Query 028707
Match_columns 205
No_of_seqs 228 out of 1225
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 15:44:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028707.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028707hhsearch_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 3.9E-77 8.5E-82 506.8 16.4 198 8-205 2-201 (202)
2 KOG3204 60S ribosomal protein 100.0 2.8E-66 6E-71 435.8 12.9 193 6-205 2-195 (197)
3 TIGR01077 L13_A_E ribosomal pr 100.0 5.3E-55 1.1E-59 354.4 8.8 142 12-154 1-142 (142)
4 PRK06394 rpl13p 50S ribosomal 100.0 3.4E-50 7.3E-55 327.6 10.1 141 9-151 2-143 (146)
5 PRK09216 rplM 50S ribosomal pr 100.0 1.6E-44 3.5E-49 293.7 8.0 119 1-130 5-141 (144)
6 TIGR01066 rplM_bact ribosomal 100.0 3.8E-44 8.2E-49 290.3 8.2 111 4-121 6-134 (140)
7 COG0102 RplM Ribosomal protein 100.0 1.3E-43 2.8E-48 288.5 9.9 122 2-134 6-146 (148)
8 CHL00159 rpl13 ribosomal prote 100.0 1.7E-43 3.6E-48 287.4 8.5 114 1-121 6-137 (143)
9 PF00572 Ribosomal_L13: Riboso 100.0 6.8E-42 1.5E-46 273.4 7.7 109 11-126 1-127 (128)
10 PLN00205 ribisomal protein L13 100.0 8.5E-41 1.8E-45 282.0 9.1 113 6-125 12-142 (191)
11 cd00392 Ribosomal_L13 Ribosoma 100.0 2.6E-38 5.6E-43 248.4 8.0 96 11-113 1-114 (114)
12 KOG3203 Mitochondrial/chloropl 100.0 2.4E-34 5.3E-39 235.0 7.0 108 5-119 17-142 (165)
13 PF12953 DUF3842: Domain of un 60.0 11 0.00023 30.8 3.2 14 34-47 53-66 (131)
14 PHA02754 hypothetical protein; 56.4 19 0.00041 25.8 3.6 16 34-49 43-58 (67)
15 COG1717 RPL32 Ribosomal protei 55.1 8.4 0.00018 31.5 1.9 73 51-154 38-110 (133)
16 PF00436 SSB: Single-strand bi 47.7 19 0.00041 26.2 2.6 23 20-42 54-76 (104)
17 KOG1154 Gamma-glutamyl kinase 45.5 20 0.00044 32.5 2.9 33 16-48 26-61 (285)
18 COG0629 Ssb Single-stranded DN 40.0 29 0.00063 28.5 2.9 22 20-41 57-78 (167)
19 PRK05853 hypothetical protein; 39.4 27 0.00059 29.1 2.6 23 20-42 49-71 (161)
20 cd04496 SSB_OBF SSB_OBF: A sub 38.3 33 0.00071 24.5 2.7 23 20-42 50-72 (100)
21 PF03447 NAD_binding_3: Homose 37.8 49 0.0011 24.8 3.7 36 9-46 59-94 (117)
22 PF00650 CRAL_TRIO: CRAL/TRIO 36.1 28 0.0006 26.7 2.1 72 35-112 61-136 (159)
23 PRK08182 single-stranded DNA-b 35.8 33 0.00072 27.9 2.6 23 20-42 60-82 (148)
24 PRK07772 single-stranded DNA-b 35.1 33 0.00072 29.2 2.5 22 20-41 59-80 (186)
25 PRK06752 single-stranded DNA-b 34.8 37 0.0008 26.0 2.6 23 19-41 52-74 (112)
26 PRK07274 single-stranded DNA-b 34.4 34 0.00073 27.1 2.3 29 9-41 46-74 (131)
27 PRK08486 single-stranded DNA-b 32.8 36 0.00078 28.9 2.4 22 20-41 55-76 (182)
28 TIGR00621 ssb single stranded 31.2 39 0.00084 27.8 2.3 23 20-42 57-79 (164)
29 PRK13732 single-stranded DNA-b 31.1 39 0.00085 28.5 2.3 23 20-42 60-82 (175)
30 PRK08763 single-stranded DNA-b 30.6 41 0.00089 28.1 2.4 22 20-41 58-79 (164)
31 PF07552 Coat_X: Spore Coat Pr 30.2 57 0.0012 23.1 2.7 18 34-51 19-36 (60)
32 PRK07275 single-stranded DNA-b 30.0 43 0.00093 27.8 2.3 23 19-41 52-74 (162)
33 PRK07459 single-stranded DNA-b 29.7 45 0.00097 26.2 2.3 22 20-41 50-71 (121)
34 KOG1481 Cysteine synthase [Ami 29.4 54 0.0012 30.7 3.1 50 12-65 318-374 (391)
35 PF05651 Diacid_rec: Putative 29.3 71 0.0015 25.7 3.5 27 23-49 4-32 (135)
36 PRK09010 single-stranded DNA-b 28.5 46 0.00099 28.2 2.3 24 19-42 59-82 (177)
37 PRK06751 single-stranded DNA-b 27.0 49 0.0011 27.9 2.2 22 20-41 53-74 (173)
38 PRK06863 single-stranded DNA-b 24.3 67 0.0014 26.9 2.5 29 10-42 52-80 (168)
39 cd02430 PTH2 Peptidyl-tRNA hyd 23.7 1.9E+02 0.0041 22.7 4.8 24 9-32 2-26 (115)
40 PRK05733 single-stranded DNA-b 23.0 74 0.0016 26.8 2.5 28 10-41 53-80 (172)
41 PF02254 TrkA_N: TrkA-N domain 23.0 88 0.0019 22.9 2.8 25 21-45 6-31 (116)
42 PRK06958 single-stranded DNA-b 22.3 78 0.0017 27.0 2.6 28 10-41 52-79 (182)
43 PF04989 CmcI: Cephalosporin h 21.8 80 0.0017 27.4 2.6 32 8-40 110-145 (206)
44 PRK03759 isopentenyl-diphospha 21.6 1.5E+02 0.0032 24.3 4.1 26 5-30 2-27 (184)
45 COG4091 Predicted homoserine d 20.8 1.4E+02 0.003 28.8 4.1 40 11-52 103-143 (438)
46 KOG1772 Vacuolar H+-ATPase V1 20.5 2E+02 0.0043 22.8 4.3 41 155-196 6-47 (108)
47 PRK06719 precorrin-2 dehydroge 20.5 1.9E+02 0.0041 23.4 4.5 32 11-42 6-43 (157)
48 PF09756 DDRGK: DDRGK domain; 20.4 44 0.00095 28.6 0.7 27 137-163 110-137 (188)
49 PF09012 FeoC: FeoC like trans 20.2 52 0.0011 22.9 0.9 26 138-163 12-38 (69)
No 1
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=100.00 E-value=3.9e-77 Score=506.83 Aligned_cols=198 Identities=57% Similarity=0.961 Sum_probs=194.6
Q ss_pred cceEEEEeCCCCcchhHHHHHHHHHhCCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCCCcccccCchHHHHH
Q 028707 8 CAKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKILWR 87 (205)
Q Consensus 8 ~~~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~g~~~~r~P~~I~~r 87 (205)
+.+|+||||+||+||||||+||+.|++||+|||||||+|+|||+++++|.||++|+++++++||..||||+|+|++||++
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 45899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccCCCCChhhHHHhhcCceecCCCCCccccccccCCchhhhhhcCCCCCeeehhhhhhhhCcccccccc-hhHHHHH
Q 028707 88 TIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQKGHKYCLLGRLSSEVGWNYYDTIK-VSKKRKE 166 (205)
Q Consensus 88 aVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP~al~v~rl~p~rk~~~LG~ls~~vGWk~~~~v~-le~krk~ 166 (205)
||||||||||++|+++|+||+||+|+||||+++++++||+|+++.+|+|+++||+|||||++|||+|+|+|+ ||++|++
T Consensus 82 aVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~k~~vvp~A~r~~rl~~~~ky~~lg~ls~~vGwky~~vv~~le~krk~ 161 (202)
T PTZ00068 82 TVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSALRVLRLKPERPYTVLGDLSAHVGWKYADVVAKLEEKRKE 161 (202)
T ss_pred HHhhhCCCCChhHHHHHhCCEEecCCCCchhccCcccccchhhhhccCCCCceeeHHHHHHHhCccHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999 9999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh-ccHHHhhccCCC
Q 028707 167 RAQVAYERRKQLAKLRVKAEKAAEERL-GPQLEIIAPIKY 205 (205)
Q Consensus 167 k~~~~~~~k~~~~~~~~~a~~~~~~~~-~~~~~~l~~~g~ 205 (205)
++++||++|++.++++++|++++.+++ .+++++|+++||
T Consensus 162 k~~~~~~~k~~~~k~~~~a~~~~~~~~~~~~~~~l~~~gy 201 (202)
T PTZ00068 162 RAAAYYKKKVKLRKAWKEARKKALAKLPKAIVAVLKKFGY 201 (202)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHcCC
Confidence 999999999999999999999999999 679999999998
No 2
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-66 Score=435.83 Aligned_cols=193 Identities=55% Similarity=0.948 Sum_probs=189.3
Q ss_pred cccceEEEEeCCCCcchhHHHHHHHHHhCCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCCCcccccCchHHH
Q 028707 6 GICAKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIL 85 (205)
Q Consensus 6 ~~~~~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~g~~~~r~P~~I~ 85 (205)
+...+..+||+.||++|||||+|||+|+.|++||||+||.|+|||++++|+ .||+++|++| ||||+|.|++||
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 456788999999999999999999999999999999999999999999999 7899999999 899999999999
Q ss_pred HHHHhccCCCCChhhHHHhhcCceecCCCCCccccccccCCchhhhhhcCCCCCeeehhhhhhhhCcccccccc-hhHHH
Q 028707 86 WRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQKGHKYCLLGRLSSEVGWNYYDTIK-VSKKR 164 (205)
Q Consensus 86 ~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP~al~v~rl~p~rk~~~LG~ls~~vGWk~~~~v~-le~kr 164 (205)
+++||||+|||+++|+.++++|++|+|+|+|||.++++++|.|+++.+|+|++|||+||+|||+|||||+++++ |||+|
T Consensus 75 ~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r~v~p~a~~v~~lk~~~K~c~lG~L~~eVGWkyq~vtatLEeKR 154 (197)
T KOG3204|consen 75 QKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKRLVVPVAFQVLRLKPYKKYCLLGRLSHEVGWKYQAVTATLEEKR 154 (197)
T ss_pred HHhhccccccCCCccHHHHHHHHHhCCCCChhhhcCCccCCcceeeecccCCceeEEeccchhhhcchhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999 99999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHhhccCCC
Q 028707 165 KERAQVAYERRKQLAKLRVKAEKAAEERLGPQLEIIAPIKY 205 (205)
Q Consensus 165 k~k~~~~~~~k~~~~~~~~~a~~~~~~~~~~~~~~l~~~g~ 205 (205)
|+|+++||++|+++++++++|++|++++|++++++|+++||
T Consensus 155 KeK~~~~y~kKkql~kl~~~Aekn~~kkidky~e~l~~~g~ 195 (197)
T KOG3204|consen 155 KEKAKIHYQKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGL 195 (197)
T ss_pred hHhhhhhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhccc
Confidence 99999999999999999999999999999999999999997
No 3
>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=5.3e-55 Score=354.41 Aligned_cols=142 Identities=57% Similarity=0.948 Sum_probs=136.6
Q ss_pred EEEeCCCCcchhHHHHHHHHHhCCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCCCcccccCchHHHHHHHhc
Q 028707 12 VVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKILWRTIRG 91 (205)
Q Consensus 12 ~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~g~~~~r~P~~I~~raVrG 91 (205)
+||||+||+||||||.||+.|+|||+|||||||+|.+||++++++.||.++.+..+..+|..|++++++|++||++||+|
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 58999999999999999999999999999999999999999999999998777788888877999999999999999999
Q ss_pred cCCCCChhhHHHhhcCceecCCCCCccccccccCCchhhhhhcCCCCCeeehhhhhhhhCccc
Q 028707 92 MIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQKGHKYCLLGRLSSEVGWNY 154 (205)
Q Consensus 92 MLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP~al~v~rl~p~rk~~~LG~ls~~vGWk~ 154 (205)
|||+++.+|+.+|+||+||+|+||||++|+++++|+|+ +.+++|.||||+|||||+.|||||
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 99986799999999999999999999999999999998 899999999999999999999997
No 4
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=100.00 E-value=3.4e-50 Score=327.60 Aligned_cols=141 Identities=43% Similarity=0.616 Sum_probs=134.7
Q ss_pred ceEEEEeCCCCcchhHHHHHHHHHhCCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCC-CcccccCchHHHHH
Q 028707 9 AKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSH-GPIHFRAPAKILWR 87 (205)
Q Consensus 9 ~~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~-g~~~~r~P~~I~~r 87 (205)
++.+||||+||+||||||.||+.|++||+|||||||+|.+||++++++.+|.+|++.++..||+. +++++++|++||++
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 45799999999999999999999999999999999999999999999999999999999999965 99999999999999
Q ss_pred HHhccCCCCChhhHHHhhcCceecCCCCCccccccccCCchhhhhhcCCCCCeeehhhhhhhhC
Q 028707 88 TIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQKGHKYCLLGRLSSEVG 151 (205)
Q Consensus 88 aVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP~al~v~rl~p~rk~~~LG~ls~~vG 151 (205)
||+||||+||.+|+.+|+||+||+|+||||.+|+++++|.|+. .++. +|+||+|||||+++|
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 9999999889999999999999999999999999999999986 6787 699999999999999
No 5
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00 E-value=1.6e-44 Score=293.69 Aligned_cols=119 Identities=29% Similarity=0.529 Sum_probs=111.7
Q ss_pred CCCCCcccceEEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhccccc
Q 028707 1 MVSGSGICAKRVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMN 68 (205)
Q Consensus 1 ~~~~~~~~~~w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~ 68 (205)
|+++..+.++|+||||+||+||||||.||+.|+ |||+|||||||+|.|||+++++|.||. |+
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 456677889999999999999999999999999 999999999999999999999999996 99
Q ss_pred ccCCC------CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccccccccCCchhh
Q 028707 69 TKPSH------GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALK 130 (205)
Q Consensus 69 ~~P~~------g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP~al~ 130 (205)
++||+ +++++|+|++||++||+|||| +|.+|+.+|+||+||+|++|||++|+ |..+.
T Consensus 79 g~pGglk~~~~~~~~~r~P~~il~~aVrgMLP-kn~lgr~~~~rLkvy~G~~hp~~~q~----p~~~~ 141 (144)
T PRK09216 79 GYPGGLKEITFGELLAKKPERVIEKAVKGMLP-KNPLGRAMFKKLKVYAGAEHPHAAQQ----PEVLE 141 (144)
T ss_pred ccCCCCEEecHHHHhhhCHHHHHHHHHHhcCC-CCccHHHHHhCcEEeCCCCCCccccC----CEecc
Confidence 99986 899999999999999999999 59999999999999999999999998 66543
No 6
>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=3.8e-44 Score=290.31 Aligned_cols=111 Identities=32% Similarity=0.508 Sum_probs=107.0
Q ss_pred CCcccceEEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccC
Q 028707 4 GSGICAKRVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKP 71 (205)
Q Consensus 4 ~~~~~~~w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P 71 (205)
..++.++|+||||+||+||||||.||+.|+ |||+|||||||+|.|||+++++|.||. |++||
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 457789999999999999999999999999 999999999999999999999999996 99999
Q ss_pred CC------CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccccc
Q 028707 72 SH------GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTK 121 (205)
Q Consensus 72 ~~------g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k 121 (205)
|+ +++++|+|++||++||+|||| ||.+|+.+|+||+||+|+||||++|+
T Consensus 80 gg~k~~~~~~~~~r~P~~ii~~aVrGMLP-kn~lgr~~l~rLkvy~G~~hp~~~q~ 134 (140)
T TIGR01066 80 GGLKSRTFEEMIARKPERVLEHAVKGMLP-KNRLGRKLFKKLKVYAGSEHPHEAQK 134 (140)
T ss_pred CccccccHHHhhhcCHHHHHHHHHHhcCC-CCccHHHHHhCeEEeCCCCCChhhcC
Confidence 86 899999999999999999999 69999999999999999999999998
No 7
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-43 Score=288.46 Aligned_cols=122 Identities=41% Similarity=0.652 Sum_probs=112.6
Q ss_pred CCCCcccceEEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhcccccc
Q 028707 2 VSGSGICAKRVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNT 69 (205)
Q Consensus 2 ~~~~~~~~~w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~ 69 (205)
+++..+.++|+||||+|++||||||.||++|+ |||+|||||||+|+|||++..++.||+ |++
T Consensus 6 ~k~~~~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~------hs~ 79 (148)
T COG0102 6 AKPSEVERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYR------HSG 79 (148)
T ss_pred cCcccccceEEEEeCCCCChHHHHHHHHHHHhcCCCCCcCcCcCCCCEEEEEeceeeEEecccccceEEEE------eec
Confidence 46667899999999999999999999999998 679999999999999999999999997 889
Q ss_pred cCCC-------CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccccccccCCchhhhhhc
Q 028707 70 KPSH-------GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRL 134 (205)
Q Consensus 70 ~P~~-------g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP~al~v~rl 134 (205)
+||+ +++++|.|++||++||+||||+ |++|+++|+||+||.|+||||..|+ |+++.+..+
T Consensus 80 ~~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk-~~lGr~~~krLkVy~G~~h~~~aq~----p~~l~~~~~ 146 (148)
T COG0102 80 YPGGLKNPTRGGPLAPRRPERILERAVRGMLPK-NPLGRAALKRLKVYAGIPHPHEAQK----PEALELKLL 146 (148)
T ss_pred cCCcccccccccccccCCHHHHHHHHHhccCCC-ChhHHHHHhCceEecCCCCcccccc----chhhhhhcc
Confidence 9973 7888899999999999999996 9999999999999999999999997 988766443
No 8
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00 E-value=1.7e-43 Score=287.35 Aligned_cols=114 Identities=30% Similarity=0.479 Sum_probs=107.9
Q ss_pred CCCCCcccceEEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhccccc
Q 028707 1 MVSGSGICAKRVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMN 68 (205)
Q Consensus 1 ~~~~~~~~~~w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~ 68 (205)
++++..+.++|+||||+||+||||||.||+.|+ |||+|||||||+|.+||+++++|.||+ |+
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 356778899999999999999999999999999 999999999999999999999998764 99
Q ss_pred ccCCC------CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccccc
Q 028707 69 TKPSH------GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTK 121 (205)
Q Consensus 69 ~~P~~------g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k 121 (205)
+|||+ +++++++|++||++||+|||| ||.+|+.+|+||+||+|++|||++|+
T Consensus 80 g~pGg~k~~~~~~~~~r~P~~il~~aV~gMLP-kn~lgr~~~~rLkvy~G~~hph~aq~ 137 (143)
T CHL00159 80 GRPGGLKIETFEELQNRLPNRIIEKAVKGMLP-KGPLGRKLFTKLKVYKGESHPHVAQK 137 (143)
T ss_pred CCCCCcccccHHHHhhcCHHHHHHHHHHhcCC-CChhHHHHHhCCEEeCCCCCCccccC
Confidence 99985 689999999999999999999 59999999999999999999999998
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=6.8e-42 Score=273.37 Aligned_cols=109 Identities=43% Similarity=0.670 Sum_probs=102.5
Q ss_pred EEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCC-----
Q 028707 11 RVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSH----- 73 (205)
Q Consensus 11 w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~----- 73 (205)
|+||||+||+||||||.||+.|+ |||+|||||||+|.+||+++.++.||. |++|||+
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 7888875
Q ss_pred -CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccccccccCC
Q 028707 74 -GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIP 126 (205)
Q Consensus 74 -g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP 126 (205)
+.+++++|++||++||+||||+ |.+|+.+|+||+||+|+||||++|+++++|
T Consensus 75 ~~~~~~~~P~~i~~~aVrgMLP~-n~~g~~~l~rL~vy~g~~hp~~~~~~~~~~ 127 (128)
T PF00572_consen 75 AKGLHEKDPSRILKRAVRGMLPK-NKLGREALKRLKVYPGEPHPHAAQKPVVLE 127 (128)
T ss_dssp CHHHHCSSHHHHHHHHHHTTSTT-SHHHHHHHTTEEEESSSSCSTTSSSCBEEE
T ss_pred hhhhhhcCHHHHHHHHHHHHCCC-ChhhhHHhhceEEECCCCCChhccCCEeCC
Confidence 4556699999999999999996 999999999999999999999999976654
No 10
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=100.00 E-value=8.5e-41 Score=281.99 Aligned_cols=113 Identities=19% Similarity=0.334 Sum_probs=104.9
Q ss_pred cccceEEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCC
Q 028707 6 GICAKRVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSH 73 (205)
Q Consensus 6 ~~~~~w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~ 73 (205)
.-.++|+||||+||+||||||.||+.|+ |||+|||||||+|.|||++|.+|.||. |++|||+
T Consensus 12 ~~~r~W~VIDA~~~iLGRLAS~IAk~L~GKhKP~ytP~~D~GD~VVVINAekI~lTG~K~~~K~Y~~------htgypGg 85 (191)
T PLN00205 12 LEGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFYRW------HTGYIGH 85 (191)
T ss_pred cCCCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEeccEEEEeCChhhcceEEE------ecCCCCC
Confidence 3468899999999999999999999999 999999999999999999999999886 9999986
Q ss_pred ------CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccccccccC
Q 028707 74 ------GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVI 125 (205)
Q Consensus 74 ------g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vv 125 (205)
+++++++|++||++||+||||+ |.+|+.+++||+||+|+||||++|+.+++
T Consensus 86 lk~~~~~~~~~r~P~~Il~kAVrGMLPk-n~lr~~~~krLkVY~G~~hp~~~q~p~~~ 142 (191)
T PLN00205 86 LKERSLKDQMAKDPTEVIRKAVLRMLPR-NRLRDDRDRKLRIFAGSEHPFGDKPLEPF 142 (191)
T ss_pred cccccHHHHhccCHHHHHHHHHHhcCCC-CchHHHHHhCCEEECCCCCChhccCCeEe
Confidence 7899999999999999999996 77777799999999999999999986443
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=2.6e-38 Score=248.41 Aligned_cols=96 Identities=54% Similarity=0.783 Sum_probs=91.6
Q ss_pred EEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCC-----
Q 028707 11 RVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSH----- 73 (205)
Q Consensus 11 w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~----- 73 (205)
|+||||+||+||||||.||+.|+ |||+|||||||+|.+||+++++|.||. |++||++
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 89999999999999999999999 499999999999999999999999997 7777764
Q ss_pred -CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCC
Q 028707 74 -GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGV 113 (205)
Q Consensus 74 -g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~ 113 (205)
+++++++|++||++||+|||| ||.+|+++|+||+||+|+
T Consensus 75 ~~~~~~~~P~~il~~aV~gMLP-kn~~g~~~l~rLkvy~g~ 114 (114)
T cd00392 75 AGPLHPRAPERILKRAVRGMLP-KNKLGRAALKRLKVYEGA 114 (114)
T ss_pred cchhhhhCHHHHHHHHHHhcCC-CChhHHHHHhCcEEeCCC
Confidence 999999999999999999999 799999999999999985
No 12
>KOG3203 consensus Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-34 Score=234.96 Aligned_cols=108 Identities=31% Similarity=0.443 Sum_probs=101.4
Q ss_pred CcccceEEEEeCCCCcchhHHHHHHHHHh------------CCCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCC
Q 028707 5 SGICAKRVVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPS 72 (205)
Q Consensus 5 ~~~~~~w~vIDA~g~iLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~ 72 (205)
.+|++.|+||||++++||||||.||..|+ |||+|||+||++|.+||++|.+|.|+. |+||||
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 36789999999999999999999999997 999999999999999999999999886 999999
Q ss_pred C------CcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccc
Q 028707 73 H------GPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDK 119 (205)
Q Consensus 73 ~------g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~ 119 (205)
+ ..++.|+|++|+++||+|||| ||.+++..++||++|+|.+||+..
T Consensus 91 ~lk~~~~~q~~~rdp~~Iv~~AV~gMLP-kN~Lrr~~~~rL~lf~g~e~p~~~ 142 (165)
T KOG3203|consen 91 GLKQTTADQLADRDPCRIVRLAVYGMLP-KNLLRRRRMQRLHLFPGEEHPEKV 142 (165)
T ss_pred chhhhHHHHHhhhCHHHHHHHHHHhhCc-cchHHHHHhheeeccCCccCchhh
Confidence 7 667889999999999999999 699999999999999999999543
No 13
>PF12953 DUF3842: Domain of unknown function (DUF3842); InterPro: IPR024208 This family of proteins has no known function.
Probab=59.96 E-value=11 Score=30.83 Aligned_cols=14 Identities=21% Similarity=0.430 Sum_probs=11.5
Q ss_pred CCCEEEEEeeceeE
Q 028707 34 NGQKVVVVRCEEIC 47 (205)
Q Consensus 34 ~Gd~VVVVNaeki~ 47 (205)
+|+.-||+||.++-
T Consensus 53 TGENaIv~n~~~aD 66 (131)
T PF12953_consen 53 TGENAIVVNARKAD 66 (131)
T ss_pred cccchheeccCCCC
Confidence 78888999988864
No 14
>PHA02754 hypothetical protein; Provisional
Probab=56.38 E-value=19 Score=25.82 Aligned_cols=16 Identities=38% Similarity=0.688 Sum_probs=14.0
Q ss_pred CCCEEEEEeeceeEee
Q 028707 34 NGQKVVVVRCEEICIS 49 (205)
Q Consensus 34 ~Gd~VVVVNaeki~iS 49 (205)
.||++|||-++.|.|.
T Consensus 43 SGdkIVVi~aD~I~i~ 58 (67)
T PHA02754 43 SGDKIVVITADAIKIE 58 (67)
T ss_pred cCCEEEEEEcceEEEE
Confidence 7999999999988774
No 15
>COG1717 RPL32 Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]
Probab=55.14 E-value=8.4 Score=31.46 Aligned_cols=73 Identities=22% Similarity=0.388 Sum_probs=40.9
Q ss_pred ccchhhhHHhhhhcccccccCCCCcccccCchHHHHHHHhccCCCCChhhHHHhhcCceecCCCCCccccccccCCchhh
Q 028707 51 GLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALK 130 (205)
Q Consensus 51 ~k~r~K~~y~~~l~kr~~~~P~~g~~~~r~P~~I~~raVrGMLP~K~~~G~~al~rLkvy~G~p~p~~~~k~~vvP~al~ 130 (205)
+.||.-.--.+-+|.+..++|.--..-+++| .+||||.|. | ++-+-|| ..-+
T Consensus 38 ~~WRrPrG~dsK~Rr~~kg~p~~v~iGyrsP-----k~vRglhPS----G---~~~VlV~----------------Nv~d 89 (133)
T COG1717 38 EKWRRPRGIDSKMRRKLKGKPPMVKIGYRSP-----KAVRGLHPS----G---YEEVLVH----------------NVKD 89 (133)
T ss_pred hhccCCCCchHHHHHHhcCCCCCcccCCCCc-----HhhcccCCC----c---cceeeee----------------cHHH
Confidence 3343333333334445556665444457888 589999995 2 3333333 1224
Q ss_pred hhhcCCCCCeeehhhhhhhhCccc
Q 028707 131 VLRLQKGHKYCLLGRLSSEVGWNY 154 (205)
Q Consensus 131 v~rl~p~rk~~~LG~ls~~vGWk~ 154 (205)
+..|.|.+. -.+||+.||-+-
T Consensus 90 Le~ldp~~~---aarIAs~VG~rK 110 (133)
T COG1717 90 LEKLDPETQ---AARIASTVGARK 110 (133)
T ss_pred HhhcCchhH---HHHHHHhhhHHH
Confidence 456776655 678888888643
No 16
>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=47.72 E-value=19 Score=26.17 Aligned_cols=23 Identities=35% Similarity=0.446 Sum_probs=16.8
Q ss_pred cchhHHHHHHHHHhCCCEEEEEe
Q 028707 20 MLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
+.|.+|..++..|..||.|.|.-
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 45899999999999999887754
No 17
>KOG1154 consensus Gamma-glutamyl kinase [Amino acid transport and metabolism]
Probab=45.52 E-value=20 Score=32.47 Aligned_cols=33 Identities=27% Similarity=0.415 Sum_probs=25.7
Q ss_pred CCCCcchhHHHHHHHHH---hCCCEEEEEeeceeEe
Q 028707 16 ARHHMLGRLASVLAKEL---LNGQKVVVVRCEEICI 48 (205)
Q Consensus 16 A~g~iLGRLAS~VAk~L---l~Gd~VVVVNaeki~i 48 (205)
..|--||||||+|-... +.|..|++|-+-.|.+
T Consensus 26 ~~~laLgrla~IVEqV~~L~~~G~evilVSSGaVA~ 61 (285)
T KOG1154|consen 26 TCGLALGRLASIVEQVSELQRMGREVILVSSGAVAF 61 (285)
T ss_pred CccchHHHHHHHHHHHHHHHhcCceEEEEecchhhh
Confidence 34558999999875543 5899999998877765
No 18
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=40.00 E-value=29 Score=28.45 Aligned_cols=22 Identities=36% Similarity=0.401 Sum_probs=20.0
Q ss_pred cchhHHHHHHHHHhCCCEEEEE
Q 028707 20 MLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
+.|++|..++..|..|+.|+|.
T Consensus 57 ~wgk~Ae~~~~yl~KG~~V~Ve 78 (167)
T COG0629 57 IWGKLAENAAEYLKKGSLVYVE 78 (167)
T ss_pred EehHHHHHHHHHhcCCCEEEEE
Confidence 5799999999999999998875
No 19
>PRK05853 hypothetical protein; Validated
Probab=39.38 E-value=27 Score=29.13 Aligned_cols=23 Identities=35% Similarity=0.471 Sum_probs=20.6
Q ss_pred cchhHHHHHHHHHhCCCEEEEEe
Q 028707 20 MLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
+.|+||..|++.|..|+.|+|.-
T Consensus 49 ~wg~lAe~v~~~L~KG~~V~V~G 71 (161)
T PRK05853 49 CWGRLVTGVGAALGKGAPVIVVG 71 (161)
T ss_pred EEhHHHHHHHHHcCCCCEEEEEE
Confidence 67899999999999999998864
No 20
>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=38.33 E-value=33 Score=24.54 Aligned_cols=23 Identities=39% Similarity=0.401 Sum_probs=19.7
Q ss_pred cchhHHHHHHHHHhCCCEEEEEe
Q 028707 20 MLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
+-|.+|..+++.|..||.|+|.-
T Consensus 50 ~~g~~a~~~~~~~~kG~~V~v~G 72 (100)
T cd04496 50 AFGKLAENAAKYLKKGDLVYVEG 72 (100)
T ss_pred EEhHHHHHHHHHhCCCCEEEEEE
Confidence 55679999999999999988754
No 21
>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=37.77 E-value=49 Score=24.76 Aligned_cols=36 Identities=25% Similarity=0.296 Sum_probs=25.7
Q ss_pred ceEEEEeCCCCcchhHHHHHHHHHhCCCEEEEEeecee
Q 028707 9 AKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEI 46 (205)
Q Consensus 9 ~~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVNaeki 46 (205)
+--+|||+.+. .-++..+...|..|-+||..|-.-+
T Consensus 59 ~~dvvVE~t~~--~~~~~~~~~~L~~G~~VVt~nk~al 94 (117)
T PF03447_consen 59 DIDVVVECTSS--EAVAEYYEKALERGKHVVTANKGAL 94 (117)
T ss_dssp T-SEEEE-SSC--HHHHHHHHHHHHTTCEEEES-HHHH
T ss_pred CCCEEEECCCc--hHHHHHHHHHHHCCCeEEEECHHHh
Confidence 35689999776 5567888888899999999885543
No 22
>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=36.15 E-value=28 Score=26.74 Aligned_cols=72 Identities=13% Similarity=0.220 Sum_probs=41.6
Q ss_pred CCEEEEEeeceeEeeCccchhhhHHhhhhcccccccCCC-CcccccCch---HHHHHHHhccCCCCChhhHHHhhcCcee
Q 028707 35 GQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKPSH-GPIHFRAPA---KILWRTIRGMIPHKTKRGAAALARLKAY 110 (205)
Q Consensus 35 Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~kr~~~~P~~-g~~~~r~P~---~I~~raVrGMLP~K~~~G~~al~rLkvy 110 (205)
+..++|++++++.++--.+........++.--...||.+ +.+|.-++. ..+|+.++.+||. ...+++.++
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 578999999999976433222222333333335679987 555544433 3678999999993 567889988
Q ss_pred cC
Q 028707 111 EG 112 (205)
Q Consensus 111 ~G 112 (205)
.+
T Consensus 135 ~~ 136 (159)
T PF00650_consen 135 SG 136 (159)
T ss_dssp CT
T ss_pred CC
Confidence 54
No 23
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=35.84 E-value=33 Score=27.95 Aligned_cols=23 Identities=26% Similarity=0.245 Sum_probs=20.0
Q ss_pred cchhHHHHHHHHHhCCCEEEEEe
Q 028707 20 MLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
+.|++|..+++.|..|+.|.|.-
T Consensus 60 ~wg~~Ae~v~~~l~KG~~V~V~G 82 (148)
T PRK08182 60 LWHRDAEHWARLYQKGMRVLVEG 82 (148)
T ss_pred EEhHHHHHHHHhcCCCCEEEEEE
Confidence 67889999999999999888753
No 24
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=35.06 E-value=33 Score=29.25 Aligned_cols=22 Identities=27% Similarity=0.437 Sum_probs=20.1
Q ss_pred cchhHHHHHHHHHhCCCEEEEE
Q 028707 20 MLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
+.|.+|..||+.|..||.|+|.
T Consensus 59 ~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 59 IWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred EecHHHHHHHHhcCCCCEEEEE
Confidence 6789999999999999999886
No 25
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=34.83 E-value=37 Score=25.98 Aligned_cols=23 Identities=13% Similarity=0.085 Sum_probs=20.0
Q ss_pred CcchhHHHHHHHHHhCCCEEEEE
Q 028707 19 HMLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 19 ~iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
-+.|++|..++..|..|+.|.|.
T Consensus 52 ~~wg~~Ae~~~~~l~KG~~V~V~ 74 (112)
T PRK06752 52 VVWRKSAENVTEYCTKGSLVGIT 74 (112)
T ss_pred EEehHHHHHHHHhcCCCCEEEEE
Confidence 36788999999999999998875
No 26
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=34.40 E-value=34 Score=27.13 Aligned_cols=29 Identities=28% Similarity=0.316 Sum_probs=22.7
Q ss_pred ceEEEEeCCCCcchhHHHHHHHHHhCCCEEEEE
Q 028707 9 AKRVVVDARHHMLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 9 ~~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
..|+-|= +.|++|..++..|..|+.|.|-
T Consensus 46 t~w~~v~----~fg~~Ae~v~~~l~KG~~V~V~ 74 (131)
T PRK07274 46 ADFINVV----LWGKLAETLASYASKGSLISID 74 (131)
T ss_pred EEEEEEE----EehHHHHHHHHHcCCCCEEEEE
Confidence 3465553 5689999999999999998774
No 27
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=32.78 E-value=36 Score=28.86 Aligned_cols=22 Identities=32% Similarity=0.560 Sum_probs=18.9
Q ss_pred cchhHHHHHHHHHhCCCEEEEE
Q 028707 20 MLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
+.|++|..+++.|..|+.|.|.
T Consensus 55 ~fg~~AE~~~~~l~KG~~V~Ve 76 (182)
T PRK08486 55 LFGRTAEIANQYLSKGSKVLIE 76 (182)
T ss_pred EEhHHHHHHHHHcCCCCEEEEE
Confidence 5799999999999988887763
No 28
>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=31.19 E-value=39 Score=27.82 Aligned_cols=23 Identities=43% Similarity=0.522 Sum_probs=20.4
Q ss_pred cchhHHHHHHHHHhCCCEEEEEe
Q 028707 20 MLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
+.|++|..+++.|..|+.|+|.-
T Consensus 57 ~wg~~Ae~~~~~l~KG~~V~V~G 79 (164)
T TIGR00621 57 IFGRLAEVAAQYLKKGSLVYVEG 79 (164)
T ss_pred EehHHHHHHHHhCCCCCEEEEEE
Confidence 67899999999999999998853
No 29
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=31.11 E-value=39 Score=28.53 Aligned_cols=23 Identities=30% Similarity=0.507 Sum_probs=20.3
Q ss_pred cchhHHHHHHHHHhCCCEEEEEe
Q 028707 20 MLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
+.|++|..++..|..|+.|+|.-
T Consensus 60 ~wgk~Ae~v~~~L~KG~~V~VeG 82 (175)
T PRK13732 60 LFGKLAEVAGEYLRKGAQVYIEG 82 (175)
T ss_pred EecHHHHHHHHhcCCCCEEEEEE
Confidence 67889999999999999998853
No 30
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=30.63 E-value=41 Score=28.07 Aligned_cols=22 Identities=18% Similarity=0.448 Sum_probs=19.5
Q ss_pred cchhHHHHHHHHHhCCCEEEEE
Q 028707 20 MLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
+.|.+|..|+..|..|+.|.|-
T Consensus 58 ~fgk~Ae~v~~~L~KGs~V~Ve 79 (164)
T PRK08763 58 FFGKLGEIAGEYLRKGSQCYIE 79 (164)
T ss_pred EehHHHHHHHHhcCCCCEEEEE
Confidence 6789999999999999988874
No 31
>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=30.23 E-value=57 Score=23.10 Aligned_cols=18 Identities=11% Similarity=0.300 Sum_probs=15.7
Q ss_pred CCCEEEEEeeceeEeeCc
Q 028707 34 NGQKVVVVRCEEICISGG 51 (205)
Q Consensus 34 ~Gd~VVVVNaeki~iSG~ 51 (205)
.-++++|.||+++.+|-.
T Consensus 19 s~q~I~I~dS~~V~Vttt 36 (60)
T PF07552_consen 19 SRQKIIIKDSCNVTVTTT 36 (60)
T ss_pred cceEEEEEcCCCCEEeeh
Confidence 578999999999999854
No 32
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=29.96 E-value=43 Score=27.84 Aligned_cols=23 Identities=22% Similarity=0.104 Sum_probs=19.8
Q ss_pred CcchhHHHHHHHHHhCCCEEEEE
Q 028707 19 HMLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 19 ~iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
-+.|++|..+|+.|..|+.|.|-
T Consensus 52 v~wgk~Ae~~~~~l~KG~~V~Ve 74 (162)
T PRK07275 52 VIWRQQAENLANWAKKGALIGVT 74 (162)
T ss_pred EEEcHHHHHHHHHcCCCCEEEEE
Confidence 37899999999999999888764
No 33
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=29.68 E-value=45 Score=26.18 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=19.3
Q ss_pred cchhHHHHHHHHHhCCCEEEEE
Q 028707 20 MLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
+.|++|..+++.|..|+.|.|.
T Consensus 50 ~wg~~Ae~~~~~l~KG~~V~V~ 71 (121)
T PRK07459 50 IWGKTAQVAADYVKKGSLIGIT 71 (121)
T ss_pred EehHHHHHHHHHcCCCCEEEEE
Confidence 5789999999999999888775
No 34
>KOG1481 consensus Cysteine synthase [Amino acid transport and metabolism]
Probab=29.40 E-value=54 Score=30.67 Aligned_cols=50 Identities=28% Similarity=0.394 Sum_probs=40.2
Q ss_pred EEEeCCCCcchhH-------HHHHHHHHhCCCEEEEEeeceeEeeCccchhhhHHhhhhcc
Q 028707 12 VVVDARHHMLGRL-------ASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRK 65 (205)
Q Consensus 12 ~vIDA~g~iLGRL-------AS~VAk~Ll~Gd~VVVVNaeki~iSG~k~r~K~~y~~~l~k 65 (205)
+++|-+|..+|-- |-.|||.|-.|..||.|-|+ ||.+.-.|.+-..||+.
T Consensus 318 ~Ll~~dGLFvGsSsa~N~VaAv~vAk~LgpG~~iVtilCD----sG~rh~sk~~~~~~l~~ 374 (391)
T KOG1481|consen 318 YLLDNDGLFVGSSSALNCVAAVRVAKTLGPGHTIVTILCD----SGSRHLSKLFSESFLES 374 (391)
T ss_pred HhhhcCceEecchhhHHHHHHHHHHHhcCCCceEEEEEeC----CcchHHHHhcCHHHHhh
Confidence 5677788888864 55789999999999999998 79988888766677764
No 35
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=29.26 E-value=71 Score=25.66 Aligned_cols=27 Identities=22% Similarity=0.386 Sum_probs=22.7
Q ss_pred hHHHHHHHHHh--CCCEEEEEeeceeEee
Q 028707 23 RLASVLAKELL--NGQKVVVVRCEEICIS 49 (205)
Q Consensus 23 RLAS~VAk~Ll--~Gd~VVVVNaeki~iS 49 (205)
.||..|+..+. .|..|.|.|++.+.|-
T Consensus 4 ~~Aq~Iv~~~~~~i~~~inimd~~G~IIA 32 (135)
T PF05651_consen 4 ELAQKIVDEIMEIIGYNINIMDENGIIIA 32 (135)
T ss_pred HHHHHHHHHHHHHcCCCEEEECCCcEEEe
Confidence 47777887776 7999999999999883
No 36
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=28.53 E-value=46 Score=28.16 Aligned_cols=24 Identities=29% Similarity=0.463 Sum_probs=20.7
Q ss_pred CcchhHHHHHHHHHhCCCEEEEEe
Q 028707 19 HMLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 19 ~iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
-+.|++|..+++.|..|+.|.|.-
T Consensus 59 ~~fgk~Ae~~~~~L~KGs~V~VeG 82 (177)
T PRK09010 59 VLFGKLAEVAGEYLRKGSQVYIEG 82 (177)
T ss_pred EEehhHHHHHHHhcCCCCEEEEEE
Confidence 477899999999999999988853
No 37
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=27.04 E-value=49 Score=27.87 Aligned_cols=22 Identities=23% Similarity=0.143 Sum_probs=19.1
Q ss_pred cchhHHHHHHHHHhCCCEEEEE
Q 028707 20 MLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 20 iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
+.|++|..++..|..|+.|+|.
T Consensus 53 ~wgk~Ae~~~~~l~KG~~V~Ve 74 (173)
T PRK06751 53 IWRKQAENVANYLKKGSLAGVD 74 (173)
T ss_pred EeCcHHHHHHHHcCCCCEEEEE
Confidence 6788999999999999888774
No 38
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=24.30 E-value=67 Score=26.95 Aligned_cols=29 Identities=24% Similarity=0.197 Sum_probs=23.4
Q ss_pred eEEEEeCCCCcchhHHHHHHHHHhCCCEEEEEe
Q 028707 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVVR 42 (205)
Q Consensus 10 ~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVVN 42 (205)
.|+-|. +.|++|..+++.|..|+.|.|.-
T Consensus 52 ~w~~Vv----~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 52 EWHRIV----FYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred eEEEEE----EEhHHHHHHHHHCCCCCEEEEEE
Confidence 476664 57889999999999999988753
No 39
>cd02430 PTH2 Peptidyl-tRNA hydrolase, type 2 (PTH2). Peptidyl-tRNA hydrolase (PTH) activity releases tRNA from the premature translation termination product peptidyl-tRNA, therefore allowing the tRNA and peptide to be reused in protein synthesis. PTH2 is present in archaea and eukaryotes.
Probab=23.69 E-value=1.9e+02 Score=22.69 Aligned_cols=24 Identities=21% Similarity=0.169 Sum_probs=16.9
Q ss_pred ceEEEEeCC-CCcchhHHHHHHHHH
Q 028707 9 AKRVVVDAR-HHMLGRLASVLAKEL 32 (205)
Q Consensus 9 ~~w~vIDA~-g~iLGRLAS~VAk~L 32 (205)
++.++|..+ +.-.|.+|+++|---
T Consensus 2 K~vivVr~DL~m~~GKiaAQ~~HAa 26 (115)
T cd02430 2 KMVLVVRNDLKMGKGKIAAQCAHAA 26 (115)
T ss_pred EEEEEEeCCCCCCcchHHHHHHHHH
Confidence 355666654 788899999987543
No 40
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=23.00 E-value=74 Score=26.80 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=22.9
Q ss_pred eEEEEeCCCCcchhHHHHHHHHHhCCCEEEEE
Q 028707 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 10 ~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
.|+-|. +.|++|..++..|..|+.|.|-
T Consensus 53 ~w~~Vv----~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 53 EWHRVS----LFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred eEEEEE----EehHHHHHHHHHhCCCCEEEEE
Confidence 466554 6788999999999999998874
No 41
>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=22.99 E-value=88 Score=22.88 Aligned_cols=25 Identities=32% Similarity=0.567 Sum_probs=20.4
Q ss_pred chhHHHHHHHHHhCCC-EEEEEeece
Q 028707 21 LGRLASVLAKELLNGQ-KVVVVRCEE 45 (205)
Q Consensus 21 LGRLAS~VAk~Ll~Gd-~VVVVNaek 45 (205)
.|+++..+|+.|..+. .|+||..+.
T Consensus 6 ~g~~~~~i~~~L~~~~~~vvvid~d~ 31 (116)
T PF02254_consen 6 YGRIGREIAEQLKEGGIDVVVIDRDP 31 (116)
T ss_dssp -SHHHHHHHHHHHHTTSEEEEEESSH
T ss_pred CCHHHHHHHHHHHhCCCEEEEEECCc
Confidence 3799999999999776 788887664
No 42
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=22.35 E-value=78 Score=27.00 Aligned_cols=28 Identities=29% Similarity=0.444 Sum_probs=22.2
Q ss_pred eEEEEeCCCCcchhHHHHHHHHHhCCCEEEEE
Q 028707 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVV 41 (205)
Q Consensus 10 ~w~vIDA~g~iLGRLAS~VAk~Ll~Gd~VVVV 41 (205)
.|+-|- +.|.+|..+++.|..|+.|.|.
T Consensus 52 ~w~~V~----~fGk~AE~v~~~LkKGs~V~Ve 79 (182)
T PRK06958 52 EWHRVA----FFGRLAEIVGEYLKKGSSVYIE 79 (182)
T ss_pred eEEEEE----EehHHHHHHHHHhCCCCEEEEE
Confidence 455543 6788999999999999888874
No 43
>PF04989 CmcI: Cephalosporin hydroxylase; InterPro: IPR007072 This entry contains Rhamnosyl O-methyltransferase which catalyses the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD) []. Members of this family are about 220 amino acids long. It also includes the CmcI protein O85726 from SWISSPROT, which is presumed to represent the cephalosporin-7--hydroxylase []. However this has not been experimentally verified.; GO: 0008168 methyltransferase activity, 0008610 lipid biosynthetic process; PDB: 2BR4_B 2BR3_E 2BR5_E 2BM8_J 2BM9_E.
Probab=21.80 E-value=80 Score=27.45 Aligned_cols=32 Identities=22% Similarity=0.288 Sum_probs=22.1
Q ss_pred cceEEEEe-CC---CCcchhHHHHHHHHHhCCCEEEE
Q 028707 8 CAKRVVVD-AR---HHMLGRLASVLAKELLNGQKVVV 40 (205)
Q Consensus 8 ~~~w~vID-A~---g~iLGRLAS~VAk~Ll~Gd~VVV 40 (205)
...|+||| +. .|+++-|.. .+..+..|++.||
T Consensus 110 ~~~vlVilDs~H~~~hvl~eL~~-y~plv~~G~Y~IV 145 (206)
T PF04989_consen 110 PHPVLVILDSSHTHEHVLAELEA-YAPLVSPGSYLIV 145 (206)
T ss_dssp -SSEEEEESS----SSHHHHHHH-HHHT--TT-EEEE
T ss_pred CCceEEEECCCccHHHHHHHHHH-hCccCCCCCEEEE
Confidence 34566665 55 699999998 8998999999988
No 44
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=21.60 E-value=1.5e+02 Score=24.30 Aligned_cols=26 Identities=15% Similarity=0.017 Sum_probs=21.3
Q ss_pred CcccceEEEEeCCCCcchhHHHHHHH
Q 028707 5 SGICAKRVVVDARHHMLGRLASVLAK 30 (205)
Q Consensus 5 ~~~~~~w~vIDA~g~iLGRLAS~VAk 30 (205)
|+-++.|.|+|..|..+|+.....+.
T Consensus 2 ~~~~E~~~~vd~~~~~~g~~~r~~~~ 27 (184)
T PRK03759 2 MMETELVVLLDEQGVPTGTAEKAAAH 27 (184)
T ss_pred CCCceeEEEECCCCCCcccccHHHHH
Confidence 44567799999999999997777775
No 45
>COG4091 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=20.81 E-value=1.4e+02 Score=28.79 Aligned_cols=40 Identities=23% Similarity=0.360 Sum_probs=29.1
Q ss_pred EEEEeCCCCcchhHHHHHHH-HHhCCCEEEEEeeceeEeeCcc
Q 028707 11 RVVVDARHHMLGRLASVLAK-ELLNGQKVVVVRCEEICISGGL 52 (205)
Q Consensus 11 w~vIDA~g~iLGRLAS~VAk-~Ll~Gd~VVVVNaeki~iSG~k 52 (205)
-.||||+|++. ..+.++- .++.|.+||.+|.|-=+.-|..
T Consensus 103 dvIIdATG~p~--vGA~~~l~Ai~h~KHlVMmNVEaDvtIGp~ 143 (438)
T COG4091 103 DVIIDATGVPE--VGAKIALEAILHGKHLVMMNVEADVTIGPI 143 (438)
T ss_pred eEEEEcCCCcc--hhhHhHHHHHhcCCeEEEEEeeeceeecHH
Confidence 37999999985 3444443 3468999999999865555653
No 46
>KOG1772 consensus Vacuolar H+-ATPase V1 sector, subunit G [Energy production and conversion]
Probab=20.49 E-value=2e+02 Score=22.81 Aligned_cols=41 Identities=12% Similarity=0.229 Sum_probs=22.6
Q ss_pred ccccc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccH
Q 028707 155 YDTIK-VSKKRKERAQVAYERRKQLAKLRVKAEKAAEERLGPQ 196 (205)
Q Consensus 155 ~~~v~-le~krk~k~~~~~~~k~~~~~~~~~a~~~~~~~~~~~ 196 (205)
+.+-. |.+...+...+--.+|.. .+..++|+.++...|+.|
T Consensus 6 qGIqQLLqAEK~A~e~V~~ARk~K-~~RLKQAKeEA~~Eie~y 47 (108)
T KOG1772|consen 6 QGIQQLLQAEKRAAEKVEEARKRK-LRRLKQAKEEAEKEIEEY 47 (108)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 34444 666666655444444433 333477777777666553
No 47
>PRK06719 precorrin-2 dehydrogenase; Validated
Probab=20.49 E-value=1.9e+02 Score=23.38 Aligned_cols=32 Identities=25% Similarity=0.367 Sum_probs=24.6
Q ss_pred EEEEeCCCCcc-----hhHHHHHHHHHh-CCCEEEEEe
Q 028707 11 RVVVDARHHML-----GRLASVLAKELL-NGQKVVVVR 42 (205)
Q Consensus 11 w~vIDA~g~iL-----GRLAS~VAk~Ll-~Gd~VVVVN 42 (205)
++.+|-+|+-. |+.|...|+.|+ .|..|+||+
T Consensus 6 P~~l~l~~~~vlVvGGG~va~rka~~Ll~~ga~V~VIs 43 (157)
T PRK06719 6 PLMFNLHNKVVVIIGGGKIAYRKASGLKDTGAFVTVVS 43 (157)
T ss_pred ceEEEcCCCEEEEECCCHHHHHHHHHHHhCCCEEEEEc
Confidence 46667666643 789999888776 799999995
No 48
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=20.39 E-value=44 Score=28.64 Aligned_cols=27 Identities=30% Similarity=0.391 Sum_probs=20.2
Q ss_pred CCCeeehhhhhhhhCcccccccc-hhHH
Q 028707 137 GHKYCLLGRLSSEVGWNYYDTIK-VSKK 163 (205)
Q Consensus 137 ~rk~~~LG~ls~~vGWk~~~~v~-le~k 163 (205)
.+|.|.|.+||.++|-+-+++++ +.+-
T Consensus 110 ~~Kvv~ledla~~f~l~t~~~i~ri~~L 137 (188)
T PF09756_consen 110 EHKVVNLEDLAAEFGLRTQDVINRIQEL 137 (188)
T ss_dssp H-SEE-HHHHHHHH-S-HHHHHHHHHHH
T ss_pred HcceeeHHHHHHHcCCCHHHHHHHHHHH
Confidence 47999999999999999999998 6654
No 49
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=20.17 E-value=52 Score=22.87 Aligned_cols=26 Identities=15% Similarity=0.092 Sum_probs=19.8
Q ss_pred CCeeehhhhhhhhCcccccccc-hhHH
Q 028707 138 HKYCLLGRLSSEVGWNYYDTIK-VSKK 163 (205)
Q Consensus 138 rk~~~LG~ls~~vGWk~~~~v~-le~k 163 (205)
+.-+++++||.++|+..+.+-+ ||.+
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4668999999999999988888 7765
Done!