Query 030330
Match_columns 179
No_of_seqs 153 out of 1213
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 12:05:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030330.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030330hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00068 60S ribosomal protein 100.0 1.1E-61 2.4E-66 403.7 9.1 152 8-159 2-153 (202)
2 TIGR01077 L13_A_E ribosomal pr 100.0 5.4E-55 1.2E-59 346.9 8.8 142 12-154 1-142 (142)
3 PRK06394 rpl13p 50S ribosomal 100.0 3.3E-50 7.2E-55 320.8 9.9 141 9-151 2-143 (146)
4 PRK09216 rplM 50S ribosomal pr 100.0 3.5E-46 7.5E-51 297.1 7.2 120 1-131 5-142 (144)
5 TIGR01066 rplM_bact ribosomal 100.0 1.3E-45 2.9E-50 292.6 7.4 115 4-129 6-138 (140)
6 COG0102 RplM Ribosomal protein 100.0 2.8E-45 6E-50 292.2 9.2 122 1-133 5-145 (148)
7 CHL00159 rpl13 ribosomal prote 100.0 1.7E-45 3.7E-50 292.8 7.7 118 1-129 6-141 (143)
8 KOG3204 60S ribosomal protein 100.0 1.6E-43 3.4E-48 292.1 5.7 147 6-159 2-148 (197)
9 PF00572 Ribosomal_L13: Riboso 100.0 5E-43 1.1E-47 274.0 6.6 108 11-125 1-126 (128)
10 PLN00205 ribisomal protein L13 100.0 9.1E-42 2E-46 281.9 7.7 111 7-124 13-141 (191)
11 cd00392 Ribosomal_L13 Ribosoma 100.0 2.4E-39 5.1E-44 249.0 7.2 96 11-113 1-114 (114)
12 KOG3203 Mitochondrial/chloropl 100.0 2.7E-37 5.9E-42 247.3 6.5 107 5-118 17-141 (165)
13 PF00436 SSB: Single-strand bi 57.7 11 0.00023 26.8 2.7 23 20-42 54-76 (104)
14 PF12953 DUF3842: Domain of un 55.3 16 0.00034 29.2 3.4 14 34-47 53-66 (131)
15 PRK05853 hypothetical protein; 50.1 16 0.00035 29.8 2.8 23 20-42 49-71 (161)
16 cd04496 SSB_OBF SSB_OBF: A sub 48.0 20 0.00043 25.1 2.7 23 20-42 50-72 (100)
17 COG0629 Ssb Single-stranded DN 46.4 21 0.00045 28.6 2.9 22 20-41 57-78 (167)
18 PRK07274 single-stranded DNA-b 44.1 21 0.00045 27.7 2.5 30 9-42 46-75 (131)
19 PRK08182 single-stranded DNA-b 43.7 23 0.0005 28.2 2.7 23 20-42 60-82 (148)
20 PRK07772 single-stranded DNA-b 43.6 22 0.00048 29.7 2.7 22 20-41 59-80 (186)
21 PRK06752 single-stranded DNA-b 43.4 24 0.00053 26.4 2.7 22 20-41 53-74 (112)
22 PRK08486 single-stranded DNA-b 40.6 25 0.00053 29.2 2.5 22 20-41 55-76 (182)
23 PRK07275 single-stranded DNA-b 39.1 27 0.00058 28.4 2.5 22 20-41 53-74 (162)
24 PRK07459 single-stranded DNA-b 38.9 28 0.00061 26.7 2.5 23 20-42 50-72 (121)
25 TIGR00621 ssb single stranded 38.0 26 0.00057 28.1 2.3 23 20-42 57-79 (164)
26 COG1717 RPL32 Ribosomal protei 37.0 28 0.00061 27.8 2.2 28 63-95 50-77 (133)
27 PHA02754 hypothetical protein; 36.6 47 0.001 23.3 3.0 15 34-48 43-57 (67)
28 PRK13732 single-stranded DNA-b 36.6 29 0.00062 28.7 2.3 29 10-42 54-82 (175)
29 PRK06863 single-stranded DNA-b 36.0 44 0.00096 27.4 3.3 30 9-42 51-80 (168)
30 PRK08763 single-stranded DNA-b 36.0 31 0.00066 28.2 2.4 22 20-41 58-79 (164)
31 PRK06751 single-stranded DNA-b 35.8 30 0.00066 28.4 2.3 28 10-41 47-74 (173)
32 PF08980 DUF1883: Domain of un 35.5 25 0.00054 26.5 1.6 48 32-84 11-58 (94)
33 PF03447 NAD_binding_3: Homose 35.0 60 0.0013 23.7 3.7 34 10-45 60-93 (117)
34 PRK09010 single-stranded DNA-b 34.1 33 0.00072 28.3 2.3 30 9-42 53-82 (177)
35 KOG1154 Gamma-glutamyl kinase 34.1 48 0.001 29.5 3.4 33 16-48 26-61 (285)
36 PRK05733 single-stranded DNA-b 31.2 69 0.0015 26.3 3.7 29 9-41 52-80 (172)
37 PRK06958 single-stranded DNA-b 27.7 55 0.0012 27.3 2.6 30 9-42 51-80 (182)
38 PF00650 CRAL_TRIO: CRAL/TRIO 27.5 50 0.0011 24.7 2.2 73 35-113 61-137 (159)
39 PF07552 Coat_X: Spore Coat Pr 24.7 74 0.0016 22.0 2.4 18 34-51 19-36 (60)
40 PRK06293 single-stranded DNA-b 24.4 66 0.0014 26.3 2.4 23 20-42 49-71 (161)
41 PF04379 DUF525: Protein of un 23.3 54 0.0012 24.1 1.6 14 6-19 30-43 (90)
42 COG1795 Formaldehyde-activatin 22.7 1.5E+02 0.0032 24.6 4.1 40 20-61 79-130 (170)
43 KOG1481 Cysteine synthase [Ami 22.4 94 0.002 28.5 3.2 51 12-66 318-375 (391)
44 PRK06642 single-stranded DNA-b 21.7 78 0.0017 25.3 2.4 22 21-42 60-82 (152)
45 COG4091 Predicted homoserine d 21.3 1.3E+02 0.0028 28.4 3.9 41 11-53 103-144 (438)
46 PF02254 TrkA_N: TrkA-N domain 21.0 1.1E+02 0.0023 21.9 2.8 27 21-47 6-33 (116)
47 PF03446 NAD_binding_2: NAD bi 20.6 1.2E+02 0.0027 23.5 3.3 22 21-42 9-31 (163)
No 1
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=100.00 E-value=1.1e-61 Score=403.73 Aligned_cols=152 Identities=65% Similarity=1.121 Sum_probs=148.5
Q ss_pred ceeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCCCCCCcCCcchhHHH
Q 030330 8 CAKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWR 87 (179)
Q Consensus 8 ~~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~g~~~~r~P~~Il~r 87 (179)
..+|+||||+||+||||||+||+.|++||+|||||||+|+|||+++++|.||+++++++++.||..||+|+|+|++||++
T Consensus 2 ~~~w~vIDA~g~vLGRLAS~VAk~Ll~Gd~VVVVNaeki~iTG~k~~~K~~y~~~lk~~~~~nP~~g~~~~r~P~~Il~r 81 (202)
T PTZ00068 2 FKKVIVIDCKGHLLGRLASVVAKELLLGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNTNPRRGPFHHRAPSDIFWR 81 (202)
T ss_pred CCceEEEECCCCcHHHHHHHHHHHHhCCCEEEEEecceeEeecchhhheeeeEeeeEeeccCCCCcchhcccCHHHHHHH
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccCCCCChhHHHHhccCceecCCCCChhhhccccCCchhhhhhcCCCCCeEEhhhhhHhhCccccceEE
Q 030330 88 TVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVGWNYYDTIR 159 (179)
Q Consensus 88 aVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al~~~~l~~~~k~~~lGel~~~~Gwk~~~v~~ 159 (179)
||||||||||++|+++|+||+||+|+||||++++++++|+|+++.+++|+++||||||||++|||||++||+
T Consensus 82 aVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~k~~vvp~A~r~~rl~~~~ky~~lg~ls~~vGwky~~vv~ 153 (202)
T PTZ00068 82 TVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSALRVLRLKPERPYTVLGDLSAHVGWKYADVVA 153 (202)
T ss_pred HHhhhCCCCChhHHHHHhCCEEecCCCCchhccCcccccchhhhhccCCCCceeeHHHHHHHhCccHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999874
No 2
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=100.00 E-value=5.4e-55 Score=346.93 Aligned_cols=142 Identities=58% Similarity=0.951 Sum_probs=135.3
Q ss_pred EEEeCCCCCchhHHHHHHHHHhCCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCCCCCCcCCcchhHHHHHhc
Q 030330 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRG 91 (179)
Q Consensus 12 ~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~g~~~~r~P~~Il~raVrG 91 (179)
+||||+||+||||||.||+.|++||+|||||||+|.+||+|+++|.||+++.++.+..+|..+++++++|++||++||+|
T Consensus 1 ivIDA~~~vlGRLAs~IA~~L~~Gd~VvViNaeki~~TG~k~~~k~~y~~~~~~g~~~~~~~~~~~~r~P~~il~~aVrG 80 (142)
T TIGR01077 1 TVIDGSGHILGRLASVVAKQLLNGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRG 80 (142)
T ss_pred CEEeCCCCchHHHHHHHHHHHhcCCEEEEEechHheecCchhhheeEEEEECCCCCcccCCHHHhhhcCHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999997767677777767999999999999999999
Q ss_pred cCCCCChhHHHHhccCceecCCCCChhhhccccCCchhhhhhcCCCCCeEEhhhhhHhhCccc
Q 030330 92 MIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVGWNY 154 (179)
Q Consensus 92 MLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al~~~~l~~~~k~~~lGel~~~~Gwk~ 154 (179)
|||+|+.+|+.+++||+||+|+||||++|+++++|+|+ +.+++|.||||+|||||+.+||||
T Consensus 81 MLPk~~~~Gr~~~krLkvy~G~~h~~~~qk~~~~~~a~-~~~~~~~~~~~~lg~l~~~~G~k~ 142 (142)
T TIGR01077 81 MLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-VSRLSPTRKYVTLGELAKFLGWKF 142 (142)
T ss_pred hCCCCChhHHHHHhCcEEecCCCCCccccCccccChhh-hhccCCCCceEEHHHHHHHhCCcC
Confidence 99997799999999999999999999999999999998 899999999999999999999996
No 3
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=100.00 E-value=3.3e-50 Score=320.80 Aligned_cols=141 Identities=43% Similarity=0.611 Sum_probs=133.8
Q ss_pred eeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCC-CCCCcCCcchhHHH
Q 030330 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH-GPIHFRAPAKIFWR 87 (179)
Q Consensus 9 ~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~-g~~~~r~P~~Il~r 87 (179)
++.+||||+||+||||||.||+.|++||+|||||||+|.+||+|++++.+|.+|.+.++..||+. +++++++|++||++
T Consensus 2 ~~~~viDA~~~vlGRLAs~IA~~L~~Gd~VVViNa~kv~~tG~K~~~~~~y~~~~~~k~~~np~~~~~~~~r~P~~il~~ 81 (146)
T PRK06394 2 EAMVVIDAEGQILGRLASYVAKRLLEGEEVVIVNAEKAVITGNRERVIEKYKQRRERGSHYNPYRNGPKYPRRPDRIFKR 81 (146)
T ss_pred CccEEEECCCCchHHHHHHHHHHHhCCCEEEEEechheEecCchhhheeeEeCCCCCcccCCCCChHHhhhcCHHHHHHH
Confidence 35689999999999999999999999999999999999999999999989988888899999965 99999999999999
Q ss_pred HHhccCCCCChhHHHHhccCceecCCCCChhhhccccCCchhhhhhcCCCCCeEEhhhhhHhhC
Q 030330 88 TVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVG 151 (179)
Q Consensus 88 aVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al~~~~l~~~~k~~~lGel~~~~G 151 (179)
||+||||+||++|+.+++||+||+|+||||++|+++++|.|+. ++++ +++||||||||+++|
T Consensus 82 AV~gMLP~kn~~gr~~~~rLkvy~G~~h~~~~qkp~~~~~a~~-~~~~-~~k~~~lgel~~~~G 143 (146)
T PRK06394 82 TIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEADL-SRLS-TIKYVTLGEVSKELG 143 (146)
T ss_pred HHHhcCCCCChhHHHHHhCcEEecCCCCCcccCCCEEecHHHH-hccC-CCCcEEHHHHHHHhC
Confidence 9999999779999999999999999999999999999999986 6777 689999999999999
No 4
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00 E-value=3.5e-46 Score=297.10 Aligned_cols=120 Identities=29% Similarity=0.511 Sum_probs=113.2
Q ss_pred CCCCCccceeEEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccc
Q 030330 1 MVSGSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMN 68 (179)
Q Consensus 1 ~~~~~~~~~~w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~ 68 (179)
+++++.++++|+||||+||+||||||.||+.|+ |||+|||||||+|.+||++|++|.||+ |+
T Consensus 5 ~~~~~~~~~~W~viDA~~~~lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~------ht 78 (144)
T PRK09216 5 SAKPAEVERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYYR------HS 78 (144)
T ss_pred cCChhhcCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEeCceeEEcCchHhheeeEE------ec
Confidence 457788899999999999999999999999999 999999999999999999999999997 89
Q ss_pred cCCCC------CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCCCCChhhhccccCCchhhh
Q 030330 69 TKPSH------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKV 131 (179)
Q Consensus 69 g~Pg~------g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al~~ 131 (179)
||||+ +++++|+|++||++|||||||+ |++|+.+++||+||+|++|||++|+ |+.+++
T Consensus 79 g~pGglk~~~~~~~~~r~P~~il~~aVrgMLPk-n~lgr~~~~rLkvy~G~~hp~~~q~----p~~~~~ 142 (144)
T PRK09216 79 GYPGGLKEITFGELLAKKPERVIEKAVKGMLPK-NPLGRAMFKKLKVYAGAEHPHAAQQ----PEVLEI 142 (144)
T ss_pred ccCCCCEEecHHHHhhhCHHHHHHHHHHhcCCC-CccHHHHHhCcEEeCCCCCCccccC----CEeccc
Confidence 99986 8899999999999999999997 9999999999999999999999999 776643
No 5
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=100.00 E-value=1.3e-45 Score=292.59 Aligned_cols=115 Identities=32% Similarity=0.489 Sum_probs=109.5
Q ss_pred CCccceeEEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccccCC
Q 030330 4 GSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71 (179)
Q Consensus 4 ~~~~~~~w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~P 71 (179)
+++++++|+||||+||+||||||.||+.|+ |||+|||||||+|.+||++|++|.||. |+|||
T Consensus 6 ~~~~~r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~------htg~p 79 (140)
T TIGR01066 6 SDDKKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYR------HSGYP 79 (140)
T ss_pred hhhhcccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEeccEEEEeCchhhceeeEE------EcccC
Confidence 567899999999999999999999999999 999999999999999999999999997 89999
Q ss_pred CC------CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCCCCChhhhccccCCchh
Q 030330 72 SH------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129 (179)
Q Consensus 72 g~------g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al 129 (179)
|+ +++++++|++||++|||||||+ |++|+++|+||+||+|+||||++|+ |..+
T Consensus 80 gg~k~~~~~~~~~r~P~~ii~~aVrGMLPk-n~lgr~~l~rLkvy~G~~hp~~~q~----p~~~ 138 (140)
T TIGR01066 80 GGLKSRTFEEMIARKPERVLEHAVKGMLPK-NRLGRKLFKKLKVYAGSEHPHEAQK----PIVL 138 (140)
T ss_pred CccccccHHHhhhcCHHHHHHHHHHhcCCC-CccHHHHHhCeEEeCCCCCChhhcC----Ceec
Confidence 86 8899999999999999999995 9999999999999999999999998 7654
No 6
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-45 Score=292.17 Aligned_cols=122 Identities=39% Similarity=0.620 Sum_probs=113.5
Q ss_pred CCCCCccceeEEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccc
Q 030330 1 MVSGSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMN 68 (179)
Q Consensus 1 ~~~~~~~~~~w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~ 68 (179)
++++++++++|+||||+|++||||||.||+.|+ |||+|||||||||+|||+|..+|.||+ |+
T Consensus 5 ~~k~~~~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~------hs 78 (148)
T COG0102 5 TAKPSEVERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYR------HS 78 (148)
T ss_pred ccCcccccceEEEEeCCCCChHHHHHHHHHHHhcCCCCCcCcCcCCCCEEEEEeceeeEEecccccceEEEE------ee
Confidence 467888999999999999999999999999998 679999999999999999999999997 89
Q ss_pred cCCCC-------CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCCCCChhhhccccCCchhhhhh
Q 030330 69 TKPSH-------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLR 133 (179)
Q Consensus 69 g~Pg~-------g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al~~~~ 133 (179)
+|||+ +++++|.|++||++||+||||+ |++||++|+||+||.|+||||.+|+ |+++++..
T Consensus 79 ~~~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk-~~lGr~~~krLkVy~G~~h~~~aq~----p~~l~~~~ 145 (148)
T COG0102 79 GYPGGLKNPTRGGPLAPRRPERILERAVRGMLPK-NPLGRAALKRLKVYAGIPHPHEAQK----PEALELKL 145 (148)
T ss_pred ccCCcccccccccccccCCHHHHHHHHHhccCCC-ChhHHHHHhCceEecCCCCcccccc----chhhhhhc
Confidence 99974 7777799999999999999998 9999999999999999999999998 98876544
No 7
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00 E-value=1.7e-45 Score=292.82 Aligned_cols=118 Identities=29% Similarity=0.450 Sum_probs=110.7
Q ss_pred CCCCCccceeEEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccc
Q 030330 1 MVSGSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMN 68 (179)
Q Consensus 1 ~~~~~~~~~~w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~ 68 (179)
++++.++.++|+||||+||+||||||.||+.|+ |||+|||||||+|.+||+||++|.||+ |+
T Consensus 6 ~~~~~~~~r~W~viDA~~~~lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViNa~kv~~TG~K~~~K~y~~------ht 79 (143)
T CHL00159 6 IPSKDYKNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFYVR------HS 79 (143)
T ss_pred cCCchhcCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEecceeEEeCchhhheEEEe------cC
Confidence 467788999999999999999999999999998 999999999999999999999998765 99
Q ss_pred cCCCC------CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCCCCChhhhccccCCchh
Q 030330 69 TKPSH------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129 (179)
Q Consensus 69 g~Pg~------g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al 129 (179)
||||+ +++++++|++||++||+||||+ |++|+.+++||+||+|++|||++|+ |+.+
T Consensus 80 g~pGg~k~~~~~~~~~r~P~~il~~aV~gMLPk-n~lgr~~~~rLkvy~G~~hph~aq~----p~~~ 141 (143)
T CHL00159 80 GRPGGLKIETFEELQNRLPNRIIEKAVKGMLPK-GPLGRKLFTKLKVYKGESHPHVAQK----PIKI 141 (143)
T ss_pred CCCCCcccccHHHHhhcCHHHHHHHHHHhcCCC-ChhHHHHHhCCEEeCCCCCCccccC----Ceec
Confidence 99986 6899999999999999999996 9999999999999999999999999 7654
No 8
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-43 Score=292.08 Aligned_cols=147 Identities=61% Similarity=1.039 Sum_probs=142.0
Q ss_pred ccceeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCCCCCCcCCcchhH
Q 030330 6 GICAKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIF 85 (179)
Q Consensus 6 ~~~~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~g~~~~r~P~~Il 85 (179)
+...+-.+||+.||++|||||.|||.|+.|++||||.||.|+|||+.+++| .||++++++| ||||++.|++||
T Consensus 2 ~~~~~~~vidg~~hllGrlAa~vaK~ll~g~kvvvvr~E~i~isg~f~r~k----~~lrk~~~~n---g~~hfr~ps~i~ 74 (197)
T KOG3204|consen 2 MLEVKLVVIDGRGHLLGRLAAIVAKQLLLGRKVVVVRCEEINISGNFYRNK----LFLRKRLNRN---GPFHFRAPSRIL 74 (197)
T ss_pred cceEEEeeccchhhhhhhHHHHHHHHHhcCCeEEEEEEeEEEEecceecch----HHHhhhhccc---CcchhhhHHHHH
Confidence 456778999999999999999999999999999999999999999999999 7889999988 999999999999
Q ss_pred HHHHhccCCCCChhHHHHhccCceecCCCCChhhhccccCCchhhhhhcCCCCCeEEhhhhhHhhCccccceEE
Q 030330 86 WRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVGWNYYDTIR 159 (179)
Q Consensus 86 ~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~P~al~~~~l~~~~k~~~lGel~~~~Gwk~~~v~~ 159 (179)
+++||||+|+|+++|+.+++||++|+|.|+|++.++++++|.|+++.+++|.+|||+||.|++++||||++|++
T Consensus 75 ~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r~v~p~a~~v~~lk~~~K~c~lG~L~~eVGWkyq~vta 148 (197)
T KOG3204|consen 75 QKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKRLVVPVAFQVLRLKPYKKYCLLGRLSHEVGWKYQAVTA 148 (197)
T ss_pred HHhhccccccCCCccHHHHHHHHHhCCCCChhhhcCCccCCcceeeecccCCceeEEeccchhhhcchhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999875
No 9
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 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 L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=100.00 E-value=5e-43 Score=274.01 Aligned_cols=108 Identities=43% Similarity=0.657 Sum_probs=102.1
Q ss_pred EEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCC-----
Q 030330 11 RVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH----- 73 (179)
Q Consensus 11 w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~----- 73 (179)
|+||||+||+||||||.||+.|+ +||+|||||||+|.+||++|++|.||. |++|||+
T Consensus 1 W~viDA~~~~lGRLAs~iAk~L~GKhk~~y~p~~d~Gd~VvViNae~i~~tG~k~~~k~y~~------h~~~~g~~~~~~ 74 (128)
T PF00572_consen 1 WYVIDAKGQILGRLASKIAKLLLGKHKPTYTPNVDCGDHVVVINAEKIVLTGKKWRQKVYYR------HTGYPGGLKNPT 74 (128)
T ss_dssp EEEEETTTBBHHHHHHHHHHHHCTTSSTSSBTTSSTTEEEEEECGGGBEESSHHHHHHHHHH------EHSSSTSCEEEE
T ss_pred CEEEeCCCCchHHHHHHHHHHHhCCCCCccCcCccCCCEEEEEcCeeeEecCCeecceEEEe------ecccchhhcccc
Confidence 99999999999999999999999 999999999999999999999999997 8999986
Q ss_pred -CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCCCCChhhhccccC
Q 030330 74 -GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVI 125 (179)
Q Consensus 74 -g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~~ 125 (179)
+.+++++|++||++|||||||+ |.+|+++|+||+||+|+||||++|+.+++
T Consensus 75 ~~~~~~~~P~~i~~~aVrgMLP~-n~~g~~~l~rL~vy~g~~hp~~~~~~~~~ 126 (128)
T PF00572_consen 75 AKGLHEKDPSRILKRAVRGMLPK-NKLGREALKRLKVYPGEPHPHAAQKPVVL 126 (128)
T ss_dssp CHHHHCSSHHHHHHHHHHTTSTT-SHHHHHHHTTEEEESSSSCSTTSSSCBEE
T ss_pred hhhhhhcCHHHHHHHHHHHHCCC-ChhhhHHhhceEEECCCCCChhccCCEeC
Confidence 4566799999999999999998 99999999999999999999999995554
No 10
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=100.00 E-value=9.1e-42 Score=281.92 Aligned_cols=111 Identities=20% Similarity=0.325 Sum_probs=104.4
Q ss_pred cceeEEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCC-
Q 030330 7 ICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH- 73 (179)
Q Consensus 7 ~~~~w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~- 73 (179)
-.++|+||||+||+||||||+||+.|+ |||+|||||||+|.+||+||.+|.||. |+||||+
T Consensus 13 ~~r~W~VIDA~~~iLGRLAS~IAk~L~GKhKP~ytP~~D~GD~VVVINAekI~lTG~K~~~K~Y~~------htgypGgl 86 (191)
T PLN00205 13 EGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFYRW------HTGYIGHL 86 (191)
T ss_pred CCCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEeccEEEEeCChhhcceEEE------ecCCCCCc
Confidence 468999999999999999999999999 999999999999999999999999887 8999997
Q ss_pred -----CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCCCCChhhhcccc
Q 030330 74 -----GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMV 124 (179)
Q Consensus 74 -----g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~~qk~~~ 124 (179)
+++++++|++||++||+||||+ |.+|+.+++||+||+|+||||++|+.+.
T Consensus 87 k~~~~~~~~~r~P~~Il~kAVrGMLPk-n~lr~~~~krLkVY~G~~hp~~~q~p~~ 141 (191)
T PLN00205 87 KERSLKDQMAKDPTEVIRKAVLRMLPR-NRLRDDRDRKLRIFAGSEHPFGDKPLEP 141 (191)
T ss_pred ccccHHHHhccCHHHHHHHHHHhcCCC-CchHHHHHhCCEEECCCCCChhccCCeE
Confidence 7799999999999999999998 7888889999999999999999998544
No 11
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=100.00 E-value=2.4e-39 Score=248.97 Aligned_cols=96 Identities=52% Similarity=0.756 Sum_probs=91.7
Q ss_pred EEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCC-----
Q 030330 11 RVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH----- 73 (179)
Q Consensus 11 w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~----- 73 (179)
|+||||+||+||||||.||+.|+ |||+|||||||+|.+||+++++|.||. |++||++
T Consensus 1 w~viDA~~~~lGRlAs~iA~~L~gKhKp~y~p~~d~Gd~VvViNa~~i~~tG~k~~~k~y~~------~~~~~g~~~~~~ 74 (114)
T cd00392 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYYR------HTGYPGGLKNPT 74 (114)
T ss_pred CEEEeCCCCchHHHHHHHHHHHcCCCCCCcCCCccCCCEEEEEeccEEEEeCchhhccceEE------eccCCCCCccCC
Confidence 99999999999999999999998 499999999999999999999999997 8888875
Q ss_pred -CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCC
Q 030330 74 -GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGV 113 (179)
Q Consensus 74 -g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~ 113 (179)
+++++++|++||++||+||||+ |++|+++|+||+||+|+
T Consensus 75 ~~~~~~~~P~~il~~aV~gMLPk-n~~g~~~l~rLkvy~g~ 114 (114)
T cd00392 75 AGPLHPRAPERILKRAVRGMLPK-NKLGRAALKRLKVYEGA 114 (114)
T ss_pred cchhhhhCHHHHHHHHHHhcCCC-ChhHHHHHhCcEEeCCC
Confidence 9999999999999999999995 99999999999999985
No 12
>KOG3203 consensus Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-37 Score=247.29 Aligned_cols=107 Identities=31% Similarity=0.431 Sum_probs=101.1
Q ss_pred CccceeEEEEeCCCCCchhHHHHHHHHHh------------CCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCC
Q 030330 5 SGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPS 72 (179)
Q Consensus 5 ~~~~~~w~VIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg 72 (179)
..|+|.|+||||++++||||||.||..|+ |||+|||+||++|.+||+||.+|.|+. |+||||
T Consensus 17 ~afaRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K~~qk~Y~~------HsGyPG 90 (165)
T KOG3203|consen 17 LAFARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWEQKIYRS------HSGYPG 90 (165)
T ss_pred HHHhhhheeeccccCchHHHHHHHHHHHhhccCCccCCccCCCCEEEEecchhheeccchhhhhhhhh------cCCCCC
Confidence 46789999999999999999999999996 899999999999999999999999887 999999
Q ss_pred C------CCCCcCCcchhHHHHHhccCCCCChhHHHHhccCceecCCCCChh
Q 030330 73 H------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYD 118 (179)
Q Consensus 73 ~------g~~~~r~P~~Il~raVrGMLPkkn~~Gr~al~rLkvy~G~p~p~~ 118 (179)
+ ..++.|+|++|+++||+||||+ |.+||..++||++|+|++||+.
T Consensus 91 ~lk~~~~~q~~~rdp~~Iv~~AV~gMLPk-N~Lrr~~~~rL~lf~g~e~p~~ 141 (165)
T KOG3203|consen 91 GLKQTTADQLADRDPCRIVRLAVYGMLPK-NLLRRRRMQRLHLFPGEEHPEK 141 (165)
T ss_pred chhhhHHHHHhhhCHHHHHHHHHHhhCcc-chHHHHHhheeeccCCccCchh
Confidence 7 6778899999999999999997 9999999999999999999944
No 13
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=57.70 E-value=11 Score=26.81 Aligned_cols=23 Identities=35% Similarity=0.413 Sum_probs=16.5
Q ss_pred CchhHHHHHHHHHhCCCEEEEEe
Q 030330 20 MLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
.-|.+|..+++.|..||.|.|.=
T Consensus 54 ~~g~~A~~~~~~l~kG~~V~V~G 76 (104)
T PF00436_consen 54 AWGKLAENVAEYLKKGDRVYVEG 76 (104)
T ss_dssp EEHHHHHHHHHH--TT-EEEEEE
T ss_pred eeeecccccceEEcCCCEEEEEE
Confidence 35889999999999999887753
No 14
>PF12953 DUF3842: Domain of unknown function (DUF3842); InterPro: IPR024208 This family of proteins has no known function.
Probab=55.33 E-value=16 Score=29.22 Aligned_cols=14 Identities=14% Similarity=0.351 Sum_probs=11.2
Q ss_pred CCCEEEEEecCccc
Q 030330 34 NGQKVVAVRCEEIC 47 (179)
Q Consensus 34 ~Gd~VVVVNaeki~ 47 (179)
+|+.-||+||.++-
T Consensus 53 TGENaIv~n~~~aD 66 (131)
T PF12953_consen 53 TGENAIVVNARKAD 66 (131)
T ss_pred cccchheeccCCCC
Confidence 57888888888864
No 15
>PRK05853 hypothetical protein; Validated
Probab=50.14 E-value=16 Score=29.81 Aligned_cols=23 Identities=35% Similarity=0.429 Sum_probs=20.5
Q ss_pred CchhHHHHHHHHHhCCCEEEEEe
Q 030330 20 MLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
.-|++|..++++|..|+.|+|.-
T Consensus 49 ~wg~lAe~v~~~L~KG~~V~V~G 71 (161)
T PRK05853 49 CWGRLVTGVGAALGKGAPVIVVG 71 (161)
T ss_pred EEhHHHHHHHHHcCCCCEEEEEE
Confidence 67889999999999999998864
No 16
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=47.98 E-value=20 Score=25.09 Aligned_cols=23 Identities=35% Similarity=0.364 Sum_probs=19.3
Q ss_pred CchhHHHHHHHHHhCCCEEEEEe
Q 030330 20 MLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
.-|.+|..+++.|..||.|.|.-
T Consensus 50 ~~g~~a~~~~~~~~kG~~V~v~G 72 (100)
T cd04496 50 AFGKLAENAAKYLKKGDLVYVEG 72 (100)
T ss_pred EEhHHHHHHHHHhCCCCEEEEEE
Confidence 45669999999999999988754
No 17
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=46.41 E-value=21 Score=28.64 Aligned_cols=22 Identities=32% Similarity=0.362 Sum_probs=19.8
Q ss_pred CchhHHHHHHHHHhCCCEEEEE
Q 030330 20 MLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
+.|++|..++++|..|+.|+|.
T Consensus 57 ~wgk~Ae~~~~yl~KG~~V~Ve 78 (167)
T COG0629 57 IWGKLAENAAEYLKKGSLVYVE 78 (167)
T ss_pred EehHHHHHHHHHhcCCCEEEEE
Confidence 5799999999999999998875
No 18
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=44.15 E-value=21 Score=27.67 Aligned_cols=30 Identities=23% Similarity=0.221 Sum_probs=23.6
Q ss_pred eeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEe
Q 030330 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 9 ~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
..|+-|- +-|++|..+++.|..|+.|.|.-
T Consensus 46 t~w~~v~----~fg~~Ae~v~~~l~KG~~V~V~G 75 (131)
T PRK07274 46 ADFINVV----LWGKLAETLASYASKGSLISIDG 75 (131)
T ss_pred EEEEEEE----EehHHHHHHHHHcCCCCEEEEEE
Confidence 4576554 45889999999999999988753
No 19
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=43.72 E-value=23 Score=28.22 Aligned_cols=23 Identities=22% Similarity=0.167 Sum_probs=19.9
Q ss_pred CchhHHHHHHHHHhCCCEEEEEe
Q 030330 20 MLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
.-|++|..+++.|..|+.|.|.-
T Consensus 60 ~wg~~Ae~v~~~l~KG~~V~V~G 82 (148)
T PRK08182 60 LWHRDAEHWARLYQKGMRVLVEG 82 (148)
T ss_pred EEhHHHHHHHHhcCCCCEEEEEE
Confidence 56889999999999999988753
No 20
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=43.63 E-value=22 Score=29.66 Aligned_cols=22 Identities=27% Similarity=0.403 Sum_probs=19.9
Q ss_pred CchhHHHHHHHHHhCCCEEEEE
Q 030330 20 MLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
+.|++|..||+.|..||.|+|.
T Consensus 59 ~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 59 IWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred EecHHHHHHHHhcCCCCEEEEE
Confidence 6688999999999999999886
No 21
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=43.45 E-value=24 Score=26.35 Aligned_cols=22 Identities=18% Similarity=0.075 Sum_probs=19.3
Q ss_pred CchhHHHHHHHHHhCCCEEEEE
Q 030330 20 MLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
+.|++|..+++.|..||.|.|.
T Consensus 53 ~wg~~Ae~~~~~l~KG~~V~V~ 74 (112)
T PRK06752 53 VWRKSAENVTEYCTKGSLVGIT 74 (112)
T ss_pred EehHHHHHHHHhcCCCCEEEEE
Confidence 5678999999999999998875
No 22
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=40.60 E-value=25 Score=29.17 Aligned_cols=22 Identities=36% Similarity=0.534 Sum_probs=18.6
Q ss_pred CchhHHHHHHHHHhCCCEEEEE
Q 030330 20 MLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
+-|++|..+++.|..|+.|.|.
T Consensus 55 ~fg~~AE~~~~~l~KG~~V~Ve 76 (182)
T PRK08486 55 LFGRTAEIANQYLSKGSKVLIE 76 (182)
T ss_pred EEhHHHHHHHHHcCCCCEEEEE
Confidence 4789999999999988877764
No 23
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=39.07 E-value=27 Score=28.38 Aligned_cols=22 Identities=14% Similarity=0.047 Sum_probs=19.2
Q ss_pred CchhHHHHHHHHHhCCCEEEEE
Q 030330 20 MLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
+.|++|..+|++|..|+.|.|-
T Consensus 53 ~wgk~Ae~~~~~l~KG~~V~Ve 74 (162)
T PRK07275 53 IWRQQAENLANWAKKGALIGVT 74 (162)
T ss_pred EEcHHHHHHHHHcCCCCEEEEE
Confidence 6789999999999999887764
No 24
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=38.90 E-value=28 Score=26.70 Aligned_cols=23 Identities=17% Similarity=0.277 Sum_probs=19.7
Q ss_pred CchhHHHHHHHHHhCCCEEEEEe
Q 030330 20 MLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
..|++|..++++|..|+.|.|.-
T Consensus 50 ~wg~~Ae~~~~~l~KG~~V~V~G 72 (121)
T PRK07459 50 IWGKTAQVAADYVKKGSLIGITG 72 (121)
T ss_pred EehHHHHHHHHHcCCCCEEEEEE
Confidence 57889999999999999888753
No 25
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.01 E-value=26 Score=28.13 Aligned_cols=23 Identities=35% Similarity=0.489 Sum_probs=20.1
Q ss_pred CchhHHHHHHHHHhCCCEEEEEe
Q 030330 20 MLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
+.|++|..+++.|..|+.|.|.=
T Consensus 57 ~wg~~Ae~~~~~l~KG~~V~V~G 79 (164)
T TIGR00621 57 IFGRLAEVAAQYLKKGSLVYVEG 79 (164)
T ss_pred EehHHHHHHHHhCCCCCEEEEEE
Confidence 67889999999999999988854
No 26
>COG1717 RPL32 Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]
Probab=36.97 E-value=28 Score=27.82 Aligned_cols=28 Identities=36% Similarity=0.815 Sum_probs=17.7
Q ss_pred hhcccccCCCCCCCCcCCcchhHHHHHhccCCC
Q 030330 63 LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPH 95 (179)
Q Consensus 63 l~kr~~g~Pg~g~~~~r~P~~Il~raVrGMLPk 95 (179)
+|++..|+|.--..-++.| .+||||.|.
T Consensus 50 ~Rr~~kg~p~~v~iGyrsP-----k~vRglhPS 77 (133)
T COG1717 50 MRRKLKGKPPMVKIGYRSP-----KAVRGLHPS 77 (133)
T ss_pred HHHHhcCCCCCcccCCCCc-----HhhcccCCC
Confidence 4445555554433445667 589999996
No 27
>PHA02754 hypothetical protein; Provisional
Probab=36.59 E-value=47 Score=23.32 Aligned_cols=15 Identities=27% Similarity=0.623 Sum_probs=13.0
Q ss_pred CCCEEEEEecCcccc
Q 030330 34 NGQKVVAVRCEEICM 48 (179)
Q Consensus 34 ~Gd~VVVVNaeki~i 48 (179)
.||++|||-|+.|.+
T Consensus 43 SGdkIVVi~aD~I~i 57 (67)
T PHA02754 43 SGDKIVVITADAIKI 57 (67)
T ss_pred cCCEEEEEEcceEEE
Confidence 599999999998876
No 28
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=36.57 E-value=29 Score=28.67 Aligned_cols=29 Identities=24% Similarity=0.324 Sum_probs=22.9
Q ss_pred eEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEe
Q 030330 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 10 ~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
.|+-|- +.|++|..++++|..|+.|.|.-
T Consensus 54 ~w~~Vv----~wgk~Ae~v~~~L~KG~~V~VeG 82 (175)
T PRK13732 54 EWHRVV----LFGKLAEVAGEYLRKGAQVYIEG 82 (175)
T ss_pred eEEEEE----EecHHHHHHHHhcCCCCEEEEEE
Confidence 455554 56789999999999999988853
No 29
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=36.00 E-value=44 Score=27.38 Aligned_cols=30 Identities=17% Similarity=0.172 Sum_probs=23.9
Q ss_pred eeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEe
Q 030330 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 9 ~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
..|+-|. +.|++|..+++.|..|+.|.|.=
T Consensus 51 t~w~~Vv----~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 51 TEWHRIV----FYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred ceEEEEE----EEhHHHHHHHHHCCCCCEEEEEE
Confidence 3577664 56889999999999999888753
No 30
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=35.99 E-value=31 Score=28.18 Aligned_cols=22 Identities=23% Similarity=0.422 Sum_probs=19.3
Q ss_pred CchhHHHHHHHHHhCCCEEEEE
Q 030330 20 MLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
+.|++|..+++.|..|+.|.|-
T Consensus 58 ~fgk~Ae~v~~~L~KGs~V~Ve 79 (164)
T PRK08763 58 FFGKLGEIAGEYLRKGSQCYIE 79 (164)
T ss_pred EehHHHHHHHHhcCCCCEEEEE
Confidence 5689999999999999988875
No 31
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=35.78 E-value=30 Score=28.43 Aligned_cols=28 Identities=18% Similarity=0.030 Sum_probs=21.9
Q ss_pred eEEEEeCCCCCchhHHHHHHHHHhCCCEEEEE
Q 030330 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 10 ~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
.|+-|= +-|++|..+|+.|..|+.|.|.
T Consensus 47 dwi~~v----~wgk~Ae~~~~~l~KG~~V~Ve 74 (173)
T PRK06751 47 DFINCV----IWRKQAENVANYLKKGSLAGVD 74 (173)
T ss_pred EEEEEE----EeCcHHHHHHHHcCCCCEEEEE
Confidence 465543 6678999999999999888774
No 32
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A.
Probab=35.50 E-value=25 Score=26.54 Aligned_cols=48 Identities=21% Similarity=0.274 Sum_probs=11.4
Q ss_pred HhCCCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCCCCCCcCCcchh
Q 030330 32 LLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKI 84 (179)
Q Consensus 32 Ll~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~g~~~~r~P~~I 84 (179)
|..||-|+|...+...| ...+-.-|..|.+.+.-.|-|+ +..++|.+|
T Consensus 11 ~~~Gd~V~V~ls~~~nV---~LMd~~Nf~~y~~g~~~~y~GG--~~~~~Pa~i 58 (94)
T PF08980_consen 11 LKRGDTVVVRLSHQANV---RLMDDSNFQRYKNGRRFKYIGG--VAKRSPARI 58 (94)
T ss_dssp --TT-------SSS----------HHHHHHHHHHTT---S-------SSS---
T ss_pred cCCCCEEEEEeCCcccE---EEcChhHhhhhccCCcceEEee--ecccCceEE
Confidence 45788888888777766 2222224544444444444443 556666654
No 33
>PF03447 NAD_binding_3: Homoserine dehydrogenase, NAD binding domain; InterPro: IPR005106 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Homoserine dehydrogenase (1.1.1.3 from EC) catalyses the third step in the aspartate pathway; theNAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine [, ]. Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (P31116 from SWISSPROT) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain []. The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet. This entry represents the NAD(P)-binding domain of aspartate and homoserine dehydrogenase. Asparate dehydrogenase (1.4.1.21 from EC) is strictly specific for L-aspartate as substrate and catalyses the first step in NAD biosynthesis from aspartate. The enzyme has a higher affinity for NAD+ than NADP+ []. Note that the C terminus of the protein contributes a helix to this domain that is not covered by this model.; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 3ING_A 3MTJ_A 3DO5_A 3JSA_A 3C8M_A 1J5P_A 1H2H_A 2EJW_E 1TVE_A 1EBU_D ....
Probab=35.00 E-value=60 Score=23.68 Aligned_cols=34 Identities=26% Similarity=0.288 Sum_probs=24.1
Q ss_pred eEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEecCc
Q 030330 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEE 45 (179)
Q Consensus 10 ~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaek 45 (179)
--+|||+.+. .-++..+...|..|-+||..|-.-
T Consensus 60 ~dvvVE~t~~--~~~~~~~~~~L~~G~~VVt~nk~a 93 (117)
T PF03447_consen 60 IDVVVECTSS--EAVAEYYEKALERGKHVVTANKGA 93 (117)
T ss_dssp -SEEEE-SSC--HHHHHHHHHHHHTTCEEEES-HHH
T ss_pred CCEEEECCCc--hHHHHHHHHHHHCCCeEEEECHHH
Confidence 3489999766 456778888888999999988543
No 34
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=34.15 E-value=33 Score=28.35 Aligned_cols=30 Identities=23% Similarity=0.335 Sum_probs=23.2
Q ss_pred eeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEe
Q 030330 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 9 ~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
..|+=| .+.|++|..+++.|..|+.|.|.-
T Consensus 53 t~w~~V----~~fgk~Ae~~~~~L~KGs~V~VeG 82 (177)
T PRK09010 53 TEWHRV----VLFGKLAEVAGEYLRKGSQVYIEG 82 (177)
T ss_pred eEEEEE----EEehhHHHHHHHhcCCCCEEEEEE
Confidence 346555 367889999999999999888753
No 35
>KOG1154 consensus Gamma-glutamyl kinase [Amino acid transport and metabolism]
Probab=34.12 E-value=48 Score=29.49 Aligned_cols=33 Identities=33% Similarity=0.416 Sum_probs=25.6
Q ss_pred CCCCCchhHHHHHHHHH---hCCCEEEEEecCcccc
Q 030330 16 ARHHMLGRLASIVAKEL---LNGQKVVAVRCEEICM 48 (179)
Q Consensus 16 A~g~iLGRLAS~VAk~L---l~Gd~VVVVNaeki~i 48 (179)
..|--|||||++|-..- +.|.+|++|-+.-|.+
T Consensus 26 ~~~laLgrla~IVEqV~~L~~~G~evilVSSGaVA~ 61 (285)
T KOG1154|consen 26 TCGLALGRLASIVEQVSELQRMGREVILVSSGAVAF 61 (285)
T ss_pred CccchHHHHHHHHHHHHHHHhcCceEEEEecchhhh
Confidence 34458999999875543 4899999999888776
No 36
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=31.25 E-value=69 Score=26.33 Aligned_cols=29 Identities=24% Similarity=0.371 Sum_probs=23.3
Q ss_pred eeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEE
Q 030330 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAV 41 (179)
Q Consensus 9 ~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVV 41 (179)
-.|+-|. +.|++|..+++.|..|+.|.|-
T Consensus 52 T~w~~Vv----~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 52 TEWHRVS----LFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred ceEEEEE----EehHHHHHHHHHhCCCCEEEEE
Confidence 4566665 5678999999999999998874
No 37
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=27.71 E-value=55 Score=27.28 Aligned_cols=30 Identities=33% Similarity=0.395 Sum_probs=22.9
Q ss_pred eeEEEEeCCCCCchhHHHHHHHHHhCCCEEEEEe
Q 030330 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 9 ~~w~VIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
-.|+-|- +.|++|..+++.|..|+.|.|.=
T Consensus 51 T~w~~V~----~fGk~AE~v~~~LkKGs~V~VeG 80 (182)
T PRK06958 51 TEWHRVA----FFGRLAEIVGEYLKKGSSVYIEG 80 (182)
T ss_pred ceEEEEE----EehHHHHHHHHHhCCCCEEEEEE
Confidence 3466554 56789999999999998887753
No 38
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=27.49 E-value=50 Score=24.68 Aligned_cols=73 Identities=12% Similarity=0.159 Sum_probs=41.7
Q ss_pred CCEEEEEecCcccccCccchhhhHhhhhhhcccccCCCC-CCCCcCCcch---hHHHHHhccCCCCChhHHHHhccCcee
Q 030330 35 GQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH-GPIHFRAPAK---IFWRTVRGMIPHKTKRGAAALARLKAY 110 (179)
Q Consensus 35 Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr~~g~Pg~-g~~~~r~P~~---Il~raVrGMLPkkn~~Gr~al~rLkvy 110 (179)
...++|++++++.++--.+......+...+--...||.+ +.++--++.. .+++.++.+||. +..+|++++
T Consensus 61 ~~~~~iiD~~g~~~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~------~~~~ki~~~ 134 (159)
T PF00650_consen 61 EGIVVIIDLSGFSLSNFDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSP------KTREKIVFH 134 (159)
T ss_dssp H-EEEEEE-TT--HHHHHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-H------HHHCTEEEE
T ss_pred eeEEEEEeCCCceEeccccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCH------hhheeEEEE
Confidence 467899999999976433222333333444445679987 4455444333 677889999985 355889998
Q ss_pred cCC
Q 030330 111 EGV 113 (179)
Q Consensus 111 ~G~ 113 (179)
.+.
T Consensus 135 ~~~ 137 (159)
T PF00650_consen 135 SGS 137 (159)
T ss_dssp CTT
T ss_pred CCc
Confidence 553
No 39
>PF07552 Coat_X: Spore Coat Protein X and V domain; InterPro: IPR011428 This domain is found in the Bacilli coat protein X as a tandem repeat and as a single domain in coat protein V. The proteins are found in the insoluble fraction [].; GO: 0030435 sporulation resulting in formation of a cellular spore, 0031160 spore wall
Probab=24.68 E-value=74 Score=22.03 Aligned_cols=18 Identities=11% Similarity=0.200 Sum_probs=15.0
Q ss_pred CCCEEEEEecCcccccCc
Q 030330 34 NGQKVVAVRCEEICMSGG 51 (179)
Q Consensus 34 ~Gd~VVVVNaeki~isG~ 51 (179)
.-++++|.||+++.+|-.
T Consensus 19 s~q~I~I~dS~~V~Vttt 36 (60)
T PF07552_consen 19 SRQKIIIKDSCNVTVTTT 36 (60)
T ss_pred cceEEEEEcCCCCEEeeh
Confidence 357999999999998754
No 40
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=24.44 E-value=66 Score=26.28 Aligned_cols=23 Identities=17% Similarity=0.203 Sum_probs=19.5
Q ss_pred CchhHHHHHHHHHhCCCEEEEEe
Q 030330 20 MLGRLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (179)
.-|.+|..+++.|..|+.|.|.-
T Consensus 49 awg~~Ae~v~~yL~KG~~V~VeG 71 (161)
T PRK06293 49 IWGNRYDKMLPYLKKGSGVIVAG 71 (161)
T ss_pred EEhHHHHHHHHhCCCCCEEEEEE
Confidence 46789999999999999988753
No 41
>PF04379 DUF525: Protein of unknown function (DUF525); InterPro: IPR007474 This domain is found in the bacterial protein ApaG and at the C termini of some F-box proteins (IPR001810 from INTERPRO). F-box proteins contain a carboxy-terminal domain that interacts with protein substrates []. The ApaG domain is ~125 amino acids in length, and is named after the bacterial ApaG protein, of which it forms the core. The Salmonella typhimurium ApaG domain protein, CorD, is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different ApaG proteins show a fold of several beta-sheets. The ApaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [, , ].; PDB: 2F1E_A 1XVS_A 1TZA_A 1XQ4_D.
Probab=23.35 E-value=54 Score=24.12 Aligned_cols=14 Identities=21% Similarity=0.347 Sum_probs=11.2
Q ss_pred ccceeEEEEeCCCC
Q 030330 6 GICAKRVVVDARHH 19 (179)
Q Consensus 6 ~~~~~w~VIDA~g~ 19 (179)
-..|.|.|.|++|+
T Consensus 30 L~sR~W~I~d~~g~ 43 (90)
T PF04379_consen 30 LLSRHWIITDADGH 43 (90)
T ss_dssp EEEEEEEEEETTS-
T ss_pred EEccEEEEEeCCCC
Confidence 45799999999985
No 42
>COG1795 Formaldehyde-activating enzyme nesessary for methanogenesis [Energy production and conversion]
Probab=22.72 E-value=1.5e+02 Score=24.63 Aligned_cols=40 Identities=23% Similarity=0.266 Sum_probs=22.0
Q ss_pred CchhHHHHHHHHH----hCC--------CEEEEEecCcccccCccchhhhHhhh
Q 030330 20 MLGRLASIVAKEL----LNG--------QKVVAVRCEEICMSGGLVRQKMKYMR 61 (179)
Q Consensus 20 iLGRLAS~VAk~L----l~G--------d~VVVVNaeki~isG~k~~~K~~y~~ 61 (179)
+.|-.-+-|||-. ..| |.|||+|. -|.+.-. ..+|+|+..
T Consensus 79 ~fGpaQ~AVAkAVadsveegiip~e~~dd~vvi~sv-fv~~~a~-d~~kiY~yn 130 (170)
T COG1795 79 IFGPAQAAVAKAVADSVEEGIIPREQADDVVVIVSV-FVHPEAE-DKRKIYQYN 130 (170)
T ss_pred hhcHHHHHHHHHHHHHHHhcCCChhHhcCEEEEEEe-EeCcccc-cHHHHHHHh
Confidence 4455445555544 344 77777776 5655443 445655543
No 43
>KOG1481 consensus Cysteine synthase [Amino acid transport and metabolism]
Probab=22.43 E-value=94 Score=28.53 Aligned_cols=51 Identities=29% Similarity=0.416 Sum_probs=38.8
Q ss_pred EEEeCCCCCchhH-------HHHHHHHHhCCCEEEEEecCcccccCccchhhhHhhhhhhcc
Q 030330 12 VVVDARHHMLGRL-------ASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKR 66 (179)
Q Consensus 12 ~VIDA~g~iLGRL-------AS~VAk~Ll~Gd~VVVVNaeki~isG~k~~~K~~y~~~l~kr 66 (179)
+++|-+|.-+|-- |-.|||.|-.|..||.|=|+ ||.+.-.|.+-..||+.+
T Consensus 318 ~Ll~~dGLFvGsSsa~N~VaAv~vAk~LgpG~~iVtilCD----sG~rh~sk~~~~~~l~~~ 375 (391)
T KOG1481|consen 318 YLLDNDGLFVGSSSALNCVAAVRVAKTLGPGHTIVTILCD----SGSRHLSKLFSESFLESK 375 (391)
T ss_pred HhhhcCceEecchhhHHHHHHHHHHHhcCCCceEEEEEeC----CcchHHHHhcCHHHHhhc
Confidence 5667777777753 56789999999999999998 688877776555676643
No 44
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=21.73 E-value=78 Score=25.27 Aligned_cols=22 Identities=23% Similarity=0.342 Sum_probs=18.3
Q ss_pred ch-hHHHHHHHHHhCCCEEEEEe
Q 030330 21 LG-RLASIVAKELLNGQKVVAVR 42 (179)
Q Consensus 21 LG-RLAS~VAk~Ll~Gd~VVVVN 42 (179)
.| ++|..++++|..|+.|.|.-
T Consensus 60 ~g~~~Ae~~~~~l~KG~~V~V~G 82 (152)
T PRK06642 60 FSEGLVSVVERYVTKGSKLYIEG 82 (152)
T ss_pred eChHHHHHHHHhCCCCCEEEEEE
Confidence 46 49999999999999988753
No 45
>COG4091 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=21.30 E-value=1.3e+02 Score=28.36 Aligned_cols=41 Identities=24% Similarity=0.375 Sum_probs=29.9
Q ss_pred EEEEeCCCCCchhHHHHHHHH-HhCCCEEEEEecCcccccCccc
Q 030330 11 RVVVDARHHMLGRLASIVAKE-LLNGQKVVAVRCEEICMSGGLV 53 (179)
Q Consensus 11 w~VIDA~g~iLGRLAS~VAk~-Ll~Gd~VVVVNaeki~isG~k~ 53 (179)
-.||||+|++. .++.++-. ++.|.|||..|.|-=+.-|.-.
T Consensus 103 dvIIdATG~p~--vGA~~~l~Ai~h~KHlVMmNVEaDvtIGp~L 144 (438)
T COG4091 103 DVIIDATGVPE--VGAKIALEAILHGKHLVMMNVEADVTIGPIL 144 (438)
T ss_pred eEEEEcCCCcc--hhhHhHHHHHhcCCeEEEEEeeeceeecHHH
Confidence 36999999975 34444433 4589999999999766667643
No 46
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=20.98 E-value=1.1e+02 Score=21.89 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=21.0
Q ss_pred chhHHHHHHHHHhCCC-EEEEEecCccc
Q 030330 21 LGRLASIVAKELLNGQ-KVVAVRCEEIC 47 (179)
Q Consensus 21 LGRLAS~VAk~Ll~Gd-~VVVVNaeki~ 47 (179)
.|+++..+|+.|..+. .|++|..+.-.
T Consensus 6 ~g~~~~~i~~~L~~~~~~vvvid~d~~~ 33 (116)
T PF02254_consen 6 YGRIGREIAEQLKEGGIDVVVIDRDPER 33 (116)
T ss_dssp -SHHHHHHHHHHHHTTSEEEEEESSHHH
T ss_pred CCHHHHHHHHHHHhCCCEEEEEECCcHH
Confidence 3799999999998766 78888866543
No 47
>PF03446 NAD_binding_2: NAD binding domain of 6-phosphogluconate dehydrogenase; InterPro: IPR006115 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) [, ]. Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequence are highly conserved []. The protein is a homodimer in which the monomers act independently []: each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet []. NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket []. This family represents the NADP binding domain of 6-phosphogluconate dehydrogenase which adopts a Rossman fold. The C-terminal domain is described in IPR006114 from INTERPRO.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0006098 pentose-phosphate shunt, 0055114 oxidation-reduction process; PDB: 3AX6_D 3PDU_G 3Q3C_A 3OBB_A 4DLL_B 1PGP_A 1PGN_A 2PGD_A 1PGQ_A 1PGO_A ....
Probab=20.60 E-value=1.2e+02 Score=23.54 Aligned_cols=22 Identities=32% Similarity=0.514 Sum_probs=19.3
Q ss_pred chhHHHHHHHHHh-CCCEEEEEe
Q 030330 21 LGRLASIVAKELL-NGQKVVAVR 42 (179)
Q Consensus 21 LGRLAS~VAk~Ll-~Gd~VVVVN 42 (179)
+|++.+.+|+.|+ .|..|.+.|
T Consensus 9 lG~mG~~~a~~L~~~g~~v~~~d 31 (163)
T PF03446_consen 9 LGNMGSAMARNLAKAGYEVTVYD 31 (163)
T ss_dssp -SHHHHHHHHHHHHTTTEEEEEE
T ss_pred hHHHHHHHHHHHHhcCCeEEeec
Confidence 6999999999987 799999988
Done!