Query 030580
Match_columns 175
No_of_seqs 135 out of 1096
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 15:53:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030580hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00034 rpl22 ribosomal prote 100.0 5.2E-35 1.1E-39 225.6 11.8 95 81-175 6-100 (117)
2 PRK00565 rplV 50S ribosomal pr 100.0 9.6E-35 2.1E-39 221.9 10.7 93 83-175 1-93 (112)
3 TIGR01044 rplV_bact ribosomal 100.0 8.1E-35 1.8E-39 219.6 9.4 89 87-175 1-89 (103)
4 COG0091 RplV Ribosomal protein 100.0 2.7E-35 5.9E-40 228.7 6.9 95 81-175 7-101 (120)
5 cd00336 Ribosomal_L22 Ribosoma 100.0 8.1E-32 1.8E-36 201.9 10.6 91 85-175 1-91 (105)
6 PF00237 Ribosomal_L22: Riboso 100.0 5.8E-32 1.2E-36 203.0 4.8 89 87-175 1-89 (105)
7 TIGR01038 L22_arch ribosomal p 100.0 2.9E-30 6.2E-35 207.1 11.1 94 81-175 8-133 (150)
8 PRK04223 rpl22p 50S ribosomal 100.0 4.5E-30 9.6E-35 206.5 11.7 94 81-175 12-135 (153)
9 PRK12279 50S ribosomal protein 100.0 3.1E-30 6.7E-35 226.7 10.5 93 83-175 1-94 (311)
10 PTZ00178 60S ribosomal protein 100.0 1.5E-29 3.2E-34 208.4 10.8 94 81-175 11-136 (181)
11 KOG1711 Mitochondrial/chloropl 99.9 6.4E-24 1.4E-28 178.5 5.5 108 66-174 54-162 (218)
12 KOG3353 60S ribosomal protein 99.4 4E-14 8.7E-19 116.4 -1.5 90 84-174 8-129 (175)
13 TIGR03419 NifU_clost FeS clust 70.2 13 0.00027 28.5 5.3 59 84-142 49-118 (121)
14 PRK11325 scaffold protein; Pro 56.8 19 0.00042 27.8 4.1 59 84-142 55-123 (127)
15 TIGR01999 iscU FeS cluster ass 54.4 23 0.0005 27.1 4.1 59 84-142 53-121 (124)
16 PF01592 NifU_N: NifU-like N t 42.6 47 0.001 25.3 4.2 59 84-142 53-122 (126)
17 PF12637 TSCPD: TSCPD domain; 39.0 1.6E+02 0.0034 21.7 7.0 39 82-120 23-66 (95)
18 TIGR02000 NifU_proper Fe-S clu 36.9 1E+02 0.0022 27.3 6.0 59 84-142 54-123 (290)
19 COG0822 IscU NifU homolog invo 30.5 58 0.0013 26.2 3.1 35 84-118 56-90 (150)
20 cd06664 IscU_like Iron-sulfur 29.7 63 0.0014 24.1 3.0 36 84-119 50-85 (123)
21 PF13852 DUF4197: Protein of u 28.5 83 0.0018 26.6 3.8 20 101-120 85-104 (202)
22 PF01466 Skp1: Skp1 family, di 28.0 74 0.0016 22.3 3.0 21 100-120 37-57 (78)
23 PF13286 HD_assoc: Phosphohydr 25.3 90 0.002 21.9 3.1 22 97-118 69-90 (92)
24 PF03793 PASTA: PASTA domain; 25.0 47 0.001 21.7 1.4 15 106-120 6-20 (63)
25 PF03448 MgtE_N: MgtE intracel 22.8 69 0.0015 22.5 2.1 42 98-139 50-91 (102)
26 TIGR01994 SUF_scaf_2 SUF syste 20.0 1.2E+02 0.0027 23.5 3.1 36 84-119 53-88 (137)
No 1
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00 E-value=5.2e-35 Score=225.62 Aligned_cols=95 Identities=71% Similarity=1.088 Sum_probs=92.9
Q ss_pred CCceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcC
Q 030580 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNE 160 (175)
Q Consensus 81 ~~~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~k 160 (175)
.+++++|..+++++||+|+++||++||||+|+||+.||+|+|+|+|+.|+++|+||.+||++++|+|+|+|||.|+|||+
T Consensus 6 ~~~~~~A~~~~ir~SpkK~r~va~~IRG~~v~~A~~~L~~~pkk~a~~i~klL~sA~aNA~~~~gld~d~L~I~~i~v~~ 85 (117)
T CHL00034 6 STTEVYALAKYIRMSAHKARRVIDQIRGRSYEEALMILEFMPYRACYPILKLVYSAAANASHNMGLNKANLFISKAEVDE 85 (117)
T ss_pred CCceEEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHHHCcHHHHHHHHHHHHHHHHHHHHccCCCccceEEEEEEECC
Confidence 45899999999999999999999999999999999999999999999999999999999998999999999999999999
Q ss_pred CCCCCCCccCCCCCC
Q 030580 161 ATSAKRPRPKAQGRE 175 (175)
Q Consensus 161 Gp~lKR~~pRArGRA 175 (175)
||++||++||||||+
T Consensus 86 G~~~KR~~prArGRa 100 (117)
T CHL00034 86 GPTLKRFRPRAQGRS 100 (117)
T ss_pred CCccCCCCcccCCCC
Confidence 999999999999996
No 2
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00 E-value=9.6e-35 Score=221.93 Aligned_cols=93 Identities=42% Similarity=0.595 Sum_probs=91.2
Q ss_pred ceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcCCC
Q 030580 83 AEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEAT 162 (175)
Q Consensus 83 ~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~kGp 162 (175)
|+++|.++++++||+|+++|+++||||+|+||+.||+|+|+|+|+.|+++|+||.+||++++|+|+|+|||.++|||+||
T Consensus 1 ~~~~A~~~~~~~SpkK~~~v~~~IrG~~v~~A~~~L~~~pkk~a~~i~k~L~sA~aNA~~~~g~d~~~L~I~~~~v~~G~ 80 (112)
T PRK00565 1 MEAKAKARYVRVSPRKARLVADLIRGKKVEEALAILKFSPKKAARLVKKVLKSAIANAENNHGLDIDNLVVKEAYVDEGP 80 (112)
T ss_pred CceEEEeCccccCHHHHHHHHHHHcCCcHHHHHHHHHHCcHhHHHHHHHHHHHHHHHHHhccCCChhHeEEEEEEECCCC
Confidence 57899999999999999999999999999999999999999999999999999999999989999999999999999999
Q ss_pred CCCCCccCCCCCC
Q 030580 163 SAKRPRPKAQGRE 175 (175)
Q Consensus 163 ~lKR~~pRArGRA 175 (175)
++||++||||||+
T Consensus 81 ~~Kr~~~rArGR~ 93 (112)
T PRK00565 81 TLKRFRPRARGRA 93 (112)
T ss_pred ccCCCCCCcCCCC
Confidence 9999999999996
No 3
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=100.00 E-value=8.1e-35 Score=219.63 Aligned_cols=89 Identities=42% Similarity=0.599 Sum_probs=87.0
Q ss_pred EEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcCCCCCCC
Q 030580 87 ASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKR 166 (175)
Q Consensus 87 A~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~kGp~lKR 166 (175)
|..+++++||+|+++|+++||||+|+||+.||+|+|+|+|+.|+|+|+||.+||++++|+|+|+|||+|+|||+||++||
T Consensus 1 a~~r~~r~SpkK~~~va~~IrG~~v~~A~~~L~f~pkk~a~~i~klL~sA~aNA~~~~~ld~~~L~I~~~~v~~G~~~kr 80 (103)
T TIGR01044 1 AKARFVRISPRKARLVADLIRGKSVSQALDILRFTPKKAAPLIKKVLASAIANAEHNYGLDADNLVVVTIFVDEGPTLKR 80 (103)
T ss_pred CcccccccCHHHHHHHHHHHcCCcHHHHHHHHhhCCHhHHHHHHHHHHHHHHHHHHccCCChHheEEEEEEECCCCcccC
Confidence 56899999999999999999999999999999999999999999999999999998899999999999999999999999
Q ss_pred CccCCCCCC
Q 030580 167 PRPKAQGRE 175 (175)
Q Consensus 167 ~~pRArGRA 175 (175)
++|||||||
T Consensus 81 ~~~rarGRa 89 (103)
T TIGR01044 81 IRPRAKGRA 89 (103)
T ss_pred CCCCCCCCC
Confidence 999999997
No 4
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-35 Score=228.75 Aligned_cols=95 Identities=39% Similarity=0.565 Sum_probs=92.9
Q ss_pred CCceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcC
Q 030580 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNE 160 (175)
Q Consensus 81 ~~~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~k 160 (175)
..++++|..+++++||+|+++||++||||++++|+.+|+|+|+|+|+.|+|+|+||++||++|+|||+|+|||.|||||+
T Consensus 7 ~~~~akA~~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~~~pkKaa~~v~KvL~sA~aNAe~n~gLd~d~L~V~~i~v~~ 86 (120)
T COG0091 7 PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILEFVPKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDK 86 (120)
T ss_pred hhhhhHhhhccCcCChHHHHHHHHHHcCCcHHHHHHHHHhChHHHHHHHHHHHHHHHhhHHhccCCChHHEEEEEEEeCC
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCccCCCCCC
Q 030580 161 ATSAKRPRPKAQGRE 175 (175)
Q Consensus 161 Gp~lKR~~pRArGRA 175 (175)
||++||++|||||||
T Consensus 87 gp~lKR~~pRA~GRa 101 (120)
T COG0091 87 GPVLKRFMPRARGRA 101 (120)
T ss_pred CceeeeecccccCcc
Confidence 999999999999997
No 5
>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=99.97 E-value=8.1e-32 Score=201.93 Aligned_cols=91 Identities=41% Similarity=0.532 Sum_probs=88.4
Q ss_pred EEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcCCCCC
Q 030580 85 VSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSA 164 (175)
Q Consensus 85 ~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~kGp~l 164 (175)
++|..+++++||+|+++++++||||+++||+.||+|+++|+|+.|+++|+||.+||++++++|+|+|||.++|||+||++
T Consensus 1 ~~a~~~~i~~S~kK~~~v~~~Irg~~v~~A~~~L~~~~kk~a~~i~k~l~sa~~nA~~~~~~~~~~L~I~~~~v~~g~~~ 80 (105)
T cd00336 1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLEFVPKKAAKIILKLLKSAEANAENNGLDDPDKLYIKHIQVNKGPTL 80 (105)
T ss_pred CEEEEccCccCHHHHHHHHHHHcCCcHHHHHHHHHhCCHHHHHHHHHHHHHHHHhHHHcCCCCccceEEEEEEECCCCcc
Confidence 37899999999999999999999999999999999999999999999999999999988888899999999999999999
Q ss_pred CCCccCCCCCC
Q 030580 165 KRPRPKAQGRE 175 (175)
Q Consensus 165 KR~~pRArGRA 175 (175)
||++||||||+
T Consensus 81 kr~~~rarGR~ 91 (105)
T cd00336 81 KRRRPRARGRA 91 (105)
T ss_pred cCCCcCCCCCC
Confidence 99999999996
No 6
>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=99.97 E-value=5.8e-32 Score=202.98 Aligned_cols=89 Identities=38% Similarity=0.535 Sum_probs=86.0
Q ss_pred EEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcCCCCCCC
Q 030580 87 ASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKR 166 (175)
Q Consensus 87 A~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~kGp~lKR 166 (175)
|..+++++||||+++++++|+||+++||+.||+|+|+|+|+.|+++|+||.+||++++|+|+|+|||.++|||+||++||
T Consensus 1 A~~~~i~~S~kk~~~v~~~Irg~~v~~A~~~L~~~~~k~a~~i~k~L~~a~~nA~~~~g~d~~~L~I~~~~v~~g~~~kr 80 (105)
T PF00237_consen 1 AKLRNIRISPKKLREVARLIRGMSVDEAIAQLKFVPKKAAKFILKLLKSAIANAENNKGLDPDNLYISEIWVNKGPYLKR 80 (105)
T ss_dssp EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHCTSTCGGEEEEEEEEEEEEEEEE
T ss_pred CccccccCCHHHHHHHHHHHcCCCHHHHHHHHHhCcHHHHHHHHhhHHHHHhhcccccccccCceEEEEEEEEecccccC
Confidence 67899999999999999999999999999999999999999999999999999998899999999999999999999999
Q ss_pred CccCCCCCC
Q 030580 167 PRPKAQGRE 175 (175)
Q Consensus 167 ~~pRArGRA 175 (175)
++||||||+
T Consensus 81 ~~~rArGR~ 89 (105)
T PF00237_consen 81 IRPRARGRA 89 (105)
T ss_dssp EEEECTTEE
T ss_pred CCcCcCCCc
Confidence 999999985
No 7
>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=99.97 E-value=2.9e-30 Score=207.09 Aligned_cols=94 Identities=29% Similarity=0.375 Sum_probs=91.0
Q ss_pred CCceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhh--------------------------------CCccchhH
Q 030580 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------------------------------MPYRACYP 128 (175)
Q Consensus 81 ~~~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~f--------------------------------spKKaAk~ 128 (175)
..++++|..+++++||+|+++||++||||++++|+.+|+| ||+|+|+.
T Consensus 8 ~~~~akA~~~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~~~gR~P~Kaa~~ 87 (150)
T TIGR01038 8 PTKSAKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKEWGWTAGRYPVKAAKF 87 (150)
T ss_pred CCeeEEEEeCCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccccCCCchHHHHH
Confidence 3468999999999999999999999999999999999999 99999999
Q ss_pred HHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcCCCCCCCCccCCCCCC
Q 030580 129 IFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGRE 175 (175)
Q Consensus 129 I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~kGp~lKR~~pRArGRA 175 (175)
|+|+|+||.+||++ +|+|+|+|||.+|+||+||++||++|||+|||
T Consensus 88 i~klL~sA~aNA~~-~gld~d~L~I~~i~vnkg~~~kR~~prA~GRa 133 (150)
T TIGR01038 88 ILKVLQNAEANAEY-KGLDVEKLVIIHIQANKGPKIRRWMPRAFGRA 133 (150)
T ss_pred HHHHHHHHHHHHHh-cCCChhHeEEEEEEECCCCccCCCCCccCCCC
Confidence 99999999999986 79999999999999999999999999999997
No 8
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=99.97 E-value=4.5e-30 Score=206.55 Aligned_cols=94 Identities=28% Similarity=0.361 Sum_probs=91.5
Q ss_pred CCceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhh------------------------------CCccchhHHH
Q 030580 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL------------------------------MPYRACYPIF 130 (175)
Q Consensus 81 ~~~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~f------------------------------spKKaAk~I~ 130 (175)
.+++++|.++++++||+|+++||++||||++++|+.+|+| ||+|+|+.|+
T Consensus 12 ~~~~akA~~~~~rvS~kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~gr~PkKaa~~i~ 91 (153)
T PRK04223 12 PEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGIDGWPAGRYPVKAAKAFL 91 (153)
T ss_pred CCceEEEEeCCCccChHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccCCCchHHHHHHH
Confidence 5579999999999999999999999999999999999999 9999999999
Q ss_pred HHHHHHHHhhhhcCCCCCCCeEEEEEEEcCCCCCCCCccCCCCCC
Q 030580 131 KLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGRE 175 (175)
Q Consensus 131 KlL~SA~aNAe~~~glD~d~L~I~ea~V~kGp~lKR~~pRArGRA 175 (175)
|+|+||++||++ +|+|+|+|||.+|+||+||++||++|||+|||
T Consensus 92 KlL~sA~aNA~~-~gld~d~L~I~~i~v~kg~~~kR~~prA~GRa 135 (153)
T PRK04223 92 KLLENAEANAEY-KGLDTEKLVIVHIAAHKGRVIKGYMPRAFGRA 135 (153)
T ss_pred HHHHHHHHHHHh-cCCChhHeEEEEEEECCCCCCCCcCcccCCCC
Confidence 999999999986 79999999999999999999999999999997
No 9
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=99.96 E-value=3.1e-30 Score=226.70 Aligned_cols=93 Identities=28% Similarity=0.381 Sum_probs=91.0
Q ss_pred ceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhh-hcCCCCCCCeEEEEEEEcCC
Q 030580 83 AEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGV-HNMGFNEASLVIAKAEVNEA 161 (175)
Q Consensus 83 ~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe-~~~glD~d~L~I~ea~V~kG 161 (175)
|+++|+++++++||+|+|+||++||||++++|+.+|+|+|+|+|..|+++|+||.+||+ +|+|+|.|+|||.+|+||+|
T Consensus 1 M~akA~~r~iriSpkK~R~Va~~IRGk~v~~Al~~L~~~PkKaA~~I~KlLkSA~ANAe~~n~gld~d~L~I~~~~VdkG 80 (311)
T PRK12279 1 MTNKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILSNTPKKFAPIVLKLLNSAISNVQHNSKDMDPSKLYIYKIVANQG 80 (311)
T ss_pred CceEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhcCCChhHeEEEEEEECCC
Confidence 67999999999999999999999999999999999999999999999999999999999 57999999999999999999
Q ss_pred CCCCCCccCCCCCC
Q 030580 162 TSAKRPRPKAQGRE 175 (175)
Q Consensus 162 p~lKR~~pRArGRA 175 (175)
|++||++|||||||
T Consensus 81 p~lKR~~PRArGRA 94 (311)
T PRK12279 81 PTMKRTLPRAKGSA 94 (311)
T ss_pred CcccCCCCccCCCC
Confidence 99999999999997
No 10
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=99.96 E-value=1.5e-29 Score=208.36 Aligned_cols=94 Identities=23% Similarity=0.303 Sum_probs=91.3
Q ss_pred CCceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhh--------------------------------CCccchhH
Q 030580 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------------------------------MPYRACYP 128 (175)
Q Consensus 81 ~~~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~f--------------------------------spKKaAk~ 128 (175)
.+++++|..+++++||+|+++||++||||++++|+++|+| +|+|+|+.
T Consensus 11 ~~~~akA~~~~~riSpkk~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~~~~~~GR~P~KaA~~ 90 (181)
T PTZ00178 11 PSKSAKAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKEFGHTQGRWPEKSVKF 90 (181)
T ss_pred CCceEEEEeCCcccchHHHHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCccccccccccccccCcCcHHHHHH
Confidence 5579999999999999999999999999999999999997 89999999
Q ss_pred HHHHHHHHHHhhhhcCCCCCCCeEEEEEEEcCCCCCCCCccCCCCCC
Q 030580 129 IFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGRE 175 (175)
Q Consensus 129 I~KlL~SA~aNAe~~~glD~d~L~I~ea~V~kGp~lKR~~pRArGRA 175 (175)
|+|+|+||.+||+ ++|+|+|+|||.+|.||+||++||++|||+|||
T Consensus 91 i~KlL~SA~aNAe-~~gld~d~L~I~~i~v~kG~~lKR~~pRA~GRA 136 (181)
T PTZ00178 91 VLSLLKNAEANAE-AKGLDVEKLVISHVQVNRAPRGRRRTYRAHGRI 136 (181)
T ss_pred HHHHHHHHHHHHH-hcCCChhHeEEEEEEECCCcccCCCCCccCCCc
Confidence 9999999999999 589999999999999999999999999999997
No 11
>KOG1711 consensus Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=6.4e-24 Score=178.49 Aligned_cols=108 Identities=35% Similarity=0.479 Sum_probs=97.9
Q ss_pred HhcCCCCCCCCCCCCCCceEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHhhhhcCC
Q 030580 66 QKRGISPPNNRNKTNKKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMG 145 (175)
Q Consensus 66 ~~~g~~~~~~~~k~~~~~e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aNAe~~~g 145 (175)
+++-..||.-.-++.. .++.|....++.|++|++.+|+||+||+|+|||.||+|++||+|+.|.++|.+|.+||.+++|
T Consensus 54 ~~Ki~~~~~l~~~p~~-~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~~s~kK~a~~i~~~l~~A~~nA~~~~g 132 (218)
T KOG1711|consen 54 RNKIVYPPQLPFEPKR-PEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLEFSDKKAAKTIAEVLLSARANAVHNHG 132 (218)
T ss_pred hccccCcccCCCCCcc-hhHHHHHHHHHhCHHHHHHHHHHHcCCCHHHHHHHhhcchHHHHHHHHHHHHHHHhhhHHhcC
Confidence 3344445555544433 789999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeEE-EEEEEcCCCCCCCCccCCCCC
Q 030580 146 FNEASLVI-AKAEVNEATSAKRPRPKAQGR 174 (175)
Q Consensus 146 lD~d~L~I-~ea~V~kGp~lKR~~pRArGR 174 (175)
+|+++||| .++++++|-++||+.++||||
T Consensus 133 l~~~~l~v~~~~t~~~g~~~Krl~~hargr 162 (218)
T KOG1711|consen 133 LDPDSLLVVAEATVGQGNELKRLKVHARGR 162 (218)
T ss_pred CCccceEEEEeeecccchhhhheeeeccCc
Confidence 99999988 999999999999999999997
No 12
>KOG3353 consensus 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=99.37 E-value=4e-14 Score=116.44 Aligned_cols=90 Identities=22% Similarity=0.313 Sum_probs=86.0
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhh--------------------------------CCccchhHHHH
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------------------------------MPYRACYPIFK 131 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~f--------------------------------spKKaAk~I~K 131 (175)
.+++.+.++++|++++++.+..|+++++..|+.+|.. ||+|+|.+++.
T Consensus 8 ~~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkksaefll~ 87 (175)
T KOG3353|consen 8 SCKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKKSAEFLLH 87 (175)
T ss_pred hhhcccccEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhhhccccCcccchHHHHHHH
Confidence 5688999999999999999999999999999999982 89999999999
Q ss_pred HHHHHHHhhhhcCCCCCCCeEEEEEEEcCCCCCCCCccCCCCC
Q 030580 132 LIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGR 174 (175)
Q Consensus 132 lL~SA~aNAe~~~glD~d~L~I~ea~V~kGp~lKR~~pRArGR 174 (175)
+|++|.+||+. +|+|+|.|+|.++.|+++|.+.|.+|||+||
T Consensus 88 ~LkN~esnaEl-kgldVDsLvIehiqvnkApKm~~rtyraHg~ 129 (175)
T KOG3353|consen 88 MLKNAESNAEL-KGLDVDSLVIEHIQVNKAPKMRRRTYRAHGR 129 (175)
T ss_pred HHHhhhhcccc-cCcCcceeEeeehhhcccchhhhHHHHhhcc
Confidence 99999999998 6899999999999999999999999999998
No 13
>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=70.23 E-value=13 Score=28.52 Aligned_cols=59 Identities=14% Similarity=0.061 Sum_probs=45.7
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHh---------hC--CccchhHHHHHHHHHHHhhhh
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE---------LM--PYRACYPIFKLIYSAAANGVH 142 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~---------fs--pKKaAk~I~KlL~SA~aNAe~ 142 (175)
+++..+.-.-+|--=.-.++.+|.|++++||..+.. +. ..+.|....+.|+.|+.+...
T Consensus 49 d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y~~ 118 (121)
T TIGR03419 49 DVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYRE 118 (121)
T ss_pred EEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHh
Confidence 556666667777777889999999999999887664 12 344788888999999888754
No 14
>PRK11325 scaffold protein; Provisional
Probab=56.85 E-value=19 Score=27.76 Aligned_cols=59 Identities=15% Similarity=0.110 Sum_probs=45.3
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHhh--------CC--ccchhHHHHHHHHHHHhhhh
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------MP--YRACYPIFKLIYSAAANGVH 142 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~f--------sp--KKaAk~I~KlL~SA~aNAe~ 142 (175)
+++..+.-.-+|-==.-.++.+|.|++++||..+..- .| .+.|....+.|+.|+.+...
T Consensus 55 d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~~ 123 (127)
T PRK11325 55 DAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYKS 123 (127)
T ss_pred EEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHh
Confidence 4566666677777778899999999999999876542 23 44788888999999888743
No 15
>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=54.41 E-value=23 Score=27.13 Aligned_cols=59 Identities=19% Similarity=0.122 Sum_probs=43.9
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHh--------hCC--ccchhHHHHHHHHHHHhhhh
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE--------LMP--YRACYPIFKLIYSAAANGVH 142 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~--------fsp--KKaAk~I~KlL~SA~aNAe~ 142 (175)
+++..+.---+|--=.-.++.+|.|++++||..+-. ..| .+.|....+.|+.|+.+...
T Consensus 53 d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~~ 121 (124)
T TIGR01999 53 DAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKS 121 (124)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHHH
Confidence 455556666667777789999999999999987654 223 44788888899888887643
No 16
>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=42.63 E-value=47 Score=25.33 Aligned_cols=59 Identities=17% Similarity=0.093 Sum_probs=41.7
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHH-----hh------CCccchhHHHHHHHHHHHhhhh
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMIL-----EL------MPYRACYPIFKLIYSAAANGVH 142 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL-----~f------spKKaAk~I~KlL~SA~aNAe~ 142 (175)
+++..+.--.+|--=.-.++.+|.|++++||..+- ++ .....+.....+|..|+++...
T Consensus 53 d~~f~~~GC~~~~Asas~~~~~i~gk~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~~ 122 (126)
T PF01592_consen 53 DAKFQGFGCAISIASASMMCELIKGKTLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYPA 122 (126)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHTTSBHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEeecChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHh
Confidence 45555555666667788999999999999995331 11 2234577888899999888643
No 17
>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=38.98 E-value=1.6e+02 Score=21.67 Aligned_cols=39 Identities=18% Similarity=0.046 Sum_probs=32.2
Q ss_pred CceEEEEeCccccCHHHHHHHHHHH-----cCCCHHHHHHHHhh
Q 030580 82 KAEVSASARYLHMSAHKVRRVIDQI-----RGRSYEETLMILEL 120 (175)
Q Consensus 82 ~~e~kA~~r~iriSpKKlr~Var~I-----RGk~V~eAi~qL~f 120 (175)
+.|+........-..-.+--++++| .|+++++.+.+|+-
T Consensus 23 p~Evf~~~~~~Gg~~~~~~ai~rliS~~Lr~G~~~~~ii~~L~g 66 (95)
T PF12637_consen 23 PFEVFINVGKAGGCSGNLEAIARLISLALRSGVPPEEIIDQLRG 66 (95)
T ss_pred ceEEEEecCcCCCchHHHHHHHHHHHHHHHcCCCHHHHHHHhcC
Confidence 4567666666665588899999999 99999999999995
No 18
>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=36.92 E-value=1e+02 Score=27.30 Aligned_cols=59 Identities=15% Similarity=0.093 Sum_probs=44.3
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHh------h---CC--ccchhHHHHHHHHHHHhhhh
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE------L---MP--YRACYPIFKLIYSAAANGVH 142 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~------f---sp--KKaAk~I~KlL~SA~aNAe~ 142 (175)
+++..+.---+|-==.-.++.+|.|++++||..+.. | .| .+.|.+..+.|+.|+.+...
T Consensus 54 d~~F~~~GCais~ASAs~~~eli~Gktv~ea~~i~~~di~~~L~~lpp~r~~CA~La~~Al~~Al~~y~~ 123 (290)
T TIGR02000 54 DAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRG 123 (290)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHHhhHHHHHHHHcCCChhhchHHHHHHHHHHHHHHHHhc
Confidence 455555556666666789999999999999987764 2 23 34677888999999988854
No 19
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=30.46 E-value=58 Score=26.16 Aligned_cols=35 Identities=14% Similarity=0.220 Sum_probs=28.9
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHH
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMIL 118 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL 118 (175)
.++..+.-.-+|--=.-.++.+|.|++++||+.+.
T Consensus 56 d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 56 DAKFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred EEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 45566666677777788999999999999999988
No 20
>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=29.74 E-value=63 Score=24.13 Aligned_cols=36 Identities=17% Similarity=0.277 Sum_probs=30.0
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHh
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE 119 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~ 119 (175)
+++..+.---+|--=+..+++++.|++++||..++.
T Consensus 50 d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 50 DAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 456666667777777889999999999999999886
No 21
>PF13852 DUF4197: Protein of unknown function (DUF4197)
Probab=28.53 E-value=83 Score=26.59 Aligned_cols=20 Identities=25% Similarity=0.270 Sum_probs=17.4
Q ss_pred HHHHHHcCCCHHHHHHHHhh
Q 030580 101 RVIDQIRGRSYEETLMILEL 120 (175)
Q Consensus 101 ~Var~IRGk~V~eAi~qL~f 120 (175)
-+.+.|+.|+++||..+|.=
T Consensus 85 if~~AI~~Ms~~DA~~IL~G 104 (202)
T PF13852_consen 85 IFVDAIKSMSIQDAKGILNG 104 (202)
T ss_pred HHHHHHHhCCHHhHHHHhcC
Confidence 35689999999999999993
No 22
>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=27.98 E-value=74 Score=22.31 Aligned_cols=21 Identities=24% Similarity=0.410 Sum_probs=16.6
Q ss_pred HHHHHHHcCCCHHHHHHHHhh
Q 030580 100 RRVIDQIRGRSYEETLMILEL 120 (175)
Q Consensus 100 r~Var~IRGk~V~eAi~qL~f 120 (175)
..||+.|+||++++--.++..
T Consensus 37 ~~iA~~i~gks~eeir~~fgi 57 (78)
T PF01466_consen 37 KYIANMIKGKSPEEIRKYFGI 57 (78)
T ss_dssp HHHHHHHTTS-HHHHHHHHT-
T ss_pred HHHHHHhcCCCHHHHHHHcCC
Confidence 467899999999999888874
No 23
>PF13286 HD_assoc: Phosphohydrolase-associated domain; PDB: 2DQB_D.
Probab=25.31 E-value=90 Score=21.86 Aligned_cols=22 Identities=27% Similarity=0.320 Sum_probs=18.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHH
Q 030580 97 HKVRRVIDQIRGRSYEETLMIL 118 (175)
Q Consensus 97 KKlr~Var~IRGk~V~eAi~qL 118 (175)
.+.+.|+|.|.||+=..|+...
T Consensus 69 ~~~r~v~DyIaGMTD~yA~~~~ 90 (92)
T PF13286_consen 69 SRARVVCDYIAGMTDRYALRLY 90 (92)
T ss_dssp -HHHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHhhcCcHHHHHHHH
Confidence 7899999999999999998754
No 24
>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=25.00 E-value=47 Score=21.65 Aligned_cols=15 Identities=40% Similarity=0.640 Sum_probs=12.2
Q ss_pred HcCCCHHHHHHHHhh
Q 030580 106 IRGRSYEETLMILEL 120 (175)
Q Consensus 106 IRGk~V~eAi~qL~f 120 (175)
+.||++++|..+|+-
T Consensus 6 ~~g~~~~~a~~~l~~ 20 (63)
T PF03793_consen 6 LVGMTYDEAKSILEA 20 (63)
T ss_dssp TTTSBHHHHHHHHHH
T ss_pred cCCCcHHHHHHHHHH
Confidence 568999999888874
No 25
>PF03448 MgtE_N: MgtE intracellular N domain; InterPro: IPR006668 This domain is found at the N terminus of eubacterial magnesium transporters of the MgtE family IPR006667 from INTERPRO. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter [] shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains.; PDB: 2YVX_D 2ZY9_A 2YVZ_B 2YVY_A 2OUX_A 3KXR_A.
Probab=22.84 E-value=69 Score=22.55 Aligned_cols=42 Identities=10% Similarity=0.115 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhCCccchhHHHHHHHHHHHh
Q 030580 98 KVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAAN 139 (175)
Q Consensus 98 Klr~Var~IRGk~V~eAi~qL~fspKKaAk~I~KlL~SA~aN 139 (175)
....++..+.+|+.++|...|...|..-...|+..|......
T Consensus 50 ~~~~~a~il~~m~~dd~~~ll~~L~~~~~~~il~~l~~~~~~ 91 (102)
T PF03448_consen 50 SPEEAAEILAEMDSDDAADLLEELPEEQREKILAALDEEERE 91 (102)
T ss_dssp -HHHHHHHHCCS-HHHHHHHHCCSHHHHHHHHHHCS-HHHHH
T ss_pred CHHHHHHHHHccChHHHHHHHHHCCHHHHHHHHHcCCHHHHH
Confidence 345677889999999999999999888888777777554443
No 26
>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=20.02 E-value=1.2e+02 Score=23.51 Aligned_cols=36 Identities=19% Similarity=0.363 Sum_probs=29.2
Q ss_pred eEEEEeCccccCHHHHHHHHHHHcCCCHHHHHHHHh
Q 030580 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE 119 (175)
Q Consensus 84 e~kA~~r~iriSpKKlr~Var~IRGk~V~eAi~qL~ 119 (175)
.++..+.-.-+|-==...++.+|.|++++||....+
T Consensus 53 d~~f~~~GCais~Asas~~~e~i~Gk~~~ea~~l~~ 88 (137)
T TIGR01994 53 DIAFEGEGCSISQASASMMTELIKGKTVEEALSLVE 88 (137)
T ss_pred EEEEEecccHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 455566666677777889999999999999998875
Done!