Query 040446
Match_columns 270
No_of_seqs 184 out of 1151
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 08:33:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040446.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040446hhsearch_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 2.6E-38 5.6E-43 259.9 14.2 112 106-217 6-117 (117)
2 PRK00565 rplV 50S ribosomal pr 100.0 3.4E-38 7.3E-43 256.8 13.2 110 109-218 2-111 (112)
3 COG0091 RplV Ribosomal protein 100.0 2.6E-38 5.7E-43 261.3 10.2 111 108-218 9-119 (120)
4 TIGR01044 rplV_bact ribosomal 100.0 1.3E-37 2.7E-42 250.3 10.9 103 112-214 1-103 (103)
5 KOG1711 Mitochondrial/chloropl 100.0 1.6E-37 3.5E-42 276.8 7.8 177 70-258 23-212 (218)
6 PRK12279 50S ribosomal protein 100.0 2.8E-36 6.1E-41 282.1 14.1 145 109-257 2-147 (311)
7 PF00237 Ribosomal_L22: Riboso 100.0 1.2E-36 2.5E-41 243.6 8.6 105 112-216 1-105 (105)
8 cd00336 Ribosomal_L22 Ribosoma 100.0 2.2E-35 4.8E-40 235.9 12.5 105 110-214 1-105 (105)
9 TIGR01038 L22_arch ribosomal p 100.0 2.1E-33 4.6E-38 239.9 13.2 109 108-217 10-150 (150)
10 PRK04223 rpl22p 50S ribosomal 100.0 3.3E-33 7.1E-38 239.3 13.7 110 107-217 13-152 (153)
11 PTZ00178 60S ribosomal protein 100.0 6.9E-33 1.5E-37 242.8 12.8 110 108-218 13-154 (181)
12 KOG3353 60S ribosomal protein 99.4 4.1E-15 8.8E-20 130.2 -4.5 108 110-218 9-148 (175)
13 TIGR03419 NifU_clost FeS clust 52.9 68 0.0015 26.3 7.0 61 107-167 47-118 (121)
14 PF12637 TSCPD: TSCPD domain; 43.3 88 0.0019 24.7 6.0 41 107-147 23-68 (95)
15 PRK11325 scaffold protein; Pro 42.0 58 0.0013 27.0 5.0 59 108-166 54-122 (127)
16 TIGR01999 iscU FeS cluster ass 40.7 72 0.0016 26.2 5.3 59 108-166 52-120 (124)
17 PF03448 MgtE_N: MgtE intracel 33.6 88 0.0019 23.7 4.5 42 124-165 51-92 (102)
18 PF01592 NifU_N: NifU-like N t 30.2 99 0.0021 25.3 4.5 59 108-166 52-121 (126)
19 TIGR02000 NifU_proper Fe-S clu 28.4 1.9E+02 0.0041 27.5 6.7 60 108-167 53-123 (290)
20 PF13852 DUF4197: Protein of u 24.2 1.2E+02 0.0026 27.5 4.3 37 125-161 84-120 (202)
21 cd06664 IscU_like Iron-sulfur 21.1 1.1E+02 0.0023 24.6 3.1 39 107-145 48-86 (123)
No 1
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00 E-value=2.6e-38 Score=259.89 Aligned_cols=112 Identities=33% Similarity=0.469 Sum_probs=108.8
Q ss_pred CCceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHhhHhCCCCCCCeEEEEEEecC
Q 040446 106 KPAKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANATHNHGLDPDRLLVAEAFVGK 185 (270)
Q Consensus 106 k~~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA~~~~GlD~d~L~I~ea~Vnk 185 (270)
+..+++|..+++++||+|+++||++||||+|+||+.||+|+|+|+|+.|+++|+||.+||++++|+|+|+|||++||||+
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 44679999999999999999999999999999999999999999999999999999999988999999999999999999
Q ss_pred CcccccccccCCCCccccccCceeEEEEEEec
Q 040446 186 GFFKKRVSYHSKGRSGIKVRPECRLTVVVREL 217 (270)
Q Consensus 186 G~~~KR~~pRARGRa~~irk~~~HItVVLkE~ 217 (270)
||++||++||||||++++++++|||+|+|+|.
T Consensus 86 G~~~KR~~prArGRa~~i~k~~sHI~Vvl~e~ 117 (117)
T CHL00034 86 GPTLKRFRPRAQGRSYPIKKPTCHITIVLKDI 117 (117)
T ss_pred CCccCCCCcccCCCCCcccCCCccEEEEEecC
Confidence 99999999999999999999999999999873
No 2
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00 E-value=3.4e-38 Score=256.78 Aligned_cols=110 Identities=42% Similarity=0.563 Sum_probs=107.4
Q ss_pred eEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHhhHhCCCCCCCeEEEEEEecCCcc
Q 040446 109 KVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANATHNHGLDPDRLLVAEAFVGKGFF 188 (270)
Q Consensus 109 evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~ 188 (270)
+++|..+++++||+|+++||++||||+|+||+.||+|+|+|+|+.|+++|+||.+||++++|+|+|+|||+++|||+|++
T Consensus 2 ~~~A~~~~~~~SpkK~~~v~~~IrG~~v~~A~~~L~~~pkk~a~~i~k~L~sA~aNA~~~~g~d~~~L~I~~~~v~~G~~ 81 (112)
T PRK00565 2 EAKAKARYVRVSPRKARLVADLIRGKKVEEALAILKFSPKKAARLVKKVLKSAIANAENNHGLDIDNLVVKEAYVDEGPT 81 (112)
T ss_pred ceEEEeCccccCHHHHHHHHHHHcCCcHHHHHHHHHHCcHhHHHHHHHHHHHHHHHHHhccCCChhHeEEEEEEECCCCc
Confidence 47899999999999999999999999999999999999999999999999999999998899999999999999999999
Q ss_pred cccccccCCCCccccccCceeEEEEEEecC
Q 040446 189 KKRVSYHSKGRSGIKVRPECRLTVVVRELT 218 (270)
Q Consensus 189 ~KR~~pRARGRa~~irk~~~HItVVLkE~~ 218 (270)
+||++||||||++++++++|||+|+|+|.+
T Consensus 82 ~Kr~~~rArGR~~~i~k~~~hi~vvL~e~~ 111 (112)
T PRK00565 82 LKRFRPRARGRASRIRKRTSHITVVVAEKE 111 (112)
T ss_pred cCCCCCCcCCCCCccccCCccEEEEEEecC
Confidence 999999999999999999999999999863
No 3
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-38 Score=261.31 Aligned_cols=111 Identities=42% Similarity=0.546 Sum_probs=108.0
Q ss_pred ceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHhhHhCCCCCCCeEEEEEEecCCc
Q 040446 108 AKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANATHNHGLDPDRLLVAEAFVGKGF 187 (270)
Q Consensus 108 ~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~ 187 (270)
.+++|..+++++||+|+++||++||||++++|+.+|+|+|+|+|+.|.|+|+||++||++|+|||+|+|||.|||||+||
T Consensus 9 ~~akA~~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~~~pkKaa~~v~KvL~sA~aNAe~n~gLd~d~L~V~~i~v~~gp 88 (120)
T COG0091 9 MEAKAKARYLRISPKKARLVADLIRGKKVAEALAILEFVPKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDKGP 88 (120)
T ss_pred hhhHhhhccCcCChHHHHHHHHHHcCCcHHHHHHHHHhChHHHHHHHHHHHHHHHhhHHhccCCChHHEEEEEEEeCCCc
Confidence 45789999999999999999999999999999999999999999999999999999999889999999999999999999
Q ss_pred ccccccccCCCCccccccCceeEEEEEEecC
Q 040446 188 FKKRVSYHSKGRSGIKVRPECRLTVVVRELT 218 (270)
Q Consensus 188 ~~KR~~pRARGRa~~irk~~~HItVVLkE~~ 218 (270)
++||++||||||+++|.+|+|||||||+|..
T Consensus 89 ~lKR~~pRA~GRa~~i~k~tshItvvv~e~~ 119 (120)
T COG0091 89 VLKRFMPRARGRATRINKRTSHITVVVREKE 119 (120)
T ss_pred eeeeecccccCccccccCCCceEEEEEeecC
Confidence 9999999999999999999999999999863
No 4
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=100.00 E-value=1.3e-37 Score=250.28 Aligned_cols=103 Identities=43% Similarity=0.531 Sum_probs=100.8
Q ss_pred EEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHhhHhCCCCCCCeEEEEEEecCCccccc
Q 040446 112 AVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANATHNHGLDPDRLLVAEAFVGKGFFKKR 191 (270)
Q Consensus 112 A~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~~KR 191 (270)
|..+++++||+|+++||++||||+|+||+.||+|+|+|+|+.|+|+|+||.+||++++|+|+|+|||+++|||+|+++||
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 46789999999999999999999999999999999999999999999999999988999999999999999999999999
Q ss_pred ccccCCCCccccccCceeEEEEE
Q 040446 192 VSYHSKGRSGIKVRPECRLTVVV 214 (270)
Q Consensus 192 ~~pRARGRa~~irk~~~HItVVL 214 (270)
++||||||++++++++|||+|||
T Consensus 81 ~~~rarGRa~~i~k~~~hi~vvl 103 (103)
T TIGR01044 81 IRPRAKGRASRIRKRTSHITVVV 103 (103)
T ss_pred CCCCCCCCCCcccCCCccEEEeC
Confidence 99999999999999999999986
No 5
>KOG1711 consensus Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-37 Score=276.77 Aligned_cols=177 Identities=44% Similarity=0.588 Sum_probs=155.2
Q ss_pred cchhhhhhcCCCCCCccCCcc---cccCCCCccccccc---------cCCceEEEEeCCCccCHHHHHHHHHHHcCCCHH
Q 040446 70 ISSTRKLLANSSDETPVSSPL---LAIESGKADDQKVV---------SKPAKVQAVLKGIKQSPKKINLVAALVRGMRVE 137 (270)
Q Consensus 70 ~s~s~~~~~~~~~~~~~~~pl---~~~~~~k~~~~~~v---------~k~~evkA~~r~iriSpKKlr~VarlIRGm~V~ 137 (270)
++|.+.+ +.+++|+.+++ .++++++||+++++ +++.+|+|..+.|++||||++.+|+||+||+|+
T Consensus 23 ~rs~~~L---~~~~~~~s~i~s~~al~~~~k~E~~~Ki~~~~~l~~~p~~~eVya~~~~Ik~S~kK~~~l~~lirgm~v~ 99 (218)
T KOG1711|consen 23 IRSFRKL---QADEQPVSDIESSPALLGSEKWEERNKIVYPPQLPFEPKRPEVYACSKSIKSSPKKVWLLARLIRGMSVE 99 (218)
T ss_pred ccchHhh---hccCCCccchhhChhhcchHHHHHhccccCcccCCCCCcchhHHHHHHHHHhCHHHHHHHHHHHcCCCHH
Confidence 4444444 66788888887 48999999999544 466899999999999999999999999999999
Q ss_pred HHHHHHhhchhhhHHHHHHHHHHHHHHhhHhCCCCCCCeEE-EEEEecCCcccccccccCCCCccccccCceeEEEEEEe
Q 040446 138 DALLQLQVTIKRAAKTVYQVIHSARANATHNHGLDPDRLLV-AEAFVGKGFFKKRVSYHSKGRSGIKVRPECRLTVVVRE 216 (270)
Q Consensus 138 eAi~qL~fs~KKaAk~V~KlL~sA~aNA~~~~GlD~d~L~I-~ea~VnkG~~~KR~~pRARGRa~~irk~~~HItVVLkE 216 (270)
|||+||+|++||+|+.|+++|.+|.+||.+++|+|+++||| +++|+++|.++||+.+|||||.++|++++|||+|+|+|
T Consensus 100 ~AL~Ql~~s~kK~a~~i~~~l~~A~~nA~~~~gl~~~~l~v~~~~t~~~g~~~Krl~~hargr~~ii~~~yvhi~v~L~e 179 (218)
T KOG1711|consen 100 EALMQLEFSDKKAAKTIAEVLLSARANAVHNHGLDPDSLLVVAEATVGQGNELKRLKVHARGRFGIIRRPYVHIFVKLEE 179 (218)
T ss_pred HHHHHhhcchHHHHHHHHHHHHHHHhhhHHhcCCCccceEEEEeeecccchhhhheeeeccCcccceecceeeEEEEEee
Confidence 99999999999999999999999999999999999999888 99999999999999999999999999999999999999
Q ss_pred cCcHHHHHHHHHhHHHHHHhhHhhhhccccccccCcccccCC
Q 040446 217 LTAEEEAQIARLRVHKFRKLTKREQRLVPHQLIETTPIWNRR 258 (270)
Q Consensus 217 ~~~~~~~~~~~~r~~~~k~~~~k~~r~~~~~~l~~~pvw~~~ 258 (270)
+++..+. +-....+.....+|..|.++|+..--
T Consensus 180 ~s~~~~~---------~~~~~~~~~~~e~~~~l~~~pi~~~~ 212 (218)
T KOG1711|consen 180 GSPPQQR---------YPGKKAKHHSSEYWQQLRSRPIYSSG 212 (218)
T ss_pred cCCCchh---------hhhhhcchhcchhhhccCCcceEecC
Confidence 9886653 11123446667899999999997643
No 6
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=100.00 E-value=2.8e-36 Score=282.11 Aligned_cols=145 Identities=25% Similarity=0.351 Sum_probs=135.7
Q ss_pred eEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHhh-HhCCCCCCCeEEEEEEecCCc
Q 040446 109 KVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANAT-HNHGLDPDRLLVAEAFVGKGF 187 (270)
Q Consensus 109 evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA~-~~~GlD~d~L~I~ea~VnkG~ 187 (270)
+++|..+++++||+|+++||++||||+|++|+.+|+|+|+|+|..|+++|+||.+||+ +++|||.|+|||.+|+||+|+
T Consensus 2 ~akA~~r~iriSpkK~R~Va~~IRGk~v~~Al~~L~~~PkKaA~~I~KlLkSA~ANAe~~n~gld~d~L~I~~~~VdkGp 81 (311)
T PRK12279 2 TNKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILSNTPKKFAPIVLKLLNSAISNVQHNSKDMDPSKLYIYKIVANQGP 81 (311)
T ss_pred ceEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhcCCChhHeEEEEEEECCCC
Confidence 4789999999999999999999999999999999999999999999999999999999 579999999999999999999
Q ss_pred ccccccccCCCCccccccCceeEEEEEEecCcHHHHHHHHHhHHHHHHhhHhhhhccccccccCcccccC
Q 040446 188 FKKRVSYHSKGRSGIKVRPECRLTVVVRELTAEEEAQIARLRVHKFRKLTKREQRLVPHQLIETTPIWNR 257 (270)
Q Consensus 188 ~~KR~~pRARGRa~~irk~~~HItVVLkE~~~~~~~~~~~~r~~~~k~~~~k~~r~~~~~~l~~~pvw~~ 257 (270)
++||++||||||+++|++++|||+|+|.|...+++++++..|. ++.+++....||.++++.|+=-+
T Consensus 82 ~lKR~~PRArGRA~~i~KrtsHItIvl~e~~~~~~~~~~~~k~----~~~~~~~~~~~~~~~~~~~~~~~ 147 (311)
T PRK12279 82 TMKRTLPRAKGSADQLFKRTTHLEIVLSDDVNEREKELAAIKA----KKSKKPLPVEPKAKVETKKVAKP 147 (311)
T ss_pred cccCCCCccCCCCCcccCCCccEEEEEecCCchhhHhhhhhhc----ccccccccCCCccccccCCCCCC
Confidence 9999999999999999999999999999998888877776665 45778889999999999987544
No 7
>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=1.2e-36 Score=243.57 Aligned_cols=105 Identities=44% Similarity=0.684 Sum_probs=102.4
Q ss_pred EEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHhhHhCCCCCCCeEEEEEEecCCccccc
Q 040446 112 AVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANATHNHGLDPDRLLVAEAFVGKGFFKKR 191 (270)
Q Consensus 112 A~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~~KR 191 (270)
|..+++++||||++++|++||||+++||+.||+|+|+|+|+.|+++|++|.+||++++|+|+|+|||+++|||+|+++||
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 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCccccccCceeEEEEEEe
Q 040446 192 VSYHSKGRSGIKVRPECRLTVVVRE 216 (270)
Q Consensus 192 ~~pRARGRa~~irk~~~HItVVLkE 216 (270)
++||||||++++++++|||+|+|+|
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 9999999999999999999999997
No 8
>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=2.2e-35 Score=235.91 Aligned_cols=105 Identities=40% Similarity=0.537 Sum_probs=102.3
Q ss_pred EEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHhhHhCCCCCCCeEEEEEEecCCccc
Q 040446 110 VQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANATHNHGLDPDRLLVAEAFVGKGFFK 189 (270)
Q Consensus 110 vkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~~ 189 (270)
++|..+++++||||+++|+++||||+++||+.||+|+++|+|+.|+++|+||.+||++++|+|+|+|||+++|||+|+++
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 47899999999999999999999999999999999999999999999999999999988888899999999999999999
Q ss_pred ccccccCCCCccccccCceeEEEEE
Q 040446 190 KRVSYHSKGRSGIKVRPECRLTVVV 214 (270)
Q Consensus 190 KR~~pRARGRa~~irk~~~HItVVL 214 (270)
||++||||||++++++++|||+|+|
T Consensus 81 kr~~~rarGR~~~~~k~~~hi~ivl 105 (105)
T cd00336 81 KRRRPRARGRANPIRKRTCHITVVL 105 (105)
T ss_pred cCCCcCCCCCCcccccCceeEEEeC
Confidence 9999999999999999999999986
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=2.1e-33 Score=239.86 Aligned_cols=109 Identities=27% Similarity=0.290 Sum_probs=105.6
Q ss_pred ceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhh--------------------------------chhhhHHHHH
Q 040446 108 AKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQV--------------------------------TIKRAAKTVY 155 (270)
Q Consensus 108 ~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~f--------------------------------s~KKaAk~V~ 155 (270)
.+++|..+++++||+|+++||++||||++++|+.+|+| .|+|+|+.|+
T Consensus 10 ~~akA~~~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~~~gR~P~Kaa~~i~ 89 (150)
T TIGR01038 10 KSAKARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKEWGWTAGRYPVKAAKFIL 89 (150)
T ss_pred eeEEEEeCCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccccCCCchHHHHHHH
Confidence 46899999999999999999999999999999999999 7999999999
Q ss_pred HHHHHHHHHhhHhCCCCCCCeEEEEEEecCCcccccccccCCCCccccccCceeEEEEEEec
Q 040446 156 QVIHSARANATHNHGLDPDRLLVAEAFVGKGFFKKRVSYHSKGRSGIKVRPECRLTVVVREL 217 (270)
Q Consensus 156 KlL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~~KR~~pRARGRa~~irk~~~HItVVLkE~ 217 (270)
++|+||.+||+ ++|||+|+|||.+|.||+|+++||++|||+||+++|++++|||+|+|.|.
T Consensus 90 klL~sA~aNA~-~~gld~d~L~I~~i~vnkg~~~kR~~prA~GRa~~~~k~~~HI~Iil~e~ 150 (150)
T TIGR01038 90 KVLQNAEANAE-YKGLDVEKLVIIHIQANKGPKIRRWMPRAFGRATPYNSSPTHIELVVEEK 150 (150)
T ss_pred HHHHHHHHHHH-hcCCChhHeEEEEEEECCCCccCCCCCccCCCCCcccCCCceEEEEEecC
Confidence 99999999998 58999999999999999999999999999999999999999999999874
No 10
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=100.00 E-value=3.3e-33 Score=239.34 Aligned_cols=110 Identities=26% Similarity=0.349 Sum_probs=106.5
Q ss_pred CceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhh------------------------------chhhhHHHHHH
Q 040446 107 PAKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQV------------------------------TIKRAAKTVYQ 156 (270)
Q Consensus 107 ~~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~f------------------------------s~KKaAk~V~K 156 (270)
..+++|..+++++||+|+++||++||||+++||+.+|+| .|+|+|+.|+|
T Consensus 13 ~~~akA~~~~~rvS~kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~gr~PkKaa~~i~K 92 (153)
T PRK04223 13 EKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGIDGWPAGRYPVKAAKAFLK 92 (153)
T ss_pred CceEEEEeCCCccChHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccCCCchHHHHHHHH
Confidence 456899999999999999999999999999999999999 79999999999
Q ss_pred HHHHHHHHhhHhCCCCCCCeEEEEEEecCCcccccccccCCCCccccccCceeEEEEEEec
Q 040446 157 VIHSARANATHNHGLDPDRLLVAEAFVGKGFFKKRVSYHSKGRSGIKVRPECRLTVVVREL 217 (270)
Q Consensus 157 lL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~~KR~~pRARGRa~~irk~~~HItVVLkE~ 217 (270)
+|+||.+||+ ++|||+|+|||++|.||+|+++||++|||+||++++.+++|||+|+|+|.
T Consensus 93 lL~sA~aNA~-~~gld~d~L~I~~i~v~kg~~~kR~~prA~GRa~~~~k~~sHI~Iil~e~ 152 (153)
T PRK04223 93 LLENAEANAE-YKGLDTEKLVIVHIAAHKGRVIKGYMPRAFGRATPKNTETVNIEVILEEV 152 (153)
T ss_pred HHHHHHHHHH-hcCCChhHeEEEEEEECCCCCCCCcCcccCCCCCcccCCCceEEEEEEeC
Confidence 9999999998 58999999999999999999999999999999999999999999999985
No 11
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=6.9e-33 Score=242.80 Aligned_cols=110 Identities=22% Similarity=0.331 Sum_probs=106.9
Q ss_pred ceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhh--------------------------------chhhhHHHHH
Q 040446 108 AKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQV--------------------------------TIKRAAKTVY 155 (270)
Q Consensus 108 ~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~f--------------------------------s~KKaAk~V~ 155 (270)
.+++|..+++++||+|+++||++||||++++|+++|+| .|+|+|..|+
T Consensus 13 ~~akA~~~~~riSpkk~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~~~~~~GR~P~KaA~~i~ 92 (181)
T PTZ00178 13 KSAKAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKEFGHTQGRWPEKSVKFVL 92 (181)
T ss_pred ceEEEEeCCcccchHHHHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCccccccccccccccCcCcHHHHHHHH
Confidence 46899999999999999999999999999999999998 7999999999
Q ss_pred HHHHHHHHHhhHhCCCCCCCeEEEEEEecCCcccccccccCCCCccccccCceeEEEEEEecC
Q 040446 156 QVIHSARANATHNHGLDPDRLLVAEAFVGKGFFKKRVSYHSKGRSGIKVRPECRLTVVVRELT 218 (270)
Q Consensus 156 KlL~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~~KR~~pRARGRa~~irk~~~HItVVLkE~~ 218 (270)
|+|+||.+||+ ++|+|+|+|||.+|.||+|+++||++|||+||+++|++++|||+|||+|.+
T Consensus 93 KlL~SA~aNAe-~~gld~d~L~I~~i~v~kG~~lKR~~pRA~GRA~~i~k~t~HI~Ivl~e~~ 154 (181)
T PTZ00178 93 SLLKNAEANAE-AKGLDVEKLVISHVQVNRAPRGRRRTYRAHGRINPFMSSPCHIELIATEKD 154 (181)
T ss_pred HHHHHHHHHHH-hcCCChhHeEEEEEEECCCcccCCCCCccCCCcCcccCCceeEEEEEEEcc
Confidence 99999999999 799999999999999999999999999999999999999999999999864
No 12
>KOG3353 consensus 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=99.42 E-value=4.1e-15 Score=130.22 Aligned_cols=108 Identities=22% Similarity=0.319 Sum_probs=102.2
Q ss_pred EEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhc--------------------------------hhhhHHHHHHH
Q 040446 110 VQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVT--------------------------------IKRAAKTVYQV 157 (270)
Q Consensus 110 vkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs--------------------------------~KKaAk~V~Kl 157 (270)
+++.+.++++++|..++.+..|+++++..|+.+|..+ |+|+|.+++.+
T Consensus 9 ~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkksaefll~~ 88 (175)
T KOG3353|consen 9 CKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKKSAEFLLHM 88 (175)
T ss_pred hhcccccEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhhhccccCcccchHHHHHHHH
Confidence 5678899999999999999999999999999999886 48999999999
Q ss_pred HHHHHHHhhHhCCCCCCCeEEEEEEecCCcccccccccCCCCccccccCceeEEEEEEecC
Q 040446 158 IHSARANATHNHGLDPDRLLVAEAFVGKGFFKKRVSYHSKGRSGIKVRPECRLTVVVRELT 218 (270)
Q Consensus 158 L~sA~aNA~~~~GlD~d~L~I~ea~VnkG~~~KR~~pRARGRa~~irk~~~HItVVLkE~~ 218 (270)
|++|..||+ .+|+|.|.|+|.++.||++|.+.+.+|||+||.+++-..+|||++||.|..
T Consensus 89 LkN~esnaE-lkgldVDsLvIehiqvnkApKm~~rtyraHg~in~y~ssP~hie~il~~ke 148 (175)
T KOG3353|consen 89 LKNAESNAE-LKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKE 148 (175)
T ss_pred HHhhhhccc-ccCcCcceeEeeehhhcccchhhhHHHHhhcccccccCChHHHHHHHHhhc
Confidence 999999999 689999999999999999999999999999999999999999999998763
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=52.91 E-value=68 Score=26.28 Aligned_cols=61 Identities=13% Similarity=0.114 Sum_probs=47.4
Q ss_pred CceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhh-----------chhhhHHHHHHHHHHHHHHhhH
Q 040446 107 PAKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQV-----------TIKRAAKTVYQVIHSARANATH 167 (270)
Q Consensus 107 ~~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~f-----------s~KKaAk~V~KlL~sA~aNA~~ 167 (270)
-.+++.....--+|.==+-.++++|.|++++||..+..- ...+.|....+.|+.|+.+...
T Consensus 47 I~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~~~~i~~~l~~l~~~r~~CA~la~~al~~a~~~y~~ 118 (121)
T TIGR03419 47 IKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYRE 118 (121)
T ss_pred EEEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHh
Confidence 345666677778888889999999999999998876642 1256888888899988887653
No 14
>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=43.33 E-value=88 Score=24.73 Aligned_cols=41 Identities=20% Similarity=0.223 Sum_probs=32.4
Q ss_pred CceEEEEeCCCccCHHHHHHHHHHH-----cCCCHHHHHHHHhhch
Q 040446 107 PAKVQAVLKGIKQSPKKINLVAALV-----RGMRVEDALLQLQVTI 147 (270)
Q Consensus 107 ~~evkA~~r~iriSpKKlr~VarlI-----RGm~V~eAi~qL~fs~ 147 (270)
|-|+.......--..--+.-++++| .|+++++.+.+|+-..
T Consensus 23 p~Evf~~~~~~Gg~~~~~~ai~rliS~~Lr~G~~~~~ii~~L~gi~ 68 (95)
T PF12637_consen 23 PFEVFINVGKAGGCSGNLEAIARLISLALRSGVPPEEIIDQLRGIR 68 (95)
T ss_pred ceEEEEecCcCCCchHHHHHHHHHHHHHHHcCCCHHHHHHHhcCCC
Confidence 5566665555544477888999999 9999999999999863
No 15
>PRK11325 scaffold protein; Provisional
Probab=41.96 E-value=58 Score=26.99 Aligned_cols=59 Identities=17% Similarity=0.145 Sum_probs=46.4
Q ss_pred ceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhhc----------hhhhHHHHHHHHHHHHHHhh
Q 040446 108 AKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQVT----------IKRAAKTVYQVIHSARANAT 166 (270)
Q Consensus 108 ~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~fs----------~KKaAk~V~KlL~sA~aNA~ 166 (270)
..+.-....--+|.==+-.++.+|.|++++||..+-... ..+.|....+.|+.|+.+..
T Consensus 54 ~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~ 122 (127)
T PRK11325 54 EDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYK 122 (127)
T ss_pred EEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHH
Confidence 456677777788888899999999999999998765431 24678888888888887764
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=40.75 E-value=72 Score=26.21 Aligned_cols=59 Identities=15% Similarity=0.129 Sum_probs=45.5
Q ss_pred ceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhh--------c--hhhhHHHHHHHHHHHHHHhh
Q 040446 108 AKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQV--------T--IKRAAKTVYQVIHSARANAT 166 (270)
Q Consensus 108 ~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~f--------s--~KKaAk~V~KlL~sA~aNA~ 166 (270)
.+++.....--+|.==+-.++++|.|++++||..+-.. - ..+.|....+.|+.|+.+..
T Consensus 52 ~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~ 120 (124)
T TIGR01999 52 EDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYK 120 (124)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHH
Confidence 45666677777888888999999999999999876532 1 24578888888888887765
No 17
>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=33.58 E-value=88 Score=23.71 Aligned_cols=42 Identities=12% Similarity=0.132 Sum_probs=32.6
Q ss_pred HHHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHHHHHh
Q 040446 124 INLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSARANA 165 (270)
Q Consensus 124 lr~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA~aNA 165 (270)
...++..+.+|+.++|...|...+......|+..|.......
T Consensus 51 ~~~~a~il~~m~~dd~~~ll~~L~~~~~~~il~~l~~~~~~~ 92 (102)
T PF03448_consen 51 PEEAAEILAEMDSDDAADLLEELPEEQREKILAALDEEEREE 92 (102)
T ss_dssp HHHHHHHHCCS-HHHHHHHHCCSHHHHHHHHHHCS-HHHHHH
T ss_pred HHHHHHHHHccChHHHHHHHHHCCHHHHHHHHHcCCHHHHHH
Confidence 345677899999999999999999988888888886655443
No 18
>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=30.24 E-value=99 Score=25.31 Aligned_cols=59 Identities=17% Similarity=0.174 Sum_probs=43.2
Q ss_pred ceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHH-----hhc------hhhhHHHHHHHHHHHHHHhh
Q 040446 108 AKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQL-----QVT------IKRAAKTVYQVIHSARANAT 166 (270)
Q Consensus 108 ~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL-----~fs------~KKaAk~V~KlL~sA~aNA~ 166 (270)
..++.....-.+|.==+-.++.+|.|+++++|..+- ++. ....+.....+|..|+.+-.
T Consensus 52 ~d~~f~~~GC~~~~Asas~~~~~i~gk~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~ 121 (126)
T PF01592_consen 52 KDAKFQGFGCAISIASASMMCELIKGKTLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYP 121 (126)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHTTSBHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEeecChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHH
Confidence 456666777778888899999999999999995321 221 24567777788888887754
No 19
>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=28.43 E-value=1.9e+02 Score=27.49 Aligned_cols=60 Identities=12% Similarity=0.128 Sum_probs=46.3
Q ss_pred ceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHh------h---c--hhhhHHHHHHHHHHHHHHhhH
Q 040446 108 AKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQ------V---T--IKRAAKTVYQVIHSARANATH 167 (270)
Q Consensus 108 ~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~------f---s--~KKaAk~V~KlL~sA~aNA~~ 167 (270)
..++.....--+|.==+-.++.+|.|++++||+.+.. | . ..+.|....+.|+.|+++...
T Consensus 53 ~d~~F~~~GCais~ASAs~~~eli~Gktv~ea~~i~~~di~~~L~~lpp~r~~CA~La~~Al~~Al~~y~~ 123 (290)
T TIGR02000 53 VDAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVSNQDIADYLGGLPPEKMHCSVMGQEALEAAIANYRG 123 (290)
T ss_pred EEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHHhhHHHHHHHHcCCChhhchHHHHHHHHHHHHHHHHhc
Confidence 3556666777777777899999999999999887764 1 1 245778888999999988763
No 20
>PF13852 DUF4197: Protein of unknown function (DUF4197)
Probab=24.23 E-value=1.2e+02 Score=27.49 Aligned_cols=37 Identities=14% Similarity=0.122 Sum_probs=25.1
Q ss_pred HHHHHHHcCCCHHHHHHHHhhchhhhHHHHHHHHHHH
Q 040446 125 NLVAALVRGMRVEDALLQLQVTIKRAAKTVYQVIHSA 161 (270)
Q Consensus 125 r~VarlIRGm~V~eAi~qL~fs~KKaAk~V~KlL~sA 161 (270)
-.+.+.|+.|+++||..+|.=.+.-|..++.+-....
T Consensus 84 ~if~~AI~~Ms~~DA~~IL~G~d~AAT~ylr~~t~~~ 120 (202)
T PF13852_consen 84 PIFVDAIKSMSIQDAKGILNGGDDAATQYLRRKTSAQ 120 (202)
T ss_pred HHHHHHHHhCCHHhHHHHhcCCCcHHHHHHHHhhHHH
Confidence 3457899999999999999965544444444433333
No 21
>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=21.09 E-value=1.1e+02 Score=24.60 Aligned_cols=39 Identities=21% Similarity=0.218 Sum_probs=31.8
Q ss_pred CceEEEEeCCCccCHHHHHHHHHHHcCCCHHHHHHHHhh
Q 040446 107 PAKVQAVLKGIKQSPKKINLVAALVRGMRVEDALLQLQV 145 (270)
Q Consensus 107 ~~evkA~~r~iriSpKKlr~VarlIRGm~V~eAi~qL~f 145 (270)
-..+.-....--+|.==+..+++++.|++++||..++.-
T Consensus 48 I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~~ 86 (123)
T cd06664 48 ITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLNK 86 (123)
T ss_pred EEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 345566677777888889999999999999999987753
Done!