Query gi|254780265|ref|YP_003064678.1| 30S ribosomal protein S7 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 156
No_of_seqs 109 out of 1439
Neff 6.0
Searched_HMMs 39220
Date Tue May 24 09:25:55 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780265.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01029 rpsG_bact ribosomal 100.0 0 0 450.6 15.4 154 3-156 1-159 (159)
2 PRK05302 30S ribosomal protein 100.0 0 0 411.3 18.2 156 1-156 1-156 (156)
3 CHL00053 rps7 ribosomal protei 100.0 0 0 394.4 18.4 155 1-155 1-155 (155)
4 pfam00177 Ribosomal_S7 Ribosom 100.0 0 0 352.6 17.7 149 1-149 1-149 (149)
5 COG0049 RpsG Ribosomal protein 100.0 0 0 354.1 16.1 148 2-149 1-148 (148)
6 PTZ00091 40S ribosomal protein 100.0 2.8E-45 0 293.6 15.7 132 18-149 51-191 (191)
7 PRK04027 30S ribosomal protein 100.0 7.3E-44 0 284.5 15.7 131 19-149 56-195 (195)
8 KOG3291 consensus 100.0 1.8E-43 0 282.1 12.9 148 2-149 58-208 (208)
9 TIGR01028 S7_S5_E_A ribosomal 100.0 2.6E-36 6.7E-41 239.0 4.7 133 17-149 48-206 (206)
10 TIGR00542 hxl6Piso_put hexulos 73.1 7 0.00018 19.8 4.4 69 54-128 88-157 (290)
11 cd05133 RasGAP_IQGAP1 IQGAP1 i 56.4 17 0.00043 17.5 4.3 52 19-70 35-91 (360)
12 cd05131 RasGAP_IQGAP2 IQGAP2 i 55.9 9.4 0.00024 19.1 2.4 52 19-70 35-91 (339)
13 KOG3960 consensus 53.5 16 0.00041 17.7 3.2 35 41-75 131-171 (284)
14 TIGR01059 gyrB DNA gyrase, B s 52.2 18 0.00046 17.4 3.3 57 12-72 340-396 (818)
15 pfam04120 Iron_permease Low af 36.6 29 0.00073 16.1 2.4 36 97-133 52-87 (133)
16 TIGR02339 thermosome_arch ther 30.4 44 0.0011 15.0 4.0 32 33-64 425-460 (522)
17 cd00822 TopoII_Trans_DNA_gyras 30.1 45 0.0011 15.0 3.0 14 116-129 148-161 (172)
18 KOG1567 consensus 30.1 45 0.0011 15.0 7.4 92 11-130 89-188 (344)
19 COG3623 SgaU Putative L-xylulo 28.8 17 0.00043 17.5 0.1 56 55-111 91-147 (287)
20 pfam02607 B12-binding_2 B12 bi 28.7 37 0.00095 15.4 1.9 74 22-104 3-76 (78)
21 pfam07300 consensus 27.6 47 0.0012 14.9 2.2 35 97-132 52-86 (111)
22 pfam00204 DNA_gyraseB DNA gyra 27.5 50 0.0013 14.7 2.9 14 116-129 149-162 (173)
23 COG2861 Uncharacterized protei 26.7 34 0.00087 15.7 1.4 79 59-148 109-206 (250)
24 TIGR03188 histidine_hisI phosp 24.9 56 0.0014 14.4 5.4 42 26-67 20-61 (84)
25 PRK13489 chemoreceptor glutami 23.8 46 0.0012 14.9 1.6 20 17-36 80-99 (237)
26 COG2117 Predicted subunit of t 23.4 54 0.0014 14.5 1.9 98 39-138 60-162 (198)
27 TIGR02876 spore_yqfD sporulati 22.7 44 0.0011 15.0 1.3 15 20-34 15-29 (406)
No 1
>TIGR01029 rpsG_bact ribosomal protein S7; InterPro: IPR005717 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 , . This model describes the bacterial and organellar branch of the ribosomal protein S7 family (includes prokaroytic S7 and eukaryotic S5).; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=450.57 Aligned_cols=154 Identities=55% Similarity=0.950 Sum_probs=153.2
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHCCCCEEEEEEEEC
Q ss_conf 989997555799974378799999999976695999999999999866742488-6389999999842754047787524
Q gi|254780265|r 3 RRRRAVVREVLPDPKFSDFVVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKK-DPVALFRQALINVTPQFEVRTRRVG 81 (156)
Q Consensus 3 Rr~~~~kr~~~pD~~y~~~lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~-npi~il~~Ai~n~~P~~evk~~r~g 81 (156)
||+.+.+|.++|||+|+|.||++|||.||+||||++|++|||+||+.|+++|++ ||+++|++||+||+|.+||+++|+|
T Consensus 1 Rk~~a~kR~~~~Dp~Y~~~Lv~kfin~~M~~GKKs~A~~IvY~al~~i~~k~~~~~pl~vf~~AlenVkP~~EVk~RRVG 80 (159)
T TIGR01029 1 RKRRAEKRKILPDPVYGSVLVAKFINRVMKDGKKSLAESIVYKALERIAKKTGEEDPLEVFEKALENVKPLLEVKSRRVG 80 (159)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEEEEEEEEC
T ss_conf 98987763179885124789999998731148630467899999999998718841688999998627872467645654
Q ss_pred CCCEECEEECCHHHHHHHHHHHHHHHHHHC----CCCCHHHHHHHHHHHHHCCCCCCEECHHHHHHHHHHHHHHHCCCC
Q ss_conf 630000010485799999999999999857----999989999999999973888726307889999999888532569
Q gi|254780265|r 82 GAAYSVPGEITSKRSQALAIRWLIMAARKR----NETTMIDRLGGEIIDAANNRGVAVRKREETHKVAEANRAFSHYRW 156 (156)
Q Consensus 82 G~~yqvP~~i~~~r~~~lAirWii~~a~~r----~~~~~~~~La~Eii~A~~~~g~aikkK~elhk~A~aNRa~ah~Rw 156 (156)
|+|||||++|.+.||..|||||||++|++| ++++|.++||+||+||++++|.|||||||+|||||||||||||||
T Consensus 81 GaTYQVP~EV~~~R~~aLA~RWi~~aArkR~~G~~~~~M~~~La~El~dA~~~~G~A~KKkEDtHrMAEANkAFaHyRW 159 (159)
T TIGR01029 81 GATYQVPVEVREERREALAIRWIVEAARKRRMGKSGKTMAERLANELLDAANNTGAAIKKKEDTHRMAEANKAFAHYRW 159 (159)
T ss_pred CCCCCCCEEECCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHCCCC
T ss_conf 8665022255761336679999999874236888997888899999999970588525403444208887446422699
No 2
>PRK05302 30S ribosomal protein S7; Validated
Probab=100.00 E-value=0 Score=411.33 Aligned_cols=156 Identities=62% Similarity=1.032 Sum_probs=155.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEE
Q ss_conf 98989997555799974378799999999976695999999999999866742488638999999984275404778752
Q gi|254780265|r 1 MSRRRRAVVREVLPDPKFSDFVVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRV 80 (156)
Q Consensus 1 m~Rr~~~~kr~~~pD~~y~~~lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~ 80 (156)
||||++++||.++|||+|+|++|++|||+||++|||++|++|+|+||++|+++|++||++||++||+|++|.+||+++|+
T Consensus 1 msrr~~~~kr~~~~dp~y~~~lv~kfiN~lMk~GKK~~A~kiv~~al~~I~~~t~~nPi~vl~~AI~Nv~P~~ev~s~r~ 80 (156)
T PRK05302 1 MPRRRRAPKREILPDPKYGSVLVAKFINKLMLDGKKSVAEKIVYGALDIIEEKTGKDPLEVFEKALENVKPVVEVKSRRV 80 (156)
T ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHEEEEEE
T ss_conf 98999998887999966587899999999885446999999999999999986537839999999996797531365650
Q ss_pred CCCCEECEEECCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEECHHHHHHHHHHHHHHHCCCC
Q ss_conf 4630000010485799999999999999857999989999999999973888726307889999999888532569
Q gi|254780265|r 81 GGAAYSVPGEITSKRSQALAIRWLIMAARKRNETTMIDRLGGEIIDAANNRGVAVRKREETHKVAEANRAFSHYRW 156 (156)
Q Consensus 81 gG~~yqvP~~i~~~r~~~lAirWii~~a~~r~~~~~~~~La~Eii~A~~~~g~aikkK~elhk~A~aNRa~ah~Rw 156 (156)
||++||||+||++.||++||||||+++|++|++++|+++||+||++|++|+|.|++||||+||||+||||||||||
T Consensus 81 GG~~yqVPv~i~~~Rr~~lAirWii~aar~r~~k~~~~~La~Eii~A~~~~g~aikKK~e~hK~AeaNRa~ah~rw 156 (156)
T PRK05302 81 GGATYQVPVEVRPERRQALAMRWLVEAARKRGEKTMAERLANELLDAANNRGAAVKKREDTHRMAEANKAFAHYRW 156 (156)
T ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 8655870576777799999999999999866999889999999999996678512138999999999776630068
No 3
>CHL00053 rps7 ribosomal protein S7
Probab=100.00 E-value=0 Score=394.36 Aligned_cols=155 Identities=50% Similarity=0.789 Sum_probs=154.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEE
Q ss_conf 98989997555799974378799999999976695999999999999866742488638999999984275404778752
Q gi|254780265|r 1 MSRRRRAVVREVLPDPKFSDFVVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRV 80 (156)
Q Consensus 1 m~Rr~~~~kr~~~pD~~y~~~lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~ 80 (156)
||||+.++||.++|||+|+|++|++|||+||++|||++|++|||+||++|+++|++||++||++||+|++|.+||+++|+
T Consensus 1 m~rr~~~~kr~~~~d~~y~~~lv~kfin~lM~~GKK~~A~~Iv~~al~~I~~~t~~~Pi~vl~~Ai~N~~P~vevks~rv 80 (155)
T CHL00053 1 MSRRGTAKKRTAKSDPIYRNRLVNMLVNRILKHGKKSLAYRIVYRALKKIQQKTETNPLSVLRQAIRNVTPDVEVKARRV 80 (155)
T ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCEEEEEEC
T ss_conf 98999998787999977587999999999984450999999999999999988079878999999997598504676521
Q ss_pred CCCCEECEEECCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEECHHHHHHHHHHHHHHHCCC
Q ss_conf 463000001048579999999999999985799998999999999997388872630788999999988853256
Q gi|254780265|r 81 GGAAYSVPGEITSKRSQALAIRWLIMAARKRNETTMIDRLGGEIIDAANNRGVAVRKREETHKVAEANRAFSHYR 155 (156)
Q Consensus 81 gG~~yqvP~~i~~~r~~~lAirWii~~a~~r~~~~~~~~La~Eii~A~~~~g~aikkK~elhk~A~aNRa~ah~R 155 (156)
||++||||+||++.|+++||||||+++|++|++++|+++||+||+||++|+|.|++||||+||||+|||||||||
T Consensus 81 GG~~yqVPv~v~~~Rr~~lAirWii~aar~r~~k~~~~~La~Eii~A~~~~g~avkKk~e~hk~AeaNRafah~R 155 (155)
T CHL00053 81 GGSTYQVPIEIGSTRGKALAIRWLLKASRKRSGRNMAFKLSSELVDAAKGSGNAIRKKEETHRMAEANRAFAHFR 155 (155)
T ss_pred CCEEEEEEEEECHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 873688500007879999999999999986589988999999999999677833347889999999866141479
No 4
>pfam00177 Ribosomal_S7 Ribosomal protein S7p/S5e. This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.
Probab=100.00 E-value=0 Score=352.62 Aligned_cols=149 Identities=55% Similarity=0.894 Sum_probs=147.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEE
Q ss_conf 98989997555799974378799999999976695999999999999866742488638999999984275404778752
Q gi|254780265|r 1 MSRRRRAVVREVLPDPKFSDFVVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRV 80 (156)
Q Consensus 1 m~Rr~~~~kr~~~pD~~y~~~lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~ 80 (156)
|||++++.++.+.|||+|+|++|++|||+||++|||++|++|+|+||++|++++++||+++|++||+|++|.+||+++|+
T Consensus 1 M~r~~~~~kr~~~~d~~~~~~lv~k~iN~lM~~GKK~~A~kiv~~al~~I~~~~~~~Pi~vl~~Ai~n~~P~~ev~s~r~ 80 (149)
T pfam00177 1 MPRRGRAKKREVLPDPKYNSRLVEKLINKLMKDGKKSLAEKIVYKAFEIIEEKTGKNPLEVLVQAIENVKPRVEVKSRRV 80 (149)
T ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCEEEEECC
T ss_conf 98999998887899977688899999999885143999999999999999985569879999999997699502576203
Q ss_pred CCCCEECEEECCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEECHHHHHHHHHHHH
Q ss_conf 463000001048579999999999999985799998999999999997388872630788999999988
Q gi|254780265|r 81 GGAAYSVPGEITSKRSQALAIRWLIMAARKRNETTMIDRLGGEIIDAANNRGVAVRKREETHKVAEANR 149 (156)
Q Consensus 81 gG~~yqvP~~i~~~r~~~lAirWii~~a~~r~~~~~~~~La~Eii~A~~~~g~aikkK~elhk~A~aNR 149 (156)
||++||||+||++.|+++||||||+++|++|++++|+++||+||++|++|+|.|++||+|+||+|+|||
T Consensus 81 GG~~yqvPv~v~~~r~~~lAirWii~~ar~r~~~~~~~~La~Eii~A~~~~g~aikKk~e~hk~A~aNR 149 (149)
T pfam00177 81 GGATYQVPVEVSPERRVALAIRWILKAARKRSGKSMAEKLANELIDAANNKGSAIKKKEETHKMAEANR 149 (149)
T ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCEEEEHHHHHHHHHHCC
T ss_conf 877788555378889999999999999987599988999999999999689975540899999998568
No 5
>COG0049 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=354.11 Aligned_cols=148 Identities=55% Similarity=0.927 Sum_probs=146.6
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEEC
Q ss_conf 89899975557999743787999999999766959999999999998667424886389999999842754047787524
Q gi|254780265|r 2 SRRRRAVVREVLPDPKFSDFVVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRVG 81 (156)
Q Consensus 2 ~Rr~~~~kr~~~pD~~y~~~lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~g 81 (156)
+|++++.++..+|||+|+|.+|++|||.||++|||++|++|||.||++|+++|++||+++|++||+|++|.+||+++++|
T Consensus 1 ~r~~~~~kr~~~~dpk~~~~iv~rliN~iM~~GKK~~A~~Ivy~A~~ii~~kTg~~Piqvf~~Ai~N~~P~~Ev~srrvG 80 (148)
T COG0049 1 PRRHTAGKREVLPDPKYNSVIVERLINKIMRDGKKSLAEKIVYGAFDIIEKKTGQNPLQVFEKAIENVKPREEVKSRRVG 80 (148)
T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHEEEEEC
T ss_conf 99987775567898641249999999999980538999999999999999997898699999999843866540345667
Q ss_pred CCCEECEEECCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEECHHHHHHHHHHHH
Q ss_conf 63000001048579999999999999985799998999999999997388872630788999999988
Q gi|254780265|r 82 GAAYSVPGEITSKRSQALAIRWLIMAARKRNETTMIDRLGGEIIDAANNRGVAVRKREETHKVAEANR 149 (156)
Q Consensus 82 G~~yqvP~~i~~~r~~~lAirWii~~a~~r~~~~~~~~La~Eii~A~~~~g~aikkK~elhk~A~aNR 149 (156)
|++||||++++|.||++||||||+++|+++++++|+++||+||+||++|.|.||+||||+||||+|||
T Consensus 81 Ga~yqvpVeV~p~RR~~lAlrwi~~~Ar~r~~ktm~erLA~Eli~Aan~~g~AikKked~hRmAeAnr 148 (148)
T COG0049 81 GATYQVPVEVRPRRRVALALRWIVEGARKRNEKTMAERLANELIDAANNTGAAIKKKEDTHRMAEANR 148 (148)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC
T ss_conf 71157467367889999999999999986598879999999999987088612233898999998539
No 6
>PTZ00091 40S ribosomal protein S5; Provisional
Probab=100.00 E-value=2.8e-45 Score=293.63 Aligned_cols=132 Identities=30% Similarity=0.429 Sum_probs=127.5
Q ss_pred CCCHHHHHHHHHHHHC----CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEECCCCEECEEECCH
Q ss_conf 3787999999999766----959999999999998667424886389999999842754047787524630000010485
Q gi|254780265|r 18 FSDFVVAKFMNAIMYG----GKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRVGGAAYSVPGEITS 93 (156)
Q Consensus 18 y~~~lv~kliN~lMk~----GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~gG~~yqvP~~i~~ 93 (156)
-+.++|++|||.||.+ |||++|++|||+||++|+++|++||++||++||+|++|.+|++++++||++||+|++++|
T Consensus 51 ~~~~IVERlin~lM~~g~n~GKK~~A~~Iv~~AfdiI~~kT~~nPlqV~~~Ai~N~~PreEv~~~r~GG~~yqv~VdVsp 130 (191)
T PTZ00091 51 AQCPIVERLANSLMFHGRNNGKKLKAVRIVRHAFEIIHLLTDKNPLQVLVDAVQKGGPREDSTRVGSGGVVRRQAVDVSP 130 (191)
T ss_pred CCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCEEEEEEEECCEEEEECEECCH
T ss_conf 56852499888876058777709999999999999999985898499999999841871689999737776783435363
Q ss_pred HHHHHHHHHHHHHHHHH---CCCCCHHHHHHHHHHHHHCCCCC--CEECHHHHHHHHHHHH
Q ss_conf 79999999999999985---79999899999999999738887--2630788999999988
Q gi|254780265|r 94 KRSQALAIRWLIMAARK---RNETTMIDRLGGEIIDAANNRGV--AVRKREETHKVAEANR 149 (156)
Q Consensus 94 ~r~~~lAirWii~~a~~---r~~~~~~~~La~Eii~A~~~~g~--aikkK~elhk~A~aNR 149 (156)
.||++||||||++++++ |++++|+++||+||++|++|.|. ||+||||+||||+|||
T Consensus 131 ~Rrv~lAlrwi~~gar~~afr~~ksm~e~LA~Eli~Aa~~~~~s~AIkKKee~eRmAeanR 191 (191)
T PTZ00091 131 MRRVNEAIYLLCKGAREAAFRNLKTIAECLADEIINASKGSSNSYAIKKKDEVERVAKANR 191 (191)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCEECHHHHHHHHHHCC
T ss_conf 7899999999999999870159883999999999999728888754230788999887548
No 7
>PRK04027 30S ribosomal protein S7P; Reviewed
Probab=100.00 E-value=7.3e-44 Score=284.52 Aligned_cols=131 Identities=37% Similarity=0.591 Sum_probs=126.9
Q ss_pred CCHHHHHHHHHHHHC----CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEECCCCEECEEECCHH
Q ss_conf 787999999999766----9599999999999986674248863899999998427540477875246300000104857
Q gi|254780265|r 19 SDFVVAKFMNAIMYG----GKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRVGGAAYSVPGEITSK 94 (156)
Q Consensus 19 ~~~lv~kliN~lMk~----GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~gG~~yqvP~~i~~~ 94 (156)
+.++|++|||.||++ |||++|++||++||++|+++|++||++||++||+|++|.+|++++++||++||+|++++|.
T Consensus 56 ~~~IVERlin~lM~~grntGKK~~A~kIV~~AfdiI~~kT~~NPiqVlv~Ai~N~~PreEvt~i~~GG~~y~~~Vdvsp~ 135 (195)
T PRK04027 56 EVPIVERLINKLMRTGRNTGKKQKAYNIVKEAFDIIEKRTKQNPIQVLVDAIENAAPREETTRIKYGGIAYPVAVDVSPQ 135 (195)
T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCEEEEEEEECCEEEEEEEECCCH
T ss_conf 57419999888863265543599999999999999999867996999999998358702468988888888741204714
Q ss_pred HHHHHHHHHHHHHHHH---CCCCCHHHHHHHHHHHHHCC--CCCCEECHHHHHHHHHHHH
Q ss_conf 9999999999999985---79999899999999999738--8872630788999999988
Q gi|254780265|r 95 RSQALAIRWLIMAARK---RNETTMIDRLGGEIIDAANN--RGVAVRKREETHKVAEANR 149 (156)
Q Consensus 95 r~~~lAirWii~~a~~---r~~~~~~~~La~Eii~A~~~--~g~aikkK~elhk~A~aNR 149 (156)
||+++|||||++++++ |++++|+++||+||++|++| .|.||+||||+||||+|||
T Consensus 136 Rrv~lAlr~i~~gar~~afr~~ksm~e~LA~Eli~Aa~~~~~syAIkKKeE~eR~A~a~R 195 (195)
T PRK04027 136 RRVDLALRNIAEGARQASFKNKKSIAECLADEIIAAANNDPKSYAVRKKEEIERVAKSAR 195 (195)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCEECHHHHHHHHHHCC
T ss_conf 789999999999999872169774999999999999718987752010788998887558
No 8
>KOG3291 consensus
Probab=100.00 E-value=1.8e-43 Score=282.11 Aligned_cols=148 Identities=34% Similarity=0.515 Sum_probs=141.6
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEEC
Q ss_conf 89899975557999743787999999999766959999999999998667424886389999999842754047787524
Q gi|254780265|r 2 SRRRRAVVREVLPDPKFSDFVVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRVG 81 (156)
Q Consensus 2 ~Rr~~~~kr~~~pD~~y~~~lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~g 81 (156)
+....+++++.+.++.|.|.++++|+|++|++|||.+|++||+.||++|+..|++||++||++||+|++|+++++.+.+|
T Consensus 58 ~~~~~~~~~~~ka~~~~~e~l~~~l~n~~~~~GKK~~a~~Iv~~aleiI~~~t~~NPiqvl~~AI~n~~P~~~~~~i~r~ 137 (208)
T KOG3291 58 SAGRYAKKRFRKAQCPIVERLINKLMNHIMKNGKKLLARRIVKHALEIIKRLTERNPIQVLVQAIENCGPLEDVTRIGRA 137 (208)
T ss_pred CCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHCEEECCC
T ss_conf 41000023332111418889999999998714607999999999999999971478899999999814854540010346
Q ss_pred CCCEECEEECCHHHHHHHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHCCCCCCEECHHHHHHHHHHHH
Q ss_conf 63000001048579999999999999985799---998999999999997388872630788999999988
Q gi|254780265|r 82 GAAYSVPGEITSKRSQALAIRWLIMAARKRNE---TTMIDRLGGEIIDAANNRGVAVRKREETHKVAEANR 149 (156)
Q Consensus 82 G~~yqvP~~i~~~r~~~lAirWii~~a~~r~~---~~~~~~La~Eii~A~~~~g~aikkK~elhk~A~aNR 149 (156)
|++||||+||++.||.++||+||+++|++++. ++|++||++||++|++|+|+|++||||+|++|++||
T Consensus 138 g~~~~vpv~v~~~rr~~~Ai~wi~~~ar~~~~~~~~~~ae~La~ELi~Aakgs~~aikKKdeLhr~a~sNR 208 (208)
T KOG3291 138 GTTYQVPVPVSPLRRVNLAIKWILTGARERSFRNIKTLAECLADELIAAAKGSGNAIKKKDELHRMAEANR 208 (208)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC
T ss_conf 43787035678089999999999999986112342519999999999997077405454899998886149
No 9
>TIGR01028 S7_S5_E_A ribosomal protein S7; InterPro: IPR005716 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 , . This family describes the members from the eukaryotic cytosol and the Archaea of the family that includes ribosomal protein S7 of bacteria and S5 of eukaryotes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=2.6e-36 Score=239.03 Aligned_cols=133 Identities=32% Similarity=0.524 Sum_probs=127.0
Q ss_pred CCCCHHHHHHHHHHHH--------------------CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf 4378799999999976--------------------69599999999999986674248863899999998427540477
Q gi|254780265|r 17 KFSDFVVAKFMNAIMY--------------------GGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVR 76 (156)
Q Consensus 17 ~y~~~lv~kliN~lMk--------------------~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk 76 (156)
+-+.++||+|||.+|+ +|||.+|.+||..||++|+.+|++||||||++||+|.+|..+++
T Consensus 48 Ka~~~IVERLiNkvMr~gg~hykvaghf~Rre~n~l~GKK~~A~~IVk~AFeII~~~T~~NPiQVLV~AI~NagPREdtt 127 (206)
T TIGR01028 48 KAKVPIVERLINKVMRKGGSHYKVAGHFMRRERNSLNGKKLKAYKIVKEAFEIIEKRTKKNPIQVLVDAIENAGPREDTT 127 (206)
T ss_pred CCCCCEEEECCHHHHCCCCCCEEEHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCE
T ss_conf 47421676410024216886100011212023324540268899999999999875508996489845231588975403
Q ss_pred EEEECCCCEECEEECCHHHHHHHHHHHHHHHHHH---CCCCCHHHHHHHHHHHHHCCC---CCCEECHHHHHHHHHHHH
Q ss_conf 8752463000001048579999999999999985---799998999999999997388---872630788999999988
Q gi|254780265|r 77 TRRVGGAAYSVPGEITSKRSQALAIRWLIMAARK---RNETTMIDRLGGEIIDAANNR---GVAVRKREETHKVAEANR 149 (156)
Q Consensus 77 ~~r~gG~~yqvP~~i~~~r~~~lAirWii~~a~~---r~~~~~~~~La~Eii~A~~~~---g~aikkK~elhk~A~aNR 149 (156)
++..||..|++.|++||.||+++||+.|..+|+. |+.+++++|||+|||.|+++. |.||+||||++|.|.+||
T Consensus 128 Ri~~GGi~~~~AVD~Sp~RRvd~Al~~ia~GA~~AAfk~kksIae~LA~Eii~AA~~~~~~SyA~~KK~E~ERvA~SaR 206 (206)
T TIGR01028 128 RIKYGGIAYRQAVDVSPLRRVDVALRNIALGAREAAFKNKKSIAECLAEEIIAAAKGDMSKSYAIKKKEELERVAKSAR 206 (206)
T ss_pred EECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCCHHHCCCCC
T ss_conf 7526750321125307424799999999999999973078878888799999997103454300113521000101479
No 10
>TIGR00542 hxl6Piso_put hexulose-6-phosphate isomerase, putative; InterPro: IPR004560 This family shows similarity to other isomerases. Putative identification as hexulose-6-phosphate isomerase has been reported. This family is conserved at better than 40 0dentity among the four known examples from three species: Escherichia coli (SgbU and SgaU), Haemophilus influenzae, and Mycoplasma pneumoniae. The rarity of the family, high level of conservation, and proposed catabolic role suggests lateral transfer may be a part of the evolutionary history of this protein.; GO: 0016861 intramolecular oxidoreductase activity interconverting aldoses and ketoses, 0005975 carbohydrate metabolic process.
Probab=73.10 E-value=7 Score=19.84 Aligned_cols=69 Identities=16% Similarity=0.228 Sum_probs=59.5
Q ss_pred CCCCHHHHHHHHHHHCCCCEEEEEEEECCC-CEECEEECCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 488638999999984275404778752463-000001048579999999999999985799998999999999997
Q gi|254780265|r 54 EKKDPVALFRQALINVTPQFEVRTRRVGGA-AYSVPGEITSKRSQALAIRWLIMAARKRNETTMIDRLGGEIIDAA 128 (156)
Q Consensus 54 ~~~npi~il~~Ai~n~~P~~evk~~r~gG~-~yqvP~~i~~~r~~~lAirWii~~a~~r~~~~~~~~La~Eii~A~ 128 (156)
+.+..++|+.+||.= +-.+++|.+-..|= +|.-|-+-.-.|+..-+|+|-++-|.+ ....||-||||..
T Consensus 88 ~r~~~~eIm~KAi~L-a~~lGIR~IQLAgYDVYYe~~d~eT~~~F~~gl~~~velA~~-----~qVtlA~EiMDtp 157 (290)
T TIGR00542 88 VRQQGLEIMEKAIQL-ARDLGIRIIQLAGYDVYYEEHDEETRRRFIEGLKKAVELAAK-----AQVTLAVEIMDTP 157 (290)
T ss_pred HHHHHHHHHHHHHHH-HHHCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHH
T ss_conf 999999999999999-975796066223330033557604589999889999999987-----5465346664133
No 11
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=56.44 E-value=17 Score=17.52 Aligned_cols=52 Identities=17% Similarity=0.235 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHCCHHHH-----HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 78799999999976695999-----99999999986674248863899999998427
Q gi|254780265|r 19 SDFVVAKFMNAIMYGGKKSV-----AVSIVYGAFDLVEKKEKKDPVALFRQALINVT 70 (156)
Q Consensus 19 ~~~lv~kliN~lMk~GKK~~-----A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~ 70 (156)
.++.+.+++-.-.++|.-.. -..++.+.++.-....+.||++|+...|.+.-
T Consensus 35 ~N~~~~km~~~y~R~~~g~~~Lk~iL~~~V~~Ii~d~~LdlE~dP~~IY~~~in~~E 91 (360)
T cd05133 35 GNPTVIKMVVSFNRGARGQNALRQILAPVVKEIMDDKSLNIKTDPVDIYKSWVNQME 91 (360)
T ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 580999999998548753599999999999998448667740788999999998888
No 12
>cd05131 RasGAP_IQGAP2 IQGAP2 is a member of the IQGAP family that contains a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeat, a single WW domain, four IQ motifs which mediate interactions with calmodulin, and a Ras-GTPase-activating protein (GAP)-related domain that binds Rho family GTPases. IQGAP2 and IQGAP3 play important roles in the regulation of the cytoskeleton for axon outgrowth in hippocampal neurons and are thought to stay in a common regulatory pathway. The results of RNA interference studies indicated that IQGAP3 partially compensates functions of IQGAP2, but has lesser ability than IQGAP2 to promote axon outgrowth in hippocampal neuron. Morevover, IQGAP2 is required for the cadherin-mediated cell-to-cell adhesion in Xenopus laevis embryos.
Probab=55.88 E-value=9.4 Score=19.07 Aligned_cols=52 Identities=12% Similarity=0.174 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHCCHHHHH-----HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 787999999999766959999-----9999999986674248863899999998427
Q gi|254780265|r 19 SDFVVAKFMNAIMYGGKKSVA-----VSIVYGAFDLVEKKEKKDPVALFRQALINVT 70 (156)
Q Consensus 19 ~~~lv~kliN~lMk~GKK~~A-----~kIv~~al~~I~~~~~~npi~il~~Ai~n~~ 70 (156)
.++.+.+++-.-.++|.-... ..++.+.++.-....+.||++|+...|.+.-
T Consensus 35 ~N~~~~km~~~y~R~~~g~~yLk~iL~~~V~~Ii~d~~Ldle~dP~~IY~~~in~~E 91 (339)
T cd05131 35 GNPTVIKMVVSFNRGARGQNTLRQLLAPVVKEIIEDKSLIINTNPVEVYKAWVNQLE 91 (339)
T ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 482899999999648732699999999999998658767730788999999999888
No 13
>KOG3960 consensus
Probab=53.51 E-value=16 Score=17.68 Aligned_cols=35 Identities=20% Similarity=0.406 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHCCCCH------HHHHHHHHHHCCCCEEE
Q ss_conf 999999986674248863------89999999842754047
Q gi|254780265|r 41 SIVYGAFDLVEKKEKKDP------VALFRQALINVTPQFEV 75 (156)
Q Consensus 41 kIv~~al~~I~~~~~~np------i~il~~Ai~n~~P~~ev 75 (156)
+=|+.||+.++..|-.|| ++||..||+-+--+..+
T Consensus 131 kKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~L 171 (284)
T KOG3960 131 KKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQAL 171 (284)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 99999999998623799434550899999999999999999
No 14
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=52.19 E-value=18 Score=17.38 Aligned_cols=57 Identities=21% Similarity=0.347 Sum_probs=35.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 7999743787999999999766959999999999998667424886389999999842754
Q gi|254780265|r 12 VLPDPKFSDFVVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQ 72 (156)
Q Consensus 12 ~~pD~~y~~~lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~ 72 (156)
-.|||.|...+=.||.|.= =|+..+.++++.|...-+.-+...-.|+.+||.-+.=.
T Consensus 340 KvP~PqFEGQTK~KLGNsE----Vr~~V~~~v~e~l~~f~eeNP~~Ak~Iv~K~~~AA~AR 396 (818)
T TIGR01059 340 KVPDPQFEGQTKTKLGNSE----VRSIVESLVYEKLTEFFEENPTEAKAIVEKAIEAARAR 396 (818)
T ss_pred ECCCCCCCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 1487897883223464641----67778888799999997529068999999999999998
No 15
>pfam04120 Iron_permease Low affinity iron permease.
Probab=36.60 E-value=29 Score=16.15 Aligned_cols=36 Identities=25% Similarity=0.413 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf 9999999999998579999899999999999738887
Q gi|254780265|r 97 QALAIRWLIMAARKRNETTMIDRLGGEIIDAANNRGV 133 (156)
Q Consensus 97 ~~lAirWii~~a~~r~~~~~~~~La~Eii~A~~~~g~ 133 (156)
+..-|=.|++.+.+|-+.-+..|| +||+.|.++-.+
T Consensus 52 ITFLMVfLIQ~tqnrD~~Al~~KL-dELi~a~~~A~n 87 (133)
T pfam04120 52 ITFLMVFLIQNTQNRDDAALQLKL-DELIRATNNAKN 87 (133)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHH-HHHHHHHHHCCC
T ss_conf 999999999735551178899999-999998774006
No 16
>TIGR02339 thermosome_arch thermosome, various subunits, archaeal; InterPro: IPR012714 Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacteria), a toroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=30.42 E-value=44 Score=15.01 Aligned_cols=32 Identities=19% Similarity=0.457 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHHHHHH----HHHCCCCHHHHHHH
Q ss_conf 695999999999999866----74248863899999
Q gi|254780265|r 33 GGKKSVAVSIVYGAFDLV----EKKEKKDPVALFRQ 64 (156)
Q Consensus 33 ~GKK~~A~kIv~~al~~I----~~~~~~npi~il~~ 64 (156)
.||..+|-.=|-+||+.| .+..+.|||..|.+
T Consensus 425 ~GrEQLA~eaFAdALE~iP~~LAENAGlDPID~Lv~ 460 (522)
T TIGR02339 425 GGREQLAIEAFADALEEIPRILAENAGLDPIDALVE 460 (522)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 870368889999998889999986338688899999
No 17
>cd00822 TopoII_Trans_DNA_gyrase TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a
Probab=30.13 E-value=45 Score=14.98 Aligned_cols=14 Identities=21% Similarity=0.098 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHC
Q ss_conf 89999999999973
Q gi|254780265|r 116 MIDRLGGEIIDAAN 129 (156)
Q Consensus 116 ~~~~La~Eii~A~~ 129 (156)
.+..+.+.++.+.+
T Consensus 148 ~a~~Ii~k~i~~a~ 161 (172)
T cd00822 148 EAKKILEKAILAAK 161 (172)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999999999
No 18
>KOG1567 consensus
Probab=30.07 E-value=45 Score=14.97 Aligned_cols=92 Identities=18% Similarity=0.327 Sum_probs=59.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHCCCCHH--HHHHHHHHHCCCCEEEEEEEECC
Q ss_conf 57999743787999999999766------95999999999999866742488638--99999998427540477875246
Q gi|254780265|r 11 EVLPDPKFSDFVVAKFMNAIMYG------GKKSVAVSIVYGAFDLVEKKEKKDPV--ALFRQALINVTPQFEVRTRRVGG 82 (156)
Q Consensus 11 ~~~pD~~y~~~lv~kliN~lMk~------GKK~~A~kIv~~al~~I~~~~~~npi--~il~~Ai~n~~P~~evk~~r~gG 82 (156)
+...|-++|-.++++|-+-+-.. |=-..-++|-......+=..+-+||- ..|..||+++ |.+
T Consensus 89 faasdGivnenl~Erfs~evqv~ear~fygfqIaiENIHSEmYSlLidtyIrD~ker~~LFnAI~t~-p~v--------- 158 (344)
T KOG1567 89 FAASDGIVNENLVERFSQEVQVPEARCFYGFQIAIENIHSEMYSLLIDTYIRDPKEREFLFNAIETI-PEV--------- 158 (344)
T ss_pred HHCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH-HHH---------
T ss_conf 8436650438999988888615110000224779988789999999999856906665799998723-777---------
Q ss_pred CCEECEEECCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
Q ss_conf 300000104857999999999999998579999899999999999738
Q gi|254780265|r 83 AAYSVPGEITSKRSQALAIRWLIMAARKRNETTMIDRLGGEIIDAANN 130 (156)
Q Consensus 83 ~~yqvP~~i~~~r~~~lAirWii~~a~~r~~~~~~~~La~Eii~A~~~ 130 (156)
...-..|+|||-+ +..+++++|+. .+|.+|
T Consensus 159 -----------k~KAdWalrWI~d-----~~s~faeRlvA--FAavEG 188 (344)
T KOG1567 159 -----------KKKADWALRWISD-----KDSLFAERLVA--FAAVEG 188 (344)
T ss_pred -----------HHHHHHHHHHHCC-----CCCCHHHHHHH--HHHHHH
T ss_conf -----------7777999988527-----87509999999--998741
No 19
>COG3623 SgaU Putative L-xylulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=28.81 E-value=17 Score=17.51 Aligned_cols=56 Identities=13% Similarity=0.347 Sum_probs=44.3
Q ss_pred CCCHHHHHHHHHHHCCCCEEEEEEEECCC-CEECEEECCHHHHHHHHHHHHHHHHHHC
Q ss_conf 88638999999984275404778752463-0000010485799999999999999857
Q gi|254780265|r 55 KKDPVALFRQALINVTPQFEVRTRRVGGA-AYSVPGEITSKRSQALAIRWLIMAARKR 111 (156)
Q Consensus 55 ~~npi~il~~Ai~n~~P~~evk~~r~gG~-~yqvP~~i~~~r~~~lAirWii~~a~~r 111 (156)
.+..++|+.+||.-+ -.+++|++-..|- +|.-|-.-...+|.--+|+|-++-|.+-
T Consensus 91 r~~aleiM~KaI~LA-~dLGIRtIQLAGYDVYYE~~d~eT~~rFi~g~~~a~~lA~~a 147 (287)
T COG3623 91 RQQALEIMEKAIQLA-QDLGIRTIQLAGYDVYYEEADEETRQRFIEGLKWAVELAARA 147 (287)
T ss_pred HHHHHHHHHHHHHHH-HHHCCEEEEECCCEEEECCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999-970842676324234414688789999999899999999861
No 20
>pfam02607 B12-binding_2 B12 binding domain. This B12 binding domain is found in methionine synthase EC:2.1.1.13, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of pfam02310. The structure of this domain is known, it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.
Probab=28.68 E-value=37 Score=15.44 Aligned_cols=74 Identities=22% Similarity=0.342 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEEECCCCEECEEECCHHHHHHHHH
Q ss_conf 99999999976695999999999999866742488638999999984275404778752463000001048579999999
Q gi|254780265|r 22 VVAKFMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALINVTPQFEVRTRRVGGAAYSVPGEITSKRSQALAI 101 (156)
Q Consensus 22 lv~kliN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~n~~P~~evk~~r~gG~~yqvP~~i~~~r~~~lAi 101 (156)
+.+++.+. +.+|.+......+..+++ .+.+|+.++.+++. |-+++...+.+...|++|--+-.-+...-|+
T Consensus 3 ~~~~l~~a-v~~g~~~~v~~~v~~aL~-----~g~~p~~ii~~~L~---~gM~~VG~~f~~ge~flPell~aaeam~~~~ 73 (78)
T pfam02607 3 LLEKLAEA-VLDGDEEGVEELVEEALA-----EGVDPLEIINEGLI---PGMDEVGDLFEKGEYFLPQLLMSAEAMKAAV 73 (78)
T ss_pred HHHHHHHH-HHHCCHHHHHHHHHHHHH-----CCCCHHHHHHHHHH---HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 89999999-982888779999999998-----39987999998878---9999999986279862899999999999998
Q ss_pred HHH
Q ss_conf 999
Q gi|254780265|r 102 RWL 104 (156)
Q Consensus 102 rWi 104 (156)
..|
T Consensus 74 ~~L 76 (78)
T pfam02607 74 DIL 76 (78)
T ss_pred HHC
T ss_conf 560
No 21
>pfam07300 consensus
Probab=27.61 E-value=47 Score=14.87 Aligned_cols=35 Identities=20% Similarity=0.389 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf 999999999999857999989999999999973888
Q gi|254780265|r 97 QALAIRWLIMAARKRNETTMIDRLGGEIIDAANNRG 132 (156)
Q Consensus 97 ~~lAirWii~~a~~r~~~~~~~~La~Eii~A~~~~g 132 (156)
++.=|-.|++.+.+|.+.-+..|| +||+.|..+-+
T Consensus 52 iTFLmVfLIQntqnRD~~Aiq~KL-DELi~a~~~A~ 86 (111)
T pfam07300 52 ITFLMVFLIQNTQNRDTAALQAKL-DELIRATAEAR 86 (111)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHH-HHHHHHHHHHH
T ss_conf 999999999710112078999889-99999999999
No 22
>pfam00204 DNA_gyraseB DNA gyrase B. This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.
Probab=27.50 E-value=50 Score=14.70 Aligned_cols=14 Identities=14% Similarity=0.264 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHHHC
Q ss_conf 89999999999973
Q gi|254780265|r 116 MIDRLGGEIIDAAN 129 (156)
Q Consensus 116 ~~~~La~Eii~A~~ 129 (156)
.+..+.+-++.+.+
T Consensus 149 ~a~~Ii~k~~~~~~ 162 (173)
T pfam00204 149 IAKKILEKALAAAK 162 (173)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999999999
No 23
>COG2861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.73 E-value=34 Score=15.70 Aligned_cols=79 Identities=18% Similarity=0.281 Sum_probs=46.5
Q ss_pred HHHHHHHHHHCCCCEEEEEEEECCCCEECEEECCHHHHHHHHHHHHHHHHHHCC---------CCCHHHHHHHHH-----
Q ss_conf 899999998427540477875246300000104857999999999999998579---------999899999999-----
Q gi|254780265|r 59 VALFRQALINVTPQFEVRTRRVGGAAYSVPGEITSKRSQALAIRWLIMAARKRN---------ETTMIDRLGGEI----- 124 (156)
Q Consensus 59 i~il~~Ai~n~~P~~evk~~r~gG~~yqvP~~i~~~r~~~lAirWii~~a~~r~---------~~~~~~~La~Ei----- 124 (156)
..-++.|..+++=.+.+ .+|.= +..-...-||+|+.++-.++. +.+.+.++|.|+
T Consensus 109 ~~rl~~a~~~v~~~~Gl-------nNhmG----s~~tsn~~aM~~~m~~Lk~r~l~flDs~T~a~S~a~~iAk~~gVp~~ 177 (250)
T COG2861 109 LRRLRKAMNKVPDAVGL-------NNHMG----SRFTSNEDAMEKLMEALKERGLYFLDSGTIANSLAGKIAKEIGVPVI 177 (250)
T ss_pred HHHHHHHHHHCCCCEEE-------HHHHH----HHHCCCHHHHHHHHHHHHHCCEEEECCCCCCCCHHHHHHHHCCCCEE
T ss_conf 99999998638651300-------12332----33017699999999999877968972665202020666763387523
Q ss_pred -----HHHHCCCCCCEECHHHHHHHHHHH
Q ss_conf -----999738887263078899999998
Q gi|254780265|r 125 -----IDAANNRGVAVRKREETHKVAEAN 148 (156)
Q Consensus 125 -----i~A~~~~g~aikkK~elhk~A~aN 148 (156)
+|.........++-+.+.+.|..|
T Consensus 178 ~rdvfLD~e~~~~~V~kql~~~~~~Ark~ 206 (250)
T COG2861 178 KRDVFLDDEDTEAAVLKQLDAAEKLARKN 206 (250)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 40133048678999999999999999866
No 24
>TIGR03188 histidine_hisI phosphoribosyl-ATP pyrophosphohydrolase. This enzyme, phosphoribosyl-ATP pyrophosphohydrolase, catalyses the second step in the histidine biosynthesis pathway. It often occurs as a fusion protein. This model a somewhat narrower scope than pfam01503, as some paralogs that appear to be functionally distinct are excluded from this model.
Probab=24.86 E-value=56 Score=14.41 Aligned_cols=42 Identities=14% Similarity=0.143 Sum_probs=33.3
Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 999997669599999999999986674248863899999998
Q gi|254780265|r 26 FMNAIMYGGKKSVAVSIVYGAFDLVEKKEKKDPVALFRQALI 67 (156)
Q Consensus 26 liN~lMk~GKK~~A~kIv~~al~~I~~~~~~npi~il~~Ai~ 67 (156)
.+..|+.+|....+.|+...|.+.+-.-.+.|+-.+.+++-+
T Consensus 20 YT~~L~~~G~~~i~~Ki~EEa~E~i~A~~~~~~~~~i~E~AD 61 (84)
T TIGR03188 20 YTARLFAKGLDKILKKVGEEAVEVVIAAKNGDKEELVYEAAD 61 (84)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 899998862889999999899999999980888889999998
No 25
>PRK13489 chemoreceptor glutamine deamidase CheD; Provisional
Probab=23.84 E-value=46 Score=14.88 Aligned_cols=20 Identities=10% Similarity=0.554 Sum_probs=17.5
Q ss_pred CCCCHHHHHHHHHHHHCCHH
Q ss_conf 43787999999999766959
Q gi|254780265|r 17 KFSDFVVAKFMNAIMYGGKK 36 (156)
Q Consensus 17 ~y~~~lv~kliN~lMk~GKK 36 (156)
.|.+.-++.|||-|++.|-+
T Consensus 80 RYG~~AME~LIN~llk~Ga~ 99 (237)
T PRK13489 80 RYGAYAMEVLINELIKAGGR 99 (237)
T ss_pred HHHHHHHHHHHHHHHHCCCC
T ss_conf 07999999999999986884
No 26
>COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=23.43 E-value=54 Score=14.46 Aligned_cols=98 Identities=19% Similarity=0.205 Sum_probs=65.9
Q ss_pred HHHHHHHHHHH-HHHHCCCCHHHHHH-HHHHHCCCCEEEEEEEECCCC-EECEEECCHHHHHHHHHHHHHHHHHHCC--C
Q ss_conf 99999999986-67424886389999-999842754047787524630-0000104857999999999999998579--9
Q gi|254780265|r 39 AVSIVYGAFDL-VEKKEKKDPVALFR-QALINVTPQFEVRTRRVGGAA-YSVPGEITSKRSQALAIRWLIMAARKRN--E 113 (156)
Q Consensus 39 A~kIv~~al~~-I~~~~~~npi~il~-~Ai~n~~P~~evk~~r~gG~~-yqvP~~i~~~r~~~lAirWii~~a~~r~--~ 113 (156)
-+.|+.+|.+. |+...+.|.|+.++ .|++-++-. ++..+--|... -.||. ++....++|-.|.=++..+--. |
T Consensus 60 dr~ile~A~em~iedg~P~~aIq~iH~~alE~~A~r-~~~~iaDGTRRDDrvP~-ls~~~~qSLEdR~nv~Yi~PL~G~G 137 (198)
T COG2117 60 DREILEDAVEMIIEDGYPRNAIQYIHEMALEALASR-EVDRIADGTRRDDRVPK-LSRSEAQSLEDRLNVQYIRPLLGLG 137 (198)
T ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH-HHHHHCCCCCCCCCCCC-CCHHHHHHHHHHCCCEEECCCCCCC
T ss_conf 889999999999853898508899999999999877-78887578744566764-2498875188751864553033446
Q ss_pred CCHHHHHHHHHHHHHCCCCCCEECH
Q ss_conf 9989999999999973888726307
Q gi|254780265|r 114 TTMIDRLGGEIIDAANNRGVAVRKR 138 (156)
Q Consensus 114 ~~~~~~La~Eii~A~~~~g~aikkK 138 (156)
......|+.+++..-++.|..+.+-
T Consensus 138 ~kti~~Lv~~~f~~e~~~Se~~~k~ 162 (198)
T COG2117 138 YKTIRRLVSAIFILEEGPSEKIEKA 162 (198)
T ss_pred HHHHHHHHHHHEEEECCCCCCCCCC
T ss_conf 7899999887734101665555553
No 27
>TIGR02876 spore_yqfD sporulation protein YqfD; InterPro: IPR010690 This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (P54469 from SWISSPROT) is known to be essential for efficient sporulation although its exact function is unknown ..
Probab=22.66 E-value=44 Score=15.03 Aligned_cols=15 Identities=20% Similarity=0.326 Sum_probs=10.1
Q ss_pred CHHHHHHHHHHHHCC
Q ss_conf 879999999997669
Q gi|254780265|r 20 DFVVAKFMNAIMYGG 34 (156)
Q Consensus 20 ~~lv~kliN~lMk~G 34 (156)
..-++||+|.||++|
T Consensus 15 G~~iErFlN~~~~~g 29 (406)
T TIGR02876 15 GEDIERFLNLCWRNG 29 (406)
T ss_pred ECCCHHHHHHHHHCC
T ss_conf 167027888988787
Done!