Query psy10065
Match_columns 215
No_of_seqs 234 out of 1053
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 16:59:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10065.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10065hhsearch_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 6.1E-70 1.3E-74 463.6 17.4 173 42-214 3-175 (193)
2 PRK04027 30S ribosomal protein 100.0 1.3E-69 2.9E-74 462.3 17.9 174 38-214 4-177 (195)
3 TIGR01028 S7_S5_E_A ribosomal 100.0 8.4E-66 1.8E-70 436.7 16.8 168 44-214 1-168 (186)
4 KOG3291|consensus 100.0 1.2E-58 2.6E-63 397.0 13.3 180 36-215 14-193 (208)
5 COG0049 RpsG Ribosomal protein 100.0 3.2E-47 7E-52 312.0 14.9 132 77-215 2-133 (148)
6 PRK05302 30S ribosomal protein 100.0 1.3E-37 2.8E-42 257.7 16.1 128 80-215 2-134 (156)
7 TIGR01029 rpsG_bact ribosomal 100.0 2E-37 4.4E-42 256.1 15.3 118 90-215 14-132 (154)
8 CHL00053 rps7 ribosomal protei 100.0 4E-37 8.6E-42 254.5 16.0 118 90-215 16-134 (155)
9 PF00177 Ribosomal_S7: Ribosom 100.0 2.3E-36 5.1E-41 247.3 14.7 129 77-214 1-132 (148)
10 KOG3960|consensus 64.8 7.3 0.00016 35.6 3.4 34 119-152 131-170 (284)
11 PF02607 B12-binding_2: B12 bi 47.9 31 0.00067 24.3 3.7 41 94-144 2-42 (79)
12 PF13374 TPR_10: Tetratricopep 37.3 87 0.0019 18.4 4.1 35 98-136 6-40 (42)
13 PF05848 CtsR: Firmicute trans 24.7 89 0.0019 26.3 3.3 50 151-211 58-107 (152)
14 COG4463 CtsR Transcriptional r 22.7 2.1E+02 0.0046 24.1 5.1 30 152-182 59-89 (153)
15 KOG3324|consensus 22.2 95 0.0021 27.4 3.1 37 95-131 112-148 (206)
16 TIGR03188 histidine_hisI phosp 20.3 3.2E+02 0.0069 20.6 5.3 41 99-143 19-59 (84)
No 1
>PTZ00091 40S ribosomal protein S5; Provisional
Probab=100.00 E-value=6.1e-70 Score=463.58 Aligned_cols=173 Identities=77% Similarity=1.177 Sum_probs=167.6
Q ss_pred CcccceeccccCCCceeecCCcccceeccccccceecCCCCcccccccCccCChhHHHHHHHhhccccccchHHHHHHHH
Q psy10065 42 LPEIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSLMMHGRNNAKKLMAVRIV 121 (215)
Q Consensus 42 ~~~~klF~kw~~~~v~v~D~~l~~yi~~~~k~~~~~phs~gr~~~krf~k~~~piverliN~LM~~g~n~GKK~~A~rIV 121 (215)
..++|||||||++||+|+||||++||+++++.++++|||+|||++|+|+|++||||+||||.||++|+|+|||++|++||
T Consensus 3 ~~~~~lf~kw~~~~v~~~d~~l~~yi~~~~~~~~~~pht~gr~~~k~f~k~~~~iVerLiN~lM~~grn~GKK~~A~~IV 82 (193)
T PTZ00091 3 ANEPKLFGKWSYDDVQVSDLSLKDYIAVTTKASVFVPHTAGRYQKKRFRKAQCPIVERLVNSLMFHGRNNGKKLLAVRIV 82 (193)
T ss_pred CccchhhCCcCcccCeecCcCHHHHhhcccCCceeeccccchhhcCccCcccCHHHHHHHHHHhccCccCCcHHHHHHHH
Confidence 45689999999999999999999999999988899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhCCChhHHHHHHHHhcCCccceEEeccCCeeeEEeeecChhHHHHHHHHHHHHHHHhhhcCCCCcHHHHH
Q psy10065 122 KHAFEIIHLLTGENPLQILVTAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECV 201 (215)
Q Consensus 122 ~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~Rig~gG~~yqvPV~vsp~Rr~~lAiwlI~~~ar~~~~r~~ks~~e~L 201 (215)
|+||++|+++|++||+|||++||+|++|++|++|+++||++|||||||+|.||++|||+||++|||+++||++++|++||
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 99999999999999999999999999999999999999999999999999999999995555999999999999999999
Q ss_pred HHHHHHHhcccCC
Q psy10065 202 ADELINAAKFNQN 214 (215)
Q Consensus 202 A~EII~Aa~~~g~ 214 (215)
|+|||+|++|+|+
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=1.3e-69 Score=462.31 Aligned_cols=174 Identities=50% Similarity=0.748 Sum_probs=167.0
Q ss_pred CCCCCcccceeccccCCCceeecCCcccceeccccccceecCCCCcccccccCccCChhHHHHHHHhhccccccchHHHH
Q psy10065 38 APAELPEIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSLMMHGRNNAKKLMA 117 (215)
Q Consensus 38 ~~~~~~~~klF~kw~~~~v~v~D~~l~~yi~~~~k~~~~~phs~gr~~~krf~k~~~piverliN~LM~~g~n~GKK~~A 117 (215)
....+.++|||||||++||+|+||||++||+++| +++|||+|||++|+|.|++||||+||||+||++|+|+|||++|
T Consensus 4 ~~~~~~~~~lf~kw~~~~v~~~d~~l~~yi~~~~---~~~pht~gr~~~k~f~k~~~~iVerLiN~lM~~~~n~GKK~~A 80 (195)
T PRK04027 4 EEAEPMEIKLFGKWDVEEVEVRDPSLKRYINLTP---VLVPHTGGRHAKKQFGKAEVPIVERLINKLMRTERNTGKKQKA 80 (195)
T ss_pred ccccchhhhhhCCCCccceeEcccchHhheeecc---eecCcccccccccCcccccCHHHHHHHHHHhccCccCCcHHHH
Confidence 3456778999999999999999999999999998 9999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCChhHHHHHHHHhcCCccceEEeccCCeeeEEeeecChhHHHHHHHHHHHHHHHhhhcCCCCcH
Q psy10065 118 VRIVKHAFEIIHLLTGENPLQILVTAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTI 197 (215)
Q Consensus 118 ~rIV~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~Rig~gG~~yqvPV~vsp~Rr~~lAiwlI~~~ar~~~~r~~ks~ 197 (215)
++|||+||++|+++|++||+|||++||+|++|++|++++++||++|||||||+|.||++|||+||++|||+++||++++|
T Consensus 81 ~~Iv~~AfeiI~~kT~~nPiqVl~~AI~N~~P~~Ev~~~r~GG~tyqvpVdV~p~Rr~~lAirwI~~~ar~r~fr~~ksm 160 (195)
T PRK04027 81 YNIVKEAFEIIEKRTKQNPIQVLVDAIENAAPREETTRIKYGGISYPKAVDVSPQRRVDLALRFIAEGARQASFKNKKSI 160 (195)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCeEEEEEecCCEEEEeeeecCHHHHHHHHHHHHHHHHHhccccCCCCH
Confidence 99999999999999999999999999999999999999999999999999999999999999555599999999999999
Q ss_pred HHHHHHHHHHHhcccCC
Q psy10065 198 AECVADELINAAKFNQN 214 (215)
Q Consensus 198 ~e~LA~EII~Aa~~~g~ 214 (215)
++|||+|||+|++|+++
T Consensus 161 ~e~LA~ElidAa~~~~~ 177 (195)
T PRK04027 161 EEALAEEIIAAANNDPK 177 (195)
T ss_pred HHHHHHHHHHHHcCCCC
Confidence 99999999999999643
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=8.4e-66 Score=436.71 Aligned_cols=168 Identities=64% Similarity=0.966 Sum_probs=162.7
Q ss_pred ccceeccccCCCceeecCCcccceeccccccceecCCCCcccccccCccCChhHHHHHHHhhccccccchHHHHHHHHHH
Q psy10065 44 EIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSLMMHGRNNAKKLMAVRIVKH 123 (215)
Q Consensus 44 ~~klF~kw~~~~v~v~D~~l~~yi~~~~k~~~~~phs~gr~~~krf~k~~~piverliN~LM~~g~n~GKK~~A~rIV~~ 123 (215)
++|||||||++||+|+||||.+||++++ +++|||+|||++|+|+|+++|+|+||||+||++|+|+|||++|++|||+
T Consensus 1 ~~~lf~kw~~~~v~~~d~~l~~yi~~~~---~~~pht~gr~~~k~f~k~~~~iV~rliN~lM~~g~n~GKK~~A~kIv~~ 77 (186)
T TIGR01028 1 EIKVFGKWSTDDVEVKDPSLKDYINLEP---KYVPHTAGRHAKKQFRKAKVPIVERLINKVMRSGRNNGKKLKAYRIVKE 77 (186)
T ss_pred CccccCCcCCccceecCCCHHhhhhcCc---eeccchhhhhhccccCcccCHHHHHHHHHHhccCcCCCcHHHHHHHHHH
Confidence 4799999999999999999999999998 8999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCChhHHHHHHHHhcCCccceEEeccCCeeeEEeeecChhHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHH
Q psy10065 124 AFEIIHLLTGENPLQILVTAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECVAD 203 (215)
Q Consensus 124 AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~Rig~gG~~yqvPV~vsp~Rr~~lAiwlI~~~ar~~~~r~~ks~~e~LA~ 203 (215)
||++|+++|++||++||++||+|++|++|+++++.||++|||||||+|.||++|||+||++|||+++||++++|++|||+
T Consensus 78 A~~iI~~~t~~nPi~vl~~AI~N~~P~~ev~~~r~GG~~yqVPv~v~p~Rr~~lAirWI~~~ar~~~~R~~k~m~~~LA~ 157 (186)
T TIGR01028 78 AFEIIEKRTGENPIQVLVDAIENAGPREDTTRIGYGGIVYRQAVDISPLRRVDQALRNIALGAREAAFRNKKSIAECLAE 157 (186)
T ss_pred HHHHHHHHhCCChHHHHHHHHHcCCCCeEEEEEecCCEEEEeccccCHHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999555599999899999999999999
Q ss_pred HHHHHhcccCC
Q psy10065 204 ELINAAKFNQN 214 (215)
Q Consensus 204 EII~Aa~~~g~ 214 (215)
|||+|++|+|+
T Consensus 158 Eii~A~~~~g~ 168 (186)
T TIGR01028 158 EIILAANGDSK 168 (186)
T ss_pred HHHHHHhCCCC
Confidence 99999999964
No 4
>KOG3291|consensus
Probab=100.00 E-value=1.2e-58 Score=396.97 Aligned_cols=180 Identities=66% Similarity=0.902 Sum_probs=174.9
Q ss_pred CCCCCCCcccceeccccCCCceeecCCcccceeccccccceecCCCCcccccccCccCChhHHHHHHHhhccccccchHH
Q psy10065 36 IAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSLMMHGRNNAKKL 115 (215)
Q Consensus 36 ~~~~~~~~~~klF~kw~~~~v~v~D~~l~~yi~~~~k~~~~~phs~gr~~~krf~k~~~piverliN~LM~~g~n~GKK~ 115 (215)
++.+...++++||++|++++++++|+||.|||+++|++..++||++|+++.++|.|+.||++++|+|+||++|+|+|||.
T Consensus 14 ~~~~~~~~~~~~f~~~s~~~~~~~d~sl~dy~~~~~k~~~~~~~~~~~~~~~~~~ka~~~~~e~l~~~l~n~~~~~GKK~ 93 (208)
T KOG3291|consen 14 AERVAETGEIKLFEKWSEDSVEFSDISLQDYIALKPKDLTQLPHSAGRYAKKRFRKAQCPIVERLINKLMNHIMKNGKKL 93 (208)
T ss_pred hhhhcccchhHHHHHhhcccccccccccccccccccccccccccccchhhhhhhhhccccHHHHHHHHHHHHHHhcccHH
Confidence 44577788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCChhHHHHHHHHhcCCccceEEeccCCeeeEEeeecChhHHHHHHHHHHHHHHHhhhcCCCC
Q psy10065 116 MAVRIVKHAFEIIHLLTGENPLQILVTAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIK 195 (215)
Q Consensus 116 ~A~rIV~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~Rig~gG~~yqvPV~vsp~Rr~~lAiwlI~~~ar~~~~r~~k 195 (215)
+|++||++||++|+++|++||+|||++||+||+|+++++++|+||++|||||||+|.||+++|||||+++||+++|++.+
T Consensus 94 ~a~~Iv~~aleiI~~~t~~NPiqvl~~AI~n~~P~~~~~~i~r~g~~~~vpv~v~~~rr~~~Ai~wi~~~ar~~~~~~~~ 173 (208)
T KOG3291|consen 94 LARRIVKHALEIIKRLTERNPIQVLVQAIENCGPLEDVTRIGRAGTTYQVPVPVSPLRRVNLAIKWILTGARERSFRNIK 173 (208)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCchhhceeecccceEEEecccCCcHHHHHHHHHHHHHHHHhccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999998888999999999999
Q ss_pred cHHHHHHHHHHHHhcccCCC
Q psy10065 196 TIAECVADELINAAKFNQNR 215 (215)
Q Consensus 196 s~~e~LA~EII~Aa~~~g~s 215 (215)
+|++|||+|||+|++|+|++
T Consensus 174 ~~ae~La~ELi~Aakgs~~a 193 (208)
T KOG3291|consen 174 TLAECLADELIAAAKGSGNA 193 (208)
T ss_pred cHHHHHHHHHHHHHhCCchh
Confidence 99999999999999999974
No 5
>COG0049 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-47 Score=312.04 Aligned_cols=132 Identities=42% Similarity=0.523 Sum_probs=126.4
Q ss_pred ecCCCCcccccccCccCChhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHhcCCccceEEe
Q psy10065 77 LPHSAGRYAAKRFRKAQCPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENPLQILVTAIINSGPREDSTRI 156 (215)
Q Consensus 77 ~phs~gr~~~krf~k~~~piverliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~Ri 156 (215)
.||+.|++....|++++++||+||||.||++ |||++|++|||.||++|+++|++||||||++||+|++|++|++++
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 RRHTAGKREVLPDPKYNSVIVERLINKIMRD----GKKSLAEKIVYGAFDIIEKKTGQNPLQVFEKAIENVKPREEVKSR 77 (148)
T ss_pred CCCCCCcccCCCCcccccHHHHHHHHHHHHh----ccHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHhcCchhheeee
Confidence 6899999999999999999999999999998 999999999999999999999999999999999999999999999
Q ss_pred ccCCeeeEEeeecChhHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHHHHHhcccCCC
Q psy10065 157 GRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECVADELINAAKFNQNR 215 (215)
Q Consensus 157 g~gG~~yqvPV~vsp~Rr~~lAiwlI~~~ar~~~~r~~ks~~e~LA~EII~Aa~~~g~s 215 (215)
++||.+|||||||+|.||++|||+||+.+||+ +++++|++|||+|||||+||+|.|
T Consensus 78 rvGGa~yqvpVeV~p~RR~~lAlrwi~~~Ar~---r~~ktm~erLA~Eli~Aan~~g~A 133 (148)
T COG0049 78 RVGGATYQVPVEVRPRRRVALALRWIVEGARK---RNEKTMAERLANELIDAANNTGAA 133 (148)
T ss_pred eeCCeeeEecCccCHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHcCCcch
Confidence 99999999999999999999999445499996 689999999999999999999864
No 6
>PRK05302 30S ribosomal protein S7; Validated
Probab=100.00 E-value=1.3e-37 Score=257.74 Aligned_cols=128 Identities=35% Similarity=0.476 Sum_probs=116.4
Q ss_pred CCCcccccc----cCccCChhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHhcCCccceEE
Q psy10065 80 SAGRYAAKR----FRKAQCPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENPLQILVTAIINSGPREDSTR 155 (215)
Q Consensus 80 s~gr~~~kr----f~k~~~piverliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~R 155 (215)
++.+.++|+ -+.+++|+|++|||+||++ |||++|++||++||++|++.|++||++||++||+|++|.+|+++
T Consensus 2 ~r~~~~~~~~~~~d~~~~~~lv~~lin~lmk~----GKK~~A~kI~~~al~~I~~~~~~npl~il~~Ai~nv~P~~evk~ 77 (156)
T PRK05302 2 PRRRRAPKREVLPDPKYGSVLVTKFINKLMLD----GKKSVAEKIVYGALDIIEEKTGKDPLEVFEKALENVKPVVEVKS 77 (156)
T ss_pred CCCCCCCCCCCCCCCCcCCHHHHHHHHHHhhc----ccHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHhCCCCeEEee
Confidence 444444443 3567899999999999998 99999999999999999999999999999999999999999998
Q ss_pred eccCCeeeEEeeecChhHHHHHHH-HHHHHHHHhhhcCCCCcHHHHHHHHHHHHhcccCCC
Q psy10065 156 IGRAGTVRRQAVDVSPLRRVNQAI-WLLCTGAREAAFRNIKTIAECVADELINAAKFNQNR 215 (215)
Q Consensus 156 ig~gG~~yqvPV~vsp~Rr~~lAi-wlI~~~ar~~~~r~~ks~~e~LA~EII~Aa~~~g~s 215 (215)
++.||.+||||++|+|.||+++|| |+| ++|++ |++++|+++||+|||+|++++|.+
T Consensus 78 ~r~gG~~~~vP~~i~~~rr~~lAirwil-~~a~~---r~~~~~~~~La~Eii~A~~~~g~a 134 (156)
T PRK05302 78 RRVGGATYQVPVEVRPERRQALAMRWLV-EAARK---RGEKTMAERLANELLDAANNRGAA 134 (156)
T ss_pred eccCCEEEEEeEEeCHHHHHHHHHHHHH-HHHHH---cCCCCHHHHHHHHHHHHHhCCCCe
Confidence 899999999999999999999999 666 89985 678999999999999999999974
No 7
>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=2e-37 Score=256.15 Aligned_cols=118 Identities=33% Similarity=0.463 Sum_probs=112.1
Q ss_pred CccCChhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHhcCCccceEEeccCCeeeEEeeec
Q psy10065 90 RKAQCPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENPLQILVTAIINSGPREDSTRIGRAGTVRRQAVDV 169 (215)
Q Consensus 90 ~k~~~piverliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~Rig~gG~~yqvPV~v 169 (215)
+.+++|+|++|||+||++ |||++|++||++||++|++.|++||++||++||+|++|.+|+++++.||.+||||++|
T Consensus 14 ~~y~~~lv~~lin~lM~~----GKK~~A~kI~~~al~~i~~~~~~nPi~vl~~Ai~nv~P~~evk~~r~gG~~yqvP~~v 89 (154)
T TIGR01029 14 PVYGSVLLNKFINRVMKD----GKKSLAESIVYKAFERIAKKTGEDPLEVFEQALENVKPLVEVKSRRVGGATYQVPVEV 89 (154)
T ss_pred CccCCHHHHHHHHHHHhc----ccHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCCeeeEEeecCCEEEEEeeEc
Confidence 457899999999999998 9999999999999999999999999999999999999999999889999999999999
Q ss_pred ChhHHHHHHH-HHHHHHHHhhhcCCCCcHHHHHHHHHHHHhcccCCC
Q psy10065 170 SPLRRVNQAI-WLLCTGAREAAFRNIKTIAECVADELINAAKFNQNR 215 (215)
Q Consensus 170 sp~Rr~~lAi-wlI~~~ar~~~~r~~ks~~e~LA~EII~Aa~~~g~s 215 (215)
+|.||+++|| |++ ++|++ |++++|+++||+|||+|++++|.+
T Consensus 90 ~~~rr~~lAirWil-~~a~~---r~~~~~~~~La~Eii~A~~~~g~a 132 (154)
T TIGR01029 90 RPSRRYALAIRWLI-EAARK---RGGKSMAERLANEILDAANNTGAA 132 (154)
T ss_pred CHHHHHHHHHHHHH-HHHHh---cCCCCHHHHHHHHHHHHHhCCCce
Confidence 9999999999 666 89996 678999999999999999999975
No 8
>CHL00053 rps7 ribosomal protein S7
Probab=100.00 E-value=4e-37 Score=254.52 Aligned_cols=118 Identities=31% Similarity=0.403 Sum_probs=111.1
Q ss_pred CccCChhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHhcCCccceEEeccCCeeeEEeeec
Q psy10065 90 RKAQCPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENPLQILVTAIINSGPREDSTRIGRAGTVRRQAVDV 169 (215)
Q Consensus 90 ~k~~~piverliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~Rig~gG~~yqvPV~v 169 (215)
+.+++++|++|||+||++ |||++|++||++||++|++.|++||++||++||+|++|.+|++.++.||.+||||++|
T Consensus 16 ~~~~~~lv~~lin~lm~~----GKK~~A~kIv~~al~~i~~~~~~npi~vl~~Ai~N~~P~~evk~~r~gG~~~qvPv~v 91 (155)
T CHL00053 16 PIYRNRLVNMLVNRILKS----GKKSLAYRIVYRALKKIQQKTEKNPLSVLRQAIRNVTPDVEVKARRVGGSTYQVPIEI 91 (155)
T ss_pred CCcCcHHHHHHHHHHHhc----ccHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCcEEEEEEeeCCEEEEEeeEc
Confidence 457899999999999998 9999999999999999999999999999999999999999988888899999999999
Q ss_pred ChhHHHHHHH-HHHHHHHHhhhcCCCCcHHHHHHHHHHHHhcccCCC
Q psy10065 170 SPLRRVNQAI-WLLCTGAREAAFRNIKTIAECVADELINAAKFNQNR 215 (215)
Q Consensus 170 sp~Rr~~lAi-wlI~~~ar~~~~r~~ks~~e~LA~EII~Aa~~~g~s 215 (215)
+|.||+++|| |+| ++|++ |++++|+++||+||++|++|+|++
T Consensus 92 ~~~rr~~lAirWil-~~ar~---r~~~~~~~~La~Eii~A~~~~g~a 134 (155)
T CHL00053 92 GSTRGKALAIRWLL-KASRK---RSGRNMAFKLSSELVDAAKGSGNA 134 (155)
T ss_pred CHHHHHHHHHHHHH-HHHHh---cCCCCHHHHHHHHHHHHHhCCCch
Confidence 9999999999 666 89986 557799999999999999999974
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=2.3e-36 Score=247.34 Aligned_cols=129 Identities=38% Similarity=0.533 Sum_probs=119.8
Q ss_pred ecCCCCccccc--ccCccCChhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHhcCCccceE
Q psy10065 77 LPHSAGRYAAK--RFRKAQCPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENPLQILVTAIINSGPREDST 154 (215)
Q Consensus 77 ~phs~gr~~~k--rf~k~~~piverliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nPiqVl~~AI~N~~P~~es~ 154 (215)
.||+ |+|.++ ..+++++|++++|||.||++ |||++|++||++||++|++.+++||++||++||+|++|.++++
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-GRYKKKKIPDPKFNDPLVKKFINRLMKD----GKKSKAEKIVYKALEIIKKKTNKNPIQILKQAIENVKPLVEVR 75 (148)
T ss_dssp SSTS-SS-SSSS-SBTTTCGHHHHHHHHHHHST----TBHHHHHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHS-SEEEE
T ss_pred CCCC-CCCCCCCCCCcccccHHHHHHHHHHHHH----hHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHhccceeee
Confidence 3677 899988 56789999999999999998 9999999999999999999999999999999999999999999
Q ss_pred EeccCCeeeEEeeecChhHHHHHHH-HHHHHHHHhhhcCCCCcHHHHHHHHHHHHhcccCC
Q psy10065 155 RIGRAGTVRRQAVDVSPLRRVNQAI-WLLCTGAREAAFRNIKTIAECVADELINAAKFNQN 214 (215)
Q Consensus 155 Rig~gG~~yqvPV~vsp~Rr~~lAi-wlI~~~ar~~~~r~~ks~~e~LA~EII~Aa~~~g~ 214 (215)
+++.||.+||||++++|.||+++|| |+| ++++ +|++++|+++||+||++|++++|.
T Consensus 76 ~~k~gg~~~~vP~~i~~~r~~~lAikWi~-~~~~---~r~~~~~~~~La~Eii~a~~~~g~ 132 (148)
T PF00177_consen 76 SIKKGGKTYQVPVPISPKRRIFLAIKWIL-EAAR---KRKEKSFSERLANEIIDASNNKGS 132 (148)
T ss_dssp EEEETTEEEEEEEEETHHHHHHHHHHHHH-HHHH---TSSSSSHHHHHHHHHHHHHTTSSH
T ss_pred eeccCceeEEEEEeecHHHHHHHHHHHHH-HHHh---hcccchHHHHHHHHHHHHHcCCcH
Confidence 9999999999999999999999999 777 8998 477899999999999999999985
No 10
>KOG3960|consensus
Probab=64.83 E-value=7.3 Score=35.58 Aligned_cols=34 Identities=32% Similarity=0.397 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhCCCh------hHHHHHHHHhcCCccc
Q psy10065 119 RIVKHAFEIIHLLTGENP------LQILVTAIINSGPRED 152 (215)
Q Consensus 119 rIV~~AfeiI~~~t~~nP------iqVl~~AI~N~~P~~e 152 (215)
+=|.+|||.+++.|--|| ++||..||+-+-=+++
T Consensus 131 kKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~ 170 (284)
T KOG3960|consen 131 KKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQA 170 (284)
T ss_pred HHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHH
Confidence 458999999999998887 6799999987765554
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=47.90 E-value=31 Score=24.28 Aligned_cols=41 Identities=22% Similarity=0.377 Sum_probs=32.3
Q ss_pred ChhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCChhHHHHHHH
Q psy10065 94 CPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENPLQILVTAI 144 (215)
Q Consensus 94 ~piverliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nPiqVl~~AI 144 (215)
.++.++|.+.++. |....+.+++.++++ ++.+|..++.+.+
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 3678999999997 899999999998887 3577888777655
No 12
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=37.27 E-value=87 Score=18.36 Aligned_cols=35 Identities=23% Similarity=0.328 Sum_probs=22.0
Q ss_pred HHHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCCh
Q psy10065 98 ERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENP 136 (215)
Q Consensus 98 erliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nP 136 (215)
..|.+.++.. |+...|..+..+++++-++..+.|+
T Consensus 6 ~~la~~~~~~----g~~~~A~~~~~~al~~~~~~~G~~H 40 (42)
T PF13374_consen 6 NNLANAYRAQ----GRYEEALELLEEALEIRERLLGPDH 40 (42)
T ss_dssp HHHHHHHHHC----T-HHHHHHHHHHHHHHH--------
T ss_pred HHHHHHHHhh----hhcchhhHHHHHHHHHHHHHhcccc
Confidence 4566667776 9999999999999999888776653
No 13
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=24.74 E-value=89 Score=26.30 Aligned_cols=50 Identities=22% Similarity=0.242 Sum_probs=25.1
Q ss_pred cceEEeccCCeeeEEeeecChhHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHHHHHhcc
Q psy10065 151 EDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECVADELINAAKF 211 (215)
Q Consensus 151 ~es~Rig~gG~~yqvPV~vsp~Rr~~lAiwlI~~~ar~~~~r~~ks~~e~LA~EII~Aa~~ 211 (215)
+||+| ||||..+-+=|++......-. .++ + .-+.++.+.=|..||+..-.
T Consensus 58 VESrR-GGGGyIRI~rv~~~~~~~~~~--~l~-----~---~ig~~is~~~a~~ii~~L~e 107 (152)
T PF05848_consen 58 VESRR-GGGGYIRIVRVPLDDEEDLLD--HLI-----E---SIGDSISQQDAEDIIQRLLE 107 (152)
T ss_dssp EEEE--STT-EEEEEEEEESTCHHHHH--HHH-----C---CS-S---HHHHHHHHHHHHH
T ss_pred EEecc-CCCceEEEEEEccCCcHHHHH--HHH-----H---HhcCcCCHHHHHHHHHHHHH
Confidence 45766 889987777777776443211 111 1 22456667777777765543
No 14
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=22.66 E-value=2.1e+02 Score=24.14 Aligned_cols=30 Identities=30% Similarity=0.413 Sum_probs=21.1
Q ss_pred ceEEeccCCeeeEEeeecChhHHHHHHH-HHH
Q psy10065 152 DSTRIGRAGTVRRQAVDVSPLRRVNQAI-WLL 182 (215)
Q Consensus 152 es~Rig~gG~~yqvPV~vsp~Rr~~lAi-wlI 182 (215)
||+| ||||+.+-.-|.-+..-..--+| -.|
T Consensus 59 ESKR-GGGGYIRI~Kv~~~~~~~~i~~l~~~I 89 (153)
T COG4463 59 ESKR-GGGGYIRIIKVEYSDNHELINALLQLI 89 (153)
T ss_pred Eeec-CCCceEEEEEecccchHHHHHHHHHHH
Confidence 4555 88898888888888777655555 444
No 15
>KOG3324|consensus
Probab=22.24 E-value=95 Score=27.44 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=32.9
Q ss_pred hhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHH
Q psy10065 95 PIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLL 131 (215)
Q Consensus 95 piverliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~ 131 (215)
|-..|.+|+.|++|+-=|+-.=+.-++|.+||.+=..
T Consensus 112 lr~nrILN~~t~~G~~~gN~lG~laL~YsaiesgI~~ 148 (206)
T KOG3324|consen 112 LRLNRILNSVTRRGRFWGNTLGSLALMYSAIESGIEA 148 (206)
T ss_pred hhHHHHhhhccccccccccchhHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999987543
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=20.30 E-value=3.2e+02 Score=20.61 Aligned_cols=41 Identities=12% Similarity=0.177 Sum_probs=31.3
Q ss_pred HHHHHhhccccccchHHHHHHHHHHHHHHHHHHhCCChhHHHHHH
Q psy10065 99 RLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGENPLQILVTA 143 (215)
Q Consensus 99 rliN~LM~~g~n~GKK~~A~rIV~~AfeiI~~~t~~nPiqVl~~A 143 (215)
.-++.|+.+ |...++.++..+|.|.|---.+.|+=++...+
T Consensus 19 SYT~~L~~~----G~~ki~kKvgEEa~E~iiAa~~~d~~~~~~E~ 59 (84)
T TIGR03188 19 SYTARLFAK----GLDKILKKVGEEAVEVVIAAKNGDKEELVYEA 59 (84)
T ss_pred cHHHHHHhC----cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 456777776 99999999999999998776666666655443
Done!