Query 028585
Match_columns 207
No_of_seqs 201 out of 1034
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 13:49:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028585.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028585hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00091 40S ribosomal protein 100.0 7.2E-80 1.6E-84 518.5 18.8 191 16-207 3-193 (193)
2 PRK04027 30S ribosomal protein 100.0 1.8E-79 3.9E-84 517.1 19.0 189 15-207 7-195 (195)
3 TIGR01028 S7_S5_E_A ribosomal 100.0 2.2E-76 4.9E-81 496.0 17.9 186 18-207 1-186 (186)
4 KOG3291 Ribosomal protein S7 [ 100.0 3.4E-66 7.3E-71 438.3 14.9 191 14-207 18-208 (208)
5 COG0049 RpsG Ribosomal protein 100.0 6E-56 1.3E-60 359.0 16.5 147 52-207 2-148 (148)
6 TIGR01029 rpsG_bact ribosomal 100.0 5.9E-46 1.3E-50 304.2 17.2 137 62-207 11-147 (154)
7 PRK05302 30S ribosomal protein 100.0 2E-45 4.3E-50 301.7 17.1 136 63-207 14-149 (156)
8 PF00177 Ribosomal_S7: Ribosom 100.0 6.2E-45 1.3E-49 295.7 17.8 146 52-207 1-148 (148)
9 CHL00053 rps7 ribosomal protei 100.0 7E-45 1.5E-49 298.1 17.0 136 63-207 14-149 (155)
10 KOG3960 Myogenic helix-loop-he 52.0 17 0.00036 32.8 3.4 35 93-127 130-170 (284)
11 PF02607 B12-binding_2: B12 bi 40.3 42 0.00091 23.3 3.4 41 69-119 2-42 (79)
12 PF09974 DUF2209: Uncharacteri 34.3 96 0.0021 25.1 4.9 57 111-180 53-109 (128)
13 PF13374 TPR_10: Tetratricopep 29.8 1.2E+02 0.0025 17.5 4.1 35 72-110 5-39 (42)
14 KOG3291 Ribosomal protein S7 [ 21.8 65 0.0014 28.1 2.0 26 61-86 68-93 (208)
No 1
>PTZ00091 40S ribosomal protein S5; Provisional
Probab=100.00 E-value=7.2e-80 Score=518.55 Aligned_cols=191 Identities=79% Similarity=1.192 Sum_probs=186.2
Q ss_pred CCcccceeccCCCCceecCCCCccceeeccCCcceeeecCCCccccccccccCchhHHHHHHHhhcCCCCCccHHHHHHH
Q 028585 16 HYDVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRI 95 (207)
Q Consensus 16 ~~~~~lf~kw~~~~v~v~D~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piverliN~LM~~g~~~GKK~~A~rI 95 (207)
..++|||||||++||+|.||||.+||++++ |.++|+|||+|||++|+|+|++||+|+||||.||++|||+|||++|++|
T Consensus 3 ~~~~~lf~kw~~~~v~~~d~~l~~yi~~~~-~~~~~~pht~gr~~~k~f~k~~~~iVerLiN~lM~~grn~GKK~~A~~I 81 (193)
T PTZ00091 3 ANEPKLFGKWSYDDVQVSDLSLKDYIAVTT-KASVFVPHTAGRYQKKRFRKAQCPIVERLVNSLMFHGRNNGKKLLAVRI 81 (193)
T ss_pred CccchhhCCcCcccCeecCcCHHHHhhccc-CCceeeccccchhhcCccCcccCHHHHHHHHHHhccCccCCcHHHHHHH
Confidence 357899999999999999999999999983 4569999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCChHHHHHHHHHhcCCccceeeeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHH
Q 028585 96 VKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAEC 175 (207)
Q Consensus 96 v~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri~~gG~~~~vpv~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~ 175 (207)
|++||++|++.|++||+|||++||+|++|++|++|+++||++||+||||+|.||+++||+||+++|++++||+.++|++|
T Consensus 82 V~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~e~~ri~~GG~~yqvpVdVsp~Rr~~lAirwI~~~ar~~~fR~~ks~~e~ 161 (193)
T PTZ00091 82 VKHAFEIIHLLTDKNPLQVLVDAVQNGGPREDSTRVGSGGVVRRQAVDVSPLRRVNQAIYLICKGAREAAFRNIKTIAEC 161 (193)
T ss_pred HHHHHHHHHHHHCCChHHHHHHHHHhCCCCeeeEEeecCCeEEEEeeecChHHHHHHHHHHHHHHHHhhcccCCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 176 LADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 176 LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
||+|||+|++|+|+||||+||||+||||+|||
T Consensus 162 LA~Eli~Aa~~~~~s~AikKKeE~hR~AeANR 193 (193)
T PTZ00091 162 LADEIINASKESSNSYAIKKKDEVERVAKANR 193 (193)
T ss_pred HHHHHHHHHhCCCCCcceehHHHHHHHHHhcC
Confidence 99999999999999999999999999999998
No 2
>PRK04027 30S ribosomal protein S7P; Reviewed
Probab=100.00 E-value=1.8e-79 Score=517.12 Aligned_cols=189 Identities=52% Similarity=0.797 Sum_probs=185.9
Q ss_pred CCCcccceeccCCCCceecCCCCccceeeccCCcceeeecCCCccccccccccCchhHHHHHHHhhcCCCCCccHHHHHH
Q 028585 15 PHYDVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVR 94 (207)
Q Consensus 15 ~~~~~~lf~kw~~~~v~v~D~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piverliN~LM~~g~~~GKK~~A~r 94 (207)
...++|||||||++||+|.||||++||+++ ++|+|||+|||++|+|.|++||+|+||||.||++|+|+|||++|++
T Consensus 7 ~~~~~~lf~kw~~~~v~~~d~~l~~yi~~~----~~~~pht~gr~~~k~f~k~~~~iVerLiN~lM~~~~n~GKK~~A~~ 82 (195)
T PRK04027 7 EPMEIKLFGKWDVEEVEVRDPSLKRYINLT----PVLVPHTGGRHAKKQFGKAEVPIVERLINKLMRTERNTGKKQKAYN 82 (195)
T ss_pred cchhhhhhCCCCccceeEcccchHhheeec----ceecCcccccccccCcccccCHHHHHHHHHHhccCccCCcHHHHHH
Confidence 456899999999999999999999999998 8999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCChHHHHHHHHHhcCCccceeeeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhhcCCCcCcHHH
Q 028585 95 IVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAE 174 (207)
Q Consensus 95 Iv~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri~~gG~~~~vpv~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e 174 (207)
||++||++|+++|++||+|||++||+|++|++|++++++||++||+||||+|.||+++||+||+++|++++||+.++|++
T Consensus 83 Iv~~AfeiI~~kT~~nPiqVl~~AI~N~~P~~Ev~~~r~GG~tyqvpVdV~p~Rr~~lAirwI~~~ar~r~fr~~ksm~e 162 (195)
T PRK04027 83 IVKEAFEIIEKRTKQNPIQVLVDAIENAAPREETTRIKYGGISYPKAVDVSPQRRVDLALRFIAEGARQASFKNKKSIEE 162 (195)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCeEEEEEecCCEEEEeeeecCHHHHHHHHHHHHHHHHHhccccCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 175 CLADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 175 ~LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
|||+|||+|++|+++||||+||||+||||+|||
T Consensus 163 ~LA~ElidAa~~~~~g~AikKKeE~hRmAeANr 195 (195)
T PRK04027 163 ALAEEIIAAANNDPKSYAVRKKEEIERVAKSAR 195 (195)
T ss_pred HHHHHHHHHHcCCCCCceeecHHHHHHHHHhcC
Confidence 999999999999988899999999999999998
No 3
>TIGR01028 S7_S5_E_A ribosomal protein S7(archaeal)/S5(eukaryotic). This model describes the members from the eukaryotic cytosol and the Archaea of the family that includes ribosomal protein S7 of bacteria and S5 of eukaryotes. A separate model describes bacterial and organellar S7.
Probab=100.00 E-value=2.2e-76 Score=495.98 Aligned_cols=186 Identities=65% Similarity=0.980 Sum_probs=183.3
Q ss_pred cccceeccCCCCceecCCCCccceeeccCCcceeeecCCCccccccccccCchhHHHHHHHhhcCCCCCccHHHHHHHHH
Q 028585 18 DVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVK 97 (207)
Q Consensus 18 ~~~lf~kw~~~~v~v~D~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piverliN~LM~~g~~~GKK~~A~rIv~ 97 (207)
+++||||||++||+|.||||.+||+++ ++++|||+|||++|+|+|+++|+|++|||.||++|+|+|||++|++||+
T Consensus 1 ~~~lf~kw~~~~v~~~d~~l~~yi~~~----~~~~pht~gr~~~k~f~k~~~~iV~rliN~lM~~g~n~GKK~~A~kIv~ 76 (186)
T TIGR01028 1 EIKVFGKWSTDDVEVKDPSLKDYINLE----PKYVPHTAGRHAKKQFRKAKVPIVERLINKVMRSGRNNGKKLKAYRIVK 76 (186)
T ss_pred CccccCCcCCccceecCCCHHhhhhcC----ceeccchhhhhhccccCcccCHHHHHHHHHHhccCcCCCcHHHHHHHHH
Confidence 479999999999999999999999998 7999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHhcCCccceeeeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHHHH
Q 028585 98 HAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLA 177 (207)
Q Consensus 98 ~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri~~gG~~~~vpv~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~LA 177 (207)
+||++|++.|++||++||++||+|++|++|++++++||++|||||||+|.||+++||+||+++|++++||+.++|++|||
T Consensus 77 ~A~~iI~~~t~~nPi~vl~~AI~N~~P~~ev~~~r~GG~~yqVPv~v~p~Rr~~lAirWI~~~ar~~~~R~~k~m~~~LA 156 (186)
T TIGR01028 77 EAFEIIEKRTGENPIQVLVDAIENAGPREDTTRIGYGGIVYRQAVDISPLRRVDQALRNIALGAREAAFRNKKSIAECLA 156 (186)
T ss_pred HHHHHHHHHhCCChHHHHHHHHHcCCCCeEEEEEecCCEEEEeccccCHHHHHHHHHHHHHHHHHHhcccCCCcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 178 DELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 178 ~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
+|||+|++|+|+||||+||||+||||+|||
T Consensus 157 ~Eii~A~~~~g~g~AikKKeE~hr~AeaNR 186 (186)
T TIGR01028 157 EEIILAANGDSKSYAIKKKEELERVAKSAR 186 (186)
T ss_pred HHHHHHHhCCCCCceeehHHHHHHHHHhcC
Confidence 999999999998899999999999999998
No 4
>KOG3291 consensus Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.4e-66 Score=438.29 Aligned_cols=191 Identities=64% Similarity=0.949 Sum_probs=186.9
Q ss_pred CCCCcccceeccCCCCceecCCCCccceeeccCCcceeeecCCCccccccccccCchhHHHHHHHhhcCCCCCccHHHHH
Q 028585 14 QPHYDVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAV 93 (207)
Q Consensus 14 ~~~~~~~lf~kw~~~~v~v~D~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piverliN~LM~~g~~~GKK~~A~ 93 (207)
...+++++|++|++++|+++|+||.|||++++ |+..++||++|+++.++|.|+.||++++|+|+||++|+|+|||.+|+
T Consensus 18 ~~~~~~~~f~~~s~~~~~~~d~sl~dy~~~~~-k~~~~~~~~~~~~~~~~~~ka~~~~~e~l~~~l~n~~~~~GKK~~a~ 96 (208)
T KOG3291|consen 18 AETGEIKLFEKWSEDSVEFSDISLQDYIALKP-KDLTQLPHSAGRYAKKRFRKAQCPIVERLINKLMNHIMKNGKKLLAR 96 (208)
T ss_pred cccchhHHHHHhhccccccccccccccccccc-ccccccccccchhhhhhhhhccccHHHHHHHHHHHHHHhcccHHHHH
Confidence 45578999999999999999999999999996 48899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCChHHHHHHHHHhcCCccceeeeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhhcCCCcCcHH
Q 028585 94 RIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIA 173 (207)
Q Consensus 94 rIv~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri~~gG~~~~vpv~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~ 173 (207)
+||++||++|+++|++||+|||++||+|++|+++++++++||++|++||||+|.||+++||+||+++|++++|++.++|+
T Consensus 97 ~Iv~~aleiI~~~t~~NPiqvl~~AI~n~~P~~~~~~i~r~g~~~~vpv~v~~~rr~~~Ai~wi~~~ar~~~~~~~~~~a 176 (208)
T KOG3291|consen 97 RIVKHALEIIKRLTERNPIQVLVQAIENCGPLEDVTRIGRAGTTYQVPVPVSPLRRVNLAIKWILTGARERSFRNIKTLA 176 (208)
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcCchhhceeecccceEEEecccCCcHHHHHHHHHHHHHHHHhccccccccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 174 ECLADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 174 e~LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
||||+|||+|++|+|+ ||+||||+||+|++||
T Consensus 177 e~La~ELi~Aakgs~~--aikKKdeLhr~a~sNR 208 (208)
T KOG3291|consen 177 ECLADELIAAAKGSGN--AIKKKDELHRMAEANR 208 (208)
T ss_pred HHHHHHHHHHHhCCch--hhhhHHHHHHHHhccC
Confidence 9999999999999998 9999999999999998
No 5
>COG0049 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6e-56 Score=359.01 Aligned_cols=147 Identities=46% Similarity=0.584 Sum_probs=144.6
Q ss_pred eecCCCccccccccccCchhHHHHHHHhhcCCCCCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCccceeee
Q 028585 52 VPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRI 131 (207)
Q Consensus 52 ~pht~gr~~~k~f~k~~~piverliN~LM~~g~~~GKK~~A~rIv~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri 131 (207)
.||++|++...+|+++++++|+||||.||+ +|||++|++|||.||++|+++|++||||||++||+|++|++|+++.
T Consensus 2 r~~~~~kr~~~~dpk~~~~iv~rliN~iM~----~GKK~~A~~Ivy~Af~ii~~kTg~~Piqvf~~Ai~N~~P~~Ev~sr 77 (148)
T COG0049 2 RRHTAGKREVLPDPKYNSVIVERLINKIMR----DGKKSLAEKIVYGAFDIIEKKTGQNPLQVFEKAIENVKPREEVKSR 77 (148)
T ss_pred CCCCCCcccCCCCcccccHHHHHHHHHHHH----hccHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHhcCchhheeee
Confidence 689999999999999999999999999999 8999999999999999999999999999999999999999999999
Q ss_pred ecCCeeEEEeeecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHHHHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 132 GSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 132 ~~gG~~~~vpv~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
++||.+|||||||+|.||+++||+||+.+|++ +++++|++|||+|||+|++|+| +|||||||+||||+|||
T Consensus 78 rvGGa~yqvpVeV~p~RR~~lAlrwi~~~Ar~---r~~ktm~erLA~Eli~Aan~~g--~AikKked~hRmAeAnr 148 (148)
T COG0049 78 RVGGATYQVPVEVRPRRRVALALRWIVEGARK---RNEKTMAERLANELIDAANNTG--AAIKKKEDTHRMAEANR 148 (148)
T ss_pred eeCCeeeEecCccCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHcCCc--chhhhHHHHHHHHHhcC
Confidence 99999999999999999999999999999999 7889999999999999999999 69999999999999998
No 6
>TIGR01029 rpsG_bact ribosomal protein S7, bacterial/organelle. This model describes the bacterial and organellar branch of the ribosomal protein S7 family (includes prokaroytic S7 and eukaryotic S5). The eukaryotic and archaeal branch is described by model TIGR01028.
Probab=100.00 E-value=5.9e-46 Score=304.25 Aligned_cols=137 Identities=31% Similarity=0.434 Sum_probs=132.3
Q ss_pred ccccccCchhHHHHHHHhhcCCCCCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCccceeeeecCCeeEEEe
Q 028585 62 KRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQA 141 (207)
Q Consensus 62 k~f~k~~~piverliN~LM~~g~~~GKK~~A~rIv~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri~~gG~~~~vp 141 (207)
.+.+.+++|+|++|||+||+ +|||++|++||++||++|+..|++||++||++||+|++|.+|+++++.||.+||||
T Consensus 11 ~~d~~y~~~lv~~lin~lM~----~GKK~~A~kI~~~al~~i~~~~~~nPi~vl~~Ai~nv~P~~evk~~r~gG~~yqvP 86 (154)
T TIGR01029 11 PPDPVYGSVLLNKFINRVMK----DGKKSLAESIVYKAFERIAKKTGEDPLEVFEQALENVKPLVEVKSRRVGGATYQVP 86 (154)
T ss_pred CCCCccCCHHHHHHHHHHHh----cccHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCCeeeEEeecCCEEEEEe
Confidence 35778889999999999999 79999999999999999999999999999999999999999999999999999999
Q ss_pred eecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHHHHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 142 VDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 142 v~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
++|+|.||+++||+||+++|++ |+.++|+++||+|||+|++++|. |++||||+||+|++||
T Consensus 87 ~~v~~~rr~~lAirWil~~a~~---r~~~~~~~~La~Eii~A~~~~g~--aikkKee~hk~AeaNR 147 (154)
T TIGR01029 87 VEVRPSRRYALAIRWLIEAARK---RGGKSMAERLANEILDAANNTGA--AIKKREDTHRMAEANK 147 (154)
T ss_pred eEcCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHhCCCc--eeeHHHHHHHHHHHhH
Confidence 9999999999999999999999 67899999999999999999986 9999999999999997
No 7
>PRK05302 30S ribosomal protein S7; Validated
Probab=100.00 E-value=2e-45 Score=301.72 Aligned_cols=136 Identities=34% Similarity=0.483 Sum_probs=131.9
Q ss_pred cccccCchhHHHHHHHhhcCCCCCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCccceeeeecCCeeEEEee
Q 028585 63 RFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAV 142 (207)
Q Consensus 63 ~f~k~~~piverliN~LM~~g~~~GKK~~A~rIv~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri~~gG~~~~vpv 142 (207)
..+.++||+|++|||+||+ +|||++|++||++||++|+..|++||++||++||+|++|.+|+++++.||.+||||+
T Consensus 14 ~d~~~~~~lv~~lin~lmk----~GKK~~A~kI~~~al~~I~~~~~~npl~il~~Ai~nv~P~~evk~~r~gG~~~~vP~ 89 (156)
T PRK05302 14 PDPKYGSVLVTKFINKLML----DGKKSVAEKIVYGALDIIEEKTGKDPLEVFEKALENVKPVVEVKSRRVGGATYQVPV 89 (156)
T ss_pred CCCCcCCHHHHHHHHHHhh----cccHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHhCCCCeEEeeeccCCEEEEEeE
Confidence 4788899999999999999 799999999999999999999999999999999999999999999999999999999
Q ss_pred ecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHHHHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 143 DISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 143 ~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
+|+|.||+++||+||+++|++ |+.++|+++||+|||+|++++|. |++||||+||+|++||
T Consensus 90 ~i~~~rr~~lAirwil~~a~~---r~~~~~~~~La~Eii~A~~~~g~--aikkK~e~hk~A~aNR 149 (156)
T PRK05302 90 EVRPERRQALAMRWLVEAARK---RGEKTMAERLANELLDAANNRGA--AVKKREDTHRMAEANK 149 (156)
T ss_pred EeCHHHHHHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHhCCCC--eeehHHHHHHHHHHhh
Confidence 999999999999999999998 67799999999999999999986 9999999999999997
No 8
>PF00177 Ribosomal_S7: Ribosomal protein S7p/S5e; InterPro: IPR023798 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S7 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S7 is known to bind directly to part of the 3'end of 16S ribosomal RNA. It belongs to a family of ribosomal proteins which have been grouped on the basis of sequence similarities [, , ]. This entry represents the S7 structural domain, which consists of a bundle of six helices and an extended beta hairpin between helices 3 and 4, with two or more RNA-binding sites on its surface [].; PDB: 3IZ6_F 3V28_G 2WRN_G 2HHH_G 2V46_G 3KNL_G 2UUC_G 2Y16_G 2Y0W_G 2J02_G ....
Probab=100.00 E-value=6.2e-45 Score=295.67 Aligned_cols=146 Identities=40% Similarity=0.561 Sum_probs=139.0
Q ss_pred eecCCCccccc--cccccCchhHHHHHHHhhcCCCCCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCcccee
Q 028585 52 VPHTAGRYSVK--RFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDAT 129 (207)
Q Consensus 52 ~pht~gr~~~k--~f~k~~~piverliN~LM~~g~~~GKK~~A~rIv~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ 129 (207)
.||+ |+|+++ .++++++|++++|||.||+ +|||.+|++||+++|++|+..|++||+++|++||+|++|.++++
T Consensus 1 m~~~-~~~~k~~~~~~~~~~~lv~k~in~lmk----~GkK~~A~~i~~~al~~i~~~~~~npi~il~~Ai~n~~P~~~v~ 75 (148)
T PF00177_consen 1 MSRK-GRYKKKKIPDPKFNDPLVKKFINRLMK----DGKKSKAEKIVYKALEIIKKKTNKNPIQILKQAIENVKPLVEVR 75 (148)
T ss_dssp SSTS-SS-SSSS-SBTTTCGHHHHHHHHHHHS----TTBHHHHHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHS-SEEEE
T ss_pred CCCC-CCCCCCCCCCcccccHHHHHHHHHHHH----HhHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHhccceeee
Confidence 4788 999999 7889999999999999999 89999999999999999999999999999999999999999999
Q ss_pred eeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHHHHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 130 RIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 130 ri~~gG~~~~vpv~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
+++.||++|++|++|+|.||+++||+||+++|++ +++++|+++||+||++|++|+|. |++||+|+||+|++||
T Consensus 76 ~~k~gg~~~~vP~~i~~~r~~~lAikWi~~~~~~---r~~~~~~~~La~Eii~a~~~~g~--aikkK~~lhk~A~~NR 148 (148)
T PF00177_consen 76 SIKKGGKTYQVPVPISPKRRIFLAIKWILEAARK---RKEKSFSERLANEIIDASNNKGS--AIKKKEELHKMAEANR 148 (148)
T ss_dssp EEEETTEEEEEEEEETHHHHHHHHHHHHHHHHHT---SSSSSHHHHHHHHHHHHHTTSSH--HHHHHHHHHHHHHHTG
T ss_pred eeccCceeEEEEEeecHHHHHHHHHHHHHHHHhh---cccchHHHHHHHHHHHHHcCCcH--HHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999997 77899999999999999999885 9999999999999998
No 9
>CHL00053 rps7 ribosomal protein S7
Probab=100.00 E-value=7e-45 Score=298.11 Aligned_cols=136 Identities=34% Similarity=0.451 Sum_probs=131.0
Q ss_pred cccccCchhHHHHHHHhhcCCCCCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCccceeeeecCCeeEEEee
Q 028585 63 RFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAV 142 (207)
Q Consensus 63 ~f~k~~~piverliN~LM~~g~~~GKK~~A~rIv~~af~iI~~~t~~nPi~vl~~AI~N~~P~~e~~ri~~gG~~~~vpv 142 (207)
..+.+++++|++|||+||+ +|||.+|++||++||++|++.|++||+++|++||+|++|.+|+++++.||.+||+|+
T Consensus 14 ~d~~~~~~lv~~lin~lm~----~GKK~~A~kIv~~al~~i~~~~~~npi~vl~~Ai~N~~P~~evk~~r~gG~~~qvPv 89 (155)
T CHL00053 14 PDPIYRNRLVNMLVNRILK----SGKKSLAYRIVYRALKKIQQKTEKNPLSVLRQAIRNVTPDVEVKARRVGGSTYQVPI 89 (155)
T ss_pred CCCCcCcHHHHHHHHHHHh----cccHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCcEEEEEEeeCCEEEEEee
Confidence 4677889999999999999 899999999999999999999999999999999999999999999999999999999
Q ss_pred ecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHHHHHHHHHHHcCCCChhhhHhhHHHHHHHHhcC
Q 028585 143 DISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR 207 (207)
Q Consensus 143 ~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~s~aikKK~elhr~A~aNR 207 (207)
+|+|.||+++||+||+++|++ ++.++|+++||+||++|++|+|+ ||+||+|+||+|++||
T Consensus 90 ~v~~~rr~~lAirWil~~ar~---r~~~~~~~~La~Eii~A~~~~g~--aikkK~e~hk~A~aNR 149 (155)
T CHL00053 90 EIGSTRGKALAIRWLLKASRK---RSGRNMAFKLSSELVDAAKGSGN--AIRKKEETHRMAEANR 149 (155)
T ss_pred EcCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHhCCCc--hhhhHHHHHHHHHHhH
Confidence 999999999999999999999 55679999999999999999997 9999999999999997
No 10
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=51.98 E-value=17 Score=32.80 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhhcCCCh------HHHHHHHHHhcCCccc
Q 028585 93 VRIVKHAMEIIHLLTDQNP------IQVIVDAVINSGPRED 127 (207)
Q Consensus 93 ~rIv~~af~iI~~~t~~nP------i~vl~~AI~N~~P~~e 127 (207)
.+=|.+|||.++..|--|| ++||..||+-+-=+++
T Consensus 130 LkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~ 170 (284)
T KOG3960|consen 130 LKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQA 170 (284)
T ss_pred HHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHH
Confidence 3558999999999998888 5689999877665554
No 11
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=40.34 E-value=42 Score=23.32 Aligned_cols=41 Identities=22% Similarity=0.406 Sum_probs=31.9
Q ss_pred chhHHHHHHHhhcCCCCCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHH
Q 028585 69 CPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAV 119 (207)
Q Consensus 69 ~piverliN~LM~~g~~~GKK~~A~rIv~~af~iI~~~t~~nPi~vl~~AI 119 (207)
.++.++|.+.++. |....+..++.+++. ++.+|..++.+.+
T Consensus 2 ~~~~~~l~~al~~-----~d~~~~~~~~~~~l~-----~g~~~~~i~~~~l 42 (79)
T PF02607_consen 2 EELIERLLDALLA-----GDEEEAEALLEEALA-----QGYPPEDIIEEIL 42 (79)
T ss_dssp HHHHHHHHHHHHT-----T-CCHHHHHHHHHHH-----CSSSTTHHHHHTH
T ss_pred hHHHHHHHHHHHh-----CCHHHHHHHHHHHHH-----cCCCHHHHHHHHH
Confidence 3678999999998 888999999998886 3567777776655
No 12
>PF09974 DUF2209: Uncharacterized protein conserved in archaea (DUF2209); InterPro: IPR014514 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=34.29 E-value=96 Score=25.12 Aligned_cols=57 Identities=18% Similarity=0.134 Sum_probs=43.3
Q ss_pred hHHHHHHHHHhcCCccceeeeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhhcCCCcCcHHHHHHHHH
Q 028585 111 PIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADEL 180 (207)
Q Consensus 111 Pi~vl~~AI~N~~P~~e~~ri~~gG~~~~vpv~vsp~rr~~lAirwI~~~ar~~~~r~~k~~~e~LA~Ei 180 (207)
-++++.+++.+..-..+-+=+-=.|-.|..| .|..++...+.|+-.+|++|+.|=||
T Consensus 53 iv~~v~e~v~~~~~~~eg~IvaE~Gefyn~p-------------~w~v~s~l~~~fkY~ES~gEr~aIei 109 (128)
T PF09974_consen 53 IVQEVEEAVSKLSEDFEGTIVAEKGEFYNEP-------------EWRVESILGREFKYPESIGEREAIEI 109 (128)
T ss_pred HHHHHHHHHhccccccCceEEeeccccccCh-------------HHHHHHHhccccccchhHHHHHHHHH
Confidence 3667788888887444433333346777776 68899999999999999999999998
No 13
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=29.81 E-value=1.2e+02 Score=17.53 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=22.8
Q ss_pred HHHHHHHhhcCCCCCccHHHHHHHHHHHHHHHHhhcCCC
Q 028585 72 VERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQN 110 (207)
Q Consensus 72 verliN~LM~~g~~~GKK~~A~rIv~~af~iI~~~t~~n 110 (207)
...|-+.++. .|+-..|..+..+++++-....+.|
T Consensus 5 ~~~la~~~~~----~g~~~~A~~~~~~al~~~~~~~G~~ 39 (42)
T PF13374_consen 5 LNNLANAYRA----QGRYEEALELLEEALEIRERLLGPD 39 (42)
T ss_dssp HHHHHHHHHH----CT-HHHHHHHHHHHHHHH-------
T ss_pred HHHHHHHHHh----hhhcchhhHHHHHHHHHHHHHhccc
Confidence 3456677777 7999999999999999988776655
No 14
>KOG3291 consensus Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=21.82 E-value=65 Score=28.12 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=21.2
Q ss_pred cccccccCchhHHHHHHHhhcCCCCC
Q 028585 61 VKRFRKAQCPIVERLTNSLMMHGRNN 86 (207)
Q Consensus 61 ~k~f~k~~~piverliN~LM~~g~~~ 86 (207)
.|-.+...++++.+|+|++|++|.+-
T Consensus 68 ~ka~~~~~e~l~~~l~n~~~~~GKK~ 93 (208)
T KOG3291|consen 68 RKAQCPIVERLINKLMNHIMKNGKKL 93 (208)
T ss_pred hhccccHHHHHHHHHHHHHHhcccHH
Confidence 34444578899999999999999874
Done!