Query psy11361
Match_columns 200
No_of_seqs 116 out of 1065
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 16:25:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11361.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11361hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00178 60S ribosomal protein 100.0 1.2E-56 2.6E-61 376.7 17.6 178 1-196 1-178 (181)
2 TIGR01038 L22_arch ribosomal p 100.0 4.6E-56 1E-60 363.6 15.8 150 4-168 1-150 (150)
3 PRK04223 rpl22p 50S ribosomal 100.0 1.6E-54 3.4E-59 355.6 16.0 151 1-169 3-153 (153)
4 KOG3353|consensus 100.0 6.5E-45 1.4E-49 304.2 -0.9 170 7-191 1-170 (175)
5 COG0091 RplV Ribosomal protein 100.0 1.8E-38 3.9E-43 252.1 10.3 118 4-169 1-119 (120)
6 CHL00034 rpl22 ribosomal prote 100.0 2.5E-36 5.4E-41 237.9 13.2 112 10-168 5-117 (117)
7 PRK00565 rplV 50S ribosomal pr 100.0 2.7E-35 5.9E-40 229.6 12.6 109 14-169 2-111 (112)
8 TIGR01044 rplV_bact ribosomal 100.0 4.3E-35 9.4E-40 225.7 10.4 102 17-165 1-103 (103)
9 PF00237 Ribosomal_L22: Riboso 100.0 4.8E-34 1E-38 218.5 8.3 104 17-167 1-105 (105)
10 PRK12279 50S ribosomal protein 100.0 1.7E-33 3.8E-38 252.7 11.6 112 13-171 1-114 (311)
11 cd00336 Ribosomal_L22 Ribosoma 100.0 3.2E-32 6.8E-37 208.1 12.0 104 15-165 1-105 (105)
12 KOG1711|consensus 99.9 6.4E-22 1.4E-26 170.4 7.5 123 3-174 62-186 (218)
13 KOG3353|consensus 96.3 0.00068 1.5E-08 57.7 -1.0 77 80-156 15-118 (175)
14 COG0091 RplV Ribosomal protein 75.0 1.2 2.7E-05 35.8 0.7 22 132-153 64-86 (120)
15 PRK11235 bifunctional antitoxi 74.2 13 0.00028 28.0 6.0 66 27-112 14-80 (80)
16 TIGR01999 iscU FeS cluster ass 71.6 23 0.00049 27.8 7.1 70 13-104 52-121 (124)
17 PRK11325 scaffold protein; Pro 69.4 21 0.00046 28.2 6.5 69 13-103 54-122 (127)
18 PF12637 TSCPD: TSCPD domain; 62.4 26 0.00056 26.5 5.5 53 26-98 37-94 (95)
19 TIGR03419 NifU_clost FeS clust 60.7 59 0.0013 25.4 7.5 70 13-104 48-118 (121)
20 TIGR01994 SUF_scaf_2 SUF syste 57.4 41 0.0009 26.9 6.2 76 13-99 52-136 (137)
21 KOG3361|consensus 55.9 21 0.00046 30.0 4.4 53 29-103 96-148 (157)
22 CHL00034 rpl22 ribosomal prote 54.9 7.9 0.00017 30.7 1.7 19 135-153 67-85 (117)
23 COG3077 RelB DNA-damage-induci 53.3 21 0.00045 27.5 3.7 31 29-60 19-49 (88)
24 TIGR02384 RelB_DinJ addiction 53.2 46 0.00099 24.8 5.4 33 27-60 15-47 (83)
25 TIGR01038 L22_arch ribosomal p 51.1 7.8 0.00017 32.2 1.1 24 132-155 97-120 (150)
26 PF01713 Smr: Smr domain; Int 49.3 18 0.0004 25.8 2.7 36 36-71 3-40 (83)
27 PF04221 RelB: RelB antitoxin; 49.1 24 0.00052 25.8 3.4 33 27-60 14-46 (83)
28 PF01592 NifU_N: NifU-like N t 47.2 90 0.002 24.3 6.5 70 12-103 51-121 (126)
29 PRK04223 rpl22p 50S ribosomal 44.7 11 0.00024 31.4 1.1 23 132-154 99-121 (153)
30 PF00237 Ribosomal_L22: Riboso 42.5 13 0.00028 28.3 1.1 19 136-154 57-75 (105)
31 TIGR01044 rplV_bact ribosomal 40.3 16 0.00035 28.1 1.3 19 135-153 56-74 (103)
32 COG1094 Predicted RNA-binding 36.7 29 0.00063 30.3 2.5 30 21-50 59-89 (194)
33 cd06664 IscU_like Iron-sulfur 33.0 1.9E+02 0.0041 22.0 6.3 42 13-54 49-90 (123)
34 TIGR02000 NifU_proper Fe-S clu 31.2 2.1E+02 0.0045 26.0 7.1 70 13-104 53-123 (290)
35 smart00463 SMR Small MutS-rela 26.8 58 0.0013 23.0 2.3 23 36-58 6-28 (80)
36 PF03793 PASTA: PASTA domain; 25.8 58 0.0012 21.7 2.0 15 36-50 6-20 (63)
37 PTZ00178 60S ribosomal protein 25.6 36 0.00079 29.3 1.2 23 132-154 100-122 (181)
38 PF13286 HD_assoc: Phosphohydr 21.9 1.1E+02 0.0024 22.0 3.0 23 27-49 69-91 (92)
39 COG0822 IscU NifU homolog invo 21.4 1.9E+02 0.0041 23.8 4.6 84 14-103 56-142 (150)
40 PF11116 DUF2624: Protein of u 21.1 37 0.00081 26.0 0.4 25 18-42 25-49 (85)
No 1
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=1.2e-56 Score=376.73 Aligned_cols=178 Identities=62% Similarity=1.037 Sum_probs=167.3
Q ss_pred CcccCCCCCCCCceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCC
Q psy11361 1 MGRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQ 80 (200)
Q Consensus 1 m~~YS~~~~d~~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~ 80 (200)
|++||++.+|++++++|..++++|||+|+++||++||||++++|++||++||++|++|||+|||+|+||++|.++||.++
T Consensus 1 ~~~Ys~~~~n~~~~akA~~~~~riSpkk~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~~~~~~ 80 (181)
T PTZ00178 1 MVKYARKPQNPSKSAKAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKEFGHTQ 80 (181)
T ss_pred CCccccCCCCCCceEEEEeCCcccchHHHHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCcccccccccccccc
Confidence 89999999779999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhhHHHHHHHHHHHHHhhhhcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCce
Q psy11361 81 GRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCH 160 (200)
Q Consensus 81 GR~P~Kaa~~~lklLksA~aNA~~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~H 160 (200)
||||+|||..|+|+|+||++||+++|+|+|+|||.||.||+|++++|++|||+| |++||.+++||
T Consensus 81 GR~P~KaA~~i~KlL~SA~aNAe~~gld~d~L~I~~i~v~kG~~lKR~~pRA~G---------------RA~~i~k~t~H 145 (181)
T PTZ00178 81 GRWPEKSVKFVLSLLKNAEANAEAKGLDVEKLVISHVQVNRAPRGRRRTYRAHG---------------RINPFMSSPCH 145 (181)
T ss_pred CcCcHHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCcccCCCCCccCC---------------CcCcccCCcee
Confidence 999999999999999999999999999999999999999999999999999999 99999999999
Q ss_pred EEEEEeeCccccCCCCCCCccccccCHHHHHHHHHh
Q psy11361 161 IEVILSERERVVAKPREDEPHKKKISKKKLARAKEK 196 (200)
Q Consensus 161 I~ivl~e~~~~~~k~~~~~~~~kk~~~~~~~~~~~~ 196 (200)
|+|+|+|.+..+++ .++.+ ||..+|.|++.+-.
T Consensus 146 I~Ivl~e~~~~~~~--~~~~~-~~~~~~~~~~~~~~ 178 (181)
T PTZ00178 146 IELIATEKDETVPK--PKEAP-KKQTKKQLARSKLR 178 (181)
T ss_pred EEEEEEEccccccc--chhhh-hhhhHHHHHHHHhh
Confidence 99999998866665 34444 45567888887643
No 2
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=100.00 E-value=4.6e-56 Score=363.64 Aligned_cols=150 Identities=55% Similarity=0.929 Sum_probs=148.1
Q ss_pred cCCCCCCCCceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCC
Q psy11361 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRW 83 (200)
Q Consensus 4 YS~~~~d~~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~ 83 (200)
||++++||+++++|.++++++||+|+++||++||||++++|+++|++||++|+||||+||++|+||++|+.+|||++|||
T Consensus 1 ys~~~~~~~~~akA~~~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~~~gR~ 80 (150)
T TIGR01038 1 YSYKPEDPTKSAKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKEWGWTAGRY 80 (150)
T ss_pred CCcCCCCCCeeEEEEeCCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccccCCC
Confidence 99999889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHHHHHHHHHHhhhhcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEE
Q psy11361 84 PRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEV 163 (200)
Q Consensus 84 P~Kaa~~~lklLksA~aNA~~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~i 163 (200)
|+|||.+|++||+||++||+++|||+|+|||.||+||+||+++|++|||+| |++||.+++|||+|
T Consensus 81 P~Kaa~~i~klL~sA~aNA~~~gld~d~L~I~~i~vnkg~~~kR~~prA~G---------------Ra~~~~k~~~HI~I 145 (150)
T TIGR01038 81 PVKAAKFILKVLQNAEANAEYKGLDVEKLVIIHIQANKGPKIRRWMPRAFG---------------RATPYNSSPTHIEL 145 (150)
T ss_pred chHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCCccCCCCCccCC---------------CCCcccCCCceEEE
Confidence 999999999999999999999999999999999999999999999999999 99999999999999
Q ss_pred EEeeC
Q psy11361 164 ILSER 168 (200)
Q Consensus 164 vl~e~ 168 (200)
+|+|.
T Consensus 146 il~e~ 150 (150)
T TIGR01038 146 VVEEK 150 (150)
T ss_pred EEecC
Confidence 99874
No 3
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=100.00 E-value=1.6e-54 Score=355.62 Aligned_cols=151 Identities=39% Similarity=0.567 Sum_probs=147.7
Q ss_pred CcccCCCCCCCCceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCC
Q psy11361 1 MGRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQ 80 (200)
Q Consensus 1 m~~YS~~~~d~~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~ 80 (200)
|++||+++ +++++++|.++++++||+|+++||++||||++++|+++|++||++|+||||+||++|+||++|+ |||++
T Consensus 3 ~~~ys~~~-~~~~~akA~~~~~rvS~kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~--~~~~~ 79 (153)
T PRK04223 3 RINYSVKA-DPEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGI--DGWPA 79 (153)
T ss_pred ccccccCC-CCCceEEEEeCCCccChHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccc--ccccc
Confidence 67999999 7999999999999999999999999999999999999999999999999999999999999998 89999
Q ss_pred CCCchhhHHHHHHHHHHHHHhhhhcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCce
Q psy11361 81 GRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCH 160 (200)
Q Consensus 81 GR~P~Kaa~~~lklLksA~aNA~~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~H 160 (200)
||||+|+|.+|+++|+||++||+++|||+|+|||+||+||+|++++|++|||+| |++++.+++||
T Consensus 80 gr~PkKaa~~i~KlL~sA~aNA~~~gld~d~L~I~~i~v~kg~~~kR~~prA~G---------------Ra~~~~k~~sH 144 (153)
T PRK04223 80 GRYPVKAAKAFLKLLENAEANAEYKGLDTEKLVIVHIAAHKGRVIKGYMPRAFG---------------RATPKNTETVN 144 (153)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCCCCCCcCcccCC---------------CCCcccCCCce
Confidence 999999999999999999999999999999999999999999999999999999 99999999999
Q ss_pred EEEEEeeCc
Q psy11361 161 IEVILSERE 169 (200)
Q Consensus 161 I~ivl~e~~ 169 (200)
|+|+|+|.+
T Consensus 145 I~Iil~e~~ 153 (153)
T PRK04223 145 IEVILEEVE 153 (153)
T ss_pred EEEEEEeCC
Confidence 999999853
No 4
>KOG3353|consensus
Probab=100.00 E-value=6.5e-45 Score=304.24 Aligned_cols=170 Identities=74% Similarity=1.178 Sum_probs=167.4
Q ss_pred CCCCCCceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchh
Q psy11361 7 EPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRK 86 (200)
Q Consensus 7 ~~~d~~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~K 86 (200)
+++++++.|+|++.++++|||++++.+..|+++++..|+.+|.+|+.+++|+||.+|++|+|+..|+++|||.+||||+|
T Consensus 1 ~~~~~~k~~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkk 80 (175)
T KOG3353|consen 1 DPENPTKSCKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKK 80 (175)
T ss_pred CccccchhhhcccccEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhhhccccCcccch
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhhhhcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEEEEe
Q psy11361 87 SADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILS 166 (200)
Q Consensus 87 aa~~~lklLksA~aNA~~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ivl~ 166 (200)
+|++++.+|+||++||+.+|+|+|.|+|+||+||++|++.|+|||||| |.+++++.+|||++||+
T Consensus 81 saefll~~LkN~esnaElkgldVDsLvIehiqvnkApKm~~rtyraHg---------------~in~y~ssP~hie~il~ 145 (175)
T KOG3353|consen 81 SAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHG---------------RINPYMSSPCHIEMILT 145 (175)
T ss_pred HHHHHHHHHHhhhhcccccCcCcceeEeeehhhcccchhhhHHHHhhc---------------ccccccCChHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred eCccccCCCCCCCccccccCHHHHH
Q psy11361 167 ERERVVAKPREDEPHKKKISKKKLA 191 (200)
Q Consensus 167 e~~~~~~k~~~~~~~~kk~~~~~~~ 191 (200)
|.++++++++++.|++++++.++++
T Consensus 146 ~ke~~v~k~e~~~~~~~~~~~~~~~ 170 (175)
T KOG3353|consen 146 EKEQIVPKPEEEVAQKKKISQKKLK 170 (175)
T ss_pred hhcccCCChhhhhchhccccHHHHH
Confidence 9999999999999999999999993
No 5
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-38 Score=252.09 Aligned_cols=118 Identities=35% Similarity=0.564 Sum_probs=114.1
Q ss_pred cCCCCCCCCceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCC
Q psy11361 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRW 83 (200)
Q Consensus 4 YS~~~~d~~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~ 83 (200)
||+... ++++++|.++++++||+|+++||++||||++.+|+.+|+ | .
T Consensus 1 y~~~~~-~~~~akA~~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~----------~----------------------~ 47 (120)
T COG0091 1 YSAKVE-PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILE----------F----------------------V 47 (120)
T ss_pred CCcccc-hhhhhHhhhccCcCChHHHHHHHHHHcCCcHHHHHHHHH----------h----------------------C
Confidence 778875 899999999999999999999999999999999999999 8 8
Q ss_pred chhhHHHHHHHHHHHHHhhhh-cCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEE
Q psy11361 84 PRKSADFLLQLLKNAESNADY-RGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIE 162 (200)
Q Consensus 84 P~Kaa~~~lklLksA~aNA~~-~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ 162 (200)
|+|||+.|+|+|+||++||++ +|||+|+|||.||+||+||++||++|||+| |++++.+++|||+
T Consensus 48 pkKaa~~v~KvL~sA~aNAe~n~gLd~d~L~V~~i~v~~gp~lKR~~pRA~G---------------Ra~~i~k~tshIt 112 (120)
T COG0091 48 PKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDKGPVLKRFMPRARG---------------RATRINKRTSHIT 112 (120)
T ss_pred hHHHHHHHHHHHHHHHhhHHhccCCChHHEEEEEEEeCCCceeeeecccccC---------------ccccccCCCceEE
Confidence 999999999999999999997 799999999999999999999999999999 9999999999999
Q ss_pred EEEeeCc
Q psy11361 163 VILSERE 169 (200)
Q Consensus 163 ivl~e~~ 169 (200)
|+|+|.+
T Consensus 113 vvv~e~~ 119 (120)
T COG0091 113 VVVREKE 119 (120)
T ss_pred EEEeecC
Confidence 9999864
No 6
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00 E-value=2.5e-36 Score=237.92 Aligned_cols=112 Identities=27% Similarity=0.447 Sum_probs=108.3
Q ss_pred CCCceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHH
Q psy11361 10 NPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSAD 89 (200)
Q Consensus 10 d~~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~ 89 (200)
.++++++|..+++++||+|+++||++||||++++|+.||+ | .|+|+|.
T Consensus 5 ~~~~~~~A~~~~ir~SpkK~r~va~~IRG~~v~~A~~~L~----------~----------------------~pkk~a~ 52 (117)
T CHL00034 5 KSTTEVYALAKYIRMSAHKARRVIDQIRGRSYEEALMILE----------F----------------------MPYRACY 52 (117)
T ss_pred CCCceEEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHH----------H----------------------CcHHHHH
Confidence 4678999999999999999999999999999999999999 8 9999999
Q ss_pred HHHHHHHHHHHhhh-hcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEEEEeeC
Q psy11361 90 FLLQLLKNAESNAD-YRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSER 168 (200)
Q Consensus 90 ~~lklLksA~aNA~-~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ivl~e~ 168 (200)
.|+++|+||++||+ ++|||+|+|||.||+||+||++||++|||+| |++++.+++|||+|+|+|.
T Consensus 53 ~i~klL~sA~aNA~~~~gld~d~L~I~~i~v~~G~~~KR~~prArG---------------Ra~~i~k~~sHI~Vvl~e~ 117 (117)
T CHL00034 53 PILKLVYSAAANASHNMGLNKANLFISKAEVDEGPTLKRFRPRAQG---------------RSYPIKKPTCHITIVLKDI 117 (117)
T ss_pred HHHHHHHHHHHHHHHccCCCccceEEEEEEECCCCccCCCCcccCC---------------CCCcccCCCccEEEEEecC
Confidence 99999999999995 8899999999999999999999999999999 9999999999999999873
No 7
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00 E-value=2.7e-35 Score=229.58 Aligned_cols=109 Identities=34% Similarity=0.524 Sum_probs=106.2
Q ss_pred eEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHHH
Q psy11361 14 SCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQ 93 (200)
Q Consensus 14 ~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~lk 93 (200)
.++|.++++++||+|+++||++|+||++++|+.+|+ | ||+|+|..|++
T Consensus 2 ~~~A~~~~~~~SpkK~~~v~~~IrG~~v~~A~~~L~----------~----------------------~pkk~a~~i~k 49 (112)
T PRK00565 2 EAKAKARYVRVSPRKARLVADLIRGKKVEEALAILK----------F----------------------SPKKAARLVKK 49 (112)
T ss_pred ceEEEeCccccCHHHHHHHHHHHcCCcHHHHHHHHH----------H----------------------CcHhHHHHHHH
Confidence 478999999999999999999999999999999999 8 99999999999
Q ss_pred HHHHHHHhhhh-cCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEEEEeeCc
Q psy11361 94 LLKNAESNADY-RGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERE 169 (200)
Q Consensus 94 lLksA~aNA~~-~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ivl~e~~ 169 (200)
+|+||.+||++ .|+|+|+|||.|++||+|+++||++|||+| |++++.+++|||+|+|+|.+
T Consensus 50 ~L~sA~aNA~~~~g~d~~~L~I~~~~v~~G~~~Kr~~~rArG---------------R~~~i~k~~~hi~vvL~e~~ 111 (112)
T PRK00565 50 VLKSAIANAENNHGLDIDNLVVKEAYVDEGPTLKRFRPRARG---------------RASRIRKRTSHITVVVAEKE 111 (112)
T ss_pred HHHHHHHHHHhccCCChhHeEEEEEEECCCCccCCCCCCcCC---------------CCCccccCCccEEEEEEecC
Confidence 99999999996 899999999999999999999999999999 99999999999999999864
No 8
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=100.00 E-value=4.3e-35 Score=225.72 Aligned_cols=102 Identities=31% Similarity=0.499 Sum_probs=99.2
Q ss_pred EeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHHHHHH
Q psy11361 17 ARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLK 96 (200)
Q Consensus 17 A~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~lklLk 96 (200)
|.++++++||+|+++||++||||++++|+.||+ | ||+|+|..|+++|+
T Consensus 1 a~~r~~r~SpkK~~~va~~IrG~~v~~A~~~L~----------f----------------------~pkk~a~~i~klL~ 48 (103)
T TIGR01044 1 AKARFVRISPRKARLVADLIRGKSVSQALDILR----------F----------------------TPKKAAPLIKKVLA 48 (103)
T ss_pred CcccccccCHHHHHHHHHHHcCCcHHHHHHHHh----------h----------------------CCHhHHHHHHHHHH
Confidence 467999999999999999999999999999999 9 99999999999999
Q ss_pred HHHHhhh-hcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEEEE
Q psy11361 97 NAESNAD-YRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVIL 165 (200)
Q Consensus 97 sA~aNA~-~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ivl 165 (200)
||.+||+ ++|+|+|+|||.|++||+|+++||++|||+| |++++.+++|||+|+|
T Consensus 49 sA~aNA~~~~~ld~~~L~I~~~~v~~G~~~kr~~~rarG---------------Ra~~i~k~~~hi~vvl 103 (103)
T TIGR01044 49 SAIANAEHNYGLDADNLVVVTIFVDEGPTLKRIRPRAKG---------------RASRIRKRTSHITVVV 103 (103)
T ss_pred HHHHHHHHccCCChHheEEEEEEECCCCcccCCCCCCCC---------------CCCcccCCCccEEEeC
Confidence 9999996 7899999999999999999999999999999 9999999999999986
No 9
>PF00237 Ribosomal_L22: Ribosomal protein L22p/L17e; InterPro: IPR001063 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 L22 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L22 is known to bind 23S rRNA. It belongs to a family of ribosomal proteins which includes: bacterial L22; algal and plant chloroplast L22 (in legumes L22 is encoded in the nucleus instead of the chloroplast); cyanelle L22; archaebacterial L22; mammalian L17; plant L17 and yeast YL17.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CD6_R 1Q7Y_S 1VQ6_R 1YI2_R 1QVF_Q 3CCR_R 3CCU_R 3CCL_R 1YJ9_R 3CCQ_R ....
Probab=100.00 E-value=4.8e-34 Score=218.45 Aligned_cols=104 Identities=44% Similarity=0.650 Sum_probs=101.0
Q ss_pred EeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHHHHHH
Q psy11361 17 ARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLK 96 (200)
Q Consensus 17 A~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~lklLk 96 (200)
|..+++++||+|++++|++|+||++++|+.+|+ | .|+|+|.+|+++|+
T Consensus 1 A~~~~i~~S~kk~~~v~~~Irg~~v~~A~~~L~----------~----------------------~~~k~a~~i~k~L~ 48 (105)
T PF00237_consen 1 AKLRNIRISPKKLREVARLIRGMSVDEAIAQLK----------F----------------------VPKKAAKFILKLLK 48 (105)
T ss_dssp EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHH----------H----------------------HSSHHHHHHHHHHH
T ss_pred CccccccCCHHHHHHHHHHHcCCCHHHHHHHHH----------h----------------------CcHHHHHHHHhhHH
Confidence 678999999999999999999999999999999 8 89999999999999
Q ss_pred HHHHhhh-hcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEEEEee
Q psy11361 97 NAESNAD-YRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSE 167 (200)
Q Consensus 97 sA~aNA~-~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ivl~e 167 (200)
||.+||+ ++|+|+|+|||++++||+|+.++|++|||+| |++++.+++|||+|+|+|
T Consensus 49 ~a~~nA~~~~g~d~~~L~I~~~~v~~g~~~kr~~~rArG---------------R~~~~~k~~~hi~vvl~E 105 (105)
T PF00237_consen 49 SAIANAENNKGLDPDNLYISEIWVNKGPYLKRIRPRARG---------------RAGPIRKRTSHITVVLKE 105 (105)
T ss_dssp HHHHHHHHHCTSTCGGEEEEEEEEEEEEEEEEEEEECTT---------------EEEEEEEEEEEEEEEEEE
T ss_pred HHHhhcccccccccCceEEEEEEEEecccccCCCcCcCC---------------CccCeecCceEEEEEEeC
Confidence 9999999 8999999999999999999999999999999 999999999999999987
No 10
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=100.00 E-value=1.7e-33 Score=252.68 Aligned_cols=112 Identities=26% Similarity=0.430 Sum_probs=107.3
Q ss_pred ceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHH
Q psy11361 13 KSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLL 92 (200)
Q Consensus 13 k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~l 92 (200)
++++|.++++++||+|+|+||++||||++++|+.+|+ | +|+|+|..|+
T Consensus 1 M~akA~~r~iriSpkK~R~Va~~IRGk~v~~Al~~L~----------~----------------------~PkKaA~~I~ 48 (311)
T PRK12279 1 MTNKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILS----------N----------------------TPKKFAPIVL 48 (311)
T ss_pred CceEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHH----------h----------------------CCHHHHHHHH
Confidence 3589999999999999999999999999999999999 8 8999999999
Q ss_pred HHHHHHHHhhh--hcCCCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEEEEeeCcc
Q psy11361 93 QLLKNAESNAD--YRGLDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERER 170 (200)
Q Consensus 93 klLksA~aNA~--~~gld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ivl~e~~~ 170 (200)
+||+||.+||+ ++|||.|+|||.||+||+|+++||++|||+| |+++|.+++|||+|+|+|...
T Consensus 49 KlLkSA~ANAe~~n~gld~d~L~I~~~~VdkGp~lKR~~PRArG---------------RA~~i~KrtsHItIvl~e~~~ 113 (311)
T PRK12279 49 KLLNSAISNVQHNSKDMDPSKLYIYKIVANQGPTMKRTLPRAKG---------------SADQLFKRTTHLEIVLSDDVN 113 (311)
T ss_pred HHHHHHHHHHHHhhcCCChhHeEEEEEEECCCCcccCCCCccCC---------------CCCcccCCCccEEEEEecCCc
Confidence 99999999999 6899999999999999999999999999999 999999999999999987554
Q ss_pred c
Q psy11361 171 V 171 (200)
Q Consensus 171 ~ 171 (200)
.
T Consensus 114 ~ 114 (311)
T PRK12279 114 E 114 (311)
T ss_pred h
Confidence 3
No 11
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=99.98 E-value=3.2e-32 Score=208.14 Aligned_cols=104 Identities=46% Similarity=0.737 Sum_probs=99.5
Q ss_pred EEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHHHH
Q psy11361 15 CKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQL 94 (200)
Q Consensus 15 ~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~lkl 94 (200)
++|..+++++||+|+++++++|+||++++|+.+|+ | .|+|+|..|+++
T Consensus 1 ~~a~~~~i~~S~kK~~~v~~~Irg~~v~~A~~~L~----------~----------------------~~kk~a~~i~k~ 48 (105)
T cd00336 1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLE----------F----------------------VPKKAAKIILKL 48 (105)
T ss_pred CEEEEccCccCHHHHHHHHHHHcCCcHHHHHHHHH----------h----------------------CCHHHHHHHHHH
Confidence 46889999999999999999999999999999999 8 999999999999
Q ss_pred HHHHHHhhhhcC-CCCCCeEEEEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCceEEEEE
Q psy11361 95 LKNAESNADYRG-LDTDRLVIEHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVIL 165 (200)
Q Consensus 95 LksA~aNA~~~g-ld~d~L~I~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~HI~ivl 165 (200)
|+||.+||++.+ +|+|+|||.|++||+||.++|++|||+| |++++.+++|||+|+|
T Consensus 49 l~sa~~nA~~~~~~~~~~L~I~~~~v~~g~~~kr~~~rarG---------------R~~~~~k~~~hi~ivl 105 (105)
T cd00336 49 LKSAEANAENNGLDDPDKLYIKHIQVNKGPTLKRRRPRARG---------------RANPIRKRTCHITVVL 105 (105)
T ss_pred HHHHHHhHHHcCCCCccceEEEEEEECCCCcccCCCcCCCC---------------CCcccccCceeEEEeC
Confidence 999999999654 5699999999999999999999999999 9999999999999986
No 12
>KOG1711|consensus
Probab=99.86 E-value=6.4e-22 Score=170.36 Aligned_cols=123 Identities=25% Similarity=0.309 Sum_probs=113.3
Q ss_pred ccCCCCCCCCceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCC
Q psy11361 3 RYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGR 82 (200)
Q Consensus 3 ~YS~~~~d~~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR 82 (200)
.|+++|. . .++.|....++.|+||++.+|++|+||++++||.+|+ |
T Consensus 62 ~l~~~p~-~-~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~----------~---------------------- 107 (218)
T KOG1711|consen 62 QLPFEPK-R-PEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLE----------F---------------------- 107 (218)
T ss_pred cCCCCCc-c-hhHHHHHHHHHhCHHHHHHHHHHHcCCCHHHHHHHhh----------c----------------------
Confidence 4566652 2 6778888999999999999999999999999999999 9
Q ss_pred CchhhHHHHHHHHHHHHHhhh-hcCCCCCCeEE-EEEEecCCCccccceeccCCCccCCCCcceeeeeeeeccCCCCCce
Q psy11361 83 WPRKSADFLLQLLKNAESNAD-YRGLDTDRLVI-EHIQVNRAPRLRRRTYRAHGNYRGLDTDRLVIEHIQVNPYMSSPCH 160 (200)
Q Consensus 83 ~P~Kaa~~~lklLksA~aNA~-~~gld~d~L~I-~~i~vnkg~~~kR~~~RA~G~~~~~~~~~l~~~~~Ra~~~~k~~~H 160 (200)
+++|+|..|.++|.+|.+||- ++|||+++|+| .++++++|..+||..++||| |-+++.+++||
T Consensus 108 s~kK~a~~i~~~l~~A~~nA~~~~gl~~~~l~v~~~~t~~~g~~~Krl~~harg---------------r~~ii~~~yvh 172 (218)
T KOG1711|consen 108 SDKKAAKTIAEVLLSARANAVHNHGLDPDSLLVVAEATVGQGNELKRLKVHARG---------------RFGIIRRPYVH 172 (218)
T ss_pred chHHHHHHHHHHHHHHHhhhHHhcCCCccceEEEEeeecccchhhhheeeeccC---------------cccceecceee
Confidence 999999999999999999997 79999999999 99999999999999999999 99999999999
Q ss_pred EEEEEeeCccccCC
Q psy11361 161 IEVILSERERVVAK 174 (200)
Q Consensus 161 I~ivl~e~~~~~~k 174 (200)
|+|+|.|...+-.+
T Consensus 173 i~v~L~e~s~~~~~ 186 (218)
T KOG1711|consen 173 IFVKLEEGSPPQQR 186 (218)
T ss_pred EEEEEeecCCCchh
Confidence 99999998766544
No 13
>KOG3353|consensus
Probab=96.30 E-value=0.00068 Score=57.67 Aligned_cols=77 Identities=27% Similarity=0.123 Sum_probs=56.2
Q ss_pred CCCCchhhHHHHHHHHHHHHHhhhh-cCCCCCCeEEEEEEecCCCcccccee--------------------------cc
Q psy11361 80 QGRWPRKSADFLLQLLKNAESNADY-RGLDTDRLVIEHIQVNRAPRLRRRTY--------------------------RA 132 (200)
Q Consensus 80 ~GR~P~Kaa~~~lklLksA~aNA~~-~gld~d~L~I~~i~vnkg~~~kR~~~--------------------------RA 132 (200)
..|++-|...+..+.|.....+... .-.|....-+...+.+.|+.+-+... .+
T Consensus 15 ~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkksaefll~~LkN~es 94 (175)
T KOG3353|consen 15 NLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKKSAEFLLHMLKNAES 94 (175)
T ss_pred cEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhhhccccCcccchHHHHHHHHHHhhhh
Confidence 4568888999999999988888763 33466666667777766665443222 34
Q ss_pred CCCccCCCCcceeeeeeeeccCCC
Q psy11361 133 HGNYRGLDTDRLVIEHIQVNPYMS 156 (200)
Q Consensus 133 ~G~~~~~~~~~l~~~~~Ra~~~~k 156 (200)
+.+++||||||||||||+++...+
T Consensus 95 naElkgldVDsLvIehiqvnkApK 118 (175)
T KOG3353|consen 95 NAELKGLDVDSLVIEHIQVNKAPK 118 (175)
T ss_pred cccccCcCcceeEeeehhhcccch
Confidence 468999999999999998877554
No 14
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=75.01 E-value=1.2 Score=35.83 Aligned_cols=22 Identities=45% Similarity=0.827 Sum_probs=18.4
Q ss_pred cCCCc-cCCCCcceeeeeeeecc
Q psy11361 132 AHGNY-RGLDTDRLVIEHIQVNP 153 (200)
Q Consensus 132 A~G~~-~~~~~~~l~~~~~Ra~~ 153 (200)
|.+++ .|||+|.|+|.|++++.
T Consensus 64 aNAe~n~gLd~d~L~V~~i~v~~ 86 (120)
T COG0091 64 ANAENNKGLDPDKLVVSHIAVDK 86 (120)
T ss_pred hhHHhccCCChHHEEEEEEEeCC
Confidence 44566 68999999999999874
No 15
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=74.24 E-value=13 Score=27.96 Aligned_cols=66 Identities=14% Similarity=0.191 Sum_probs=48.0
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHHHHHHHHHHhhhh-c
Q psy11361 27 KNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADY-R 105 (200)
Q Consensus 27 Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~lklLksA~aNA~~-~ 105 (200)
+.+.++++.+ |+++..|+..+-.-+....-+||. . ..+--.-..++..++.+.+|-.. .
T Consensus 14 ~~A~~vl~~l-Gls~S~Ai~~fl~qi~~~~~iPF~-----------~--------~~~s~ed~~~l~~~re~~~~~~~~~ 73 (80)
T PRK11235 14 ARAYAVLEKL-GVTPSEALRLLLQYVAENGRLPFK-----------T--------VLLSDEDAALLETVRERLANPQKGI 73 (80)
T ss_pred HHHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCCCC-----------C--------CCCCHHHHHHHHHHHHHHhCCCCCe
Confidence 3577788888 999999999999999999999991 0 12334566788888888887652 2
Q ss_pred CCCCCCe
Q psy11361 106 GLDTDRL 112 (200)
Q Consensus 106 gld~d~L 112 (200)
.++.|+|
T Consensus 74 ~~~~d~l 80 (80)
T PRK11235 74 RVTLDDL 80 (80)
T ss_pred eeecCcC
Confidence 3555543
No 16
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=71.57 E-value=23 Score=27.83 Aligned_cols=70 Identities=11% Similarity=0.031 Sum_probs=50.8
Q ss_pred ceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHH
Q psy11361 13 KSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLL 92 (200)
Q Consensus 13 k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~l 92 (200)
..++-.+...-+|.-=+--++.+|.|+++++|..+....+....-+|- .-.++|....
T Consensus 52 ~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~~~i~~~lg~p~----------------------~r~~CA~l~~ 109 (124)
T TIGR01999 52 EDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKNTEIAKELSLPP----------------------VKLHCSLLAE 109 (124)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccHHHHHHHcCCCc----------------------ccchHHHHHH
Confidence 344555566677777788999999999999999998764433222221 2256899999
Q ss_pred HHHHHHHHhhhh
Q psy11361 93 QLLKNAESNADY 104 (200)
Q Consensus 93 klLksA~aNA~~ 104 (200)
+.|+.|..+...
T Consensus 110 ~al~~a~~~y~~ 121 (124)
T TIGR01999 110 DAIKAAIKDYKS 121 (124)
T ss_pred HHHHHHHHHHHH
Confidence 999999888754
No 17
>PRK11325 scaffold protein; Provisional
Probab=69.36 E-value=21 Score=28.21 Aligned_cols=69 Identities=9% Similarity=0.008 Sum_probs=52.1
Q ss_pred ceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHH
Q psy11361 13 KSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLL 92 (200)
Q Consensus 13 k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~l 92 (200)
..++-.+...-+|--=+--++.++.|+++++|..+....+....-+|- --.++|....
T Consensus 54 ~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~~~i~~~lg~p~----------------------~r~~CA~la~ 111 (127)
T PRK11325 54 EDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALPP----------------------VKIHCSILAE 111 (127)
T ss_pred EEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHcCCCc----------------------ccchHHHHHH
Confidence 455666677778888889999999999999999998865543222332 2256899999
Q ss_pred HHHHHHHHhhh
Q psy11361 93 QLLKNAESNAD 103 (200)
Q Consensus 93 klLksA~aNA~ 103 (200)
+.|+.|..+..
T Consensus 112 ~al~~a~~~y~ 122 (127)
T PRK11325 112 DAIKAAIADYK 122 (127)
T ss_pred HHHHHHHHHHH
Confidence 99999988765
No 18
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=62.38 E-value=26 Score=26.54 Aligned_cols=53 Identities=23% Similarity=0.260 Sum_probs=40.1
Q ss_pred hHHHHHHHhhh-----cCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHHHHHHHH
Q psy11361 26 FKNTRETAKTI-----SKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNA 98 (200)
Q Consensus 26 ~Kk~r~va~~I-----rg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~lklLksA 98 (200)
.-.+.-++++| .|+++++.+..|.. |.+ .+.|+..|++..-.++.|.++|+..
T Consensus 37 ~~~~~ai~rliS~~Lr~G~~~~~ii~~L~g-------i~~-------------~~~~~~~~~~~~S~~D~Ia~~L~~~ 94 (95)
T PF12637_consen 37 SGNLEAIARLISLALRSGVPPEEIIDQLRG-------IRC-------------GPSGTVGGSRVTSCPDAIAKALEEH 94 (95)
T ss_pred hHHHHHHHHHHHHHHHcCCCHHHHHHHhcC-------CCC-------------CCCCccCCCccCcHHHHHHHHHHHh
Confidence 78889999999 99999999999982 111 1224445567778888888888764
No 19
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=60.71 E-value=59 Score=25.42 Aligned_cols=70 Identities=13% Similarity=0.116 Sum_probs=50.4
Q ss_pred ceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHH-HHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHH
Q psy11361 13 KSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKN-VKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFL 91 (200)
Q Consensus 13 k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~-Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~ 91 (200)
..++-.+...-+|--=+-.++.+|.|+++++|..+..+ ++..=.-+|- .-.++|...
T Consensus 48 ~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~~~i~~~l~~l~~----------------------~r~~CA~la 105 (121)
T TIGR03419 48 KDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPP----------------------VKMHCSVLA 105 (121)
T ss_pred EEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhhHHHHHHHcCCCc----------------------ccCHHHHHH
Confidence 34555566677777788899999999999999999874 2222122231 345789999
Q ss_pred HHHHHHHHHhhhh
Q psy11361 92 LQLLKNAESNADY 104 (200)
Q Consensus 92 lklLksA~aNA~~ 104 (200)
.+.|+.|..+...
T Consensus 106 ~~al~~a~~~y~~ 118 (121)
T TIGR03419 106 EEAIHKAINDYRE 118 (121)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999887753
No 20
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=57.44 E-value=41 Score=26.85 Aligned_cols=76 Identities=14% Similarity=0.188 Sum_probs=48.2
Q ss_pred ceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccC---------CCCCCC
Q psy11361 13 KSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWG---------TTQGRW 83 (200)
Q Consensus 13 k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g---------~~~GR~ 83 (200)
..++-.+...-+|--=+-.++..|.|+++++|..++++ |..+-.+.+--.....|| ..++|
T Consensus 52 ~d~~f~~~GCais~Asas~~~e~i~Gk~~~ea~~l~~~---------~~~ml~~~~~~~~~~~l~dl~~l~~v~~~p~R- 121 (137)
T TIGR01994 52 EDIAFEGEGCSISQASASMMTELIKGKTVEEALSLVEA---------FSEMIQGQETDEDEEKLGDAEALAGVAKFPAR- 121 (137)
T ss_pred EEEEEEecccHHHHHHHHHHHHHHcCCCHHHHHHHHHH---------HHHHHhcCCCCccccccchHHHhhccccCcch-
Confidence 34455566667777778899999999999999999875 333322211100111222 13344
Q ss_pred chhhHHHHHHHHHHHH
Q psy11361 84 PRKSADFLLQLLKNAE 99 (200)
Q Consensus 84 P~Kaa~~~lklLksA~ 99 (200)
.++|-.-.+.|+.|.
T Consensus 122 -~~Ca~L~~~al~~al 136 (137)
T TIGR01994 122 -IKCATLAWKALERAL 136 (137)
T ss_pred -HHHHHHHHHHHHHHh
Confidence 678888888888775
No 21
>KOG3361|consensus
Probab=55.89 E-value=21 Score=29.96 Aligned_cols=53 Identities=11% Similarity=0.036 Sum_probs=41.2
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcchhhcccCCCCCCCchhhHHHHHHHHHHHHHhhh
Q psy11361 29 TRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNAD 103 (200)
Q Consensus 29 ~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~lklLksA~aNA~ 103 (200)
.-.....|+||+++||..+=+.=|+++.|.|= ..--++-.-...|+.|+.+-.
T Consensus 96 SS~aTewvkgkt~dea~kIkNteIAKeL~LPP----------------------VKLHCSMLAEDAIKaAikdyk 148 (157)
T KOG3361|consen 96 SSLATEWVKGKTLDEALKIKNTEIAKELSLPP----------------------VKLHCSMLAEDAIKAAIKDYK 148 (157)
T ss_pred hHHHHHHHccccHHHHHhcccHHHHHhccCCc----------------------hhhhhHHHHHHHHHHHHHHHH
Confidence 44567789999999999999999999999994 222345555678888887765
No 22
>CHL00034 rpl22 ribosomal protein L22
Probab=54.89 E-value=7.9 Score=30.70 Aligned_cols=19 Identities=26% Similarity=0.455 Sum_probs=16.9
Q ss_pred CccCCCCcceeeeeeeecc
Q psy11361 135 NYRGLDTDRLVIEHIQVNP 153 (200)
Q Consensus 135 ~~~~~~~~~l~~~~~Ra~~ 153 (200)
+..|||+|.|+|.+++++.
T Consensus 67 ~~~gld~d~L~I~~i~v~~ 85 (117)
T CHL00034 67 HNMGLNKANLFISKAEVDE 85 (117)
T ss_pred HccCCCccceEEEEEEECC
Confidence 5678999999999999975
No 23
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=53.32 E-value=21 Score=27.54 Aligned_cols=31 Identities=13% Similarity=0.314 Sum_probs=27.8
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHhccccccc
Q psy11361 29 TRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60 (200)
Q Consensus 29 ~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf 60 (200)
+..|+..+ |+++.+||.++-.=+.....+||
T Consensus 19 A~~Vl~~m-Glt~S~airm~L~~va~~~~lPf 49 (88)
T COG3077 19 ATAVLEEM-GLTISDAIRMFLTKVAREGALPF 49 (88)
T ss_pred HHHHHHHh-CCCHHHHHHHHHHHHHHcCCCCc
Confidence 56677777 99999999999888999999999
No 24
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=53.15 E-value=46 Score=24.75 Aligned_cols=33 Identities=15% Similarity=0.232 Sum_probs=28.5
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHhccccccc
Q psy11361 27 KNTRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60 (200)
Q Consensus 27 Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf 60 (200)
..+..+++.+ |++..+|+..+=.=+....-+||
T Consensus 15 ~~a~~i~~~l-Gl~~s~ai~~fl~qvv~~~~lPF 47 (83)
T TIGR02384 15 KEAYAVFEEL-GLTPSTAIRMFLKQVIREQGLPF 47 (83)
T ss_pred HHHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCCC
Confidence 3466778888 99999999988888889999999
No 25
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=51.14 E-value=7.8 Score=32.23 Aligned_cols=24 Identities=50% Similarity=0.757 Sum_probs=19.9
Q ss_pred cCCCccCCCCcceeeeeeeeccCC
Q psy11361 132 AHGNYRGLDTDRLVIEHIQVNPYM 155 (200)
Q Consensus 132 A~G~~~~~~~~~l~~~~~Ra~~~~ 155 (200)
|..++.|||+|+|+|.|+.++.-.
T Consensus 97 aNA~~~gld~d~L~I~~i~vnkg~ 120 (150)
T TIGR01038 97 ANAEYKGLDVEKLVIIHIQANKGP 120 (150)
T ss_pred HHHHhcCCChhHeEEEEEEECCCC
Confidence 455678999999999999998643
No 26
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=49.33 E-value=18 Score=25.78 Aligned_cols=36 Identities=17% Similarity=0.258 Sum_probs=24.9
Q ss_pred hcCCCHHHHHHHHHHHHhc--cccccceeecCCCCcch
Q psy11361 36 ISKMPLRRAIKFLKNVKDQ--LECVPFRRYNGGVGRCA 71 (200)
Q Consensus 36 Irg~~l~~Ai~~L~~Vi~k--k~~VPf~ryn~gvgh~~ 71 (200)
+.||++++|+.+|.+.|.. ..-+...+.-.|.|+++
T Consensus 3 LHG~~~~eA~~~l~~~l~~~~~~~~~~~~II~G~G~hS 40 (83)
T PF01713_consen 3 LHGLTVEEALRALEEFLDEARQRGIRELRIITGKGNHS 40 (83)
T ss_dssp -TTS-HHHHHHHHHHHHHHHHHTTHSEEEEE--STCTC
T ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCCEEEEEeccCCCC
Confidence 4699999999999999866 34556666667888775
No 27
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=49.13 E-value=24 Score=25.82 Aligned_cols=33 Identities=15% Similarity=0.275 Sum_probs=25.1
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHhccccccc
Q psy11361 27 KNTRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60 (200)
Q Consensus 27 Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf 60 (200)
..+..+++.+ |+++..|+..+-.=+.....+||
T Consensus 14 ~~a~~il~~~-Glt~s~ai~~fl~qiv~~~~iPF 46 (83)
T PF04221_consen 14 EEAEAILEEL-GLTLSDAINMFLKQIVREGGIPF 46 (83)
T ss_dssp HHHHHHHHHT-T--HHHHHHHHHHHHHHHSS-S-
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHHHHHhCCCCc
Confidence 3567788888 99999999998888889999999
No 28
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=47.17 E-value=90 Score=24.34 Aligned_cols=70 Identities=17% Similarity=0.151 Sum_probs=46.7
Q ss_pred CceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhcccc-ccceeecCCCCcchhhcccCCCCCCCchhhHHH
Q psy11361 12 TKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLEC-VPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADF 90 (200)
Q Consensus 12 ~k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~-VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~ 90 (200)
-..++-.+..-.+|.-=+-.++.+|.|+++++|..+-.+-|....- +|= .-...+..
T Consensus 51 I~d~~f~~~GC~~~~Asas~~~~~i~gk~l~ea~~i~~~~i~~~l~~~~~----------------------~~~~~~~l 108 (126)
T PF01592_consen 51 IKDAKFQGFGCAISIASASMMCELIKGKTLEEALKITAEDIEEALGGLPP----------------------ERQHCAEL 108 (126)
T ss_dssp EEEEEEEEESSHHHHHHHHHHHHHHTTSBHHHHHCHHHHHHHHHHTC-CG----------------------TCGHHHHH
T ss_pred EEEEEEEeecChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccc----------------------CcccHHHH
Confidence 3455666677788888889999999999999997654322211111 221 22346777
Q ss_pred HHHHHHHHHHhhh
Q psy11361 91 LLQLLKNAESNAD 103 (200)
Q Consensus 91 ~lklLksA~aNA~ 103 (200)
...+|..|.++-.
T Consensus 109 ~~~al~~av~~y~ 121 (126)
T PF01592_consen 109 ADDALKAAVADYP 121 (126)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 8888888887764
No 29
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=44.66 E-value=11 Score=31.39 Aligned_cols=23 Identities=48% Similarity=0.793 Sum_probs=19.5
Q ss_pred cCCCccCCCCcceeeeeeeeccC
Q psy11361 132 AHGNYRGLDTDRLVIEHIQVNPY 154 (200)
Q Consensus 132 A~G~~~~~~~~~l~~~~~Ra~~~ 154 (200)
|..+++|||+|+|+|.|+.++.-
T Consensus 99 aNA~~~gld~d~L~I~~i~v~kg 121 (153)
T PRK04223 99 ANAEYKGLDTEKLVIVHIAAHKG 121 (153)
T ss_pred HHHHhcCCChhHeEEEEEEECCC
Confidence 45567899999999999999864
No 30
>PF00237 Ribosomal_L22: Ribosomal protein L22p/L17e; InterPro: IPR001063 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 L22 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L22 is known to bind 23S rRNA. It belongs to a family of ribosomal proteins which includes: bacterial L22; algal and plant chloroplast L22 (in legumes L22 is encoded in the nucleus instead of the chloroplast); cyanelle L22; archaebacterial L22; mammalian L17; plant L17 and yeast YL17.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CD6_R 1Q7Y_S 1VQ6_R 1YI2_R 1QVF_Q 3CCR_R 3CCU_R 3CCL_R 1YJ9_R 3CCQ_R ....
Probab=42.54 E-value=13 Score=28.30 Aligned_cols=19 Identities=47% Similarity=0.581 Sum_probs=16.9
Q ss_pred ccCCCCcceeeeeeeeccC
Q psy11361 136 YRGLDTDRLVIEHIQVNPY 154 (200)
Q Consensus 136 ~~~~~~~~l~~~~~Ra~~~ 154 (200)
..|+|.|.|+|.++.++.-
T Consensus 57 ~~g~d~~~L~I~~~~v~~g 75 (105)
T PF00237_consen 57 NKGLDPDNLYISEIWVNKG 75 (105)
T ss_dssp HCTSTCGGEEEEEEEEEEE
T ss_pred ccccccCceEEEEEEEEec
Confidence 6789999999999998863
No 31
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=40.27 E-value=16 Score=28.11 Aligned_cols=19 Identities=42% Similarity=0.592 Sum_probs=16.6
Q ss_pred CccCCCCcceeeeeeeecc
Q psy11361 135 NYRGLDTDRLVIEHIQVNP 153 (200)
Q Consensus 135 ~~~~~~~~~l~~~~~Ra~~ 153 (200)
++.|||.|.|.|.++.++.
T Consensus 56 ~~~~ld~~~L~I~~~~v~~ 74 (103)
T TIGR01044 56 HNYGLDADNLVVVTIFVDE 74 (103)
T ss_pred HccCCChHheEEEEEEECC
Confidence 4568999999999999985
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=36.68 E-value=29 Score=30.26 Aligned_cols=30 Identities=23% Similarity=0.447 Sum_probs=27.4
Q ss_pred CcccchHHHHHHHhhh-cCCCHHHHHHHHHH
Q psy11361 21 NLRVHFKNTRETAKTI-SKMPLRRAIKFLKN 50 (200)
Q Consensus 21 ~~rvS~Kk~r~va~~I-rg~~l~~Ai~~L~~ 50 (200)
.=+.++.+++++.++| +|.+.++|+.+|++
T Consensus 59 ~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~d 89 (194)
T COG1094 59 EDPLALLKARDVVKAIGRGFPPEKALKLLED 89 (194)
T ss_pred CChHHHHHHHHHHHHHhcCCCHHHHHHHhcC
Confidence 4688999999999999 79999999999995
No 33
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=33.00 E-value=1.9e+02 Score=22.04 Aligned_cols=42 Identities=17% Similarity=0.179 Sum_probs=34.1
Q ss_pred ceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhc
Q psy11361 13 KSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQ 54 (200)
Q Consensus 13 k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~k 54 (200)
..++-.+...-+|--=+-.+++++.|+++++|..++.+.+..
T Consensus 49 ~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~~~~~~ 90 (123)
T cd06664 49 TDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLNKDIAM 90 (123)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 345556677778888889999999999999999999875544
No 34
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=31.19 E-value=2.1e+02 Score=26.00 Aligned_cols=70 Identities=11% Similarity=0.003 Sum_probs=50.1
Q ss_pred ceEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhcc-ccccceeecCCCCcchhhcccCCCCCCCchhhHHHH
Q psy11361 13 KSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQL-ECVPFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFL 91 (200)
Q Consensus 13 k~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk-~~VPf~ryn~gvgh~~~~~~~g~~~GR~P~Kaa~~~ 91 (200)
..++-.+..--+|.-=+-.++.+|.|+++++|..+..+-|... .-+|- .-.+.|...
T Consensus 53 ~d~~F~~~GCais~ASAs~~~eli~Gktv~ea~~i~~~di~~~L~~lpp----------------------~r~~CA~La 110 (290)
T TIGR02000 53 VDAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVSNQDIADYLGGLPP----------------------EKMHCSVMG 110 (290)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHHhhHHHHHHHHcCCCh----------------------hhchHHHHH
Confidence 3555566777778888889999999999999999986433221 11221 234688888
Q ss_pred HHHHHHHHHhhhh
Q psy11361 92 LQLLKNAESNADY 104 (200)
Q Consensus 92 lklLksA~aNA~~ 104 (200)
.+.|+.|..+...
T Consensus 111 ~~Al~~Al~~y~~ 123 (290)
T TIGR02000 111 QEALEAAIANYRG 123 (290)
T ss_pred HHHHHHHHHHHhc
Confidence 8999999888763
No 35
>smart00463 SMR Small MutS-related domain.
Probab=26.81 E-value=58 Score=23.01 Aligned_cols=23 Identities=9% Similarity=0.179 Sum_probs=18.3
Q ss_pred hcCCCHHHHHHHHHHHHhccccc
Q psy11361 36 ISKMPLRRAIKFLKNVKDQLECV 58 (200)
Q Consensus 36 Irg~~l~~Ai~~L~~Vi~kk~~V 58 (200)
+.||++++|+..|...|+.-..-
T Consensus 6 LHG~~~~eA~~~l~~~l~~~~~~ 28 (80)
T smart00463 6 LHGLTVEEALTALDKFLNNARLK 28 (80)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHc
Confidence 46999999999999877754443
No 36
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=25.78 E-value=58 Score=21.75 Aligned_cols=15 Identities=20% Similarity=0.257 Sum_probs=13.6
Q ss_pred hcCCCHHHHHHHHHH
Q psy11361 36 ISKMPLRRAIKFLKN 50 (200)
Q Consensus 36 Irg~~l~~Ai~~L~~ 50 (200)
+.||++++|...|++
T Consensus 6 ~~g~~~~~a~~~l~~ 20 (63)
T PF03793_consen 6 LVGMTYDEAKSILEA 20 (63)
T ss_dssp TTTSBHHHHHHHHHH
T ss_pred cCCCcHHHHHHHHHH
Confidence 579999999999995
No 37
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=25.61 E-value=36 Score=29.29 Aligned_cols=23 Identities=48% Similarity=0.778 Sum_probs=19.1
Q ss_pred cCCCccCCCCcceeeeeeeeccC
Q psy11361 132 AHGNYRGLDTDRLVIEHIQVNPY 154 (200)
Q Consensus 132 A~G~~~~~~~~~l~~~~~Ra~~~ 154 (200)
|..++.|||+|.|+|.|+.++.-
T Consensus 100 aNAe~~gld~d~L~I~~i~v~kG 122 (181)
T PTZ00178 100 ANAEAKGLDVEKLVISHVQVNRA 122 (181)
T ss_pred HHHHhcCCChhHeEEEEEEECCC
Confidence 45567899999999999998753
No 38
>PF13286 HD_assoc: Phosphohydrolase-associated domain; PDB: 2DQB_D.
Probab=21.95 E-value=1.1e+02 Score=21.98 Aligned_cols=23 Identities=22% Similarity=0.314 Sum_probs=18.5
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHH
Q psy11361 27 KNTRETAKTISKMPLRRAIKFLK 49 (200)
Q Consensus 27 Kk~r~va~~Irg~~l~~Ai~~L~ 49 (200)
...+.|+|.|.||+=.-|+...+
T Consensus 69 ~~~r~v~DyIaGMTD~yA~~~~~ 91 (92)
T PF13286_consen 69 SRARVVCDYIAGMTDRYALRLYQ 91 (92)
T ss_dssp -HHHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHhhcCcHHHHHHHHc
Confidence 57889999999999999987654
No 39
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=21.39 E-value=1.9e+02 Score=23.83 Aligned_cols=84 Identities=15% Similarity=0.081 Sum_probs=49.2
Q ss_pred eEEEeeCCcccchHHHHHHHhhhcCCCHHHHHHHHHHHHhccccccceeecCCCCcch-hhcccCCCCCCCch--hhHHH
Q psy11361 14 SCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRYNGGVGRCA-QAKQWGTTQGRWPR--KSADF 90 (200)
Q Consensus 14 ~~kA~~~~~rvS~Kk~r~va~~Irg~~l~~Ai~~L~~Vi~kk~~VPf~ryn~gvgh~~-~~~~~g~~~GR~P~--Kaa~~ 90 (200)
.++=.+...-+|.-=+-.++.+|.|++++||+++.++..+--+ ..++..+.. +.-...++.--+|. +++-.
T Consensus 56 d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~~~~~~m~~------~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L 129 (150)
T COG0822 56 DAKFKGFGCAISIASSSMMTELVKGKTLDEALKITEAFTDMAK------ELGGDPDDRLGDLVALAGVALPPARIKCSLL 129 (150)
T ss_pred EEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH------HcCCCccchhhhhHhhhhhccccccccchhc
Confidence 4455566777788888899999999999999999965222111 001111111 00011122222555 45666
Q ss_pred HHHHHHHHHHhhh
Q psy11361 91 LLQLLKNAESNAD 103 (200)
Q Consensus 91 ~lklLksA~aNA~ 103 (200)
-.+.|+.|..+..
T Consensus 130 ~~~al~~ai~~~~ 142 (150)
T COG0822 130 AWDALKAAIKDYK 142 (150)
T ss_pred cHHHHHHHHHHhh
Confidence 6688888887765
No 40
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=21.07 E-value=37 Score=25.99 Aligned_cols=25 Identities=12% Similarity=0.223 Sum_probs=22.3
Q ss_pred eeCCcccchHHHHHHHhhhcCCCHH
Q psy11361 18 RGSNLRVHFKNTRETAKTISKMPLR 42 (200)
Q Consensus 18 ~~~~~rvS~Kk~r~va~~Irg~~l~ 42 (200)
...+++++.+.+..|++.+||.+++
T Consensus 25 kqy~i~it~~QA~~I~~~lr~k~in 49 (85)
T PF11116_consen 25 KQYNISITKKQAEQIANILRGKNIN 49 (85)
T ss_pred HHhCCCCCHHHHHHHHHHHhcCCCC
Confidence 4578999999999999999999873
Done!