Query 033167
Match_columns 125
No_of_seqs 132 out of 858
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 10:38:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033167hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0292 RplT Ribosomal protein 100.0 7E-55 1.5E-59 319.8 12.6 106 2-107 13-118 (118)
2 PTZ00030 60S ribosomal protein 100.0 1.9E-54 4.2E-59 320.0 13.7 116 1-116 3-118 (121)
3 TIGR01032 rplT_bact ribosomal 100.0 2.6E-53 5.7E-58 310.8 11.7 102 2-103 12-113 (113)
4 PRK05185 rplT 50S ribosomal pr 100.0 6.9E-53 1.5E-57 308.8 11.9 103 2-104 12-114 (114)
5 CHL00068 rpl20 ribosomal prote 100.0 9.7E-53 2.1E-57 308.6 12.0 102 2-103 13-114 (115)
6 PF00453 Ribosomal_L20: Riboso 100.0 2.6E-51 5.7E-56 297.9 10.8 97 2-98 12-108 (108)
7 PRK14537 50S ribosomal protein 100.0 2.8E-50 6E-55 322.8 12.1 105 2-106 13-117 (230)
8 KOG4707 Mitochondrial/chloropl 100.0 1.8E-37 3.8E-42 235.1 6.6 115 1-115 19-133 (147)
9 COG3514 Uncharacterized protei 68.7 2.4 5.2E-05 30.6 0.9 13 49-61 76-88 (93)
10 PF05225 HTH_psq: helix-turn-h 54.5 11 0.00024 23.0 1.9 21 54-74 19-39 (45)
11 PF03683 UPF0175: Uncharacteri 54.0 16 0.00034 24.5 2.8 27 54-80 37-63 (76)
12 PRK03573 transcriptional regul 53.8 78 0.0017 22.5 6.7 60 45-104 11-72 (144)
13 PRK01905 DNA-binding protein F 50.9 69 0.0015 21.3 5.6 25 53-77 52-76 (77)
14 PF12558 DUF3744: ATP-binding 50.6 37 0.00081 22.7 4.2 45 58-102 5-50 (74)
15 PF00126 HTH_1: Bacterial regu 46.1 13 0.00029 23.2 1.4 31 52-82 14-44 (60)
16 PF07818 HCNGP: HCNGP-like pro 44.9 29 0.00063 24.6 3.1 37 66-103 18-54 (96)
17 PF01527 HTH_Tnp_1: Transposas 42.5 24 0.00051 22.4 2.2 24 52-75 24-47 (76)
18 PF11333 DUF3135: Protein of u 40.1 31 0.00067 24.0 2.6 21 83-103 8-28 (83)
19 PF13404 HTH_AsnC-type: AsnC-t 39.1 33 0.00072 20.6 2.3 25 78-102 3-27 (42)
20 PF03050 DDE_Tnp_IS66: Transpo 37.3 52 0.0011 25.9 3.8 54 60-113 18-71 (271)
21 PF02954 HTH_8: Bacterial regu 35.4 39 0.00084 19.9 2.2 22 53-74 20-41 (42)
22 PF11527 ARL2_Bind_BART: The A 34.5 97 0.0021 22.1 4.5 58 44-101 51-112 (121)
23 PF14384 DUF4415: Domain of un 33.7 24 0.00053 22.8 1.2 12 50-61 50-61 (62)
24 COG5304 Uncharacterized protei 30.9 59 0.0013 23.5 2.8 24 50-73 62-85 (92)
25 PF06480 FtsH_ext: FtsH Extrac 30.0 23 0.00049 23.2 0.6 18 60-77 27-44 (110)
26 PF12668 DUF3791: Protein of u 29.0 65 0.0014 20.6 2.6 52 51-104 5-56 (62)
27 PRK13877 conjugal transfer rel 28.9 1E+02 0.0022 22.6 3.9 40 52-99 23-62 (114)
28 KOG4343 bZIP transcription fac 27.7 1.3E+02 0.0028 28.3 5.1 62 19-91 278-339 (655)
29 PRK13696 hypothetical protein; 27.5 96 0.0021 20.8 3.2 33 53-88 15-47 (62)
30 PF13443 HTH_26: Cro/C1-type H 27.1 1.5E+02 0.0033 17.9 5.5 45 54-103 2-48 (63)
31 PF08809 DUF1799: Phage relate 26.6 87 0.0019 21.7 3.1 38 58-95 41-80 (83)
32 smart00344 HTH_ASNC helix_turn 26.4 55 0.0012 22.1 2.0 24 78-101 3-26 (108)
33 COG1352 CheR Methylase of chem 26.1 1.6E+02 0.0035 24.4 5.0 54 51-105 28-88 (268)
34 PHA01513 mnt Mnt 25.9 2.4E+02 0.0052 19.8 5.4 53 52-104 18-76 (82)
35 PF15410 PH_9: Pleckstrin homo 25.1 41 0.00088 23.9 1.2 11 48-58 108-118 (119)
36 COG2005 ModE N-terminal domain 24.9 62 0.0013 24.4 2.2 28 52-79 32-59 (130)
37 PF01402 RHH_1: Ribbon-helix-h 23.6 97 0.0021 17.3 2.4 23 52-74 12-34 (39)
38 PF05678 VQ: VQ motif; InterP 23.5 66 0.0014 18.6 1.7 14 90-103 10-23 (31)
39 PF00570 HRDC: HRDC domain Blo 23.3 1.3E+02 0.0029 18.5 3.3 45 45-100 4-48 (68)
40 PF02042 RWP-RK: RWP-RK domain 22.8 1.3E+02 0.0028 19.3 3.1 35 44-78 8-42 (52)
41 PF01121 CoaE: Dephospho-CoA k 22.0 1.1E+02 0.0024 23.5 3.1 23 78-100 62-84 (180)
42 PRK00081 coaE dephospho-CoA ki 21.8 80 0.0017 23.9 2.3 23 78-100 64-86 (194)
43 KOG0942 E3 ubiquitin protein l 21.5 1E+02 0.0023 30.4 3.4 25 28-52 34-58 (1001)
44 PF08681 DUF1778: Protein of u 20.8 2E+02 0.0044 19.2 3.9 49 53-101 13-63 (80)
45 PRK00430 fis global DNA-bindin 20.7 1.1E+02 0.0024 21.4 2.7 25 53-77 70-94 (95)
46 PF04627 ATP-synt_Eps: Mitocho 20.2 65 0.0014 20.4 1.3 15 58-72 4-18 (50)
47 TIGR00637 ModE_repress ModE mo 20.1 58 0.0013 22.8 1.1 31 52-82 17-47 (99)
48 PF04708 Pox_F16: Poxvirus F16 20.0 1E+02 0.0022 25.4 2.6 40 48-88 165-210 (218)
No 1
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7e-55 Score=319.76 Aligned_cols=106 Identities=49% Similarity=0.917 Sum_probs=103.9
Q ss_pred cHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhh
Q 033167 2 NKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNR 81 (125)
Q Consensus 2 ~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNR 81 (125)
.||+|||+||||||+++++||+|+|+|++|++|||+|||++|||||+|||+|||||+|++|+|||+||+||+++||+|||
T Consensus 13 RrKkiLK~AKG~~G~r~~~~r~Akq~v~ka~~yaYrdRr~rKRdFR~LWI~RINAA~R~~GlsYS~fi~gLkkA~I~inR 92 (118)
T COG0292 13 RRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQRKRDFRKLWIARINAAARENGLSYSRFINGLKKAGIEIDR 92 (118)
T ss_pred HHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHcCchhhH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhhChHHHHHHHHHHHhhCC
Q 033167 82 KVLSELSMHEPYSFKALVDISRNAFP 107 (125)
Q Consensus 82 K~La~LAi~dp~sF~~Lv~~ak~~~~ 107 (125)
||||||||+||.+|.+||+.++.+++
T Consensus 93 KvLadlAi~d~~aF~~lv~~aK~al~ 118 (118)
T COG0292 93 KVLADLAINDPAAFAALVEKAKAALA 118 (118)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHHhcC
Confidence 99999999999999999999998764
No 2
>PTZ00030 60S ribosomal protein L20; Provisional
Probab=100.00 E-value=1.9e-54 Score=320.00 Aligned_cols=116 Identities=53% Similarity=0.879 Sum_probs=110.7
Q ss_pred CcHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchh
Q 033167 1 MNKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLN 80 (125)
Q Consensus 1 ~~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LN 80 (125)
++|++||++|+||+|++|+|||+|+|+|+|||+|||+|||+|||+||+|||+|||||+|++|++||.||++|+++||.||
T Consensus 3 ~rrkkilk~AkGf~G~~s~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~~L~k~~i~LN 82 (121)
T PTZ00030 3 IPRDKVFKLAKGFRGRSKNCFKLARNRVMKALLYSYISRRKRKRILRVHWIQTINAATREHNMTYSRFINGLNNSNIQLN 82 (121)
T ss_pred chHHHHHHHhcccCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCCc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHhhhChHHHHHHHHHHHhhCCCCCCCCCCC
Q 033167 81 RKVLSELSMHEPYSFKALVDISRNAFPGNKNIVHPP 116 (125)
Q Consensus 81 RK~La~LAi~dp~sF~~Lv~~ak~~~~~~~~~~~~~ 116 (125)
|||||||||+||.+|++||+.++.+++..+..|-..
T Consensus 83 RK~Ls~LAi~dp~sF~~lv~~~k~~l~~~~~~~~~~ 118 (121)
T PTZ00030 83 RKILANLAITEPFSFKALVDESKYQLNERKEKPRDI 118 (121)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHhcccccccccc
Confidence 999999999999999999999999887776665544
No 3
>TIGR01032 rplT_bact ribosomal protein L20. This protein binds directly to 23s ribosomal RNA and is necessary for the in vitro assembly process of the 50s ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. GO process changed accordingly
Probab=100.00 E-value=2.6e-53 Score=310.76 Aligned_cols=102 Identities=54% Similarity=0.960 Sum_probs=100.2
Q ss_pred cHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhh
Q 033167 2 NKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNR 81 (125)
Q Consensus 2 ~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNR 81 (125)
.|++||++|+||+|++|+|||+|+|+|+|||+|||+|||+|||+||+|||+|||||+|++|+|||.||++|+++||.|||
T Consensus 12 rrkkilk~akGf~G~~s~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~~L~~~~i~LnR 91 (113)
T TIGR01032 12 RRKKILKQAKGFRGTRKRHYRVAKQTVIKAMAYAYRDRRQRKRDFRSLWITRINAAARQHGLSYSRFINGLKKANIEINR 91 (113)
T ss_pred HHHHHHHHhcccCCccccchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCccH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhhChHHHHHHHHHHH
Q 033167 82 KVLSELSMHEPYSFKALVDISR 103 (125)
Q Consensus 82 K~La~LAi~dp~sF~~Lv~~ak 103 (125)
|||||||++||.+|++||+.++
T Consensus 92 KvLa~lAi~dp~~F~~lv~~~k 113 (113)
T TIGR01032 92 KVLSELAINDPEAFAEIVEQAK 113 (113)
T ss_pred HHHHHHHhcCHHHHHHHHHHhC
Confidence 9999999999999999999874
No 4
>PRK05185 rplT 50S ribosomal protein L20; Provisional
Probab=100.00 E-value=6.9e-53 Score=308.85 Aligned_cols=103 Identities=51% Similarity=0.930 Sum_probs=101.0
Q ss_pred cHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhh
Q 033167 2 NKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNR 81 (125)
Q Consensus 2 ~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNR 81 (125)
.|++||++|+||+|++++||++|+|+|+|||+|||+|||+|||+||+|||+||||++|++|+|||+||++|+++||.|||
T Consensus 12 rrkkilk~akGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~~L~~~~i~LNR 91 (114)
T PRK05185 12 RRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQKKRDFRKLWIARINAAARQNGLSYSRFINGLKKAGIEIDR 91 (114)
T ss_pred HHHHHHHHhcccCCccccchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCccH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhhChHHHHHHHHHHHh
Q 033167 82 KVLSELSMHEPYSFKALVDISRN 104 (125)
Q Consensus 82 K~La~LAi~dp~sF~~Lv~~ak~ 104 (125)
||||||||+||.+|++||+.++.
T Consensus 92 K~La~lAi~dp~~F~~lv~~~k~ 114 (114)
T PRK05185 92 KVLADLAVNDPAAFAALVEKAKA 114 (114)
T ss_pred HHHHHHHhcCHHHHHHHHHHHhC
Confidence 99999999999999999999863
No 5
>CHL00068 rpl20 ribosomal protein L20
Probab=100.00 E-value=9.7e-53 Score=308.61 Aligned_cols=102 Identities=45% Similarity=0.785 Sum_probs=100.0
Q ss_pred cHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhh
Q 033167 2 NKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNR 81 (125)
Q Consensus 2 ~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNR 81 (125)
.|++||++|+||+|++++||++|+|+|+|||+|||+|||+|||+||+|||+|||||+|++|+|||+||++|+++||.|||
T Consensus 13 rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi~gL~~~~i~LnR 92 (115)
T CHL00068 13 RRKKILKFASGFRGAHSRLFRTANQQKMKALVSSYRDRKKKKRDFRRLWITRINAAIRENGVSYSKFIHNLYKNQILLNR 92 (115)
T ss_pred HHHHHHHHhccCCCcccccHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCccH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhhChHHHHHHHHHHH
Q 033167 82 KVLSELSMHEPYSFKALVDISR 103 (125)
Q Consensus 82 K~La~LAi~dp~sF~~Lv~~ak 103 (125)
|||||||++||.+|++||+.+.
T Consensus 93 KvLa~LAi~dp~~F~~lv~~~~ 114 (115)
T CHL00068 93 KILAQIAILDPNCFYTISNKII 114 (115)
T ss_pred HHHHHHHhcCHHHHHHHHHHHh
Confidence 9999999999999999999763
No 6
>PF00453 Ribosomal_L20: Ribosomal protein L20; InterPro: IPR005813 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 [, ]. L20 is a protein from the large (50S) subunit; in Escherichia coli it is known to bind directly to the 23S rRNA, and is required for ribosome assembly, but does not take part in protein synthesis. It belongs to a family of ribosomal proteins, including L20 from eubacteria, plant and alga chloroplasts and cyanelles [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_S 3CF5_N 3PIO_N 3PIP_N 2ZJQ_N 2ZJR_N 2ZJP_N 3DLL_N 3KIT_U 2X9U_U ....
Probab=100.00 E-value=2.6e-51 Score=297.93 Aligned_cols=97 Identities=61% Similarity=1.080 Sum_probs=95.8
Q ss_pred cHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhh
Q 033167 2 NKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNR 81 (125)
Q Consensus 2 ~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNR 81 (125)
+|++||++|+||+|++++|||+|+|+|+|||+|||+|||+|||+||+|||+|||||+|++|++||.||++|+++||.|||
T Consensus 12 rrkkilk~akGf~G~~~~~~r~a~q~v~kal~yay~~Rk~kKR~fR~lWI~RINAa~r~~g~~Ys~fi~~L~~~~i~LNR 91 (108)
T PF00453_consen 12 RRKKILKLAKGFRGRRSNCYRIAKQQVMKALQYAYRDRKLKKRDFRRLWITRINAAAREHGLSYSRFINGLKKANIELNR 91 (108)
T ss_dssp HHHHHHHHTTTSSGGGGTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSTHHHHHHHHHHCTSSTSC
T ss_pred HHHHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHhCCcCcH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhhChHHHHHH
Q 033167 82 KVLSELSMHEPYSFKAL 98 (125)
Q Consensus 82 K~La~LAi~dp~sF~~L 98 (125)
||||||||+||.+|++|
T Consensus 92 KiLa~LAi~dp~~F~~L 108 (108)
T PF00453_consen 92 KILADLAINDPESFKSL 108 (108)
T ss_dssp TTGGGHHTSSHHHHHHH
T ss_pred HHHHHHHhcCHHHHhhC
Confidence 99999999999999987
No 7
>PRK14537 50S ribosomal protein L20/unknown domain fusion protein; Provisional
Probab=100.00 E-value=2.8e-50 Score=322.78 Aligned_cols=105 Identities=42% Similarity=0.798 Sum_probs=103.1
Q ss_pred cHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhh
Q 033167 2 NKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNR 81 (125)
Q Consensus 2 ~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNR 81 (125)
.|++||++|+||||++|+|||+|+|+|+|||+|||+|||+|||+||+|||+|||||+|++|++||.||+||+++||.|||
T Consensus 13 RRKKILKlAKGfrGrrs~lyR~A~q~V~KAL~YAYrdRK~KKRdFR~LWItRINAAaR~~GlsYS~fI~gLkka~I~LNR 92 (230)
T PRK14537 13 RRKKVLKMAKGYFGSKSTLYKTAHEQVMRSLQYAYRDRKQRKRDFRKLWISRINAGAMLCGIKYSRLMHGLALAKVDINR 92 (230)
T ss_pred HHHHHHHHhcccCCccccchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCccH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhhChHHHHHHHHHHHhhC
Q 033167 82 KVLSELSMHEPYSFKALVDISRNAF 106 (125)
Q Consensus 82 K~La~LAi~dp~sF~~Lv~~ak~~~ 106 (125)
||||||||+||.+|.+||+.++.++
T Consensus 93 KvLAdLAI~Dp~sF~~Lv~~ak~al 117 (230)
T PRK14537 93 KVLSDLAHLQPEVFVQYVELAKKFL 117 (230)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999765
No 8
>KOG4707 consensus Mitochondrial/chloroplast ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-37 Score=235.12 Aligned_cols=115 Identities=53% Similarity=0.888 Sum_probs=109.8
Q ss_pred CcHHHHHHHhhccccCCcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchh
Q 033167 1 MNKKEIFKLAKGFRGRAKNCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLN 80 (125)
Q Consensus 1 ~~Rkkilk~AkGfrG~~s~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LN 80 (125)
|.|++|+++|+||||++++|||.|.++|+|||+|+++||.+||++||.|||+||||++++||+.||.|+++|.+++|.||
T Consensus 19 ~rr~~l~k~Aa~frgr~~~~~r~A~r~v~rAlvy~~k~R~~kK~~mr~lwieRv~A~~~e~gv~y~~F~~~L~k~~ilLn 98 (147)
T KOG4707|consen 19 MRRQELFKFAAHFRGRKRRCYRLAVRTVIRALVYATKDRYLKKRDMRTLWIERVNAGAAEHGVRYSPFKHGLHKSPILLN 98 (147)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhccccccccCCccccccchh
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHhhhChHHHHHHHHHHHhhCCCCCCCCCC
Q 033167 81 RKVLSELSMHEPYSFKALVDISRNAFPGNKNIVHP 115 (125)
Q Consensus 81 RK~La~LAi~dp~sF~~Lv~~ak~~~~~~~~~~~~ 115 (125)
||+|||||++||.+|.+||+.++.......+++.+
T Consensus 99 ~k~Lsqlai~eP~sf~~lv~~~k~r~~g~~~i~q~ 133 (147)
T KOG4707|consen 99 RKVLSQLAIVEPRSFCALVVLSKERHPGMHPILQP 133 (147)
T ss_pred HHHhhhhhhhCchhhhhHhhccHhhCCCCCcccCh
Confidence 99999999999999999999999977777666653
No 9
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.73 E-value=2.4 Score=30.61 Aligned_cols=13 Identities=54% Similarity=0.698 Sum_probs=11.4
Q ss_pred hHHHHHHHHhhcC
Q 033167 49 LWIQRINAGTRQH 61 (125)
Q Consensus 49 LWI~RINAa~R~~ 61 (125)
=|-+|||++.|++
T Consensus 76 GwQtRiN~aLR~~ 88 (93)
T COG3514 76 GWQTRINAALRQY 88 (93)
T ss_pred cHHHHHHHHHHHH
Confidence 4999999999974
No 10
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=54.46 E-value=11 Score=23.02 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=15.1
Q ss_pred HHHHhhcCCCChHHHHHHHHH
Q 033167 54 INAGTRQHGVNYGNFMHGLMK 74 (125)
Q Consensus 54 INAa~R~~GlsYs~fi~~Lkk 74 (125)
|..|++.||+++|.+..-++.
T Consensus 19 ~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 19 IRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHcC
Confidence 567999999999998866554
No 11
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=54.00 E-value=16 Score=24.46 Aligned_cols=27 Identities=19% Similarity=0.333 Sum_probs=24.2
Q ss_pred HHHHhhcCCCChHHHHHHHHHcCcchh
Q 033167 54 INAGTRQHGVNYGNFMHGLMKENIQLN 80 (125)
Q Consensus 54 INAa~R~~GlsYs~fi~~Lkk~~i~LN 80 (125)
+..|++..|+|--.|+..|++.||.+|
T Consensus 37 ~gkAAelag~s~~eF~~~L~~~gI~~~ 63 (76)
T PF03683_consen 37 LGKAAELAGMSRWEFLELLKERGIPIN 63 (76)
T ss_pred HHHHHHHhCCCHHHHHHHHHHCCCCCC
Confidence 346889999999999999999999976
No 12
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=53.80 E-value=78 Score=22.51 Aligned_cols=60 Identities=12% Similarity=0.151 Sum_probs=44.8
Q ss_pred HHHHhHHHHHHHHhhcCCCChHHH--HHHHHHcCcchhhhHHHHHhhhChHHHHHHHHHHHh
Q 033167 45 DMRSLWIQRINAGTRQHGVNYGNF--MHGLMKENIQLNRKVLSELSMHEPYSFKALVDISRN 104 (125)
Q Consensus 45 ~fR~LWI~RINAa~R~~GlsYs~f--i~~Lkk~~i~LNRK~La~LAi~dp~sF~~Lv~~ak~ 104 (125)
.+-++|-..++.....+|++.+.| +..|...+-.+.-.-|++.--.|+.+...+++.-..
T Consensus 11 ~~~~~~~~~~~~~l~~~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 11 RLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 355677777888899999999886 555655443355678888889999999988875543
No 13
>PRK01905 DNA-binding protein Fis; Provisional
Probab=50.94 E-value=69 Score=21.27 Aligned_cols=25 Identities=12% Similarity=0.222 Sum_probs=22.3
Q ss_pred HHHHHhhcCCCChHHHHHHHHHcCc
Q 033167 53 RINAGTRQHGVNYGNFMHGLMKENI 77 (125)
Q Consensus 53 RINAa~R~~GlsYs~fi~~Lkk~~i 77 (125)
-+..+++..|++.+.|...|++.||
T Consensus 52 n~s~aAr~LGIsrstL~rklkk~gi 76 (77)
T PRK01905 52 NQSLAAEYLGINRNTLRKKLQQHGL 76 (77)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 4778999999999999999998876
No 14
>PF12558 DUF3744: ATP-binding cassette cobalt transporter; InterPro: IPR022216 This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with PF00005 from PFAM. There is a conserved REP sequence motif. There is a single completely conserved residue P that may be functionally important. The proteins in this family are frequently annotated as ABC Cobalt transporters however there is little accompanying literature to confirm this. ; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
Probab=50.56 E-value=37 Score=22.66 Aligned_cols=45 Identities=18% Similarity=0.231 Sum_probs=36.3
Q ss_pred hhcCCCChHHHHHHHHHcCcchhhhH-HHHHhhhChHHHHHHHHHH
Q 033167 58 TRQHGVNYGNFMHGLMKENIQLNRKV-LSELSMHEPYSFKALVDIS 102 (125)
Q Consensus 58 ~R~~GlsYs~fi~~Lkk~~i~LNRK~-La~LAi~dp~sF~~Lv~~a 102 (125)
..++||-=.=++..|+.+||.|+... |++|.-.|-..++.-+..-
T Consensus 5 L~~~GIREPLYitALk~ag~~l~~~~~l~~l~~l~~~~~~~~l~~w 50 (74)
T PF12558_consen 5 LEQNGIREPLYITALKYAGVDLTKEDHLSDLDNLDLSDVKEKLQQW 50 (74)
T ss_pred HhhcCCCccHHHHHHHHcCCCcccCCCccCHHHCCcHHHHHHHHHH
Confidence 35688888889999999999999988 8988888877776665443
No 15
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=46.15 E-value=13 Score=23.17 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=24.5
Q ss_pred HHHHHHhhcCCCChHHHHHHHHHcCcchhhh
Q 033167 52 QRINAGTRQHGVNYGNFMHGLMKENIQLNRK 82 (125)
Q Consensus 52 ~RINAa~R~~GlsYs~fi~~Lkk~~i~LNRK 82 (125)
.-|.+|++..|+|++.+-..|++..=.|+.+
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhCCe
Confidence 3578999999999999988888766665554
No 16
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=44.87 E-value=29 Score=24.61 Aligned_cols=37 Identities=19% Similarity=0.445 Sum_probs=31.6
Q ss_pred HHHHHHHHHcCcchhhhHHHHHhhhChHHHHHHHHHHH
Q 033167 66 GNFMHGLMKENIQLNRKVLSELSMHEPYSFKALVDISR 103 (125)
Q Consensus 66 s~fi~~Lkk~~i~LNRK~La~LAi~dp~sF~~Lv~~ak 103 (125)
.+|. .|++.|+.+|.++-..-+..+|.-+..|++.+-
T Consensus 18 ~~fl-~lk~~G~~fN~~L~~s~~frNP~i~ekLi~~~~ 54 (96)
T PF07818_consen 18 AKFL-ELKRQGIHFNDRLQNSKSFRNPSILEKLIEFFG 54 (96)
T ss_pred HHHH-HHHHcCCCHHHHHHHccccCChHHHHHHHHHcC
Confidence 4543 466699999999999999999999999998765
No 17
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=42.52 E-value=24 Score=22.36 Aligned_cols=24 Identities=8% Similarity=0.135 Sum_probs=19.8
Q ss_pred HHHHHHhhcCCCChHHHHHHHHHc
Q 033167 52 QRINAGTRQHGVNYGNFMHGLMKE 75 (125)
Q Consensus 52 ~RINAa~R~~GlsYs~fi~~Lkk~ 75 (125)
..|+..|+++||+.+.|-+-+++.
T Consensus 24 ~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 24 ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CceEeeecccccccccccHHHHHH
Confidence 568899999999999998887766
No 18
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=40.08 E-value=31 Score=24.02 Aligned_cols=21 Identities=29% Similarity=0.374 Sum_probs=17.2
Q ss_pred HHHHHhhhChHHHHHHHHHHH
Q 033167 83 VLSELSMHEPYSFKALVDISR 103 (125)
Q Consensus 83 ~La~LAi~dp~sF~~Lv~~ak 103 (125)
-|.+||-.||+.|.+|-...-
T Consensus 8 ~L~~LA~~dPe~fe~lr~~~~ 28 (83)
T PF11333_consen 8 ELKELAQNDPEAFEQLRQELI 28 (83)
T ss_pred HHHHHHHhCHHHHHHHHHHHH
Confidence 578999999999999865443
No 19
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=39.09 E-value=33 Score=20.58 Aligned_cols=25 Identities=28% Similarity=0.373 Sum_probs=19.5
Q ss_pred chhhhHHHHHhhhChHHHHHHHHHH
Q 033167 78 QLNRKVLSELSMHEPYSFKALVDIS 102 (125)
Q Consensus 78 ~LNRK~La~LAi~dp~sF~~Lv~~a 102 (125)
.+|+++|..|--.-..+|..|.+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l 27 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL 27 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH
Confidence 4799999999999999999887643
No 20
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=37.27 E-value=52 Score=25.95 Aligned_cols=54 Identities=9% Similarity=0.076 Sum_probs=47.3
Q ss_pred cCCCChHHHHHHHHHcCcchhhhHHHHHhhhChHHHHHHHHHHHhhCCCCCCCC
Q 033167 60 QHGVNYGNFMHGLMKENIQLNRKVLSELSMHEPYSFKALVDISRNAFPGNKNIV 113 (125)
Q Consensus 60 ~~GlsYs~fi~~Lkk~~i~LNRK~La~LAi~dp~sF~~Lv~~ak~~~~~~~~~~ 113 (125)
.+++|+.+....|...|+.|.+.+|+++-..-...++.+++..++.+...+++-
T Consensus 18 ~~~lp~~r~~~~~~~~G~~is~~ti~~~~~~~~~~l~~~~~~l~~~~~~~~~~~ 71 (271)
T PF03050_consen 18 VYHLPLYRIQQMLEDLGITISRGTIANWIKRVAEALKPLYEALKEELRSSPVVH 71 (271)
T ss_pred cCCCCHHHHhhhhhccceeeccchhHhHhhhhhhhhhhhhhhhhhhccccceec
Confidence 578999999999999999999999999999999999999999888776555543
No 21
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=35.41 E-value=39 Score=19.90 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=17.1
Q ss_pred HHHHHhhcCCCChHHHHHHHHH
Q 033167 53 RINAGTRQHGVNYGNFMHGLMK 74 (125)
Q Consensus 53 RINAa~R~~GlsYs~fi~~Lkk 74 (125)
.+..+|+..|||.+.|-..|++
T Consensus 20 n~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 20 NVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHh
Confidence 3567999999999999888875
No 22
>PF11527 ARL2_Bind_BART: The ARF-like 2 binding protein BART; InterPro: IPR023379 This domain is found in ADP-ribosylation factor-like 2 (ARF2) binding protein, also known as BART, and in uncharacterised proteins. BART binds specifically to ARF2.GTP with a high affinity. However, it does not bind to ARF2.GDP. It is thought that this specific interaction is due to BART being the first identified ARF2-specific effector. The function is not completely characterised []. BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1 []. ; PDB: 2K0S_A 2K9A_A 3DOF_B 3DOE_B.
Probab=34.49 E-value=97 Score=22.13 Aligned_cols=58 Identities=10% Similarity=0.216 Sum_probs=48.8
Q ss_pred HHHHHhHHHHHHHHhhcCCCChHHHHHHH---HHcCcchhhhHHHHH-hhhChHHHHHHHHH
Q 033167 44 RDMRSLWIQRINAGTRQHGVNYGNFMHGL---MKENIQLNRKVLSEL-SMHEPYSFKALVDI 101 (125)
Q Consensus 44 R~fR~LWI~RINAa~R~~GlsYs~fi~~L---kk~~i~LNRK~La~L-Ai~dp~sF~~Lv~~ 101 (125)
.+|+.|==.-|...+...|+|=..|...+ ....-.+.+.++..| |..|-.+|+.+.-.
T Consensus 51 ~ey~~lvE~~le~~l~~~g~s~e~f~~~~~~~~~~~~~~~~~i~e~Lla~~DF~~Fk~mM~~ 112 (121)
T PF11527_consen 51 QEYKELVEKLLEEFLEELGISMEEFEEACLSEESQKDEIAGEIFEQLLAADDFEAFKEMMVQ 112 (121)
T ss_dssp HHHHHHHHHHHHHHHHSTTSSHHCHHHHH---TCCCCCSSCCCHHHHCGGC-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhcccchhhhHHHHHHHHHHccHHHHHHHHHH
Confidence 35777777778888889999999999999 888888999999998 99999999998644
No 23
>PF14384 DUF4415: Domain of unknown function (DUF4415)
Probab=33.75 E-value=24 Score=22.83 Aligned_cols=12 Identities=33% Similarity=0.498 Sum_probs=10.9
Q ss_pred HHHHHHHHhhcC
Q 033167 50 WIQRINAGTRQH 61 (125)
Q Consensus 50 WI~RINAa~R~~ 61 (125)
|-+|||.+.|.+
T Consensus 50 yQtriN~~Lr~~ 61 (62)
T PF14384_consen 50 YQTRINEALRKY 61 (62)
T ss_pred HHHHHHHHHHHh
Confidence 999999999875
No 24
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.88 E-value=59 Score=23.48 Aligned_cols=24 Identities=13% Similarity=0.426 Sum_probs=18.8
Q ss_pred HHHHHHHHhhcCCCChHHHHHHHH
Q 033167 50 WIQRINAGTRQHGVNYGNFMHGLM 73 (125)
Q Consensus 50 WI~RINAa~R~~GlsYs~fi~~Lk 73 (125)
=+.+|---+-.+||+|.+||..+-
T Consensus 62 dLeaIK~kaSa~GlpYQtyIreiL 85 (92)
T COG5304 62 DLEAIKQKASAEGLPYQTYIREIL 85 (92)
T ss_pred HHHHHHHHHhhcCCcHHHHHHHHH
Confidence 456676667789999999998753
No 25
>PF06480 FtsH_ext: FtsH Extracellular; InterPro: IPR011546 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found in the FtsH family of proteins that include FtsH a membrane-bound ATP-dependent protease universally conserved in prokaryotes []. The FtsH peptidases, which belong to MEROPS peptidase family M41 (clan MA(E)), efficiently degrade proteins that have a low thermodynamic stability - e.g. they lack robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni (Leuconostoc oenos) FtsH is involved in protection against environmental stress [], and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded. The precise function of this N-terminal region is unclear. ; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016021 integral to membrane; PDB: 2LNA_A.
Probab=30.03 E-value=23 Score=23.24 Aligned_cols=18 Identities=28% Similarity=0.588 Sum_probs=12.0
Q ss_pred cCCCChHHHHHHHHHcCc
Q 033167 60 QHGVNYGNFMHGLMKENI 77 (125)
Q Consensus 60 ~~GlsYs~fi~~Lkk~~i 77 (125)
..-++||.|++.|...+|
T Consensus 27 ~~~i~YS~F~~~l~~g~V 44 (110)
T PF06480_consen 27 TKEISYSEFLQMLEKGNV 44 (110)
T ss_dssp SEE--HHHHHHTGGGT-E
T ss_pred CcEECHHHHHHHHHcCCE
Confidence 345899999999987765
No 26
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=29.02 E-value=65 Score=20.57 Aligned_cols=52 Identities=6% Similarity=0.017 Sum_probs=39.5
Q ss_pred HHHHHHHhhcCCCChHHHHHHHHHcCcchhhhHHHHHhhhChHHHHHHHHHHHh
Q 033167 51 IQRINAGTRQHGVNYGNFMHGLMKENIQLNRKVLSELSMHEPYSFKALVDISRN 104 (125)
Q Consensus 51 I~RINAa~R~~GlsYs~fi~~Lkk~~i~LNRK~La~LAi~dp~sF~~Lv~~ak~ 104 (125)
+.=|...++.+|+|...-.+-|++.|+. + =+...--+..-.++.-+|+..-.
T Consensus 5 v~~Ie~~A~~~~~s~~ea~~~~~~~~~~-~-~i~~~Yd~lHt~s~~yivedi~~ 56 (62)
T PF12668_consen 5 VFCIEEFAKKLNISGEEAYNYFKRSGVI-D-YIIDCYDVLHTQSDEYIVEDIIE 56 (62)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHcCcH-H-HHHHcchHHHHCcHHHHHHHHHH
Confidence 3458889999999999999999999853 4 66666666666777777765543
No 27
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=28.85 E-value=1e+02 Score=22.58 Aligned_cols=40 Identities=10% Similarity=0.151 Sum_probs=27.2
Q ss_pred HHHHHHhhcCCCChHHHHHHHHHcCcchhhhHHHHHhhhChHHHHHHH
Q 033167 52 QRINAGTRQHGVNYGNFMHGLMKENIQLNRKVLSELSMHEPYSFKALV 99 (125)
Q Consensus 52 ~RINAa~R~~GlsYs~fi~~Lkk~~i~LNRK~La~LAi~dp~sF~~Lv 99 (125)
..|..=+++.|+|-|.|+..+-...+. = +..|++.|..|+
T Consensus 23 ~~I~~kA~~AGlS~SeYLR~~aLg~~I-----~---s~~D~e~v~eL~ 62 (114)
T PRK13877 23 AEIEANAAAAGLSVARYLRDVGQGYQI-----K---GVIDYEYVRELA 62 (114)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHcCCCc-----c---ccCCHHHHHHHH
Confidence 357788899999999999888653333 2 234555555555
No 28
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=27.73 E-value=1.3e+02 Score=28.28 Aligned_cols=62 Identities=29% Similarity=0.383 Sum_probs=47.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhhhHHHHHhhhC
Q 033167 19 NCIRIARERVEKALQYSYRDRRNKKRDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNRKVLSELSMHE 91 (125)
Q Consensus 19 ~~~R~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNRK~La~LAi~d 91 (125)
.+|+. .|+++|--.||--.||+||--+-.| -+||+++..++ ..|++.|+.|-|. |..|+-.+
T Consensus 278 kv~kr-qQRmIKNResA~~SRkKKKEy~~~L-e~rLq~ll~En--------e~Lk~ENatLk~q-L~~l~~En 339 (655)
T KOG4343|consen 278 KVLKR-QQRMIKNRESACQSRKKKKEYMLGL-EARLQALLSEN--------EQLKKENATLKRQ-LDELVSEN 339 (655)
T ss_pred HHHHH-HHHHHhhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH--------HHHHhhhHHHHHH-HHHHhhcC
Confidence 44544 4699999999999998887666544 68999999886 5699999999776 45555444
No 29
>PRK13696 hypothetical protein; Provisional
Probab=27.51 E-value=96 Score=20.77 Aligned_cols=33 Identities=12% Similarity=0.146 Sum_probs=24.5
Q ss_pred HHHHHhhcCCCChHHHHHHHHHcCcchhhhHHHHHh
Q 033167 53 RINAGTRQHGVNYGNFMHGLMKENIQLNRKVLSELS 88 (125)
Q Consensus 53 RINAa~R~~GlsYs~fi~~Lkk~~i~LNRK~La~LA 88 (125)
+|+ ...-|.|+|.|+..|- ....-|++.|-+++
T Consensus 15 ~L~--~kk~~~SFSevi~~L~-~~~~~~~~~l~~~~ 47 (62)
T PRK13696 15 KLL--EIKGDKSFSEVIRELI-EKKKGNLDKLMKAF 47 (62)
T ss_pred HHH--HHhCCCCHHHHHHHHH-HHhhccHHHHHHHH
Confidence 455 4557899999999998 55566777776665
No 30
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=27.06 E-value=1.5e+02 Score=17.91 Aligned_cols=45 Identities=16% Similarity=0.250 Sum_probs=19.0
Q ss_pred HHHHhhcCCCChHHHHHHHHHcCcchhhhHHHHHhhhC--hHHHHHHHHHHH
Q 033167 54 INAGTRQHGVNYGNFMHGLMKENIQLNRKVLSELSMHE--PYSFKALVDISR 103 (125)
Q Consensus 54 INAa~R~~GlsYs~fi~~Lkk~~i~LNRK~La~LAi~d--p~sF~~Lv~~ak 103 (125)
|.-...+.|++.+.+-..+ .+++..|+.+--.+ +-++..|...+.
T Consensus 2 L~~~m~~~~it~~~La~~~-----gis~~tl~~~~~~~~~~~~~~~l~~ia~ 48 (63)
T PF13443_consen 2 LKELMAERGITQKDLARKT-----GISRSTLSRILNGKPSNPSLDTLEKIAK 48 (63)
T ss_dssp HHHHHHHTT--HHHHHHHH-----T--HHHHHHHHTTT-----HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH-----CcCHHHHHHHHhcccccccHHHHHHHHH
Confidence 3344455566555554433 44555555555544 344555554444
No 31
>PF08809 DUF1799: Phage related hypothetical protein (DUF1799); InterPro: IPR014915 This entry is represented by the Bacteriophage TLS, TfmB. The characteristics of the protein distribution suggest prophage matches.
Probab=26.65 E-value=87 Score=21.67 Aligned_cols=38 Identities=16% Similarity=0.298 Sum_probs=30.6
Q ss_pred hhcCCCChHHHHHHHHHcCcchhhh--HHHHHhhhChHHH
Q 033167 58 TRQHGVNYGNFMHGLMKENIQLNRK--VLSELSMHEPYSF 95 (125)
Q Consensus 58 ~R~~GlsYs~fi~~Lkk~~i~LNRK--~La~LAi~dp~sF 95 (125)
.--.||.|+..-..+...||..... ++.+|-+-|..+-
T Consensus 41 ~g~~GLDY~al~~~~~~~gi~~~~~~~~~~~lrvmE~~AL 80 (83)
T PF08809_consen 41 GGPTGLDYGALPAVMDLMGIDDEDRPELFDDLRVMEAAAL 80 (83)
T ss_pred CcCccccHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHH
Confidence 3457999999999999999976544 8999888776554
No 32
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.39 E-value=55 Score=22.09 Aligned_cols=24 Identities=29% Similarity=0.465 Sum_probs=18.7
Q ss_pred chhhhHHHHHhhhChHHHHHHHHH
Q 033167 78 QLNRKVLSELSMHEPYSFKALVDI 101 (125)
Q Consensus 78 ~LNRK~La~LAi~dp~sF~~Lv~~ 101 (125)
.+|+++|..|....+.++..|.+.
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~ 26 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKK 26 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHH
Confidence 368888888888888888877663
No 33
>COG1352 CheR Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]
Probab=26.14 E-value=1.6e+02 Score=24.41 Aligned_cols=54 Identities=19% Similarity=0.365 Sum_probs=42.9
Q ss_pred HHHHHHHhhcCCCC-hHHHHHHHHHcCcchhhhHHHHHhhh------ChHHHHHHHHHHHhh
Q 033167 51 IQRINAGTRQHGVN-YGNFMHGLMKENIQLNRKVLSELSMH------EPYSFKALVDISRNA 105 (125)
Q Consensus 51 I~RINAa~R~~Gls-Ys~fi~~Lkk~~i~LNRK~La~LAi~------dp~sF~~Lv~~ak~~ 105 (125)
-.||+.-.+..|+. |..+.+.|... =..=.-+|..|.++ ||..|..|-+.+.-.
T Consensus 28 ~~Rl~~~~~~~~~~~~~~y~~~l~~~-~~e~~~~l~~ltin~T~FFR~~~~f~~l~~~v~p~ 88 (268)
T COG1352 28 YRRLSRRLRKLGLKNFEEYLNLLESD-SEELQAFLDALTINVTEFFRDPEHFEELRDEVLPE 88 (268)
T ss_pred HHHHHHHHHHhCcccHHHHHHHHhCC-HHHHHHHHHHhhhccchhccCcHHHHHHHHHHHHH
Confidence 46889999999997 99999999888 33334567777775 799999999888753
No 34
>PHA01513 mnt Mnt
Probab=25.90 E-value=2.4e+02 Score=19.81 Aligned_cols=53 Identities=9% Similarity=0.149 Sum_probs=38.2
Q ss_pred HHHHHHhhcCCCChHHHHHHHHHcCcchh------hhHHHHHhhhChHHHHHHHHHHHh
Q 033167 52 QRINAGTRQHGVNYGNFMHGLMKENIQLN------RKVLSELSMHEPYSFKALVDISRN 104 (125)
Q Consensus 52 ~RINAa~R~~GlsYs~fi~~Lkk~~i~LN------RK~La~LAi~dp~sF~~Lv~~ak~ 104 (125)
.+|-.++..+|.|=+..+-.+-..-+.-. ++-+-.+|-.+++.|+.++-..-.
T Consensus 18 ~rL~~aA~~nGRSmNaeIv~~Le~al~~~~~~~g~~~~~~~~a~~~~~~~~~~~~~~l~ 76 (82)
T PHA01513 18 EKLKQRAKANGRSLNAELVQIVQDALSKPSPVTGYRDDAERLADEQSELVKKMVFDTLK 76 (82)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778889999998877776655443211 556778999999999988755443
No 35
>PF15410 PH_9: Pleckstrin homology domain; PDB: 1WJM_A 1BTN_A 1MPH_A.
Probab=25.06 E-value=41 Score=23.93 Aligned_cols=11 Identities=36% Similarity=0.706 Sum_probs=8.5
Q ss_pred HhHHHHHHHHh
Q 033167 48 SLWIQRINAGT 58 (125)
Q Consensus 48 ~LWI~RINAa~ 58 (125)
.-||.+||.+|
T Consensus 108 ~~Wi~~IN~~A 118 (119)
T PF15410_consen 108 NEWIDAINYAA 118 (119)
T ss_dssp HHHHHHHHHH-
T ss_pred HHHHHHHhhhc
Confidence 46999999876
No 36
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=24.89 E-value=62 Score=24.45 Aligned_cols=28 Identities=21% Similarity=0.266 Sum_probs=19.8
Q ss_pred HHHHHHhhcCCCChHHHHHHHHHcCcch
Q 033167 52 QRINAGTRQHGVNYGNFMHGLMKENIQL 79 (125)
Q Consensus 52 ~RINAa~R~~GlsYs~fi~~Lkk~~i~L 79 (125)
+-|++|++.-|+||-.=-..++..|=.+
T Consensus 32 GSIs~AAk~~GiSYk~AW~~i~~~n~~~ 59 (130)
T COG2005 32 GSISAAAKAAGISYKSAWDYIKALNRLL 59 (130)
T ss_pred CCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 4589999999999966555555544333
No 37
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=23.61 E-value=97 Score=17.35 Aligned_cols=23 Identities=9% Similarity=0.341 Sum_probs=19.1
Q ss_pred HHHHHHhhcCCCChHHHHHHHHH
Q 033167 52 QRINAGTRQHGVNYGNFMHGLMK 74 (125)
Q Consensus 52 ~RINAa~R~~GlsYs~fi~~Lkk 74 (125)
.+|+..|.+.|+|=|.||..+-.
T Consensus 12 ~~l~~~a~~~g~s~s~~ir~ai~ 34 (39)
T PF01402_consen 12 ERLDELAKELGRSRSELIREAIR 34 (39)
T ss_dssp HHHHHHHHHHTSSHHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHH
Confidence 57888999999999999887643
No 38
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=23.48 E-value=66 Score=18.61 Aligned_cols=14 Identities=36% Similarity=0.589 Sum_probs=11.3
Q ss_pred hChHHHHHHHHHHH
Q 033167 90 HEPYSFKALVDISR 103 (125)
Q Consensus 90 ~dp~sF~~Lv~~ak 103 (125)
.||..|.+||..--
T Consensus 10 ~d~~~Fr~lVQ~LT 23 (31)
T PF05678_consen 10 TDPSNFRALVQRLT 23 (31)
T ss_pred eCHHHHHHHHHHhH
Confidence 58999999996543
No 39
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=23.35 E-value=1.3e+02 Score=18.53 Aligned_cols=45 Identities=22% Similarity=0.217 Sum_probs=30.5
Q ss_pred HHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcchhhhHHHHHhhhChHHHHHHHH
Q 033167 45 DMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQLNRKVLSELSMHEPYSFKALVD 100 (125)
Q Consensus 45 ~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~LNRK~La~LAi~dp~sF~~Lv~ 100 (125)
-++.||--|=.-| ++.|++.+. -++-.+|-+||..-|.+-..|..
T Consensus 4 ~~~~L~~~R~~~A-~~~~~~~~~----------Il~~~~L~~ia~~~P~s~~~L~~ 48 (68)
T PF00570_consen 4 LLKALKEWREELA-REEDVPPYR----------ILSDEALLEIAKRLPTSIEELLQ 48 (68)
T ss_dssp HHHHHHHHHHHHH-HHHTS-HHH----------HS-HHHHHHHHHH--SSHHHHHT
T ss_pred HHHHHHHHHHHHH-HHcCcCccc----------ccCHHHHHHHHHhCCCCHHHHHH
Confidence 4667777776665 566776655 46788999999999999888764
No 40
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=22.79 E-value=1.3e+02 Score=19.32 Aligned_cols=35 Identities=14% Similarity=0.245 Sum_probs=28.1
Q ss_pred HHHHHhHHHHHHHHhhcCCCChHHHHHHHHHcCcc
Q 033167 44 RDMRSLWIQRINAGTRQHGVNYGNFMHGLMKENIQ 78 (125)
Q Consensus 44 R~fR~LWI~RINAa~R~~GlsYs~fi~~Lkk~~i~ 78 (125)
-+++...---|+.||++.|++-+.|..-..+.||.
T Consensus 8 ~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 8 EDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred HHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 35555556678899999999999999988888873
No 41
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The crystal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases [].; GO: 0004140 dephospho-CoA kinase activity, 0005524 ATP binding, 0015937 coenzyme A biosynthetic process; PDB: 1VHL_A 1N3B_A 1VIY_A 1VHT_B 1T3H_B 1UF9_C 2F6R_A 2GRJ_D 2IF2_C 1JJV_A.
Probab=22.02 E-value=1.1e+02 Score=23.46 Aligned_cols=23 Identities=30% Similarity=0.603 Sum_probs=18.4
Q ss_pred chhhhHHHHHhhhChHHHHHHHH
Q 033167 78 QLNRKVLSELSMHEPYSFKALVD 100 (125)
Q Consensus 78 ~LNRK~La~LAi~dp~sF~~Lv~ 100 (125)
.|||+.|+++...||..-+.|=+
T Consensus 62 ~idR~~L~~~vF~d~~~~~~L~~ 84 (180)
T PF01121_consen 62 EIDRKKLAEIVFSDPEKLKKLEN 84 (180)
T ss_dssp SB-HHHHHHHHTTSHHHHHHHHH
T ss_pred CChHHHHHHHHhcCHHHHHHHHH
Confidence 59999999999999987766633
No 42
>PRK00081 coaE dephospho-CoA kinase; Reviewed
Probab=21.81 E-value=80 Score=23.94 Aligned_cols=23 Identities=35% Similarity=0.471 Sum_probs=20.0
Q ss_pred chhhhHHHHHhhhChHHHHHHHH
Q 033167 78 QLNRKVLSELSMHEPYSFKALVD 100 (125)
Q Consensus 78 ~LNRK~La~LAi~dp~sF~~Lv~ 100 (125)
.+||+.|+++...||.....|-+
T Consensus 64 ~idr~~L~~~vf~~~~~~~~L~~ 86 (194)
T PRK00081 64 ELDRAKLRELVFSDPEARKKLEA 86 (194)
T ss_pred CcCHHHHHHHHhCCHHHHHHHHH
Confidence 59999999999999999886643
No 43
>KOG0942 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.46 E-value=1e+02 Score=30.43 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHhhHHHHHHhHHH
Q 033167 28 VEKALQYSYRDRRNKKRDMRSLWIQ 52 (125)
Q Consensus 28 v~kAl~yayrdRk~kKR~fR~LWI~ 52 (125)
+..++.-+|++|++.|++||.-|+.
T Consensus 34 ~vQs~~Rg~~~r~~~~~~~R~~fd~ 58 (1001)
T KOG0942|consen 34 KVQSFWRGFRVRHNQKLLFREEFDA 58 (1001)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4557778999999999999999985
No 44
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=20.79 E-value=2e+02 Score=19.20 Aligned_cols=49 Identities=20% Similarity=0.230 Sum_probs=32.0
Q ss_pred HHHHHhhcCCCChHHHHHH--HHHcCcchhhhHHHHHhhhChHHHHHHHHH
Q 033167 53 RINAGTRQHGVNYGNFMHG--LMKENIQLNRKVLSELSMHEPYSFKALVDI 101 (125)
Q Consensus 53 RINAa~R~~GlsYs~fi~~--Lkk~~i~LNRK~La~LAi~dp~sF~~Lv~~ 101 (125)
.|..|+...|.|.|.||-. +..+.=.|...-.-.|.-.|-..|..+++.
T Consensus 13 li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aLd~ 63 (80)
T PF08681_consen 13 LIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAALDN 63 (80)
T ss_dssp HHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH-
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHHhC
Confidence 4677899999999999864 444444455555556666666666666653
No 45
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=20.73 E-value=1.1e+02 Score=21.35 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=22.2
Q ss_pred HHHHHhhcCCCChHHHHHHHHHcCc
Q 033167 53 RINAGTRQHGVNYGNFMHGLMKENI 77 (125)
Q Consensus 53 RINAa~R~~GlsYs~fi~~Lkk~~i 77 (125)
.+..+++..|++.+.|-..|++.||
T Consensus 70 n~s~AAr~LGIsRsTL~rKLkr~gi 94 (95)
T PRK00430 70 NQTRAALMLGINRGTLRKKLKKYGM 94 (95)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 4778999999999999999998775
No 46
>PF04627 ATP-synt_Eps: Mitochondrial ATP synthase epsilon chain; InterPro: IPR006721 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This family constitutes the mitochondrial ATP synthase epsilon subunit, which is distinct from the bacterial epsilon subunit (the latter being homologous to the mitochondrial delta subunit, IPR001469 from INTERPRO). The mitochondrial epsilon subunit is located in the stalk region of the F1 complex, and acts as an inhibitor of the ATPase catalytic core. The epsilon subunit can assume two conformations, contracted and extended, where the latter inhibits ATP hydrolysis. The conformation of the epsilon subunit is determined by the direction of rotation of the gamma subunit, and possibly by the presence of ADP. The extended epsilon subunit is thought to become extended in the presence of ADP, thereby acting as a safety lock to prevent wasteful ATP hydrolysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1); PDB: 3OEH_R 3OE7_1 3OFN_R 3OEE_I 2HLD_I 3FKS_I 2WPD_I 3ZRY_I 2V7Q_I 1H8E_I ....
Probab=20.20 E-value=65 Score=20.42 Aligned_cols=15 Identities=20% Similarity=0.395 Sum_probs=9.4
Q ss_pred hhcCCCChHHHHHHH
Q 033167 58 TRQHGVNYGNFMHGL 72 (125)
Q Consensus 58 ~R~~GlsYs~fi~~L 72 (125)
-|.-|+||++|.+-.
T Consensus 4 WR~AGlsY~~Ys~ia 18 (50)
T PF04627_consen 4 WRAAGLSYNKYSNIA 18 (50)
T ss_dssp STTSS--HHHHHHHH
T ss_pred HHHhCcCHHHHHHHH
Confidence 467899999986644
No 47
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=20.08 E-value=58 Score=22.77 Aligned_cols=31 Identities=13% Similarity=0.162 Sum_probs=24.2
Q ss_pred HHHHHHhhcCCCChHHHHHHHHHcCcchhhh
Q 033167 52 QRINAGTRQHGVNYGNFMHGLMKENIQLNRK 82 (125)
Q Consensus 52 ~RINAa~R~~GlsYs~fi~~Lkk~~i~LNRK 82 (125)
..|..|++..|+||+..-..+++.+=.|+-+
T Consensus 17 gSis~AA~~L~iS~stvs~~I~~LE~~lg~~ 47 (99)
T TIGR00637 17 GSISQAAKDAGISYKSAWDYIRAMNNLSGEP 47 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 4688999999999998888887765555443
No 48
>PF04708 Pox_F16: Poxvirus F16 protein; InterPro: IPR006798 This entry represents the Poxvirus F16 proteins.
Probab=20.02 E-value=1e+02 Score=25.42 Aligned_cols=40 Identities=15% Similarity=0.413 Sum_probs=27.4
Q ss_pred HhHHHHHHHHhhcCC------CChHHHHHHHHHcCcchhhhHHHHHh
Q 033167 48 SLWIQRINAGTRQHG------VNYGNFMHGLMKENIQLNRKVLSELS 88 (125)
Q Consensus 48 ~LWI~RINAa~R~~G------lsYs~fi~~Lkk~~i~LNRK~La~LA 88 (125)
.||++..=.-....+ ++|.+||+.+++-+. .+..-+.++.
T Consensus 165 ~lWv~~~L~~~~~~~~~~~~v~~fk~Fi~kik~l~~-~~~~~i~~IC 210 (218)
T PF04708_consen 165 SLWVTSVLNQSNKRKRNGLNVISFKRFINKIKKLKK-KENSDIDEIC 210 (218)
T ss_pred chHHHHHhccccCccccchhHHHHHHHHHHHHHhcc-cchhhHHHHH
Confidence 577766433222222 689999999999887 7777777664
Done!