Query 044569
Match_columns 116
No_of_seqs 138 out of 1052
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:35:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044569hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00030 rpl23 ribosomal prote 99.9 8.5E-24 1.8E-28 148.7 6.9 76 22-113 2-90 (93)
2 PRK05738 rplW 50S ribosomal pr 99.9 9.4E-23 2E-27 142.3 6.3 74 23-111 3-89 (92)
3 PF00276 Ribosomal_L23: Riboso 99.9 3E-22 6.4E-27 139.0 4.2 75 22-111 2-89 (91)
4 PRK12280 rplW 50S ribosomal pr 99.8 2.1E-21 4.5E-26 148.0 6.2 75 22-112 5-92 (158)
5 COG0089 RplW Ribosomal protein 99.8 2.8E-21 6E-26 136.8 5.8 76 22-112 3-92 (94)
6 PRK14548 50S ribosomal protein 99.6 1.9E-15 4.2E-20 104.8 5.0 57 23-107 4-73 (84)
7 TIGR03636 L23_arch archaeal ri 99.5 8.5E-15 1.8E-19 100.0 5.1 53 27-107 1-66 (77)
8 PTZ00191 60S ribosomal protein 99.5 3.8E-14 8.3E-19 107.0 3.5 61 23-111 65-139 (145)
9 KOG4089 Predicted mitochondria 98.7 3.5E-08 7.7E-13 76.2 5.0 77 35-111 17-113 (165)
10 KOG1751 60s ribosomal protein 97.3 0.00028 6E-09 54.4 3.4 42 51-106 90-145 (157)
11 PF12969 DUF3857: Domain of Un 38.1 88 0.0019 22.2 4.8 70 42-111 14-99 (177)
12 PF10610 Tafi-CsgC: Thin aggre 34.0 43 0.00094 24.5 2.6 21 92-112 77-97 (106)
13 COG3175 COX11 Cytochrome oxida 32.6 1.1E+02 0.0025 24.5 5.0 57 52-110 91-147 (195)
14 PF09143 AvrPphF-ORF-2: AvrPph 30.3 37 0.00081 26.8 1.9 20 94-113 156-175 (175)
15 PF00677 Lum_binding: Lumazine 23.2 53 0.0012 22.0 1.4 15 101-115 33-47 (85)
16 KOG0814 Glyoxylase [General fu 21.3 64 0.0014 26.3 1.7 22 94-115 92-113 (237)
No 1
>CHL00030 rpl23 ribosomal protein L23
Probab=99.90 E-value=8.5e-24 Score=148.73 Aligned_cols=76 Identities=16% Similarity=0.137 Sum_probs=69.9
Q ss_pred eeEEecccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCe
Q 044569 22 EWEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGL 88 (116)
Q Consensus 22 ~~~~~~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~ 88 (116)
+++.+|.+||++... . +.|+|+|+|+++| ||+|.+|||++++||.||+|++
T Consensus 2 ~iI~~PivTEKs~~l---------------~-e~n~y~F~V~~~anK~eIK~avE~lf~VkV~~VNt~~~~~k~kr~~~~ 65 (93)
T CHL00030 2 DGIKYPVFTDKSIRL---------------L-EKNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMGPI 65 (93)
T ss_pred ceeccceeCHHHHHh---------------h-HCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEcCCCccccCCc
Confidence 357789999999887 5 5699999999999 9999999999999999999999
Q ss_pred eeecCCeeEEEEEcCCCCEEeeeee
Q 044569 89 LNAKPDYKKAYVTSPPRTRFRCGRI 113 (116)
Q Consensus 89 ~Gk~~~yKKAyVTL~~G~~Idf~~~ 113 (116)
.|++++||||||||++|++|||-..
T Consensus 66 ~G~~~~~KKAiVtL~~g~~I~~~~~ 90 (93)
T CHL00030 66 MGHKMHYKRMIITLQPGYSIPLFRE 90 (93)
T ss_pred ccccCCcEEEEEEcCCcCEeccccc
Confidence 9999999999999999999998643
No 2
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=99.88 E-value=9.4e-23 Score=142.34 Aligned_cols=74 Identities=27% Similarity=0.348 Sum_probs=69.7
Q ss_pred eEEecccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCee
Q 044569 23 WEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGLL 89 (116)
Q Consensus 23 ~~~~~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~~ 89 (116)
+++.|.+||++... .++.|+|+|.|+++| ||+|.+|||++++||.||+|+..
T Consensus 3 ii~~P~~TEKs~~~---------------~e~~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~VnT~~~~gk~kr~~~~~ 67 (92)
T PRK05738 3 VIKRPVITEKSTLL---------------MEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKTKRFGRRI 67 (92)
T ss_pred cccccccCHHHHHh---------------HHhCCEEEEEECCCCCHHHHHHHHHHHcCCceeEEEEEEeCCceeeecccc
Confidence 57789999999887 677899999999999 99999999999999999999999
Q ss_pred eecCCeeEEEEEcCCCCEEeee
Q 044569 90 NAKPDYKKAYVTSPPRTRFRCG 111 (116)
Q Consensus 90 Gk~~~yKKAyVTL~~G~~Idf~ 111 (116)
|++++||||||||++|++|||-
T Consensus 68 g~~~~~KKA~VtL~~g~~i~~~ 89 (92)
T PRK05738 68 GKRSDWKKAIVTLAEGQKIDFF 89 (92)
T ss_pred cccCCcEEEEEEcCCCCEEecc
Confidence 9999999999999999999984
No 3
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 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 [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=99.86 E-value=3e-22 Score=138.98 Aligned_cols=75 Identities=28% Similarity=0.325 Sum_probs=67.0
Q ss_pred eeEEecccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCe
Q 044569 22 EWEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGL 88 (116)
Q Consensus 22 ~~~~~~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~ 88 (116)
++++.|.+||++... .++.|+|+|+|+++| ||+|.+|||+++.||.+|.|+.
T Consensus 2 ~ii~~p~iTeKs~~~---------------~~~~n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR~g~~ 66 (91)
T PF00276_consen 2 DIIKKPVITEKSMKL---------------LENPNQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKRKGKF 66 (91)
T ss_dssp TTEEEE--SHHHHHH---------------HHHSSEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEESSSC
T ss_pred CEeecceecHhHHHh---------------hhcCCEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceEeCCc
Confidence 467889999998887 778899999999999 9999999999999999999999
Q ss_pred eeecCCeeEEEEEcCCCCEEeee
Q 044569 89 LNAKPDYKKAYVTSPPRTRFRCG 111 (116)
Q Consensus 89 ~Gk~~~yKKAyVTL~~G~~Idf~ 111 (116)
.|++++||||||+|++|+.||+.
T Consensus 67 ~g~~~~~KKaiVtL~~~~~i~~~ 89 (91)
T PF00276_consen 67 VGKTKDYKKAIVTLKEGDKIPLF 89 (91)
T ss_dssp EEEE-EEEEEEEEESTTSCHHHH
T ss_pred cccCCCcEEEEEEeCCCCccccc
Confidence 99999999999999999999874
No 4
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.84 E-value=2.1e-21 Score=147.98 Aligned_cols=75 Identities=21% Similarity=0.137 Sum_probs=68.4
Q ss_pred eeEEecccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCe
Q 044569 22 EWEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGL 88 (116)
Q Consensus 22 ~~~~~~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~ 88 (116)
+++++|.+||++..+ . +.|+|+|.|+++| ||+|.+|||+|++||.||+|++
T Consensus 5 ~iIk~PviTEKs~~l---------------~-e~N~ytF~V~~~anK~eIK~AVE~iF~VkV~~VNT~~~~~K~KR~g~~ 68 (158)
T PRK12280 5 EVIKKPILTEKSYSL---------------M-SKNVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLGRF 68 (158)
T ss_pred hhhhccccCHHHHhh---------------h-hCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEecCCcccccCCc
Confidence 467789999998776 4 4599999999999 9999999999999999999999
Q ss_pred eeecCCeeEEEEEcCCCCEEeeee
Q 044569 89 LNAKPDYKKAYVTSPPRTRFRCGR 112 (116)
Q Consensus 89 ~Gk~~~yKKAyVTL~~G~~Idf~~ 112 (116)
.|++++||||||||++|++|||-.
T Consensus 69 ~G~~~~~KKAiVtL~~g~~I~~f~ 92 (158)
T PRK12280 69 PGFTNSYKKAYVTLAEGYSINLFP 92 (158)
T ss_pred ccccCCcEEEEEECCCCCEeeccC
Confidence 999999999999999999999743
No 5
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=2.8e-21 Score=136.79 Aligned_cols=76 Identities=26% Similarity=0.276 Sum_probs=69.7
Q ss_pred eeEEecccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCC-
Q 044569 22 EWEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGG- 87 (116)
Q Consensus 22 ~~~~~~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~- 87 (116)
.++.+|.+||++... +++.|+|+|.|+++| ||+|.+|||+|++||.||.+.
T Consensus 3 dvI~~PvvTEKa~~l---------------~~~~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNTl~~k~k~KR~~~k 67 (94)
T COG0089 3 DVIKSPVVTEKAMLL---------------MEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGVK 67 (94)
T ss_pred chhhcceecHHHHHh---------------HhhCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEeCCcceEEecc
Confidence 456788999999888 556799999999999 999999999999999999988
Q ss_pred eeeecCCeeEEEEEcCCCCEEeeee
Q 044569 88 LLNAKPDYKKAYVTSPPRTRFRCGR 112 (116)
Q Consensus 88 ~~Gk~~~yKKAyVTL~~G~~Idf~~ 112 (116)
+.|.+++||||||+|++|++||+-+
T Consensus 68 ~~G~~~~~kka~V~l~~G~~i~~~~ 92 (94)
T COG0089 68 RIGLRKDYKKAYVTLKEGQSIDFFG 92 (94)
T ss_pred ccccCcccceeEEEccCCCEEeecc
Confidence 8999999999999999999999854
No 6
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=99.58 E-value=1.9e-15 Score=104.76 Aligned_cols=57 Identities=18% Similarity=0.088 Sum_probs=52.2
Q ss_pred eEEecccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCee
Q 044569 23 WEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGLL 89 (116)
Q Consensus 23 ~~~~~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~~ 89 (116)
++.+|.+||++... .++.|+|+|.|+++| ||+|.+|||++++
T Consensus 4 iI~~PviTEK~~~~---------------~e~~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~---------- 58 (84)
T PRK14548 4 IIKYPLVTEKAMNL---------------IEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITP---------- 58 (84)
T ss_pred chhccccCHHHHHH---------------HHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcC----------
Confidence 57789999999888 777899999999999 9999999999997
Q ss_pred eecCCeeEEEEEcCCCCE
Q 044569 90 NAKPDYKKAYVTSPPRTR 107 (116)
Q Consensus 90 Gk~~~yKKAyVTL~~G~~ 107 (116)
++||||||+|++|++
T Consensus 59 ---~~~KKA~V~L~~g~~ 73 (84)
T PRK14548 59 ---KGEKKAYVKLAEEYD 73 (84)
T ss_pred ---CCcEEEEEEeCCCCc
Confidence 589999999999986
No 7
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=99.54 E-value=8.5e-15 Score=100.04 Aligned_cols=53 Identities=19% Similarity=0.145 Sum_probs=47.0
Q ss_pred cccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCeeeecC
Q 044569 27 SEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGLLNAKP 93 (116)
Q Consensus 27 ~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~~Gk~~ 93 (116)
|.+||++... .++.|+|+|.|+++| ||+|.+|||++++ +
T Consensus 1 P~iTEKs~~~---------------~e~~n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~-------------~ 52 (77)
T TIGR03636 1 PLVTEKAMNL---------------IEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITP-------------R 52 (77)
T ss_pred CcccHHHHHH---------------HHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcC-------------C
Confidence 4677877776 666799999999999 9999999999997 4
Q ss_pred CeeEEEEEcCCCCE
Q 044569 94 DYKKAYVTSPPRTR 107 (116)
Q Consensus 94 ~yKKAyVTL~~G~~ 107 (116)
+||||||||++|++
T Consensus 53 ~~KKA~VtL~~g~~ 66 (77)
T TIGR03636 53 GEKKAYVKLAEEYA 66 (77)
T ss_pred CceEEEEEECCCCc
Confidence 99999999999986
No 8
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=99.46 E-value=3.8e-14 Score=107.04 Aligned_cols=61 Identities=18% Similarity=0.132 Sum_probs=53.2
Q ss_pred eEEecccchhccceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCee
Q 044569 23 WEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGLL 89 (116)
Q Consensus 23 ~~~~~~~~~~~~~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~~ 89 (116)
++..|.+||++... .++.|+|+|.||++| ||+|.+|||++.+|
T Consensus 65 IIk~Pl~TEKa~~~---------------~E~~N~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~--------- 120 (145)
T PTZ00191 65 IIKYPLTTEKAMKK---------------IEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPD--------- 120 (145)
T ss_pred hhhcccccHHHHHH---------------HhhCCEEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCC---------
Confidence 55667777777666 677899999999999 99999999999987
Q ss_pred eecCCeeEEEEEcCCCCE-Eeee
Q 044569 90 NAKPDYKKAYVTSPPRTR-FRCG 111 (116)
Q Consensus 90 Gk~~~yKKAyVTL~~G~~-Idf~ 111 (116)
+||||||+|.+|+. ||++
T Consensus 121 ----g~KKA~V~L~~~~~aidva 139 (145)
T PTZ00191 121 ----GLKKAYIRLSPDVDALDVA 139 (145)
T ss_pred ----CceEEEEEECCCCcHHHHH
Confidence 89999999999987 9886
No 9
>KOG4089 consensus Predicted mitochondrial ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=98.65 E-value=3.5e-08 Score=76.15 Aligned_cols=77 Identities=27% Similarity=0.185 Sum_probs=63.2
Q ss_pred ceeeecCcceeeecCCCccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCC----ccccc-C-CeeeecC-C
Q 044569 35 GKQAAGNLPIKLLMPNTFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGG----KKKKW-G-GLLNAKP-D 94 (116)
Q Consensus 35 ~~vf~pn~~lklv~p~t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~G----K~KR~-g-~~~Gk~~-~ 94 (116)
..||||||||.|++|......++..|.|.+.+ |++|.+|.|....| +.++. . ...-.+. +
T Consensus 17 ~rVf~Pn~~~~l~rp~~~q~p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~Gk~~~~~k~r~~~~k~i~kdmd 96 (165)
T KOG4089|consen 17 LRVFFPNFWINLVRPLVTQPPKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHGKDYKKTKKRLQSPKRIKKDMD 96 (165)
T ss_pred eeEecchhHHhhhcccccCCCceEEEEcchhhccccHHHHHHHhcCCceeeeeeeeeechhhhcceecccccceeecccc
Confidence 67899999999999976678899999999999 99999999999999 33321 1 1223445 9
Q ss_pred eeEEEEEcCCCCEEeee
Q 044569 95 YKKAYVTSPPRTRFRCG 111 (116)
Q Consensus 95 yKKAyVTL~~G~~Idf~ 111 (116)
++=|||.+..|+++.|-
T Consensus 97 ~p~~Yv~~pr~~~~~~P 113 (165)
T KOG4089|consen 97 EPVAYVEEPRGSKFSFP 113 (165)
T ss_pred cceeeecCCCCccccCC
Confidence 99999999999988663
No 10
>KOG1751 consensus 60s ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=97.26 E-value=0.00028 Score=54.37 Aligned_cols=42 Identities=26% Similarity=0.328 Sum_probs=36.6
Q ss_pred CccCCCeEEEEEcCCC-------------CCeEeeEEEEeeCCcccccCCeeeecCCe-eEEEEEcCCCC
Q 044569 51 TFQNIKEIAAKTIPSN-------------GFEVDEARTLNKGGKKKKWGGLLNAKPDY-KKAYVTSPPRT 106 (116)
Q Consensus 51 t~~~~Nqy~F~V~~~A-------------~VkV~~VnTlnv~GK~KR~g~~~Gk~~~y-KKAyVTL~~G~ 106 (116)
..++.|..+|.||..| +++|.+|||++ ++|+ |||||.|.+..
T Consensus 90 k~ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli--------------~p~g~kkayv~la~dy 145 (157)
T KOG1751|consen 90 KIEDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLI--------------RPDGEKKAYVRLAPDY 145 (157)
T ss_pred chhhCceeEEEEecccchHHHHHHHHHHhccchhhheeee--------------cCCCceeEEEecCCch
Confidence 3577899999999998 99999999998 6667 99999999763
No 11
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=38.08 E-value=88 Score=22.17 Aligned_cols=70 Identities=19% Similarity=0.251 Sum_probs=42.1
Q ss_pred cceeeecCCCccCCCeEEEEEcCCC-CCeEeeEEEEeeCCcccccCC--eee----------ecCCeeEEEEEcC---CC
Q 044569 42 LPIKLLMPNTFQNIKEIAAKTIPSN-GFEVDEARTLNKGGKKKKWGG--LLN----------AKPDYKKAYVTSP---PR 105 (116)
Q Consensus 42 ~~lklv~p~t~~~~Nqy~F~V~~~A-~VkV~~VnTlnv~GK~KR~g~--~~G----------k~~~yKKAyVTL~---~G 105 (116)
..++++..+..+..+++.+.-++.. .+++.++.+++-.|+...... +.. .=.+.|-+++.|. .|
T Consensus 14 ~~iki~~~~g~~~~~~~~i~y~~~~~~~~~~~a~v~~~dg~i~~~~~~~i~~~~~~~~~~~~~y~~~~~~~~~~p~v~~G 93 (177)
T PF12969_consen 14 QVIKILNEEGVEDYSEISISYDPDYEKLKIHKARVIRPDGKIDKLDKSDIKDRSAESASEAPIYSDSRTKVFAFPDVRVG 93 (177)
T ss_dssp EEEEE-SHHHHTSGGEEEEEE-TTTEEEEEEEEEEE-TTS-EEE--GGGEEEE--GGGTT-GGGTT-EEEEEE--S--TT
T ss_pred EEEEEcCHHHhhhcceEEEEeCCCCcEEEEEEEEEEcCCCeEEecChHHeEEeecccccccccccCcEEEEEEcCCCCCC
Confidence 3455555555666688988888887 699999999999998554321 111 2267787778765 78
Q ss_pred CEEeee
Q 044569 106 TRFRCG 111 (116)
Q Consensus 106 ~~Idf~ 111 (116)
+.|++.
T Consensus 94 diIe~~ 99 (177)
T PF12969_consen 94 DIIEYS 99 (177)
T ss_dssp -EEEEE
T ss_pred cEEEEE
Confidence 888764
No 12
>PF10610 Tafi-CsgC: Thin aggregative fimbriae synthesis protein; InterPro: IPR014491 Thin aggressive fibres known as curli fibres or fimbriae (curli; Tafi) are cell-surface protein polymers found in Salmonella typhimurium and Escherichia coli that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation []. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), which differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly [].; PDB: 2XSK_A 2Y2T_A 2Y2Y_A.
Probab=34.03 E-value=43 Score=24.53 Aligned_cols=21 Identities=19% Similarity=0.112 Sum_probs=11.3
Q ss_pred cCCeeEEEEEcCCCCEEeeee
Q 044569 92 KPDYKKAYVTSPPRTRFRCGR 112 (116)
Q Consensus 92 ~~~yKKAyVTL~~G~~Idf~~ 112 (116)
-.|+=+-+||+.+|++..+.+
T Consensus 77 p~D~v~I~VtvSDG~sl~Lsq 97 (106)
T PF10610_consen 77 PGDKVKIIVTVSDGKSLHLSQ 97 (106)
T ss_dssp TT-EEEEEEEEE-SSS-EEEE
T ss_pred CCCeEEEEEEEcCCCeEEeEe
Confidence 356666677777776666554
No 13
>COG3175 COX11 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=32.58 E-value=1.1e+02 Score=24.53 Aligned_cols=57 Identities=12% Similarity=-0.019 Sum_probs=36.4
Q ss_pred ccCCCeEEEEEcCCCCCeEeeEEEEeeCCcccccCCeeeecCCeeEEEEEcCCCCEEee
Q 044569 52 FQNIKEIAAKTIPSNGFEVDEARTLNKGGKKKKWGGLLNAKPDYKKAYVTSPPRTRFRC 110 (116)
Q Consensus 52 ~~~~Nqy~F~V~~~A~VkV~~VnTlnv~GK~KR~g~~~Gk~~~yKKAyVTL~~G~~Idf 110 (116)
..+.++..|++...++..+...-|.|+-+.. -|.+..|-.=+==-==+|++|+++++
T Consensus 91 pGet~~~~y~a~N~sd~~itg~A~~nv~P~~--Ag~YF~KveCFCFteq~L~pgE~vem 147 (195)
T COG3175 91 PGETNLIFYEAENLSDKPITGQATYNVAPGQ--AGAYFNKVECFCFTEQTLKPGETVEM 147 (195)
T ss_pred cCceEEEEEEEecCCCCCceeEEecccChhH--hhhheeeeeEEEeeecccCCCCeEec
Confidence 3567899999999999999999999987643 22222211111000126888888774
No 14
>PF09143 AvrPphF-ORF-2: AvrPphF-ORF-2; InterPro: IPR015226 Many Gram-negative pathogenic bacteria directly translocate effector proteins into eukaryotic host cells via a type III secretion system. Type III effector proteins are determinants of virulence on susceptible plant hosts; they are also the proteins that trigger specific disease resistance in resistant plant hosts. Evolution of type III effectors is dominated by competing forces: the likely requirement for conservation of virulence function, the avoidance of host defenses, and possible adaptation to new hosts. Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosylt ransferase toxins []. ; PDB: 1S21_A.
Probab=30.34 E-value=37 Score=26.83 Aligned_cols=20 Identities=20% Similarity=0.076 Sum_probs=11.2
Q ss_pred CeeEEEEEcCCCCEEeeeee
Q 044569 94 DYKKAYVTSPPRTRFRCGRI 113 (116)
Q Consensus 94 ~yKKAyVTL~~G~~Idf~~~ 113 (116)
.-.--||||.+|+++++.-|
T Consensus 156 ~~~~LIvtLP~G~~VPv~Ii 175 (175)
T PF09143_consen 156 LENALIVTLPEGQKVPVEII 175 (175)
T ss_dssp S-EEEEEE--TT-EEE-EE-
T ss_pred ccccEEEECCCCCcccceeC
Confidence 34566999999999998744
No 15
>PF00677 Lum_binding: Lumazine binding domain; InterPro: IPR001783 The following proteins have been shown [, ] to be structurally and evolutionary related: Riboflavin synthase alpha chain (2.5.1.9 from EC) (RS-alpha) (gene ribC in Escherichia coli, ribB in Bacillus subtilis and Photobacterium leiognathi, RIB5 in yeast. This enzyme synthesises riboflavin from two moles of 6,7- dimethyl-8-(1'-D-ribityl)lumazine (Lum), a pteridine-derivative. Photobacterium phosphoreum lumazine protein (LumP) (gene luxL). LumP is a protein that modulates the colour of the bioluminescence emission of bacterial luciferase. In the presence of LumP, light emission is shifted to higher energy values (shorter wavelength). LumP binds non-covalently to 6,7-dimethyl-8-(1'-D-ribityl)lumazine. Vibrio fischeri yellow fluorescent protein (YFP) (gene luxY). Like LumP, YFP modulates light emission but towards a longer wavelength. YFP binds non-covalently to FMN. These proteins seem to have evolved from the duplication of a domain of about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. RS-alpha which binds two molecules of Lum has two perfect copies of this motif, while LumP which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, YFP, which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif.; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process; PDB: 3DDY_A 1KZL_A 3A3G_B 3A35_B 3A3B_B 1I8D_C 1PKV_B 1HZE_B 1I18_B.
Probab=23.24 E-value=53 Score=22.04 Aligned_cols=15 Identities=13% Similarity=0.242 Sum_probs=12.2
Q ss_pred EcCCCCEEeeeeeee
Q 044569 101 TSPPRTRFRCGRICL 115 (116)
Q Consensus 101 TL~~G~~Idf~~~~~ 115 (116)
.+..|++|-++|+||
T Consensus 33 ~~~~g~SIavnGvcL 47 (85)
T PF00677_consen 33 DLKIGGSIAVNGVCL 47 (85)
T ss_dssp TG-TTSEEEETTEEE
T ss_pred hCccCcEEEECCeee
Confidence 366789999999998
No 16
>KOG0814 consensus Glyoxylase [General function prediction only]
Probab=21.32 E-value=64 Score=26.35 Aligned_cols=22 Identities=18% Similarity=0.057 Sum_probs=18.3
Q ss_pred CeeEEEEEcCCCCEEeeeeeee
Q 044569 94 DYKKAYVTSPPRTRFRCGRICL 115 (116)
Q Consensus 94 ~yKKAyVTL~~G~~Idf~~~~~ 115 (116)
.--||=..|.+|+.|+||++-|
T Consensus 92 SGakAD~~l~~Gd~i~~G~~~l 113 (237)
T KOG0814|consen 92 SGAKADLHLEDGDIIEIGGLKL 113 (237)
T ss_pred cccccccccCCCCEEEEccEEE
Confidence 3356778899999999999876
Done!