Query gi|254780418|ref|YP_003064831.1| 50S ribosomal protein L25/general stress protein Ctc [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 191
No_of_seqs 120 out of 1712
Neff 6.3
Searched_HMMs 39220
Date Sun May 29 16:11:26 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780418.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05618 50S ribosomal protein 100.0 0 0 391.4 22.6 187 3-191 1-187 (193)
2 TIGR00731 ctc_TL5 ribosomal pr 100.0 2.1E-36 5.2E-41 248.5 16.0 179 8-186 1-182 (182)
3 PRK05943 50S ribosomal protein 100.0 2E-28 5.1E-33 198.4 10.2 93 6-98 1-93 (93)
4 cd00495 Ribosomal_L25_TL5_CTC 99.9 6.1E-26 1.6E-30 182.8 9.5 91 6-97 1-91 (91)
5 pfam01386 Ribosomal_L25p Ribos 99.9 7.5E-26 1.9E-30 182.2 8.4 87 8-95 1-87 (87)
6 COG1825 RplY Ribosomal protein 99.9 1.9E-24 4.9E-29 173.4 7.6 92 6-98 2-93 (93)
7 pfam01000 RNA_pol_A_bac RNA po 82.1 3.3 8.3E-05 21.5 4.9 68 117-187 12-80 (117)
8 cd06928 RNAP_alpha_NTD N-termi 80.9 3.1 8E-05 21.6 4.4 29 158-187 96-124 (215)
9 CHL00013 rpoA RNA polymerase a 80.8 1.8 4.5E-05 23.1 3.1 52 131-187 91-142 (333)
10 TIGR01416 Rieske_proteo ubiqui 79.6 1.3 3.4E-05 23.9 2.2 24 140-163 36-59 (192)
11 TIGR01910 DapE-ArgE acetylorni 68.5 3.3 8.4E-05 21.4 1.9 44 7-50 371-416 (427)
12 PRK05182 DNA-directed RNA poly 65.3 8.4 0.00022 18.9 3.5 27 159-186 104-130 (306)
13 pfam12000 DUF3495 Domain of un 64.7 4.7 0.00012 20.4 2.1 22 18-39 54-75 (172)
14 TIGR00150 TIGR00150 conserved 58.9 4.2 0.00011 20.8 1.0 31 75-107 63-93 (147)
15 pfam02367 UPF0079 Uncharacteri 58.5 5.7 0.00015 19.9 1.6 30 73-104 48-77 (123)
16 KOG1421 consensus 56.6 15 0.00039 17.3 3.5 109 20-150 758-867 (955)
17 COG4856 Uncharacterized protei 54.5 17 0.00043 17.0 6.0 81 102-184 219-312 (403)
18 PRK10646 putative ATPase; Prov 54.3 12 0.0003 18.0 2.6 78 74-165 62-140 (153)
19 pfam11113 Phage_head_chap Head 51.6 19 0.00048 16.7 3.8 33 68-103 9-41 (56)
20 PRK13007 dipeptidase; Reviewed 45.3 12 0.00032 17.8 1.6 35 131-165 240-276 (354)
21 COG0802 Predicted ATPase or ki 39.1 26 0.00067 15.8 2.5 74 75-161 60-134 (149)
22 PRK00466 acetyl-lysine deacety 38.7 25 0.00064 15.9 2.4 32 5-36 112-144 (345)
23 TIGR02027 rpoA DNA-directed RN 37.6 31 0.00079 15.3 3.4 29 158-187 106-135 (324)
24 pfam06434 Aconitase_2_N Aconit 33.9 35 0.0009 15.0 4.3 36 146-185 116-151 (204)
25 PRK08652 acetylornithine deace 33.1 27 0.00069 15.7 1.8 31 6-36 111-142 (349)
26 TIGR00113 queA S-adenosylmethi 31.9 28 0.00072 15.6 1.7 64 33-101 185-253 (364)
27 PRK13983 diaminopimelate amino 30.9 40 0.001 14.6 2.9 33 133-165 275-313 (399)
28 KOG3493 consensus 30.5 21 0.00053 16.4 0.8 41 133-173 13-68 (73)
29 PRK08554 peptidase; Reviewed 29.6 38 0.00096 14.8 2.0 30 6-35 127-160 (438)
30 COG3603 Uncharacterized conser 29.4 34 0.00085 15.1 1.7 28 124-151 32-61 (128)
31 PRK08651 succinyl-diaminopimel 28.6 37 0.00094 14.9 1.8 19 130-148 241-259 (371)
32 TIGR01017 rpsD_bact ribosomal 28.5 19 0.00048 16.7 0.3 48 108-155 136-186 (217)
33 PRK04443 acetyl-lysine deacety 28.1 44 0.0011 14.4 2.3 26 6-31 116-141 (352)
34 PRK08596 acetylornithine deace 26.6 47 0.0012 14.2 2.2 24 7-30 145-168 (421)
35 PRK13009 succinyl-diaminopimel 26.1 48 0.0012 14.1 2.9 16 21-36 145-161 (375)
36 COG1049 AcnB Aconitase B [Ener 25.6 43 0.0011 14.4 1.8 100 77-185 210-320 (852)
37 cd01791 Ubl5 UBL5 (also known 23.9 53 0.0013 13.9 2.9 31 143-173 38-68 (73)
38 PRK13004 peptidase; Reviewed 23.5 50 0.0013 14.0 1.8 31 7-37 137-170 (397)
39 TIGR00020 prfB peptide chain r 21.4 59 0.0015 13.6 4.4 94 37-143 180-277 (373)
40 cd01576 AcnB_Swivel Aconitase 20.9 57 0.0014 13.7 1.6 38 120-162 91-129 (131)
41 PRK05464 Na(+)-translocating N 20.9 35 0.00091 14.9 0.6 36 118-153 159-194 (408)
No 1
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=100.00 E-value=0 Score=391.39 Aligned_cols=187 Identities=40% Similarity=0.732 Sum_probs=182.0
Q ss_pred CCEEEEEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEEEECHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEE
Q ss_conf 61699999991687617789999789943899678988556999800221001114662257996167752037861212
Q gi|254780418|r 3 QKECKLSAVMRDKVGKGSARLLRKNGQIPAIIYGNMSDPKPIALSAKDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQ 82 (191)
Q Consensus 3 m~~~~L~~~~R~~~gk~~~r~lR~~G~VPaviYG~~~e~~~i~v~~~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ 82 (191)
|++++|+|++|+.+||+++|+||++|+||||+||++.+|++++++.++|.+++++.++.+.+|+|+++|++++|++||+|
T Consensus 1 M~~~~L~a~~R~~~Gk~~~r~lR~~G~VPaViYG~~~e~~~i~v~~~~~~~~l~~~~~~~~~~~l~v~g~~~~vlikevQ 80 (193)
T PRK05618 1 METIELKAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELLKALRKEGFRSTVITLEVDGKKQKVLVKDVQ 80 (193)
T ss_pred CCCEEEEEEECCCCCCHHHHHHHHCCCCEEEEECCCCCCEEEEECHHHHHHHHHHCCCCCEEEEEEECCEEEEEEEEEEE
T ss_conf 96089999993667877899998879955999889998879998599999998625663179999989918999984103
Q ss_pred CCCCCCCEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEHHHCCCEEEECCCCCCCCCEEEE
Q ss_conf 14326846544899932897699996369960565443212311357654578888076796346832222356977999
Q gi|254780418|r 83 LDPVSDILIHADFLQVSEGSTVTVHVPVRFINENKSPGIKQGGKLNVVCHEVSLLCPANNIPDSITVDLNDLKIGDSIHM 162 (191)
Q Consensus 83 ~~p~~~~i~HvDF~~v~~~~~v~v~VPI~~~ge~~~~Gvk~GG~l~~~~~~i~v~~~p~~IPe~ievDvs~L~~Gd~i~v 162 (191)
+||+++.++|+|||+++++++++++|||+|+|+ ++|+++||+|++.+++|+|+|+|.+||++|++|||+|++||++++
T Consensus 81 ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gv~~GG~L~~~~~~i~V~~~p~~IP~~I~vDvs~L~iGd~i~v 158 (193)
T PRK05618 81 RHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGE--AAGVKRGGVLSQVLRELEVECLPKDIPEFIEVDVSGLEIGDSIHV 158 (193)
T ss_pred EHHCCCCEEEEEEEEECCCCEEEEEEEEEEECC--CCCCCCCCEEEEEEEEEEEEEEHHHCCEEEEEECHHCCCCCEEEE
T ss_conf 001149178999999479987999946798033--245248979999986899997088898189998221679986897
Q ss_pred EEEECCCCCEECCCCCCEEEEEECCCCCC
Q ss_conf 97535888678368982699994488779
Q gi|254780418|r 163 EDIRLPEKTSSMSQLNITIATIVAPISGS 191 (191)
Q Consensus 163 ~Dl~lpegv~~l~d~~~~vvsv~~P~~g~ 191 (191)
+||++|+|+++++|+|.+||+|.+||+..
T Consensus 159 ~Dl~lpegv~~~~d~~~~V~~V~~p~~~~ 187 (193)
T PRK05618 159 SDIKLPEGVKLLDDPDFVVVTVVAPAAAE 187 (193)
T ss_pred EEECCCCCEEECCCCCCEEEEEECCCCCC
T ss_conf 50058998089459995899997997536
No 2
>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form; InterPro: IPR001021 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 of 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 , . The bacterial ribosomal protein L25 is an RNA binding protein. Ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases .; GO: 0003735 structural constituent of ribosome, 0008097 5S rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=100.00 E-value=2.1e-36 Score=248.46 Aligned_cols=179 Identities=34% Similarity=0.644 Sum_probs=173.0
Q ss_pred EEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEEEE---CHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEECC
Q ss_conf 99999168761778999978994389967898855699980---022100111466225799616775203786121214
Q gi|254780418|r 8 LSAVMRDKVGKGSARLLRKNGQIPAIIYGNMSDPKPIALSA---KDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQLD 84 (191)
Q Consensus 8 L~~~~R~~~gk~~~r~lR~~G~VPaviYG~~~e~~~i~v~~---~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ~~ 84 (191)
|.++.|+.+||+++|++|++|.+||++||+|.++.++.++. ++|.+.++..+..+.++.++++|+.+++++|++|.|
T Consensus 1 l~~~~r~~~~~~~~~~~r~~g~~pa~~yg~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 80 (182)
T TIGR00731 1 LEGKSRTEFGKSAARRIRKEGRIPAVVYGKGKEPVPLELKSLVFKEFLKYLRKGGLSNTVLTLDDGGKEFKVLVKDLQLN 80 (182)
T ss_pred CEEEEEECCCHHHHHHHHHHCCCCEEEECCCCCCCCEEEHHHHHHHHHHHHHCCCCCEEEEEEECCCCEEEEEEHHHHHC
T ss_conf 93566412430456655550786478863886323213134566677876420132214676312782677630023211
Q ss_pred CCCCCEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEHHHCCCEEEECCCCCCCCCEEEEEE
Q ss_conf 32684654489993289769999636996056544321231135765457888807679634683222235697799997
Q gi|254780418|r 85 PVSDILIHADFLQVSEGSTVTVHVPVRFINENKSPGIKQGGKLNVVCHEVSLLCPANNIPDSITVDLNDLKIGDSIHMED 164 (191)
Q Consensus 85 p~~~~i~HvDF~~v~~~~~v~v~VPI~~~ge~~~~Gvk~GG~l~~~~~~i~v~~~p~~IPe~ievDvs~L~~Gd~i~v~D 164 (191)
|+++.+.|+||+.+.++++++++||+++.|+..+.|+|.||.+++..+.++++|.|.+||+++++|+++++.|++++++|
T Consensus 81 ~~~~~~~h~d~~~~~~~~~~~~~~p~~~~g~~~g~g~k~gg~l~~~~~~~~~~~~p~~~p~~~~~d~~~~~~~~~~~~~d 160 (182)
T TIGR00731 81 PVTDEVIHVDFLEVDEGVPLKLEVPIKLEGAPIGLGVKNGGILTQLKRRIEVECKPKDLPEFLELDVSGLGVGESLKLSD 160 (182)
T ss_pred CCCCEEEEEEEEEEECCCEEEEEEEEEECCCCCEEEECCCCEEEEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEE
T ss_conf 10010121012443247505888757871552102202573333322245676310137744689851479674455300
Q ss_pred EECCCCCEECCCCCCEEEEEEC
Q ss_conf 5358886783689826999944
Q gi|254780418|r 165 IRLPEKTSSMSQLNITIATIVA 186 (191)
Q Consensus 165 l~lpegv~~l~d~~~~vvsv~~ 186 (191)
+.+|+|+.++++++.+++++..
T Consensus 161 ~~~p~~~~~~~~~~~~~~~~~~ 182 (182)
T TIGR00731 161 LPLPAGVSLLTDPDEVVVTVIK 182 (182)
T ss_pred ECCCCCCEEECCCCEEEEEEEC
T ss_conf 1047871440575417888719
No 3
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=99.95 E-value=2e-28 Score=198.36 Aligned_cols=93 Identities=34% Similarity=0.527 Sum_probs=90.0
Q ss_pred EEEEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEEEECHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEECCC
Q ss_conf 99999991687617789999789943899678988556999800221001114662257996167752037861212143
Q gi|254780418|r 6 CKLSAVMRDKVGKGSARLLRKNGQIPAIIYGNMSDPKPIALSAKDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQLDP 85 (191)
Q Consensus 6 ~~L~~~~R~~~gk~~~r~lR~~G~VPaviYG~~~e~~~i~v~~~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ~~p 85 (191)
++|+|++|+..||+++|+||++|+||||+||++.+|++++++.++|.+++++.++.+.+++|+++|+++.|++||+|+||
T Consensus 1 i~L~a~~R~~~Gk~~~r~LR~~G~vPaViYG~~~~~~~i~v~~~e~~~~l~~~~~~~~~i~l~i~g~~~~vlikevQ~~P 80 (93)
T PRK05943 1 FTLNAEVRKEQGKGASRRLRRAGKFPAIIYGGGEAPISIVLDHDDVLNLQKKAEFYKEVITLVIDGKEGKVKVQAVQRHP 80 (93)
T ss_pred CEEEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEECHHHHHHHHHCCCCCCEEEEEEECCCEEEEEEEEEEECC
T ss_conf 99999991678978899999879961999889987779998599999998356764169999848929989988888378
Q ss_pred CCCCEEEEEEEEE
Q ss_conf 2684654489993
Q gi|254780418|r 86 VSDILIHADFLQV 98 (191)
Q Consensus 86 ~~~~i~HvDF~~v 98 (191)
+++.++|||||+|
T Consensus 81 v~~~i~HvDF~~V 93 (93)
T PRK05943 81 YKPKLLHIDFVRV 93 (93)
T ss_pred CCCCEEEEEEEEC
T ss_conf 8897387860759
No 4
>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L
Probab=99.93 E-value=6.1e-26 Score=182.77 Aligned_cols=91 Identities=37% Similarity=0.645 Sum_probs=86.5
Q ss_pred EEEEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEEEECHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEECCC
Q ss_conf 99999991687617789999789943899678988556999800221001114662257996167752037861212143
Q gi|254780418|r 6 CKLSAVMRDKVGKGSARLLRKNGQIPAIIYGNMSDPKPIALSAKDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQLDP 85 (191)
Q Consensus 6 ~~L~~~~R~~~gk~~~r~lR~~G~VPaviYG~~~e~~~i~v~~~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ~~p 85 (191)
.+|+|++|+..||+++|+||++|+||||+||++.++++++++.++|.+++++ .+.+++|+|+++|++.+|++||+|+||
T Consensus 1 ~~L~a~~R~~~gk~~~r~lR~~G~iPaViYG~~~~~~~i~v~~~~~~k~l~~-~~~~~~~~l~i~g~~~~v~ikevQ~~p 79 (91)
T cd00495 1 LTLKAEKREETGKGASRRLRRAGKVPAVIYGKGKEPISISVDEKELEKLLRK-EGRSTLIELNIDGKKENVLIKDVQRHP 79 (91)
T ss_pred CEEEEEECCCCCCHHHHHHHHCCCCEEEEECCCCCCEEEEEEHHHHHHHHHC-CCCCEEEEEECCCEEEEEEEEEEEECC
T ss_conf 9899999055686779999986995499975899788999949999999854-688489999608808999999999557
Q ss_pred CCCCEEEEEEEE
Q ss_conf 268465448999
Q gi|254780418|r 86 VSDILIHADFLQ 97 (191)
Q Consensus 86 ~~~~i~HvDF~~ 97 (191)
+++.++||||++
T Consensus 80 v~~~i~HvDF~~ 91 (91)
T cd00495 80 VKDKILHVDFLR 91 (91)
T ss_pred CCCCEEEEECCC
T ss_conf 889788886159
No 5
>pfam01386 Ribosomal_L25p Ribosomal L25p family. Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis, which is induced by stress.
Probab=99.93 E-value=7.5e-26 Score=182.20 Aligned_cols=87 Identities=38% Similarity=0.654 Sum_probs=83.9
Q ss_pred EEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEEEECHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEECCCCC
Q ss_conf 99999168761778999978994389967898855699980022100111466225799616775203786121214326
Q gi|254780418|r 8 LSAVMRDKVGKGSARLLRKNGQIPAIIYGNMSDPKPIALSAKDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQLDPVS 87 (191)
Q Consensus 8 L~~~~R~~~gk~~~r~lR~~G~VPaviYG~~~e~~~i~v~~~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ~~p~~ 87 (191)
|+|+.|+.+||+++|+||++|+||||+||++.+|++++++.++|.++++ .++.+.+|+|+++|+++.|++||||+||++
T Consensus 1 L~a~~R~~~gk~~~r~lR~~G~iPaViYG~~~~~~~i~v~~~~~~k~l~-~~~~~~ii~l~v~g~~~~vlikevQ~~pv~ 79 (87)
T pfam01386 1 LKAEKREETGKGASRRLRREGKVPAVIYGKGKEPVSISVDEKELEKLLR-EAGENTVIELKIDGKKENVLIKDVQRHPVK 79 (87)
T ss_pred CCEEECCCCCCHHHHHHHHCCCCEEEEECCCCCCEEEEEEHHHHHHHHH-HCCCEEEEEEECCCCEEEEEEEEEEECCCC
T ss_conf 9287825568678999998699539997589988899981999999985-479708999972892899999866737788
Q ss_pred CCEEEEEE
Q ss_conf 84654489
Q gi|254780418|r 88 DILIHADF 95 (191)
Q Consensus 88 ~~i~HvDF 95 (191)
+.++|+||
T Consensus 80 ~~i~HvDF 87 (87)
T pfam01386 80 DKILHVDF 87 (87)
T ss_pred CCEEECCC
T ss_conf 97683359
No 6
>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.9e-24 Score=173.37 Aligned_cols=92 Identities=38% Similarity=0.655 Sum_probs=88.0
Q ss_pred EEEEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEEEECHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEECCC
Q ss_conf 99999991687617789999789943899678988556999800221001114662257996167752037861212143
Q gi|254780418|r 6 CKLSAVMRDKVGKGSARLLRKNGQIPAIIYGNMSDPKPIALSAKDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQLDP 85 (191)
Q Consensus 6 ~~L~~~~R~~~gk~~~r~lR~~G~VPaviYG~~~e~~~i~v~~~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ~~p 85 (191)
++|+++.|+..||+++|+||++|++|||+||.|.+|.+++++.++|.++++..+ .|++|+|+++|++..|++|++|+||
T Consensus 2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~g~~~v~i~l~~~~~~k~~~~~~-~~~v~~l~v~g~~~~Vlvkd~Q~~p 80 (93)
T COG1825 2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGGGKEPVNIALDHHEFAKALRKLG-YSTVITLEVDGKEIKVLVKDVQRHP 80 (93)
T ss_pred CEECEEEECCCCCCHHHHHHHCCCCCEEEECCCCCCCEEEECHHHHHHHHHHCC-CCEEEEEEECCEEEEEEEHHHHHCC
T ss_conf 320206853567606666876699888998999878469974899999974214-3337999979969999861111385
Q ss_pred CCCCEEEEEEEEE
Q ss_conf 2684654489993
Q gi|254780418|r 86 VSDILIHADFLQV 98 (191)
Q Consensus 86 ~~~~i~HvDF~~v 98 (191)
+++.++|+||+++
T Consensus 81 ~~~~~~HvDf~~v 93 (93)
T COG1825 81 LTDEVQHIDFLRV 93 (93)
T ss_pred CCCCCEEEEEECC
T ss_conf 6586055522629
No 7
>pfam01000 RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain. Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal
Probab=82.06 E-value=3.3 Score=21.46 Aligned_cols=68 Identities=18% Similarity=0.166 Sum_probs=40.2
Q ss_pred CCCCCCCC-CEEEEEEEEEEEEEEHHHCCCEEEECCCCCCCCCEEEEEEEECCCCCEECCCCCCEEEEEECC
Q ss_conf 54432123-113576545788880767963468322223569779999753588867836898269999448
Q gi|254780418|r 117 KSPGIKQG-GKLNVVCHEVSLLCPANNIPDSITVDLNDLKIGDSIHMEDIRLPEKTSSMSQLNITIATIVAP 187 (191)
Q Consensus 117 ~~~Gvk~G-G~l~~~~~~i~v~~~p~~IPe~ievDvs~L~~Gd~i~v~Dl~lpegv~~l~d~~~~vvsv~~P 187 (191)
..+|+++- --+-..+.++.++.. ..-+..+.+.++.-..| .++.+||.+|++++++ +++..||++...
T Consensus 12 ~I~GV~Edv~~IilNlK~i~~~~~-~~~~~~~~~~l~~~gp~-~VtA~Di~~~~~veiv-npd~~Iatl~~~ 80 (117)
T pfam01000 12 LIPGVSEDVLEIILNLKELVCKIE-GCEECSVTLTLDVKGPG-EVTAGDLESDPDVEIV-NPDILIATLRKG 80 (117)
T ss_pred CCCCCHHHHHHHHHCCCCCEEEEC-CCCCCEEEEEEEEECCC-EEEEEEECCCCCEEEC-CCCEEEEEECCC
T ss_conf 589832609999736465399832-68881599999974583-8994016168854864-987599997899
No 8
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=80.89 E-value=3.1 Score=21.57 Aligned_cols=29 Identities=24% Similarity=0.303 Sum_probs=14.7
Q ss_pred CEEEEEEEECCCCCEECCCCCCEEEEEECC
Q ss_conf 779999753588867836898269999448
Q gi|254780418|r 158 DSIHMEDIRLPEKTSSMSQLNITIATIVAP 187 (191)
Q Consensus 158 d~i~v~Dl~lpegv~~l~d~~~~vvsv~~P 187 (191)
..++.+||.+|+++++ -+||..||++..+
T Consensus 96 ~~vtA~Di~~p~~iei-vNpdq~IaTl~~~ 124 (215)
T cd06928 96 GVVTAADIELPSGVEI-VNPDQYIATLTED 124 (215)
T ss_pred EEEEEEHCCCCCCEEE-ECCCEEEEEECCC
T ss_conf 0599203058886699-6899799997789
No 9
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=80.78 E-value=1.8 Score=23.14 Aligned_cols=52 Identities=19% Similarity=0.201 Sum_probs=26.2
Q ss_pred EEEEEEEEEHHHCCCEEEECCCCCCCCCEEEEEEEECCCCCEECCCCCCEEEEEECC
Q ss_conf 545788880767963468322223569779999753588867836898269999448
Q gi|254780418|r 131 CHEVSLLCPANNIPDSITVDLNDLKIGDSIHMEDIRLPEKTSSMSQLNITIATIVAP 187 (191)
Q Consensus 131 ~~~i~v~~~p~~IPe~ievDvs~L~~Gd~i~v~Dl~lpegv~~l~d~~~~vvsv~~P 187 (191)
+.+|.+++... -|....+++.+ .-.++.+||.+|+++++ -+|+..||++..+
T Consensus 91 LK~i~~k~~~~-~~~~~~l~~~G---p~~VtA~Di~~p~~vei-vNpd~~IATl~~~ 142 (333)
T CHL00013 91 LKEIVLRSNLY-GTQIASICVQG---PGYVTAQDIILPPSVEI-VDPTQYIATLTEP 142 (333)
T ss_pred HHHEEEECCCC-CCEEEEEEEEC---CCEEEEHHCCCCCCEEE-ECCCEEEEEECCC
T ss_conf 45438972479-85799999607---80588034168885399-7798799996799
No 10
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit; InterPro: IPR006317 These sequences represent the Proteobacterial and mitochondrial type of the Rieske [2Fe-2S] iron-sulphur subunit as found in ubiquinol-cytochrome c reductase. Not included in this group are the Rieske iron-sulphur protein as found in the cytochrome b6-f complex of the Cyanobacteria and chloroplasts. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006118 electron transport.
Probab=79.60 E-value=1.3 Score=23.92 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=19.3
Q ss_pred HHHCCCEEEECCCCCCCCCEEEEE
Q ss_conf 767963468322223569779999
Q gi|254780418|r 140 ANNIPDSITVDLNDLKIGDSIHME 163 (191)
Q Consensus 140 p~~IPe~ievDvs~L~~Gd~i~v~ 163 (191)
...+=-.+|||||+|+-|+.++|+
T Consensus 36 ~~AaGA~~eVDvs~~~~Gq~~tv~ 59 (192)
T TIGR01416 36 ALAAGAPTEVDVSKIQEGQQLTVE 59 (192)
T ss_pred HHHCCCCEEEECCCCCCCCEEEEE
T ss_conf 985788548862577988678887
No 11
>TIGR01910 DapE-ArgE acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase; InterPro: IPR010182 This group of sequences contains annotations for both acetylornithine deacetylase and succinyl-diaminopimelate desuccinylase, but does not contain any members with experimental characterization. Bacillus, Staphylococcus and Sulfolobus species contain multiple hits to this subfamily and each may have a separate activity. Determining which is which must await further laboratory research.; GO: 0009014 succinyl-diaminopimelate desuccinylase activity, 0046872 metal ion binding, 0009085 lysine biosynthetic process.
Probab=68.48 E-value=3.3 Score=21.42 Aligned_cols=44 Identities=27% Similarity=0.379 Sum_probs=32.6
Q ss_pred EEEEEEECCCCCHHHHHHHHCC--CCCEEEECCCCCCEEEEEEECH
Q ss_conf 9999991687617789999789--9438996789885569998002
Q gi|254780418|r 7 KLSAVMRDKVGKGSARLLRKNG--QIPAIIYGNMSDPKPIALSAKD 50 (191)
Q Consensus 7 ~L~~~~R~~~gk~~~r~lR~~G--~VPaviYG~~~e~~~i~v~~~~ 50 (191)
.+++..--..|.-.++-+|.+| -+|.|+||+|..-..-++++.-
T Consensus 371 g~~~~~~~s~g~TD~~~~~~~g~~d~P~ivyGPG~~~~aH~~NEyi 416 (427)
T TIGR01910 371 GIEAKVLVSSGTTDARFFRKAGGKDIPVIVYGPGELETAHQVNEYI 416 (427)
T ss_pred CCCCEEEEECCHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCE
T ss_conf 5431157643213588887458962589985488888887455651
No 12
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=65.32 E-value=8.4 Score=18.86 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=12.7
Q ss_pred EEEEEEEECCCCCEECCCCCCEEEEEEC
Q ss_conf 7999975358886783689826999944
Q gi|254780418|r 159 SIHMEDIRLPEKTSSMSQLNITIATIVA 186 (191)
Q Consensus 159 ~i~v~Dl~lpegv~~l~d~~~~vvsv~~ 186 (191)
.++.+||.+|+++++ -+|+..||++..
T Consensus 104 ~vtA~Di~~p~~vei-vnpd~~Iatl~~ 130 (306)
T PRK05182 104 EVTAGDIETDSDVEI-VNPDLVIATLNE 130 (306)
T ss_pred EEEHHHCCCCCCEEE-ECCCEEEEEECC
T ss_conf 488747489884399-689889999778
No 13
>pfam12000 DUF3495 Domain of unknown function (DUF3495). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 170 amino acids in length. This domain is found associated with pfam00534. This domain has a single completely conserved residue G that may be functionally important.
Probab=64.70 E-value=4.7 Score=20.45 Aligned_cols=22 Identities=32% Similarity=0.437 Sum_probs=18.7
Q ss_pred CHHHHHHHHCCCCCEEEECCCC
Q ss_conf 1778999978994389967898
Q gi|254780418|r 18 KGSARLLRKNGQIPAIIYGNMS 39 (191)
Q Consensus 18 k~~~r~lR~~G~VPaviYG~~~ 39 (191)
-.++.+||++|+.|-+|+|+..
T Consensus 54 ~~aa~~L~~~Gf~PDvIi~H~G 75 (172)
T pfam12000 54 ARAARQLRAQGFRPDVIVAHPG 75 (172)
T ss_pred HHHHHHHHHCCCCCCEEEECCC
T ss_conf 9999999974999998987587
No 14
>TIGR00150 TIGR00150 conserved hypothetical protein TIGR00150; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements . .
Probab=58.94 E-value=4.2 Score=20.75 Aligned_cols=31 Identities=13% Similarity=0.275 Sum_probs=21.9
Q ss_pred EEEEEEEECCCCCCCEEEEEEEEECCCCEEEEE
Q ss_conf 378612121432684654489993289769999
Q gi|254780418|r 75 HVIPKDYQLDPVSDILIHADFLQVSEGSTVTVH 107 (191)
Q Consensus 75 ~vlikevQ~~p~~~~i~HvDF~~v~~~~~v~v~ 107 (191)
..|+++.... +-.++|+||||++..++++.-
T Consensus 63 ftlv~~Y~~~--~~~~YH~DlYR~~~~~E~E~~ 93 (147)
T TIGR00150 63 FTLVNEYNEG--NLPLYHFDLYRLADPEELELL 93 (147)
T ss_pred CCEEEEEECC--CCCEEEEEEECCCCHHHHHHH
T ss_conf 2101001137--851533334205772344541
No 15
>pfam02367 UPF0079 Uncharacterized P-loop hydrolase UPF0079. This uncharacterized family contains a P-loop.
Probab=58.52 E-value=5.7 Score=19.91 Aligned_cols=30 Identities=17% Similarity=0.269 Sum_probs=20.6
Q ss_pred CEEEEEEEEECCCCCCCEEEEEEEEECCCCEE
Q ss_conf 20378612121432684654489993289769
Q gi|254780418|r 73 LVHVIPKDYQLDPVSDILIHADFLQVSEGSTV 104 (191)
Q Consensus 73 ~~~vlikevQ~~p~~~~i~HvDF~~v~~~~~v 104 (191)
....++++.+ +-+..+.|+||||+...+.+
T Consensus 48 PTF~lv~~Y~--~~~~~i~H~DlYRl~~~~e~ 77 (123)
T pfam02367 48 PTFTLVNVYE--PGKLPLYHYDLYRLEDPEEL 77 (123)
T ss_pred CCEEEEEEEC--CCCCEEEEEEEECCCCHHHH
T ss_conf 9558899970--89963999983326997789
No 16
>KOG1421 consensus
Probab=56.60 E-value=15 Score=17.26 Aligned_cols=109 Identities=16% Similarity=0.199 Sum_probs=66.7
Q ss_pred HHHHHHHCCCCCEEEECCCCCCEEEEEEECHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEECCCCCCCEEEEEEEEEC
Q ss_conf 78999978994389967898855699980022100111466225799616775203786121214326846544899932
Q gi|254780418|r 20 SARLLRKNGQIPAIIYGNMSDPKPIALSAKDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQLDPVSDILIHADFLQVS 99 (191)
Q Consensus 20 ~~r~lR~~G~VPaviYG~~~e~~~i~v~~~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ~~p~~~~i~HvDF~~v~ 99 (191)
--+|.|.++-+|--+|- ++--.--+.|.|-. .=+-|.++|+-..-| .|.| .+..+||.-+.
T Consensus 758 ~imk~e~es~~~~ql~~-------ishv~~~~~kil~~-----gdiilsvngk~itr~-~dl~------d~~eid~~ilr 818 (955)
T KOG1421 758 FIMKSEEESTIPRQLYV-------ISHVRPLLHKILGV-----GDIILSVNGKMITRL-SDLH------DFEEIDAVILR 818 (955)
T ss_pred HHHHHHHCCCCCCEEEE-------EEEECCCCCCCCCC-----CCEEEEECCEEEEEE-HHHH------HHHHHHEEEEE
T ss_conf 98655532798513799-------98422576501134-----648999567677650-2233------45531204541
Q ss_pred CCCEEEEEEEEEEEECCCCCCCC-CCCEEEEEEEEEEEEEEHHHCCCEEEEC
Q ss_conf 89769999636996056544321-2311357654578888076796346832
Q gi|254780418|r 100 EGSTVTVHVPVRFINENKSPGIK-QGGKLNVVCHEVSLLCPANNIPDSITVD 150 (191)
Q Consensus 100 ~~~~v~v~VPI~~~ge~~~~Gvk-~GG~l~~~~~~i~v~~~p~~IPe~ievD 150 (191)
.|..++++||..-.- +.+..+- .|.+||..++.+.-+ -.|+|+.+-+-
T Consensus 819 dg~~~~ikipt~p~~-et~r~vi~~gailq~ph~av~~q--~edlp~gvyvt 867 (955)
T KOG1421 819 DGIEMEIKIPTYPEY-ETSRAVIWMGAILQPPHSAVFEQ--VEDLPEGVYVT 867 (955)
T ss_pred CCCEEEEEECCCCCC-CCCEEEEEEECCCCCCHHHHHHH--HHCCCCCEEEE
T ss_conf 581899982455511-35458999703136843889998--74067753885
No 17
>COG4856 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.49 E-value=17 Score=16.98 Aligned_cols=81 Identities=17% Similarity=0.288 Sum_probs=47.2
Q ss_pred CEEEEEEEEEEEECCCCCCCCCCC---------EEEEEEEEEEEEEEHHHCCC----EEEECCCCCCCCCEEEEEEEECC
Q ss_conf 769999636996056544321231---------13576545788880767963----46832222356977999975358
Q gi|254780418|r 102 STVTVHVPVRFINENKSPGIKQGG---------KLNVVCHEVSLLCPANNIPD----SITVDLNDLKIGDSIHMEDIRLP 168 (191)
Q Consensus 102 ~~v~v~VPI~~~ge~~~~Gvk~GG---------~l~~~~~~i~v~~~p~~IPe----~ievDvs~L~~Gd~i~v~Dl~lp 168 (191)
.++.++||++=.....+.-+++-| -+..-..++.|-+.-+.+-+ .++||+|+...+..+++ +|++|
T Consensus 219 ~evn~tV~vek~sksVpv~Vk~tGslpdg~si~sit~s~~tv~I~Gs~dvLd~lseId~~vDlskI~~~t~~tv-~lpvP 297 (403)
T COG4856 219 QEVNLTVPVEKPSKSVPVNVKRTGSLPDGVSISSITPSKNTVTIVGSQDVLDNLSEIDAPVDLSKISKDTTKTV-KLPVP 297 (403)
T ss_pred CEEEEEEEEECCCCCCCEEEEECCCCCCCCCEEEEECCCCEEEEECCHHHHCCHHEEEEEEEHHHCCCCCEEEE-EEECC
T ss_conf 55789976005676453266543669987413564158865999826676201010542223645457744899-86478
Q ss_pred CCCEECCCCCCEEEEE
Q ss_conf 8867836898269999
Q gi|254780418|r 169 EKTSSMSQLNITIATI 184 (191)
Q Consensus 169 egv~~l~d~~~~vvsv 184 (191)
+|++..... .+=+.+
T Consensus 298 egv~sv~Ps-~i~v~l 312 (403)
T COG4856 298 EGVKSVSPS-SIEVRL 312 (403)
T ss_pred CCCEECCCC-EEEEEE
T ss_conf 762453775-699999
No 18
>PRK10646 putative ATPase; Provisional
Probab=54.33 E-value=12 Score=17.99 Aligned_cols=78 Identities=13% Similarity=0.265 Sum_probs=41.4
Q ss_pred EEEEEEEEECCCCCCCEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEHHHCCC-EEEECCC
Q ss_conf 037861212143268465448999328976999963699605654432123113576545788880767963-4683222
Q gi|254780418|r 74 VHVIPKDYQLDPVSDILIHADFLQVSEGSTVTVHVPVRFINENKSPGIKQGGKLNVVCHEVSLLCPANNIPD-SITVDLN 152 (191)
Q Consensus 74 ~~vlikevQ~~p~~~~i~HvDF~~v~~~~~v~v~VPI~~~ge~~~~Gvk~GG~l~~~~~~i~v~~~p~~IPe-~ievDvs 152 (191)
...++.+.+..+ ..+.|+||||+...+.+. ..|-+.. ...+++.-.-=.+. .+.-+|+ .++|.++
T Consensus 62 Tf~lv~~Y~~~~--~~~~H~DlYRl~~~~e~~------~lg~~e~--~~~~~i~lIEWpe~----~~~~lP~~~l~I~i~ 127 (153)
T PRK10646 62 TYTLVEPYTLDN--LMVYHFDLYRLADPEELE------FMGIRDY--FANDAICLVEWPQQ----GTGVLPDPDVEIHID 127 (153)
T ss_pred CEEEEEEECCCC--CEEEEEEEECCCCHHHHH------HCCCHHH--HCCCCEEEEECCCC----CCCCCCCCCEEEEEE
T ss_conf 764799732899--338999853469988998------7787888--57996999989765----101088476899999
Q ss_pred CCCCCCEEEEEEE
Q ss_conf 2356977999975
Q gi|254780418|r 153 DLKIGDSIHMEDI 165 (191)
Q Consensus 153 ~L~~Gd~i~v~Dl 165 (191)
.-+-|..+++.-.
T Consensus 128 ~~~~~R~~~i~a~ 140 (153)
T PRK10646 128 YQAQGREARVSAV 140 (153)
T ss_pred ECCCCCEEEEEEC
T ss_conf 8599847999988
No 19
>pfam11113 Phage_head_chap Head assembly gene product. This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex
Probab=51.60 E-value=19 Score=16.69 Aligned_cols=33 Identities=24% Similarity=0.136 Sum_probs=28.3
Q ss_pred CCCCCCEEEEEEEEECCCCCCCEEEEEEEEECCCCE
Q ss_conf 167752037861212143268465448999328976
Q gi|254780418|r 68 DIGKELVHVIPKDYQLDPVSDILIHADFLQVSEGST 103 (191)
Q Consensus 68 ~i~g~~~~vlikevQ~~p~~~~i~HvDF~~v~~~~~ 103 (191)
.=+|+.+.+++-+++++ +.=+++||-..+.+++
T Consensus 9 ~~dG~~hlVyi~~~~~~---dgkl~vdf~T~~e~~k 41 (56)
T pfam11113 9 LEDGEHHLVYIHKLEYD---DGKLKVDFSTPSEDEK 41 (56)
T ss_pred CCCCCEEEEEEEEEEEC---CCCEEEEEECCCCCHH
T ss_conf 58998889999998982---8958999608884146
No 20
>PRK13007 dipeptidase; Reviewed
Probab=45.31 E-value=12 Score=17.80 Aligned_cols=35 Identities=9% Similarity=0.172 Sum_probs=16.2
Q ss_pred EEEEEEEEEHHHCCCEEEECCCCC--CCCCEEEEEEE
Q ss_conf 545788880767963468322223--56977999975
Q gi|254780418|r 131 CHEVSLLCPANNIPDSITVDLNDL--KIGDSIHMEDI 165 (191)
Q Consensus 131 ~~~i~v~~~p~~IPe~ievDvs~L--~~Gd~i~v~Dl 165 (191)
.-+++++..|..=++.+.-.+..+ +.+-.+.+.+.
T Consensus 240 ~~~~d~R~~p~~~~~~v~~~l~~~~~~~~~~~~~~~~ 276 (354)
T PRK13007 240 EVNVNYRFAPDRSLEEALAHVRELFDGLDVEVEVTDL 276 (354)
T ss_pred EEEEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf 9999998699999999999999987137856999961
No 21
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=39.07 E-value=26 Score=15.78 Aligned_cols=74 Identities=11% Similarity=0.073 Sum_probs=37.5
Q ss_pred EEEEEEEECCCCCCCEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEHHHCCCEEEECCCCC
Q ss_conf 37861212143268465448999328976999963699605654432123113576545788880767963468322223
Q gi|254780418|r 75 HVIPKDYQLDPVSDILIHADFLQVSEGSTVTVHVPVRFINENKSPGIKQGGKLNVVCHEVSLLCPANNIPDSITVDLNDL 154 (191)
Q Consensus 75 ~vlikevQ~~p~~~~i~HvDF~~v~~~~~v~v~VPI~~~ge~~~~Gvk~GG~l~~~~~~i~v~~~p~~IPe~ievDvs~L 154 (191)
..++++..-. ...++|.|+||+...+.+. +.|-+.+- -..|+.-.--.+.--.++| +..|+|.++..
T Consensus 60 Ftlv~~Y~~~--~~~lyH~DlYRl~d~ee~~------~lg~~e~~--~~~gv~lIEW~e~~~~~lp---~~~l~I~i~~~ 126 (149)
T COG0802 60 FTLVEEYEEG--RLPLYHFDLYRLSDPEELD------ELGLDEYF--DGDGICLIEWPERLAELLP---DADLEITITYE 126 (149)
T ss_pred EEEEHHHCCC--CCCEEEEEEECCCCHHHHH------HCCHHHHH--CCCCEEEEECCCHHCCCCC---CCEEEEEEEEE
T ss_conf 6101211379--9877998611258867756------66988974--7784899987411215898---76289999982
Q ss_pred C-CCCEEE
Q ss_conf 5-697799
Q gi|254780418|r 155 K-IGDSIH 161 (191)
Q Consensus 155 ~-~Gd~i~ 161 (191)
. -|-.+.
T Consensus 127 ~~~~R~~~ 134 (149)
T COG0802 127 GDDGRRAE 134 (149)
T ss_pred CCCCEEEE
T ss_conf 48856999
No 22
>PRK00466 acetyl-lysine deacetylase; Validated
Probab=38.70 E-value=25 Score=15.87 Aligned_cols=32 Identities=25% Similarity=0.298 Sum_probs=22.3
Q ss_pred EEEEEEEEECCCCCHHHHHHHHCCCCCE-EEEC
Q ss_conf 6999999916876177899997899438-9967
Q gi|254780418|r 5 ECKLSAVMRDKVGKGSARLLRKNGQIPA-IIYG 36 (191)
Q Consensus 5 ~~~L~~~~R~~~gk~~~r~lR~~G~VPa-viYG 36 (191)
.+.+.+..-|+.|...++.+-+.|+-|- ++.|
T Consensus 112 ~i~~~~~~dEE~~~~G~~~l~~~~~~~d~~Ivg 144 (345)
T PRK00466 112 KVQVAALSDEEGKSKGARELVSSGKRFLYIIVG 144 (345)
T ss_pred CEEEEEEECCCCCCHHHHHHHHCCCCCCEEEEC
T ss_conf 389999917546754599999669998989984
No 23
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent.
Probab=37.55 E-value=31 Score=15.33 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=21.5
Q ss_pred CEEEEEEEE-CCCCCEECCCCCCEEEEEECC
Q ss_conf 779999753-588867836898269999448
Q gi|254780418|r 158 DSIHMEDIR-LPEKTSSMSQLNITIATIVAP 187 (191)
Q Consensus 158 d~i~v~Dl~-lpegv~~l~d~~~~vvsv~~P 187 (191)
..++.+||. -|.++++ -+||.+||++..|
T Consensus 106 ~~~~A~Di~~~~~~~Ev-vNpdl~Iatl~~~ 135 (324)
T TIGR02027 106 GVVTAGDIKAQPGGVEV-VNPDLVIATLTED 135 (324)
T ss_pred CEEEEEEEECCCCCEEE-ECCCCEEEEECCC
T ss_conf 31452200137996468-7888526674079
No 24
>pfam06434 Aconitase_2_N Aconitate hydratase 2 N-terminus. This family represents the N-terminal region of several bacterial Aconitate hydratase 2 proteins and is found in conjunction with pfam00330.
Probab=33.87 E-value=35 Score=14.96 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=25.0
Q ss_pred EEEECCCCCCCCCEEEEEEEECCCCCEECCCCCCEEEEEE
Q ss_conf 4683222235697799997535888678368982699994
Q gi|254780418|r 146 SITVDLNDLKIGDSIHMEDIRLPEKTSSMSQLNITIATIV 185 (191)
Q Consensus 146 ~ievDvs~L~~Gd~i~v~Dl~lpegv~~l~d~~~~vvsv~ 185 (191)
.|+.||++|+.||.|.+. |..-++..+..+++++-.
T Consensus 116 Pie~dv~~l~tGdvi~I~----p~~g~i~~~~g~v~~~f~ 151 (204)
T pfam06434 116 PIEADVSSLNTGDVITIY----PYEGKITKEDGEVISTFE 151 (204)
T ss_pred EEEEECCCCCCCCEEEEE----CCCCEEECCCCCEEEEEE
T ss_conf 468640316679889996----578869769997898876
No 25
>PRK08652 acetylornithine deacetylase; Provisional
Probab=33.08 E-value=27 Score=15.70 Aligned_cols=31 Identities=13% Similarity=0.176 Sum_probs=17.8
Q ss_pred EEEEEEEECCCCCHHHHHHHHCCCCCE-EEEC
Q ss_conf 999999916876177899997899438-9967
Q gi|254780418|r 6 CKLSAVMRDKVGKGSARLLRKNGQIPA-IIYG 36 (191)
Q Consensus 6 ~~L~~~~R~~~gk~~~r~lR~~G~VPa-viYG 36 (191)
+.|.....|+.|...++.+-.++.-|. .+.+
T Consensus 111 i~l~f~~dEE~g~~G~~~~~~~~~~~d~~iv~ 142 (349)
T PRK08652 111 VGIAFVSDEEKGGKGSALFAERYSTPKMAVVL 142 (349)
T ss_pred EEEEEEECCCCCCHHHHHHHHHCCCCCEEEEE
T ss_conf 89999953455866899999728888889994
No 26
>TIGR00113 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; InterPro: IPR003699 Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine. The hypermodified nucleoside is found in bacteria and eukaryotes . Queuosine is synthesized de novo exclusively in bacteria; for eukaryotes the compound is a nutrient factor. Queuosine biosynthesis protein, or S-adenosylmethionine:tRNA -ribosyltransferase-isomerase, is required for the synthesis of the queuosine precursor (oQ). ; GO: 0003824 catalytic activity, 0008616 queuosine biosynthetic process.
Probab=31.92 E-value=28 Score=15.59 Aligned_cols=64 Identities=20% Similarity=0.409 Sum_probs=44.6
Q ss_pred EEECCCCCCE-----EEEEEECHHHEEHHCCCCCEEEEEECCCCCCEEEEEEEEECCCCCCCEEEEEEEEECCC
Q ss_conf 9967898855-----69998002210011146622579961677520378612121432684654489993289
Q gi|254780418|r 33 IIYGNMSDPK-----PIALSAKDISKRLYSKNFMTTILTLDIGKELVHVIPKDYQLDPVSDILIHADFLQVSEG 101 (191)
Q Consensus 33 viYG~~~e~~-----~i~v~~~~l~k~l~~~~~~~~v~~l~i~g~~~~vlikevQ~~p~~~~i~HvDF~~v~~~ 101 (191)
.||.+..-+. .+-.++.-|.| |+..+.....++|.||=.+.. -|..+-+.++.+|-.|++|++.
T Consensus 185 TvYsk~~GavAAPTAGLHF~e~ll~k-L~~kgv~~~F~TLHVGaGTF~----pV~~~~i~dH~mH~E~~~vp~~ 253 (364)
T TIGR00113 185 TVYSKKVGAVAAPTAGLHFSEELLEK-LKAKGVEIAFVTLHVGAGTFR----PVEVENIEDHVMHAEYLEVPQE 253 (364)
T ss_pred EEEECCCCCCCCCCCCCCCCHHHHHH-HHHCCCCEEEEEEEEECCCCC----CEEECCCCCCCCCCHHEECCHH
T ss_conf 34543542000342444579889999-995798676876453054475----0244021036420000126878
No 27
>PRK13983 diaminopimelate aminotransferase; Provisional
Probab=30.85 E-value=40 Score=14.65 Aligned_cols=33 Identities=15% Similarity=0.150 Sum_probs=13.5
Q ss_pred EEEEEEEHHHCCCEEEECCCCC------CCCCEEEEEEE
Q ss_conf 5788880767963468322223------56977999975
Q gi|254780418|r 133 EVSLLCPANNIPDSITVDLNDL------KIGDSIHMEDI 165 (191)
Q Consensus 133 ~i~v~~~p~~IPe~ievDvs~L------~~Gd~i~v~Dl 165 (191)
.++++..|..=|+.+.-.+..+ +.+..+++..+
T Consensus 275 ~~d~R~~p~~~~~~v~~~i~~~~~~~~~~~~~~~~~e~~ 313 (399)
T PRK13983 275 YFDCRILPDYDLDEVLSDIEKIADEFENEYGVKIEYEIV 313 (399)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf 999985899999999999999999999870993589875
No 28
>KOG3493 consensus
Probab=30.46 E-value=21 Score=16.43 Aligned_cols=41 Identities=17% Similarity=0.306 Sum_probs=28.0
Q ss_pred EEEEEEEHH---------------HCCCEEEECCCCCCCCCEEEEEEEECCCCCEE
Q ss_conf 578888076---------------79634683222235697799997535888678
Q gi|254780418|r 133 EVSLLCPAN---------------NIPDSITVDLNDLKIGDSIHMEDIRLPEKTSS 173 (191)
Q Consensus 133 ~i~v~~~p~---------------~IPe~ievDvs~L~~Gd~i~v~Dl~lpegv~~ 173 (191)
.++|+|.|+ ..|+.|.+.--.-=+.|.|+++|.++-+|..+
T Consensus 13 KVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~l 68 (73)
T KOG3493 13 KVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNL 68 (73)
T ss_pred EEEEEECCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCE
T ss_conf 48987488665468999888751786668789876754104413566884168537
No 29
>PRK08554 peptidase; Reviewed
Probab=29.58 E-value=38 Score=14.79 Aligned_cols=30 Identities=20% Similarity=0.404 Sum_probs=16.9
Q ss_pred EEEEEEEECCCCCH----HHHHHHHCCCCCEEEE
Q ss_conf 99999991687617----7899997899438996
Q gi|254780418|r 6 CKLSAVMRDKVGKG----SARLLRKNGQIPAIIY 35 (191)
Q Consensus 6 ~~L~~~~R~~~gk~----~~r~lR~~G~VPaviY 35 (191)
+.+....=|+.|.. -+.+++..|..|..+.
T Consensus 127 i~~~~~~DEE~Gg~~~~~~~~~~~~~~~~~~~~i 160 (438)
T PRK08554 127 VIFAFTGDEEIGGAMAMHIAERLREEGKLPKYMV 160 (438)
T ss_pred EEEEEEECCCCCCCCCHHHHHHHHHCCCCCCEEE
T ss_conf 8999993465587571999999885187888899
No 30
>COG3603 Uncharacterized conserved protein [Function unknown]
Probab=29.35 E-value=34 Score=15.10 Aligned_cols=28 Identities=25% Similarity=0.593 Sum_probs=21.7
Q ss_pred CCEEEEE--EEEEEEEEEHHHCCCEEEECC
Q ss_conf 3113576--545788880767963468322
Q gi|254780418|r 124 GGKLNVV--CHEVSLLCPANNIPDSITVDL 151 (191)
Q Consensus 124 GG~l~~~--~~~i~v~~~p~~IPe~ievDv 151 (191)
+|+.... -.|+.+.|+++++|+.++++-
T Consensus 32 ~~F~sIt~t~eelsivc~~~~vp~~V~~~~ 61 (128)
T COG3603 32 PGFWSITRTPEELSIVCLADRVPDVVQIEK 61 (128)
T ss_pred CCEEEEECCCCEEEEEEECCCCCCCEEECC
T ss_conf 862788737762788850556996157548
No 31
>PRK08651 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=28.60 E-value=37 Score=14.86 Aligned_cols=19 Identities=5% Similarity=-0.041 Sum_probs=10.1
Q ss_pred EEEEEEEEEEHHHCCCEEE
Q ss_conf 6545788880767963468
Q gi|254780418|r 130 VCHEVSLLCPANNIPDSIT 148 (191)
Q Consensus 130 ~~~~i~v~~~p~~IPe~ie 148 (191)
..-+++++..|..-|+.+.
T Consensus 241 a~~~~d~R~~p~~~~~~v~ 259 (371)
T PRK08651 241 FAFSVDRRLIPEEDLEEVI 259 (371)
T ss_pred EEEEEEEECCCCCCHHHHH
T ss_conf 9999998639999999999
No 32
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 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 of 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 , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=28.54 E-value=19 Score=16.68 Aligned_cols=48 Identities=23% Similarity=0.358 Sum_probs=32.3
Q ss_pred EEEEEEECCCCCCCCC-CCEEEE--EEEEEEEEEEHHHCCCEEEECCCCCC
Q ss_conf 6369960565443212-311357--65457888807679634683222235
Q gi|254780418|r 108 VPVRFINENKSPGIKQ-GGKLNV--VCHEVSLLCPANNIPDSITVDLNDLK 155 (191)
Q Consensus 108 VPI~~~ge~~~~Gvk~-GG~l~~--~~~~i~v~~~p~~IPe~ievDvs~L~ 155 (191)
||=-++-.++-..+|+ ---... +...+|.......+|.++|+|-..|+
T Consensus 136 IPSy~v~~Gd~i~ikEk~~~~~~sni~~~~E~~~~~~~~P~~Le~d~~~~~ 186 (217)
T TIGR01017 136 IPSYQVRPGDIISIKEKSKKIPLSNIKENLELAGIQRNIPSWLEVDKDKLE 186 (217)
T ss_pred CCEEEECCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEECCCCE
T ss_conf 240670799889981032035356788876520002367863677657507
No 33
>PRK04443 acetyl-lysine deacetylase; Provisional
Probab=28.15 E-value=44 Score=14.36 Aligned_cols=26 Identities=8% Similarity=0.102 Sum_probs=12.3
Q ss_pred EEEEEEEECCCCCHHHHHHHHCCCCC
Q ss_conf 99999991687617789999789943
Q gi|254780418|r 6 CKLSAVMRDKVGKGSARLLRKNGQIP 31 (191)
Q Consensus 6 ~~L~~~~R~~~gk~~~r~lR~~G~VP 31 (191)
+.|.+..-|+.|...++.+-.+++-|
T Consensus 116 v~~~~~~dEE~g~~g~~~~~~~~~~~ 141 (352)
T PRK04443 116 VIFVGAVEEEAASSGGARLVAPRYRP 141 (352)
T ss_pred EEEEEEECCCCCCCCHHHHHHHCCCC
T ss_conf 89999832335674689998515586
No 34
>PRK08596 acetylornithine deacetylase; Validated
Probab=26.60 E-value=47 Score=14.18 Aligned_cols=24 Identities=21% Similarity=0.277 Sum_probs=10.8
Q ss_pred EEEEEEECCCCCHHHHHHHHCCCC
Q ss_conf 999999168761778999978994
Q gi|254780418|r 7 KLSAVMRDKVGKGSARLLRKNGQI 30 (191)
Q Consensus 7 ~L~~~~R~~~gk~~~r~lR~~G~V 30 (191)
.+.+..=|+.|...++.+-+.|+-
T Consensus 145 ~~~~~~dEE~g~~G~~~~~~~~~~ 168 (421)
T PRK08596 145 IFQSVIGEEVGEAGTLQCCKRGYD 168 (421)
T ss_pred EEEEEECCCCCCHHHHHHHHCCCC
T ss_conf 999993664562679999972999
No 35
>PRK13009 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=26.09 E-value=48 Score=14.12 Aligned_cols=16 Identities=25% Similarity=0.312 Sum_probs=7.6
Q ss_pred HHHHHHCCCCC-EEEEC
Q ss_conf 89999789943-89967
Q gi|254780418|r 21 ARLLRKNGQIP-AIIYG 36 (191)
Q Consensus 21 ~r~lR~~G~VP-aviYG 36 (191)
.+.++..|..| +.|.|
T Consensus 145 ~~~l~~~~~~~d~~iv~ 161 (375)
T PRK13009 145 LEWLKARGEKIDYCIVG 161 (375)
T ss_pred HHHHHHCCCCCCEEEEC
T ss_conf 88899629987889984
No 36
>COG1049 AcnB Aconitase B [Energy production and conversion]
Probab=25.59 E-value=43 Score=14.40 Aligned_cols=100 Identities=17% Similarity=0.257 Sum_probs=48.3
Q ss_pred EEEEEECCCCCCCEEE--EEEEEECCCCEEEEEEEEEEEECC-------CCCCCCCCCEEE-EEEEEEEEEEEHHHCCCE
Q ss_conf 8612121432684654--489993289769999636996056-------544321231135-765457888807679634
Q gi|254780418|r 77 IPKDYQLDPVSDILIH--ADFLQVSEGSTVTVHVPVRFINEN-------KSPGIKQGGKLN-VVCHEVSLLCPANNIPDS 146 (191)
Q Consensus 77 likevQ~~p~~~~i~H--vDF~~v~~~~~v~v~VPI~~~ge~-------~~~Gvk~GG~l~-~~~~~i~v~~~p~~IPe~ 146 (191)
.++.+|.++-++.++- =|-...-.+++--++.-+-+.|++ ..-|+-.||.+- ...++.+..+ .+ .
T Consensus 210 ~i~~i~~lk~Kg~~vayvgdvvGtGSSRkSa~NsvlW~~g~diP~VPnkr~ggivlG~~IaPIFfnT~ed~G---al--P 284 (852)
T COG1049 210 PIKQIEALKQKGHPVAYVGDVVGTGSSRKSATNSVLWHMGDDIPYVPNKRYGGIVLGGKIAPIFFNTMEDAG---AL--P 284 (852)
T ss_pred HHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEECCEECCEEEEEHHCCC---CC--C
T ss_conf 278999877549558995461125756432301032114787877875666654665712323541010057---87--5
Q ss_pred EEECCCCCCCCCEEEEEEEECCCCCEEC-CCCCCEEEEEE
Q ss_conf 6832222356977999975358886783-68982699994
Q gi|254780418|r 147 ITVDLNDLKIGDSIHMEDIRLPEKTSSM-SQLNITIATIV 185 (191)
Q Consensus 147 ievDvs~L~~Gd~i~v~Dl~lpegv~~l-~d~~~~vvsv~ 185 (191)
|++||++|+.||.|.+- |-.-++. .+..++|+.-.
T Consensus 285 I~~dv~~l~~Gdvi~i~----py~gki~~~~~ge~v~~f~ 320 (852)
T COG1049 285 IEVDVSNLEMGDVIDIY----PYEGKIRNNNTGEVVATFS 320 (852)
T ss_pred EEEEECCCCCCCEEEEE----CCCCEEECCCCCCEEEEEE
T ss_conf 37651124566458860----4677443168870777752
No 37
>cd01791 Ubl5 UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=23.91 E-value=53 Score=13.87 Aligned_cols=31 Identities=16% Similarity=0.201 Sum_probs=17.5
Q ss_pred CCCEEEECCCCCCCCCEEEEEEEECCCCCEE
Q ss_conf 9634683222235697799997535888678
Q gi|254780418|r 143 IPDSITVDLNDLKIGDSIHMEDIRLPEKTSS 173 (191)
Q Consensus 143 IPe~ievDvs~L~~Gd~i~v~Dl~lpegv~~ 173 (191)
-|+.|.+-=..--+.|.|++.|-++-.|..+
T Consensus 38 ~~~kI~Lkk~~~v~KDhitL~DYeIhdG~~l 68 (73)
T cd01791 38 RPEKIVLKKWYTIFKDHISLGDYEIHDGMNL 68 (73)
T ss_pred CHHHEEEEECCCCCCCCEEEEEEEEECCCEE
T ss_conf 8333676405620244116130566079569
No 38
>PRK13004 peptidase; Reviewed
Probab=23.52 E-value=50 Score=14.02 Aligned_cols=31 Identities=6% Similarity=0.160 Sum_probs=12.4
Q ss_pred EEEEEEECCC-CCHHHHH-HHHCCCCC-EEEECC
Q ss_conf 9999991687-6177899-99789943-899678
Q gi|254780418|r 7 KLSAVMRDKV-GKGSARL-LRKNGQIP-AIIYGN 37 (191)
Q Consensus 7 ~L~~~~R~~~-gk~~~r~-lR~~G~VP-aviYG~ 37 (191)
.+....-|+. +....+. +++.+.-| ++++|.
T Consensus 137 ~~~~~~dEE~~~g~~~~~~~~~~~~~~d~~ii~E 170 (397)
T PRK13004 137 YVTGTVQEEDCDGLAWRYIIEEDKIKPDFVVITE 170 (397)
T ss_pred EEEEEECCCCCCCHHHHHHHHHCCCCCCEEEECC
T ss_conf 9999855425676689999973799999899878
No 39
>TIGR00020 prfB peptide chain release factor 2; InterPro: IPR004374 In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a superfamily IPR000352 from INTERPRO of RF-1, RF-2, mitochondrial, RF-H, etc proteins.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=21.42 E-value=59 Score=13.56 Aligned_cols=94 Identities=14% Similarity=0.136 Sum_probs=65.5
Q ss_pred CCCCCEEEEEEECHHHEEHHCCCCCEEEEEE---CCCCCCEEEEEEEEECCCCCCCE-EEEEEEEECCCCEEEEEEEEEE
Q ss_conf 8988556999800221001114662257996---16775203786121214326846-5448999328976999963699
Q gi|254780418|r 37 NMSDPKPIALSAKDISKRLYSKNFMTTILTL---DIGKELVHVIPKDYQLDPVSDIL-IHADFLQVSEGSTVTVHVPVRF 112 (191)
Q Consensus 37 ~~~e~~~i~v~~~~l~k~l~~~~~~~~v~~l---~i~g~~~~vlikevQ~~p~~~~i-~HvDF~~v~~~~~v~v~VPI~~ 112 (191)
.|++++.|.|.-.=.==.|++..|.|+++.+ +-+++.|+-| =+|+-.|.=|.. +|||--.=+ |++.+ |
T Consensus 180 AGIKSVT~~ikG~yAYG~Lk~E~GvHRLVRISPFDa~~rRHTSF-asv~V~P~~Dd~tI~IeI~~~D----~riD~---Y 251 (373)
T TIGR00020 180 AGIKSVTILIKGEYAYGYLKSEQGVHRLVRISPFDANARRHTSF-ASVEVMPEVDDDTIDIEIKPED----VRIDT---Y 251 (373)
T ss_pred CCEEEEEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEE-EEEEECCCCCCCCCCCCCCCCC----EEEEE---E
T ss_conf 34015899985265333022687417877506666869533226-8888624035744511068875----46866---6
Q ss_pred EECCCCCCCCCCCEEEEEEEEEEEEEEHHHC
Q ss_conf 6056544321231135765457888807679
Q gi|254780418|r 113 INENKSPGIKQGGKLNVVCHEVSLLCPANNI 143 (191)
Q Consensus 113 ~ge~~~~Gvk~GG~l~~~~~~i~v~~~p~~I 143 (191)
. +.| --|-.+|..=.-|++.=.|..|
T Consensus 252 --R--aSG-AGGQhVNkTdSAVRITHiPTGi 277 (373)
T TIGR00020 252 --R--ASG-AGGQHVNKTDSAVRITHIPTGI 277 (373)
T ss_pred --E--CCC-CCCCCCCCCCCCEEEEEECCCC
T ss_conf --5--468-9897421446532654435873
No 40
>cd01576 AcnB_Swivel Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The domain structure of Aconitase B is different from other Aconitases in that he swivel domain that is found at N-terminus of B family is normally found at C-terminus for other Aconitases. In most members of the family, there is also a HEAT domain before domain 4, which is believed to play a role in protein-protein interaction.
Probab=20.89 E-value=57 Score=13.67 Aligned_cols=38 Identities=26% Similarity=0.566 Sum_probs=22.4
Q ss_pred CCCCCCEEE-EEEEEEEEEEEHHHCCCEEEECCCCCCCCCEEEE
Q ss_conf 321231135-7654578888076796346832222356977999
Q gi|254780418|r 120 GIKQGGKLN-VVCHEVSLLCPANNIPDSITVDLNDLKIGDSIHM 162 (191)
Q Consensus 120 Gvk~GG~l~-~~~~~i~v~~~p~~IPe~ievDvs~L~~Gd~i~v 162 (191)
|+-.|+.+- ....+.+..+ .|| |+.||+.|+.||.|.+
T Consensus 91 gv~~g~~IaPIFfnT~edsG---alp--ie~dv~~~~~gdvi~i 129 (131)
T cd01576 91 GVVLGGKIAPIFFNTAEDSG---ALP--IQLDVSVLDMGDILNI 129 (131)
T ss_pred EEEECCCCCCEEEECCCCCC---CEE--EEEECCCCCCCCEEEC
T ss_conf 68868817535772112257---604--7853342456887734
No 41
>PRK05464 Na(+)-translocating NADH-quinone reductase subunit F; Provisional
Probab=20.86 E-value=35 Score=14.95 Aligned_cols=36 Identities=14% Similarity=0.244 Sum_probs=19.0
Q ss_pred CCCCCCCCEEEEEEEEEEEEEEHHHCCCEEEECCCC
Q ss_conf 443212311357654578888076796346832222
Q gi|254780418|r 118 SPGIKQGGKLNVVCHEVSLLCPANNIPDSITVDLND 153 (191)
Q Consensus 118 ~~Gvk~GG~l~~~~~~i~v~~~p~~IPe~ievDvs~ 153 (191)
....|.||.+|.....-++.-.+-|||+...-|-..
T Consensus 159 ~~~fkaG~yiQi~iP~~~~~~~~~di~~~y~~dW~~ 194 (408)
T PRK05464 159 EVPFRAGGYIQIEAPPHKVKYKDFDIPEEYRGDWEK 194 (408)
T ss_pred CCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 452025877999637631464513553777888875
Done!