04203 2 MDREKIEEAVKEALEEA---PKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAKGELALQAKEAGA 78 (215)
T ss_pred CcHHHHHHHHHHHHHhc---ccCCCCceEEEEEEecCCCCCccCceeeEEEECCCCCCCCcEEEEEcChHhHHHHHHcCC
Confidence 57888999988876533 7789999999999999999984 9999999999999999999999999999999999999
Q ss_pred C-ccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCCCCCccccc
Q 031803 83 D-YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCYSPRIPGVQ 148 (152)
Q Consensus 83 ~-~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~~~~~~~~~ 148 (152)
+ ++|.++|.++.++++.+|+|+.+||+|||||+||+.|+++||+.|+|++|||+|++.+.|+.+.+
T Consensus 79 ~~v~~~e~L~~i~~~~k~~rkl~~~fD~~lA~~~im~~l~k~LGk~lgprgkmP~p~~~t~di~~~i 145 (215)
T PRK04203 79 DYVITREELEELGGDKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGPRGKMPTPLPPNADIKPLV 145 (215)
T ss_pred CEEeCHHHHHHHhcChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCcCCCCCHHHHH
Confidence 9 66777788888888999999999999999999999999999999999999999999887877543
No 4
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-38 Score=254.26 Aligned_cols=134 Identities=31% Similarity=0.485 Sum_probs=115.2
Q ss_pred cHHHHHHHHHHHHHhhhhhccCCCceeEEEEEEecccCCC-CCCceeeeEEccCCCCCCcEEEEecCchhHHHHHHcCCC
Q 031803 5 QSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQ-KDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLD 83 (152)
Q Consensus 5 ~~~~l~~av~~~~~~~~~~~~~kf~esvel~i~lk~~d~k-~~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~aGa~ 83 (152)
+....+. |.+|++++++.+.++|+||||++|+| ++|++ +++++||+|.|||++|+..||||||+++.+++|++|||+
T Consensus 16 d~~~~~~-i~eai~~~ke~~~~kF~etVevav~L-~vD~~k~dq~vrg~VvLP~g~gk~vrV~Vfa~g~~~~~A~~AGad 93 (228)
T COG0081 16 DRNKLYS-LEEAVKLLKETSKRKFDETVEVAVNL-KVDPRKPDQRVRGSVVLPNGTGKTVRVAVFADGEKAEEAKAAGAD 93 (228)
T ss_pred hhhhhhh-HHHHHHHHHhccccCcceEEEEEEEc-ccCCCCcccccceeEECCCCCCCccEEEEEcChHhHHHHHHcCCC
Confidence 3334443 56666667777889999999999999 59997 699999999999999999999999999999999999999
Q ss_pred ccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCC--CCCCccc
Q 031803 84 YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPC--YSPRIPG 146 (152)
Q Consensus 84 ~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~--~~~~~~~ 146 (152)
+||++||.+.+++++ ..+||+|||||+|||.+ +.|||.|+|+|+||+|++ ++.|+.+
T Consensus 94 ~Vg~edl~e~ik~~r-----~~~fD~~IAtpdmM~~v-~~LG~vLGPRGlMP~Pk~gTvt~Dv~~ 152 (228)
T COG0081 94 YVGGEDLIELIKNGR-----AKDFDVFIATPDMMPLV-GKLGKVLGPRGLMPNPKTGTVTDDVAK 152 (228)
T ss_pred EecHHHHHHHHhCcc-----hhcCCEEEECchHHHHH-HHHhhhcCCCCCCCCCCCCCCCcCHHH
Confidence 999999999988874 38999999999999998 667777777777777777 5778764
No 5
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=100.00 E-value=3.3e-37 Score=249.81 Aligned_cols=128 Identities=21% Similarity=0.354 Sum_probs=109.1
Q ss_pred HHHHHHhhhhhccCCCceeEEEEEEecccCCC-CCCceeeeEEccCCCCCCcEEEEecCchhHHHHHHcCCCccCHHHHH
Q 031803 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQ-KDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEGLK 91 (152)
Q Consensus 13 v~~~~~~~~~~~~~kf~esvel~i~lk~~d~k-~~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~aGa~~vg~~eL~ 91 (152)
+.+|++.+++.+.++|+||||++|+| |+|++ +++++||+|.|||+++++.+|||||+++++++|+++||++||++||+
T Consensus 22 l~eAi~~~k~~~~~kF~esvel~i~L-~id~kk~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~eAk~aGad~vg~edLi 100 (229)
T CHL00129 22 PEEAINLLKETATAKFIETAEAHISL-NIDPKYADQQLRTTVTLPKGTGKTIRIAVLTNEEKITEAKNAGADIVGSDDLI 100 (229)
T ss_pred HHHHHHHHHHhCcCCCCccEEEEEEE-CCCCCCCCCceeeEEECCCCCCCCcEEEEECChHhHHHHHHcCCCEeCHHHHH
Confidence 44555556666889999999999999 99999 59999999999999999999999999999999999999999999998
Q ss_pred HHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCCC--CCccccc
Q 031803 92 KLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCYS--PRIPGVQ 148 (152)
Q Consensus 92 k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~~--~~~~~~~ 148 (152)
+.++++ ..+||+|||||++|++|+| |||.|+|+|+||+|.+++ +|+.+.+
T Consensus 101 ~~ik~~------~~~fd~~iAt~d~m~~l~k-LgriLGprGlMP~pk~gTvt~di~~~V 152 (229)
T CHL00129 101 EEITKG------NLDFDLLIATPDMMPKLAK-LGRVLGPRGLMPSPKSGTVTTDLASAI 152 (229)
T ss_pred HHHHcC------cccCCEEEECHHHHHHHHH-hcCcccccCCCCCCCCCCccccHHHHH
Confidence 655443 3799999999999999887 777777777777777665 7877543
No 6
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=100.00 E-value=8.6e-36 Score=241.63 Aligned_cols=128 Identities=23% Similarity=0.364 Sum_probs=108.1
Q ss_pred HHHHHHhhhhhccCCCceeEEEEEEecccCCCC-CCceeeeEEccCCCCCCcEEEEecCchhHHHHHHcCCCccCHHHHH
Q 031803 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEGLK 91 (152)
Q Consensus 13 v~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~-~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~aGa~~vg~~eL~ 91 (152)
+.+|++.+++.+.++|+||||++|+| |+|+++ ++++||+|.|||+++++.||||||+++++++|+++||++||++||+
T Consensus 22 l~eAi~~lk~~~~~kF~esvel~v~L-~id~kK~~~~irg~v~LP~~~gk~~kI~Vfa~~~~~~~Ak~aGa~~vg~eeLi 100 (230)
T PRK05424 22 LEEAIALVKETATAKFDETVDVAVNL-GVDPRKADQQVRGAVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADIVGGEDLI 100 (230)
T ss_pred HHHHHHHHHhhccCCCCCcEEEEEEe-CCCCCCCCCeeeEEEECCCCCCCCcEEEEECChHhHHHHHHcCCCEeCHHHHH
Confidence 33444445555788999999999999 999995 9999999999999999999999999999999999999999999998
Q ss_pred HHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCCC--CCccccc
Q 031803 92 KLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCYS--PRIPGVQ 148 (152)
Q Consensus 92 k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~~--~~~~~~~ 148 (152)
+.++++. .+||+|||||++||+|++ |||.|+|+|+||+|.+++ +|+.+.+
T Consensus 101 ~~ik~~~------~~fd~~iat~~~m~~l~~-Lg~iLGPrGlMP~pk~gTv~~di~~~I 152 (230)
T PRK05424 101 EKIKGGW------LDFDVVIATPDMMGKVGK-LGRILGPRGLMPNPKTGTVTMDVAKAV 152 (230)
T ss_pred HHHhcCC------CcCCEEEECHHHHHHHHH-hccccccccCCCCCCCCCcchhHHHHH
Confidence 7776542 489999999999999886 777777777777776665 7877543
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=3.1e-35 Score=238.00 Aligned_cols=128 Identities=25% Similarity=0.388 Sum_probs=104.9
Q ss_pred HHHHHHhhhhhccCCCceeEEEEEEecccCCCC-CCceeeeEEccCCCCCCcEEEEecCchhHHHHHHcCCCccCHHHHH
Q 031803 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEGLK 91 (152)
Q Consensus 13 v~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~-~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~aGa~~vg~~eL~ 91 (152)
+.+|++.+++.+.++|+||||++|+| |+|+++ ++++||+|.|||+++++.||||||+++++++|+++||++||++||+
T Consensus 21 l~eAi~~lk~~~~~~f~esvel~i~L-~id~kK~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~~Ak~aGa~~vg~~eLi 99 (227)
T TIGR01169 21 LDEAIALLKETATAKFDETVEVAIRL-GIDPRKSDQQVRGTVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADYVGSDDLI 99 (227)
T ss_pred HHHHHHHHHhhccCCCCCCEEEEEEE-CcCCCcCCCeeeEEEECCCCCCCCcEEEEEcCchhHHHHHHcCCCEeCHHHHH
Confidence 34444445556888999999999999 999996 9999999999999999999999999999999999999999999998
Q ss_pred HHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCC--CCCccccc
Q 031803 92 KLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCY--SPRIPGVQ 148 (152)
Q Consensus 92 k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~--~~~~~~~~ 148 (152)
+.++++ ..+||+|||||++||+|+ .||+.|+|+|+||++..+ ++|+.+.+
T Consensus 100 ~~ik~~------~~~fd~~iat~~~m~~l~-~Lg~iLGPrGlMP~~k~gtv~~di~~~I 151 (227)
T TIGR01169 100 EKIKKG------WLDFDVVIATPDMMRVVG-KLGRILGPRGLMPNPKTGTVTADVAKAV 151 (227)
T ss_pred HHHHcC------CccCCEEEECHHHHHHHH-HhccccccccCCCCCCCCCccccHHHHH
Confidence 755444 389999999999999986 455555555555555555 47877554
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=2.6e-34 Score=217.78 Aligned_cols=127 Identities=20% Similarity=0.259 Sum_probs=99.5
Q ss_pred HHHHHHhhhhhccC--CCceeEEEEEEecccCCCCCCceeeeEEccCCCCCCcEEEEecCchh-HHHHHHcCCCccCHHH
Q 031803 13 VSSIVQYSKETKKR--NFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQH-VEEAEKIGLDYMDVEG 89 (152)
Q Consensus 13 v~~~~~~~~~~~~~--kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~~k~~kI~Vf~~~~~-~~~Ak~aGa~~vg~~e 89 (152)
|.+|++++++.... +|+||||++|+| |++.+ ..++||+|.|||+++++.||||||++++ +++|+++||+++|++|
T Consensus 3 i~eA~~~lk~~~~~~~~~~etvel~i~L-~~~~~-~~~irg~v~LP~~~~k~~kV~Vf~~~~~~~~~Ak~aGa~~vg~ed 80 (141)
T TIGR01170 3 VIKAFVYLKTKSISMYVPKQSVNLDIGL-LMELG-KESVQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGGDD 80 (141)
T ss_pred HHHHHHHHHHhcccCCCCCceEEEEEEE-CCCCC-CCCceEEEECCCCCCCCCEEEEECCChHHHHHHHHcCCCEeCHHH
Confidence 45556666666555 999999999999 77765 3459999999999999999999999987 6889999999999999
Q ss_pred HHHHhhchHHHHHhhhc-ccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCCC--CCccccc
Q 031803 90 LKKLNKNKKLVKKLAKK-YHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCYS--PRIPGVQ 148 (152)
Q Consensus 90 L~k~~k~~~~~kkl~~~-fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~~--~~~~~~~ 148 (152)
|++.+++++ .+ ||+|||||++|++|+ .||+.|+|+|+||++.+++ +|+.+.+
T Consensus 81 Li~~i~~g~------~~~fd~~iA~~~~m~~l~-~Lg~iLGprGlMP~~k~gTv~~di~~~I 135 (141)
T TIGR01170 81 LIKKIEDGE------IKPFDYLIAHPDIVPELA-QLRRLLGPKGLMPSPKRGTVGDNLLSMI 135 (141)
T ss_pred HHHHHhcCC------cccccEEEECHHHHHHHH-HhhcccccCcCCCCCCCCCcccCHHHHH
Confidence 865444432 55 999999999999977 5555555555555555554 7877543
No 9
>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=4e-30 Score=203.77 Aligned_cols=145 Identities=69% Similarity=0.991 Sum_probs=140.9
Q ss_pred CCcccHHHHHHHHHHHHHhhhhhccCCCceeEEEEEEecccCCCCCCceeeeEEccCCCCCCcEEEEecCchhHHHHHHc
Q 031803 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKI 80 (152)
Q Consensus 1 ~~~~~~~~l~~av~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~a 80 (152)
|++++++++.+||.+++...++.+.++|.+||++|++|||||+.++.++.|++.|||.+++..++|||++..++.+|++.
T Consensus 2 ~sk~~~~~l~~~v~~i~~~~~~~k~~~~~~tielQi~Lk~ydp~Kdkr~s~~~~l~~~~~p~~k~cv~gd~~h~~~ak~~ 81 (218)
T KOG1570|consen 2 SSKVEEEALREAVAEILLRSKEFKNRNFVETIELQINLKNYDPQKDKRFSGSVKLPHAPRPKMKVCVIGDQQHCDEAKAI 81 (218)
T ss_pred CcchhHHHHHHHHHHHHhccccccCccceeeeeeeecccccChhHhCcccceEecCCCCCccceeeeechHHHHHHhhcC
Confidence 58899999999999999988888999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCCCCCcc
Q 031803 81 GLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCYSPRIP 145 (152)
Q Consensus 81 Ga~~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~~~~~~ 145 (152)
|.+.+..++|++..++++.++|+++.||+|||+.+++.+|.|+|||||...||+|+++.++||+-
T Consensus 82 ~~p~m~~d~lkklnk~Kklvkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~l~~~d~l~ 146 (218)
T KOG1570|consen 82 DLPAMDIDALKKLNKNKKLVKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSLLVHGDSLY 146 (218)
T ss_pred CCCCcCHHHHhcCcccchHHHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCccccchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999875
No 10
>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=99.96 E-value=3.1e-28 Score=193.01 Aligned_cols=134 Identities=38% Similarity=0.535 Sum_probs=119.4
Q ss_pred HHHHHHHHHhhhhhccCCCceeEEEEEEecccCCCCCCceeeeEEccCCCCCCcEEEEecCchhHHHHHHcCCCccCHHH
Q 031803 10 REAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMDVEG 89 (152)
Q Consensus 10 ~~av~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~~k~~kI~Vf~~~~~~~~Ak~aGa~~vg~~e 89 (152)
.+|++.+.++.. ...+|+|+|+++|+|+.++.++++++++.|.|||+++++.+|||||+++.+++|+++|++++|+++
T Consensus 2 ~~Ai~~l~~~~~--~~~~~~~~v~l~i~l~~~~~~~~~~~~~~i~LPh~~~~~~~i~v~~~d~~~~~a~~~~a~vig~~~ 79 (208)
T cd00403 2 EEAIKALKKTSV--KKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQAKEAKAAGADVVGGED 79 (208)
T ss_pred HHHHHHHHHhcc--ccCCCCceEEEEEEeCCCCCccccccceeEECCCCCCCCeEEEEEcChHhHHHHHHcCCCEEcHHH
Confidence 356666554332 467999999999999877756789999999999999999999999999999999999999999999
Q ss_pred HHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCCC--CCCccc
Q 031803 90 LKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPCY--SPRIPG 146 (152)
Q Consensus 90 L~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~~--~~~~~~ 146 (152)
|++.+++++.+ +|+.+||+|||++++|+.+.+.||+.|+|++|||+++.. ++|+.+
T Consensus 80 L~~~~~~~~~~-~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~~~t~~~~l~~ 137 (208)
T cd00403 80 LKKKIKNGEAK-KLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTEDLAK 137 (208)
T ss_pred HHHHhhcchhh-hhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCCCCCCcccHHH
Confidence 99998888877 999999999999999999999999999999999999987 677764
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=99.89 E-value=1e-23 Score=168.01 Aligned_cols=123 Identities=33% Similarity=0.477 Sum_probs=107.1
Q ss_pred ccCCCceeEEEEEEecccCCCCCCce-eeeEEccCCCC-CCcEEEEecCchhHHH---------HHHcCCCccCHHHHHH
Q 031803 24 KKRNFTETIELQIGLKNYDPQKDKRF-SGSVKLPHIPR-PKMKVCMLGDAQHVEE---------AEKIGLDYMDVEGLKK 92 (152)
Q Consensus 24 ~~~kf~esvel~i~lk~~d~k~~~~i-~g~i~LPh~~~-k~~kI~Vf~~~~~~~~---------Ak~aGa~~vg~~eL~k 92 (152)
...+|+++|+|+|+++.++.+++.++ ++.|.|||++. ++.+||||+++.+.+. +.++|+.++|+++|.+
T Consensus 16 ~~~~~~~~v~l~i~~~~~~~~~~~~~~~~~i~LPh~~~~~~~~vcli~~d~~~~~~~~~~~~~~~~~~~~~vi~~~~L~~ 95 (220)
T PF00687_consen 16 EDDNFDESVYLQITLKKIPKKKDKSFKPGRIPLPHPLYIKNSKVCLIVKDPQKKAKEKEKLEEKAVEAGAKVIGGEELKK 95 (220)
T ss_dssp CCSSSSTEEEEEEEESSSTTSSCTST-EEEEEBSTSSS-SSSBEEEEESCHHHHHH-------HHHHTTCSEEECHHHHH
T ss_pred ccCCCCcEEEEEEEeCcCCCccccccccceeeecCCCCCCccEEEEEecCcchhhhhhhhhhhhhhhcccceecHHHHHH
Confidence 66799999999999987777777788 99999999998 8999999997765433 4678999999999998
Q ss_pred HhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCC-CCCCCCCCCCCC-CCCccc
Q 031803 93 LNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGL-NKAGKKVPYPCY-SPRIPG 146 (152)
Q Consensus 93 ~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL-~p~~K~pt~v~~-~~~~~~ 146 (152)
..+..+..++|+.+||+|||++++|+.+++.||+.| +|++|||+++.- ++++.+
T Consensus 96 ~~~~~~~~r~l~~~~d~flad~~i~~~l~~~Lgk~~~~~k~k~P~~v~~~~~~l~~ 151 (220)
T PF00687_consen 96 KYKTIEAKRKLAKSYDFFLADPRIMPKLPKLLGKIFYGKKGKMPIPVTLSKEDLKE 151 (220)
T ss_dssp HHCHHHHCHHHHHCSSEEEEEGGGHHHHHHHTHHHH-CCTTTSCEEBSSHTSCHHH
T ss_pred HHHHHHHHHHHHhhcCEEEECHHHHHHHHHhhhhheecccCCcceEEeccchhHHH
Confidence 866667777899999999999999999999999977 899999999876 367764
No 12
>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=99.82 E-value=2.8e-20 Score=154.67 Aligned_cols=128 Identities=23% Similarity=0.326 Sum_probs=100.3
Q ss_pred HHHHHHhhhhhccC----CCceeEEEEEEecccCCC----CCCceeeeEEccCCCC--CCcEEEEecCc-hhHHHHHHcC
Q 031803 13 VSSIVQYSKETKKR----NFTETIELQIGLKNYDPQ----KDKRFSGSVKLPHIPR--PKMKVCMLGDA-QHVEEAEKIG 81 (152)
Q Consensus 13 v~~~~~~~~~~~~~----kf~esvel~i~lk~~d~k----~~~~i~g~i~LPh~~~--k~~kI~Vf~~~-~~~~~Ak~aG 81 (152)
|+++++..++..-. .=.+++.+.|.| |+... +...+.+++..|||++ ...+|+||+++ +..++|+|+|
T Consensus 92 vq~a~~~~ke~~~~sa~~~pk~~~~l~i~l-~~~a~~~~k~~~~~~~~v~vP~Pf~~ge~r~IavFtn~~~kveeArEaG 170 (323)
T KOG1569|consen 92 VQKAVHLHKELQILSAYNVPKQPVNLRIEL-NMLAEKETKGVAPLQGSVTVPHPFAHGEIRKIAVFTNDASKVEEAREAG 170 (323)
T ss_pred HHHHHHHHHHhccchhhhCCCCceeeeEEe-eeeeeeeccccCCCceeEeccccCCCCceEEEEEecCChHHHHHHHhcc
Confidence 55666544333111 224667777776 55433 4788899999999994 46689999987 6789999999
Q ss_pred CCccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhh---hhhcCCCCCCCCCCCCCCCCCCcccccc
Q 031803 82 LDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIP---RLLGPGLNKAGKKVPYPCYSPRIPGVQS 149 (152)
Q Consensus 82 a~~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~---riLGpgL~p~~K~pt~v~~~~~~~~~~~ 149 (152)
|+++||.||++.+++++ +..+||+++|+|||||.|. ++|||. ||+.|.+|+ |+||+|++.
T Consensus 171 A~l~GG~dLIkkI~~Ge----i~~Dyd~~vA~Pdim~~l~~Lr~iL~~r-~Pn~k~gtv---g~nipemie 233 (323)
T KOG1569|consen 171 AALAGGTDLIKKIKSGE----IVADYDFYVAHPDIMPELNRLRKILGPR-FPNPKRGTV---GRNIPEMIE 233 (323)
T ss_pred ccccccHHHHHHhhcCe----EEEeeceeeecchHHHHHHHHHHHhccc-CCCcccCcc---ccchHHHHH
Confidence 99999999988777775 5677999999999999864 889999 999999998 999998863
No 13
>KOG1685 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.54 E-value=6.5e-08 Score=82.57 Aligned_cols=109 Identities=21% Similarity=0.295 Sum_probs=82.9
Q ss_pred CCceeEEEEEEecccCCCCCCceeeeEEccCCC----C--CCcEEEEecCchhH---------HHHHHcCCC----ccCH
Q 031803 27 NFTETIELQIGLKNYDPQKDKRFSGSVKLPHIP----R--PKMKVCMLGDAQHV---------EEAEKIGLD----YMDV 87 (152)
Q Consensus 27 kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~----~--k~~kI~Vf~~~~~~---------~~Ak~aGa~----~vg~ 87 (152)
++...++++.+. +.-. +.++. .|++||.+ - ....||+|.++... +...++|.+ +++.
T Consensus 51 k~~~~~~~~k~~-~~~~-~~n~~--~IP~k~~~~~~~~~~~~~~vcLIvkD~~~~~~t~~~~~d~l~~~gi~~itkVI~~ 126 (343)
T KOG1685|consen 51 KNVYKVVLQKNT-PQKV-GTNKL--KIPLKHLLKKLLLKHDDTDVCLIVKDLQQSYLTEEDAEDLLESEGIKSITKVISL 126 (343)
T ss_pred hhhHHHHHHHhc-cccc-ccccc--cccCcchhcccccCCCCCceEEEecCchhccccHHHHHHHHHHcCCccceeeeeh
Confidence 555666666665 2211 12222 34455554 2 46799999976432 444577988 8899
Q ss_pred HHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcCCCCCCCCCCCCCC
Q 031803 88 EGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGPGLNKAGKKVPYPC 139 (152)
Q Consensus 88 ~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGpgL~p~~K~pt~v~ 139 (152)
..|....+..++.++|+.+||+|||+.+++|.|+++||+.++...|.|.++.
T Consensus 127 ~~LK~~yksyeaKr~L~~sfDlflaD~RV~~~LP~llGK~f~q~kk~Pv~i~ 178 (343)
T KOG1685|consen 127 SKLKRDYKSYEAKRKLLSSFDLFLADDRVIPLLPKLLGKEFYQKKKVPVSIR 178 (343)
T ss_pred HHHHHHHHHHHHHHHHHhhccEEEEcchhHhHHHHHhhhhhcccccCceEEE
Confidence 9999999999999999999999999999999999999999999999998763
No 14
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=96.87 E-value=0.0024 Score=48.04 Aligned_cols=59 Identities=22% Similarity=0.340 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHhhhhhccCCCc---eeEEEEEEecccCCC---CCCceeeeEEccCCCCCCc-EEEEe
Q 031803 8 ALREAVSSIVQYSKETKKRNFT---ETIELQIGLKNYDPQ---KDKRFSGSVKLPHIPRPKM-KVCML 68 (152)
Q Consensus 8 ~l~~av~~~~~~~~~~~~~kf~---esvel~i~lk~~d~k---~~~~i~g~i~LPh~~~k~~-kI~Vf 68 (152)
.|++ |+.|+..++..+..+|+ |.|++.++| |+-.- +..++-+.|.|||++..+. +|+||
T Consensus 68 ~Iye-ve~Ai~mLKkfQ~lDfT~pkQ~VYldL~L-dm~l~KKkkVePF~s~i~lPypF~~eiNKv~VF 133 (133)
T PF13003_consen 68 PIYE-VEKAIDMLKKFQILDFTSPKQPVYLDLTL-DMKLEKKKKVEPFASVILLPYPFTSEINKVLVF 133 (133)
T ss_pred cHHH-HHHHHHHHHhcccccCCCCCCcEEEeeee-hhhhccccccCCCccceecccccccccceeeeC
Confidence 4555 67777777766666666 889999998 44433 2889999999999996555 99987
No 15
>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=96.67 E-value=0.001 Score=50.56 Aligned_cols=24 Identities=38% Similarity=0.509 Sum_probs=21.3
Q ss_pred HhhhhhhhcC-CCCCCCCCCCCCCC
Q 031803 117 IKQIPRLLGP-GLNKAGKKVPYPCY 140 (152)
Q Consensus 117 m~~l~riLGp-gL~p~~K~pt~v~~ 140 (152)
++.|||+||| ||||++|.||++.+
T Consensus 106 l~~Lg~iLGprGlMP~~k~gTv~~d 130 (141)
T TIGR01170 106 LAQLRRLLGPKGLMPSPKRGTVGDN 130 (141)
T ss_pred HHHhhcccccCcCCCCCCCCCcccC
Confidence 3469999999 99999999999876
No 16
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=96.24 E-value=0.0025 Score=52.04 Aligned_cols=105 Identities=18% Similarity=0.249 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHhhhh----h---------ccCCCceeEEEEEEecccCCCCCCceeeeEEccCCCC----CCcEEEEecC
Q 031803 8 ALREAVSSIVQYSKE----T---------KKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPR----PKMKVCMLGD 70 (152)
Q Consensus 8 ~l~~av~~~~~~~~~----~---------~~~kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~~----k~~kI~Vf~~ 70 (152)
.|.+||+.+++.... + ..++=++.|.=.|.|.+ ...+..+ .+.|-.+-. ++.-.-+++.
T Consensus 21 ~l~eAi~~~k~~~~~kF~esvel~i~L~id~kk~~~~irg~v~LP~-~~gk~~k---V~Vfa~~~~~~eAk~aGad~vg~ 96 (229)
T CHL00129 21 SPEEAINLLKETATAKFIETAEAHISLNIDPKYADQQLRTTVTLPK-GTGKTIR---IAVLTNEEKITEAKNAGADIVGS 96 (229)
T ss_pred CHHHHHHHHHHhCcCCCCccEEEEEEECCCCCCCCCceeeEEECCC-CCCCCcE---EEEECChHhHHHHHHcCCCEeCH
Confidence 567888888853211 1 12233566777777731 2222333 477766531 1112334444
Q ss_pred chhHHHHHHcCCC----ccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcC-CCCCCCCCCCCCCC
Q 031803 71 AQHVEEAEKIGLD----YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGP-GLNKAGKKVPYPCY 140 (152)
Q Consensus 71 ~~~~~~Ak~aGa~----~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGp-gL~p~~K~pt~v~~ 140 (152)
++..+++++ |+. ++...++... ++.|||+||| ||||++|.||++.+
T Consensus 97 edLi~~ik~-~~~~fd~~iAt~d~m~~-----------------------l~kLgriLGprGlMP~pk~gTvt~d 147 (229)
T CHL00129 97 DDLIEEITK-GNLDFDLLIATPDMMPK-----------------------LAKLGRVLGPRGLMPSPKSGTVTTD 147 (229)
T ss_pred HHHHHHHHc-CcccCCEEEECHHHHHH-----------------------HHHhcCcccccCCCCCCCCCCcccc
Confidence 555555544 442 3444443221 4458999999 99999999998876
No 17
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=96.22 E-value=0.0031 Score=51.48 Aligned_cols=110 Identities=20% Similarity=0.238 Sum_probs=66.5
Q ss_pred CcccHHHHHHHHHHHHHhhhhh-------------ccCCCceeEEEEEEecccCCCCCCceeeeEEccCCCCCCc-EE--
Q 031803 2 SKLQSDALREAVSSIVQYSKET-------------KKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKM-KV-- 65 (152)
Q Consensus 2 ~~~~~~~l~~av~~~~~~~~~~-------------~~~kf~esvel~i~lk~~d~k~~~~i~g~i~LPh~~~k~~-kI-- 65 (152)
.+.+...|.+||+.+++..... ..++=+|.|.=.|.|.+ -+.+..+ .+.+.++-.-+. +=
T Consensus 16 d~~~~~~i~eai~~~ke~~~~kF~etVevav~L~vD~~k~dq~vrg~VvLP~-g~gk~vr---V~Vfa~g~~~~~A~~AG 91 (228)
T COG0081 16 DRNKLYSLEEAVKLLKETSKRKFDETVEVAVNLKVDPRKPDQRVRGSVVLPN-GTGKTVR---VAVFADGEKAEEAKAAG 91 (228)
T ss_pred hhhhhhhHHHHHHHHHhccccCcceEEEEEEEcccCCCCcccccceeEECCC-CCCCccE---EEEEcChHhHHHHHHcC
Confidence 3567788999999998742221 33456788888899832 1123444 477787642111 11
Q ss_pred --EEecCchhHHHHHHcC-CC----ccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcC-CCCCCCCCCCC
Q 031803 66 --CMLGDAQHVEEAEKIG-LD----YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGP-GLNKAGKKVPY 137 (152)
Q Consensus 66 --~Vf~~~~~~~~Ak~aG-a~----~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGp-gL~p~~K~pt~ 137 (152)
.|.. ++..+.++. | +. ++-..++..++ ..||++||| ||||++|.||+
T Consensus 92 ad~Vg~-edl~e~ik~-~r~~~fD~~IAtpdmM~~v-----------------------~~LG~vLGPRGlMP~Pk~gTv 146 (228)
T COG0081 92 ADYVGG-EDLIELIKN-GRAKDFDVFIATPDMMPLV-----------------------GKLGKVLGPRGLMPNPKTGTV 146 (228)
T ss_pred CCEecH-HHHHHHHhC-cchhcCCEEEECchHHHHH-----------------------HHHhhhcCCCCCCCCCCCCCC
Confidence 1333 444443333 3 22 44444443332 568999999 99999999999
Q ss_pred CCC
Q 031803 138 PCY 140 (152)
Q Consensus 138 v~~ 140 (152)
.++
T Consensus 147 t~D 149 (228)
T COG0081 147 TDD 149 (228)
T ss_pred CcC
Confidence 876
No 18
>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=95.91 E-value=0.0044 Score=50.44 Aligned_cols=24 Identities=29% Similarity=0.461 Sum_probs=21.3
Q ss_pred HhhhhhhhcC-CCCCCCCCCCCCCC
Q 031803 117 IKQIPRLLGP-GLNKAGKKVPYPCY 140 (152)
Q Consensus 117 m~~l~riLGp-gL~p~~K~pt~v~~ 140 (152)
++.|||+||| ||||++|.||++.+
T Consensus 122 l~~Lg~iLGPrGlMP~~k~gtv~~d 146 (227)
T TIGR01169 122 VGKLGRILGPRGLMPNPKTGTVTAD 146 (227)
T ss_pred HHHhccccccccCCCCCCCCCcccc
Confidence 3468999999 99999999998876
No 19
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=95.87 E-value=0.0041 Score=50.71 Aligned_cols=24 Identities=29% Similarity=0.441 Sum_probs=21.2
Q ss_pred HhhhhhhhcC-CCCCCCCCCCCCCC
Q 031803 117 IKQIPRLLGP-GLNKAGKKVPYPCY 140 (152)
Q Consensus 117 m~~l~riLGp-gL~p~~K~pt~v~~ 140 (152)
++.|||+||| ||||++|.||++.+
T Consensus 123 l~~Lg~iLGPrGlMP~pk~gTv~~d 147 (230)
T PRK05424 123 VGKLGRILGPRGLMPNPKTGTVTMD 147 (230)
T ss_pred HHHhccccccccCCCCCCCCCcchh
Confidence 4459999999 99999999998876
No 20
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=88.28 E-value=0.33 Score=39.07 Aligned_cols=21 Identities=24% Similarity=0.284 Sum_probs=18.5
Q ss_pred Hhh-hhhhhcC-CCCCCCCCCCC
Q 031803 117 IKQ-IPRLLGP-GLNKAGKKVPY 137 (152)
Q Consensus 117 m~~-l~riLGp-gL~p~~K~pt~ 137 (152)
++. ||++||| |+||+++.+|.
T Consensus 117 l~k~LGk~lgprgkmP~p~~~t~ 139 (215)
T PRK04203 117 IGRYLGPVLGPRGKMPTPLPPNA 139 (215)
T ss_pred HHHHHhhhcCcCCCCCCCcCCCC
Confidence 554 8999999 99999999986
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=76.11 E-value=11 Score=26.41 Aligned_cols=51 Identities=16% Similarity=0.144 Sum_probs=33.7
Q ss_pred CCcEEEEecCch---------hHHHHHHcCCC----ccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhh
Q 031803 61 PKMKVCMLGDAQ---------HVEEAEKIGLD----YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIP 121 (152)
Q Consensus 61 k~~kI~Vf~~~~---------~~~~Ak~aGa~----~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~ 121 (152)
+..+|+++|... ..+.+++.|.+ ..+..++.+. ..+||+++.+|.+--.+.
T Consensus 2 ~~~~ILl~C~~G~sSS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~~----------~~~~Dvill~pqi~~~~~ 65 (95)
T TIGR00853 2 NETNILLLCAAGMSTSLLVNKMNKAAEEYGVPVKIAAGSYGAAGEK----------LDDADVVLLAPQVAYMLP 65 (95)
T ss_pred CccEEEEECCCchhHHHHHHHHHHHHHHCCCcEEEEEecHHHHHhh----------cCCCCEEEECchHHHHHH
Confidence 356899999643 23666778887 3344444322 267999999999875543
No 22
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=66.93 E-value=18 Score=25.92 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=31.5
Q ss_pred EEEEecCch---------hHHHHHHcCCCc----cCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhh
Q 031803 64 KVCMLGDAQ---------HVEEAEKIGLDY----MDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQ 119 (152)
Q Consensus 64 kI~Vf~~~~---------~~~~Ak~aGa~~----vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~ 119 (152)
+|+++|.+. ..+.|++.|.++ .+..++.+...+ .+||+++.+|++--.
T Consensus 3 kILlvCg~G~STSlla~k~k~~~~e~gi~~~i~a~~~~e~~~~~~~--------~~~DvIll~PQi~~~ 63 (104)
T PRK09590 3 KALIICAAGMSSSMMAKKTTEYLKEQGKDIEVDAITATEGEKAIAA--------AEYDLYLVSPQTKMY 63 (104)
T ss_pred EEEEECCCchHHHHHHHHHHHHHHHCCCceEEEEecHHHHHHhhcc--------CCCCEEEEChHHHHH
Confidence 688888642 235667778873 566665443211 369999999987643
No 23
>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=62.58 E-value=6 Score=31.02 Aligned_cols=26 Identities=23% Similarity=0.203 Sum_probs=20.8
Q ss_pred hhHhhhhhhhcC-CCCCCCCCCCCCCC
Q 031803 115 SVIKQIPRLLGP-GLNKAGKKVPYPCY 140 (152)
Q Consensus 115 ~im~~l~riLGp-gL~p~~K~pt~v~~ 140 (152)
.+...+||+||| ++||..+.+|...+
T Consensus 108 ~~~~~lgk~~~~k~k~P~~~~~t~~~~ 134 (208)
T cd00403 108 LLPKLLGKVLGPRGKMPNPKTGTVTED 134 (208)
T ss_pred HHHHHhccccccCCCCCcCCCCCCccc
Confidence 345679999999 99999999875544
No 24
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=58.48 E-value=33 Score=24.50 Aligned_cols=55 Identities=24% Similarity=0.433 Sum_probs=40.6
Q ss_pred cEEEEecCchhHHHHHHcCCC---ccCHHHHHHHhhchHHHHHhh-hcccEEEEchhhHhhhhhh
Q 031803 63 MKVCMLGDAQHVEEAEKIGLD---YMDVEGLKKLNKNKKLVKKLA-KKYHAFLASESVIKQIPRL 123 (152)
Q Consensus 63 ~kI~Vf~~~~~~~~Ak~aGa~---~vg~~eL~k~~k~~~~~kkl~-~~fd~~lAt~~im~~l~ri 123 (152)
.||+|++|.+.+-=-+-+|++ +.+.+++.+... ++. .+|-.++.|.++...+...
T Consensus 4 ~kIaVIGD~dtv~GFrLaGi~~~~v~~~ee~~~~i~------~l~~~d~gII~Ite~~a~~i~~~ 62 (104)
T PRK01395 4 YKIGVVGDKDSILPFKALGIDVFPVIDEQEAINTLR------KLAMEDYGIIYITEQIAADIPET 62 (104)
T ss_pred eeEEEEECHHHHHHHHHcCCeeEEecChHHHHHHHH------HHhcCCcEEEEEcHHHHHHhHHH
Confidence 489999998888777888998 335666654432 232 5699999999999887643
No 25
>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=55.72 E-value=30 Score=24.57 Aligned_cols=46 Identities=11% Similarity=0.101 Sum_probs=29.9
Q ss_pred EEEEecCch---------hHHHHHHcCCCc----cCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhh
Q 031803 64 KVCMLGDAQ---------HVEEAEKIGLDY----MDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQ 119 (152)
Q Consensus 64 kI~Vf~~~~---------~~~~Ak~aGa~~----vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~ 119 (152)
+|+++|.+- ..+.|++.|.++ .+..++.+. ..+||.++.+|.+--.
T Consensus 2 ~Ill~C~~GaSSs~la~km~~~a~~~gi~~~i~a~~~~e~~~~----------~~~~Dvill~PQv~~~ 60 (99)
T cd05565 2 NVLVLCAGGGTSGLLANALNKGAKERGVPLEAAAGAYGSHYDM----------IPDYDLVILAPQMASY 60 (99)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHHHh----------ccCCCEEEEcChHHHH
Confidence 588888532 346778888873 244444322 2689999999986543
No 26
>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=50.98 E-value=49 Score=22.89 Aligned_cols=48 Identities=21% Similarity=0.227 Sum_probs=29.7
Q ss_pred EEEEecCch---------hHHHHHHcCCC----ccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhh
Q 031803 64 KVCMLGDAQ---------HVEEAEKIGLD----YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIP 121 (152)
Q Consensus 64 kI~Vf~~~~---------~~~~Ak~aGa~----~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~ 121 (152)
+|+++|... ..+.+++.|.+ ..+..++.+ ...+||.++.+|.+.-.+.
T Consensus 1 kIl~~Cg~G~sTS~~~~ki~~~~~~~~~~~~v~~~~~~~~~~----------~~~~~Diil~~Pqv~~~~~ 61 (96)
T cd05564 1 KILLVCSAGMSTSILVKKMKKAAEKRGIDAEIEAVPESELEE----------YIDDADVVLLGPQVRYMLD 61 (96)
T ss_pred CEEEEcCCCchHHHHHHHHHHHHHHCCCceEEEEecHHHHHH----------hcCCCCEEEEChhHHHHHH
Confidence 467777532 23556677776 334444432 1267999999999876544
No 27
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=47.27 E-value=11 Score=29.97 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=23.2
Q ss_pred cEEEEecCchhHHHHHHcCCCccCHH
Q 031803 63 MKVCMLGDAQHVEEAEKIGLDYMDVE 88 (152)
Q Consensus 63 ~kI~Vf~~~~~~~~Ak~aGa~~vg~~ 88 (152)
.|||=+++.+.++.|.++||+++|.-
T Consensus 3 vKICGit~~eda~~~~~~GaD~iGfI 28 (207)
T PRK13958 3 LKFCGFTTIKDVTAASQLPIDAIGFI 28 (207)
T ss_pred EEEcCCCcHHHHHHHHHcCCCEEEEe
Confidence 68999999999999999999988874
No 28
>COG0135 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=45.03 E-value=12 Score=30.11 Aligned_cols=26 Identities=35% Similarity=0.632 Sum_probs=22.7
Q ss_pred CcEEEEecCchhHHHHHHcCCCccCH
Q 031803 62 KMKVCMLGDAQHVEEAEKIGLDYMDV 87 (152)
Q Consensus 62 ~~kI~Vf~~~~~~~~Ak~aGa~~vg~ 87 (152)
..|||=++..+.++.|.++||+++|.
T Consensus 3 ~vKICGlt~~eda~~a~~~gad~iG~ 28 (208)
T COG0135 3 KVKICGLTRLEDAKAAAKAGADYIGF 28 (208)
T ss_pred ceEECCCCCHHHHHHHHHcCCCEEEE
Confidence 46899999999999999999997764
No 29
>PRK01222 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=40.43 E-value=15 Score=29.18 Aligned_cols=26 Identities=23% Similarity=0.498 Sum_probs=23.2
Q ss_pred cEEEEecCchhHHHHHHcCCCccCHH
Q 031803 63 MKVCMLGDAQHVEEAEKIGLDYMDVE 88 (152)
Q Consensus 63 ~kI~Vf~~~~~~~~Ak~aGa~~vg~~ 88 (152)
.|||=+.+.+.++.|.++||+++|.-
T Consensus 5 vKICGi~~~eda~~~~~~Gad~iGfI 30 (210)
T PRK01222 5 VKICGITTPEDAEAAAELGADAIGFV 30 (210)
T ss_pred EEECCCCcHHHHHHHHHcCCCEEEEc
Confidence 68998999899999999999988874
No 30
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=39.84 E-value=80 Score=22.41 Aligned_cols=46 Identities=22% Similarity=0.176 Sum_probs=33.3
Q ss_pred eeeeEEccCCCC--CCcEEEEecCch----hHHHHHHcCCCccCHHHHHHHh
Q 031803 49 FSGSVKLPHIPR--PKMKVCMLGDAQ----HVEEAEKIGLDYMDVEGLKKLN 94 (152)
Q Consensus 49 i~g~i~LPh~~~--k~~kI~Vf~~~~----~~~~Ak~aGa~~vg~~eL~k~~ 94 (152)
.|..+.|-+..+ +-.+|..-+.|+ .++.|+++|+++.-..+|.+..
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 455666666664 344777777765 4588999999999888887765
No 31
>PRK10499 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIB; Provisional
Probab=39.68 E-value=76 Score=22.50 Aligned_cols=51 Identities=12% Similarity=0.150 Sum_probs=32.6
Q ss_pred cEEEEecCch---------hHHHHHHcCCC----ccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhh
Q 031803 63 MKVCMLGDAQ---------HVEEAEKIGLD----YMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRL 123 (152)
Q Consensus 63 ~kI~Vf~~~~---------~~~~Ak~aGa~----~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~ri 123 (152)
.||+++|..- ..+++++.|.+ .++.+.... . ..+||++|..|++.-.+..+
T Consensus 4 kkIllvC~~G~sTSll~~km~~~~~~~gi~~~V~A~~~~~~~~---~-------~~~~DviLl~Pqi~~~~~~i 67 (106)
T PRK10499 4 KHIYLFCSAGMSTSLLVSKMRAQAEKYEVPVIIEAFPETLAGE---K-------GQNADVVLLGPQIAYMLPEI 67 (106)
T ss_pred CEEEEECCCCccHHHHHHHHHHHHHHCCCCEEEEEeecchhhc---c-------ccCCCEEEECHHHHHHHHHH
Confidence 4799999642 23566777887 233332222 1 25799999999988766533
No 32
>PF00697 PRAI: N-(5'phosphoribosyl)anthranilate (PRA) isomerase; InterPro: IPR001240 Indole-3-glycerol phosphate synthase (IGPS) (see IPR001468 from INTERPRO) catalyzes the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyzes N-(5-phosphoribosyl)anthranilate isomerase (PRAI) activity, the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (GATase) N-terminal domain (see IPR000991 from INTERPRO). Phosphoribosylanthranilate isomerase (PRAI) is monomeric and labile in most mesophilic microorganisms, but dimeric and stable in the hyperthermophile Thermotoga maritima (tPRAI) []. The comparison to the known 2.0 A structure of PRAI from Escherichia coli (ePRAI) shows that tPRAI has the complete TIM- or (beta alp ha)8-barrel fold, whereas helix alpha5 in ePRAI is replaced by a loop. The subunits of tPRAI associate via the N-terminal faces of their central beta-barrels. Two long, symmetry-related loops that protrude reciprocally into cavities of the other subunit provide for multiple hydrophobic interactions. Moreover, the side chains of the N-terminal methionines and the C-terminal leucines of both subunits are immobilized in a hydrophobic cluster, and the number of salt bridges is increased in tPRAI. These features appear to be mainly responsible for the high thermostability of tPRAI []. ; GO: 0004640 phosphoribosylanthranilate isomerase activity, 0006568 tryptophan metabolic process; PDB: 1V5X_A 1PII_A 1JCM_P 2KZH_A 1LBM_A 1DL3_A 1NSJ_A.
Probab=38.61 E-value=20 Score=28.00 Aligned_cols=26 Identities=23% Similarity=0.539 Sum_probs=20.1
Q ss_pred cEEEEecCchhHHHHHHcCCCccCHH
Q 031803 63 MKVCMLGDAQHVEEAEKIGLDYMDVE 88 (152)
Q Consensus 63 ~kI~Vf~~~~~~~~Ak~aGa~~vg~~ 88 (152)
.|||=+++.+.+..|.++|++++|..
T Consensus 1 vKICGi~~~~da~~~~~~g~d~~Gfi 26 (197)
T PF00697_consen 1 VKICGITRPEDARLAAELGADYLGFI 26 (197)
T ss_dssp EEEE---SHHHHHHHHHHTSSEEEEE
T ss_pred CeECCCCcHHHHHHHHHcCCCEEeee
Confidence 48999999999999999999988764
No 33
>KOG1198 consensus Zinc-binding oxidoreductase [Energy production and conversion; General function prediction only]
Probab=37.12 E-value=54 Score=28.17 Aligned_cols=46 Identities=24% Similarity=0.268 Sum_probs=29.3
Q ss_pred CcEEEEecCchhHHHHHHcCCCc-c--CHHHHHHHhhchHHHHHhhhcccEEEE
Q 031803 62 KMKVCMLGDAQHVEEAEKIGLDY-M--DVEGLKKLNKNKKLVKKLAKKYHAFLA 112 (152)
Q Consensus 62 ~~kI~Vf~~~~~~~~Ak~aGa~~-v--g~~eL~k~~k~~~~~kkl~~~fd~~lA 112 (152)
-.+|.+.|..+..+-+++.||+. + ..+++.+..++. .-..||++|-
T Consensus 183 ~~~v~t~~s~e~~~l~k~lGAd~vvdy~~~~~~e~~kk~-----~~~~~DvVlD 231 (347)
T KOG1198|consen 183 AIKVVTACSKEKLELVKKLGADEVVDYKDENVVELIKKY-----TGKGVDVVLD 231 (347)
T ss_pred CcEEEEEcccchHHHHHHcCCcEeecCCCHHHHHHHHhh-----cCCCccEEEE
Confidence 35788888888888888888883 3 334444443321 0146999876
No 34
>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=36.78 E-value=53 Score=25.10 Aligned_cols=86 Identities=14% Similarity=0.205 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHHhhhhhccCCCceeEEEEEEecccCCCC----CCceee-eEEccCC--------------CCC-CcEE
Q 031803 6 SDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQK----DKRFSG-SVKLPHI--------------PRP-KMKV 65 (152)
Q Consensus 6 ~~~l~~av~~~~~~~~~~~~~kf~esvel~i~lk~~d~k~----~~~i~g-~i~LPh~--------------~~k-~~kI 65 (152)
.+.|..|=+.+++.+.+.. .+.. .++.|.+-++.... ...+.| .|.+-.. .+. ...|
T Consensus 21 ~~~l~~aR~~Li~~L~~y~--~~~~-~~v~VVFDa~~~~~~~~~~~~~~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v 97 (166)
T PF05991_consen 21 RGDLEAARERLIEMLSEYA--QFSG-YEVIVVFDAYKVPGGSEEREEYGGIEVVFTKEGETADDYIERLVRELKNRPRQV 97 (166)
T ss_pred cCCHHHHHHHHHHHHHHHh--cccC-CEEEEEEeCCcCCCCCceeeeeCceEEEECCCCCCHHHHHHHHHHHhccCCCeE
Confidence 3455556556665554322 3433 77888885444332 111222 3444432 112 4799
Q ss_pred EEecCc-hhHHHHHHcCCCccCHHHHHHHh
Q 031803 66 CMLGDA-QHVEEAEKIGLDYMDVEGLKKLN 94 (152)
Q Consensus 66 ~Vf~~~-~~~~~Ak~aGa~~vg~~eL~k~~ 94 (152)
+|.+++ .....|+..||..++.+++....
T Consensus 98 ~VVTSD~~iq~~~~~~GA~~iss~ef~~~l 127 (166)
T PF05991_consen 98 TVVTSDREIQRAARGRGAKRISSEEFLREL 127 (166)
T ss_pred EEEeCCHHHHHHHhhCCCEEEcHHHHHHHH
Confidence 999965 45677889999999999976443
No 35
>PLN02363 phosphoribosylanthranilate isomerase
Probab=36.47 E-value=20 Score=29.68 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=24.2
Q ss_pred CCcEEEEecCchhHHHHHHcCCCccCHH
Q 031803 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVE 88 (152)
Q Consensus 61 k~~kI~Vf~~~~~~~~Ak~aGa~~vg~~ 88 (152)
...|||=+.+.+.+..|.++||+++|.-
T Consensus 47 ~~VKICGit~~eda~~a~~~GaD~iGfI 74 (256)
T PLN02363 47 PLVKMCGITSARDAAMAVEAGADFIGMI 74 (256)
T ss_pred ceEEECCCCcHHHHHHHHHcCCCEEEEe
Confidence 3469999999999999999999988874
No 36
>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=35.34 E-value=1.1e+02 Score=20.87 Aligned_cols=51 Identities=22% Similarity=0.384 Sum_probs=36.9
Q ss_pred EEEecCchhHHHHHHcCCC--cc--CHHHHHHHhhchHHHHHhh--hcccEEEEchhhHhhhh
Q 031803 65 VCMLGDAQHVEEAEKIGLD--YM--DVEGLKKLNKNKKLVKKLA--KKYHAFLASESVIKQIP 121 (152)
Q Consensus 65 I~Vf~~~~~~~~Ak~aGa~--~v--g~~eL~k~~k~~~~~kkl~--~~fd~~lAt~~im~~l~ 121 (152)
|+|+++.+...==+-+|++ ++ ..+++.+..+ ++. .++-.++-|.+++..+.
T Consensus 1 IavIGd~~~v~gFrLaGv~~~~~~~~~ee~~~~l~------~l~~~~~~gIIii~e~~~~~~~ 57 (95)
T PF01990_consen 1 IAVIGDRDTVLGFRLAGVEGVYVNTDPEEAEEALK------ELLKDEDVGIIIITEDLAEKIR 57 (95)
T ss_dssp EEEEE-HHHHHHHHHTTSEEEEESHSHHHHHHHHH------HHHHHTTEEEEEEEHHHHTTHH
T ss_pred CEEEeCHHHHHHHHHcCCCCccCCCCHHHHHHHHH------HHhcCCCccEEEeeHHHHHHHH
Confidence 6889988877777888998 33 5666655442 233 57999999999998765
No 37
>PTZ00469 60S ribosomal subunit protein L18; Provisional
Probab=35.12 E-value=1.3e+02 Score=24.02 Aligned_cols=73 Identities=15% Similarity=0.169 Sum_probs=49.2
Q ss_pred CCcEEEEecCch-hHHHHHHcCCCccCHHHHHHHhhchHHHHHhhhcccEEEEchhhHhhhhhhhcC--CCCCCCCCCCC
Q 031803 61 PKMKVCMLGDAQ-HVEEAEKIGLDYMDVEGLKKLNKNKKLVKKLAKKYHAFLASESVIKQIPRLLGP--GLNKAGKKVPY 137 (152)
Q Consensus 61 k~~kI~Vf~~~~-~~~~Ak~aGa~~vg~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~~l~riLGp--gL~p~~K~pt~ 137 (152)
++.+||+|-=.+ ..+.-.+||-.++..++|....=. .+...+|..|.--.+..+.+|+ |.=-....|-+
T Consensus 95 pkvtVaAL~fS~~Ar~kI~~AGGe~lT~dqLa~~~P~--------G~nv~Ll~g~r~~R~a~khfg~apg~p~s~t~P~v 166 (187)
T PTZ00469 95 KKLKVCALRFTETARKRILDAGGECLTFDQLALKYPT--------GQKCILLRGPTKARTAEKHFGKAPGRPKSKARPYV 166 (187)
T ss_pred CceEEEEEecCHHHHHHHHHhCCEEEeHHHHHHHCCC--------CCceEEEECCCchhHHHHhcCCCCCCCCCCCCCce
Confidence 356899988444 455667889999999999775422 3456677777777888888887 33334345554
Q ss_pred CCCC
Q 031803 138 PCYS 141 (152)
Q Consensus 138 v~~~ 141 (152)
...|
T Consensus 167 ~skg 170 (187)
T PTZ00469 167 RSKG 170 (187)
T ss_pred eccc
Confidence 4443
No 38
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=34.09 E-value=1.4e+02 Score=20.89 Aligned_cols=53 Identities=13% Similarity=0.361 Sum_probs=38.2
Q ss_pred cEEEEecCchhHHHHHHcCCC--c-cCH-HHHHHHhhchHHHHHh--hhcccEEEEchhhHhhhh
Q 031803 63 MKVCMLGDAQHVEEAEKIGLD--Y-MDV-EGLKKLNKNKKLVKKL--AKKYHAFLASESVIKQIP 121 (152)
Q Consensus 63 ~kI~Vf~~~~~~~~Ak~aGa~--~-vg~-~eL~k~~k~~~~~kkl--~~~fd~~lAt~~im~~l~ 121 (152)
.||+|++|.+.+.--+-+|+. + +.. +|+.+.+ +++ ..+|-.++.|.++...+.
T Consensus 1 mkIaVIGD~dtv~GFrLaGi~~~~~~~~~ee~~~~l------~~l~~~~d~gII~Ite~~~~~i~ 59 (100)
T PRK02228 1 MEIAVIGSPEFTTGFRLAGIRKVYEVPDDEKLDEAV------EEVLEDDDVGILVMHDDDLEKLP 59 (100)
T ss_pred CEEEEEeCHHHHHHHHHcCCceEEeeCCHHHHHHHH------HHHhhCCCEEEEEEehhHhHhhH
Confidence 379999998888888899997 3 344 4454433 223 256999999999887765
No 39
>cd00405 PRAI Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric, monofunctional and thermolabile, but in some thermophile organisms PRAI is dimeric for reasons of stability and in others it is fused to other components of the tryptophan biosynthesis pathway to form multifunctional enzymes.
Probab=32.17 E-value=27 Score=27.12 Aligned_cols=27 Identities=19% Similarity=0.265 Sum_probs=22.4
Q ss_pred cEEEEecCchhHHHHHHcCCCccCHHH
Q 031803 63 MKVCMLGDAQHVEEAEKIGLDYMDVEG 89 (152)
Q Consensus 63 ~kI~Vf~~~~~~~~Ak~aGa~~vg~~e 89 (152)
.|||=+.+.+.++.|.++|++++|.-.
T Consensus 1 vKiCGi~~~ed~~~a~~~Gvd~ig~i~ 27 (203)
T cd00405 1 VKICGITTLEDALAAAEAGADAIGFIF 27 (203)
T ss_pred CEECCCCCHHHHHHHHHcCCCEEEEec
Confidence 378888888899999999999887653
No 40
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=30.88 E-value=36 Score=23.19 Aligned_cols=26 Identities=15% Similarity=0.262 Sum_probs=20.7
Q ss_pred hhHHHHHHcCCCccCHHHHHHHhhch
Q 031803 72 QHVEEAEKIGLDYMDVEGLKKLNKNK 97 (152)
Q Consensus 72 ~~~~~Ak~aGa~~vg~~eL~k~~k~~ 97 (152)
.+.+.|.+||++-...+||..+...|
T Consensus 53 aQ~EMA~eAgi~~~rID~IA~fLNqW 78 (81)
T PF10820_consen 53 AQQEMASEAGIDEQRIDDIANFLNQW 78 (81)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHHh
Confidence 35688899999988889988776555
No 41
>PF04481 DUF561: Protein of unknown function (DUF561); InterPro: IPR007570 Protein in this entry are of unknown function and are found in cyanobacteria and the chloroplasts of algae. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=29.59 E-value=72 Score=26.38 Aligned_cols=51 Identities=16% Similarity=0.294 Sum_probs=35.5
Q ss_pred EEEec-CchhHHHHHHcCCCcc---------------CHHHHHHHhhchHHHHHhhhcccEEEEchhhHh
Q 031803 65 VCMLG-DAQHVEEAEKIGLDYM---------------DVEGLKKLNKNKKLVKKLAKKYHAFLASESVIK 118 (152)
Q Consensus 65 I~Vf~-~~~~~~~Ak~aGa~~v---------------g~~eL~k~~k~~~~~kkl~~~fd~~lAt~~im~ 118 (152)
|||=+ +.+..-.|.+|||+.+ +.+|+..+. ++-|+|+-+-..++.-|.++|
T Consensus 64 ICVSaVep~~f~~aV~AGAdliEIGNfDsFY~qGr~f~a~eVL~Lt---~~tR~LLP~~~LsVTVPHiL~ 130 (242)
T PF04481_consen 64 ICVSAVEPELFVAAVKAGADLIEIGNFDSFYAQGRRFSAEEVLALT---RETRSLLPDITLSVTVPHILP 130 (242)
T ss_pred eEeecCCHHHHHHHHHhCCCEEEecchHHHHhcCCeecHHHHHHHH---HHHHHhCCCCceEEecCcccc
Confidence 99988 6677788999999954 233333332 345667777777888887776
No 42
>PRK03957 V-type ATP synthase subunit F; Provisional
Probab=29.16 E-value=2e+02 Score=20.07 Aligned_cols=52 Identities=23% Similarity=0.338 Sum_probs=37.7
Q ss_pred EEEEecCchhHHHHHHcCCC---ccC-HHHHHHHhhchHHHHHhh--hcccEEEEchhhHhhhh
Q 031803 64 KVCMLGDAQHVEEAEKIGLD---YMD-VEGLKKLNKNKKLVKKLA--KKYHAFLASESVIKQIP 121 (152)
Q Consensus 64 kI~Vf~~~~~~~~Ak~aGa~---~vg-~~eL~k~~k~~~~~kkl~--~~fd~~lAt~~im~~l~ 121 (152)
||+|++|.+..-==+-+|+. .+. .+|+.+.. +++. .+|-.++.|.++...+.
T Consensus 2 kIaVIgD~dtv~GFrLaGi~~~~~v~~~ee~~~~l------~~l~~~~d~gII~ite~~~~~i~ 59 (100)
T PRK03957 2 KIAVVGDRDTVTGFRLAGLTEVYEVKNPEEAKNAI------KELVENDEIGIIIITERIAEEIR 59 (100)
T ss_pred EEEEEeCHHHHHHHHHcCCCceEEeCCHHHHHHHH------HHHhhCCCeEEEEEcHHHHHHHH
Confidence 79999998877777888995 333 35554433 3344 56999999999998875
No 43
>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....
Probab=28.89 E-value=17 Score=24.11 Aligned_cols=21 Identities=10% Similarity=0.278 Sum_probs=14.4
Q ss_pred hcccEEEEchhhH-hhhhhhhc
Q 031803 105 KKYHAFLASESVI-KQIPRLLG 125 (152)
Q Consensus 105 ~~fd~~lAt~~im-~~l~riLG 125 (152)
.+||++|.+|++- ..+.+..+
T Consensus 46 ~~~D~il~~~~i~~~~~~~~~~ 67 (90)
T PF02302_consen 46 DDADLILLTPQIAYEDLKEFAG 67 (90)
T ss_dssp TT-SEEEEEESSGGHHHHHHTT
T ss_pred CCCcEEEEcCccchhhhhhhcC
Confidence 6799999999887 35554444
No 44
>PRK00536 speE spermidine synthase; Provisional
Probab=28.59 E-value=91 Score=25.90 Aligned_cols=72 Identities=15% Similarity=0.197 Sum_probs=41.0
Q ss_pred CCCcEEEEecCch--hHHHHHHc--CCCccCHHH-HHHHhhch--H--------------HHHHh-hhcccEEEEc----
Q 031803 60 RPKMKVCMLGDAQ--HVEEAEKI--GLDYMDVEG-LKKLNKNK--K--------------LVKKL-AKKYHAFLAS---- 113 (152)
Q Consensus 60 ~k~~kI~Vf~~~~--~~~~Ak~a--Ga~~vg~~e-L~k~~k~~--~--------------~~kkl-~~~fd~~lAt---- 113 (152)
+.+.+|+|++.|+ .+.|..+. -++.|-.++ +.+..+.. . ..++- ...||++|.+
T Consensus 71 ~~pk~VLIiGGGDGg~~REvLkh~~~v~mVeID~~Vv~~~k~~lP~~~~~~~DpRv~l~~~~~~~~~~~fDVIIvDs~~~ 150 (262)
T PRK00536 71 KELKEVLIVDGFDLELAHQLFKYDTHVDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIICLQEPD 150 (262)
T ss_pred CCCCeEEEEcCCchHHHHHHHCcCCeeEEEECCHHHHHHHHHHCHHHHHhhcCCCEEEeehhhhccCCcCCEEEEcCCCC
Confidence 4567999999765 34455443 345565555 44444331 0 11111 2569999997
Q ss_pred hhhHhhhhhhhcC-CCCCC
Q 031803 114 ESVIKQIPRLLGP-GLNKA 131 (152)
Q Consensus 114 ~~im~~l~riLGp-gL~p~ 131 (152)
++....+.|.|.| |+|-.
T Consensus 151 ~~fy~~~~~~L~~~Gi~v~ 169 (262)
T PRK00536 151 IHKIDGLKRMLKEDGVFIS 169 (262)
T ss_pred hHHHHHHHHhcCCCcEEEE
Confidence 3444456677777 66543
No 45
>PF01262 AlaDh_PNT_C: Alanine dehydrogenase/PNT, C-terminal domain; InterPro: IPR007698 Alanine dehydrogenases (1.4.1.1 from EC) and pyridine nucleotide transhydrogenase (1.6.1.1 from EC) have been shown to share regions of similarity []. Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. Pyridine nucleotide transhydrogenase catalyzes the reduction of NADP+ to NADPH with the concomitant oxidation of NADH to NAD+. This enzyme is located in the plasma membrane of prokaryotes and in the inner membrane of the mitochondria of eukaryotes. The transhydrogenation between NADH and NADP is coupled with the translocation of a proton across the membrane. In prokaryotes the enzyme is composed of two different subunits, an alpha chain (gene pntA) and a beta chain (gene pntB), while in eukaryotes it is a single chain protein. The sequence of alanine dehydrogenase from several bacterial species are related with those of the alpha subunit of bacterial pyridine nucleotide transhydrogenase and of the N-terminal half of the eukaryotic enzyme. The two most conserved regions correspond respectively to the N-terminal extremity of these proteins and to a central glycine-rich region which is part of the NAD(H)-binding site. This is a C-terminal domain of alanine dehydrogenases (1.4.1.1 from EC). This domain is also found in the lysine 2-oxoglutarate reductases. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1KOL_A 2EEZ_F 1L7E_C 1PTJ_B 1NM5_A 1HZZ_B 1U2G_B 2FSV_A 2FR8_A 1U2D_A ....
Probab=26.40 E-value=24 Score=26.60 Aligned_cols=37 Identities=22% Similarity=0.243 Sum_probs=24.4
Q ss_pred EEccCCCCCCcEEEEecCch----hHHHHHHcCCCccCHHHH
Q 031803 53 VKLPHIPRPKMKVCMLGDAQ----HVEEAEKIGLDYMDVEGL 90 (152)
Q Consensus 53 i~LPh~~~k~~kI~Vf~~~~----~~~~Ak~aGa~~vg~~eL 90 (152)
...|.++ ++.+|+|++.|. .++.|+..|+.++..++.
T Consensus 12 ~~~~~~~-~p~~vvv~G~G~vg~gA~~~~~~lGa~v~~~d~~ 52 (168)
T PF01262_consen 12 LGGPGGV-PPAKVVVTGAGRVGQGAAEIAKGLGAEVVVPDER 52 (168)
T ss_dssp ECTTTEE--T-EEEEESTSHHHHHHHHHHHHTT-EEEEEESS
T ss_pred ccCCCCC-CCeEEEEECCCHHHHHHHHHHhHCCCEEEeccCC
Confidence 3345555 568999999875 467778899998776664
No 46
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=26.12 E-value=2.4e+02 Score=19.99 Aligned_cols=67 Identities=16% Similarity=0.190 Sum_probs=43.3
Q ss_pred EEEEecCchhHHHHHHcCCC---ccCHHH-HHHHhhchHHHHHhh-hcccEEEEchhhHhhhhh-hhcCCCCCCCCCCCC
Q 031803 64 KVCMLGDAQHVEEAEKIGLD---YMDVEG-LKKLNKNKKLVKKLA-KKYHAFLASESVIKQIPR-LLGPGLNKAGKKVPY 137 (152)
Q Consensus 64 kI~Vf~~~~~~~~Ak~aGa~---~vg~~e-L~k~~k~~~~~kkl~-~~fd~~lAt~~im~~l~r-iLGpgL~p~~K~pt~ 137 (152)
+|+|+++.+..-=-+.+|.+ .+..+| ..++ .+.++ .+|-.++.|.++...+.+ .+- -+.+...|.+
T Consensus 4 kIaVvGd~DtilGFrlaGi~~v~~~~~~e~~~~~------~~~l~~~~~gII~iTE~~a~~i~~~~i~--~~~~~~~P~I 75 (104)
T PRK01189 4 CITVIGERDVVLGFRLLGIGDTIEAEGKDLVKKF------LEIFNNPKCKYIFVSESTKNMFDKNTLR--SLESSSKPLV 75 (104)
T ss_pred eEEEEcCHHHHHHHHHcCCceEEEcCCHHHHHHH------HHHHhcCCeEEEEEEHHHHhhCCHHHHH--HHhccCCCeE
Confidence 79999999888778889996 333333 3222 22344 469999999999988862 211 1224455655
Q ss_pred C
Q 031803 138 P 138 (152)
Q Consensus 138 v 138 (152)
+
T Consensus 76 I 76 (104)
T PRK01189 76 V 76 (104)
T ss_pred E
Confidence 5
No 47
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=25.24 E-value=1.1e+02 Score=25.73 Aligned_cols=20 Identities=15% Similarity=0.267 Sum_probs=9.6
Q ss_pred hHHHHHHcCCCccCHHHHHH
Q 031803 73 HVEEAEKIGLDYMDVEGLKK 92 (152)
Q Consensus 73 ~~~~Ak~aGa~~vg~~eL~k 92 (152)
..+.|++.|+.+++.+++.+
T Consensus 284 K~~kA~~~gi~ii~e~~f~~ 303 (313)
T PRK06063 284 KGYHARQLGVPVLDEAAFLE 303 (313)
T ss_pred HHHHHHHcCCccccHHHHHH
Confidence 34445555555555555433
No 48
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=24.79 E-value=83 Score=22.62 Aligned_cols=55 Identities=27% Similarity=0.399 Sum_probs=37.0
Q ss_pred cEEEEecCchhHHHHHHcCCC--c-cCHHH--HHHHhhchHHHHHhh-hcccEEEEchhhHhhhhhh
Q 031803 63 MKVCMLGDAQHVEEAEKIGLD--Y-MDVEG--LKKLNKNKKLVKKLA-KKYHAFLASESVIKQIPRL 123 (152)
Q Consensus 63 ~kI~Vf~~~~~~~~Ak~aGa~--~-vg~~e--L~k~~k~~~~~kkl~-~~fd~~lAt~~im~~l~ri 123 (152)
.+|||+++.+...==+=+|++ + +..++ +.+.. ++|+ .+|..++-|.+++..+...
T Consensus 3 ~~I~VIGd~dtvtGFrLaGv~~~~v~~~~~~~~~~~~------~~l~~~~~~iIiite~~a~~i~~~ 63 (104)
T COG1436 3 MKIAVIGDRDTVTGFRLAGVRVVYVADDEEDELRAAL------RVLAEDDVGIILITEDLAEKIREE 63 (104)
T ss_pred eEEEEEEccchhhceeeecceeEEEecChhHHHHHHH------HhhccCCceEEEEeHHHHhhhHHH
Confidence 489999998876555566777 2 44443 43333 2233 3799999999999887643
No 49
>TIGR02922 conserved hypothetical protein TIGR02922. Two members of this family are found in Colwellia psychrerythraea 34H and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by TIGR02595.
Probab=24.76 E-value=48 Score=22.01 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=20.8
Q ss_pred ceeeeEEccCCCCCCcEEEEecCch
Q 031803 48 RFSGSVKLPHIPRPKMKVCMLGDAQ 72 (152)
Q Consensus 48 ~i~g~i~LPh~~~k~~kI~Vf~~~~ 72 (152)
.-.|.+.+|..+++-..|.+.|.|+
T Consensus 30 ~~~GrvmiPqeFkrGKsIiAV~EGe 54 (67)
T TIGR02922 30 NESGRVMIPQEFKRGKSIIAVCEGE 54 (67)
T ss_pred cccccEEcchHHcCCCeEEEEEecc
Confidence 3457899999998888899999876
No 50
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=24.07 E-value=21 Score=24.86 Aligned_cols=54 Identities=11% Similarity=0.052 Sum_probs=28.5
Q ss_pred CCcEEEEecCchhH----HHHHHcCCC--ccCHH--HHHHHhh-chHHHHHhhhcccEEEEch
Q 031803 61 PKMKVCMLGDAQHV----EEAEKIGLD--YMDVE--GLKKLNK-NKKLVKKLAKKYHAFLASE 114 (152)
Q Consensus 61 k~~kI~Vf~~~~~~----~~Ak~aGa~--~vg~~--eL~k~~k-~~~~~kkl~~~fd~~lAt~ 114 (152)
+..+|+|++.|+.+ +...++||+ +++.+ ...+... ..+........++++++.+
T Consensus 6 ~~~~vlVvGgG~va~~k~~~Ll~~gA~v~vis~~~~~~~~~i~~~~~~~~~~l~~~~lV~~at 68 (103)
T PF13241_consen 6 KGKRVLVVGGGPVAARKARLLLEAGAKVTVISPEIEFSEGLIQLIRREFEEDLDGADLVFAAT 68 (103)
T ss_dssp TT-EEEEEEESHHHHHHHHHHCCCTBEEEEEESSEHHHHTSCEEEESS-GGGCTTESEEEE-S
T ss_pred CCCEEEEECCCHHHHHHHHHHHhCCCEEEEECCchhhhhhHHHHHhhhHHHHHhhheEEEecC
Confidence 45689999988643 333467888 55555 3333221 0011122345678887755
No 51
>KOG2697 consensus Histidinol dehydrogenase [Amino acid transport and metabolism]
Probab=23.57 E-value=49 Score=28.87 Aligned_cols=19 Identities=21% Similarity=0.469 Sum_probs=13.4
Q ss_pred hHhhhhhhhcC--CCCCCCCC
Q 031803 116 VIKQIPRLLGP--GLNKAGKK 134 (152)
Q Consensus 116 im~~l~riLGp--gL~p~~K~ 134 (152)
-.|++-+|||| .+--..||
T Consensus 206 ~~PKV~KIfGPGNQfVTAAKM 226 (446)
T KOG2697|consen 206 SCPKVEKIFGPGNQFVTAAKM 226 (446)
T ss_pred cCcchhhhcCCchhhhhhhhh
Confidence 36888899999 45455565
No 52
>PF04413 Glycos_transf_N: 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); InterPro: IPR007507 This is a domain found in proteins that transfer activated sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. Proteins bearing this domain transfer UDP, ADP, GDP or CMP linked sugars. This region is flanked at the N terminus by a signal peptide and at the C terminus by a glycosyl transferase group 1 domain (IPR001296 from INTERPRO). The eukaryotic glycogen synthases may be distant members of this bacterial family [].; GO: 0005529 sugar binding, 0016740 transferase activity, 0005975 carbohydrate metabolic process; PDB: 2XCI_A 2XCU_B.
Probab=23.04 E-value=1.6e+02 Score=22.74 Aligned_cols=68 Identities=16% Similarity=0.183 Sum_probs=29.8
Q ss_pred eEEccCCCC---------CCcEEEEecCch----hHHHHHHcCCCccCHHH-HH-HHhhc----hHHHHHhhhcccEEEE
Q 031803 52 SVKLPHIPR---------PKMKVCMLGDAQ----HVEEAEKIGLDYMDVEG-LK-KLNKN----KKLVKKLAKKYHAFLA 112 (152)
Q Consensus 52 ~i~LPh~~~---------k~~kI~Vf~~~~----~~~~Ak~aGa~~vg~~e-L~-k~~k~----~~~~kkl~~~fd~~lA 112 (152)
.+.+|.... =..++||++..| ...+|++.|+.++-..- +. +-... ....+.+...||.++|
T Consensus 76 ~~~~P~D~~~~~~rfl~~~~P~~~i~~EtElWPnll~~a~~~~ip~~LvNarls~~s~~~~~~~~~~~r~~l~~f~~i~a 155 (186)
T PF04413_consen 76 VQYLPLDFPWAVRRFLDHWRPDLLIWVETELWPNLLREAKRRGIPVVLVNARLSERSFRRYRRFPFLFRPLLSRFDRILA 155 (186)
T ss_dssp EEE---SSHHHHHHHHHHH--SEEEEES----HHHHHH-----S-EEEEEE--------------HHHHHHGGG-SEEEE
T ss_pred EEEeCccCHHHHHHHHHHhCCCEEEEEccccCHHHHHHHhhcCCCEEEEeeeeccccchhhhhhHHHHHHHHHhCCEEEE
Confidence 455776641 134889999876 57889999999442111 21 11111 2356667788999999
Q ss_pred chhhHhh
Q 031803 113 SESVIKQ 119 (152)
Q Consensus 113 t~~im~~ 119 (152)
..+--.+
T Consensus 156 qs~~da~ 162 (186)
T PF04413_consen 156 QSEADAE 162 (186)
T ss_dssp SSHHHHH
T ss_pred CCHHHHH
Confidence 7665544
No 53
>COG5583 Uncharacterized small protein [Function unknown]
Probab=22.03 E-value=2.2e+02 Score=18.24 Aligned_cols=24 Identities=4% Similarity=0.223 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHhhhhhccCCCceeEEEEEE
Q 031803 7 DALREAVSSIVQYSKETKKRNFTETIELQIG 37 (152)
Q Consensus 7 ~~l~~av~~~~~~~~~~~~~kf~esvel~i~ 37 (152)
+.+.+-|..+++.+ +| -||++.|+
T Consensus 8 ~~~~ekI~~~Le~l------ky-GsV~ItVh 31 (54)
T COG5583 8 PEVIEKIKKALEGL------KY-GSVTITVH 31 (54)
T ss_pred hHHHHHHHHHHhhc------cc-ceEEEEEE
Confidence 34445577777777 66 77888776
No 54
>PF09558 DUF2375: Protein of unknown function (DUF2375); InterPro: IPR014271 Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by IPR013424 from INTERPRO.
Probab=21.95 E-value=58 Score=21.94 Aligned_cols=24 Identities=21% Similarity=0.248 Sum_probs=19.8
Q ss_pred eeeeEEccCCCCCCcEEEEecCch
Q 031803 49 FSGSVKLPHIPRPKMKVCMLGDAQ 72 (152)
Q Consensus 49 i~g~i~LPh~~~k~~kI~Vf~~~~ 72 (152)
-.|.+.+|..+++-..|.+.++|+
T Consensus 33 ~~grv~iP~~Fr~GKsIiAVleGe 56 (71)
T PF09558_consen 33 ESGRVMIPQSFRRGKSIIAVLEGE 56 (71)
T ss_pred cCccEEChHHHcCCceEEEEEcCc
Confidence 356899999998888888888875
No 55
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=21.93 E-value=3.4e+02 Score=23.58 Aligned_cols=75 Identities=24% Similarity=0.406 Sum_probs=39.5
Q ss_pred EEccCCCC--CCcEEEEecCchhHHHHHHc-CCC----ccCHHH-HHHHhhch--------------HHH----HHhhhc
Q 031803 53 VKLPHIPR--PKMKVCMLGDAQHVEEAEKI-GLD----YMDVEG-LKKLNKNK--------------KLV----KKLAKK 106 (152)
Q Consensus 53 i~LPh~~~--k~~kI~Vf~~~~~~~~Ak~a-Ga~----~vg~~e-L~k~~k~~--------------~~~----kkl~~~ 106 (152)
+.|=|..| ...+|.|.++++.--.|... |-+ +|..+| |++++..- ..+ -++...
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 44455543 23358888877654334322 222 667777 65544211 000 124457
Q ss_pred ccEEEEchh-hHhhhhhhhcCC
Q 031803 107 YHAFLASES-VIKQIPRLLGPG 127 (152)
Q Consensus 107 fd~~lAt~~-im~~l~riLGpg 127 (152)
||.|+++|- -++.+--.||+|
T Consensus 222 FDvfiTDPpeTi~alk~FlgRG 243 (354)
T COG1568 222 FDVFITDPPETIKALKLFLGRG 243 (354)
T ss_pred CCeeecCchhhHHHHHHHHhcc
Confidence 999999875 445444455554
No 56
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=21.78 E-value=51 Score=22.49 Aligned_cols=14 Identities=14% Similarity=0.029 Sum_probs=10.9
Q ss_pred hHHHHHHcCCC-ccC
Q 031803 73 HVEEAEKIGLD-YMD 86 (152)
Q Consensus 73 ~~~~Ak~aGa~-~vg 86 (152)
+.++|++.||+ +||
T Consensus 34 M~e~A~~lGAnAVVG 48 (74)
T TIGR03884 34 LREKVKAKGGMGLIA 48 (74)
T ss_pred HHHHHHHcCCCEEEE
Confidence 56889999999 444
No 57
>PRK09427 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional
Probab=21.69 E-value=45 Score=29.92 Aligned_cols=28 Identities=29% Similarity=0.296 Sum_probs=24.2
Q ss_pred CCcEEEEecCchhHHHHHHcCCCccCHH
Q 031803 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVE 88 (152)
Q Consensus 61 k~~kI~Vf~~~~~~~~Ak~aGa~~vg~~ 88 (152)
...|||=+.+.+.+..|.++||+++|.-
T Consensus 257 ~~vKICGit~~eda~~a~~~GaD~lGfI 284 (454)
T PRK09427 257 GENKVCGLTRPQDAKAAYDAGAVYGGLI 284 (454)
T ss_pred cccccCCCCCHHHHHHHHhCCCCEEeeE
Confidence 3579999999999999999999988873
No 58
>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=21.03 E-value=1e+02 Score=25.55 Aligned_cols=57 Identities=16% Similarity=0.270 Sum_probs=26.0
Q ss_pred CCcEEEEecCchhHHHHHHc-----CCCccCHHH-HHHHhhchHH-------------H----HHhhhcccEEEEchhhH
Q 031803 61 PKMKVCMLGDAQHVEEAEKI-----GLDYMDVEG-LKKLNKNKKL-------------V----KKLAKKYHAFLASESVI 117 (152)
Q Consensus 61 k~~kI~Vf~~~~~~~~Ak~a-----Ga~~vg~~e-L~k~~k~~~~-------------~----kkl~~~fd~~lAt~~im 117 (152)
...+|++++|++....|.+. .+.++..+| |.+.++..-. + ..+...||.|++.|---
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 34578888877754444333 222667776 5555432211 1 22446799999987643
Done!