Query 030658
Match_columns 173
No_of_seqs 116 out of 1063
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 02:38:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030658hhsearch_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 2E-57 4.4E-62 368.0 16.7 164 1-165 1-164 (181)
2 TIGR01038 L22_arch ribosomal p 100.0 7.1E-56 1.5E-60 350.4 15.9 150 4-154 1-150 (150)
3 PRK04223 rpl22p 50S ribosomal 100.0 5.2E-55 1.1E-59 346.5 16.1 151 1-155 3-153 (153)
4 COG0091 RplV Ribosomal protein 100.0 4.3E-41 9.2E-46 257.3 10.1 118 4-155 1-119 (120)
5 CHL00034 rpl22 ribosomal prote 100.0 1.3E-38 2.9E-43 242.8 12.9 112 10-154 5-117 (117)
6 PRK00565 rplV 50S ribosomal pr 100.0 1.9E-38 4.2E-43 239.9 12.4 110 13-155 1-111 (112)
7 TIGR01044 rplV_bact ribosomal 100.0 1.6E-37 3.4E-42 232.0 10.2 102 17-151 1-103 (103)
8 PF00237 Ribosomal_L22: Riboso 100.0 2.3E-36 5E-41 225.2 9.3 104 17-153 1-105 (105)
9 cd00336 Ribosomal_L22 Ribosoma 100.0 1.1E-34 2.3E-39 216.1 12.1 104 15-151 1-105 (105)
10 PRK12279 50S ribosomal protein 100.0 1.1E-34 2.4E-39 251.5 11.9 113 13-158 1-115 (311)
11 KOG3353 60S ribosomal protein 100.0 7.6E-37 1.6E-41 246.1 -2.9 158 7-165 1-158 (175)
12 KOG1711 Mitochondrial/chloropl 99.9 1.7E-25 3.8E-30 184.7 7.8 122 4-160 63-186 (218)
13 KOG3361 Iron binding protein i 68.9 10 0.00022 30.2 4.5 34 30-63 97-130 (157)
14 PRK11235 bifunctional antitoxi 67.4 21 0.00045 25.6 5.5 55 28-103 15-69 (80)
15 COG3077 RelB DNA-damage-induci 65.0 11 0.00024 27.6 3.8 34 29-63 19-52 (88)
16 TIGR01999 iscU FeS cluster ass 63.9 45 0.00098 25.1 7.2 69 14-105 53-121 (124)
17 PRK11325 scaffold protein; Pro 60.4 46 0.00099 25.3 6.7 69 14-105 55-123 (127)
18 PF12637 TSCPD: TSCPD domain; 59.5 28 0.00061 25.2 5.2 36 15-50 26-66 (95)
19 PF01713 Smr: Smr domain; Int 54.9 14 0.00031 25.4 2.9 37 36-72 3-41 (83)
20 PF04221 RelB: RelB antitoxin; 53.5 19 0.00042 25.3 3.4 35 27-62 14-48 (83)
21 TIGR03419 NifU_clost FeS clust 42.8 1.4E+02 0.0031 22.3 7.6 69 14-105 49-118 (121)
22 TIGR02384 RelB_DinJ addiction 38.6 58 0.0013 23.1 3.9 33 28-61 16-48 (83)
23 COG1094 Predicted RNA-binding 37.3 30 0.00065 28.9 2.5 30 21-50 59-89 (194)
24 TIGR02000 NifU_proper Fe-S clu 36.8 1.3E+02 0.0028 26.3 6.5 70 14-105 54-123 (290)
25 PF03793 PASTA: PASTA domain; 31.6 35 0.00076 22.0 1.7 15 36-50 6-20 (63)
26 PF13852 DUF4197: Protein of u 30.8 54 0.0012 27.3 3.1 20 30-49 84-103 (202)
27 PF01592 NifU_N: NifU-like N t 30.8 1.9E+02 0.0042 21.6 5.9 34 14-47 53-86 (126)
28 COG0822 IscU NifU homolog invo 30.0 1.1E+02 0.0024 24.2 4.6 37 14-50 56-92 (150)
29 smart00463 SMR Small MutS-rela 27.8 51 0.0011 22.4 2.1 21 36-56 6-26 (80)
30 PF01466 Skp1: Skp1 family, di 27.8 76 0.0017 21.9 3.0 21 29-49 36-56 (78)
31 PF11116 DUF2624: Protein of u 27.7 28 0.00061 25.3 0.8 26 17-42 24-49 (85)
32 cd06664 IscU_like Iron-sulfur 27.6 1.5E+02 0.0032 21.8 4.7 38 14-51 50-87 (123)
33 PF04485 NblA: Phycobilisome d 25.9 1.3E+02 0.0028 20.0 3.6 24 28-51 11-34 (53)
34 PF13286 HD_assoc: Phosphohydr 24.8 1E+02 0.0022 21.3 3.3 23 27-49 69-91 (92)
35 PF07778 CENP-I: Mis6 ; Inter 22.0 74 0.0016 30.2 2.6 46 39-113 56-101 (511)
36 PF06738 DUF1212: Protein of u 21.7 1.3E+02 0.0028 23.8 3.6 39 17-55 55-98 (193)
No 1
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=2e-57 Score=367.97 Aligned_cols=164 Identities=67% Similarity=1.065 Sum_probs=158.2
Q ss_pred CccccCCCCCCCceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCC
Q 030658 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNG 80 (173)
Q Consensus 1 ~~~y~~~~~~~~~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~ 80 (173)
||+||++.+|++++++|..+++++||+|+++||++||||++++|+++|++||++|++|||+||++++||++++.+ ||.+
T Consensus 1 ~~~Ys~~~~n~~~~akA~~~~~riSpkk~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~-~~~~ 79 (181)
T PTZ00178 1 MVKYARKPQNPSKSAKAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKE-FGHT 79 (181)
T ss_pred CCccccCCCCCCceEEEEeCCcccchHHHHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCccccccccc-cccc
Confidence 899999997799999999999999999999999999999999999999999999999999999999999999987 8999
Q ss_pred CCCCchhhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeCCccCCC
Q 030658 81 QGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKK 160 (173)
Q Consensus 81 ~gr~p~Kaa~~i~k~L~sa~~NA~~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~~~~~~~ 160 (173)
+||||+|+|..|+|+|+||++||+++|+|+|+|||.||.||+|++++|++|||+||++++++++|||+|+|+|.++.+++
T Consensus 80 ~GR~P~KaA~~i~KlL~SA~aNAe~~gld~d~L~I~~i~v~kG~~lKR~~pRA~GRA~~i~k~t~HI~Ivl~e~~~~~~~ 159 (181)
T PTZ00178 80 QGRWPEKSVKFVLSLLKNAEANAEAKGLDVEKLVISHVQVNRAPRGRRRTYRAHGRINPFMSSPCHIELIATEKDETVPK 159 (181)
T ss_pred cCcCcHHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCcccCCCCCccCCCcCcccCCceeEEEEEEEccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998888876
Q ss_pred Ccchh
Q 030658 161 EPETQ 165 (173)
Q Consensus 161 ~~~~~ 165 (173)
+.+.|
T Consensus 160 ~~~~~ 164 (181)
T PTZ00178 160 PKEAP 164 (181)
T ss_pred chhhh
Confidence 55543
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=7.1e-56 Score=350.43 Aligned_cols=150 Identities=58% Similarity=0.871 Sum_probs=147.5
Q ss_pred ccCCCCCCCceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCC
Q 030658 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGR 83 (173)
Q Consensus 4 y~~~~~~~~~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr 83 (173)
||++++|++++++|..+++++||+|+++||++||||++++|+.+|++|+++|+||||++|++|+||++++.+ |||++||
T Consensus 1 ys~~~~~~~~~akA~~~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~-~~~~~gR 79 (150)
T TIGR01038 1 YSYKPEDPTKSAKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKE-WGWTAGR 79 (150)
T ss_pred CCcCCCCCCeeEEEEeCCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccc-cccccCC
Confidence 999998899999999999999999999999999999999999999999999999999999999999999988 7999999
Q ss_pred CchhhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeC
Q 030658 84 WPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEK 154 (173)
Q Consensus 84 ~p~Kaa~~i~k~L~sa~~NA~~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~ 154 (173)
||+|+|..|+|+|+||++||+++|+|+|+|||.||+||+|+.+||++|||+||++++++++|||+|+|+|+
T Consensus 80 ~P~Kaa~~i~klL~sA~aNA~~~gld~d~L~I~~i~vnkg~~~kR~~prA~GRa~~~~k~~~HI~Iil~e~ 150 (150)
T TIGR01038 80 YPVKAAKFILKVLQNAEANAEYKGLDVEKLVIIHIQANKGPKIRRWMPRAFGRATPYNSSPTHIELVVEEK 150 (150)
T ss_pred CchHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCCccCCCCCccCCCCCcccCCCceEEEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999874
No 3
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=100.00 E-value=5.2e-55 Score=346.48 Aligned_cols=151 Identities=42% Similarity=0.598 Sum_probs=147.3
Q ss_pred CccccCCCCCCCceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCC
Q 030658 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNG 80 (173)
Q Consensus 1 ~~~y~~~~~~~~~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~ 80 (173)
|++||+++ +++++++|.++++++||+|+++||++||||++++|+++|++|+++|+||||++|++|+||++++ +||+
T Consensus 3 ~~~ys~~~-~~~~~akA~~~~~rvS~kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~---~~~~ 78 (153)
T PRK04223 3 RINYSVKA-DPEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGI---DGWP 78 (153)
T ss_pred ccccccCC-CCCceEEEEeCCCccChHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccc---cccc
Confidence 67899999 6999999999999999999999999999999999999999999999999999999999999987 7899
Q ss_pred CCCCchhhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeCC
Q 030658 81 QGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKE 155 (173)
Q Consensus 81 ~gr~p~Kaa~~i~k~L~sa~~NA~~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~~ 155 (173)
+||||+|+|+.|+|+|+||++||+++|+|+|+|||+||+||+|+.++|++|||+||++++.+++|||+|+|+|.+
T Consensus 79 ~gr~PkKaa~~i~KlL~sA~aNA~~~gld~d~L~I~~i~v~kg~~~kR~~prA~GRa~~~~k~~sHI~Iil~e~~ 153 (153)
T PRK04223 79 AGRYPVKAAKAFLKLLENAEANAEYKGLDTEKLVIVHIAAHKGRVIKGYMPRAFGRATPKNTETVNIEVILEEVE 153 (153)
T ss_pred cCCCchHHHHHHHHHHHHHHHHHHhcCCChhHeEEEEEEECCCCCCCCcCcccCCCCCcccCCCceEEEEEEeCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999853
No 4
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-41 Score=257.26 Aligned_cols=118 Identities=37% Similarity=0.483 Sum_probs=114.0
Q ss_pred ccCCCCCCCceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCC
Q 030658 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGR 83 (173)
Q Consensus 4 y~~~~~~~~~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr 83 (173)
||++.. ++++++|..+++++||+|+++||++||||++++|+.+|+ |
T Consensus 1 y~~~~~-~~~~akA~~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~---------------------------~------ 46 (120)
T COG0091 1 YSAKVE-PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILE---------------------------F------ 46 (120)
T ss_pred CCcccc-hhhhhHhhhccCcCChHHHHHHHHHHcCCcHHHHHHHHH---------------------------h------
Confidence 788875 889999999999999999999999999999999999999 5
Q ss_pred CchhhhHHHHHHHHHHHHHHHH-cCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeCC
Q 030658 84 WPVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKE 155 (173)
Q Consensus 84 ~p~Kaa~~i~k~L~sa~~NA~~-kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~~ 155 (173)
.|+|+|+.|+|+|+||++||++ +|||+|+|||.||+||+|+++||++|||+||++++++++|||||+|+|.+
T Consensus 47 ~pkKaa~~v~KvL~sA~aNAe~n~gLd~d~L~V~~i~v~~gp~lKR~~pRA~GRa~~i~k~tshItvvv~e~~ 119 (120)
T COG0091 47 VPKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDKGPVLKRFMPRARGRATRINKRTSHITVVVREKE 119 (120)
T ss_pred ChHHHHHHHHHHHHHHHhhHHhccCCChHHEEEEEEEeCCCceeeeecccccCccccccCCCceEEEEEeecC
Confidence 7999999999999999999999 79999999999999999999999999999999999999999999999964
No 5
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00 E-value=1.3e-38 Score=242.77 Aligned_cols=112 Identities=29% Similarity=0.401 Sum_probs=107.4
Q ss_pred CCCceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhh
Q 030658 10 NPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSA 89 (173)
Q Consensus 10 ~~~~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa 89 (173)
.++++++|..+++++||+|+++||++||||++++|+.||+ | .|+|+|
T Consensus 5 ~~~~~~~A~~~~ir~SpkK~r~va~~IRG~~v~~A~~~L~---------------------------~------~pkk~a 51 (117)
T CHL00034 5 KSTTEVYALAKYIRMSAHKARRVIDQIRGRSYEEALMILE---------------------------F------MPYRAC 51 (117)
T ss_pred CCCceEEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------H------CcHHHH
Confidence 3568999999999999999999999999999999999999 5 799999
Q ss_pred HHHHHHHHHHHHHHH-HcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeC
Q 030658 90 KFILDLLKNAESNAE-VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEK 154 (173)
Q Consensus 90 ~~i~k~L~sa~~NA~-~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~ 154 (173)
+.|+++|+||++||+ ++|+|+|+|||.|++||+|+++||++|||+||++++++++|||+|+|+|.
T Consensus 52 ~~i~klL~sA~aNA~~~~gld~d~L~I~~i~v~~G~~~KR~~prArGRa~~i~k~~sHI~Vvl~e~ 117 (117)
T CHL00034 52 YPILKLVYSAAANASHNMGLNKANLFISKAEVDEGPTLKRFRPRAQGRSYPIKKPTCHITIVLKDI 117 (117)
T ss_pred HHHHHHHHHHHHHHHHccCCCccceEEEEEEECCCCccCCCCcccCCCCCcccCCCccEEEEEecC
Confidence 999999999999995 58999999999999999999999999999999999999999999999873
No 6
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00 E-value=1.9e-38 Score=239.93 Aligned_cols=110 Identities=32% Similarity=0.424 Sum_probs=106.6
Q ss_pred ceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHH
Q 030658 13 KSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFI 92 (173)
Q Consensus 13 ~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i 92 (173)
++++|..+++++||+|+++||++||||++++|+.||+ | ||+|+|..|
T Consensus 1 ~~~~A~~~~~~~SpkK~~~v~~~IrG~~v~~A~~~L~---------------------------~------~pkk~a~~i 47 (112)
T PRK00565 1 MEAKAKARYVRVSPRKARLVADLIRGKKVEEALAILK---------------------------F------SPKKAARLV 47 (112)
T ss_pred CceEEEeCccccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------H------CcHhHHHHH
Confidence 3689999999999999999999999999999999999 5 899999999
Q ss_pred HHHHHHHHHHHHH-cCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeCC
Q 030658 93 LDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKE 155 (173)
Q Consensus 93 ~k~L~sa~~NA~~-kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~~ 155 (173)
+++|+||.+||++ +|+|+|+|||.|+|||+|+++||++|||+||++++++++|||+|+|+|.+
T Consensus 48 ~k~L~sA~aNA~~~~g~d~~~L~I~~~~v~~G~~~Kr~~~rArGR~~~i~k~~~hi~vvL~e~~ 111 (112)
T PRK00565 48 KKVLKSAIANAENNHGLDIDNLVVKEAYVDEGPTLKRFRPRARGRASRIRKRTSHITVVVAEKE 111 (112)
T ss_pred HHHHHHHHHHHHhccCCChhHeEEEEEEECCCCccCCCCCCcCCCCCccccCCccEEEEEEecC
Confidence 9999999999998 89999999999999999999999999999999999999999999999964
No 7
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=100.00 E-value=1.6e-37 Score=231.97 Aligned_cols=102 Identities=30% Similarity=0.384 Sum_probs=98.8
Q ss_pred EeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHHHHH
Q 030658 17 ARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLL 96 (173)
Q Consensus 17 A~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~k~L 96 (173)
|..+++++||+|+++||++||||+++||+.||+ | ||+|+|..|+|+|
T Consensus 1 a~~r~~r~SpkK~~~va~~IrG~~v~~A~~~L~---------------------------f------~pkk~a~~i~klL 47 (103)
T TIGR01044 1 AKARFVRISPRKARLVADLIRGKSVSQALDILR---------------------------F------TPKKAAPLIKKVL 47 (103)
T ss_pred CcccccccCHHHHHHHHHHHcCCcHHHHHHHHh---------------------------h------CCHhHHHHHHHHH
Confidence 568999999999999999999999999999999 6 9999999999999
Q ss_pred HHHHHHHH-HcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEe
Q 030658 97 KNAESNAE-VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTL 151 (173)
Q Consensus 97 ~sa~~NA~-~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL 151 (173)
+||.+||+ ++|+|+|+|||.|++||+|+++||++|||+||++++++++|||+|+|
T Consensus 48 ~sA~aNA~~~~~ld~~~L~I~~~~v~~G~~~kr~~~rarGRa~~i~k~~~hi~vvl 103 (103)
T TIGR01044 48 ASAIANAEHNYGLDADNLVVVTIFVDEGPTLKRIRPRAKGRASRIRKRTSHITVVV 103 (103)
T ss_pred HHHHHHHHHccCCChHheEEEEEEECCCCcccCCCCCCCCCCCcccCCCccEEEeC
Confidence 99999996 58999999999999999999999999999999999999999999986
No 8
>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=2.3e-36 Score=225.25 Aligned_cols=104 Identities=44% Similarity=0.561 Sum_probs=100.4
Q ss_pred EeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHHHHH
Q 030658 17 ARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLL 96 (173)
Q Consensus 17 A~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~k~L 96 (173)
|..+++++||||++++|++||||++++|+.||++ .|+|+|..|+++|
T Consensus 1 A~~~~i~~S~kk~~~v~~~Irg~~v~~A~~~L~~---------------------------------~~~k~a~~i~k~L 47 (105)
T PF00237_consen 1 AKLRNIRISPKKLREVARLIRGMSVDEAIAQLKF---------------------------------VPKKAAKFILKLL 47 (105)
T ss_dssp EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHH---------------------------------HSSHHHHHHHHHH
T ss_pred CccccccCCHHHHHHHHHHHcCCCHHHHHHHHHh---------------------------------CcHHHHHHHHhhH
Confidence 6789999999999999999999999999999994 6999999999999
Q ss_pred HHHHHHHH-HcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeee
Q 030658 97 KNAESNAE-VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSE 153 (173)
Q Consensus 97 ~sa~~NA~-~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E 153 (173)
+||.+||+ ++|+|+|+|||.++|||+|++++|++|||+||++++++++|||+|+|+|
T Consensus 48 ~~a~~nA~~~~g~d~~~L~I~~~~v~~g~~~kr~~~rArGR~~~~~k~~~hi~vvl~E 105 (105)
T PF00237_consen 48 KSAIANAENNKGLDPDNLYISEIWVNKGPYLKRIRPRARGRAGPIRKRTSHITVVLKE 105 (105)
T ss_dssp HHHHHHHHHHCTSTCGGEEEEEEEEEEEEEEEEEEEECTTEEEEEEEEEEEEEEEEEE
T ss_pred HHHHhhcccccccccCceEEEEEEEEecccccCCCcCcCCCccCeecCceEEEEEEeC
Confidence 99999999 7999999999999999999999999999999999999999999999998
No 9
>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=100.00 E-value=1.1e-34 Score=216.06 Aligned_cols=104 Identities=48% Similarity=0.664 Sum_probs=99.7
Q ss_pred EEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHHH
Q 030658 15 CKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILD 94 (173)
Q Consensus 15 ~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~k 94 (173)
++|..+++++||+|+++||++||||+++||+.||+ | .|+|+|..|++
T Consensus 1 ~~a~~~~i~~S~kK~~~v~~~Irg~~v~~A~~~L~---------------------------~------~~kk~a~~i~k 47 (105)
T cd00336 1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLE---------------------------F------VPKKAAKIILK 47 (105)
T ss_pred CEEEEccCccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------h------CCHHHHHHHHH
Confidence 47899999999999999999999999999999999 5 79999999999
Q ss_pred HHHHHHHHHHHcC-CCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEe
Q 030658 95 LLKNAESNAEVKG-LDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTL 151 (173)
Q Consensus 95 ~L~sa~~NA~~kg-ld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL 151 (173)
+|+||.+||++++ +|+|+|||.|+|||+|++++|++|||+||++++++++|||+|+|
T Consensus 48 ~l~sa~~nA~~~~~~~~~~L~I~~~~v~~g~~~kr~~~rarGR~~~~~k~~~hi~ivl 105 (105)
T cd00336 48 LLKSAEANAENNGLDDPDKLYIKHIQVNKGPTLKRRRPRARGRANPIRKRTCHITVVL 105 (105)
T ss_pred HHHHHHHhHHHcCCCCccceEEEEEEECCCCcccCCCcCCCCCCcccccCceeEEEeC
Confidence 9999999999865 56999999999999999999999999999999999999999986
No 10
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=100.00 E-value=1.1e-34 Score=251.46 Aligned_cols=113 Identities=27% Similarity=0.397 Sum_probs=107.7
Q ss_pred ceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHH
Q 030658 13 KSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFI 92 (173)
Q Consensus 13 ~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i 92 (173)
|+++|..+++++||+|+++||++||||++++|+.+|+ | +|+|+|..|
T Consensus 1 M~akA~~r~iriSpkK~R~Va~~IRGk~v~~Al~~L~---------------------------~------~PkKaA~~I 47 (311)
T PRK12279 1 MTNKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILS---------------------------N------TPKKFAPIV 47 (311)
T ss_pred CceEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHH---------------------------h------CCHHHHHHH
Confidence 4689999999999999999999999999999999999 5 899999999
Q ss_pred HHHHHHHHHHHH--HcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeCCccC
Q 030658 93 LDLLKNAESNAE--VKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPV 158 (173)
Q Consensus 93 ~k~L~sa~~NA~--~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~~~~~ 158 (173)
+++|+||++||+ ++|+|+|+|||.||+||+|+.+||++|||+||++++++++|||+|+|.|...+.
T Consensus 48 ~KlLkSA~ANAe~~n~gld~d~L~I~~~~VdkGp~lKR~~PRArGRA~~i~KrtsHItIvl~e~~~~~ 115 (311)
T PRK12279 48 LKLLNSAISNVQHNSKDMDPSKLYIYKIVANQGPTMKRTLPRAKGSADQLFKRTTHLEIVLSDDVNER 115 (311)
T ss_pred HHHHHHHHHHHHHhhcCCChhHeEEEEEEECCCCcccCCCCccCCCCCcccCCCccEEEEEecCCchh
Confidence 999999999999 489999999999999999999999999999999999999999999999855543
No 11
>KOG3353 consensus 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.6e-37 Score=246.15 Aligned_cols=158 Identities=69% Similarity=1.058 Sum_probs=154.1
Q ss_pred CCCCCCceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCch
Q 030658 7 EPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPV 86 (173)
Q Consensus 7 ~~~~~~~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~ 86 (173)
+|+++++.++|.+.++++|+|++++.+..|+++++..|+.+|.+|+.+++|+||++|+.|+|+..++++ |||.+||||+
T Consensus 1 ~~~~~~k~~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~-~~~~~~rwpk 79 (175)
T KOG3353|consen 1 DPENPTKSCKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQ-WGWTQGRWPK 79 (175)
T ss_pred CccccchhhhcccccEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhh-hccccCcccc
Confidence 367888999999999999999999999999999999999999999999999999999999999999987 8999999999
Q ss_pred hhhHHHHHHHHHHHHHHHHcCCCCCCeEEEEEEEecCCccccceecCCCccccccccceEEEEEeeeCCccCCCCcchh
Q 030658 87 KSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKKEPETQ 165 (173)
Q Consensus 87 Kaa~~i~k~L~sa~~NA~~kgld~d~L~I~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~~~~~~~~~~~~ 165 (173)
|++++++.+|+||.+||+.+|+|+|.|+|.|+.||+++.+.+.+|||+||.+++.+.+|||++||+|.++++|+++|+-
T Consensus 80 ksaefll~~LkN~esnaElkgldVDsLvIehiqvnkApKm~~rtyraHg~in~y~ssP~hie~il~~ke~~v~k~e~~~ 158 (175)
T KOG3353|consen 80 KSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQIVPKPEEEV 158 (175)
T ss_pred hHHHHHHHHHHhhhhcccccCcCcceeEeeehhhcccchhhhHHHHhhcccccccCChHHHHHHHHhhcccCCChhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999974
No 12
>KOG1711 consensus Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=1.7e-25 Score=184.74 Aligned_cols=122 Identities=28% Similarity=0.318 Sum_probs=113.3
Q ss_pred ccCCCCCCCceEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCC
Q 030658 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGR 83 (173)
Q Consensus 4 y~~~~~~~~~~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr 83 (173)
|++.|. . .++.|....++.|+||++.+|++|+||++++|+.||+ |
T Consensus 63 l~~~p~-~-~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~---------------------------~------ 107 (218)
T KOG1711|consen 63 LPFEPK-R-PEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLE---------------------------F------ 107 (218)
T ss_pred CCCCCc-c-hhHHHHHHHHHhCHHHHHHHHHHHcCCCHHHHHHHhh---------------------------c------
Confidence 455553 2 6888999999999999999999999999999999999 6
Q ss_pred CchhhhHHHHHHHHHHHHHHHH-cCCCCCCeEE-EEEEEecCCccccceecCCCccccccccceEEEEEeeeCCccCCC
Q 030658 84 WPVKSAKFILDLLKNAESNAEV-KGLDVDALYI-SHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKK 160 (173)
Q Consensus 84 ~p~Kaa~~i~k~L~sa~~NA~~-kgld~d~L~I-~~~~v~kG~~~kr~~pRArGRa~~~~k~~~hI~IvL~E~~~~~~~ 160 (173)
+++|+|..|.++|.+|.+||.+ +|+|+++||| .++++++|.++||..++||||.+++++++|||+++|.|.+.+..+
T Consensus 108 s~kK~a~~i~~~l~~A~~nA~~~~gl~~~~l~v~~~~t~~~g~~~Krl~~hargr~~ii~~~yvhi~v~L~e~s~~~~~ 186 (218)
T KOG1711|consen 108 SDKKAAKTIAEVLLSARANAVHNHGLDPDSLLVVAEATVGQGNELKRLKVHARGRFGIIRRPYVHIFVKLEEGSPPQQR 186 (218)
T ss_pred chHHHHHHHHHHHHHHHhhhHHhcCCCccceEEEEeeecccchhhhheeeeccCcccceecceeeEEEEEeecCCCchh
Confidence 8999999999999999999976 7999999999 999999999999999999999999999999999999998887765
No 13
>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]
Probab=68.86 E-value=10 Score=30.23 Aligned_cols=34 Identities=12% Similarity=0.194 Sum_probs=29.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHhhcccccceeee
Q 030658 30 RETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63 (173)
Q Consensus 30 ~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~ 63 (173)
......|+||+++||+.+=+.-|+++.++|=.+.
T Consensus 97 S~aTewvkgkt~dea~kIkNteIAKeL~LPPVKL 130 (157)
T KOG3361|consen 97 SLATEWVKGKTLDEALKIKNTEIAKELSLPPVKL 130 (157)
T ss_pred HHHHHHHccccHHHHHhcccHHHHHhccCCchhh
Confidence 4566789999999999988888999999996655
No 14
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=67.43 E-value=21 Score=25.62 Aligned_cols=55 Identities=15% Similarity=0.227 Sum_probs=41.4
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHHHHHHHHHHHH
Q 030658 28 NTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNA 103 (173)
Q Consensus 28 K~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~k~L~sa~~NA 103 (173)
.+..++..+ |++..+|+..+-.-+....-+||.--. +.-.-..++...+++++|-
T Consensus 15 ~A~~vl~~l-Gls~S~Ai~~fl~qi~~~~~iPF~~~~--------------------~s~ed~~~l~~~re~~~~~ 69 (80)
T PRK11235 15 RAYAVLEKL-GVTPSEALRLLLQYVAENGRLPFKTVL--------------------LSDEDAALLETVRERLANP 69 (80)
T ss_pred HHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCCCCCCC--------------------CCHHHHHHHHHHHHHHhCC
Confidence 567788887 999999999988888888899977542 2224566777777777664
No 15
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=64.98 E-value=11 Score=27.60 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=29.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHhhcccccceeee
Q 030658 29 TRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63 (173)
Q Consensus 29 ~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~ 63 (173)
+..|+..+ |+++.+|+..+=.=+..+..+||.-.
T Consensus 19 A~~Vl~~m-Glt~S~airm~L~~va~~~~lPfdl~ 52 (88)
T COG3077 19 ATAVLEEM-GLTISDAIRMFLTKVAREGALPFDLR 52 (88)
T ss_pred HHHHHHHh-CCCHHHHHHHHHHHHHHcCCCCcccc
Confidence 56677777 99999999998888899999998765
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=63.92 E-value=45 Score=25.13 Aligned_cols=69 Identities=12% Similarity=0.054 Sum_probs=48.5
Q ss_pred eEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHH
Q 030658 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFIL 93 (173)
Q Consensus 14 ~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~ 93 (173)
.++-....-.+|.-=+-.++++|.|+++++|..+....+... .|.+.. -.++|....
T Consensus 53 d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~~~i~~~---------------------lg~p~~--r~~CA~l~~ 109 (124)
T TIGR01999 53 DAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKNTEIAKE---------------------LSLPPV--KLHCSLLAE 109 (124)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccHHHHHHH---------------------cCCCcc--cchHHHHHH
Confidence 445555666677777889999999999999999877432211 222222 256888889
Q ss_pred HHHHHHHHHHHH
Q 030658 94 DLLKNAESNAEV 105 (173)
Q Consensus 94 k~L~sa~~NA~~ 105 (173)
+.|+.|+.+...
T Consensus 110 ~al~~a~~~y~~ 121 (124)
T TIGR01999 110 DAIKAAIKDYKS 121 (124)
T ss_pred HHHHHHHHHHHH
Confidence 999998887654
No 17
>PRK11325 scaffold protein; Provisional
Probab=60.41 E-value=46 Score=25.31 Aligned_cols=69 Identities=10% Similarity=0.043 Sum_probs=50.2
Q ss_pred eEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHH
Q 030658 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFIL 93 (173)
Q Consensus 14 ~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~ 93 (173)
.++-....-.+|.==+-.++.+|.|+++++|..+....+... +|.+..| .++|....
T Consensus 55 d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~~~i~~~---------------------lg~p~~r--~~CA~la~ 111 (127)
T PRK11325 55 DAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEE---------------------LALPPVK--IHCSILAE 111 (127)
T ss_pred EEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHH---------------------cCCCccc--chHHHHHH
Confidence 555666777778888899999999999999999877533221 2222222 56888888
Q ss_pred HHHHHHHHHHHH
Q 030658 94 DLLKNAESNAEV 105 (173)
Q Consensus 94 k~L~sa~~NA~~ 105 (173)
+.|+.|+.+...
T Consensus 112 ~al~~a~~~y~~ 123 (127)
T PRK11325 112 DAIKAAIADYKS 123 (127)
T ss_pred HHHHHHHHHHHh
Confidence 999998877643
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=59.46 E-value=28 Score=25.23 Aligned_cols=36 Identities=14% Similarity=-0.019 Sum_probs=27.5
Q ss_pred EEEeeCCCccchHHHHHHHHHH-----hCCCHHHHHHHHHH
Q 030658 15 CKARGSDLRVHFKNTRETAHAI-----RKLPLTKAKRYLED 50 (173)
Q Consensus 15 ~kA~~~~~riS~KK~~~va~~I-----rG~~v~~A~~~L~~ 50 (173)
+-......--..-.+.-++++| .|+++++.+++|+.
T Consensus 26 vf~~~~~~Gg~~~~~~ai~rliS~~Lr~G~~~~~ii~~L~g 66 (95)
T PF12637_consen 26 VFINVGKAGGCSGNLEAIARLISLALRSGVPPEEIIDQLRG 66 (95)
T ss_pred EEEecCcCCCchHHHHHHHHHHHHHHHcCCCHHHHHHHhcC
Confidence 4344333333377889999999 99999999999994
No 19
>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=54.91 E-value=14 Score=25.42 Aligned_cols=37 Identities=24% Similarity=0.401 Sum_probs=25.5
Q ss_pred HhCCCHHHHHHHHHHHhhc--ccccceeeecCCCccchh
Q 030658 36 IRKLPLTKAKRYLEDVMAH--KQAIPFTRFCGGVGRTAQ 72 (173)
Q Consensus 36 IrG~~v~~A~~~L~~V~~~--k~~iP~~r~~~~~~~~~~ 72 (173)
+.||++++|+..|+..+.. ..-+...+.--|.|++|.
T Consensus 3 LHG~~~~eA~~~l~~~l~~~~~~~~~~~~II~G~G~hS~ 41 (83)
T PF01713_consen 3 LHGLTVEEALRALEEFLDEARQRGIRELRIITGKGNHSK 41 (83)
T ss_dssp -TTS-HHHHHHHHHHHHHHHHHTTHSEEEEE--STCTCC
T ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCCEEEEEeccCCCCC
Confidence 4699999999999998754 456677777777777763
No 20
>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=53.46 E-value=19 Score=25.28 Aligned_cols=35 Identities=17% Similarity=0.309 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceee
Q 030658 27 KNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTR 62 (173)
Q Consensus 27 KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r 62 (173)
..+..|+..+ |++..+|+..+-.=+..+..|||.-
T Consensus 14 ~~a~~il~~~-Glt~s~ai~~fl~qiv~~~~iPF~~ 48 (83)
T PF04221_consen 14 EEAEAILEEL-GLTLSDAINMFLKQIVREGGIPFEL 48 (83)
T ss_dssp HHHHHHHHHT-T--HHHHHHHHHHHHHHHSS-S---
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHHHHHhCCCCccc
Confidence 3567777777 9999999998887778888899743
No 21
>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=42.78 E-value=1.4e+02 Score=22.33 Aligned_cols=69 Identities=9% Similarity=0.026 Sum_probs=49.1
Q ss_pred eEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCC-CCCCCCchhhhHHH
Q 030658 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHP-NGQGRWPVKSAKFI 92 (173)
Q Consensus 14 ~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g-~~~gr~p~Kaa~~i 92 (173)
.++-....-.+|.-=+-.++.+|.|++++||..+...-+. +.+| .+.. -.++|...
T Consensus 49 d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~~~i~---------------------~~l~~l~~~--r~~CA~la 105 (121)
T TIGR03419 49 DVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVA---------------------EALDGLPPV--KMHCSVLA 105 (121)
T ss_pred EEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhhHHHH---------------------HHHcCCCcc--cCHHHHHH
Confidence 4555666677777778899999999999999998763110 0122 2222 35788999
Q ss_pred HHHHHHHHHHHHH
Q 030658 93 LDLLKNAESNAEV 105 (173)
Q Consensus 93 ~k~L~sa~~NA~~ 105 (173)
.+.|+.|+.+...
T Consensus 106 ~~al~~a~~~y~~ 118 (121)
T TIGR03419 106 EEAIHKAINDYRE 118 (121)
T ss_pred HHHHHHHHHHHHh
Confidence 9999998887654
No 22
>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=38.56 E-value=58 Score=23.11 Aligned_cols=33 Identities=18% Similarity=0.295 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhhccccccee
Q 030658 28 NTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61 (173)
Q Consensus 28 K~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~ 61 (173)
.+..|++.+ |++..+|+..+=.=+.+..-+||.
T Consensus 16 ~a~~i~~~l-Gl~~s~ai~~fl~qvv~~~~lPF~ 48 (83)
T TIGR02384 16 EAYAVFEEL-GLTPSTAIRMFLKQVIREQGLPFD 48 (83)
T ss_pred HHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCCCC
Confidence 456677777 999999999877767777888854
No 23
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=37.28 E-value=30 Score=28.87 Aligned_cols=30 Identities=33% Similarity=0.489 Sum_probs=27.3
Q ss_pred CCccchHHHHHHHHHH-hCCCHHHHHHHHHH
Q 030658 21 DLRVHFKNTRETAHAI-RKLPLTKAKRYLED 50 (173)
Q Consensus 21 ~~riS~KK~~~va~~I-rG~~v~~A~~~L~~ 50 (173)
.=|.+..|++.+.++| +|.+.++|+.+|++
T Consensus 59 ~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~d 89 (194)
T COG1094 59 EDPLALLKARDVVKAIGRGFPPEKALKLLED 89 (194)
T ss_pred CChHHHHHHHHHHHHHhcCCCHHHHHHHhcC
Confidence 4678899999999999 59999999999997
No 24
>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=36.81 E-value=1.3e+02 Score=26.31 Aligned_cols=70 Identities=11% Similarity=0.029 Sum_probs=47.9
Q ss_pred eEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHH
Q 030658 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFIL 93 (173)
Q Consensus 14 ~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~ 93 (173)
.++-....-.+|.==+-.++.+|+|++++||..+...-+... + .|.+.. -.++|....
T Consensus 54 d~~F~~~GCais~ASAs~~~eli~Gktv~ea~~i~~~di~~~-------L-------------~~lpp~--r~~CA~La~ 111 (290)
T TIGR02000 54 DAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVSNQDIADY-------L-------------GGLPPE--KMHCSVMGQ 111 (290)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHHhhHHHHHHH-------H-------------cCCChh--hchHHHHHH
Confidence 445555666677777889999999999999999886322110 0 012212 356888888
Q ss_pred HHHHHHHHHHHH
Q 030658 94 DLLKNAESNAEV 105 (173)
Q Consensus 94 k~L~sa~~NA~~ 105 (173)
+.|+.|+.+...
T Consensus 112 ~Al~~Al~~y~~ 123 (290)
T TIGR02000 112 EALEAAIANYRG 123 (290)
T ss_pred HHHHHHHHHHhc
Confidence 999998888764
No 25
>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=31.57 E-value=35 Score=21.98 Aligned_cols=15 Identities=27% Similarity=0.352 Sum_probs=13.7
Q ss_pred HhCCCHHHHHHHHHH
Q 030658 36 IRKLPLTKAKRYLED 50 (173)
Q Consensus 36 IrG~~v~~A~~~L~~ 50 (173)
+.||++++|...|++
T Consensus 6 ~~g~~~~~a~~~l~~ 20 (63)
T PF03793_consen 6 LVGMTYDEAKSILEA 20 (63)
T ss_dssp TTTSBHHHHHHHHHH
T ss_pred cCCCcHHHHHHHHHH
Confidence 569999999999996
No 26
>PF13852 DUF4197: Protein of unknown function (DUF4197)
Probab=30.77 E-value=54 Score=27.27 Aligned_cols=20 Identities=25% Similarity=0.321 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 030658 30 RETAHAIRKLPLTKAKRYLE 49 (173)
Q Consensus 30 ~~va~~IrG~~v~~A~~~L~ 49 (173)
--+.++|+.|+++||..+|.
T Consensus 84 ~if~~AI~~Ms~~DA~~IL~ 103 (202)
T PF13852_consen 84 PIFVDAIKSMSIQDAKGILN 103 (202)
T ss_pred HHHHHHHHhCCHHhHHHHhc
Confidence 34678999999999999998
No 27
>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=30.76 E-value=1.9e+02 Score=21.58 Aligned_cols=34 Identities=15% Similarity=0.179 Sum_probs=27.4
Q ss_pred eEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHH
Q 030658 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRY 47 (173)
Q Consensus 14 ~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~ 47 (173)
.++.....-.+|.-=+..++.+|.|+++++|..+
T Consensus 53 d~~f~~~GC~~~~Asas~~~~~i~gk~l~ea~~i 86 (126)
T PF01592_consen 53 DAKFQGFGCAISIASASMMCELIKGKTLEEALKI 86 (126)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHTTSBHHHHHCH
T ss_pred EEEEEeecChHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 4555666677777788999999999999999654
No 28
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=30.03 E-value=1.1e+02 Score=24.17 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=29.3
Q ss_pred eEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHH
Q 030658 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLED 50 (173)
Q Consensus 14 ~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~ 50 (173)
.++-....-.+|.-=+..++.+|.|++++||+...+.
T Consensus 56 d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~~~ 92 (150)
T COG0822 56 DAKFKGFGCAISIASSSMMTELVKGKTLDEALKITEA 92 (150)
T ss_pred EEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3444556666777778899999999999999998854
No 29
>smart00463 SMR Small MutS-related domain.
Probab=27.80 E-value=51 Score=22.41 Aligned_cols=21 Identities=14% Similarity=0.308 Sum_probs=16.8
Q ss_pred HhCCCHHHHHHHHHHHhhccc
Q 030658 36 IRKLPLTKAKRYLEDVMAHKQ 56 (173)
Q Consensus 36 IrG~~v~~A~~~L~~V~~~k~ 56 (173)
+.||++++|+..|+..|+.-.
T Consensus 6 LHG~~~~eA~~~l~~~l~~~~ 26 (80)
T smart00463 6 LHGLTVEEALTALDKFLNNAR 26 (80)
T ss_pred cCCCCHHHHHHHHHHHHHHHH
Confidence 469999999999998765433
No 30
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=27.77 E-value=76 Score=21.87 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCCHHHHHHHHH
Q 030658 29 TRETAHAIRKLPLTKAKRYLE 49 (173)
Q Consensus 29 ~~~va~~IrG~~v~~A~~~L~ 49 (173)
+..||+.|+|+|+++-..+|.
T Consensus 36 ~~~iA~~i~gks~eeir~~fg 56 (78)
T PF01466_consen 36 CKYIANMIKGKSPEEIRKYFG 56 (78)
T ss_dssp HHHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHhcCCCHHHHHHHcC
Confidence 356889999999999888876
No 31
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=27.73 E-value=28 Score=25.34 Aligned_cols=26 Identities=12% Similarity=0.267 Sum_probs=22.5
Q ss_pred EeeCCCccchHHHHHHHHHHhCCCHH
Q 030658 17 ARGSDLRVHFKNTRETAHAIRKLPLT 42 (173)
Q Consensus 17 A~~~~~riS~KK~~~va~~IrG~~v~ 42 (173)
|.-.+++++.+.+..|+..+||.+++
T Consensus 24 skqy~i~it~~QA~~I~~~lr~k~in 49 (85)
T PF11116_consen 24 SKQYNISITKKQAEQIANILRGKNIN 49 (85)
T ss_pred HHHhCCCCCHHHHHHHHHHHhcCCCC
Confidence 34568999999999999999999864
No 32
>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=27.56 E-value=1.5e+02 Score=21.82 Aligned_cols=38 Identities=16% Similarity=0.177 Sum_probs=31.2
Q ss_pred eEEEeeCCCccchHHHHHHHHHHhCCCHHHHHHHHHHH
Q 030658 14 SCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDV 51 (173)
Q Consensus 14 ~~kA~~~~~riS~KK~~~va~~IrG~~v~~A~~~L~~V 51 (173)
.++-....-.+|.-=+..+++.+.|+++++|..++...
T Consensus 50 d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~~~ 87 (123)
T cd06664 50 DAKFQGFGCAISIASASLLTELIKGKTLDEALKLLNKD 87 (123)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 44555666677777888999999999999999999864
No 33
>PF04485 NblA: Phycobilisome degradation protein nblA ; InterPro: IPR007574 In the cyanobacterium Synechococcus species PCC 7942 (P35087 from SWISSPROT), nblA triggers degradation of light-harvesting phycobiliproteins in response to deprivation nutrients including nitrogen, phosphorus and sulphur. The mechanism of nblA function is not known, but it has been hypothesised that nblA may act by disrupting phycobilisome structure, activating a protease or tagging phycobiliproteins for proteolysis. Members of this family have also been identified in the chloroplasts of some red algae.; PDB: 3CS5_D 1OJH_L 2QDO_B 2Q8V_A.
Probab=25.94 E-value=1.3e+02 Score=20.03 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=20.6
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHH
Q 030658 28 NTRETAHAIRKLPLTKAKRYLEDV 51 (173)
Q Consensus 28 K~~~va~~IrG~~v~~A~~~L~~V 51 (173)
+++...++|..|+.++|.++|-.+
T Consensus 11 ~L~~~~~qv~~ls~Eqaq~~Lve~ 34 (53)
T PF04485_consen 11 KLRSFKDQVQKLSREQAQELLVEL 34 (53)
T ss_dssp HHHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCHHHHHHHHHHH
Confidence 677889999999999999999875
No 34
>PF13286 HD_assoc: Phosphohydrolase-associated domain; PDB: 2DQB_D.
Probab=24.81 E-value=1e+02 Score=21.29 Aligned_cols=23 Identities=17% Similarity=0.120 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Q 030658 27 KNTRETAHAIRKLPLTKAKRYLE 49 (173)
Q Consensus 27 KK~~~va~~IrG~~v~~A~~~L~ 49 (173)
.+.+.||+.|.|||=.-|+..-+
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 57899999999999888887543
No 35
>PF07778 CENP-I: Mis6 ; InterPro: IPR012485 Centromere protein Cenp-I (also known as Mis6) is an essential centromere connector protein acting during G1-S phase of the cell cycle. Mis6 is thought to be required for recruiting Cenp-A, the centromere- specific histone H3 variant; an important event for centromere function and chromosome segregation during mitosis [, ].
Probab=22.05 E-value=74 Score=30.19 Aligned_cols=46 Identities=30% Similarity=0.275 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHhhcccccceeeecCCCccchhhhcCCCCCCCCCchhhhHHHHHHHHHHHHHHHHcCCCCCCe
Q 030658 39 LPLTKAKRYLEDVMAHKQAIPFTRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDAL 113 (173)
Q Consensus 39 ~~v~~A~~~L~~V~~~k~~iP~~r~~~~~~~~~~~~~~~g~~~gr~p~Kaa~~i~k~L~sa~~NA~~kgld~d~L 113 (173)
-++++|+.+|+++ . . +-+++-...+.+.|+...+.|-..|+++|.|
T Consensus 56 ~~l~~ai~~l~~~----------------------~--~-----~~~~~~~~~~~~~i~~l~s~A~~~GL~~~~l 101 (511)
T PF07778_consen 56 DSLEDAIEYLEKV----------------------S--K-----VPSKRRNTSLKSTIKTLESLAYENGLSPEAL 101 (511)
T ss_pred HHHHHHHHHHHhc----------------------c--c-----cccccccchHHHHHHHHHHHHHHcCCCHHHH
Confidence 6779999999953 0 1 1344555677788999999999999998876
No 36
>PF06738 DUF1212: Protein of unknown function (DUF1212); InterPro: IPR010619 This entry represents a predicted domain found within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. Some of these sequences are predicted to be membrane proteins.
Probab=21.74 E-value=1.3e+02 Score=23.78 Aligned_cols=39 Identities=18% Similarity=0.213 Sum_probs=26.2
Q ss_pred EeeCCCccchHHHHH---HHHHH--hCCCHHHHHHHHHHHhhcc
Q 030658 17 ARGSDLRVHFKNTRE---TAHAI--RKLPLTKAKRYLEDVMAHK 55 (173)
Q Consensus 17 A~~~~~riS~KK~~~---va~~I--rG~~v~~A~~~L~~V~~~k 55 (173)
.+...-.+...++.+ +.+.+ ..++++||.+.|+.+...+
T Consensus 55 ~~v~~~~~nl~~l~~v~~l~~~~~~~~~~~~ea~~~L~~I~~~~ 98 (193)
T PF06738_consen 55 RRVPPRGVNLDKLAAVNRLSRRIVAGQLSLEEAIERLDEIDREP 98 (193)
T ss_pred EEeCCCCcCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhCC
Confidence 334455555555544 56666 5899999999999875443
Done!