Query 028649
Match_columns 206
No_of_seqs 211 out of 1219
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 14:49:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028649.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028649hhsearch_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 1E-76 2.2E-81 504.6 18.2 199 8-206 2-201 (202)
2 KOG3204 60S ribosomal protein 100.0 2.8E-66 6E-71 436.1 14.2 194 6-206 2-195 (197)
3 TIGR01077 L13_A_E ribosomal pr 100.0 2E-54 4.2E-59 351.3 8.5 142 12-154 1-142 (142)
4 PRK06394 rpl13p 50S ribosomal 100.0 1.3E-49 2.8E-54 324.4 10.0 141 9-151 2-143 (146)
5 PRK09216 rplM 50S ribosomal pr 100.0 1.4E-44 3.1E-49 294.1 7.5 119 1-130 5-141 (144)
6 TIGR01066 rplM_bact ribosomal 100.0 2.6E-44 5.5E-49 291.5 7.6 115 4-129 6-138 (140)
7 CHL00159 rpl13 ribosomal prote 100.0 1.3E-43 2.9E-48 288.1 7.8 118 1-129 6-141 (143)
8 COG0102 RplM Ribosomal protein 100.0 4.6E-43 9.9E-48 285.4 9.2 123 1-134 5-146 (148)
9 PF00572 Ribosomal_L13: Riboso 100.0 5E-42 1.1E-46 274.3 7.6 109 11-126 1-127 (128)
10 PLN00205 ribisomal protein L13 100.0 6.3E-41 1.4E-45 282.9 8.4 111 7-124 13-141 (191)
11 cd00392 Ribosomal_L13 Ribosoma 100.0 9.5E-39 2.1E-43 251.0 7.5 96 11-113 1-114 (114)
12 KOG3203 Mitochondrial/chloropl 100.0 9.7E-36 2.1E-40 243.3 7.0 108 5-119 17-142 (165)
13 PHA02754 hypothetical protein; 53.0 21 0.00046 25.6 3.4 16 34-49 43-58 (67)
14 PF12953 DUF3842: Domain of un 52.9 18 0.00039 29.5 3.5 14 34-47 53-66 (131)
15 PF00650 CRAL_TRIO: CRAL/TRIO 49.8 14 0.0003 28.5 2.3 73 35-113 61-137 (159)
16 PF00436 SSB: Single-strand bi 49.8 17 0.00036 26.5 2.6 23 20-42 54-76 (104)
17 COG1717 RPL32 Ribosomal protei 42.1 28 0.0006 28.5 3.0 76 52-158 39-114 (133)
18 PRK05853 hypothetical protein; 42.0 24 0.00052 29.5 2.7 23 20-42 49-71 (161)
19 cd04496 SSB_OBF SSB_OBF: A sub 41.9 27 0.00058 25.0 2.7 23 20-42 50-72 (100)
20 KOG1154 Gamma-glutamyl kinase 41.4 28 0.00061 31.6 3.2 37 12-48 20-61 (285)
21 PF05651 Diacid_rec: Putative 41.0 35 0.00076 27.5 3.4 27 23-49 4-32 (135)
22 PF03447 NAD_binding_3: Homose 40.8 45 0.00098 25.0 3.9 36 10-47 60-95 (117)
23 COG0629 Ssb Single-stranded DN 40.6 27 0.00059 28.7 2.8 22 20-41 57-78 (167)
24 PF09756 DDRGK: DDRGK domain; 39.7 29 0.00062 29.8 2.9 29 137-165 110-138 (188)
25 PRK08182 single-stranded DNA-b 37.9 30 0.00066 28.2 2.7 23 20-42 60-82 (148)
26 PRK06752 single-stranded DNA-b 37.4 30 0.00066 26.5 2.5 24 19-42 52-75 (112)
27 PRK07772 single-stranded DNA-b 36.7 29 0.00063 29.6 2.5 22 20-41 59-80 (186)
28 PRK07274 single-stranded DNA-b 35.9 30 0.00065 27.4 2.3 29 10-42 47-75 (131)
29 PF04760 IF2_N: Translation in 34.3 42 0.00091 22.2 2.5 22 140-161 3-24 (54)
30 PRK08486 single-stranded DNA-b 34.0 32 0.0007 29.2 2.3 22 20-41 55-76 (182)
31 PRK07459 single-stranded DNA-b 32.9 38 0.00083 26.6 2.4 23 20-42 50-72 (121)
32 PRK08763 single-stranded DNA-b 32.8 35 0.00076 28.5 2.3 22 20-41 58-79 (164)
33 PRK13732 single-stranded DNA-b 32.5 38 0.00082 28.6 2.5 23 20-42 60-82 (175)
34 TIGR00621 ssb single stranded 32.5 38 0.00082 27.9 2.4 23 20-42 57-79 (164)
35 PRK07275 single-stranded DNA-b 32.4 36 0.00077 28.3 2.3 23 19-41 52-74 (162)
36 PRK09010 single-stranded DNA-b 30.1 40 0.00087 28.5 2.2 24 19-42 59-82 (177)
37 PRK06751 single-stranded DNA-b 28.7 42 0.00092 28.3 2.1 22 20-41 53-74 (173)
38 PF07552 Coat_X: Spore Coat Pr 28.6 63 0.0014 22.9 2.6 19 34-52 19-37 (60)
39 PF09012 FeoC: FeoC like trans 27.5 80 0.0017 21.9 3.1 27 138-164 12-38 (69)
40 KOG1481 Cysteine synthase [Ami 26.3 66 0.0014 30.1 3.1 50 12-65 318-374 (391)
41 PF04989 CmcI: Cephalosporin h 26.3 60 0.0013 28.2 2.7 32 8-40 110-145 (206)
42 PRK06863 single-stranded DNA-b 26.3 56 0.0012 27.4 2.4 29 10-42 52-80 (168)
43 smart00516 SEC14 Domain in hom 25.3 63 0.0014 24.7 2.4 69 35-112 62-134 (158)
44 PRK05733 single-stranded DNA-b 25.0 62 0.0013 27.3 2.5 28 10-41 53-80 (172)
45 PRK06958 single-stranded DNA-b 24.3 66 0.0014 27.5 2.5 29 10-42 52-80 (182)
46 PRK11477 carbohydrate diacid t 23.8 75 0.0016 29.0 3.0 33 19-51 5-39 (385)
47 cd02430 PTH2 Peptidyl-tRNA hyd 23.2 2E+02 0.0044 22.5 4.9 24 9-32 2-26 (115)
48 PRK08444 hypothetical protein; 23.0 3.9E+02 0.0084 24.8 7.5 128 19-164 27-160 (353)
49 PF11524 SeleniumBinding: Sele 22.7 55 0.0012 24.6 1.5 33 136-169 16-48 (81)
50 PF12324 HTH_15: Helix-turn-he 21.8 90 0.002 23.3 2.5 28 137-164 35-62 (77)
51 COG4091 Predicted homoserine d 21.6 1.2E+02 0.0027 29.1 3.9 41 11-53 103-144 (438)
52 PF14419 SPOUT_MTase_2: AF2226 21.4 1.5E+02 0.0033 25.3 4.1 36 10-45 95-130 (173)
53 PF01726 LexA_DNA_bind: LexA D 21.3 86 0.0019 22.1 2.2 12 142-153 27-38 (65)
54 PF02254 TrkA_N: TrkA-N domain 20.8 1.1E+02 0.0023 22.4 2.8 26 21-46 6-32 (116)
55 PRK03759 isopentenyl-diphospha 20.7 1.5E+02 0.0033 24.3 3.9 27 4-30 1-27 (184)
No 1
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=100.00 E-value=1e-76 Score=504.61 Aligned_cols=199 Identities=59% Similarity=0.977 Sum_probs=195.6
Q ss_pred cceEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCCCCccccCccHHHHH
Q 028649 8 CAKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWR 87 (206)
Q Consensus 8 ~~~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~g~~~~r~P~~I~~r 87 (206)
+.+|+||||+||+||||||+||+.|+|||+|||||||+|+|||++++++.||+.|+++++++||..||+|+|+|++||++
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 HHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchhhhhhcCCCCCeeehhhhhhhhCcchHHHHHHHHHHHHH
Q 028649 88 TVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVGWNYYDTIRELEKKRKE 167 (206)
Q Consensus 88 aVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~v~~l~p~rk~~~lg~ls~~vGWk~~~~v~~le~krk~ 167 (206)
||||||||||.+|+++|+||+||+|+||||+++++++||+|+++.+|+|+|+||+|||||++|||+|+|+|++||++|++
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 99999999899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh-hhHHHhhccCCC
Q 028649 168 RSQVAYERKKQLNKLRAKAEKVAEEKL-GSQLDILAPVKY 206 (206)
Q Consensus 168 k~~~~~~~k~~~~~~~~~a~~~~~~~~-~~~~~~l~~~g~ 206 (206)
++++||++|++.++++++|++++++++ .+++++|+++||
T Consensus 162 k~~~~~~~k~~~~k~~~~a~~~~~~~~~~~~~~~l~~~gy 201 (202)
T PTZ00068 162 RAAAYYKKKVKLRKAWKEARKKALAKLPKAIVAVLKKFGY 201 (202)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHcCC
Confidence 999999999999999999999999999 689999999998
No 2
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-66 Score=436.09 Aligned_cols=194 Identities=56% Similarity=0.939 Sum_probs=190.2
Q ss_pred cccceEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCCCCccccCccHHH
Q 028649 6 GICAKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIF 85 (206)
Q Consensus 6 ~~~~~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~g~~~~r~P~~I~ 85 (206)
+...+..+||+.||++|||||+|||+|+.|++||||+||+|+|||++|||+ .||+++|++| ||||+|.|++||
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 446788999999999999999999999999999999999999999999999 7999999999 899999999999
Q ss_pred HHHHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchhhhhhcCCCCCeeehhhhhhhhCcchHHHHHHHHHHH
Q 028649 86 WRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVGWNYYDTIRELEKKR 165 (206)
Q Consensus 86 ~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~v~~l~p~rk~~~lg~ls~~vGWk~~~~v~~le~kr 165 (206)
+++||||+||++++|+.++++|.+|+|+|+||+.++++++|.|++|++|+|++|||+||+|||+|||+|+|++++||+||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHhhccCCC
Q 028649 166 KERSQVAYERKKQLNKLRAKAEKVAEEKLGSQLDILAPVKY 206 (206)
Q Consensus 166 k~k~~~~~~~k~~~~~~~~~a~~~~~~~~~~~~~~l~~~g~ 206 (206)
|+|+++||.+|+++++++++|+++++++|++++++|+++||
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=2e-54 Score=351.30 Aligned_cols=142 Identities=58% Similarity=0.951 Sum_probs=135.5
Q ss_pred EEEeCCCCchhhHHHHHHHHHhCCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCCCCccccCccHHHHHHHhc
Q 028649 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRG 91 (206)
Q Consensus 12 ~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~g~~~~r~P~~I~~raVrG 91 (206)
+||||+||+||||||.||+.|+|||+|||||||+|.+||++++++.||..+....+..+|..|++|+++|++||++||+|
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 58999999999999999999999999999999999999999999999986667777777777999999999999999999
Q ss_pred cCCCCChhhHHHhhcCccccCCCCChhhhccccCCchhhhhhcCCCCCeeehhhhhhhhCcch
Q 028649 92 MIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVGWNY 154 (206)
Q Consensus 92 MLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~v~~l~p~rk~~~lg~ls~~vGWk~ 154 (206)
|||+++.+|+.+|+||+||+|+||||++|+++++|+|+ +.+++|.||||+|||||+.+||||
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 99976799999999999999999999999999999998 999999999999999999999997
No 4
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=100.00 E-value=1.3e-49 Score=324.40 Aligned_cols=141 Identities=43% Similarity=0.611 Sum_probs=134.3
Q ss_pred ceEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCC-CCccccCccHHHHH
Q 028649 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH-GPIHFRAPAKIFWR 87 (206)
Q Consensus 9 ~~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~-g~~~~r~P~~I~~r 87 (206)
++.+||||+||+||||||.||+.|++||+|||||||+|.+||++++++.+|..|++.++..||.. +++|+++|++||++
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 45789999999999999999999999999999999999999999999999988888899999964 99999999999999
Q ss_pred HHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchhhhhhcCCCCCeeehhhhhhhhC
Q 028649 88 TVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCLLGRLASEVG 151 (206)
Q Consensus 88 aVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~v~~l~p~rk~~~lg~ls~~vG 151 (206)
||+||||+||.+|+.+|+||+||+|+||||.+|+++++|.|+. .++. +|+||+|||||+++|
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 6777 699999999999999
No 5
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=100.00 E-value=1.4e-44 Score=294.13 Aligned_cols=119 Identities=30% Similarity=0.514 Sum_probs=112.1
Q ss_pred CCCCCcccceEEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhccccc
Q 028649 1 MVSGSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMN 68 (206)
Q Consensus 1 ~~~~~~~~~~w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~ 68 (206)
|+++..+.++|+||||+||+||||||.||+.|+ |||+|||||||+|.|||++|++|.||+ |+
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 999999999999999999999999997 99
Q ss_pred ccCCC------CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchhh
Q 028649 69 TKPSH------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALK 130 (206)
Q Consensus 69 ~~P~~------g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~ 130 (206)
+|||+ +++++++|++||++||+|||| +|.+|+.+|+||+||+|++|||++|+ |..+.
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 76553
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=2.6e-44 Score=291.50 Aligned_cols=115 Identities=33% Similarity=0.497 Sum_probs=109.6
Q ss_pred CCcccceEEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhcccccccC
Q 028649 4 GSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71 (206)
Q Consensus 4 ~~~~~~~w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P 71 (206)
+.++.++|+||||+||+||||||.||+.|+ |||+|||||||+|.|||++|+++.||. |++||
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 999999999999999999999999997 99999
Q ss_pred CC------CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchh
Q 028649 72 SH------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129 (206)
Q Consensus 72 ~~------g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al 129 (206)
|+ +++++++|++||++||+|||| ||.+|+.+|+||+||+|+||||++|+ |..+
T Consensus 80 gg~k~~~~~~~~~r~P~~ii~~aVrGMLP-kn~lgr~~l~rLkvy~G~~hp~~~q~----p~~~ 138 (140)
T TIGR01066 80 GGLKSRTFEEMIARKPERVLEHAVKGMLP-KNRLGRKLFKKLKVYAGSEHPHEAQK----PIVL 138 (140)
T ss_pred CccccccHHHhhhcCHHHHHHHHHHhcCC-CCccHHHHHhCeEEeCCCCCChhhcC----Ceec
Confidence 86 899999999999999999999 69999999999999999999999998 6554
No 7
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=100.00 E-value=1.3e-43 Score=288.10 Aligned_cols=118 Identities=30% Similarity=0.458 Sum_probs=110.4
Q ss_pred CCCCCcccceEEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhccccc
Q 028649 1 MVSGSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMN 68 (206)
Q Consensus 1 ~~~~~~~~~~w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~ 68 (206)
|+++..+.++|+||||+||+||||||.||+.|+ |||+|||||||+|.+||++|++|.||+ |+
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 999999999999999999999998775 99
Q ss_pred ccCCC------CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchh
Q 028649 69 TKPSH------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129 (206)
Q Consensus 69 ~~P~~------g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al 129 (206)
+|||+ +++++++|++||++||+|||| ||.+|+.+|+||+||+|.+|||++|+ |..+
T Consensus 80 g~pGg~k~~~~~~~~~r~P~~il~~aV~gMLP-kn~lgr~~~~rLkvy~G~~hph~aq~----p~~~ 141 (143)
T CHL00159 80 GRPGGLKIETFEELQNRLPNRIIEKAVKGMLP-KGPLGRKLFTKLKVYKGESHPHVAQK----PIKI 141 (143)
T ss_pred CCCCCcccccHHHHhhcCHHHHHHHHHHhcCC-CChhHHHHHhCCEEeCCCCCCccccC----Ceec
Confidence 99985 689999999999999999999 69999999999999999999999998 6554
No 8
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.6e-43 Score=285.40 Aligned_cols=123 Identities=40% Similarity=0.625 Sum_probs=113.7
Q ss_pred CCCCCcccceEEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhccccc
Q 028649 1 MVSGSGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMN 68 (206)
Q Consensus 1 ~~~~~~~~~~w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~ 68 (206)
++++..+.++|+||||+|++||||||.||+.|+ |||+|||||||+|+|||++..++.||+ |+
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 356677899999999999999999999999998 679999999999999999999999997 99
Q ss_pred ccCCC-------CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchhhhhhc
Q 028649 69 TKPSH-------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRL 134 (206)
Q Consensus 69 ~~P~~-------g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~v~~l 134 (206)
+|||+ +++++|.|++||++||+||||+ |++||++|+||+||.|+||||..|+ |+++.+..+
T Consensus 79 ~~~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk-~~lGr~~~krLkVy~G~~h~~~aq~----p~~l~~~~~ 146 (148)
T COG0102 79 GYPGGLKNPTRGGPLAPRRPERILERAVRGMLPK-NPLGRAALKRLKVYAGIPHPHEAQK----PEALELKLL 146 (148)
T ss_pred ccCCcccccccccccccCCHHHHHHHHHhccCCC-ChhHHHHHhCceEecCCCCcccccc----chhhhhhcc
Confidence 99974 7888899999999999999996 9999999999999999999999998 988766443
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-42 Score=274.31 Aligned_cols=109 Identities=42% Similarity=0.650 Sum_probs=103.0
Q ss_pred EEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCC-----
Q 028649 11 RVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH----- 73 (206)
Q Consensus 11 w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~----- 73 (206)
|+||||+||+||||||.||+.|+ |||+|||||||+|.+||++|+++.||. |++|||+
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 999999999999999999999999998 8999986
Q ss_pred -CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCC
Q 028649 74 -GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIP 126 (206)
Q Consensus 74 -g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP 126 (206)
+.+++++|++||++||+||||+ |.+|+.+|+||+||+|+||||++|+++++|
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 4666799999999999999995 999999999999999999999999966654
No 10
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=100.00 E-value=6.3e-41 Score=282.94 Aligned_cols=111 Identities=20% Similarity=0.325 Sum_probs=104.1
Q ss_pred ccceEEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCC-
Q 028649 7 ICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH- 73 (206)
Q Consensus 7 ~~~~w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~- 73 (206)
-.++|+||||+||+||||||.||+.|+ |||+|||||||+|.|||++|.+|.||+ ||+|||+
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 367899999999999999999999999 999999999999999999999999987 9999996
Q ss_pred -----CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhhhcccc
Q 028649 74 -----GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMV 124 (206)
Q Consensus 74 -----g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~v 124 (206)
+++++++|++||++||+||||+ |.+|+.+++||+||+|+||||++|+.++
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 7899999999999999999995 7777779999999999999999998533
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=9.5e-39 Score=251.02 Aligned_cols=96 Identities=53% Similarity=0.765 Sum_probs=92.4
Q ss_pred EEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCC-----
Q 028649 11 RVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH----- 73 (206)
Q Consensus 11 w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~----- 73 (206)
|+||||+||+||||||.||+.|+ |||+|||||||+|.+||++++++.||. |++||++
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 599999999999999999999999998 8888875
Q ss_pred -CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCC
Q 028649 74 -GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGV 113 (206)
Q Consensus 74 -g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~ 113 (206)
+++++++|++||++||+|||| ||.+|+++|+||+||+|+
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=9.7e-36 Score=243.29 Aligned_cols=108 Identities=31% Similarity=0.430 Sum_probs=102.5
Q ss_pred CcccceEEEEeCCCCchhhHHHHHHHHHh------------CCCEEEEEeccceeecCccchhhhHhhhhhcccccccCC
Q 028649 5 SGICAKRVVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPS 72 (206)
Q Consensus 5 ~~~~~~w~VIDA~g~~LGRLAs~VAk~Ll------------~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~ 72 (206)
.+|++.|+||||++++||||||.||..|. |||+|||+||++|.|||++|.+|.|++ |+||||
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 46889999999999999999999999997 999999999999999999999999887 999999
Q ss_pred C------CCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhh
Q 028649 73 H------GPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDK 119 (206)
Q Consensus 73 ~------g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~ 119 (206)
+ ..++.++|++|+++||+|||| ||.+++..++||++|+|.+|||+.
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 778899999999999999999 699999999999999999999653
No 13
>PHA02754 hypothetical protein; Provisional
Probab=52.99 E-value=21 Score=25.59 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=14.0
Q ss_pred CCCEEEEEeccceeec
Q 028649 34 NGQKVVAVRCEEICMS 49 (206)
Q Consensus 34 ~Gd~VVVVNae~I~is 49 (206)
.||++|||-++.|.|-
T Consensus 43 SGdkIVVi~aD~I~i~ 58 (67)
T PHA02754 43 SGDKIVVITADAIKIE 58 (67)
T ss_pred cCCEEEEEEcceEEEE
Confidence 7999999999988773
No 14
>PF12953 DUF3842: Domain of unknown function (DUF3842); InterPro: IPR024208 This family of proteins has no known function.
Probab=52.87 E-value=18 Score=29.52 Aligned_cols=14 Identities=14% Similarity=0.351 Sum_probs=10.8
Q ss_pred CCCEEEEEecccee
Q 028649 34 NGQKVVAVRCEEIC 47 (206)
Q Consensus 34 ~Gd~VVVVNae~I~ 47 (206)
+|+.-||+||.++-
T Consensus 53 TGENaIv~n~~~aD 66 (131)
T PF12953_consen 53 TGENAIVVNARKAD 66 (131)
T ss_pred cccchheeccCCCC
Confidence 68888888888764
No 15
>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=49.84 E-value=14 Score=28.50 Aligned_cols=73 Identities=12% Similarity=0.165 Sum_probs=43.2
Q ss_pred CCEEEEEeccceeecCccchhhhHhhhhhcccccccCCC-CCccccCccH---HHHHHHhccCCCCChhhHHHhhcCccc
Q 028649 35 GQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH-GPIHFRAPAK---IFWRTVRGMIPHKTKRGAAALARLKAY 110 (206)
Q Consensus 35 Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~-g~~~~r~P~~---I~~raVrGMLP~K~~~Gr~al~rLkvy 110 (206)
+..++|++++++.++--.+........++.--...||.+ +.+|.-++.. .+|+.++.+|| ....+|+.++
T Consensus 61 ~~~~~iiD~~g~~~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~------~~~~~ki~~~ 134 (159)
T PF00650_consen 61 EGIVVIIDLSGFSLSNFDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLS------PKTREKIVFH 134 (159)
T ss_dssp H-EEEEEE-TT--HHHHHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-------HHHHCTEEEE
T ss_pred eeEEEEEeCCCceEeccccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcC------HhhheeEEEE
Confidence 578999999999986444322222333333335779987 6666555444 67899999998 4566889988
Q ss_pred cCC
Q 028649 111 EGV 113 (206)
Q Consensus 111 ~G~ 113 (206)
.+.
T Consensus 135 ~~~ 137 (159)
T PF00650_consen 135 SGS 137 (159)
T ss_dssp CTT
T ss_pred CCc
Confidence 553
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=49.78 E-value=17 Score=26.48 Aligned_cols=23 Identities=35% Similarity=0.413 Sum_probs=16.8
Q ss_pred chhhHHHHHHHHHhCCCEEEEEe
Q 028649 20 MLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
+.|.+|..++..|..||.|.|.-
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 45899999999999999888754
No 17
>COG1717 RPL32 Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]
Probab=42.09 E-value=28 Score=28.51 Aligned_cols=76 Identities=25% Similarity=0.375 Sum_probs=43.4
Q ss_pred cchhhhHhhhhhcccccccCCCCCccccCccHHHHHHHhccCCCCChhhHHHhhcCccccCCCCChhhhccccCCchhhh
Q 028649 52 LVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKV 131 (206)
Q Consensus 52 k~r~k~~y~~~l~kr~~~~P~~g~~~~r~P~~I~~raVrGMLP~K~~~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~v 131 (206)
.||.-.--.+-+|++..|+|.-=..-+++| .+||||.|. | ++-+-|| ..-++
T Consensus 39 ~WRrPrG~dsK~Rr~~kg~p~~v~iGyrsP-----k~vRglhPS----G---~~~VlV~----------------Nv~dL 90 (133)
T COG1717 39 KWRRPRGIDSKMRRKLKGKPPMVKIGYRSP-----KAVRGLHPS----G---YEEVLVH----------------NVKDL 90 (133)
T ss_pred hccCCCCchHHHHHHhcCCCCCcccCCCCc-----HhhcccCCC----c---cceeeee----------------cHHHH
Confidence 344333333334445666665444456777 478999995 1 2222222 22245
Q ss_pred hhcCCCCCeeehhhhhhhhCcchHHHH
Q 028649 132 LRLQKGHKYCLLGRLASEVGWNYYDTI 158 (206)
Q Consensus 132 ~~l~p~rk~~~lg~ls~~vGWk~~~~v 158 (206)
..|.|.++ -.+||+.||.+-...+
T Consensus 91 e~ldp~~~---aarIAs~VG~rKR~eI 114 (133)
T COG1717 91 EKLDPETQ---AARIASTVGARKRIEI 114 (133)
T ss_pred hhcCchhH---HHHHHHhhhHHHHHHH
Confidence 56777655 8899999998655433
No 18
>PRK05853 hypothetical protein; Validated
Probab=42.04 E-value=24 Score=29.45 Aligned_cols=23 Identities=35% Similarity=0.429 Sum_probs=20.7
Q ss_pred chhhHHHHHHHHHhCCCEEEEEe
Q 028649 20 MLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
+.|+||..|+++|..|+.|+|.-
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 19
>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=41.89 E-value=27 Score=25.04 Aligned_cols=23 Identities=35% Similarity=0.364 Sum_probs=19.8
Q ss_pred chhhHHHHHHHHHhCCCEEEEEe
Q 028649 20 MLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
.-|.+|..+++.|..||.|+|.-
T Consensus 50 ~~g~~a~~~~~~~~kG~~V~v~G 72 (100)
T cd04496 50 AFGKLAENAAKYLKKGDLVYVEG 72 (100)
T ss_pred EEhHHHHHHHHHhCCCCEEEEEE
Confidence 45679999999999999998864
No 20
>KOG1154 consensus Gamma-glutamyl kinase [Amino acid transport and metabolism]
Probab=41.41 E-value=28 Score=31.57 Aligned_cols=37 Identities=32% Similarity=0.443 Sum_probs=28.0
Q ss_pred EEEeCC--CCchhhHHHHHHHH---HhCCCEEEEEeccceee
Q 028649 12 VVVDAR--HHMLGRLASIVAKE---LLNGQKVVAVRCEEICM 48 (206)
Q Consensus 12 ~VIDA~--g~~LGRLAs~VAk~---Ll~Gd~VVVVNae~I~i 48 (206)
.|.|.. |--|||||++|-.. =+.|..|++|-+..|.+
T Consensus 20 vit~e~~~~laLgrla~IVEqV~~L~~~G~evilVSSGaVA~ 61 (285)
T KOG1154|consen 20 VITREDTCGLALGRLASIVEQVSELQRMGREVILVSSGAVAF 61 (285)
T ss_pred EEECCCCccchHHHHHHHHHHHHHHHhcCceEEEEecchhhh
Confidence 344544 45899999987543 35899999999888877
No 21
>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=40.96 E-value=35 Score=27.48 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=23.0
Q ss_pred hHHHHHHHHHh--CCCEEEEEeccceeec
Q 028649 23 RLASIVAKELL--NGQKVVAVRCEEICMS 49 (206)
Q Consensus 23 RLAs~VAk~Ll--~Gd~VVVVNae~I~is 49 (206)
.||..|+..+. .|..|.|.|++.+.|-
T Consensus 4 ~~Aq~Iv~~~~~~i~~~inimd~~G~IIA 32 (135)
T PF05651_consen 4 ELAQKIVDEIMEIIGYNINIMDENGIIIA 32 (135)
T ss_pred HHHHHHHHHHHHHcCCCEEEECCCcEEEe
Confidence 47888888886 7999999999999983
No 22
>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=40.80 E-value=45 Score=24.98 Aligned_cols=36 Identities=25% Similarity=0.302 Sum_probs=26.0
Q ss_pred eEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEecccee
Q 028649 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEIC 47 (206)
Q Consensus 10 ~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVNae~I~ 47 (206)
--+||||.+. .-++..+...|..|-+||..|-.-+.
T Consensus 60 ~dvvVE~t~~--~~~~~~~~~~L~~G~~VVt~nk~ala 95 (117)
T PF03447_consen 60 IDVVVECTSS--EAVAEYYEKALERGKHVVTANKGALA 95 (117)
T ss_dssp -SEEEE-SSC--HHHHHHHHHHHHTTCEEEES-HHHHH
T ss_pred CCEEEECCCc--hHHHHHHHHHHHCCCeEEEECHHHhh
Confidence 4589999776 45678888888999999999865444
No 23
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=40.60 E-value=27 Score=28.65 Aligned_cols=22 Identities=32% Similarity=0.362 Sum_probs=20.0
Q ss_pred chhhHHHHHHHHHhCCCEEEEE
Q 028649 20 MLGRLASIVAKELLNGQKVVAV 41 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVV 41 (206)
+.|++|..++.+|..|+.|+|.
T Consensus 57 ~wgk~Ae~~~~yl~KG~~V~Ve 78 (167)
T COG0629 57 IWGKLAENAAEYLKKGSLVYVE 78 (167)
T ss_pred EehHHHHHHHHHhcCCCEEEEE
Confidence 5799999999999999998875
No 24
>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=39.69 E-value=29 Score=29.79 Aligned_cols=29 Identities=31% Similarity=0.397 Sum_probs=22.0
Q ss_pred CCCeeehhhhhhhhCcchHHHHHHHHHHH
Q 028649 137 GHKYCLLGRLASEVGWNYYDTIRELEKKR 165 (206)
Q Consensus 137 ~rk~~~lg~ls~~vGWk~~~~v~~le~kr 165 (206)
.+|.|.|.+||.+||-+.+|+++.+..-.
T Consensus 110 ~~Kvv~ledla~~f~l~t~~~i~ri~~L~ 138 (188)
T PF09756_consen 110 EHKVVNLEDLAAEFGLRTQDVINRIQELE 138 (188)
T ss_dssp H-SEE-HHHHHHHH-S-HHHHHHHHHHHH
T ss_pred HcceeeHHHHHHHcCCCHHHHHHHHHHHH
Confidence 47999999999999999999999887643
No 25
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=37.95 E-value=30 Score=28.19 Aligned_cols=23 Identities=22% Similarity=0.167 Sum_probs=20.3
Q ss_pred chhhHHHHHHHHHhCCCEEEEEe
Q 028649 20 MLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
+.|++|..++++|..|+.|.|.-
T Consensus 60 ~wg~~Ae~v~~~l~KG~~V~V~G 82 (148)
T PRK08182 60 LWHRDAEHWARLYQKGMRVLVEG 82 (148)
T ss_pred EEhHHHHHHHHhcCCCCEEEEEE
Confidence 67889999999999999988764
No 26
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=37.38 E-value=30 Score=26.46 Aligned_cols=24 Identities=17% Similarity=0.028 Sum_probs=20.5
Q ss_pred CchhhHHHHHHHHHhCCCEEEEEe
Q 028649 19 HMLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 19 ~~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
-+.|++|..++.+|..||.|.|.-
T Consensus 52 ~~wg~~Ae~~~~~l~KG~~V~V~G 75 (112)
T PRK06752 52 VVWRKSAENVTEYCTKGSLVGITG 75 (112)
T ss_pred EEehHHHHHHHHhcCCCCEEEEEE
Confidence 367889999999999999988753
No 27
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=36.74 E-value=29 Score=29.62 Aligned_cols=22 Identities=27% Similarity=0.403 Sum_probs=20.2
Q ss_pred chhhHHHHHHHHHhCCCEEEEE
Q 028649 20 MLGRLASIVAKELLNGQKVVAV 41 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVV 41 (206)
+.|.+|..||+.|..||.|+|.
T Consensus 59 ~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 59 IWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred EecHHHHHHHHhcCCCCEEEEE
Confidence 6789999999999999999986
No 28
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=35.86 E-value=30 Score=27.43 Aligned_cols=29 Identities=21% Similarity=0.201 Sum_probs=23.0
Q ss_pred eEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEe
Q 028649 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 10 ~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
.|+-|= +.|++|..++..|..|+.|.|.-
T Consensus 47 ~w~~v~----~fg~~Ae~v~~~l~KG~~V~V~G 75 (131)
T PRK07274 47 DFINVV----LWGKLAETLASYASKGSLISIDG 75 (131)
T ss_pred EEEEEE----EehHHHHHHHHHcCCCCEEEEEE
Confidence 465553 55889999999999999988753
No 29
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=34.27 E-value=42 Score=22.24 Aligned_cols=22 Identities=27% Similarity=0.338 Sum_probs=19.8
Q ss_pred eeehhhhhhhhCcchHHHHHHH
Q 028649 140 YCLLGRLASEVGWNYYDTIREL 161 (206)
Q Consensus 140 ~~~lg~ls~~vGWk~~~~v~~l 161 (206)
.+++.|||.++|=.-.++++.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999999998
No 30
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=33.99 E-value=32 Score=29.17 Aligned_cols=22 Identities=36% Similarity=0.534 Sum_probs=19.0
Q ss_pred chhhHHHHHHHHHhCCCEEEEE
Q 028649 20 MLGRLASIVAKELLNGQKVVAV 41 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVV 41 (206)
+.|++|..+++.|..|+.|.|.
T Consensus 55 ~fg~~AE~~~~~l~KG~~V~Ve 76 (182)
T PRK08486 55 LFGRTAEIANQYLSKGSKVLIE 76 (182)
T ss_pred EEhHHHHHHHHHcCCCCEEEEE
Confidence 5799999999999988887774
No 31
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=32.89 E-value=38 Score=26.59 Aligned_cols=23 Identities=17% Similarity=0.277 Sum_probs=19.9
Q ss_pred chhhHHHHHHHHHhCCCEEEEEe
Q 028649 20 MLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
+.|++|..++++|..|+.|.|.-
T Consensus 50 ~wg~~Ae~~~~~l~KG~~V~V~G 72 (121)
T PRK07459 50 IWGKTAQVAADYVKKGSLIGITG 72 (121)
T ss_pred EehHHHHHHHHHcCCCCEEEEEE
Confidence 57899999999999999888753
No 32
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=32.81 E-value=35 Score=28.52 Aligned_cols=22 Identities=23% Similarity=0.422 Sum_probs=19.6
Q ss_pred chhhHHHHHHHHHhCCCEEEEE
Q 028649 20 MLGRLASIVAKELLNGQKVVAV 41 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVV 41 (206)
+.|.+|..|+.+|..|+.|.|.
T Consensus 58 ~fgk~Ae~v~~~L~KGs~V~Ve 79 (164)
T PRK08763 58 FFGKLGEIAGEYLRKGSQCYIE 79 (164)
T ss_pred EehHHHHHHHHhcCCCCEEEEE
Confidence 6789999999999999988875
No 33
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=32.55 E-value=38 Score=28.64 Aligned_cols=23 Identities=26% Similarity=0.465 Sum_probs=20.4
Q ss_pred chhhHHHHHHHHHhCCCEEEEEe
Q 028649 20 MLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
+.|++|..++.+|..|+.|+|.-
T Consensus 60 ~wgk~Ae~v~~~L~KG~~V~VeG 82 (175)
T PRK13732 60 LFGKLAEVAGEYLRKGAQVYIEG 82 (175)
T ss_pred EecHHHHHHHHhcCCCCEEEEEE
Confidence 56889999999999999998864
No 34
>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=32.49 E-value=38 Score=27.90 Aligned_cols=23 Identities=35% Similarity=0.489 Sum_probs=20.5
Q ss_pred chhhHHHHHHHHHhCCCEEEEEe
Q 028649 20 MLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
+.|++|..+++.|..|+.|.|.-
T Consensus 57 ~wg~~Ae~~~~~l~KG~~V~V~G 79 (164)
T TIGR00621 57 IFGRLAEVAAQYLKKGSLVYVEG 79 (164)
T ss_pred EehHHHHHHHHhCCCCCEEEEEE
Confidence 67889999999999999998864
No 35
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=32.39 E-value=36 Score=28.34 Aligned_cols=23 Identities=13% Similarity=0.016 Sum_probs=19.9
Q ss_pred CchhhHHHHHHHHHhCCCEEEEE
Q 028649 19 HMLGRLASIVAKELLNGQKVVAV 41 (206)
Q Consensus 19 ~~LGRLAs~VAk~Ll~Gd~VVVV 41 (206)
-+.|++|..+|++|..|+.|.|-
T Consensus 52 v~wgk~Ae~~~~~l~KG~~V~Ve 74 (162)
T PRK07275 52 VIWRQQAENLANWAKKGALIGVT 74 (162)
T ss_pred EEEcHHHHHHHHHcCCCCEEEEE
Confidence 37899999999999999888774
No 36
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=30.12 E-value=40 Score=28.53 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=20.8
Q ss_pred CchhhHHHHHHHHHhCCCEEEEEe
Q 028649 19 HMLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 19 ~~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
-+.|++|..+++.|..|+.|.|.-
T Consensus 59 ~~fgk~Ae~~~~~L~KGs~V~VeG 82 (177)
T PRK09010 59 VLFGKLAEVAGEYLRKGSQVYIEG 82 (177)
T ss_pred EEehhHHHHHHHhcCCCCEEEEEE
Confidence 367899999999999999988864
No 37
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=28.73 E-value=42 Score=28.26 Aligned_cols=22 Identities=23% Similarity=0.108 Sum_probs=19.2
Q ss_pred chhhHHHHHHHHHhCCCEEEEE
Q 028649 20 MLGRLASIVAKELLNGQKVVAV 41 (206)
Q Consensus 20 ~LGRLAs~VAk~Ll~Gd~VVVV 41 (206)
+.|++|..++..|..|+.|.|.
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
>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=28.55 E-value=63 Score=22.92 Aligned_cols=19 Identities=11% Similarity=0.120 Sum_probs=16.1
Q ss_pred CCCEEEEEeccceeecCcc
Q 028649 34 NGQKVVAVRCEEICMSGGL 52 (206)
Q Consensus 34 ~Gd~VVVVNae~I~isG~k 52 (206)
.-++++|.||+++.+|-..
T Consensus 19 s~q~I~I~dS~~V~VtttD 37 (60)
T PF07552_consen 19 SRQKIIIKDSCNVTVTTTD 37 (60)
T ss_pred cceEEEEEcCCCCEEeehh
Confidence 5789999999999997553
No 39
>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=27.47 E-value=80 Score=21.90 Aligned_cols=27 Identities=26% Similarity=0.146 Sum_probs=21.1
Q ss_pred CCeeehhhhhhhhCcchHHHHHHHHHH
Q 028649 138 HKYCLLGRLASEVGWNYYDTIRELEKK 164 (206)
Q Consensus 138 rk~~~lg~ls~~vGWk~~~~v~~le~k 164 (206)
+.-+++++||.++|+....|-.-||.+
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 567899999999999999988888765
No 40
>KOG1481 consensus Cysteine synthase [Amino acid transport and metabolism]
Probab=26.30 E-value=66 Score=30.11 Aligned_cols=50 Identities=30% Similarity=0.406 Sum_probs=39.4
Q ss_pred EEEeCCCCchhhH-------HHHHHHHHhCCCEEEEEeccceeecCccchhhhHhhhhhcc
Q 028649 12 VVVDARHHMLGRL-------ASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRK 65 (206)
Q Consensus 12 ~VIDA~g~~LGRL-------As~VAk~Ll~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~k 65 (206)
+++|-+|-.+|-- |..|||.|-.|..||.|-|+ ||...-.|++-.+||+.
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 4566777777754 55789999999999999998 78888788777777764
No 41
>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=26.29 E-value=60 Score=28.23 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=22.2
Q ss_pred cceEEEEe-CC---CCchhhHHHHHHHHHhCCCEEEE
Q 028649 8 CAKRVVVD-AR---HHMLGRLASIVAKELLNGQKVVA 40 (206)
Q Consensus 8 ~~~w~VID-A~---g~~LGRLAs~VAk~Ll~Gd~VVV 40 (206)
...|+||| +. .|+++-|.. .+..+..|++.||
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 56 799999998 8999999999998
No 42
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=26.28 E-value=56 Score=27.43 Aligned_cols=29 Identities=17% Similarity=0.171 Sum_probs=23.5
Q ss_pred eEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEe
Q 028649 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 10 ~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
.|+-|. +.|++|..+++.|..|+.|.|.-
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 57889999999999999988864
No 43
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=25.32 E-value=63 Score=24.71 Aligned_cols=69 Identities=14% Similarity=0.293 Sum_probs=41.3
Q ss_pred CCEEEEEeccceeecCccchhhhHhhhhhcccccccCCC-CCccccCccHH---HHHHHhccCCCCChhhHHHhhcCccc
Q 028649 35 GQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSH-GPIHFRAPAKI---FWRTVRGMIPHKTKRGAAALARLKAY 110 (206)
Q Consensus 35 Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~-g~~~~r~P~~I---~~raVrGMLP~K~~~Gr~al~rLkvy 110 (206)
...++|++++++.++-.....-....+.+ ...||.+ ..++.-+|..+ +|..++.+|+.+ ..+++++.
T Consensus 62 ~~~~~i~D~~~~~~~~~~~~~lk~~~~~~---~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~------~~~ki~~~ 132 (158)
T smart00516 62 EGFTVIFDLKGLSMSNPDLSVLRKILKIL---QDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEK------TREKIRFV 132 (158)
T ss_pred eeEEEEEECCCCCcccccHHHHHHHHHHH---HHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChh------hhccEEEe
Confidence 46789999999887532211111111122 4567766 66666666554 558888999842 34567766
Q ss_pred cC
Q 028649 111 EG 112 (206)
Q Consensus 111 ~G 112 (206)
.+
T Consensus 133 ~~ 134 (158)
T smart00516 133 GN 134 (158)
T ss_pred CC
Confidence 65
No 44
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=24.97 E-value=62 Score=27.25 Aligned_cols=28 Identities=25% Similarity=0.377 Sum_probs=23.0
Q ss_pred eEEEEeCCCCchhhHHHHHHHHHhCCCEEEEE
Q 028649 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAV 41 (206)
Q Consensus 10 ~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVV 41 (206)
.|+-|. +.|++|..++.+|..|+.|.|.
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 6788999999999999998875
No 45
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=24.29 E-value=66 Score=27.46 Aligned_cols=29 Identities=34% Similarity=0.401 Sum_probs=22.8
Q ss_pred eEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEe
Q 028649 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVR 42 (206)
Q Consensus 10 ~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVN 42 (206)
.|+-|- +.|.+|..+++.|..|+.|.|.-
T Consensus 52 ~w~~V~----~fGk~AE~v~~~LkKGs~V~VeG 80 (182)
T PRK06958 52 EWHRVA----FFGRLAEIVGEYLKKGSSVYIEG 80 (182)
T ss_pred eEEEEE----EehHHHHHHHHHhCCCCEEEEEE
Confidence 455443 67889999999999999888853
No 46
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=23.76 E-value=75 Score=29.02 Aligned_cols=33 Identities=9% Similarity=0.200 Sum_probs=26.4
Q ss_pred CchhhHHHHHHHHHh--CCCEEEEEeccceeecCc
Q 028649 19 HMLGRLASIVAKELL--NGQKVVAVRCEEICMSGG 51 (206)
Q Consensus 19 ~~LGRLAs~VAk~Ll--~Gd~VVVVNae~I~isG~ 51 (206)
.+--.||..|+..+. .|..|.|+|.+++.|-..
T Consensus 5 ~l~~~lAq~IV~~~~~ii~~ninimd~~G~IIaS~ 39 (385)
T PRK11477 5 HLDTKMAQDIVARTMRIIDTNINVMDARGRIIGSG 39 (385)
T ss_pred ccCHHHHHHHHHHHHHHcCCCeEEECCCCEEEecC
Confidence 344568888888887 799999999999888543
No 47
>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=23.17 E-value=2e+02 Score=22.54 Aligned_cols=24 Identities=21% Similarity=0.184 Sum_probs=16.6
Q ss_pred ceEEEEeCC-CCchhhHHHHHHHHH
Q 028649 9 AKRVVVDAR-HHMLGRLASIVAKEL 32 (206)
Q Consensus 9 ~~w~VIDA~-g~~LGRLAs~VAk~L 32 (206)
++.++|... +.-.|.+|++++.--
T Consensus 2 K~vivVr~DL~m~~GKiaAQ~~HAa 26 (115)
T cd02430 2 KMVLVVRNDLKMGKGKIAAQCAHAA 26 (115)
T ss_pred EEEEEEeCCCCCCcchHHHHHHHHH
Confidence 355666644 677899999887644
No 48
>PRK08444 hypothetical protein; Provisional
Probab=22.99 E-value=3.9e+02 Score=24.76 Aligned_cols=128 Identities=14% Similarity=0.160 Sum_probs=75.7
Q ss_pred CchhhHHHHHHHHHhCCCEEEEEeccceeecCccchhhhHhhhhhcccccccCCCCCccccCccHHHHHHHhccCCCCCh
Q 028649 19 HMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTK 98 (206)
Q Consensus 19 ~~LGRLAs~VAk~Ll~Gd~VVVVNae~I~isG~k~r~k~~y~~~l~kr~~~~P~~g~~~~r~P~~I~~raVrGMLP~K~~ 98 (206)
..|+.+|..|-... +||.|..+.+..|++||- ..+.=.|..|-+ +++.+. .+ .-+|+.|+..+-...=.
T Consensus 27 ~~L~~~A~~vR~~~-~G~~Vt~~~n~~In~TN~-C~~~C~FCaf~~--~~~~~~--~y-~ls~eeI~~~a~~a~~~---- 95 (353)
T PRK08444 27 FTLGKYADKKRTKL-HGKKVYFNVNRHINPTNI-CADVCKFCAFSA--HRKNPN--PY-TMSHEEILEIVKNSVKR---- 95 (353)
T ss_pred HHHHHHHHHHHHHh-cCCEEEEEecCCcccccc-cccCCccCCCcc--CCCCCc--cc-cCCHHHHHHHHHHHHHC----
Confidence 35677777776543 799999998899999655 444445666643 344442 23 46999999987764321
Q ss_pred hhHHHhhcCccccCCCCChhhhccccCCchhhhhh-cCCCCCe--eehh---hhhhhhCcchHHHHHHHHHH
Q 028649 99 RGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLR-LQKGHKY--CLLG---RLASEVGWNYYDTIRELEKK 164 (206)
Q Consensus 99 ~Gr~al~rLkvy~G~p~p~~~~k~~vvP~al~v~~-l~p~rk~--~~lg---~ls~~vGWk~~~~v~~le~k 164 (206)
-..++.+=-|..++.+-. -+.++++..+ .-|.-.- .+.+ .+|..+|....++...|-+-
T Consensus 96 ----G~~ei~iv~G~~p~~~~e---~y~e~ir~Ik~~~p~i~i~a~s~~Ei~~~a~~~g~~~~e~l~~LkeA 160 (353)
T PRK08444 96 ----GIKEVHIVSAHNPNYGYE---WYLEIFKKIKEAYPNLHVKAMTAAEVDFLSRKFGKSYEEVLEDMLEY 160 (353)
T ss_pred ----CCCEEEEeccCCCCCCHH---HHHHHHHHHHHHCCCceEeeCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 256677766655443211 1223333222 1233222 2333 46778899999988887653
No 49
>PF11524 SeleniumBinding: Selenium binding protein; InterPro: IPR021603 Selenium is an important nutrient which needs to be regulated since lack of the nutrient leads to cell abnormalities and high concentrations are toxic.SeBP regulates the level of free selenium in the cell by sequestering the nutrient during transport. SeBP acts as a pentamer and delivers the selenium to the selenophosphate synthetase enzyme []. Each subunit is composed of an alpha helix on top of a four stranded twisted ss sheet, stabilised by hydrogen bonds []. members of this entry are restricted to the archaeal Methanococcales.; PDB: 2JZ7_D.
Probab=22.71 E-value=55 Score=24.57 Aligned_cols=33 Identities=27% Similarity=0.400 Sum_probs=26.9
Q ss_pred CCCCeeehhhhhhhhCcchHHHHHHHHHHHHHHH
Q 028649 136 KGHKYCLLGRLASEVGWNYYDTIRELEKKRKERS 169 (206)
Q Consensus 136 p~rk~~~lg~ls~~vGWk~~~~v~~le~krk~k~ 169 (206)
|+-.-|++|=+|..+- ...++++.||++-|++.
T Consensus 16 PGiely~~gIvS~~~e-nvd~li~~lee~vk~k~ 48 (81)
T PF11524_consen 16 PGIELYYLGIVSEASE-NVDELIKKLEEKVKAKG 48 (81)
T ss_dssp TTS--EEEEEEEEBSS-SHHHHHHHHHHHHHHTT
T ss_pred CCeEEEeehhHHHHHh-hHHHHHHHHHHHHHhCC
Confidence 7888999999998887 88999999999977653
No 50
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=21.76 E-value=90 Score=23.27 Aligned_cols=28 Identities=18% Similarity=0.292 Sum_probs=20.1
Q ss_pred CCCeeehhhhhhhhCcchHHHHHHHHHH
Q 028649 137 GHKYCLLGRLASEVGWNYYDTIRELEKK 164 (206)
Q Consensus 137 ~rk~~~lg~ls~~vGWk~~~~v~~le~k 164 (206)
.-.=++..+||...||...+|.+.|+.-
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 3466889999999999999999998763
No 51
>COG4091 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=21.59 E-value=1.2e+02 Score=29.14 Aligned_cols=41 Identities=22% Similarity=0.346 Sum_probs=30.0
Q ss_pred EEEEeCCCCchhhHHHHHHH-HHhCCCEEEEEeccceeecCccc
Q 028649 11 RVVVDARHHMLGRLASIVAK-ELLNGQKVVAVRCEEICMSGGLV 53 (206)
Q Consensus 11 w~VIDA~g~~LGRLAs~VAk-~Ll~Gd~VVVVNae~I~isG~k~ 53 (206)
-.||||+|++. .++.++- .++.|.|||.+|.|-=+.-|...
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 47999999985 4455544 45689999999998666556643
No 52
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=21.44 E-value=1.5e+02 Score=25.25 Aligned_cols=36 Identities=17% Similarity=0.245 Sum_probs=31.0
Q ss_pred eEEEEeCCCCchhhHHHHHHHHHhCCCEEEEEeccc
Q 028649 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEE 45 (206)
Q Consensus 10 ~w~VIDA~g~~LGRLAs~VAk~Ll~Gd~VVVVNae~ 45 (206)
--+|.|.+|..+-+++..+|+.|..++.|+|.-.+.
T Consensus 95 ~lIvtdPkG~~is~vk~~L~~~~r~~~eV~v~iGSR 130 (173)
T PF14419_consen 95 PLIVTDPKGDPISEVKDKLAEDLRYAKEVVVFIGSR 130 (173)
T ss_pred eEEEECCCCCcHHHHHHHHHHHHhhCcEEEEEEEcc
Confidence 457889999999999999999999999988765443
No 53
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=21.33 E-value=86 Score=22.07 Aligned_cols=12 Identities=17% Similarity=0.385 Sum_probs=10.4
Q ss_pred ehhhhhhhhCcc
Q 028649 142 LLGRLASEVGWN 153 (206)
Q Consensus 142 ~lg~ls~~vGWk 153 (206)
++-||+..+|++
T Consensus 27 t~rEIa~~~g~~ 38 (65)
T PF01726_consen 27 TVREIAEALGLK 38 (65)
T ss_dssp -HHHHHHHHTSS
T ss_pred CHHHHHHHhCCC
Confidence 688999999999
No 54
>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=20.85 E-value=1.1e+02 Score=22.43 Aligned_cols=26 Identities=27% Similarity=0.463 Sum_probs=20.6
Q ss_pred hhhHHHHHHHHHhCCC-EEEEEeccce
Q 028649 21 LGRLASIVAKELLNGQ-KVVAVRCEEI 46 (206)
Q Consensus 21 LGRLAs~VAk~Ll~Gd-~VVVVNae~I 46 (206)
.|+++..+|+.|..+. .|+||..+.-
T Consensus 6 ~g~~~~~i~~~L~~~~~~vvvid~d~~ 32 (116)
T PF02254_consen 6 YGRIGREIAEQLKEGGIDVVVIDRDPE 32 (116)
T ss_dssp -SHHHHHHHHHHHHTTSEEEEEESSHH
T ss_pred CCHHHHHHHHHHHhCCCEEEEEECCcH
Confidence 3789999999999776 7888876643
No 55
>PRK03759 isopentenyl-diphosphate delta-isomerase; Provisional
Probab=20.68 E-value=1.5e+02 Score=24.29 Aligned_cols=27 Identities=15% Similarity=0.001 Sum_probs=22.0
Q ss_pred CCcccceEEEEeCCCCchhhHHHHHHH
Q 028649 4 GSGICAKRVVVDARHHMLGRLASIVAK 30 (206)
Q Consensus 4 ~~~~~~~w~VIDA~g~~LGRLAs~VAk 30 (206)
+|.-++.|.|+|..|..+|+.....+.
T Consensus 1 ~~~~~E~~~~vd~~~~~~g~~~r~~~~ 27 (184)
T PRK03759 1 PMMETELVVLLDEQGVPTGTAEKAAAH 27 (184)
T ss_pred CCCCceeEEEECCCCCCcccccHHHHH
Confidence 345567899999999999997777775
Done!