Query psy9578
Match_columns 122
No_of_seqs 141 out of 855
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 23:13:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9578.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9578hhsearch_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 1.3E-62 2.9E-67 357.0 14.3 118 1-118 1-118 (118)
2 CHL00068 rpl20 ribosomal prote 100.0 1.1E-59 2.3E-64 342.7 14.4 114 1-114 1-114 (115)
3 TIGR01032 rplT_bact ribosomal 100.0 4.9E-59 1.1E-63 338.2 13.8 113 2-114 1-113 (113)
4 PRK05185 rplT 50S ribosomal pr 100.0 1.5E-58 3.2E-63 336.1 14.3 113 2-114 1-113 (114)
5 PRK14537 50S ribosomal protein 100.0 3.4E-57 7.3E-62 359.4 14.9 118 1-118 1-118 (230)
6 PF00453 Ribosomal_L20: Riboso 100.0 8.1E-57 1.8E-61 324.3 12.8 108 2-109 1-108 (108)
7 PTZ00030 60S ribosomal protein 100.0 4.4E-55 9.6E-60 320.8 13.3 110 11-120 2-111 (121)
8 KOG4707|consensus 100.0 6.8E-40 1.5E-44 245.9 7.4 117 1-117 8-124 (147)
9 COG3514 Uncharacterized protei 77.0 1.5 3.2E-05 31.4 1.4 13 60-72 76-88 (93)
10 PF03683 UPF0175: Uncharacteri 61.2 14 0.0003 24.6 3.4 27 65-91 37-63 (76)
11 PF11333 DUF3135: Protein of u 57.8 14 0.0003 25.5 3.1 20 94-113 8-27 (83)
12 PF05225 HTH_psq: helix-turn-h 57.5 12 0.00025 22.7 2.4 21 65-85 19-39 (45)
13 PRK01905 DNA-binding protein F 46.9 81 0.0018 20.7 5.4 25 64-88 52-76 (77)
14 PF07818 HCNGP: HCNGP-like pro 46.7 22 0.00047 25.0 2.7 37 76-113 17-53 (96)
15 PF14384 DUF4415: Domain of un 46.2 15 0.00032 23.7 1.6 12 61-72 50-61 (62)
16 PF01527 HTH_Tnp_1: Transposas 45.9 25 0.00053 22.1 2.7 24 63-86 24-47 (76)
17 PF00126 HTH_1: Bacterial regu 42.6 15 0.00031 22.8 1.2 30 64-93 15-44 (60)
18 PRK03573 transcriptional regul 40.8 1.3E+02 0.0028 21.2 7.5 58 56-113 11-70 (144)
19 COG5304 Uncharacterized protei 40.6 38 0.00083 24.1 3.1 23 61-83 62-84 (92)
20 PF13404 HTH_AsnC-type: AsnC-t 40.1 21 0.00046 21.2 1.6 25 89-113 3-27 (42)
21 PF12668 DUF3791: Protein of u 39.5 78 0.0017 20.0 4.3 55 62-118 5-59 (62)
22 PF02954 HTH_8: Bacterial regu 38.3 42 0.00092 19.5 2.7 21 65-85 21-41 (42)
23 PRK13877 conjugal transfer rel 34.4 1E+02 0.0022 22.3 4.7 37 63-99 23-62 (114)
24 COG1352 CheR Methylase of chem 33.9 1.1E+02 0.0023 25.2 5.2 57 60-117 26-89 (268)
25 PF01402 RHH_1: Ribbon-helix-h 33.7 68 0.0015 17.9 3.0 23 62-84 11-33 (39)
26 PRK13696 hypothetical protein; 33.5 72 0.0016 21.1 3.4 33 64-99 15-47 (62)
27 PF06480 FtsH_ext: FtsH Extrac 31.6 19 0.00042 23.5 0.5 18 72-89 28-45 (110)
28 PF15410 PH_9: Pleckstrin homo 30.8 30 0.00066 24.4 1.4 11 59-69 108-118 (119)
29 PF11527 ARL2_Bind_BART: The A 29.0 2.1E+02 0.0046 20.2 6.4 59 56-114 52-114 (121)
30 PF01121 CoaE: Dephospho-CoA k 28.9 72 0.0016 24.3 3.2 24 89-112 62-85 (180)
31 PF02042 RWP-RK: RWP-RK domain 28.6 98 0.0021 19.6 3.3 34 56-89 9-42 (52)
32 COG2005 ModE N-terminal domain 28.6 51 0.0011 24.6 2.3 28 63-90 32-59 (130)
33 PHA01513 mnt Mnt 28.4 2E+02 0.0044 19.9 5.1 51 63-113 18-74 (82)
34 KOG3955|consensus 27.7 44 0.00096 28.8 2.0 49 72-122 212-269 (361)
35 smart00344 HTH_ASNC helix_turn 26.6 41 0.00089 22.6 1.4 24 89-112 3-26 (108)
36 PRK00081 coaE dephospho-CoA ki 26.4 79 0.0017 23.8 3.1 25 88-112 63-87 (194)
37 PF00570 HRDC: HRDC domain Blo 26.2 1.3E+02 0.0028 18.4 3.6 45 56-111 4-48 (68)
38 PF08809 DUF1799: Phage relate 25.9 91 0.002 21.4 3.0 37 71-107 43-81 (83)
39 KOG4343|consensus 25.1 1.4E+02 0.003 27.8 4.8 63 30-103 278-340 (655)
40 PF01777 Ribosomal_L27e: Ribos 24.5 50 0.0011 22.9 1.5 45 74-118 24-68 (85)
41 PF13443 HTH_26: Cro/C1-type H 24.4 1.7E+02 0.0037 17.5 5.7 44 65-113 2-47 (63)
42 PF11537 DUF3227: Protein of u 24.2 66 0.0014 23.4 2.1 51 59-113 6-56 (102)
43 cd01230 PH_EFA6 EFA6 Pleckstri 23.8 50 0.0011 23.8 1.5 14 58-71 100-113 (117)
44 PF04444 Dioxygenase_N: Catech 23.5 1.2E+02 0.0026 20.4 3.2 23 62-84 12-34 (74)
45 PF03050 DDE_Tnp_IS66: Transpo 23.4 1.1E+02 0.0025 23.9 3.5 47 71-117 18-64 (271)
46 PF04627 ATP-synt_Eps: Mitocho 22.5 53 0.0011 20.6 1.2 16 69-84 4-19 (50)
47 PF05678 VQ: VQ motif; InterP 21.8 79 0.0017 18.0 1.7 15 101-115 10-24 (31)
48 COG3969 Predicted phosphoadeno 21.5 1.6E+02 0.0034 26.1 4.2 47 69-115 225-283 (407)
49 PF02662 FlpD: Methyl-viologen 21.0 83 0.0018 22.7 2.2 42 76-117 79-120 (124)
50 PHA01748 hypothetical protein 20.8 1.5E+02 0.0034 18.8 3.2 23 62-84 14-36 (60)
51 PRK00430 fis global DNA-bindin 20.7 1.4E+02 0.0029 20.8 3.1 25 64-88 70-94 (95)
No 1
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-62 Score=356.96 Aligned_cols=118 Identities=62% Similarity=0.991 Sum_probs=116.6
Q ss_pred CCcccCcHHHHHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHH
Q psy9578 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFM 80 (122)
Q Consensus 1 M~Rvkrg~~~~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi 80 (122)
|||||+|+++++|||||||+||||+|+++++|++|+|+|++|++|||+||+++|||||+|||+|||||+|++|+|||+||
T Consensus 1 M~RvK~gv~~r~RrKkiLK~AKG~~G~r~~~~r~Akq~v~ka~~yaYrdRr~rKRdFR~LWI~RINAA~R~~GlsYS~fi 80 (118)
T COG0292 1 MARVKRGVVARARRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQRKRDFRKLWIARINAAARENGLSYSRFI 80 (118)
T ss_pred CCcccccHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCCcHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCcccchhhhHHHHhhChHHHHHHHHHHHHHhc
Q psy9578 81 NGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENLT 118 (122)
Q Consensus 81 ~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k~~~~ 118 (122)
+||+++||+|||||||||||+||.+|.+||+.++.+++
T Consensus 81 ~gLkkA~I~inRKvLadlAi~d~~aF~~lv~~aK~al~ 118 (118)
T COG0292 81 NGLKKAGIEIDRKVLADLAINDPAAFAALVEKAKAALA 118 (118)
T ss_pred HHHHHcCchhhHHHHHHHHhcCHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999998874
No 2
>CHL00068 rpl20 ribosomal protein L20
Probab=100.00 E-value=1.1e-59 Score=342.65 Aligned_cols=114 Identities=51% Similarity=0.797 Sum_probs=112.6
Q ss_pred CCcccCcHHHHHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHH
Q psy9578 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFM 80 (122)
Q Consensus 1 M~Rvkrg~~~~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi 80 (122)
|||||+|+++++||++||++|+||+|++++||++|+|+|+|||+|||+||++|||+||+|||+|||||+|++|+|||+||
T Consensus 1 M~Rvk~g~~~r~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi 80 (115)
T CHL00068 1 MTRVKRGYIARKRRKKILKFASGFRGAHSRLFRTANQQKMKALVSSYRDRKKKKRDFRRLWITRINAAIRENGVSYSKFI 80 (115)
T ss_pred CCCccccHHHHHHHHHHHHHhccCCCcccccHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCcccchhhhHHHHhhChHHHHHHHHHHH
Q psy9578 81 NGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIK 114 (122)
Q Consensus 81 ~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k 114 (122)
+||+++||+|||||||||||+||.+|.+||+.+.
T Consensus 81 ~gL~~~~i~LnRKvLa~LAi~dp~~F~~lv~~~~ 114 (115)
T CHL00068 81 HNLYKNQILLNRKILAQIAILDPNCFYTISNKII 114 (115)
T ss_pred HHHHHcCCCccHHHHHHHHhcCHHHHHHHHHHHh
Confidence 9999999999999999999999999999999763
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=4.9e-59 Score=338.25 Aligned_cols=113 Identities=60% Similarity=0.960 Sum_probs=111.5
Q ss_pred CcccCcHHHHHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHH
Q psy9578 2 PRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFMN 81 (122)
Q Consensus 2 ~Rvkrg~~~~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi~ 81 (122)
||||+|+++++||++||++|+||+|++|+||++|+|+|+|||+|||+||++|||+||+|||+|||||+|++|+|||+||+
T Consensus 1 ~Rvkrg~~~r~rrkkilk~akGf~G~~s~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~ 80 (113)
T TIGR01032 1 MRVKGGVVARRRRKKILKQAKGFRGTRKRHYRVAKQTVIKAMAYAYRDRRQRKRDFRSLWITRINAAARQHGLSYSRFIN 80 (113)
T ss_pred CCCcccHHHHHHHHHHHHHhcccCCccccchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHCCcccchhhhHHHHhhChHHHHHHHHHHH
Q psy9578 82 GLKKSSIQLDRKLLASIAITDKLVFSSIVNQIK 114 (122)
Q Consensus 82 ~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k 114 (122)
+|+++||+|||||||||||+||.+|.+||+.++
T Consensus 81 ~L~~~~i~LnRKvLa~lAi~dp~~F~~lv~~~k 113 (113)
T TIGR01032 81 GLKKANIEINRKVLSELAINDPEAFAEIVEQAK 113 (113)
T ss_pred HHHHcCCCccHHHHHHHHhcCHHHHHHHHHHhC
Confidence 999999999999999999999999999999874
No 4
>PRK05185 rplT 50S ribosomal protein L20; Provisional
Probab=100.00 E-value=1.5e-58 Score=336.12 Aligned_cols=113 Identities=62% Similarity=1.002 Sum_probs=111.9
Q ss_pred CcccCcHHHHHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHH
Q psy9578 2 PRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFMN 81 (122)
Q Consensus 2 ~Rvkrg~~~~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi~ 81 (122)
||||+|+++++||++||++|+||+|++++||++|+|+|+|||+|||+||++||||||+|||+|||||+|++|+|||+||+
T Consensus 1 ~Rvk~g~~~r~rrkkilk~akGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~ 80 (114)
T PRK05185 1 ARVKRGVVARARRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQKKRDFRKLWIARINAAARQNGLSYSRFIN 80 (114)
T ss_pred CCCcccHHHHHHHHHHHHHhcccCCccccchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHCCcccchhhhHHHHhhChHHHHHHHHHHH
Q psy9578 82 GLKKSSIQLDRKLLASIAITDKLVFSSIVNQIK 114 (122)
Q Consensus 82 ~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k 114 (122)
+|+++||+|||||||||||+||.+|.+||+.++
T Consensus 81 ~L~~~~i~LNRK~La~lAi~dp~~F~~lv~~~k 113 (114)
T PRK05185 81 GLKKAGIEIDRKVLADLAVNDPAAFAALVEKAK 113 (114)
T ss_pred HHHHhCCCccHHHHHHHHhcCHHHHHHHHHHHh
Confidence 999999999999999999999999999999886
No 5
>PRK14537 50S ribosomal protein L20/unknown domain fusion protein; Provisional
Probab=100.00 E-value=3.4e-57 Score=359.42 Aligned_cols=118 Identities=42% Similarity=0.715 Sum_probs=116.3
Q ss_pred CCcccCcHHHHHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHH
Q psy9578 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFM 80 (122)
Q Consensus 1 M~Rvkrg~~~~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi 80 (122)
||||++|+++++||++||++|+||+|++|+|||+|+|+|+|||+|||+||++|||+||+|||+|||||+|++|+|||.||
T Consensus 1 M~RvkrG~~arkRRKKILKlAKGfrGrrs~lyR~A~q~V~KAL~YAYrdRK~KKRdFR~LWItRINAAaR~~GlsYS~fI 80 (230)
T PRK14537 1 MAKISFTPARHRRRKKVLKMAKGYFGSKSTLYKTAHEQVMRSLQYAYRDRKQRKRDFRKLWISRINAGAMLCGIKYSRLM 80 (230)
T ss_pred CCCcccchHHHHHHHHHHHHhcccCCccccchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCcccchhhhHHHHhhChHHHHHHHHHHHHHhc
Q psy9578 81 NGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENLT 118 (122)
Q Consensus 81 ~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k~~~~ 118 (122)
+||+++||.|||||||||||+||.+|.+||+.++.+++
T Consensus 81 ~gLkka~I~LNRKvLAdLAI~Dp~sF~~Lv~~ak~al~ 118 (230)
T PRK14537 81 HGLALAKVDINRKVLSDLAHLQPEVFVQYVELAKKFLS 118 (230)
T ss_pred HHHHHcCCCccHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998764
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=8.1e-57 Score=324.30 Aligned_cols=108 Identities=63% Similarity=1.002 Sum_probs=104.4
Q ss_pred CcccCcHHHHHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHH
Q psy9578 2 PRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFMN 81 (122)
Q Consensus 2 ~Rvkrg~~~~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi~ 81 (122)
||||+|+++++||++||++|+||+|++++||++|+|+|+|||+|||+||++|||+||+|||+|||||+|++|+|||.||+
T Consensus 1 ~Rvk~g~~~~~rrkkilk~akGf~G~~~~~~r~a~q~v~kal~yay~~Rk~kKR~fR~lWI~RINAa~r~~g~~Ys~fi~ 80 (108)
T PF00453_consen 1 MRVKRGVVARKRRKKILKLAKGFRGRRSNCYRIAKQQVMKALQYAYRDRKLKKRDFRRLWITRINAAAREHGLSYSRFIN 80 (108)
T ss_dssp --S-STTHHHHHHHHHHHHTTTSSGGGGTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSTHHHHHH
T ss_pred CCCCCchHHHHHHHHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHCCcccchhhhHHHHhhChHHHHHH
Q psy9578 82 GLKKSSIQLDRKLLASIAITDKLVFSSI 109 (122)
Q Consensus 82 ~L~k~~i~LNRKiLa~lAi~dp~~F~~l 109 (122)
+|+++||+|||||||||||+||++|++|
T Consensus 81 ~L~~~~i~LNRKiLa~LAi~dp~~F~~L 108 (108)
T PF00453_consen 81 GLKKANIELNRKILADLAINDPESFKSL 108 (108)
T ss_dssp HHHHCTSSTSCTTGGGHHTSSHHHHHHH
T ss_pred HHHHhCCcCcHHHHHHHHhcCHHHHhhC
Confidence 9999999999999999999999999986
No 7
>PTZ00030 60S ribosomal protein L20; Provisional
Probab=100.00 E-value=4.4e-55 Score=320.76 Aligned_cols=110 Identities=45% Similarity=0.817 Sum_probs=107.2
Q ss_pred HHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHCCccc
Q psy9578 11 RARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFMNGLKKSSIQL 90 (122)
Q Consensus 11 ~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi~~L~k~~i~L 90 (122)
++||++||++|+||+|++++||++|+|+|+|||+|||+||++|||+||+|||+|||||+|+||+|||.||++|+++||.|
T Consensus 2 ~~rrkkilk~AkGf~G~~s~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~~L~k~~i~L 81 (121)
T PTZ00030 2 KIPRDKVFKLAKGFRGRSKNCFKLARNRVMKALLYSYISRRKRKRILRVHWIQTINAATREHNMTYSRFINGLNNSNIQL 81 (121)
T ss_pred cchHHHHHHHhcccCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCC
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhHHHHhhChHHHHHHHHHHHHHhccc
Q psy9578 91 DRKLLASIAITDKLVFSSIVNQIKENLTNK 120 (122)
Q Consensus 91 NRKiLa~lAi~dp~~F~~lv~~~k~~~~~~ 120 (122)
||||||||||+||.+|.+||+.++.+++.+
T Consensus 82 NRK~Ls~LAi~dp~sF~~lv~~~k~~l~~~ 111 (121)
T PTZ00030 82 NRKILANLAITEPFSFKALVDESKYQLNER 111 (121)
T ss_pred cHHHHHHHHhcCHHHHHHHHHHHHHHhccc
Confidence 999999999999999999999999887654
No 8
>KOG4707|consensus
Probab=100.00 E-value=6.8e-40 Score=245.92 Aligned_cols=117 Identities=38% Similarity=0.608 Sum_probs=114.1
Q ss_pred CCcccCcHHHHHHHHHHHHHhhcccccCcchhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHH
Q psy9578 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFM 80 (122)
Q Consensus 1 M~Rvkrg~~~~~rrkkilk~AkGf~G~~~~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi 80 (122)
|.++++|++.+.|+++|+++|+||||++++|||.|.++|+|||+|+++||.+||+|||.|||+||||++++||+.||.|+
T Consensus 8 l~~~~r~~d~~~rr~~l~k~Aa~frgr~~~~~r~A~r~v~rAlvy~~k~R~~kK~~mr~lwieRv~A~~~e~gv~y~~F~ 87 (147)
T KOG4707|consen 8 LWLRNRGPDRYMRRQELFKFAAHFRGRKRRCYRLAVRTVIRALVYATKDRYLKKRDMRTLWIERVNAGAAEHGVRYSPFK 87 (147)
T ss_pred ceeeccchHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcccccccc
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCcccchhhhHHHHhhChHHHHHHHHHHHHHh
Q psy9578 81 NGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117 (122)
Q Consensus 81 ~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k~~~ 117 (122)
++|.+++|.||+|+||||||.||.||.+||+.+++..
T Consensus 88 ~~L~k~~ilLn~k~Lsqlai~eP~sf~~lv~~~k~r~ 124 (147)
T KOG4707|consen 88 HGLHKSPILLNRKVLSQLAIVEPRSFCALVVLSKERH 124 (147)
T ss_pred CCccccccchhHHHhhhhhhhCchhhhhHhhccHhhC
Confidence 9999999999999999999999999999999988743
No 9
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.97 E-value=1.5 Score=31.37 Aligned_cols=13 Identities=54% Similarity=0.838 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHhC
Q psy9578 60 LWISRINAAVREH 72 (122)
Q Consensus 60 LWI~RINAa~R~~ 72 (122)
=|-+|||++.|++
T Consensus 76 GwQtRiN~aLR~~ 88 (93)
T COG3514 76 GWQTRINAALRQY 88 (93)
T ss_pred cHHHHHHHHHHHH
Confidence 4999999999964
No 10
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=61.23 E-value=14 Score=24.55 Aligned_cols=27 Identities=22% Similarity=0.310 Sum_probs=24.3
Q ss_pred HHHHHHhCCCcHHHHHHHHHHCCcccc
Q psy9578 65 INAAVREHKMTYNTFMNGLKKSSIQLD 91 (122)
Q Consensus 65 INAa~R~~glsYs~fi~~L~k~~i~LN 91 (122)
+-.|++..|+|-..|+..|...||.+|
T Consensus 37 ~gkAAelag~s~~eF~~~L~~~gI~~~ 63 (76)
T PF03683_consen 37 LGKAAELAGMSRWEFLELLKERGIPIN 63 (76)
T ss_pred HHHHHHHhCCCHHHHHHHHHHCCCCCC
Confidence 345889999999999999999999977
No 11
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=57.85 E-value=14 Score=25.51 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=16.9
Q ss_pred hhHHHHhhChHHHHHHHHHH
Q psy9578 94 LLASIAITDKLVFSSIVNQI 113 (122)
Q Consensus 94 iLa~lAi~dp~~F~~lv~~~ 113 (122)
-|.+||-+||+.|.++-...
T Consensus 8 ~L~~LA~~dPe~fe~lr~~~ 27 (83)
T PF11333_consen 8 ELKELAQNDPEAFEQLRQEL 27 (83)
T ss_pred HHHHHHHhCHHHHHHHHHHH
Confidence 57899999999999986653
No 12
>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=57.53 E-value=12 Score=22.66 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=15.0
Q ss_pred HHHHHHhCCCcHHHHHHHHHH
Q psy9578 65 INAAVREHKMTYNTFMNGLKK 85 (122)
Q Consensus 65 INAa~R~~glsYs~fi~~L~k 85 (122)
|..|++.+|+++|.+..-++.
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 567999999999998865543
No 13
>PRK01905 DNA-binding protein Fis; Provisional
Probab=46.86 E-value=81 Score=20.74 Aligned_cols=25 Identities=16% Similarity=0.173 Sum_probs=22.1
Q ss_pred HHHHHHHhCCCcHHHHHHHHHHCCc
Q psy9578 64 RINAAVREHKMTYNTFMNGLKKSSI 88 (122)
Q Consensus 64 RINAa~R~~glsYs~fi~~L~k~~i 88 (122)
-+..+++..|++.+.+...|++.||
T Consensus 52 n~s~aAr~LGIsrstL~rklkk~gi 76 (77)
T PRK01905 52 NQSLAAEYLGINRNTLRKKLQQHGL 76 (77)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 3778999999999999999998876
No 14
>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=46.71 E-value=22 Score=25.04 Aligned_cols=37 Identities=16% Similarity=0.403 Sum_probs=31.1
Q ss_pred HHHHHHHHHHCCcccchhhhHHHHhhChHHHHHHHHHH
Q psy9578 76 YNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQI 113 (122)
Q Consensus 76 Ys~fi~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~ 113 (122)
..+|. .|++.|+.+|..+-+.-+..+|.-+..|++.+
T Consensus 17 i~~fl-~lk~~G~~fN~~L~~s~~frNP~i~ekLi~~~ 53 (96)
T PF07818_consen 17 IAKFL-ELKRQGIHFNDRLQNSKSFRNPSILEKLIEFF 53 (96)
T ss_pred HHHHH-HHHHcCCCHHHHHHHccccCChHHHHHHHHHc
Confidence 44553 46669999999999999999999999999864
No 15
>PF14384 DUF4415: Domain of unknown function (DUF4415)
Probab=46.21 E-value=15 Score=23.67 Aligned_cols=12 Identities=42% Similarity=0.670 Sum_probs=10.8
Q ss_pred HHHHHHHHHHhC
Q psy9578 61 WISRINAAVREH 72 (122)
Q Consensus 61 WI~RINAa~R~~ 72 (122)
|-+|||.+.|.+
T Consensus 50 yQtriN~~Lr~~ 61 (62)
T PF14384_consen 50 YQTRINEALRKY 61 (62)
T ss_pred HHHHHHHHHHHh
Confidence 999999999864
No 16
>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=45.90 E-value=25 Score=22.13 Aligned_cols=24 Identities=21% Similarity=0.220 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCcHHHHHHHHHHC
Q psy9578 63 SRINAAVREHKMTYNTFMNGLKKS 86 (122)
Q Consensus 63 ~RINAa~R~~glsYs~fi~~L~k~ 86 (122)
..|+..|+++|++.+.|-.=+++.
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 468899999999999888877765
No 17
>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=42.56 E-value=15 Score=22.81 Aligned_cols=30 Identities=20% Similarity=0.207 Sum_probs=22.9
Q ss_pred HHHHHHHhCCCcHHHHHHHHHHCCcccchh
Q psy9578 64 RINAAVREHKMTYNTFMNGLKKSSIQLDRK 93 (122)
Q Consensus 64 RINAa~R~~glsYs~fi~~L~k~~i~LNRK 93 (122)
-|.+|++..|+|+|.+-..|+...=.++.+
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHhCCe
Confidence 478999999999999988887765444443
No 18
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=40.76 E-value=1.3e+02 Score=21.23 Aligned_cols=58 Identities=10% Similarity=0.235 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHHhCCCcHHHH--HHHHHHCCcccchhhhHHHHhhChHHHHHHHHHH
Q psy9578 56 VFRSLWISRINAAVREHKMTYNTF--MNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQI 113 (122)
Q Consensus 56 ~fR~LWI~RINAa~R~~glsYs~f--i~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~ 113 (122)
.+-.+|-..++.....+|++.++| +..|...+=.+.-.-||+.--.++.+...+++.-
T Consensus 11 ~~~~~~~~~~~~~l~~~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~L 70 (144)
T PRK03573 11 RLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQL 70 (144)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHH
Confidence 356677788888999999998886 4555554434556778888888999888888753
No 19
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.57 E-value=38 Score=24.14 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHH
Q psy9578 61 WISRINAAVREHKMTYNTFMNGL 83 (122)
Q Consensus 61 WI~RINAa~R~~glsYs~fi~~L 83 (122)
=+.+|---+-.+||+|..||..+
T Consensus 62 dLeaIK~kaSa~GlpYQtyIrei 84 (92)
T COG5304 62 DLEAIKQKASAEGLPYQTYIREI 84 (92)
T ss_pred HHHHHHHHHhhcCCcHHHHHHHH
Confidence 46777777778999999999875
No 20
>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=40.08 E-value=21 Score=21.21 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=19.5
Q ss_pred ccchhhhHHHHhhChHHHHHHHHHH
Q psy9578 89 QLDRKLLASIAITDKLVFSSIVNQI 113 (122)
Q Consensus 89 ~LNRKiLa~lAi~dp~~F~~lv~~~ 113 (122)
++|+++|..|.-+-..+|..|.+.+
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 4799999999999999999987753
No 21
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=39.49 E-value=78 Score=19.98 Aligned_cols=55 Identities=18% Similarity=0.192 Sum_probs=42.8
Q ss_pred HHHHHHHHHhCCCcHHHHHHHHHHCCcccchhhhHHHHhhChHHHHHHHHHHHHHhc
Q psy9578 62 ISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENLT 118 (122)
Q Consensus 62 I~RINAa~R~~glsYs~fi~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k~~~~ 118 (122)
+.=|...|+.+|+|..+-.+-|++.|+. + =+...--+..-.++.-+|+..-..+.
T Consensus 5 v~~Ie~~A~~~~~s~~ea~~~~~~~~~~-~-~i~~~Yd~lHt~s~~yivedi~~~l~ 59 (62)
T PF12668_consen 5 VFCIEEFAKKLNISGEEAYNYFKRSGVI-D-YIIDCYDVLHTQSDEYIVEDIIEYLK 59 (62)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHcCcH-H-HHHHcchHHHHCcHHHHHHHHHHHHH
Confidence 4458899999999999999999999853 4 66666777777788888877655443
No 22
>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=38.29 E-value=42 Score=19.53 Aligned_cols=21 Identities=29% Similarity=0.341 Sum_probs=16.9
Q ss_pred HHHHHHhCCCcHHHHHHHHHH
Q psy9578 65 INAAVREHKMTYNTFMNGLKK 85 (122)
Q Consensus 65 INAa~R~~glsYs~fi~~L~k 85 (122)
+..+|+..|+|.+.|-..|++
T Consensus 21 ~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 21 VSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHh
Confidence 567999999999999887765
No 23
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=34.44 E-value=1e+02 Score=22.33 Aligned_cols=37 Identities=11% Similarity=0.249 Sum_probs=28.5
Q ss_pred HHHHHHHHhCCCcHHHHHHHHHHCCcc---cchhhhHHHH
Q psy9578 63 SRINAAVREHKMTYNTFMNGLKKSSIQ---LDRKLLASIA 99 (122)
Q Consensus 63 ~RINAa~R~~glsYs~fi~~L~k~~i~---LNRKiLa~lA 99 (122)
..|..=+.+.|+|-|.|+..+-...+. +|...+-||+
T Consensus 23 ~~I~~kA~~AGlS~SeYLR~~aLg~~I~s~~D~e~v~eL~ 62 (114)
T PRK13877 23 AEIEANAAAAGLSVARYLRDVGQGYQIKGVIDYEYVRELA 62 (114)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHcCCCccccCCHHHHHHHH
Confidence 357788899999999999988775554 6666666665
No 24
>COG1352 CheR Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]
Probab=33.93 E-value=1.1e+02 Score=25.25 Aligned_cols=57 Identities=19% Similarity=0.376 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHhCCCc-HHHHHHHHHHCCcccchhhhHHHHhh------ChHHHHHHHHHHHHHh
Q psy9578 60 LWISRINAAVREHKMT-YNTFMNGLKKSSIQLDRKLLASIAIT------DKLVFSSIVNQIKENL 117 (122)
Q Consensus 60 LWI~RINAa~R~~gls-Ys~fi~~L~k~~i~LNRKiLa~lAi~------dp~~F~~lv~~~k~~~ 117 (122)
+=-.||+...+..|+. |..+...|.... +.=.-+|..|.++ ||+.|..|-+.+...+
T Consensus 26 ~v~~Rl~~~~~~~~~~~~~~y~~~l~~~~-~e~~~~l~~ltin~T~FFR~~~~f~~l~~~v~p~l 89 (268)
T COG1352 26 LVYRRLSRRLRKLGLKNFEEYLNLLESDS-EELQAFLDALTINVTEFFRDPEHFEELRDEVLPEL 89 (268)
T ss_pred HHHHHHHHHHHHhCcccHHHHHHHHhCCH-HHHHHHHHHhhhccchhccCcHHHHHHHHHHHHHH
Confidence 3357899999999997 999999998883 3334567777775 7899999988877543
No 25
>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=33.71 E-value=68 Score=17.85 Aligned_cols=23 Identities=9% Similarity=0.160 Sum_probs=19.1
Q ss_pred HHHHHHHHHhCCCcHHHHHHHHH
Q psy9578 62 ISRINAAVREHKMTYNTFMNGLK 84 (122)
Q Consensus 62 I~RINAa~R~~glsYs~fi~~L~ 84 (122)
..+|+..|.+.|+|=|.||..+-
T Consensus 11 ~~~l~~~a~~~g~s~s~~ir~ai 33 (39)
T PF01402_consen 11 YERLDELAKELGRSRSELIREAI 33 (39)
T ss_dssp HHHHHHHHHHHTSSHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHH
Confidence 35788999999999999987664
No 26
>PRK13696 hypothetical protein; Provisional
Probab=33.51 E-value=72 Score=21.12 Aligned_cols=33 Identities=6% Similarity=0.028 Sum_probs=25.2
Q ss_pred HHHHHHHhCCCcHHHHHHHHHHCCcccchhhhHHHH
Q psy9578 64 RINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIA 99 (122)
Q Consensus 64 RINAa~R~~glsYs~fi~~L~k~~i~LNRKiLa~lA 99 (122)
+|+ ....|.|+|.++..|. ....-|++.|-+++
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 4568899999999998 55667777777665
No 27
>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=31.62 E-value=19 Score=23.45 Aligned_cols=18 Identities=22% Similarity=0.661 Sum_probs=11.9
Q ss_pred CCCcHHHHHHHHHHCCcc
Q psy9578 72 HKMTYNTFMNGLKKSSIQ 89 (122)
Q Consensus 72 ~glsYs~fi~~L~k~~i~ 89 (122)
.-++||.|++.|.+.+|.
T Consensus 28 ~~i~YS~F~~~l~~g~V~ 45 (110)
T PF06480_consen 28 KEISYSEFLQMLEKGNVK 45 (110)
T ss_dssp EE--HHHHHHTGGGT-EE
T ss_pred cEECHHHHHHHHHcCCEE
Confidence 347999999999887653
No 28
>PF15410 PH_9: Pleckstrin homology domain; PDB: 1WJM_A 1BTN_A 1MPH_A.
Probab=30.81 E-value=30 Score=24.40 Aligned_cols=11 Identities=45% Similarity=0.736 Sum_probs=8.5
Q ss_pred HHHHHHHHHHH
Q psy9578 59 SLWISRINAAV 69 (122)
Q Consensus 59 ~LWI~RINAa~ 69 (122)
.-||..||.+|
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 29
>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=29.00 E-value=2.1e+02 Score=20.18 Aligned_cols=59 Identities=12% Similarity=0.220 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHhCCCcHHHHHHHH---HHCCcccchhhhHHH-HhhChHHHHHHHHHHH
Q psy9578 56 VFRSLWISRINAAVREHKMTYNTFMNGL---KKSSIQLDRKLLASI-AITDKLVFSSIVNQIK 114 (122)
Q Consensus 56 ~fR~LWI~RINAa~R~~glsYs~fi~~L---~k~~i~LNRKiLa~l-Ai~dp~~F~~lv~~~k 114 (122)
.|..|=-.-|...+...|+|=..|...+ ....-.+.+.++-.| |..|-..|+.+.-.-+
T Consensus 52 ey~~lvE~~le~~l~~~g~s~e~f~~~~~~~~~~~~~~~~~i~e~Lla~~DF~~Fk~mM~~~n 114 (121)
T PF11527_consen 52 EYKELVEKLLEEFLEELGISMEEFEEACLSEESQKDEIAGEIFEQLLAADDFEAFKEMMVQYN 114 (121)
T ss_dssp HHHHHHHHHHHHHHHSTTSSHHCHHHHH---TCCCCCSSCCCHHHHCGGC-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhcccchhhhHHHHHHHHHHccHHHHHHHHHHHH
Confidence 5667777778888889999999999999 888888999999998 9999999999865433
No 30
>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=28.85 E-value=72 Score=24.29 Aligned_cols=24 Identities=33% Similarity=0.457 Sum_probs=19.3
Q ss_pred ccchhhhHHHHhhChHHHHHHHHH
Q psy9578 89 QLDRKLLASIAITDKLVFSSIVNQ 112 (122)
Q Consensus 89 ~LNRKiLa~lAi~dp~~F~~lv~~ 112 (122)
.|||+.|+++...||+.-+.|-+.
T Consensus 62 ~idR~~L~~~vF~d~~~~~~L~~i 85 (180)
T PF01121_consen 62 EIDRKKLAEIVFSDPEKLKKLENI 85 (180)
T ss_dssp SB-HHHHHHHHTTSHHHHHHHHHH
T ss_pred CChHHHHHHHHhcCHHHHHHHHHH
Confidence 599999999999999987776443
No 31
>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=28.63 E-value=98 Score=19.63 Aligned_cols=34 Identities=15% Similarity=0.188 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHhCCCcHHHHHHHHHHCCcc
Q psy9578 56 VFRSLWISRINAAVREHKMTYNTFMNGLKKSSIQ 89 (122)
Q Consensus 56 ~fR~LWI~RINAa~R~~glsYs~fi~~L~k~~i~ 89 (122)
|.+...---|+.||++.|++-+.|..-..+.||.
T Consensus 9 ~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 9 DLSQYFHLPIKEAAKELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred HHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 3344444568889999999999998888888873
No 32
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=28.60 E-value=51 Score=24.64 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCcHHHHHHHHHHCCccc
Q psy9578 63 SRINAAVREHKMTYNTFMNGLKKSSIQL 90 (122)
Q Consensus 63 ~RINAa~R~~glsYs~fi~~L~k~~i~L 90 (122)
+-|++|++.-|+||-.--..++..|=.+
T Consensus 32 GSIs~AAk~~GiSYk~AW~~i~~~n~~~ 59 (130)
T COG2005 32 GSISAAAKAAGISYKSAWDYIKALNRLL 59 (130)
T ss_pred CCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 3589999999999987766666554333
No 33
>PHA01513 mnt Mnt
Probab=28.43 E-value=2e+02 Score=19.94 Aligned_cols=51 Identities=8% Similarity=0.116 Sum_probs=37.0
Q ss_pred HHHHHHHHhCCCcHHHHHHHHHHCCcccc------hhhhHHHHhhChHHHHHHHHHH
Q psy9578 63 SRINAAVREHKMTYNTFMNGLKKSSIQLD------RKLLASIAITDKLVFSSIVNQI 113 (122)
Q Consensus 63 ~RINAa~R~~glsYs~fi~~L~k~~i~LN------RKiLa~lAi~dp~~F~~lv~~~ 113 (122)
.+|-.+|..+|.|-+..+..+-..-+.-. ++=+-.+|-.+++.|+.++-..
T Consensus 18 ~rL~~aA~~nGRSmNaeIv~~Le~al~~~~~~~g~~~~~~~~a~~~~~~~~~~~~~~ 74 (82)
T PHA01513 18 EKLKQRAKANGRSLNAELVQIVQDALSKPSPVTGYRDDAERLADEQSELVKKMVFDT 74 (82)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788899999998888777655544321 5557778888999998876543
No 34
>KOG3955|consensus
Probab=27.68 E-value=44 Score=28.76 Aligned_cols=49 Identities=20% Similarity=0.341 Sum_probs=33.2
Q ss_pred CCCcHHHHHHHHHHCCcccchhhhHHHHh---------hChHHHHHHHHHHHHHhcccCC
Q psy9578 72 HKMTYNTFMNGLKKSSIQLDRKLLASIAI---------TDKLVFSSIVNQIKENLTNKAF 122 (122)
Q Consensus 72 ~glsYs~fi~~L~k~~i~LNRKiLa~lAi---------~dp~~F~~lv~~~k~~~~~~~~ 122 (122)
.|.+-..||.-= -|++-||.|||||++ -|-+-=.-|+|.||+.|..-||
T Consensus 212 sGctLqEFmdCP--YNLAnNRQMLadLSLVGCYnlsfiPegkraqlllESAKkNLRgMaF 269 (361)
T KOG3955|consen 212 SGCPLKEFMDCP--YNLANNRQMLADLSLVGCYNLSFIPEGKRAQLLLESAKKNLRGMAF 269 (361)
T ss_pred CCccHHHHhcCc--hhhhhhHHHhhhcceeeeecccccCcchHHHHHHHHHHhhhhccee
Confidence 356677777643 366889999999985 2333345678888887765544
No 35
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.60 E-value=41 Score=22.56 Aligned_cols=24 Identities=17% Similarity=0.519 Sum_probs=19.6
Q ss_pred ccchhhhHHHHhhChHHHHHHHHH
Q psy9578 89 QLDRKLLASIAITDKLVFSSIVNQ 112 (122)
Q Consensus 89 ~LNRKiLa~lAi~dp~~F~~lv~~ 112 (122)
++|+++|..|.-+.+-++..|.+.
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~ 26 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKK 26 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHH
Confidence 468899999988888888888764
No 36
>PRK00081 coaE dephospho-CoA kinase; Reviewed
Probab=26.44 E-value=79 Score=23.81 Aligned_cols=25 Identities=20% Similarity=0.191 Sum_probs=21.2
Q ss_pred cccchhhhHHHHhhChHHHHHHHHH
Q psy9578 88 IQLDRKLLASIAITDKLVFSSIVNQ 112 (122)
Q Consensus 88 i~LNRKiLa~lAi~dp~~F~~lv~~ 112 (122)
=.+||+.|+++...||+....|-+.
T Consensus 63 g~idr~~L~~~vf~~~~~~~~L~~i 87 (194)
T PRK00081 63 GELDRAKLRELVFSDPEARKKLEAI 87 (194)
T ss_pred CCcCHHHHHHHHhCCHHHHHHHHHH
Confidence 3699999999999999998876543
No 37
>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=26.20 E-value=1.3e+02 Score=18.43 Aligned_cols=45 Identities=20% Similarity=0.162 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHhCCCcHHHHHHHHHHCCcccchhhhHHHHhhChHHHHHHHH
Q psy9578 56 VFRSLWISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVN 111 (122)
Q Consensus 56 ~fR~LWI~RINAa~R~~glsYs~fi~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~ 111 (122)
-++.||--|=.-| ++.|++.+. -++-.+|-+||..-|.+-..|..
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 4667777776666 666776555 46778999999999999888865
No 38
>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=25.92 E-value=91 Score=21.36 Aligned_cols=37 Identities=8% Similarity=0.238 Sum_probs=29.9
Q ss_pred hCCCcHHHHHHHHHHCCcccchh--hhHHHHhhChHHHH
Q psy9578 71 EHKMTYNTFMNGLKKSSIQLDRK--LLASIAITDKLVFS 107 (122)
Q Consensus 71 ~~glsYs~fi~~L~k~~i~LNRK--iLa~lAi~dp~~F~ 107 (122)
..||.|+..-..+...||..... ++++|-+-|..+..
T Consensus 43 ~~GLDY~al~~~~~~~gi~~~~~~~~~~~lrvmE~~AL~ 81 (83)
T PF08809_consen 43 PTGLDYGALPAVMDLMGIDDEDRPELFDDLRVMEAAALE 81 (83)
T ss_pred CccccHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHH
Confidence 47899999999999999976544 88888887766543
No 39
>KOG4343|consensus
Probab=25.12 E-value=1.4e+02 Score=27.82 Aligned_cols=63 Identities=25% Similarity=0.403 Sum_probs=48.3
Q ss_pred chhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHCCcccchhhhHHHHhhCh
Q psy9578 30 SVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDK 103 (122)
Q Consensus 30 ~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi~~L~k~~i~LNRKiLa~lAi~dp 103 (122)
.+|+. .|+++|--.||.-.|++||-.+-.| -+||+++..++ +.|++.|+.|-|. |..|+-.++
T Consensus 278 kv~kr-qQRmIKNResA~~SRkKKKEy~~~L-e~rLq~ll~En--------e~Lk~ENatLk~q-L~~l~~En~ 340 (655)
T KOG4343|consen 278 KVLKR-QQRMIKNRESACQSRKKKKEYMLGL-EARLQALLSEN--------EQLKKENATLKRQ-LDELVSENQ 340 (655)
T ss_pred HHHHH-HHHHHhhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH--------HHHHhhhHHHHHH-HHHHhhcCc
Confidence 34443 4689999999999999999877666 68999998886 5699999999765 445554443
No 40
>PF01777 Ribosomal_L27e: Ribosomal L27e protein family; InterPro: IPR001141 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, L27 is found in fungi, plants, algae and vertebrates [, ]. The family has a specific signature at the C terminus.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_a 4A1B_N 4A19_N 4A18_N 4A1D_N 3IZR_a.
Probab=24.50 E-value=50 Score=22.88 Aligned_cols=45 Identities=20% Similarity=0.256 Sum_probs=33.1
Q ss_pred CcHHHHHHHHHHCCcccchhhhHHHHhhChHHHHHHHHHHHHHhc
Q psy9578 74 MTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENLT 118 (122)
Q Consensus 74 lsYs~fi~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k~~~~ 118 (122)
++|+++|--=+...+..+..++..-++.||..=......++..++
T Consensus 24 iNynHlmPTRY~vd~~~~k~~v~~~~l~~~~~kk~a~k~~k~~fe 68 (85)
T PF01777_consen 24 INYNHLMPTRYSVDIPDDKTVVNKDALKDPSKKKKAKKEIKKKFE 68 (85)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCHHHHHTT--HHHHHHHHHHHHH
T ss_pred eeccceEeeeeeeechhhhcccCHHHHhChHHHHHHHHHHHHHHH
Confidence 468999887777777778888888889999877777776666553
No 41
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.38 E-value=1.7e+02 Score=17.54 Aligned_cols=44 Identities=11% Similarity=0.157 Sum_probs=18.3
Q ss_pred HHHHHHhCCCcHHHHHHHHHHCCcccchhhhHHHHhhC--hHHHHHHHHHH
Q psy9578 65 INAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITD--KLVFSSIVNQI 113 (122)
Q Consensus 65 INAa~R~~glsYs~fi~~L~k~~i~LNRKiLa~lAi~d--p~~F~~lv~~~ 113 (122)
|.-...+.|+|.+.+-... .+++..|+.+--.+ +-++..|...|
T Consensus 2 L~~~m~~~~it~~~La~~~-----gis~~tl~~~~~~~~~~~~~~~l~~ia 47 (63)
T PF13443_consen 2 LKELMAERGITQKDLARKT-----GISRSTLSRILNGKPSNPSLDTLEKIA 47 (63)
T ss_dssp HHHHHHHTT--HHHHHHHH-----T--HHHHHHHHTTT-----HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH-----CcCHHHHHHHHhcccccccHHHHHHHH
Confidence 3444555566655554433 45555555555544 34444444433
No 42
>PF11537 DUF3227: Protein of unknown function (DUF3227); InterPro: IPR021609 This archaeal family of proteins has no known function. ; PDB: 2P9X_C.
Probab=24.16 E-value=66 Score=23.36 Aligned_cols=51 Identities=18% Similarity=0.283 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHHHCCcccchhhhHHHHhhChHHHHHHHHHH
Q psy9578 59 SLWISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQI 113 (122)
Q Consensus 59 ~LWI~RINAa~R~~glsYs~fi~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~ 113 (122)
.+-+.-|-++.|+.|-..-..++.==+ -..|. .+ +||..||..|+..|...
T Consensus 6 dilv~ti~~~lr~v~p~L~~~Le~~Lr--at~~k-g~-Eia~EDP~~F~~avskl 56 (102)
T PF11537_consen 6 DILVATIKEALREVAPGLEATLEAYLR--ATYNK-GF-EIAYEDPKKFYEAVSKL 56 (102)
T ss_dssp HHHHHHHHHHHHHH-TTHHHHHHHHHH--HHHS---T-THHHH-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCccHHHHHHHHHH--HHhCC-ce-ehhhcChHHHHHHHHHH
Confidence 344566777888877665555443211 13444 33 99999999999998753
No 43
>cd01230 PH_EFA6 EFA6 Pleckstrin Homology (PH) domain. EFA6 Pleckstrin Homology (PH) domain. EFA6 is an guanine nucleotide exchange factor for ARF6, which is involved in membrane recycling. It consists of a SEC7 domain followed by a PH domain. The EFA6 PH domain regulates its association with the plasma membrane. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=23.77 E-value=50 Score=23.80 Aligned_cols=14 Identities=36% Similarity=0.631 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHh
Q psy9578 58 RSLWISRINAAVRE 71 (122)
Q Consensus 58 R~LWI~RINAa~R~ 71 (122)
..-||..||.+|-.
T Consensus 100 ~~~Wi~~I~~~~~~ 113 (117)
T cd01230 100 LQSWIERINVVAAA 113 (117)
T ss_pred HHHHHHHHHHHHHh
Confidence 45799999999854
No 44
>PF04444 Dioxygenase_N: Catechol dioxygenase N terminus; InterPro: IPR007535 This domain is the N-terminal region of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (IPR000627 from INTERPRO). Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (IPR000486 from INTERPRO) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) []. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (1.13.11.1 from EC); protocatechuate 3,4-dioxygenase (3,4-PCD) (1.13.11.3 from EC); and chlorocatechol 1,2-dioxygenase (1.13.11.1 from EC) [].; GO: 0005506 iron ion binding, 0018576 catechol 1,2-dioxygenase activity, 0009712 catechol-containing compound metabolic process, 0055114 oxidation-reduction process; PDB: 3O6R_B 1S9A_A 3O6J_A 3O5U_B 3O32_B 3HHY_A 3HHX_A 3HJS_A 3HJQ_A 3HKP_A ....
Probab=23.52 E-value=1.2e+02 Score=20.35 Aligned_cols=23 Identities=13% Similarity=0.358 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCCcHHHHHHHHH
Q psy9578 62 ISRINAAVREHKMTYNTFMNGLK 84 (122)
Q Consensus 62 I~RINAa~R~~glsYs~fi~~L~ 84 (122)
+.-|.+.++++.+|+..|..++.
T Consensus 12 v~~lh~~i~e~~lT~~E~~~av~ 34 (74)
T PF04444_consen 12 VRHLHDFIREVDLTEDEWWAAVD 34 (74)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Confidence 56788999999999998877763
No 45
>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=23.38 E-value=1.1e+02 Score=23.86 Aligned_cols=47 Identities=15% Similarity=0.166 Sum_probs=42.6
Q ss_pred hCCCcHHHHHHHHHHCCcccchhhhHHHHhhChHHHHHHHHHHHHHh
Q psy9578 71 EHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117 (122)
Q Consensus 71 ~~glsYs~fi~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k~~~ 117 (122)
.+++|+.+...-|...||.|.+.+|+++-..-.+.+..+++..++.+
T Consensus 18 ~~~lp~~r~~~~~~~~G~~is~~ti~~~~~~~~~~l~~~~~~l~~~~ 64 (271)
T PF03050_consen 18 VYHLPLYRIQQMLEDLGITISRGTIANWIKRVAEALKPLYEALKEEL 64 (271)
T ss_pred cCCCCHHHHhhhhhccceeeccchhHhHhhhhhhhhhhhhhhhhhhc
Confidence 47899999999999999999999999999999999999988887665
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=22.51 E-value=53 Score=20.62 Aligned_cols=16 Identities=25% Similarity=0.368 Sum_probs=10.1
Q ss_pred HHhCCCcHHHHHHHHH
Q psy9578 69 VREHKMTYNTFMNGLK 84 (122)
Q Consensus 69 ~R~~glsYs~fi~~L~ 84 (122)
-|.-|+||++|.+-..
T Consensus 4 WR~AGlsY~~Ys~iaA 19 (50)
T PF04627_consen 4 WRAAGLSYNKYSNIAA 19 (50)
T ss_dssp STTSS--HHHHHHHHH
T ss_pred HHHhCcCHHHHHHHHH
Confidence 3678999999976543
No 47
>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=21.82 E-value=79 Score=18.05 Aligned_cols=15 Identities=27% Similarity=0.461 Sum_probs=12.0
Q ss_pred hChHHHHHHHHHHHH
Q psy9578 101 TDKLVFSSIVNQIKE 115 (122)
Q Consensus 101 ~dp~~F~~lv~~~k~ 115 (122)
.||..|.+||...-.
T Consensus 10 ~d~~~Fr~lVQ~LTG 24 (31)
T PF05678_consen 10 TDPSNFRALVQRLTG 24 (31)
T ss_pred eCHHHHHHHHHHhHC
Confidence 489999999976543
No 48
>COG3969 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]
Probab=21.48 E-value=1.6e+02 Score=26.11 Aligned_cols=47 Identities=13% Similarity=0.244 Sum_probs=37.0
Q ss_pred HHhCCCcHHHHHHHHHHCCcccc------------hhhhHHHHhhChHHHHHHHHHHHH
Q psy9578 69 VREHKMTYNTFMNGLKKSSIQLD------------RKLLASIAITDKLVFSSIVNQIKE 115 (122)
Q Consensus 69 ~R~~glsYs~fi~~L~k~~i~LN------------RKiLa~lAi~dp~~F~~lv~~~k~ 115 (122)
--.+|.+|+.+-+.+.++|+.++ |+-|----+-||++...++.-+..
T Consensus 225 ~Ak~~~~yN~LYDlmYqAGvp~~~MRVc~Pfgd~qr~gL~LYhvIEPetW~k~~~RVsG 283 (407)
T COG3969 225 NAKFSYAYNPLYDLMYQAGVPLRQMRVCEPFGDEQRKGLWLYHVIEPETWAKMCGRVSG 283 (407)
T ss_pred HHhcCCcccHHHHHHHHcCCChhhccccCCCChhhhcccchhhhcCHHHHHHHHHHhcc
Confidence 33799999999999999999875 445555556788888888877654
No 49
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=21.00 E-value=83 Score=22.67 Aligned_cols=42 Identities=24% Similarity=0.300 Sum_probs=35.1
Q ss_pred HHHHHHHHHHCCcccchhhhHHHHhhChHHHHHHHHHHHHHh
Q psy9578 76 YNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117 (122)
Q Consensus 76 Ys~fi~~L~k~~i~LNRKiLa~lAi~dp~~F~~lv~~~k~~~ 117 (122)
...+-..|...||+=+|=-+..++..|+..|..+++..-+.+
T Consensus 79 v~~~k~~L~~~Gi~~eRv~~~~~~~~~~~~fa~~~~~f~~~i 120 (124)
T PF02662_consen 79 VERLKKLLEELGIEPERVRLYWISAPEGKRFAEIVNEFTERI 120 (124)
T ss_pred HHHHHHHHHHcCCChhHeEEEEeCcccHHHHHHHHHHHHHHH
Confidence 345667799999999999999999999999999988755443
No 50
>PHA01748 hypothetical protein
Probab=20.82 E-value=1.5e+02 Score=18.80 Aligned_cols=23 Identities=4% Similarity=0.078 Sum_probs=18.8
Q ss_pred HHHHHHHHHhCCCcHHHHHHHHH
Q psy9578 62 ISRINAAVREHKMTYNTFMNGLK 84 (122)
Q Consensus 62 I~RINAa~R~~glsYs~fi~~L~ 84 (122)
+.+|...|.++|++.|.+|...-
T Consensus 14 ~~eld~~a~~~g~~RSE~Ir~Ai 36 (60)
T PHA01748 14 LELLDRYAIKHGLNRSEAIRKAI 36 (60)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Confidence 46788899999999999887653
No 51
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=20.66 E-value=1.4e+02 Score=20.75 Aligned_cols=25 Identities=20% Similarity=0.123 Sum_probs=21.9
Q ss_pred HHHHHHHhCCCcHHHHHHHHHHCCc
Q psy9578 64 RINAAVREHKMTYNTFMNGLKKSSI 88 (122)
Q Consensus 64 RINAa~R~~glsYs~fi~~L~k~~i 88 (122)
.+..+++..|+|.+.+-..|++.||
T Consensus 70 n~s~AAr~LGIsRsTL~rKLkr~gi 94 (95)
T PRK00430 70 NQTRAALMLGINRGTLRKKLKKYGM 94 (95)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 4778999999999999999998775
Done!