Query 028931
Match_columns 201
No_of_seqs 140 out of 1126
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 04:48:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028931hhsearch_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 5.7E-41 1.2E-45 263.7 13.1 111 81-191 6-116 (117)
2 PRK00565 rplV 50S ribosomal pr 100.0 4.7E-41 1E-45 261.8 12.5 111 83-193 1-111 (112)
3 COG0091 RplV Ribosomal protein 100.0 2.3E-41 5E-46 267.1 9.3 113 81-193 7-119 (120)
4 TIGR01044 rplV_bact ribosomal 100.0 5.8E-40 1.2E-44 252.5 10.1 103 87-189 1-103 (103)
5 PF00237 Ribosomal_L22: Riboso 100.0 2.8E-38 6.1E-43 242.2 6.4 105 87-191 1-105 (105)
6 cd00336 Ribosomal_L22 Ribosoma 100.0 5.7E-37 1.2E-41 234.8 11.5 105 85-189 1-105 (105)
7 PRK04223 rpl22p 50S ribosomal 100.0 8.5E-36 1.8E-40 244.1 13.9 112 81-193 12-153 (153)
8 PRK12279 50S ribosomal protein 100.0 3.3E-36 7.1E-41 269.3 11.9 115 83-197 1-116 (311)
9 TIGR01038 L22_arch ribosomal p 100.0 7.4E-36 1.6E-40 243.7 12.9 111 81-192 8-150 (150)
10 PTZ00178 60S ribosomal protein 100.0 2.7E-35 5.8E-40 246.6 12.9 112 81-193 11-154 (181)
11 KOG1711 Mitochondrial/chloropl 100.0 3.8E-32 8.2E-37 231.7 6.2 137 53-198 48-186 (218)
12 KOG3353 60S ribosomal protein 99.5 7.1E-16 1.5E-20 128.9 -5.1 110 83-193 7-148 (175)
13 TIGR03419 NifU_clost FeS clust 62.7 30 0.00065 27.0 6.2 60 83-142 48-118 (121)
14 PRK11325 scaffold protein; Pro 46.0 57 0.0012 25.6 5.3 58 84-141 55-122 (127)
15 TIGR01999 iscU FeS cluster ass 45.7 65 0.0014 25.1 5.6 58 84-141 53-120 (124)
16 PF12637 TSCPD: TSCPD domain; 37.6 88 0.0019 23.4 5.0 38 83-120 24-66 (95)
17 PF01592 NifU_N: NifU-like N t 32.4 1.1E+02 0.0023 23.8 4.9 58 84-141 53-121 (126)
18 TIGR02000 NifU_proper Fe-S clu 31.3 2.2E+02 0.0048 25.7 7.3 59 84-142 54-123 (290)
19 COG0822 IscU NifU homolog invo 27.3 1E+02 0.0022 25.2 4.1 35 84-118 56-90 (150)
20 cd06664 IscU_like Iron-sulfur 25.6 1.2E+02 0.0027 23.0 4.1 37 83-119 49-85 (123)
21 PF11373 DUF3175: Protein of u 25.4 49 0.0011 25.1 1.7 51 95-145 31-85 (86)
22 PF13286 HD_assoc: Phosphohydr 24.0 1E+02 0.0022 22.0 3.2 22 97-118 69-90 (92)
23 PF03793 PASTA: PASTA domain; 22.9 55 0.0012 21.8 1.5 15 106-120 6-20 (63)
24 PF13852 DUF4197: Protein of u 21.7 1.3E+02 0.0029 25.8 3.9 20 101-120 85-104 (202)
25 PF01466 Skp1: Skp1 family, di 20.5 1.2E+02 0.0027 21.5 3.0 22 100-121 37-58 (78)
No 1
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00 E-value=5.7e-41 Score=263.66 Aligned_cols=111 Identities=70% Similarity=1.099 Sum_probs=108.9
Q ss_pred CCcEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHHHHHHHHhhchhcCCCCCCCeEEEEEEecC
Q 028931 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNE 160 (201)
Q Consensus 81 ~~~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~k 160 (201)
++++++|..+++++||+|+++||++||||+++||+.||+|+|+|+|+.|+++|+||.+||++++|+|+|+|||+++|||+
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 46889999999999999999999999999999999999999999999999999999999998899999999999999999
Q ss_pred CcccCCCCcCCCCcccccccCceeEEEEEEe
Q 028931 161 ATSAKRPRPKAQGRVHMIKRPTCHITVVLRD 191 (201)
Q Consensus 161 G~~lKRi~pRArGRa~~i~kr~sHItVvL~E 191 (201)
||++||++||||||++++++++|||+|+|+|
T Consensus 86 G~~~KR~~prArGRa~~i~k~~sHI~Vvl~e 116 (117)
T CHL00034 86 GPTLKRFRPRAQGRSYPIKKPTCHITIVLKD 116 (117)
T ss_pred CCccCCCCcccCCCCCcccCCCccEEEEEec
Confidence 9999999999999999999999999999987
No 2
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00 E-value=4.7e-41 Score=261.80 Aligned_cols=111 Identities=41% Similarity=0.593 Sum_probs=108.5
Q ss_pred cEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHHHHHHHHhhchhcCCCCCCCeEEEEEEecCCc
Q 028931 83 AEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEAT 162 (201)
Q Consensus 83 ~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~ 162 (201)
|+++|..+++++||+|+++||++||||+++||+.||+|+|+|+|+.|+++|+||.+||++++|+|+++|||+++|||+||
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 46899999999999999999999999999999999999999999999999999999999989999999999999999999
Q ss_pred ccCCCCcCCCCcccccccCceeEEEEEEecC
Q 028931 163 SAKRPRPKAQGRVHMIKRPTCHITVVLRDMS 193 (201)
Q Consensus 163 ~lKRi~pRArGRa~~i~kr~sHItVvL~E~~ 193 (201)
++||++||||||++++++++|||+|+|+|++
T Consensus 81 ~~Kr~~~rArGR~~~i~k~~~hi~vvL~e~~ 111 (112)
T PRK00565 81 TLKRFRPRARGRASRIRKRTSHITVVVAEKE 111 (112)
T ss_pred ccCCCCCCcCCCCCccccCCccEEEEEEecC
Confidence 9999999999999999999999999999965
No 3
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-41 Score=267.10 Aligned_cols=113 Identities=40% Similarity=0.577 Sum_probs=110.2
Q ss_pred CCcEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHHHHHHHHhhchhcCCCCCCCeEEEEEEecC
Q 028931 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNE 160 (201)
Q Consensus 81 ~~~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~k 160 (201)
+.++++|..+++++||+|+++||++||||++++|+.+|+|+|+|+|+.|+|+|+||++||++|+|||+|+|||.|||||+
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 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCCCCcCCCCcccccccCceeEEEEEEecC
Q 028931 161 ATSAKRPRPKAQGRVHMIKRPTCHITVVLRDMS 193 (201)
Q Consensus 161 G~~lKRi~pRArGRa~~i~kr~sHItVvL~E~~ 193 (201)
||++||++||||||+++|.+++|||+|+|+|.+
T Consensus 87 gp~lKR~~pRA~GRa~~i~k~tshItvvv~e~~ 119 (120)
T COG0091 87 GPVLKRFMPRARGRATRINKRTSHITVVVREKE 119 (120)
T ss_pred CceeeeecccccCccccccCCCceEEEEEeecC
Confidence 999999999999999999999999999999965
No 4
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=100.00 E-value=5.8e-40 Score=252.48 Aligned_cols=103 Identities=43% Similarity=0.616 Sum_probs=100.7
Q ss_pred EEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHHHHHHHHhhchhcCCCCCCCeEEEEEEecCCcccCC
Q 028931 87 ASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKR 166 (201)
Q Consensus 87 A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~~lKR 166 (201)
|..+++++||+|+++||++||||+++||+.||+|+|+|+|+.|+|+|+||.+||++++|+|+|+|||+|+|||+||++||
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 46789999999999999999999999999999999999999999999999999998899999999999999999999999
Q ss_pred CCcCCCCcccccccCceeEEEEE
Q 028931 167 PRPKAQGRVHMIKRPTCHITVVL 189 (201)
Q Consensus 167 i~pRArGRa~~i~kr~sHItVvL 189 (201)
++||||||++++++++|||+|+|
T Consensus 81 ~~~rarGRa~~i~k~~~hi~vvl 103 (103)
T TIGR01044 81 IRPRAKGRASRIRKRTSHITVVV 103 (103)
T ss_pred CCCCCCCCCCcccCCCccEEEeC
Confidence 99999999999999999999986
No 5
>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=2.8e-38 Score=242.25 Aligned_cols=105 Identities=40% Similarity=0.568 Sum_probs=102.0
Q ss_pred EEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHHHHHHHHhhchhcCCCCCCCeEEEEEEecCCcccCC
Q 028931 87 ASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKR 166 (201)
Q Consensus 87 A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~~lKR 166 (201)
|..+++++||+|++++|++|+||+++||+.||+|+|+|+|+.|+++|+||.+||++++|+|+|+|||+++|||+|+++||
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 57889999999999999999999999999999999999999999999999999997899999999999999999999999
Q ss_pred CCcCCCCcccccccCceeEEEEEEe
Q 028931 167 PRPKAQGRVHMIKRPTCHITVVLRD 191 (201)
Q Consensus 167 i~pRArGRa~~i~kr~sHItVvL~E 191 (201)
++||||||++++++++|||+|+|+|
T Consensus 81 ~~~rArGR~~~~~k~~~hi~vvl~E 105 (105)
T PF00237_consen 81 IRPRARGRAGPIRKRTSHITVVLKE 105 (105)
T ss_dssp EEEECTTEEEEEEEEEEEEEEEEEE
T ss_pred CCcCcCCCccCeecCceEEEEEEeC
Confidence 9999999999999999999999998
No 6
>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=5.7e-37 Score=234.80 Aligned_cols=105 Identities=44% Similarity=0.602 Sum_probs=102.1
Q ss_pred EEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHHHHHHHHhhchhcCCCCCCCeEEEEEEecCCccc
Q 028931 85 VSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSA 164 (201)
Q Consensus 85 ~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~~l 164 (201)
++|..+++++||+|+++|+++||||+++||+.||+|+|+|+|+.|+++|+||.+||++++++|+++|||+++|||+||++
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 36889999999999999999999999999999999999999999999999999999998888899999999999999999
Q ss_pred CCCCcCCCCcccccccCceeEEEEE
Q 028931 165 KRPRPKAQGRVHMIKRPTCHITVVL 189 (201)
Q Consensus 165 KRi~pRArGRa~~i~kr~sHItVvL 189 (201)
||++||||||++++++++|||+|+|
T Consensus 81 kr~~~rarGR~~~~~k~~~hi~ivl 105 (105)
T cd00336 81 KRRRPRARGRANPIRKRTCHITVVL 105 (105)
T ss_pred cCCCcCCCCCCcccccCceeEEEeC
Confidence 9999999999999999999999986
No 7
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=100.00 E-value=8.5e-36 Score=244.09 Aligned_cols=112 Identities=27% Similarity=0.358 Sum_probs=108.7
Q ss_pred CCcEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhh------------------------------CCCcchhHHH
Q 028931 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL------------------------------MPYRACYPIF 130 (201)
Q Consensus 81 ~~~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~f------------------------------spKKaA~~V~ 130 (201)
.+++++|..+++++||+|+++||++||||++++|+.+|+| +|+|+|+.|+
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 4689999999999999999999999999999999999999 9999999999
Q ss_pred HHHHHHHhhchhcCCCCCCCeEEEEEEecCCcccCCCCcCCCCcccccccCceeEEEEEEecC
Q 028931 131 KLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGRVHMIKRPTCHITVVLRDMS 193 (201)
Q Consensus 131 KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~~lKRi~pRArGRa~~i~kr~sHItVvL~E~~ 193 (201)
|+|+||.+||++ +|+|.|+|||++++||+||++||++|||+||++++.+++|||+|+|+|.+
T Consensus 92 KlL~sA~aNA~~-~gld~d~L~I~~i~v~kg~~~kR~~prA~GRa~~~~k~~sHI~Iil~e~~ 153 (153)
T PRK04223 92 KLLENAEANAEY-KGLDTEKLVIVHIAAHKGRVIKGYMPRAFGRATPKNTETVNIEVILEEVE 153 (153)
T ss_pred HHHHHHHHHHHh-cCCChhHeEEEEEEECCCCCCCCcCcccCCCCCcccCCCceEEEEEEeCC
Confidence 999999999987 69999999999999999999999999999999999999999999999853
No 8
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=100.00 E-value=3.3e-36 Score=269.28 Aligned_cols=115 Identities=28% Similarity=0.382 Sum_probs=111.0
Q ss_pred cEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHHHHHHHHhhch-hcCCCCCCCeEEEEEEecCC
Q 028931 83 AEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFKLIYSAAANGV-HNMGFNEASLVIAKAEVNEA 161 (201)
Q Consensus 83 ~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~KlL~sA~aNA~-~~~gld~d~L~I~ea~V~kG 161 (201)
|+++|..+++++||+|+|+||++||||++++|+.+|+|+|+|+|..|+++|+||.+||+ +|+|||.|+|||.+|+||+|
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 57999999999999999999999999999999999999999999999999999999999 67999999999999999999
Q ss_pred cccCCCCcCCCCcccccccCceeEEEEEEecCCCCc
Q 028931 162 TSAKRPRPKAQGRVHMIKRPTCHITVVLRDMSLDDE 197 (201)
Q Consensus 162 ~~lKRi~pRArGRa~~i~kr~sHItVvL~E~~~~~~ 197 (201)
|++||++||||||+++|++++|||+|+|+|..++++
T Consensus 81 p~lKR~~PRArGRA~~i~KrtsHItIvl~e~~~~~~ 116 (311)
T PRK12279 81 PTMKRTLPRAKGSADQLFKRTTHLEIVLSDDVNERE 116 (311)
T ss_pred CcccCCCCccCCCCCcccCCCccEEEEEecCCchhh
Confidence 999999999999999999999999999999877654
No 9
>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=7.4e-36 Score=243.75 Aligned_cols=111 Identities=27% Similarity=0.365 Sum_probs=107.6
Q ss_pred CCcEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhh--------------------------------CCCcchhH
Q 028931 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------------------------------MPYRACYP 128 (201)
Q Consensus 81 ~~~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~f--------------------------------spKKaA~~ 128 (201)
+.++++|..+++++||+|+++||++||||++++|+.+|+| +|+|+|+.
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 3578999999999999999999999999999999999999 89999999
Q ss_pred HHHHHHHHHhhchhcCCCCCCCeEEEEEEecCCcccCCCCcCCCCcccccccCceeEEEEEEec
Q 028931 129 IFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGRVHMIKRPTCHITVVLRDM 192 (201)
Q Consensus 129 V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~~lKRi~pRArGRa~~i~kr~sHItVvL~E~ 192 (201)
|+++|+||.+||++ +|+|.|+|||++++||+||++||++|||+||+++|++++|||+|+|+|+
T Consensus 88 i~klL~sA~aNA~~-~gld~d~L~I~~i~vnkg~~~kR~~prA~GRa~~~~k~~~HI~Iil~e~ 150 (150)
T TIGR01038 88 ILKVLQNAEANAEY-KGLDVEKLVIIHIQANKGPKIRRWMPRAFGRATPYNSSPTHIELVVEEK 150 (150)
T ss_pred HHHHHHHHHHHHHh-cCCChhHeEEEEEEECCCCccCCCCCccCCCCCcccCCCceEEEEEecC
Confidence 99999999999987 7999999999999999999999999999999999999999999999874
No 10
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=2.7e-35 Score=246.58 Aligned_cols=112 Identities=22% Similarity=0.347 Sum_probs=108.6
Q ss_pred CCcEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhh--------------------------------CCCcchhH
Q 028931 81 KKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------------------------------MPYRACYP 128 (201)
Q Consensus 81 ~~~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~f--------------------------------spKKaA~~ 128 (201)
++++++|..+++++||+|+++||++||||++++|+++|+| +|+|+|..
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 5789999999999999999999999999999999999997 89999999
Q ss_pred HHHHHHHHHhhchhcCCCCCCCeEEEEEEecCCcccCCCCcCCCCcccccccCceeEEEEEEecC
Q 028931 129 IFKLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGRVHMIKRPTCHITVVLRDMS 193 (201)
Q Consensus 129 V~KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~~lKRi~pRArGRa~~i~kr~sHItVvL~E~~ 193 (201)
|+|+|+||.+||+ ++|+|+|+|||.+|.||+||++||++|||+||+++|++++|||+|+|+|.+
T Consensus 91 i~KlL~SA~aNAe-~~gld~d~L~I~~i~v~kG~~lKR~~pRA~GRA~~i~k~t~HI~Ivl~e~~ 154 (181)
T PTZ00178 91 VLSLLKNAEANAE-AKGLDVEKLVISHVQVNRAPRGRRRTYRAHGRINPFMSSPCHIELIATEKD 154 (181)
T ss_pred HHHHHHHHHHHHH-hcCCChhHeEEEEEEECCCcccCCCCCccCCCcCcccCCceeEEEEEEEcc
Confidence 9999999999999 579999999999999999999999999999999999999999999999864
No 11
>KOG1711 consensus Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.8e-32 Score=231.65 Aligned_cols=137 Identities=35% Similarity=0.444 Sum_probs=125.1
Q ss_pred ccccc-ccccchhhhhcCCCCCCCcccCCCCcEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHHHH
Q 028931 53 NEIFN-SKKIISSAQKRGISPPNNRNKTNKKAEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILELMPYRACYPIFK 131 (201)
Q Consensus 53 ~~~f~-~~~~i~~~~~~g~~~~~~~~~~~~~~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V~K 131 (201)
++.|| .+|++++++..+.++ ..|++|+...|+.|++|++.+|+||+||+|+|||.||+|++||+|+.|.+
T Consensus 48 ~~k~E~~~Ki~~~~~l~~~p~---------~~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~~s~kK~a~~i~~ 118 (218)
T KOG1711|consen 48 SEKWEERNKIVYPPQLPFEPK---------RPEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLEFSDKKAAKTIAE 118 (218)
T ss_pred hHHHHHhccccCcccCCCCCc---------chhHHHHHHHHHhCHHHHHHHHHHHcCCCHHHHHHHhhcchHHHHHHHHH
Confidence 44677 458888777777633 25799999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhchhcCCCCCCCeEE-EEEEecCCcccCCCCcCCCCcccccccCceeEEEEEEecCCCCcc
Q 028931 132 LIYSAAANGVHNMGFNEASLVI-AKAEVNEATSAKRPRPKAQGRVHMIKRPTCHITVVLRDMSLDDEY 198 (201)
Q Consensus 132 lL~sA~aNA~~~~gld~d~L~I-~ea~V~kG~~lKRi~pRArGRa~~i~kr~sHItVvL~E~~~~~~~ 198 (201)
+|.+|.+||.+|+|+|+++|+| .++|+++|.++||+.++||||.++|++++|||+|+|.|+.++.-+
T Consensus 119 ~l~~A~~nA~~~~gl~~~~l~v~~~~t~~~g~~~Krl~~hargr~~ii~~~yvhi~v~L~e~s~~~~~ 186 (218)
T KOG1711|consen 119 VLLSARANAVHNHGLDPDSLLVVAEATVGQGNELKRLKVHARGRFGIIRRPYVHIFVKLEEGSPPQQR 186 (218)
T ss_pred HHHHHHhhhHHhcCCCccceEEEEeeecccchhhhheeeeccCcccceecceeeEEEEEeecCCCchh
Confidence 9999999999999999999887 999999999999999999999999999999999999999876544
No 12
>KOG3353 consensus 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=99.48 E-value=7.1e-16 Score=128.85 Aligned_cols=110 Identities=22% Similarity=0.351 Sum_probs=103.5
Q ss_pred cEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhh--------------------------------CCCcchhHHH
Q 028931 83 AEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------------------------------MPYRACYPIF 130 (201)
Q Consensus 83 ~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~f--------------------------------spKKaA~~V~ 130 (201)
..+++.+.++++|.+..++.+..|+++++..|+..|.- +|+|+|++++
T Consensus 7 k~~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkksaefll 86 (175)
T KOG3353|consen 7 KSCKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKKSAEFLL 86 (175)
T ss_pred hhhhcccccEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhhhccccCcccchHHHHHH
Confidence 45778889999999999999999999999999988882 7999999999
Q ss_pred HHHHHHHhhchhcCCCCCCCeEEEEEEecCCcccCCCCcCCCCcccccccCceeEEEEEEecC
Q 028931 131 KLIYSAAANGVHNMGFNEASLVIAKAEVNEATSAKRPRPKAQGRVHMIKRPTCHITVVLRDMS 193 (201)
Q Consensus 131 KlL~sA~aNA~~~~gld~d~L~I~ea~V~kG~~lKRi~pRArGRa~~i~kr~sHItVvL~E~~ 193 (201)
.+|++|.+||+. +|+|.|.|+|.++.||+.|.+.|.++||+||.+++.+..|||++||.|.+
T Consensus 87 ~~LkN~esnaEl-kgldVDsLvIehiqvnkApKm~~rtyraHg~in~y~ssP~hie~il~~ke 148 (175)
T KOG3353|consen 87 HMLKNAESNAEL-KGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKE 148 (175)
T ss_pred HHHHhhhhcccc-cCcCcceeEeeehhhcccchhhhHHHHhhcccccccCChHHHHHHHHhhc
Confidence 999999999998 58999999999999999999999999999999999999999999998764
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=62.70 E-value=30 Score=26.97 Aligned_cols=60 Identities=13% Similarity=0.058 Sum_probs=46.3
Q ss_pred cEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHh---------hC--CCcchhHHHHHHHHHHhhchh
Q 028931 83 AEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE---------LM--PYRACYPIFKLIYSAAANGVH 142 (201)
Q Consensus 83 ~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~---------fs--pKKaA~~V~KlL~sA~aNA~~ 142 (201)
.+++......-+|--=.-.++++|.|++++||..+.. +. ..+.|....+.|+.|+.+...
T Consensus 48 ~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y~~ 118 (121)
T TIGR03419 48 KDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYRE 118 (121)
T ss_pred EEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHh
Confidence 3577777788888888999999999999999877654 12 235677778888888877654
No 14
>PRK11325 scaffold protein; Provisional
Probab=46.00 E-value=57 Score=25.63 Aligned_cols=58 Identities=16% Similarity=0.113 Sum_probs=45.0
Q ss_pred EEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHhh--------CC--CcchhHHHHHHHHHHhhch
Q 028931 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILEL--------MP--YRACYPIFKLIYSAAANGV 141 (201)
Q Consensus 84 e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~f--------sp--KKaA~~V~KlL~sA~aNA~ 141 (201)
+++......-+|--=+-.++.+|.|++++||..+-.- .| .+.|....+.|+.|+++..
T Consensus 55 d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~ 122 (127)
T PRK11325 55 DAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYK 122 (127)
T ss_pred EEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHH
Confidence 5677777888888889999999999999999866441 22 3467777788888887764
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=45.71 E-value=65 Score=25.12 Aligned_cols=58 Identities=19% Similarity=0.125 Sum_probs=44.4
Q ss_pred EEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHh--------hCC--CcchhHHHHHHHHHHhhch
Q 028931 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE--------LMP--YRACYPIFKLIYSAAANGV 141 (201)
Q Consensus 84 e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~--------fsp--KKaA~~V~KlL~sA~aNA~ 141 (201)
+++......-+|--=.-.++++|.|++++||..+-. ..| .+.|....+.|+.|+++..
T Consensus 53 d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~ 120 (124)
T TIGR01999 53 DAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYK 120 (124)
T ss_pred EEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHH
Confidence 566777777888888899999999999999987653 123 3467777788888877764
No 16
>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=37.57 E-value=88 Score=23.43 Aligned_cols=38 Identities=18% Similarity=0.052 Sum_probs=31.2
Q ss_pred cEEEEEeCccccCHHHHHHHHHHH-----hCCCHHHHHHHHhh
Q 028931 83 AEVSASARYLHMSAHKVRRVIDQI-----RGRSYEETLMILEL 120 (201)
Q Consensus 83 ~e~~A~~r~iriSpkKlr~Var~I-----RGk~v~eAi~qL~f 120 (201)
.|+.......--..--+.-++++| .|+++++.+.+|+-
T Consensus 24 ~Evf~~~~~~Gg~~~~~~ai~rliS~~Lr~G~~~~~ii~~L~g 66 (95)
T PF12637_consen 24 FEVFINVGKAGGCSGNLEAIARLISLALRSGVPPEEIIDQLRG 66 (95)
T ss_pred eEEEEecCcCCCchHHHHHHHHHHHHHHHcCCCHHHHHHHhcC
Confidence 567666665555577888999999 99999999999995
No 17
>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=32.45 E-value=1.1e+02 Score=23.84 Aligned_cols=58 Identities=17% Similarity=0.097 Sum_probs=41.9
Q ss_pred EEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHH-----hh----C--CCcchhHHHHHHHHHHhhch
Q 028931 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMIL-----EL----M--PYRACYPIFKLIYSAAANGV 141 (201)
Q Consensus 84 e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL-----~f----s--pKKaA~~V~KlL~sA~aNA~ 141 (201)
+++.......+|--=+-.++.+|.|+++++|..+- ++ . ....+......|..|+++..
T Consensus 53 d~~f~~~GC~~~~Asas~~~~~i~gk~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~ 121 (126)
T PF01592_consen 53 DAKFQGFGCAISIASASMMCELIKGKTLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYP 121 (126)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHTTSBHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEeecChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHH
Confidence 56677777788888899999999999999995321 11 2 23345666788888887754
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=31.28 E-value=2.2e+02 Score=25.67 Aligned_cols=59 Identities=15% Similarity=0.093 Sum_probs=45.5
Q ss_pred EEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHh------h---CC--CcchhHHHHHHHHHHhhchh
Q 028931 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE------L---MP--YRACYPIFKLIYSAAANGVH 142 (201)
Q Consensus 84 e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~------f---sp--KKaA~~V~KlL~sA~aNA~~ 142 (201)
+++......-+|--=+-.++.+|.|++++||+.+.. | .| .+.|....+.|+.|+.+...
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 566667777778778899999999999999887764 2 23 34566777899999888754
No 19
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=27.28 E-value=1e+02 Score=25.18 Aligned_cols=35 Identities=14% Similarity=0.220 Sum_probs=30.7
Q ss_pred EEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHH
Q 028931 84 EVSASARYLHMSAHKVRRVIDQIRGRSYEETLMIL 118 (201)
Q Consensus 84 e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL 118 (201)
.++..+...-+|--=.-.++.+|.|++++||+...
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 56777777888888899999999999999999877
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=25.58 E-value=1.2e+02 Score=23.01 Aligned_cols=37 Identities=16% Similarity=0.275 Sum_probs=32.0
Q ss_pred cEEEEEeCccccCHHHHHHHHHHHhCCCHHHHHHHHh
Q 028931 83 AEVSASARYLHMSAHKVRRVIDQIRGRSYEETLMILE 119 (201)
Q Consensus 83 ~e~~A~~r~iriSpkKlr~Var~IRGk~v~eAi~qL~ 119 (201)
.++.......-+|--=+..+++++.|++++||..++.
T Consensus 49 ~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 49 TDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 3567777788888888999999999999999998875
No 21
>PF11373 DUF3175: Protein of unknown function (DUF3175); InterPro: IPR021513 This entry is represented by Ralstonia phage RSL1, Orf186. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=25.42 E-value=49 Score=25.11 Aligned_cols=51 Identities=12% Similarity=0.147 Sum_probs=35.9
Q ss_pred CHHHHHHHHHHHhCCCHHHHHHHHhhCCCcchhHH----HHHHHHHHhhchhcCC
Q 028931 95 SAHKVRRVIDQIRGRSYEETLMILELMPYRACYPI----FKLIYSAAANGVHNMG 145 (201)
Q Consensus 95 SpkKlr~Var~IRGk~v~eAi~qL~fspKKaA~~V----~KlL~sA~aNA~~~~g 145 (201)
|.+.--+-.+--+|.+..-|+.+|.|+-.+|.+.+ .++|+.|......-+|
T Consensus 31 SLk~Sae~S~RRk~~pf~SAMSML~FYINRAGk~L~~~rr~~LE~AK~eLR~~fG 85 (86)
T PF11373_consen 31 SLKRSAEHSRRRKATPFRSAMSMLNFYINRAGKNLPKERRAVLERAKDELRKAFG 85 (86)
T ss_pred HHHHHHHhhcccCCCchHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHhC
Confidence 34444444455678999999999999988887666 5677777766544333
No 22
>PF13286 HD_assoc: Phosphohydrolase-associated domain; PDB: 2DQB_D.
Probab=24.03 E-value=1e+02 Score=22.05 Aligned_cols=22 Identities=27% Similarity=0.320 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhCCCHHHHHHHH
Q 028931 97 HKVRRVIDQIRGRSYEETLMIL 118 (201)
Q Consensus 97 kKlr~Var~IRGk~v~eAi~qL 118 (201)
.+.+.|+|.|.||+=..|+..-
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 6899999999999999988654
No 23
>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=22.92 E-value=55 Score=21.77 Aligned_cols=15 Identities=40% Similarity=0.640 Sum_probs=10.4
Q ss_pred HhCCCHHHHHHHHhh
Q 028931 106 IRGRSYEETLMILEL 120 (201)
Q Consensus 106 IRGk~v~eAi~qL~f 120 (201)
+.||++++|..+|+-
T Consensus 6 ~~g~~~~~a~~~l~~ 20 (63)
T PF03793_consen 6 LVGMTYDEAKSILEA 20 (63)
T ss_dssp TTTSBHHHHHHHHHH
T ss_pred cCCCcHHHHHHHHHH
Confidence 457888887776653
No 24
>PF13852 DUF4197: Protein of unknown function (DUF4197)
Probab=21.70 E-value=1.3e+02 Score=25.82 Aligned_cols=20 Identities=25% Similarity=0.270 Sum_probs=17.6
Q ss_pred HHHHHHhCCCHHHHHHHHhh
Q 028931 101 RVIDQIRGRSYEETLMILEL 120 (201)
Q Consensus 101 ~Var~IRGk~v~eAi~qL~f 120 (201)
.+.+.|+.|+++||..+|.=
T Consensus 85 if~~AI~~Ms~~DA~~IL~G 104 (202)
T PF13852_consen 85 IFVDAIKSMSIQDAKGILNG 104 (202)
T ss_pred HHHHHHHhCCHHhHHHHhcC
Confidence 45688999999999999993
No 25
>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=20.45 E-value=1.2e+02 Score=21.54 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCHHHHHHHHhhC
Q 028931 100 RRVIDQIRGRSYEETLMILELM 121 (201)
Q Consensus 100 r~Var~IRGk~v~eAi~qL~fs 121 (201)
..||+.|+||++++-..++...
T Consensus 37 ~~iA~~i~gks~eeir~~fgi~ 58 (78)
T PF01466_consen 37 KYIANMIKGKSPEEIRKYFGIE 58 (78)
T ss_dssp HHHHHHHTTS-HHHHHHHHT--
T ss_pred HHHHHHhcCCCHHHHHHHcCCC
Confidence 4678999999999998888743
Done!