Query 029666
Match_columns 190
No_of_seqs 223 out of 1056
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 16:34:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029666.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029666hhsearch_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 3.3E-72 7.2E-77 466.1 18.0 172 17-189 4-175 (193)
2 PRK04027 30S ribosomal protein 100.0 5.2E-72 1.1E-76 465.8 18.1 171 15-189 7-177 (195)
3 TIGR01028 S7_S5_E_A ribosomal 100.0 4.2E-69 9.2E-74 446.1 17.2 168 18-189 1-168 (186)
4 KOG3291 Ribosomal protein S7 [ 100.0 3.8E-59 8.3E-64 390.3 12.9 175 14-189 18-192 (208)
5 COG0049 RpsG Ribosomal protein 100.0 2.1E-50 4.6E-55 322.6 14.7 131 52-189 2-132 (148)
6 TIGR01029 rpsG_bact ribosomal 100.0 3.1E-40 6.8E-45 266.8 16.5 122 62-190 11-132 (154)
7 PRK05302 30S ribosomal protein 100.0 1E-39 2.2E-44 264.3 16.4 121 63-190 14-134 (156)
8 CHL00053 rps7 ribosomal protei 100.0 2.9E-39 6.3E-44 261.3 15.8 121 63-190 14-134 (155)
9 PF00177 Ribosomal_S7: Ribosom 100.0 6.8E-39 1.5E-43 256.7 16.7 130 52-189 1-132 (148)
10 KOG3960 Myogenic helix-loop-he 62.8 8.2 0.00018 34.3 3.2 34 94-127 131-170 (284)
11 PF13317 DUF4088: Protein of u 45.0 64 0.0014 27.8 5.7 110 49-184 18-127 (229)
12 PF02607 B12-binding_2: B12 bi 44.3 35 0.00076 23.4 3.5 41 69-119 2-42 (79)
13 PF13374 TPR_10: Tetratricopep 34.6 91 0.002 17.8 3.9 35 72-110 5-39 (42)
14 COG4130 Predicted sugar epimer 27.1 26 0.00056 30.9 0.6 72 110-183 115-187 (272)
15 KOG3324 Mitochondrial import i 22.8 97 0.0021 26.6 3.2 36 70-105 112-147 (206)
16 TIGR03188 histidine_hisI phosp 22.6 2.5E+02 0.0055 20.5 5.0 41 74-118 19-59 (84)
17 PF09974 DUF2209: Uncharacteri 21.3 2.4E+02 0.0053 22.5 5.0 56 112-180 54-109 (128)
18 PRK00468 hypothetical protein; 20.3 1.1E+02 0.0025 21.8 2.7 16 149-164 50-65 (75)
No 1
>PTZ00091 40S ribosomal protein S5; Provisional
Probab=100.00 E-value=3.3e-72 Score=466.07 Aligned_cols=172 Identities=77% Similarity=1.198 Sum_probs=167.5
Q ss_pred CccceeecccCCcceecCCCccccccccccccceeeecCCCCcccccccccCchhHHHHHHHhhccCCcCccHHHHHHHH
Q 029666 17 YDVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIV 96 (190)
Q Consensus 17 ~~~klf~kw~~~~v~v~d~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv 96 (190)
.++|||||||++||+|+||||++||++++ |.++++|||+|||++++|+|++||+|+||||.||++|+|+|||++|++||
T Consensus 4 ~~~~lf~kw~~~~v~~~d~~l~~yi~~~~-~~~~~~pht~gr~~~k~f~k~~~~iVerLiN~lM~~grn~GKK~~A~~IV 82 (193)
T PTZ00091 4 NEPKLFGKWSYDDVQVSDLSLKDYIAVTT-KASVFVPHTAGRYQKKRFRKAQCPIVERLVNSLMFHGRNNGKKLLAVRIV 82 (193)
T ss_pred ccchhhCCcCcccCeecCcCHHHHhhccc-CCceeeccccchhhcCccCcccCHHHHHHHHHHhccCccCCcHHHHHHHH
Confidence 57899999999999999999999999983 45699999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHH
Q 029666 97 KHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECL 176 (190)
Q Consensus 97 ~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~L 176 (190)
|+||++|+++|++||+|||++||+|++|++|++|+++||++|||||||+|.||+++|||||+++|++++||++++|++||
T Consensus 83 ~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~e~~ri~~GG~~yqvpVdVsp~Rr~~lAirwI~~~ar~~~fR~~ks~~e~L 162 (193)
T PTZ00091 83 KHAFEIIHLLTDKNPLQVLVDAVQNGGPREDSTRVGSGGVVRRQAVDVSPLRRVNQAIYLICKGAREAAFRNIKTIAECL 162 (193)
T ss_pred HHHHHHHHHHHCCChHHHHHHHHHhCCCCeeeEEeecCCeEEEEeeecChHHHHHHHHHHHHHHHHhhcccCCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCC
Q 029666 177 ADELINAAKGSSN 189 (190)
Q Consensus 177 A~EiI~A~~~~g~ 189 (190)
|+|||+|++|+|+
T Consensus 163 A~Eli~Aa~~~~~ 175 (193)
T PTZ00091 163 ADEIINASKESSN 175 (193)
T ss_pred HHHHHHHHhCCCC
Confidence 9999999999965
No 2
>PRK04027 30S ribosomal protein S7P; Reviewed
Probab=100.00 E-value=5.2e-72 Score=465.79 Aligned_cols=171 Identities=50% Similarity=0.769 Sum_probs=167.0
Q ss_pred CCCccceeecccCCcceecCCCccccccccccccceeeecCCCCcccccccccCchhHHHHHHHhhccCCcCccHHHHHH
Q 029666 15 PHYDVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVR 94 (190)
Q Consensus 15 ~~~~~klf~kw~~~~v~v~d~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piv~rliN~lM~~~~~~GKK~~A~r 94 (190)
...++|||||||++||+|.||||++||+++ ++++|||+|||++++|.|++||+|+||||.||++|+|+|||++|++
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 446899999999999999999999999998 9999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHHH
Q 029666 95 IVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAE 174 (190)
Q Consensus 95 Iv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e 174 (190)
|||+||++|+++|++||+|||++||+|++|++|++++++||++|||||||+|.||+++|||||+++|++++||++++|++
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 HHHHHHHHHHcCCCC
Q 029666 175 CLADELINAAKGSSN 189 (190)
Q Consensus 175 ~LA~EiI~A~~~~g~ 189 (190)
|||+|||+|++|+++
T Consensus 163 ~LA~ElidAa~~~~~ 177 (195)
T PRK04027 163 ALAEEIIAAANNDPK 177 (195)
T ss_pred HHHHHHHHHHcCCCC
Confidence 999999999999754
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=4.2e-69 Score=446.14 Aligned_cols=168 Identities=64% Similarity=0.971 Sum_probs=164.9
Q ss_pred ccceeecccCCcceecCCCccccccccccccceeeecCCCCcccccccccCchhHHHHHHHhhccCCcCccHHHHHHHHH
Q 029666 18 DVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVK 97 (190)
Q Consensus 18 ~~klf~kw~~~~v~v~d~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv~ 97 (190)
+++||||||++||+|+||||.+||+++ ++++|||+|||++++|+|+++|+|++|||+||++|+|+|||++|++|||
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 HHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHH
Q 029666 98 HAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLA 177 (190)
Q Consensus 98 ~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA 177 (190)
+||++|+++|++||++||++||+|++|++|++++++||++|||||||+|.||+++|||||+++|++++||++++|++|||
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 HHHHHHHcCCCC
Q 029666 178 DELINAAKGSSN 189 (190)
Q Consensus 178 ~EiI~A~~~~g~ 189 (190)
+|||+|++|+|+
T Consensus 157 ~Eii~A~~~~g~ 168 (186)
T TIGR01028 157 EEIILAANGDSK 168 (186)
T ss_pred HHHHHHHhCCCC
Confidence 999999999974
No 4
>KOG3291 consensus Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-59 Score=390.30 Aligned_cols=175 Identities=62% Similarity=0.936 Sum_probs=170.7
Q ss_pred CCCCccceeecccCCcceecCCCccccccccccccceeeecCCCCcccccccccCchhHHHHHHHhhccCCcCccHHHHH
Q 029666 14 QPHYDVKLFNRWTFEDVQVNDISLSDYIGVQAAKHATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAV 93 (190)
Q Consensus 14 ~~~~~~klf~kw~~~~v~v~d~~l~~yi~~~~~k~~~~~pht~gr~~~k~f~k~~~piv~rliN~lM~~~~~~GKK~~A~ 93 (190)
....++++|++|++++|+++|+||.|||++++. +..++||++|+++.++|.++.||++++|+|+||++|+|+|||.+|+
T Consensus 18 ~~~~~~~~f~~~s~~~~~~~d~sl~dy~~~~~k-~~~~~~~~~~~~~~~~~~ka~~~~~e~l~~~l~n~~~~~GKK~~a~ 96 (208)
T KOG3291|consen 18 AETGEIKLFEKWSEDSVEFSDISLQDYIALKPK-DLTQLPHSAGRYAKKRFRKAQCPIVERLINKLMNHIMKNGKKLLAR 96 (208)
T ss_pred cccchhHHHHHhhcccccccccccccccccccc-cccccccccchhhhhhhhhccccHHHHHHHHHHHHHHhcccHHHHH
Confidence 345789999999999999999999999999964 8999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHH
Q 029666 94 RIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIA 173 (190)
Q Consensus 94 rIv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~ 173 (190)
+||++||++|+++|++||+|||++||+||+|++++++||+||++|||||||+|.||+++||+||+++||+++||+.++|+
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 HHHHHHHHHHHcCCCC
Q 029666 174 ECLADELINAAKGSSN 189 (190)
Q Consensus 174 e~LA~EiI~A~~~~g~ 189 (190)
+|||+|||+|++|+|+
T Consensus 177 e~La~ELi~Aakgs~~ 192 (208)
T KOG3291|consen 177 ECLADELIAAAKGSGN 192 (208)
T ss_pred HHHHHHHHHHHhCCch
Confidence 9999999999999996
No 5
>COG0049 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-50 Score=322.62 Aligned_cols=131 Identities=44% Similarity=0.553 Sum_probs=128.8
Q ss_pred eecCCCCcccccccccCchhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEe
Q 029666 52 VPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRI 131 (190)
Q Consensus 52 ~pht~gr~~~k~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri 131 (190)
.||++|++...+|+++++++|+||||.||+ +|||++|++|||.||++|+++|++||||||++||+|++|++|++++
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 9999999999999999999999999999999999999999999999
Q ss_pred ecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHHcCCCC
Q 029666 132 GSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSN 189 (190)
Q Consensus 132 ~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~ 189 (190)
++||++|||||||+|.||++|||+||+.+|++ |++++|++|||+|||||+||+|.
T Consensus 78 rvGGa~yqvpVeV~p~RR~~lAlrwi~~~Ar~---r~~ktm~erLA~Eli~Aan~~g~ 132 (148)
T COG0049 78 RVGGATYQVPVEVRPRRRVALALRWIVEGARK---RNEKTMAERLANELIDAANNTGA 132 (148)
T ss_pred eeCCeeeEecCccCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHcCCcc
Confidence 99999999999999999999999999999999 78999999999999999999985
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=3.1e-40 Score=266.81 Aligned_cols=122 Identities=29% Similarity=0.378 Sum_probs=117.4
Q ss_pred ccccccCchhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEeecCCeeEEEe
Q 029666 62 KRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQA 141 (190)
Q Consensus 62 k~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvP 141 (190)
.+.+.+++++|++|||+||+ +|||++|++||++||++|+..|++||++||++||+|++|.+|+++++.||++||||
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 35788999999999999999 89999999999999999999999999999999999999999999999999999999
Q ss_pred eecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHHcCCCCC
Q 029666 142 VDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNR 190 (190)
Q Consensus 142 v~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~~ 190 (190)
++|+|.||+++||+||+++|++ |++++|+++||+|||+|++|+|.+
T Consensus 87 ~~v~~~rr~~lAirWil~~a~~---r~~~~~~~~La~Eii~A~~~~g~a 132 (154)
T TIGR01029 87 VEVRPSRRYALAIRWLIEAARK---RGGKSMAERLANEILDAANNTGAA 132 (154)
T ss_pred eEcCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHhCCCce
Confidence 9999999999999999999999 778999999999999999999863
No 7
>PRK05302 30S ribosomal protein S7; Validated
Probab=100.00 E-value=1e-39 Score=264.28 Aligned_cols=121 Identities=32% Similarity=0.434 Sum_probs=116.9
Q ss_pred cccccCchhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEeecCCeeEEEee
Q 029666 63 RFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAV 142 (190)
Q Consensus 63 ~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvPv 142 (190)
..+.+++|+|++|||+||+ +|||++|++||++||++|+..|++||++||++||+|++|.+|+++++.||++||||+
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 5788999999999999999 899999999999999999999999999999999999999999999889999999999
Q ss_pred ecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHHcCCCCC
Q 029666 143 DISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNR 190 (190)
Q Consensus 143 ~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~~ 190 (190)
+|+|.||+++||+||+++|++ |++++|+++||+|||+|++|+|.+
T Consensus 90 ~i~~~rr~~lAirwil~~a~~---r~~~~~~~~La~Eii~A~~~~g~a 134 (156)
T PRK05302 90 EVRPERRQALAMRWLVEAARK---RGEKTMAERLANELLDAANNRGAA 134 (156)
T ss_pred EeCHHHHHHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHhCCCCe
Confidence 999999999999999999998 778999999999999999999863
No 8
>CHL00053 rps7 ribosomal protein S7
Probab=100.00 E-value=2.9e-39 Score=261.32 Aligned_cols=121 Identities=30% Similarity=0.388 Sum_probs=115.9
Q ss_pred cccccCchhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCceeeEEeecCCeeEEEee
Q 029666 63 RFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDATRIGSAGVVRRQAV 142 (190)
Q Consensus 63 ~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvPv 142 (190)
..+.++++++++|||+||+ +|||.+|++||++||++|+..|++||+++|++||+|++|.+|+++++.||++||||+
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 4778899999999999999 999999999999999999999999999999999999999999988889999999999
Q ss_pred ecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHHcCCCCC
Q 029666 143 DISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSNR 190 (190)
Q Consensus 143 ~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~~ 190 (190)
+|+|.||+++||+||+++|++ |++++|+++||+||++|++|+|++
T Consensus 90 ~v~~~rr~~lAirWil~~ar~---r~~~~~~~~La~Eii~A~~~~g~a 134 (155)
T CHL00053 90 EIGSTRGKALAIRWLLKASRK---RSGRNMAFKLSSELVDAAKGSGNA 134 (155)
T ss_pred EcCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHhCCCch
Confidence 999999999999999999999 566899999999999999999863
No 9
>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=6.8e-39 Score=256.70 Aligned_cols=130 Identities=38% Similarity=0.517 Sum_probs=123.6
Q ss_pred eecCCCCcccc--cccccCchhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCceeeE
Q 029666 52 VPHTAGRYSVK--RFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDAT 129 (190)
Q Consensus 52 ~pht~gr~~~k--~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es~ 129 (190)
.||+ |+|+++ .+++++++++++|||.||+ +|||.+|++||++||++|+..+++||+++|++||+|++|.++++
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 99999999999999999999999999999999999999999999
Q ss_pred EeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHHcCCCC
Q 029666 130 RIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAAKGSSN 189 (190)
Q Consensus 130 ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA~EiI~A~~~~g~ 189 (190)
+++.||++||||++|+|.||+++||+||+++|++ |++++|+++||+||++|++|+|.
T Consensus 76 ~~k~gg~~~~vP~~i~~~r~~~lAikWi~~~~~~---r~~~~~~~~La~Eii~a~~~~g~ 132 (148)
T PF00177_consen 76 SIKKGGKTYQVPVPISPKRRIFLAIKWILEAARK---RKEKSFSERLANEIIDASNNKGS 132 (148)
T ss_dssp EEEETTEEEEEEEEETHHHHHHHHHHHHHHHHHT---SSSSSHHHHHHHHHHHHHTTSSH
T ss_pred eeccCceeEEEEEeecHHHHHHHHHHHHHHHHhh---cccchHHHHHHHHHHHHHcCCcH
Confidence 9999999999999999999999999999999997 77899999999999999999884
No 10
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=62.85 E-value=8.2 Score=34.29 Aligned_cols=34 Identities=21% Similarity=0.319 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhhcCCCh------HHHHHHHHHhcCCcee
Q 029666 94 RIVKHAMEIIHLLTDQNP------IQVIVDAVINSGPRED 127 (190)
Q Consensus 94 rIv~~afeiI~~~t~~nP------i~vl~~AI~N~~P~~e 127 (190)
+=|.+|||.+++.|--|| ++||..||+-+-=+.+
T Consensus 131 kKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~ 170 (284)
T KOG3960|consen 131 KKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQA 170 (284)
T ss_pred HHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHH
Confidence 458999999999998886 6789999987765554
No 11
>PF13317 DUF4088: Protein of unknown function (DUF4088)
Probab=45.02 E-value=64 Score=27.82 Aligned_cols=110 Identities=18% Similarity=0.258 Sum_probs=77.3
Q ss_pred ceeeecCCCCcccccccccCchhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHhcCCceee
Q 029666 49 ATYVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAVINSGPREDA 128 (190)
Q Consensus 49 ~~~~pht~gr~~~k~f~k~~~piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~AI~N~~P~~es 128 (190)
+.|+|-+..-+-.-++-..+.|+.|+-+..||. .|.-.-|.|.+.+-|- |.+++|.. +.
T Consensus 18 ~~F~~PsF~dfLrAkLl~~~~pLTE~AV~rll~----~GqYaWAkr~~DK~~P--------d~~a~Lmr---------~A 76 (229)
T PF13317_consen 18 PQFVPPSFEDFLRAKLLDNDGPLTERAVQRLLQ----GGQYAWAKRVFDKQFP--------DVVAILMR---------QA 76 (229)
T ss_pred cCcCCccHHHHHHHHHHhcCCcchHHHHHHHHh----cchhHHHHHHhhhhcc--------HHHHHHHH---------HH
Confidence 444444444444445666778999999999999 8999999988775443 34444432 23
Q ss_pred EEeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHH
Q 029666 129 TRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADELINAA 184 (190)
Q Consensus 129 ~ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA~EiI~A~ 184 (190)
.+.|.| .-+--+-+|..++..+=-|-..-..++ ...-++.+.||..|-.++
T Consensus 77 ~~fGFg---~Avr~dWtp~e~~~~~r~WA~~i~~ea--~~D~a~~d~LAaQi~asa 127 (229)
T PF13317_consen 77 QRFGFG---FAVRSDWTPDELVAHARDWAAAILSEA--GGDAAFIDPLAAQIKASA 127 (229)
T ss_pred HHcCce---eeecCCCCHHHHHHHHHHHHHHHHHHc--CCcHHHHHHHHHHHHHHH
Confidence 455544 455568899999999999987777775 336788889988886654
No 12
>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=44.29 E-value=35 Score=23.37 Aligned_cols=41 Identities=22% Similarity=0.406 Sum_probs=31.6
Q ss_pred chhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHHH
Q 029666 69 CPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDAV 119 (190)
Q Consensus 69 ~piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~AI 119 (190)
.++.++|.+.++. |....+.+++.+++. ++.+|..++.+.+
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 4678899999988 899999999998886 3567777776644
No 13
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=34.64 E-value=91 Score=17.75 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=22.9
Q ss_pred HHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCC
Q 029666 72 VERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQN 110 (190)
Q Consensus 72 v~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~n 110 (190)
...|.+.++. .|+-..|..+..+++++-+...+.|
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 8999999999999999988776665
No 14
>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]
Probab=27.13 E-value=26 Score=30.87 Aligned_cols=72 Identities=24% Similarity=0.200 Sum_probs=60.0
Q ss_pred ChHHHHHHHHHhcCCceeeEEeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCC-CCcHHHHHHHHHHHH
Q 029666 110 NPIQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRN-IKTIAECLADELINA 183 (190)
Q Consensus 110 nPi~vl~~AI~N~~P~~es~ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~-~k~~~e~LA~EiI~A 183 (190)
-+-..++.|+.-.+|.++..-|. |-+-+.-.+++..|+-..|-+-|-.+.-++.||= ..+|.+.||.|=.-.
T Consensus 115 vr~~~lv~AlkaLkpil~~~gi~--GLVEPLGF~~csLRsk~eA~~aI~aa~g~~~fklvhDTFHHhLagE~~ff 187 (272)
T COG4130 115 VRREDLVEALKALKPILDEYGIT--GLVEPLGFRVCSLRSKAEAAEAIRAAGGERVFKLVHDTFHHHLAGETEFF 187 (272)
T ss_pred cchHHHHHHHHHhhHHHHHhCcc--ccccccCchhhhhhhHHHHHHHHHHhCCCceeeeehhhhhhhhcccceec
Confidence 36678999999999999988776 7778888999999999999999999888877763 368888898775433
No 15
>KOG3324 consensus Mitochondrial import inner membrane translocase, subunit TIM23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.75 E-value=97 Score=26.63 Aligned_cols=36 Identities=25% Similarity=0.229 Sum_probs=32.5
Q ss_pred hhHHHHHHHhhccCCcCccHHHHHHHHHHHHHHHHh
Q 029666 70 PIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHL 105 (190)
Q Consensus 70 piv~rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~ 105 (190)
+-..|.+|+.|++|+-=|+-.=+.-++|.+||.+=.
T Consensus 112 lr~nrILN~~t~~G~~~gN~lG~laL~YsaiesgI~ 147 (206)
T KOG3324|consen 112 LRLNRILNSVTRRGRFWGNTLGSLALMYSAIESGIE 147 (206)
T ss_pred hhHHHHhhhccccccccccchhHHHHHHHHHHHHHH
Confidence 568899999999999999999999999999998654
No 16
>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 Pfam model pfam01503, as some paralogs that appear to be functionally distinct are excluded from this model.
Probab=22.60 E-value=2.5e+02 Score=20.50 Aligned_cols=41 Identities=15% Similarity=0.279 Sum_probs=31.3
Q ss_pred HHHHHhhccCCcCccHHHHHHHHHHHHHHHHhhcCCChHHHHHHH
Q 029666 74 RLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLTDQNPIQVIVDA 118 (190)
Q Consensus 74 rliN~lM~~~~~~GKK~~A~rIv~~afeiI~~~t~~nPi~vl~~A 118 (190)
--++.|+. +|.-.+++++..+|.|.|---.+.|+=.+...+
T Consensus 19 SYT~~L~~----~G~~ki~kKvgEEa~E~iiAa~~~d~~~~~~E~ 59 (84)
T TIGR03188 19 SYTARLFA----KGLDKILKKVGEEAVEVVIAAKNGDKEELVYEA 59 (84)
T ss_pred cHHHHHHh----CcHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 34667787 799999999999999998776666666655443
No 17
>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=21.30 E-value=2.4e+02 Score=22.51 Aligned_cols=56 Identities=18% Similarity=0.152 Sum_probs=42.0
Q ss_pred HHHHHHHHHhcCCceeeEEeecCCeeEEEeeecChhHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Q 029666 112 IQVIVDAVINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLITTGARESAFRNIKTIAECLADEL 180 (190)
Q Consensus 112 i~vl~~AI~N~~P~~es~ri~~gG~~yqvPv~vsp~Rr~~lAirwIi~~ar~~~~r~~k~~~e~LA~Ei 180 (190)
++++.+++.+..-..|-+=+-=.|-.|..| .|...+.-.+.|+=.+|++|+.|=||
T Consensus 54 v~~v~e~v~~~~~~~eg~IvaE~Gefyn~p-------------~w~v~s~l~~~fkY~ES~gEr~aIei 109 (128)
T PF09974_consen 54 VQEVEEAVSKLSEDFEGTIVAEKGEFYNEP-------------EWRVESILGREFKYPESIGEREAIEI 109 (128)
T ss_pred HHHHHHHHhccccccCceEEeeccccccCh-------------HHHHHHHhccccccchhHHHHHHHHH
Confidence 567788888887444422222237778777 68899999999988899999999887
No 18
>PRK00468 hypothetical protein; Provisional
Probab=20.29 E-value=1.1e+02 Score=21.82 Aligned_cols=16 Identities=25% Similarity=0.318 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHhc
Q 029666 149 RVNQAIYLITTGARES 164 (190)
Q Consensus 149 r~~lAirwIi~~ar~~ 164 (190)
|.-.|||-++.+|..+
T Consensus 50 r~i~AIRtvv~aaa~k 65 (75)
T PRK00468 50 RIAKAIRTVVKAAAIK 65 (75)
T ss_pred hhHHHHHHHHHHHHhc
Confidence 7899999999999774
Done!