Query psy7141
Match_columns 215
No_of_seqs 178 out of 1159
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 19:15:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7141hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1711|consensus 100.0 1.2E-43 2.7E-48 304.2 10.5 175 29-214 36-211 (218)
2 PRK00565 rplV 50S ribosomal pr 100.0 4.2E-38 9.1E-43 247.5 11.4 109 73-182 3-111 (112)
3 CHL00034 rpl22 ribosomal prote 100.0 1.1E-37 2.3E-42 247.3 11.7 108 72-180 9-116 (117)
4 TIGR01044 rplV_bact ribosomal 100.0 1.6E-37 3.4E-42 241.2 10.4 102 76-178 2-103 (103)
5 COG0091 RplV Ribosomal protein 100.0 1.3E-37 2.8E-42 247.8 9.7 112 65-182 8-119 (120)
6 PF00237 Ribosomal_L22: Riboso 100.0 2.1E-36 4.6E-41 234.2 8.3 104 76-180 2-105 (105)
7 cd00336 Ribosomal_L22 Ribosoma 100.0 3.7E-35 8E-40 227.0 11.0 104 74-178 2-105 (105)
8 TIGR01038 L22_arch ribosomal p 100.0 2.8E-33 6.1E-38 230.6 11.4 106 74-181 13-150 (150)
9 PRK04223 rpl22p 50S ribosomal 100.0 5.3E-33 1.1E-37 229.6 11.7 108 73-182 16-153 (153)
10 PTZ00178 60S ribosomal protein 100.0 4.9E-33 1.1E-37 234.9 11.0 115 74-190 16-162 (181)
11 PRK12279 50S ribosomal protein 100.0 1.2E-32 2.6E-37 248.5 11.1 112 73-185 3-115 (311)
12 KOG3353|consensus 99.6 4.1E-17 8.9E-22 137.3 -3.6 112 75-188 11-154 (175)
13 PF12637 TSCPD: TSCPD domain; 67.3 27 0.00058 26.5 6.5 41 68-108 21-66 (95)
14 TIGR03419 NifU_clost FeS clust 60.0 26 0.00056 27.6 5.4 62 69-130 46-118 (121)
15 TIGR01999 iscU FeS cluster ass 44.9 41 0.00089 26.5 4.3 61 69-129 50-120 (124)
16 PRK11325 scaffold protein; Pro 43.5 50 0.0011 26.2 4.7 61 69-129 52-122 (127)
17 PF03448 MgtE_N: MgtE intracel 41.4 28 0.00061 25.5 2.7 44 86-129 50-93 (102)
18 PF01592 NifU_N: NifU-like N t 31.6 95 0.0021 24.3 4.5 60 71-130 52-122 (126)
19 PF03793 PASTA: PASTA domain; 29.8 31 0.00067 23.2 1.3 14 94-107 6-19 (63)
20 PF13852 DUF4197: Protein of u 29.1 86 0.0019 27.3 4.1 19 89-107 85-103 (202)
21 PF14804 Jag_N: Jag N-terminus 26.9 1.2E+02 0.0027 20.6 3.8 47 119-178 5-51 (52)
22 COG0822 IscU NifU homolog invo 24.4 71 0.0015 26.4 2.7 33 74-106 58-90 (150)
23 TIGR02000 NifU_proper Fe-S clu 24.3 1.5E+02 0.0032 27.0 5.0 60 71-130 53-123 (290)
24 PF02593 dTMP_synthase: Thymid 24.2 81 0.0017 27.8 3.1 21 86-106 157-177 (217)
25 PF11373 DUF3175: Protein of u 23.5 76 0.0017 24.3 2.4 55 79-133 27-85 (86)
26 cd06664 IscU_like Iron-sulfur 23.1 88 0.0019 24.1 2.9 39 69-107 47-85 (123)
27 PF01466 Skp1: Skp1 family, di 22.6 1E+02 0.0022 22.2 3.0 21 88-108 37-57 (78)
28 cd01785 PDZ_GEF_RA Ubiquitin-l 20.4 2E+02 0.0043 21.9 4.1 37 121-157 25-62 (85)
No 1
>KOG1711|consensus
Probab=100.00 E-value=1.2e-43 Score=304.16 Aligned_cols=175 Identities=39% Similarity=0.593 Sum_probs=162.2
Q ss_pred ccchhhhhhhhhcccCCCChhhhhhccceeCCCCCCCccCccceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHcc
Q psy7141 29 ASDLHTSQSCLKKSLAEIEVPRFTRHNNVVFPPQQEGEERRPAFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGY 108 (215)
Q Consensus 29 ~~~~ht~~~~~~~~~~~~~~~~w~~~n~~v~ppq~~~~~~r~~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f 108 (215)
.+.+|++.. .+++++|+++|+++|||+.+.+|.+ .+|+||...|++|+||||.+|++||||+|+|||.||+|
T Consensus 36 ~s~i~s~~a-------l~~~~k~E~~~Ki~~~~~l~~~p~~-~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~~ 107 (218)
T KOG1711|consen 36 VSDIESSPA-------LLGSEKWEERNKIVYPPQLPFEPKR-PEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLEF 107 (218)
T ss_pred ccchhhChh-------hcchHHHHHhccccCcccCCCCCcc-hhHHHHHHHHHhCHHHHHHHHHHHcCCCHHHHHHHhhc
Confidence 346666653 2579999999999999999999877 89999999999999999999999999999999999999
Q ss_pred CcccchHHHHHHHHHHHHHhHHhCCCCCCCCEEE-EEEEecCCcccccccccCCCCcccccccceeEEEEEeeCCCCCCC
Q psy7141 109 VAKKGAPFIRDTILEAQEMAVKDHNVEFKSNLWV-AESFVLKDIVIKGMRRHARVRMGRVEYKYCTYFVRLEEGKPPKNY 187 (215)
Q Consensus 109 ~pKKaA~~I~kvL~sA~aNA~~~~gld~~~~L~I-~e~~v~kG~~lKRir~rArGRa~~i~k~~~HI~VvL~E~~~p~~~ 187 (215)
++||+|+.|.++|.+|.+||.++||+|. ++|+| +++++++|.++||+++|||||++++++++|||||+|+|+.++.++
T Consensus 108 s~kK~a~~i~~~l~~A~~nA~~~~gl~~-~~l~v~~~~t~~~g~~~Krl~~hargr~~ii~~~yvhi~v~L~e~s~~~~~ 186 (218)
T KOG1711|consen 108 SDKKAAKTIAEVLLSARANAVHNHGLDP-DSLLVVAEATVGQGNELKRLKVHARGRFGIIRRPYVHIFVKLEEGSPPQQR 186 (218)
T ss_pred chHHHHHHHHHHHHHHHhhhHHhcCCCc-cceEEEEeeecccchhhhheeeeccCcccceecceeeEEEEEeecCCCchh
Confidence 9999999999999999999999999995 66655 999999999999999999999999999999999999999999998
Q ss_pred cCCCCCCchHHHHHHHHHhcccccccC
Q psy7141 188 YWTGPQTGPEKLEEYLQSLRYRKISSS 214 (215)
Q Consensus 188 y~~~~~~~~~~~~~~~~~~r~r~i~~~ 214 (215)
| ..+.++++.++|..+|++|.|-.|
T Consensus 187 ~--~~~~~~~~~~e~~~~l~~~pi~~~ 211 (218)
T KOG1711|consen 187 Y--PGKKAKHHSSEYWQQLRSRPIYSS 211 (218)
T ss_pred h--hhhhcchhcchhhhccCCcceEec
Confidence 5 478999999999999999988654
No 2
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00 E-value=4.2e-38 Score=247.51 Aligned_cols=109 Identities=28% Similarity=0.368 Sum_probs=105.2
Q ss_pred eeccccccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhHHhCCCCCCCCEEEEEEEecCCcc
Q psy7141 73 VCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAVKDHNVEFKSNLWVAESFVLKDIV 152 (215)
Q Consensus 73 v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~~~~gld~~~~L~I~e~~v~kG~~ 152 (215)
+.+..+++++||+|+++||++||||+++||+.||+|+|+|+|+.|+++|+||.+||++++|+| +|+|||+++|||+|++
T Consensus 3 ~~A~~~~~~~SpkK~~~v~~~IrG~~v~~A~~~L~~~pkk~a~~i~k~L~sA~aNA~~~~g~d-~~~L~I~~~~v~~G~~ 81 (112)
T PRK00565 3 AKAKARYVRVSPRKARLVADLIRGKKVEEALAILKFSPKKAARLVKKVLKSAIANAENNHGLD-IDNLVVKEAYVDEGPT 81 (112)
T ss_pred eEEEeCccccCHHHHHHHHHHHcCCcHHHHHHHHHHCcHhHHHHHHHHHHHHHHHHHhccCCC-hhHeEEEEEEECCCCc
Confidence 455699999999999999999999999999999999999999999999999999999889999 7999999999999999
Q ss_pred cccccccCCCCcccccccceeEEEEEeeCC
Q psy7141 153 IKGMRRHARVRMGRVEYKYCTYFVRLEEGK 182 (215)
Q Consensus 153 lKRir~rArGRa~~i~k~~~HI~VvL~E~~ 182 (215)
+||++||||||++++++++|||+|+|+|++
T Consensus 82 ~Kr~~~rArGR~~~i~k~~~hi~vvL~e~~ 111 (112)
T PRK00565 82 LKRFRPRARGRASRIRKRTSHITVVVAEKE 111 (112)
T ss_pred cCCCCCCcCCCCCccccCCccEEEEEEecC
Confidence 999999999999999999999999999965
No 3
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00 E-value=1.1e-37 Score=247.30 Aligned_cols=108 Identities=22% Similarity=0.278 Sum_probs=104.6
Q ss_pred eeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhHHhCCCCCCCCEEEEEEEecCCc
Q psy7141 72 FVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAVKDHNVEFKSNLWVAESFVLKDI 151 (215)
Q Consensus 72 ~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~~~~gld~~~~L~I~e~~v~kG~ 151 (215)
++++..+++++||+|+++||++||||+|+||+.||+|+|+|+|+.|+++|+||.+||++++|+| +|+|||++++||+|+
T Consensus 9 ~~~A~~~~ir~SpkK~r~va~~IRG~~v~~A~~~L~~~pkk~a~~i~klL~sA~aNA~~~~gld-~d~L~I~~i~v~~G~ 87 (117)
T CHL00034 9 EVYALAKYIRMSAHKARRVIDQIRGRSYEEALMILEFMPYRACYPILKLVYSAAANASHNMGLN-KANLFISKAEVDEGP 87 (117)
T ss_pred eEEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHHHCcHHHHHHHHHHHHHHHHHHHHccCCC-ccceEEEEEEECCCC
Confidence 4566699999999999999999999999999999999999999999999999999998889999 699999999999999
Q ss_pred ccccccccCCCCcccccccceeEEEEEee
Q psy7141 152 VIKGMRRHARVRMGRVEYKYCTYFVRLEE 180 (215)
Q Consensus 152 ~lKRir~rArGRa~~i~k~~~HI~VvL~E 180 (215)
++||++||||||++++++++|||+|+|+|
T Consensus 88 ~~KR~~prArGRa~~i~k~~sHI~Vvl~e 116 (117)
T CHL00034 88 TLKRFRPRAQGRSYPIKKPTCHITIVLKD 116 (117)
T ss_pred ccCCCCcccCCCCCcccCCCccEEEEEec
Confidence 99999999999999999999999999987
No 4
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=100.00 E-value=1.6e-37 Score=241.17 Aligned_cols=102 Identities=31% Similarity=0.381 Sum_probs=99.4
Q ss_pred cccccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhHHhCCCCCCCCEEEEEEEecCCccccc
Q psy7141 76 FKEKIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAVKDHNVEFKSNLWVAESFVLKDIVIKG 155 (215)
Q Consensus 76 ~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~~~~gld~~~~L~I~e~~v~kG~~lKR 155 (215)
..+++++||+|+++||++||||+|+||+.||+|+|+|+|+.|+++|+||.+||++++|+| +|+|||+|++||+|+++||
T Consensus 2 ~~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 2 KARFVRISPRKARLVADLIRGKSVSQALDILRFTPKKAAPLIKKVLASAIANAEHNYGLD-ADNLVVVTIFVDEGPTLKR 80 (103)
T ss_pred cccccccCHHHHHHHHHHHcCCcHHHHHHHHhhCCHhHHHHHHHHHHHHHHHHHHccCCC-hHheEEEEEEECCCCcccC
Confidence 478999999999999999999999999999999999999999999999999998889999 7999999999999999999
Q ss_pred ccccCCCCcccccccceeEEEEE
Q psy7141 156 MRRHARVRMGRVEYKYCTYFVRL 178 (215)
Q Consensus 156 ir~rArGRa~~i~k~~~HI~VvL 178 (215)
++||||||++++++++|||+|+|
T Consensus 81 ~~~rarGRa~~i~k~~~hi~vvl 103 (103)
T TIGR01044 81 IRPRAKGRASRIRKRTSHITVVV 103 (103)
T ss_pred CCCCCCCCCCcccCCCccEEEeC
Confidence 99999999999999999999986
No 5
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-37 Score=247.78 Aligned_cols=112 Identities=28% Similarity=0.333 Sum_probs=107.0
Q ss_pred CccCccceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhHHhCCCCCCCCEEEEE
Q psy7141 65 GEERRPAFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAVKDHNVEFKSNLWVAE 144 (215)
Q Consensus 65 ~~~~r~~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~~~~gld~~~~L~I~e 144 (215)
..++++. .+++++||+|+++||++||||++++|+.+|+|+|+|+|+.|.++|+||++||++++||| +|+|||.|
T Consensus 8 ~~~akA~-----~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~~~pkKaa~~v~KvL~sA~aNAe~n~gLd-~d~L~V~~ 81 (120)
T COG0091 8 EMEAKAK-----ARYLRISPKKARLVADLIRGKKVAEALAILEFVPKKAAKLVKKVLESAIANAENNKGLD-PDKLVVSH 81 (120)
T ss_pred hhhhHhh-----hccCcCChHHHHHHHHHHcCCcHHHHHHHHHhChHHHHHHHHHHHHHHHhhHHhccCCC-hHHEEEEE
Confidence 3455666 99999999999999999999999999999999999999999999999999999889999 79999999
Q ss_pred EEecCCcccccccccCCCCcccccccceeEEEEEeeCC
Q psy7141 145 SFVLKDIVIKGMRRHARVRMGRVEYKYCTYFVRLEEGK 182 (215)
Q Consensus 145 ~~v~kG~~lKRir~rArGRa~~i~k~~~HI~VvL~E~~ 182 (215)
++||+|+++||++|||+||++++++++|||+|+|+|.+
T Consensus 82 i~v~~gp~lKR~~pRA~GRa~~i~k~tshItvvv~e~~ 119 (120)
T COG0091 82 IAVDKGPVLKRFMPRARGRATRINKRTSHITVVVREKE 119 (120)
T ss_pred EEeCCCceeeeecccccCccccccCCCceEEEEEeecC
Confidence 99999999999999999999999999999999999965
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=100.00 E-value=2.1e-36 Score=234.16 Aligned_cols=104 Identities=37% Similarity=0.490 Sum_probs=100.6
Q ss_pred cccccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhHHhCCCCCCCCEEEEEEEecCCccccc
Q psy7141 76 FKEKIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAVKDHNVEFKSNLWVAESFVLKDIVIKG 155 (215)
Q Consensus 76 ~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~~~~gld~~~~L~I~e~~v~kG~~lKR 155 (215)
..+++++||||++++|++||||+++||+.||+|+|+|+|+.|+++|++|.+||++++|+| +|+|||++++||+|+++||
T Consensus 2 ~~~~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 2 KLRNIRISPKKLREVARLIRGMSVDEAIAQLKFVPKKAAKFILKLLKSAIANAENNKGLD-PDNLYISEIWVNKGPYLKR 80 (105)
T ss_dssp EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHCTST-CGGEEEEEEEEEEEEEEEE
T ss_pred ccccccCCHHHHHHHHHHHcCCCHHHHHHHHHhCcHHHHHHHHhhHHHHHhhcccccccc-cCceEEEEEEEEecccccC
Confidence 368999999999999999999999999999999999999999999999999999889999 7999999999999999999
Q ss_pred ccccCCCCcccccccceeEEEEEee
Q psy7141 156 MRRHARVRMGRVEYKYCTYFVRLEE 180 (215)
Q Consensus 156 ir~rArGRa~~i~k~~~HI~VvL~E 180 (215)
++||||||++++++++|||+|+|+|
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 7
>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=3.7e-35 Score=227.04 Aligned_cols=104 Identities=33% Similarity=0.378 Sum_probs=100.4
Q ss_pred eccccccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhHHhCCCCCCCCEEEEEEEecCCccc
Q psy7141 74 CHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAVKDHNVEFKSNLWVAESFVLKDIVI 153 (215)
Q Consensus 74 ~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~~~~gld~~~~L~I~e~~v~kG~~l 153 (215)
+++.+++++||+|++++|++||||+++||+.||+|+++|+|+.|+++|+||.+||++++++| +++|||++++||+|+++
T Consensus 2 ~a~~~~i~~S~kK~~~v~~~Irg~~v~~A~~~L~~~~kk~a~~i~k~l~sa~~nA~~~~~~~-~~~L~I~~~~v~~g~~~ 80 (105)
T cd00336 2 KAKGRYLRISPKKARLVARLIRGMSVDEALAQLEFVPKKAAKIILKLLKSAEANAENNGLDD-PDKLYIKHIQVNKGPTL 80 (105)
T ss_pred EEEEccCccCHHHHHHHHHHHcCCcHHHHHHHHHhCCHHHHHHHHHHHHHHHHhHHHcCCCC-ccceEEEEEEECCCCcc
Confidence 56689999999999999999999999999999999999999999999999999999877777 79999999999999999
Q ss_pred ccccccCCCCcccccccceeEEEEE
Q psy7141 154 KGMRRHARVRMGRVEYKYCTYFVRL 178 (215)
Q Consensus 154 KRir~rArGRa~~i~k~~~HI~VvL 178 (215)
||++||||||++++++++|||+|+|
T Consensus 81 kr~~~rarGR~~~~~k~~~hi~ivl 105 (105)
T cd00336 81 KRRRPRARGRANPIRKRTCHITVVL 105 (105)
T ss_pred cCCCcCCCCCCcccccCceeEEEeC
Confidence 9999999999999999999999986
No 8
>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=2.8e-33 Score=230.55 Aligned_cols=106 Identities=21% Similarity=0.092 Sum_probs=102.0
Q ss_pred eccccccccCHHHHHHHHHHHcCCCHHHHHHHHcc--------------------------------CcccchHHHHHHH
Q psy7141 74 CHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGY--------------------------------VAKKGAPFIRDTI 121 (215)
Q Consensus 74 ~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f--------------------------------~pKKaA~~I~kvL 121 (215)
.++.+++++||+|+++||++||||++++|+.+|+| +|+|+|+.|+++|
T Consensus 13 kA~~~~~riS~kk~r~va~~IrG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~~~gR~P~Kaa~~i~klL 92 (150)
T TIGR01038 13 KARGRNLRVSFKNARETARAIRGMELDKARKYLEDVIEMKRAVPFRRYNGKVGHRRGLKEWGWTAGRYPVKAAKFILKVL 92 (150)
T ss_pred EEEeCCCcccHHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccccCCCchHHHHHHHHHH
Confidence 45599999999999999999999999999999999 8999999999999
Q ss_pred HHHHHHhHHhCCCCCCCCEEEEEEEecCCcccccccccCCCCcccccccceeEEEEEeeC
Q psy7141 122 LEAQEMAVKDHNVEFKSNLWVAESFVLKDIVIKGMRRHARVRMGRVEYKYCTYFVRLEEG 181 (215)
Q Consensus 122 ~sA~aNA~~~~gld~~~~L~I~e~~v~kG~~lKRir~rArGRa~~i~k~~~HI~VvL~E~ 181 (215)
+||.+||++ +|+| .|+|||.+++||+|+.+||++|||+||++++++++|||+|+|+|+
T Consensus 93 ~sA~aNA~~-~gld-~d~L~I~~i~vnkg~~~kR~~prA~GRa~~~~k~~~HI~Iil~e~ 150 (150)
T TIGR01038 93 QNAEANAEY-KGLD-VEKLVIIHIQANKGPKIRRWMPRAFGRATPYNSSPTHIELVVEEK 150 (150)
T ss_pred HHHHHHHHh-cCCC-hhHeEEEEEEECCCCccCCCCCccCCCCCcccCCCceEEEEEecC
Confidence 999999985 8999 699999999999999999999999999999999999999999874
No 9
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=100.00 E-value=5.3e-33 Score=229.59 Aligned_cols=108 Identities=25% Similarity=0.168 Sum_probs=103.2
Q ss_pred eeccccccccCHHHHHHHHHHHcCCCHHHHHHHHcc------------------------------CcccchHHHHHHHH
Q psy7141 73 VCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGY------------------------------VAKKGAPFIRDTIL 122 (215)
Q Consensus 73 v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f------------------------------~pKKaA~~I~kvL~ 122 (215)
+.+..+++++||+|+++||++||||+++||+.+|+| +|+|+|+.|+++|+
T Consensus 16 akA~~~~~rvS~kk~r~va~~IRG~~v~~A~~~L~~V~~~k~~vPf~r~~~~~g~~~~~~~~~~gr~PkKaa~~i~KlL~ 95 (153)
T PRK04223 16 AKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRAVPFKRHNKKVGHRKGIDGWPAGRYPVKAAKAFLKLLE 95 (153)
T ss_pred EEEEeCCCccChHHHHHHHHHHcCCcHHHHHHHHHHHHhcccccceeeecCCccccccccccccCCCchHHHHHHHHHHH
Confidence 345599999999999999999999999999999999 89999999999999
Q ss_pred HHHHHhHHhCCCCCCCCEEEEEEEecCCcccccccccCCCCcccccccceeEEEEEeeCC
Q psy7141 123 EAQEMAVKDHNVEFKSNLWVAESFVLKDIVIKGMRRHARVRMGRVEYKYCTYFVRLEEGK 182 (215)
Q Consensus 123 sA~aNA~~~~gld~~~~L~I~e~~v~kG~~lKRir~rArGRa~~i~k~~~HI~VvL~E~~ 182 (215)
||++||++ +|+| .|+|||.+++||+|+.+||++|||+||++++.+++|||+|+|+|.+
T Consensus 96 sA~aNA~~-~gld-~d~L~I~~i~v~kg~~~kR~~prA~GRa~~~~k~~sHI~Iil~e~~ 153 (153)
T PRK04223 96 NAEANAEY-KGLD-TEKLVIVHIAAHKGRVIKGYMPRAFGRATPKNTETVNIEVILEEVE 153 (153)
T ss_pred HHHHHHHh-cCCC-hhHeEEEEEEECCCCCCCCcCcccCCCCCcccCCCceEEEEEEeCC
Confidence 99999985 8999 6999999999999999999999999999999999999999999864
No 10
>PTZ00178 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=4.9e-33 Score=234.86 Aligned_cols=115 Identities=14% Similarity=0.059 Sum_probs=107.9
Q ss_pred eccccccccCHHHHHHHHHHHcCCCHHHHHHHHcc--------------------------------CcccchHHHHHHH
Q psy7141 74 CHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGY--------------------------------VAKKGAPFIRDTI 121 (215)
Q Consensus 74 ~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f--------------------------------~pKKaA~~I~kvL 121 (215)
.++.+++++||+|+++||++||||++++|+.+|+| +|+|+|..|+++|
T Consensus 16 kA~~~~~riSpkk~r~Va~~IRGk~v~~A~~~L~~Vi~~k~~VPf~r~~~~vgh~~~~~~~~~~~GR~P~KaA~~i~KlL 95 (181)
T PTZ00178 16 KAKGSDLRVHFKNTYETARAIKGMKLARAQKYLEDVLAKKRCVPFRRFNGGVGRTAQAKEFGHTQGRWPEKSVKFVLSLL 95 (181)
T ss_pred EEEeCCcccchHHHHHHHHHHcCCcHHHHHHHHHHHHhccccccceeecCCccccccccccccccCcCcHHHHHHHHHHH
Confidence 34499999999999999999999999999999997 8999999999999
Q ss_pred HHHHHHhHHhCCCCCCCCEEEEEEEecCCcccccccccCCCCcccccccceeEEEEEeeCCCCCCCcCC
Q psy7141 122 LEAQEMAVKDHNVEFKSNLWVAESFVLKDIVIKGMRRHARVRMGRVEYKYCTYFVRLEEGKPPKNYYWT 190 (215)
Q Consensus 122 ~sA~aNA~~~~gld~~~~L~I~e~~v~kG~~lKRir~rArGRa~~i~k~~~HI~VvL~E~~~p~~~y~~ 190 (215)
+||.+||+ ++|+| +|+|||.+++||+|+++||++|||+||+++|++++|||+|+|+|.+...+.+..
T Consensus 96 ~SA~aNAe-~~gld-~d~L~I~~i~v~kG~~lKR~~pRA~GRA~~i~k~t~HI~Ivl~e~~~~~~~~~~ 162 (181)
T PTZ00178 96 KNAEANAE-AKGLD-VEKLVISHVQVNRAPRGRRRTYRAHGRINPFMSSPCHIELIATEKDETVPKPKE 162 (181)
T ss_pred HHHHHHHH-hcCCC-hhHeEEEEEEECCCcccCCCCCccCCCcCcccCCceeEEEEEEEcccccccchh
Confidence 99999999 69999 699999999999999999999999999999999999999999998777765543
No 11
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=99.98 E-value=1.2e-32 Score=248.50 Aligned_cols=112 Identities=16% Similarity=0.148 Sum_probs=106.0
Q ss_pred eeccccccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhH-HhCCCCCCCCEEEEEEEecCCc
Q psy7141 73 VCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAV-KDHNVEFKSNLWVAESFVLKDI 151 (215)
Q Consensus 73 v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~-~~~gld~~~~L~I~e~~v~kG~ 151 (215)
+.++.+++++||+|+++||++||||++++|+.+|+|+|+|+|..|+++|+||.+||+ +++|+| .|+|||.+++||+|+
T Consensus 3 akA~~r~iriSpkK~R~Va~~IRGk~v~~Al~~L~~~PkKaA~~I~KlLkSA~ANAe~~n~gld-~d~L~I~~~~VdkGp 81 (311)
T PRK12279 3 NKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILSNTPKKFAPIVLKLLNSAISNVQHNSKDMD-PSKLYIYKIVANQGP 81 (311)
T ss_pred eEEEeCCcccCHHHHHHHHHHHcCCcHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhcCCC-hhHeEEEEEEECCCC
Confidence 455699999999999999999999999999999999999999999999999999999 579999 699999999999999
Q ss_pred ccccccccCCCCcccccccceeEEEEEeeCCCCC
Q psy7141 152 VIKGMRRHARVRMGRVEYKYCTYFVRLEEGKPPK 185 (215)
Q Consensus 152 ~lKRir~rArGRa~~i~k~~~HI~VvL~E~~~p~ 185 (215)
.+||++||||||+++|++++|||+|+|.|..++.
T Consensus 82 ~lKR~~PRArGRA~~i~KrtsHItIvl~e~~~~~ 115 (311)
T PRK12279 82 TMKRTLPRAKGSADQLFKRTTHLEIVLSDDVNER 115 (311)
T ss_pred cccCCCCccCCCCCcccCCCccEEEEEecCCchh
Confidence 9999999999999999999999999999866543
No 12
>KOG3353|consensus
Probab=99.59 E-value=4.1e-17 Score=137.30 Aligned_cols=112 Identities=17% Similarity=0.081 Sum_probs=104.6
Q ss_pred ccccccccCHHHHHHHHHHHcCCCHHHHHHHHcc--------------------------------CcccchHHHHHHHH
Q psy7141 75 HFKEKIKYSPDKMWYIACLIRGMSVDQALIQLGY--------------------------------VAKKGAPFIRDTIL 122 (215)
Q Consensus 75 ~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~f--------------------------------~pKKaA~~I~kvL~ 122 (215)
.++.++++|+|..++.+..|+++++..|+..|.. +|+|+|+.++.+|+
T Consensus 11 arg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkksaefll~~Lk 90 (175)
T KOG3353|consen 11 ARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKKSAEFLLHMLK 90 (175)
T ss_pred cccccEEEEeccCcccchhhcCcccccceeeeccchhhcccccceecCCCcCccchhhhhccccCcccchHHHHHHHHHH
Confidence 3489999999999999999999999999999862 79999999999999
Q ss_pred HHHHHhHHhCCCCCCCCEEEEEEEecCCcccccccccCCCCcccccccceeEEEEEeeCCCCCCCc
Q psy7141 123 EAQEMAVKDHNVEFKSNLWVAESFVLKDIVIKGMRRHARVRMGRVEYKYCTYFVRLEEGKPPKNYY 188 (215)
Q Consensus 123 sA~aNA~~~~gld~~~~L~I~e~~v~kG~~lKRir~rArGRa~~i~k~~~HI~VvL~E~~~p~~~y 188 (215)
+|..||+. +|+|+ |.|+|.++.||+++.+.+.+|||+||.+++.+.+|||++||+|+++.+++-
T Consensus 91 N~esnaEl-kgldV-DsLvIehiqvnkApKm~~rtyraHg~in~y~ssP~hie~il~~ke~~v~k~ 154 (175)
T KOG3353|consen 91 NAESNAEL-KGLDV-DSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQIVPKP 154 (175)
T ss_pred hhhhcccc-cCcCc-ceeEeeehhhcccchhhhHHHHhhcccccccCChHHHHHHHHhhcccCCCh
Confidence 99999995 89995 999999999999999999999999999999999999999999998877653
No 13
>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=67.25 E-value=27 Score=26.52 Aligned_cols=41 Identities=27% Similarity=0.148 Sum_probs=33.9
Q ss_pred CccceeeccccccccCHHHHHHHHHHH-----cCCCHHHHHHHHcc
Q psy7141 68 RRPAFVCHFKEKIKYSPDKMWYIACLI-----RGMSVDQALIQLGY 108 (215)
Q Consensus 68 ~r~~~v~~~~~~ir~SpkK~~~va~~I-----RGm~vdeAl~qL~f 108 (215)
-+|.||.......--..-.+--++++| .|+++++.+.+|+-
T Consensus 21 g~p~Evf~~~~~~Gg~~~~~~ai~rliS~~Lr~G~~~~~ii~~L~g 66 (95)
T PF12637_consen 21 GRPFEVFINVGKAGGCSGNLEAIARLISLALRSGVPPEEIIDQLRG 66 (95)
T ss_pred CcceEEEEecCcCCCchHHHHHHHHHHHHHHHcCCCHHHHHHHhcC
Confidence 367888776665555578899999999 99999999999984
No 14
>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=59.98 E-value=26 Score=27.60 Aligned_cols=62 Identities=11% Similarity=-0.050 Sum_probs=46.7
Q ss_pred ccceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHc---------c--CcccchHHHHHHHHHHHHHhHH
Q psy7141 69 RPAFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLG---------Y--VAKKGAPFIRDTILEAQEMAVK 130 (215)
Q Consensus 69 r~~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~---------f--~pKKaA~~I~kvL~sA~aNA~~ 130 (215)
+=.++.+...-.-+|--=+-.++.+|.|++++||..+.. + ...+.|....++|+.|..+...
T Consensus 46 ~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 46 IIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYRE 118 (121)
T ss_pred EEEEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhhhHHHHHHHcCCCcccCHHHHHHHHHHHHHHHHHHh
Confidence 445566667777777778889999999999999887664 1 2345677888888888887654
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=44.91 E-value=41 Score=26.51 Aligned_cols=61 Identities=15% Similarity=-0.062 Sum_probs=44.8
Q ss_pred ccceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHc--------cCc--ccchHHHHHHHHHHHHHhH
Q psy7141 69 RPAFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLG--------YVA--KKGAPFIRDTILEAQEMAV 129 (215)
Q Consensus 69 r~~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~--------f~p--KKaA~~I~kvL~sA~aNA~ 129 (215)
+=.++.+...-.-+|--=+-.++.+|.|++++||...-. +-| .+.|....++|+.|+.+..
T Consensus 50 ~I~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~l~~~al~~a~~~y~ 120 (124)
T TIGR01999 50 IIEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKNTEIAKELSLPPVKLHCSLLAEDAIKAAIKDYK 120 (124)
T ss_pred eEEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhccHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHH
Confidence 344556666666777777889999999999999987653 123 3467778888888887765
No 16
>PRK11325 scaffold protein; Provisional
Probab=43.53 E-value=50 Score=26.23 Aligned_cols=61 Identities=11% Similarity=-0.073 Sum_probs=45.1
Q ss_pred ccceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHc-----c---Cc--ccchHHHHHHHHHHHHHhH
Q psy7141 69 RPAFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLG-----Y---VA--KKGAPFIRDTILEAQEMAV 129 (215)
Q Consensus 69 r~~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~-----f---~p--KKaA~~I~kvL~sA~aNA~ 129 (215)
+=..+.+...-.-+|-==+-.++.+|.|++++||...-. + .| .+.|....++|+.|+.+..
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~~~i~~~lg~p~~r~~CA~la~~al~~a~~~y~ 122 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYK 122 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHcCCCcccchHHHHHHHHHHHHHHHHH
Confidence 444556666667777777889999999999999987653 1 22 4467778888888887765
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=41.37 E-value=28 Score=25.47 Aligned_cols=44 Identities=16% Similarity=0.048 Sum_probs=32.3
Q ss_pred HHHHHHHHHcCCCHHHHHHHHccCcccchHHHHHHHHHHHHHhH
Q psy7141 86 KMWYIACLIRGMSVDQALIQLGYVAKKGAPFIRDTILEAQEMAV 129 (215)
Q Consensus 86 K~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I~kvL~sA~aNA~ 129 (215)
....++..+.+|+.|+|...|...|..-...|+..|........
T Consensus 50 ~~~~~a~il~~m~~dd~~~ll~~L~~~~~~~il~~l~~~~~~~i 93 (102)
T PF03448_consen 50 SPEEAAEILAEMDSDDAADLLEELPEEQREKILAALDEEEREEI 93 (102)
T ss_dssp -HHHHHHHHCCS-HHHHHHHHCCSHHHHHHHHHHCS-HHHHHHH
T ss_pred CHHHHHHHHHccChHHHHHHHHHCCHHHHHHHHHcCCHHHHHHH
Confidence 34567778889999999999999998888777777765554443
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=31.57 E-value=95 Score=24.34 Aligned_cols=60 Identities=17% Similarity=0.046 Sum_probs=39.7
Q ss_pred ceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHH--------c-cC--cccchHHHHHHHHHHHHHhHH
Q psy7141 71 AFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQL--------G-YV--AKKGAPFIRDTILEAQEMAVK 130 (215)
Q Consensus 71 ~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL--------~-f~--pKKaA~~I~kvL~sA~aNA~~ 130 (215)
..+.+...--.+|--=+-.++.+|.|++++||..+- . +. ....+.....+|..|+.+-..
T Consensus 52 ~d~~f~~~GC~~~~Asas~~~~~i~gk~l~ea~~i~~~~i~~~l~~~~~~~~~~~~l~~~al~~av~~y~~ 122 (126)
T PF01592_consen 52 KDAKFQGFGCAISIASASMMCELIKGKTLEEALKITAEDIEEALGGLPPERQHCAELADDALKAAVADYPA 122 (126)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHTTSBHHHHHCHHHHHHHHHHTC-CGTCGHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEeecChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHh
Confidence 344555555666777788999999999999995332 1 12 223355667778887776543
No 19
>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=29.75 E-value=31 Score=23.23 Aligned_cols=14 Identities=36% Similarity=0.437 Sum_probs=9.1
Q ss_pred HcCCCHHHHHHHHc
Q psy7141 94 IRGMSVDQALIQLG 107 (215)
Q Consensus 94 IRGm~vdeAl~qL~ 107 (215)
+.||++++|..+|+
T Consensus 6 ~~g~~~~~a~~~l~ 19 (63)
T PF03793_consen 6 LVGMTYDEAKSILE 19 (63)
T ss_dssp TTTSBHHHHHHHHH
T ss_pred cCCCcHHHHHHHHH
Confidence 45777777766654
No 20
>PF13852 DUF4197: Protein of unknown function (DUF4197)
Probab=29.06 E-value=86 Score=27.26 Aligned_cols=19 Identities=26% Similarity=0.226 Sum_probs=17.0
Q ss_pred HHHHHHcCCCHHHHHHHHc
Q psy7141 89 YIACLIRGMSVDQALIQLG 107 (215)
Q Consensus 89 ~va~~IRGm~vdeAl~qL~ 107 (215)
.+.+.|+.|+++||..+|.
T Consensus 85 if~~AI~~Ms~~DA~~IL~ 103 (202)
T PF13852_consen 85 IFVDAIKSMSIQDAKGILN 103 (202)
T ss_pred HHHHHHHhCCHHhHHHHhc
Confidence 4568899999999999997
No 21
>PF14804 Jag_N: Jag N-terminus; PDB: 3GKU_B.
Probab=26.89 E-value=1.2e+02 Score=20.63 Aligned_cols=47 Identities=23% Similarity=0.099 Sum_probs=23.4
Q ss_pred HHHHHHHHHhHHhCCCCCCCCEEEEEEEecCCcccccccccCCCCcccccccceeEEEEE
Q psy7141 119 DTILEAQEMAVKDHNVEFKSNLWVAESFVLKDIVIKGMRRHARVRMGRVEYKYCTYFVRL 178 (215)
Q Consensus 119 kvL~sA~aNA~~~~gld~~~~L~I~e~~v~kG~~lKRir~rArGRa~~i~k~~~HI~VvL 178 (215)
+.+++|++.|....|+. .++|-|.=+.-+ .+|-+| +.++...|.|.+
T Consensus 5 kt~eeAi~~A~~~l~~~-~~~~~~eVi~~g-----------~kGf~G-~g~k~a~I~v~~ 51 (52)
T PF14804_consen 5 KTVEEAIEKALKELGVP-REELEYEVIEEG-----------KKGFFG-FGKKPAKIRVTI 51 (52)
T ss_dssp SSHHHHHHHHHHHTT---GGGEEEEEEE-------------B---------B-EEEEEEE
T ss_pred CCHHHHHHHHHHHhCCC-hHHEEEEEEEcC-----------CCcEEe-ecceeEEEEEEE
Confidence 35778889998889998 688866544332 123344 445666666554
No 22
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=24.36 E-value=71 Score=26.38 Aligned_cols=33 Identities=18% Similarity=0.062 Sum_probs=25.9
Q ss_pred eccccccccCHHHHHHHHHHHcCCCHHHHHHHH
Q psy7141 74 CHFKEKIKYSPDKMWYIACLIRGMSVDQALIQL 106 (215)
Q Consensus 74 ~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL 106 (215)
.+...-.-+|--=+-.++.+|.|++++||+...
T Consensus 58 ~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 58 KFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred EeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 444555566666678899999999999999877
No 23
>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=24.28 E-value=1.5e+02 Score=27.05 Aligned_cols=60 Identities=10% Similarity=-0.034 Sum_probs=43.8
Q ss_pred ceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHc------c---Cc--ccchHHHHHHHHHHHHHhHH
Q psy7141 71 AFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLG------Y---VA--KKGAPFIRDTILEAQEMAVK 130 (215)
Q Consensus 71 ~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~------f---~p--KKaA~~I~kvL~sA~aNA~~ 130 (215)
..+.+...---+|--=+-.++.+|.|++++||+.+.. | .| .+-|....++|+.|+++...
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 3445555555666666789999999999999987763 2 23 34576778999999888864
No 24
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=24.17 E-value=81 Score=27.82 Aligned_cols=21 Identities=24% Similarity=0.474 Sum_probs=17.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHH
Q psy7141 86 KMWYIACLIRGMSVDQALIQL 106 (215)
Q Consensus 86 K~~~va~~IRGm~vdeAl~qL 106 (215)
=+|+||.-++||+++||-..-
T Consensus 157 sT~~vAk~l~G~~~~d~~~~~ 177 (217)
T PF02593_consen 157 STWFVAKRLIGKEVEDAPEKA 177 (217)
T ss_pred cHHHHHHHhcCCccchhhhhh
Confidence 379999999999999987543
No 25
>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=23.48 E-value=76 Score=24.26 Aligned_cols=55 Identities=15% Similarity=0.112 Sum_probs=39.5
Q ss_pred ccccCHHHHHHHHHHHcCCCHHHHHHHHccCcccchHHH----HHHHHHHHHHhHHhCC
Q psy7141 79 KIKYSPDKMWYIACLIRGMSVDQALIQLGYVAKKGAPFI----RDTILEAQEMAVKDHN 133 (215)
Q Consensus 79 ~ir~SpkK~~~va~~IRGm~vdeAl~qL~f~pKKaA~~I----~kvL~sA~aNA~~~~g 133 (215)
.|--|.|..-+..+--+|-+..-|+..|.|+-.+|.+.+ .++|+.|...-...+|
T Consensus 27 ~IA~SLk~Sae~S~RRk~~pf~SAMSML~FYINRAGk~L~~~rr~~LE~AK~eLR~~fG 85 (86)
T PF11373_consen 27 KIAASLKRSAEHSRRRKATPFRSAMSMLNFYINRAGKNLPKERRAVLERAKDELRKAFG 85 (86)
T ss_pred HHHHHHHHHHHhhcccCCCchHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHhC
Confidence 344566666666677789999999999999888886655 5677777665544333
No 26
>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=23.12 E-value=88 Score=24.08 Aligned_cols=39 Identities=23% Similarity=0.113 Sum_probs=31.2
Q ss_pred ccceeeccccccccCHHHHHHHHHHHcCCCHHHHHHHHc
Q psy7141 69 RPAFVCHFKEKIKYSPDKMWYIACLIRGMSVDQALIQLG 107 (215)
Q Consensus 69 r~~~v~~~~~~ir~SpkK~~~va~~IRGm~vdeAl~qL~ 107 (215)
+=..+.+...---+|--=+-.++.++.|++++||...+.
T Consensus 47 ~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 47 RITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred EEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 344556666777777778889999999999999998875
No 27
>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=22.58 E-value=1e+02 Score=22.20 Aligned_cols=21 Identities=33% Similarity=0.469 Sum_probs=16.6
Q ss_pred HHHHHHHcCCCHHHHHHHHcc
Q psy7141 88 WYIACLIRGMSVDQALIQLGY 108 (215)
Q Consensus 88 ~~va~~IRGm~vdeAl~qL~f 108 (215)
..||..|+|+|+++-..++..
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 467899999999999988864
No 28
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=20.43 E-value=2e+02 Score=21.93 Aligned_cols=37 Identities=27% Similarity=0.232 Sum_probs=27.5
Q ss_pred HHHHHHHhHHhCCCCCC-CCEEEEEEEecCCccccccc
Q psy7141 121 ILEAQEMAVKDHNVEFK-SNLWVAESFVLKDIVIKGMR 157 (215)
Q Consensus 121 L~sA~aNA~~~~gld~~-~~L~I~e~~v~kG~~lKRir 157 (215)
-.++...|.+++|+..+ ++.=.-|+.|+.|..+|..|
T Consensus 25 a~evv~lal~eFgi~~~s~~~sLceVtV~~~g~IKQrR 62 (85)
T cd01785 25 AHEVVMLALQEFGITAPSSNFSLCEVSVTPGGVIKQRR 62 (85)
T ss_pred HHHHHHHHHHHhCCCCCccceEEEEEEecCCceeeecc
Confidence 34666778888998743 66677899999999887544
Done!