Query 047908
Match_columns 94
No_of_seqs 125 out of 1018
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 04:28:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047908hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0846 Mitochondrial/chloropl 99.9 2.4E-25 5.2E-30 165.6 9.1 93 1-93 95-188 (274)
2 PRK05592 rplO 50S ribosomal pr 99.8 3.8E-19 8.3E-24 123.6 7.4 70 1-79 76-145 (146)
3 TIGR01071 rplO_bact ribosomal 99.8 5.1E-19 1.1E-23 122.6 7.5 70 1-78 76-145 (145)
4 PF00828 Ribosomal_L18e: Ribos 99.7 7.9E-18 1.7E-22 113.8 4.0 72 1-79 57-128 (129)
5 COG0200 RplO Ribosomal protein 99.6 6.1E-16 1.3E-20 108.3 6.7 73 1-81 79-152 (152)
6 PRK06419 rpl15p 50S ribosomal 99.6 5.8E-16 1.3E-20 107.8 6.4 67 1-80 72-145 (148)
7 PTZ00160 60S ribosomal protein 99.5 2.2E-14 4.8E-19 100.0 4.6 70 1-80 72-146 (147)
8 PRK04005 50S ribosomal protein 99.5 1.5E-13 3.2E-18 92.0 5.9 38 40-79 56-93 (111)
9 COG1727 RPL18A Ribosomal prote 99.0 9.1E-10 2E-14 74.5 5.1 58 1-80 48-105 (122)
10 PTZ00469 60S ribosomal subunit 98.6 8.1E-08 1.8E-12 69.3 5.8 42 42-87 84-127 (187)
11 PTZ00195 60S ribosomal protein 98.5 4.3E-07 9.3E-12 66.0 6.5 43 42-88 92-136 (198)
12 KOG1742 60s ribosomal protein 98.4 6.3E-08 1.4E-12 67.2 0.9 70 1-80 70-146 (147)
13 KOG1714 60s ribosomal protein 92.2 0.13 2.8E-06 37.3 2.5 34 53-88 96-129 (188)
14 PF08734 GYD: GYD domain; Int 88.7 0.63 1.4E-05 29.6 3.2 22 63-84 22-43 (91)
15 COG4274 Uncharacterized conser 76.0 3.8 8.2E-05 27.2 3.0 21 64-84 33-53 (104)
16 PF14237 DUF4339: Domain of un 60.8 9 0.0002 20.9 2.1 17 1-17 13-29 (45)
17 PF10531 SLBB: SLBB domain; I 52.0 20 0.00043 20.5 2.7 28 50-78 7-34 (59)
18 PF09494 Slx4: Slx4 endonuclea 44.3 32 0.0007 20.2 2.8 28 1-28 24-51 (64)
19 PF00542 Ribosomal_L12: Riboso 40.0 31 0.00066 20.8 2.3 16 64-79 52-67 (68)
20 PF00367 PTS_EIIB: phosphotran 30.1 42 0.0009 17.7 1.5 17 66-82 1-19 (35)
21 cd00387 Ribosomal_L7_L12 Ribos 29.7 47 0.001 22.6 2.1 15 65-79 113-127 (127)
22 COG1918 FeoA Fe2+ transport sy 29.3 77 0.0017 19.5 2.8 34 24-62 24-57 (75)
23 PF08134 cIII: cIII protein fa 29.0 40 0.00086 18.8 1.3 14 73-86 7-20 (44)
24 TIGR00001 rpmI_bact ribosomal 28.9 32 0.00068 20.6 1.0 51 39-91 11-61 (63)
25 TIGR00855 L12 ribosomal protei 27.7 67 0.0015 21.9 2.6 15 65-79 111-125 (126)
26 PF04471 Mrr_cat: Restriction 27.7 44 0.00095 20.4 1.6 35 52-89 79-113 (115)
27 PF03537 Glyco_hydro_114: Glyc 27.3 1.2E+02 0.0025 18.3 3.4 30 55-85 30-59 (74)
28 CHL00083 rpl12 ribosomal prote 26.9 70 0.0015 21.9 2.6 15 65-79 116-130 (131)
29 KOG0697 Protein phosphatase 1B 26.9 57 0.0012 25.8 2.4 19 62-80 167-185 (379)
30 PRK00157 rplL 50S ribosomal pr 26.6 72 0.0016 21.7 2.6 15 65-79 108-122 (123)
31 COG3324 Predicted enzyme relat 26.3 63 0.0014 22.0 2.2 16 64-79 83-98 (127)
32 cd00027 BRCT Breast Cancer Sup 25.4 82 0.0018 16.7 2.3 18 63-80 15-32 (72)
33 PF09926 DUF2158: Uncharacteri 24.8 44 0.00096 19.3 1.1 23 72-94 27-49 (53)
34 PF03820 Mtc: Tricarboxylate c 24.7 38 0.00083 26.3 1.1 34 51-84 273-306 (308)
35 PF07722 Peptidase_C26: Peptid 23.8 1.1E+02 0.0024 22.0 3.3 31 60-90 23-55 (217)
36 COG0291 RpmI Ribosomal protein 22.8 50 0.0011 20.1 1.1 52 40-93 13-64 (65)
37 PF00533 BRCT: BRCA1 C Terminu 22.4 79 0.0017 17.8 1.9 15 64-78 22-36 (78)
38 PRK00172 rpmI 50S ribosomal pr 21.4 47 0.001 19.9 0.8 51 39-91 12-62 (65)
39 CHL00103 rpl35 ribosomal prote 21.2 46 0.00099 20.1 0.7 50 40-91 13-62 (65)
No 1
>KOG0846 consensus Mitochondrial/chloroplast ribosomal protein L15/L10 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.4e-25 Score=165.62 Aligned_cols=93 Identities=49% Similarity=0.726 Sum_probs=87.8
Q ss_pred CcchhhHHhHHHcCCCCCCCccCHHHHHHcCC-ccCCCCCceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEE
Q 047908 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGA-IGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRR 79 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~~~~I~~~~L~~~g~-i~~~~~~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~ 79 (94)
+++|.+||.||+.|+|++.++|||++|++.|+ ..+.+.++|+|.+.|+.+++.+|+|||++||..|+++||+|||+|++
T Consensus 95 pl~L~rlq~lID~grid~~q~Idm~tL~~~g~i~p~~~eyGv~L~~~G~d~~~~~i~iEvs~aS~~AiaaIEkaGG~vtt 174 (274)
T KOG0846|consen 95 PLSLGRLQKLIDTGRIDPSQPIDMKTLKDSGLINPKGREYGVQLTADGADEFKAKINIEVSRASVQAIAAIEKAGGSVTT 174 (274)
T ss_pred cccHHHHHHHHHhcCCCccCceeHHHHHhccCCCccccccCceeeccCCccccceEEEEehhhhHHHHHHHHhcCCeEEE
Confidence 58999999999999999999999999999994 44455679999999988999999999999999999999999999999
Q ss_pred EEecHhhhhhhcCC
Q 047908 80 VHYNKLGLRALLKP 93 (94)
Q Consensus 80 ~~~~~~~l~~~~~p 93 (94)
+|||++|||+||+|
T Consensus 175 ~yy~p~~Lra~lnP 188 (274)
T KOG0846|consen 175 AYYDPLSLRAHLNP 188 (274)
T ss_pred EEEcchhhhhhcCc
Confidence 99999999999999
No 2
>PRK05592 rplO 50S ribosomal protein L15; Reviewed
Probab=99.79 E-value=3.8e-19 Score=123.56 Aligned_cols=70 Identities=33% Similarity=0.569 Sum_probs=62.7
Q ss_pred CcchhhHHhHHHcCCCCCCCccCHHHHHHcCCccCCCCCceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEE
Q 047908 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRR 79 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~~~~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~ 79 (94)
+|||++|+++ +++++||+++|++.|+|+.+ .++|||||+| +|+++|+|++++||++|+++||+|||+|++
T Consensus 76 ~VNL~~L~~~------~~~~~I~~~~L~~~gli~~~-~~~vKvLg~G--~l~~~i~I~a~~~S~sA~e~IE~aGG~v~~ 145 (146)
T PRK05592 76 VVNLGDLNKF------EEGTEVTLEALKAAGLIRKN-IKGVKVLGNG--ELTKKLTVKAHKFSKSAKEAIEAAGGKVEE 145 (146)
T ss_pred EEeHHHhhcc------CCCCeECHHHHHHCCcccCC-CcceEEEecC--ccccCEEEEEEccCHHHHHHHHHcCCEEEe
Confidence 5899999863 33468999999999999865 3589999999 999999999999999999999999999975
No 3
>TIGR01071 rplO_bact ribosomal protein L15, bacterial/organelle.
Probab=99.78 E-value=5.1e-19 Score=122.58 Aligned_cols=70 Identities=47% Similarity=0.723 Sum_probs=63.7
Q ss_pred CcchhhHHhHHHcCCCCCCCccCHHHHHHcCCccCCCCCceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEE
Q 047908 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVR 78 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~~~~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~ 78 (94)
+|||++||++++++ .+||+++|.+.++|+.. ..++||||+| +|++||+|++++||++|+++||+|||+|+
T Consensus 76 ~VNL~~L~~~~~~g-----~~i~~~~L~~~gli~~~-~~~vKvLg~G--~l~~~l~I~a~~~S~sA~ekIE~aGG~v~ 145 (145)
T TIGR01071 76 EVNLGKLAKLFPNG-----EVVTLETLKEKGLITKK-IKFVKVLGNG--KLTKPLTVKAHRVSKSAKAAIEAAGGSVE 145 (145)
T ss_pred EEEHHHHhhhhhcC-----CEecHHHHhhCccCcCC-CCceEEeCCC--CcCcCEEEEEEEECHHHHHHHHHcCCEEC
Confidence 58999999998876 38999999999999854 3579999999 99999999999999999999999999984
No 4
>PF00828 Ribosomal_L18e: Ribosomal protein L18e/L15; InterPro: IPR021131 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 [, ]. This entry represents both L15 and L18e ribosomal proteins, which share a common structure consisting mainly of parallel beta sheets (beta-alpha-beta units) with a core of three turns of irregular (beta-beta-alpha)n superhelix [, ].; PDB: 3O58_Y 1S1I_V 3O5H_Y 3IZS_O 3IZR_R 2OTL_L 1M1K_M 3G6E_L 1VQ9_L 1YIT_L ....
Probab=99.71 E-value=7.9e-18 Score=113.78 Aligned_cols=72 Identities=40% Similarity=0.595 Sum_probs=63.8
Q ss_pred CcchhhHHhHHHcCCCCCCCccCHHHHHHcCCccCCCCCceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEE
Q 047908 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRR 79 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~~~~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~ 79 (94)
+|||++|+++++..+.+.. +++.+.+.+.+++ ..++||||+| ++++|++|++++||++|+++||+|||+|++
T Consensus 57 ~vnL~~L~~~i~~~~~~~~-~~~~~~~~~~~~~----~~~~KvLg~G--~l~~~l~I~a~~~S~~A~ekIe~aGG~v~~ 128 (129)
T PF00828_consen 57 PVNLSKLQELIEKLKIDGT-EIDGKILVDAGLI----KGYVKVLGKG--ELTKPLTIKAHRFSKSAKEKIEAAGGEVVT 128 (129)
T ss_dssp EEEHHHHHHHTTTSSSSSC-ECTTSEEEECCEE----SSEEEEESSS--SSSSSEEEEESEETHHHHHHHHHTSEEEEE
T ss_pred eeeHHHHHHHHHhcccccc-ccCCceeeecccc----ccceeeeccC--CcccceEEEEEecCHHHHHHHHHcCCEEEe
Confidence 5899999999987775544 6788888888887 2589999999 999999999999999999999999999986
No 5
>COG0200 RplO Ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=99.63 E-value=6.1e-16 Score=108.32 Aligned_cols=73 Identities=37% Similarity=0.588 Sum_probs=64.1
Q ss_pred CcchhhHHhHHHcCCCCCCCccCHHHHHHcCCccCCCCCceEEEcCCcccccccEEEEEE-ecCHHHHHHHHHcCCEEEE
Q 047908 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVS-RVTVRAKAAVEAAGGSVRR 79 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~~~~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l~~~i~I~~~-~~S~~A~~~Ie~aGG~v~~ 79 (94)
+||+++|+.+++++. ++|+++|.+.++|... ..++||||+| +|++++.++++ .||++|+++||+|||+|++
T Consensus 79 ~vn~~~l~~~~~~~~-----~v~~~~l~~~~~i~~~-~~~vKvLg~G--~l~~~~~~~v~a~~S~~A~ekIe~aGG~v~~ 150 (152)
T COG0200 79 VVNLGKLAELLPEGE-----EVTLASLKAAGVIRKL-KDLVKVLGNG--KLTKAVPVKVKAKASKSAIEKIEAAGGKVEL 150 (152)
T ss_pred EEEHHHhhhhccccc-----cccHHHHhhCCeEecc-ccccEEeccC--eeccceeEEEEeeeCHHHHHHHHHcCCEEEe
Confidence 589999999876664 8999999999999875 4679999999 99977777777 9999999999999999998
Q ss_pred EE
Q 047908 80 VH 81 (94)
Q Consensus 80 ~~ 81 (94)
++
T Consensus 151 ~~ 152 (152)
T COG0200 151 IE 152 (152)
T ss_pred cC
Confidence 64
No 6
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=99.63 E-value=5.8e-16 Score=107.83 Aligned_cols=67 Identities=22% Similarity=0.468 Sum_probs=52.6
Q ss_pred CcchhhHHhHH----HcCCCCCCC---ccCHHHHHHcCCccCCCCCceEEEcCCcccccccEEEEEEecCHHHHHHHHHc
Q 047908 1 PVGLGKIAYLI----NAGKIDSHE---LITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAA 73 (94)
Q Consensus 1 ~iNL~~L~~~~----~~g~i~~~~---~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~a 73 (94)
+|||++||+++ +.|.++..+ +||+ .+ ..++||||+| ++++|++|+|+.||++|+++||+|
T Consensus 72 ~INL~~L~~l~~~l~~~g~i~~~~~~~vid~---~~--------~g~~KVLG~G--~l~~pl~Vka~~fS~~A~ekIe~a 138 (148)
T PRK06419 72 TINVGELDELADLLKAEGKAEEEDGKIVVDL---TE--------LGYDKVLGGG--KVTRPLVIKADAFSEKAIEKIEAA 138 (148)
T ss_pred eEEHHHHHHhHHHHHHCCcccccCCcceeee---cc--------CCceEEeCCC--ccCcCEEEEEeccCHHHHHHHHHc
Confidence 58999999987 345443322 2222 11 1378999999 999999999999999999999999
Q ss_pred CCEEEEE
Q 047908 74 GGSVRRV 80 (94)
Q Consensus 74 GG~v~~~ 80 (94)
||+|+++
T Consensus 139 GG~v~l~ 145 (148)
T PRK06419 139 GGEVVLS 145 (148)
T ss_pred CCEEEEe
Confidence 9999875
No 7
>PTZ00160 60S ribosomal protein L27a; Provisional
Probab=99.50 E-value=2.2e-14 Score=99.98 Aligned_cols=70 Identities=17% Similarity=0.352 Sum_probs=51.4
Q ss_pred CcchhhHHhHHHcC----CCCCCCccCHHHHHHcCCccCCCCCceEEEcCCcccc-cccEEEEEEecCHHHHHHHHHcCC
Q 047908 1 PVGLGKIAYLINAG----KIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKI-KWPIHLEVSRVTVRAKAAVEAAGG 75 (94)
Q Consensus 1 ~iNL~~L~~~~~~g----~i~~~~~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l-~~~i~I~~~~~S~~A~~~Ie~aGG 75 (94)
+|||++||+++++- .++..+....-+|.+.| ++||||+| ++ ++|++|+++.||++|+++||++||
T Consensus 72 ~INl~~L~~lv~~~~~~~~a~~~~~~~vIDl~~~g--------~~KVLG~G--~l~~~~v~Vka~~~Sk~A~ekIe~aGG 141 (147)
T PTZ00160 72 TINVDKLWSLVPEETRYKYAKKGDKAPVIDVTKAG--------YFKVLGKG--HLPKQPVIVKARYFSKKAEKKIKAVGG 141 (147)
T ss_pred eeEHHHHHHHhHHHHHHhhhhccCCceEEEeeccC--------ceEEecCC--eEcCccEEEEEeecCHHHHHHHHHcCC
Confidence 48999999998641 11111111112222222 68999999 99 779999999999999999999999
Q ss_pred EEEEE
Q 047908 76 SVRRV 80 (94)
Q Consensus 76 ~v~~~ 80 (94)
+|+++
T Consensus 142 ~v~l~ 146 (147)
T PTZ00160 142 ACVLT 146 (147)
T ss_pred EEEEc
Confidence 99875
No 8
>PRK04005 50S ribosomal protein L18e; Provisional
Probab=99.45 E-value=1.5e-13 Score=91.97 Aligned_cols=38 Identities=24% Similarity=0.420 Sum_probs=36.5
Q ss_pred ceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEE
Q 047908 40 GVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRR 79 (94)
Q Consensus 40 ~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~ 79 (94)
++||||+| +++++++|++++||++|+++||++||++++
T Consensus 56 ~~KVLg~G--~l~k~l~V~a~~~Sk~A~ekIe~aGG~v~~ 93 (111)
T PRK04005 56 PGKVLGSG--KLDHKVTVAALSFSETAKEKIEEAGGKALT 93 (111)
T ss_pred eeEEEcCc--eEcCCEEEEEeecCHHHHHHHHHcCCEEEE
Confidence 68999999 999999999999999999999999999865
No 9
>COG1727 RPL18A Ribosomal protein L18E [Translation, ribosomal structure and biogenesis]
Probab=98.98 E-value=9.1e-10 Score=74.53 Aligned_cols=58 Identities=22% Similarity=0.426 Sum_probs=47.3
Q ss_pred CcchhhHHhHHHcCCCCCCCccCHHHHHHcCCccCCCCCceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEEE
Q 047908 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRRV 80 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~~~~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~ 80 (94)
+||+++|+....+|. ++ +++ =||||.| .+.++++|-+-+||++|+++|+.|||++..+
T Consensus 48 ~VnlsKI~r~ak~~d-----~v---------vVp------GkVLg~g--~l~~kVtVaAl~FS~~A~~KI~~aGGe~~tl 105 (122)
T COG1727 48 EVNVSKINRYAKEGD-----TV---------VVP------GKVLGDG--KLDKKVTVAALRFSKTAREKIEEAGGECLTL 105 (122)
T ss_pred ceeHHHHHhhcCCCC-----EE---------EEe------eeEecCc--ccccceEEEEEecCHHHHHHHHHcCCeEeeH
Confidence 478888887765443 33 332 3899999 9999999999999999999999999998654
No 10
>PTZ00469 60S ribosomal subunit protein L18; Provisional
Probab=98.62 E-value=8.1e-08 Score=69.33 Aligned_cols=42 Identities=19% Similarity=0.320 Sum_probs=36.5
Q ss_pred EEEcCCccccc--ccEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhh
Q 047908 42 RLMGRGAEKIK--WPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGL 87 (94)
Q Consensus 42 KlLg~G~~~l~--~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l 87 (94)
|||++| .+. .+++|-|-.||++|+++|++|||+|. -|+.+.+
T Consensus 84 kVl~dg--rl~~vpkvtVaAL~fS~~Ar~kI~~AGGe~l--T~dqLa~ 127 (187)
T PTZ00469 84 SITDDK--RLYDCKKLKVCALRFTETARKRILDAGGECL--TFDQLAL 127 (187)
T ss_pred eEccCc--cccccCceEEEEEecCHHHHHHHHHhCCEEE--eHHHHHH
Confidence 799999 998 99999999999999999999999764 4555544
No 11
>PTZ00195 60S ribosomal protein L18; Provisional
Probab=98.49 E-value=4.3e-07 Score=66.02 Aligned_cols=43 Identities=16% Similarity=0.352 Sum_probs=37.1
Q ss_pred EEEcCCcccccc--cEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhhh
Q 047908 42 RLMGRGAEKIKW--PIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGLR 88 (94)
Q Consensus 42 KlLg~G~~~l~~--~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l~ 88 (94)
+|+++| .+.. +++|-|-+||++|+++|++|||+|. -|+.+.++
T Consensus 92 kVtdd~--rl~~vPkvtVaALrfS~tAr~rI~kAGGe~l--T~dQLa~~ 136 (198)
T PTZ00195 92 DVLDDV--RMARIPAMRVCALRFSKSARQSIVAAGGECL--TFDQLAMI 136 (198)
T ss_pred eEcCCc--cccccCceEEEEEecCHHHHHHHHHhCCEEE--eHHHHHHH
Confidence 799999 9987 9999999999999999999999754 45666554
No 12
>KOG1742 consensus 60s ribosomal protein L15/L27 [Translation, ribosomal structure and biogenesis]
Probab=98.43 E-value=6.3e-08 Score=67.16 Aligned_cols=70 Identities=21% Similarity=0.345 Sum_probs=50.0
Q ss_pred CcchhhHHhHHHcCCCCC-----CCccCHHHHHHcCCccCCCCCceEEEcCCccccc--ccEEEEEEecCHHHHHHHHHc
Q 047908 1 PVGLGKIAYLINAGKIDS-----HELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIK--WPIHLEVSRVTVRAKAAVEAA 73 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~-----~~~I~~~~L~~~g~i~~~~~~~vKlLg~G~~~l~--~~i~I~~~~~S~~A~~~Ie~a 73 (94)
+|||++||.++.+..-+. .....+-++.+.| +.|+||.| .|+ +|+.+++..||+.|.++|.++
T Consensus 70 ~vnldkLWtlv~~~~~~~~~~~k~g~aPvidv~~~G--------y~kvlGkg--klp~~~PvIVKak~~s~~AeekIk~~ 139 (147)
T KOG1742|consen 70 TVNLDKLWTLVREQTRVKAAKNKTGAAPVIDVVQSG--------YYKVLGKG--KLPEETPVIVKAKYFSRRAEEKIKKA 139 (147)
T ss_pred cccHHHHHHhhhHHHHHHHhccCCCCCceeeeeecc--------eeEeeccc--cCCCCCcEEEeccccCccchHHHHhc
Confidence 489999999985321110 1112222222333 56999999 875 999999999999999999999
Q ss_pred CCEEEEE
Q 047908 74 GGSVRRV 80 (94)
Q Consensus 74 GG~v~~~ 80 (94)
||.+...
T Consensus 140 gg~~~~~ 146 (147)
T KOG1742|consen 140 GGAVVLT 146 (147)
T ss_pred Cceeeec
Confidence 9998764
No 13
>KOG1714 consensus 60s ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=92.17 E-value=0.13 Score=37.28 Aligned_cols=34 Identities=26% Similarity=0.368 Sum_probs=28.7
Q ss_pred ccEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhhh
Q 047908 53 WPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGLR 88 (94)
Q Consensus 53 ~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l~ 88 (94)
.++.|.+.+||++|++.|+++||+|-+ ++.++|+
T Consensus 96 Pkl~v~al~~t~~ar~rI~kagg~i~T--lDQLal~ 129 (188)
T KOG1714|consen 96 PKLKVAALRFTKGARARILKAGGEILT--LDQLALD 129 (188)
T ss_pred ccceeeeeecccchhhhhhccCceEEe--eHHhccc
Confidence 689999999999999999999999754 5666554
No 14
>PF08734 GYD: GYD domain; InterPro: IPR014845 These proteins of unknown function are usually less than 100 amino acids in length. They may belong to the dimeric alpha/beta barrel superfamily.
Probab=88.72 E-value=0.63 Score=29.62 Aligned_cols=22 Identities=23% Similarity=0.425 Sum_probs=19.2
Q ss_pred CHHHHHHHHHcCCEEEEEEecH
Q 047908 63 TVRAKAAVEAAGGSVRRVHYNK 84 (94)
Q Consensus 63 S~~A~~~Ie~aGG~v~~~~~~~ 84 (94)
-+.+++.+|++||+++-.||+.
T Consensus 22 ~~a~~~~~e~~Gg~l~~~y~t~ 43 (91)
T PF08734_consen 22 AEAVRALIEALGGKLKSFYWTL 43 (91)
T ss_pred HHHHHHHHHHcCCEEEEEEEec
Confidence 3568899999999999999984
No 15
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=76.04 E-value=3.8 Score=27.21 Aligned_cols=21 Identities=24% Similarity=0.444 Sum_probs=19.0
Q ss_pred HHHHHHHHHcCCEEEEEEecH
Q 047908 64 VRAKAAVEAAGGSVRRVHYNK 84 (94)
Q Consensus 64 ~~A~~~Ie~aGG~v~~~~~~~ 84 (94)
+.+++..|+.||++...|||.
T Consensus 33 ~av~~~les~G~k~~~~y~T~ 53 (104)
T COG4274 33 AAVRALLESMGGKVKEQYWTL 53 (104)
T ss_pred HHHHHHHHHcCcEEEEEEEee
Confidence 578889999999999999985
No 16
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=60.83 E-value=9 Score=20.89 Aligned_cols=17 Identities=41% Similarity=0.774 Sum_probs=8.7
Q ss_pred CcchhhHHhHHHcCCCC
Q 047908 1 PVGLGKIAYLINAGKID 17 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~ 17 (94)
|+++.+|.+++.+|+|+
T Consensus 13 P~s~~el~~l~~~g~i~ 29 (45)
T PF14237_consen 13 PFSLEELRQLISSGEID 29 (45)
T ss_pred CcCHHHHHHHHHcCCCC
Confidence 34555555555555443
No 17
>PF10531 SLBB: SLBB domain; InterPro: IPR019554 The soluble ligand-binding beta-grasp domain (SLBB) contains a beta-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins; transcobalamin, intrinsic factor and the bacterial polysaccharide export proteins []. Some proteins may be part of a membrane complex involved in electron transport, others are probably involved in the export of the extracellular polysaccharide colanic acid from the cell to medium.; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1 2W8I_E 2W8H_E 2J58_D.
Probab=52.02 E-value=20 Score=20.47 Aligned_cols=28 Identities=21% Similarity=0.316 Sum_probs=22.5
Q ss_pred cccccEEEEEEecCHHHHHHHHHcCCEEE
Q 047908 50 KIKWPIHLEVSRVTVRAKAAVEAAGGSVR 78 (94)
Q Consensus 50 ~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~ 78 (94)
++.+|=++++.. ..+..++|..|||--.
T Consensus 7 ~V~~PG~~~~~~-g~tl~~~i~~AGG~~~ 34 (59)
T PF10531_consen 7 EVNRPGTYELPP-GTTLSDAIAQAGGLTP 34 (59)
T ss_dssp SBSS-EEEEEET-T-BHHHHHHCTTSBBT
T ss_pred EeCCCEEEEECC-CCcHHHHHHHhCCCCC
Confidence 888999999888 8889999999999543
No 18
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=44.34 E-value=32 Score=20.20 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=15.1
Q ss_pred CcchhhHHhHHHcCCCCCCCccCHHHHH
Q 047908 1 PVGLGKIAYLINAGKIDSHELITMKTLK 28 (94)
Q Consensus 1 ~iNL~~L~~~~~~g~i~~~~~I~~~~L~ 28 (94)
||+|++|..+.....++-...++...|+
T Consensus 24 PI~L~el~~~L~~~g~~~~~~~~~~~l~ 51 (64)
T PF09494_consen 24 PINLEELHAWLKASGIGFDRKVDPSKLK 51 (64)
T ss_pred CccHHHHHHHHHHcCCCccceeCHHHHH
Confidence 5777777777663433222345555443
No 19
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 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 [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=40.00 E-value=31 Score=20.84 Aligned_cols=16 Identities=38% Similarity=0.399 Sum_probs=12.3
Q ss_pred HHHHHHHHHcCCEEEE
Q 047908 64 VRAKAAVEAAGGSVRR 79 (94)
Q Consensus 64 ~~A~~~Ie~aGG~v~~ 79 (94)
+.++++++++|++|++
T Consensus 52 e~ik~~Le~aGa~v~l 67 (68)
T PF00542_consen 52 EEIKKKLEAAGAKVEL 67 (68)
T ss_dssp HHHHHHHHCCT-EEEE
T ss_pred HHHHHHHHHcCCEEEe
Confidence 3678889999999875
No 20
>PF00367 PTS_EIIB: phosphotransferase system, EIIB; InterPro: IPR018113 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC) [] which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA) carries the first permease-specific phoshorylation site, a histidine, which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the permease. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate in a process catalyzed by the IIC domain; this process is coupled to the transmembrane transport of the sugar. This entry covers the phosphorylation site of EIIB domains. ; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity; PDB: 3IPJ_B 3BP3_A 1O2F_B 3BP8_C 1IBA_A.
Probab=30.13 E-value=42 Score=17.71 Aligned_cols=17 Identities=41% Similarity=0.624 Sum_probs=12.0
Q ss_pred HHHHHHHcCCE--EEEEEe
Q 047908 66 AKAAVEAAGGS--VRRVHY 82 (94)
Q Consensus 66 A~~~Ie~aGG~--v~~~~~ 82 (94)
|++.|++.||. +..+.+
T Consensus 1 A~~il~~lGG~~NI~~v~~ 19 (35)
T PF00367_consen 1 AKQILEALGGKENIKSVTN 19 (35)
T ss_dssp HHHHHHHCTTCCCEEEEEE
T ss_pred ChHHHHHhCCHHHHHHHhc
Confidence 78889999994 444443
No 21
>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
Probab=29.73 E-value=47 Score=22.56 Aligned_cols=15 Identities=33% Similarity=0.415 Sum_probs=10.7
Q ss_pred HHHHHHHHcCCEEEE
Q 047908 65 RAKAAVEAAGGSVRR 79 (94)
Q Consensus 65 ~A~~~Ie~aGG~v~~ 79 (94)
..++++|++|++|++
T Consensus 113 ~ik~kLe~aGA~Vel 127 (127)
T cd00387 113 EIKKKLEEAGAKVEL 127 (127)
T ss_pred HHHHHHHHcCCEEeC
Confidence 456777888888763
No 22
>COG1918 FeoA Fe2+ transport system protein A [Inorganic ion transport and metabolism]
Probab=29.26 E-value=77 Score=19.51 Aligned_cols=34 Identities=18% Similarity=0.302 Sum_probs=26.6
Q ss_pred HHHHHHcCCccCCCCCceEEEcCCcccccccEEEEEEec
Q 047908 24 MKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRV 62 (94)
Q Consensus 24 ~~~L~~~g~i~~~~~~~vKlLg~G~~~l~~~i~I~~~~~ 62 (94)
..-|.+.|+++.. .+.++.++ -+.-|+.|++...
T Consensus 24 ~~RL~~mG~~~G~---~i~vi~~a--plgdPi~v~v~g~ 57 (75)
T COG1918 24 RRRLLSMGIVPGA---SITVVRKA--PLGDPILVEVRGT 57 (75)
T ss_pred HHHHHHcCCCCCC---EEEEEEec--CCCCCEEEEECCE
Confidence 3567888998753 68999988 8888999987653
No 23
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=29.02 E-value=40 Score=18.84 Aligned_cols=14 Identities=29% Similarity=0.330 Sum_probs=11.9
Q ss_pred cCCEEEEEEecHhh
Q 047908 73 AGGSVRRVHYNKLG 86 (94)
Q Consensus 73 aGG~v~~~~~~~~~ 86 (94)
|||-|...||-..|
T Consensus 7 aG~gvmSAyYP~ES 20 (44)
T PF08134_consen 7 AGSGVMSAYYPTES 20 (44)
T ss_pred cCceeeeeecCcHH
Confidence 78999999998765
No 24
>TIGR00001 rpmI_bact ribosomal protein L35. This ribosomal protein is found in bacteria and organelles only. It is not closely related to any eukaryotic or archaeal ribosomal protein.
Probab=28.92 E-value=32 Score=20.58 Aligned_cols=51 Identities=16% Similarity=0.094 Sum_probs=37.9
Q ss_pred CceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhhhhhc
Q 047908 39 DGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGLRALL 91 (94)
Q Consensus 39 ~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l~~~~ 91 (94)
..||+.|+| .+...=.-.-|..+.......-..++...+.--+...++.+|
T Consensus 11 KRFK~T~tG--Kvkr~~a~k~H~l~~Ks~k~kR~L~~~~~v~~~~~~~ik~~l 61 (63)
T TIGR00001 11 KRFKITGSG--KIKRKKAGKRHLLTKKSSKRKRNLRKKAIVSAGDLKRVKLLL 61 (63)
T ss_pred hheEEcCCC--CEEecccCcccccccCCHHHHHhcCCCeeECHHHHHHHHHhc
Confidence 368999999 887777777777877777777788887766655556665554
No 25
>TIGR00855 L12 ribosomal protein L7/L12. THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus.
Probab=27.74 E-value=67 Score=21.93 Aligned_cols=15 Identities=33% Similarity=0.410 Sum_probs=11.2
Q ss_pred HHHHHHHHcCCEEEE
Q 047908 65 RAKAAVEAAGGSVRR 79 (94)
Q Consensus 65 ~A~~~Ie~aGG~v~~ 79 (94)
..++++|.+|++|++
T Consensus 111 ~ik~~Le~aGa~vei 125 (126)
T TIGR00855 111 ELKKKLEEAGAKVEV 125 (126)
T ss_pred HHHHHHHHcCCEEEe
Confidence 456778888888875
No 26
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=27.68 E-value=44 Score=20.36 Aligned_cols=35 Identities=20% Similarity=0.011 Sum_probs=14.7
Q ss_pred cccEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhhhh
Q 047908 52 KWPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGLRA 89 (94)
Q Consensus 52 ~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l~~ 89 (94)
+..+.|....||..|++.+++.-+ +.-++...|..
T Consensus 79 ~~~iivt~~~~t~~a~~~~~~~~~---I~l~d~~~L~~ 113 (115)
T PF04471_consen 79 DKGIIVTSSGFTPEAKEFAEKFKN---IELIDGEDLQE 113 (115)
T ss_dssp SEEEEE-SSEE-HHHHHHHH------------------
T ss_pred CEEEEEECCcCCHHHHHHHHhhcc---ccccccccccc
Confidence 455777777899999999988322 34445444443
No 27
>PF03537 Glyco_hydro_114: Glycoside-hydrolase family GH114; InterPro: IPR004352 Eighty-one archaeal-like genes, ranging in size from 4-20kb, are clustered in 15 regions of the Thermotoga maritima genome []. Conservation of gene order between T. maritima and Archaea in many of these regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea []. One of the T. maritima sequences (hypothetical protein TM1410) shares similarity with Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ1477 and with hypothetical protein DR0705 from Deinococcus radiodurans. The sequences are characterised by relatively variable N- and C-terminal domains, and a more conserved central domain. They share no similarity with any other known, functionally or structurally characterised proteins. ; PDB: 2AAM_F.
Probab=27.27 E-value=1.2e+02 Score=18.29 Aligned_cols=30 Identities=10% Similarity=0.095 Sum_probs=19.0
Q ss_pred EEEEEEecCHHHHHHHHHcCCEEEEEEecHh
Q 047908 55 IHLEVSRVTVRAKAAVEAAGGSVRRVHYNKL 85 (94)
Q Consensus 55 i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~ 85 (94)
+.|....+|++.++.+.+.| ...+-|++-=
T Consensus 30 ~~iD~~~~~~~~I~~L~~~G-~~vicY~s~G 59 (74)
T PF03537_consen 30 VVIDLFDFSKEEIARLKAQG-KKVICYFSIG 59 (74)
T ss_dssp EEE-SBS--HHHHHHHHHTT--EEEEEEESS
T ss_pred EEECCccCCHHHHHHHHHCC-CEEEEEEeCc
Confidence 34455668999999999997 6666687643
No 28
>CHL00083 rpl12 ribosomal protein L12
Probab=26.92 E-value=70 Score=21.94 Aligned_cols=15 Identities=40% Similarity=0.423 Sum_probs=11.0
Q ss_pred HHHHHHHHcCCEEEE
Q 047908 65 RAKAAVEAAGGSVRR 79 (94)
Q Consensus 65 ~A~~~Ie~aGG~v~~ 79 (94)
..++++|.+|++|++
T Consensus 116 ~ik~~le~~Ga~v~l 130 (131)
T CHL00083 116 EAKKQLEEAGAKVII 130 (131)
T ss_pred HHHHHHHHcCCEEEe
Confidence 456777888888765
No 29
>KOG0697 consensus Protein phosphatase 1B (formerly 2C) [Signal transduction mechanisms]
Probab=26.87 E-value=57 Score=25.80 Aligned_cols=19 Identities=32% Similarity=0.373 Sum_probs=17.4
Q ss_pred cCHHHHHHHHHcCCEEEEE
Q 047908 62 VTVRAKAAVEAAGGSVRRV 80 (94)
Q Consensus 62 ~S~~A~~~Ie~aGG~v~~~ 80 (94)
++..-++.|+.|||+|.+.
T Consensus 167 ~~p~EkeRIqnAGGSVMIq 185 (379)
T KOG0697|consen 167 YLPKEKERIQNAGGSVMIQ 185 (379)
T ss_pred CChHHHHHHhcCCCeEEEE
Confidence 7889999999999999875
No 30
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=26.60 E-value=72 Score=21.68 Aligned_cols=15 Identities=33% Similarity=0.415 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCEEEE
Q 047908 65 RAKAAVEAAGGSVRR 79 (94)
Q Consensus 65 ~A~~~Ie~aGG~v~~ 79 (94)
..++++|.+|++|++
T Consensus 108 ~ik~~Le~aGa~vel 122 (123)
T PRK00157 108 EIKKKLEEAGAKVEL 122 (123)
T ss_pred HHHHHHHHcCCEEee
Confidence 466778889988875
No 31
>COG3324 Predicted enzyme related to lactoylglutathione lyase [General function prediction only]
Probab=26.29 E-value=63 Score=21.95 Aligned_cols=16 Identities=44% Similarity=0.416 Sum_probs=13.0
Q ss_pred HHHHHHHHHcCCEEEE
Q 047908 64 VRAKAAVEAAGGSVRR 79 (94)
Q Consensus 64 ~~A~~~Ie~aGG~v~~ 79 (94)
..+.++|+++||+|.-
T Consensus 83 d~~l~rv~~~GG~V~~ 98 (127)
T COG3324 83 DATLERVVAAGGKVLR 98 (127)
T ss_pred HHHHHHHHhcCCeEEe
Confidence 5678899999998764
No 32
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=25.41 E-value=82 Score=16.69 Aligned_cols=18 Identities=28% Similarity=0.344 Sum_probs=13.9
Q ss_pred CHHHHHHHHHcCCEEEEE
Q 047908 63 TVRAKAAVEAAGGSVRRV 80 (94)
Q Consensus 63 S~~A~~~Ie~aGG~v~~~ 80 (94)
-..-++.|+..||++...
T Consensus 15 ~~~l~~~i~~~Gg~v~~~ 32 (72)
T cd00027 15 RDELKELIEKLGGKVTSS 32 (72)
T ss_pred HHHHHHHHHHcCCEEecc
Confidence 356688999999987653
No 33
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=24.80 E-value=44 Score=19.32 Aligned_cols=23 Identities=30% Similarity=0.371 Sum_probs=19.8
Q ss_pred HcCCEEEEEEecHhhhhhhcCCC
Q 047908 72 AAGGSVRRVHYNKLGLRALLKPE 94 (94)
Q Consensus 72 ~aGG~v~~~~~~~~~l~~~~~p~ 94 (94)
..++.+.+..|+-.+.++..||+
T Consensus 27 ~~~~~v~C~WFd~~~~~~~~F~~ 49 (53)
T PF09926_consen 27 ASGGWVECQWFDGHGEQRETFPE 49 (53)
T ss_pred CCCCeEEEEeCCCCCccccccCh
Confidence 46789999999999998888875
No 34
>PF03820 Mtc: Tricarboxylate carrier; InterPro: IPR004686 The MTC family consists of a limited number of homologues, all from eukaryotes. One member of the family has been functionally characterised as a tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism. The rest of the characterised proteins appear to be sideroflexins involved in iron transport.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016020 membrane
Probab=24.74 E-value=38 Score=26.28 Aligned_cols=34 Identities=24% Similarity=0.271 Sum_probs=29.2
Q ss_pred ccccEEEEEEecCHHHHHHHHHcCCEEEEEEecH
Q 047908 51 IKWPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNK 84 (94)
Q Consensus 51 l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~ 84 (94)
++..-.|.++..-.+-.+.+++.|..++.+|||+
T Consensus 273 FPQ~~si~~~~LEpe~~~~~~~~g~~~~~vyyNK 306 (308)
T PF03820_consen 273 FPQRSSISVSKLEPELQELTEKKGPPPTTVYYNK 306 (308)
T ss_pred cccccccchHhcCHHHHHHHhhcCCCCCEEEeCC
Confidence 4555577888899999999999999999999996
No 35
>PF07722 Peptidase_C26: Peptidase C26; InterPro: IPR011697 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. These peptidases have gamma-glutamyl hydrolase activity; that is they catalyse the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to IPR000991 from INTERPRO, but contain extensions in four loops and at the C terminus []. They belong to MEROPS peptidase family C26 (gamma-glutamyl hydrolase family), clan PC. The majority of the sequences are classified as unassigned peptidases. ; GO: 0016787 hydrolase activity, 0006541 glutamine metabolic process; PDB: 1L9X_A 3FIJ_D.
Probab=23.81 E-value=1.1e+02 Score=21.95 Aligned_cols=31 Identities=32% Similarity=0.415 Sum_probs=22.1
Q ss_pred EecCHHHHHHHHHcCCEEEEEEec--Hhhhhhh
Q 047908 60 SRVTVRAKAAVEAAGGSVRRVHYN--KLGLRAL 90 (94)
Q Consensus 60 ~~~S~~A~~~Ie~aGG~v~~~~~~--~~~l~~~ 90 (94)
..+.++=.++|++|||.+..+.++ ...++..
T Consensus 23 ~~i~~~Yv~~i~~aG~~pv~ip~~~~~~~~~~~ 55 (217)
T PF07722_consen 23 SYIAASYVKAIEAAGGRPVPIPYDADDEELDEL 55 (217)
T ss_dssp EEEEHHHHHHHHHTT-EEEEE-SS--HHHHHHH
T ss_pred HHHhHHHHHHHHHcCCEEEEEccCCCHHHHHHH
Confidence 346777889999999999999887 5555544
No 36
>COG0291 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]
Probab=22.80 E-value=50 Score=20.10 Aligned_cols=52 Identities=15% Similarity=0.087 Sum_probs=39.8
Q ss_pred ceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhhhhhcCC
Q 047908 40 GVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGLRALLKP 93 (94)
Q Consensus 40 ~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l~~~~~p 93 (94)
.+|+.|+| .+...--..-|.++...-..+-...|...+---|-..++++|-|
T Consensus 13 RFK~T~~G--kikr~~A~k~H~l~kKs~k~kR~Lr~~~~v~~~d~k~v~~~l~~ 64 (65)
T COG0291 13 RFKITGTG--KIKRKHAGKRHILTKKSTKRKRHLRKTAVVSKADLKRVKRLLLY 64 (65)
T ss_pred heeecCCC--cEEecccccccccccCCHHHHHhccCCceeCHHHHHHHHHhccC
Confidence 68999999 99888888888888888888888888766665555555555543
No 37
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=22.40 E-value=79 Score=17.79 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=12.3
Q ss_pred HHHHHHHHHcCCEEE
Q 047908 64 VRAKAAVEAAGGSVR 78 (94)
Q Consensus 64 ~~A~~~Ie~aGG~v~ 78 (94)
+...+.|+..||++.
T Consensus 22 ~~l~~~i~~~GG~v~ 36 (78)
T PF00533_consen 22 EELEQLIKKHGGTVS 36 (78)
T ss_dssp HHHHHHHHHTTEEEE
T ss_pred HHHHHHHHHcCCEEE
Confidence 456889999999983
No 38
>PRK00172 rpmI 50S ribosomal protein L35; Reviewed
Probab=21.41 E-value=47 Score=19.90 Aligned_cols=51 Identities=14% Similarity=0.170 Sum_probs=35.8
Q ss_pred CceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhhhhhc
Q 047908 39 DGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGLRALL 91 (94)
Q Consensus 39 ~~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l~~~~ 91 (94)
..||+.|+| .+...=.-.-|.++....+..-..++...+.--+...++.+|
T Consensus 12 KRFk~T~~G--Ki~r~~a~k~H~~~~Ks~k~kR~lr~~~~v~~~~~k~ik~~l 62 (65)
T PRK00172 12 KRFKVTGSG--KVKRKHAGKRHILTKKSTKRKRQLRGTTVVSKADAKRVKRML 62 (65)
T ss_pred heeEEcCCC--CEEeccCCCccccccCCHHHHHhcCCCeeECHHHHHHHHHhc
Confidence 368999999 887666667777777777777777777665555555555544
No 39
>CHL00103 rpl35 ribosomal protein L35
Probab=21.20 E-value=46 Score=20.10 Aligned_cols=50 Identities=10% Similarity=0.108 Sum_probs=36.7
Q ss_pred ceEEEcCCcccccccEEEEEEecCHHHHHHHHHcCCEEEEEEecHhhhhhhc
Q 047908 40 GVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRRVHYNKLGLRALL 91 (94)
Q Consensus 40 ~vKlLg~G~~~l~~~i~I~~~~~S~~A~~~Ie~aGG~v~~~~~~~~~l~~~~ 91 (94)
.+|+.|+| .+...=...-|..++......-..++...+--=|...++.+|
T Consensus 13 RFKvT~sG--Kvkr~~a~k~H~l~kKs~krkR~L~~~~~v~~~d~~~ik~~l 62 (65)
T CHL00103 13 RYKKTGNG--KFLRRKAFKSHLLQKKSSKQKRKLSQTVCVSKGDSKSIKLML 62 (65)
T ss_pred eeEecCCC--CEEeccCCccccccCCCHHHHHhcCCCeeECHHHHHHHHHhc
Confidence 68999999 887777777777888777777778777655554555555554
Done!