Query 030926
Match_columns 169
No_of_seqs 117 out of 1136
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:39:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030926.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030926hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00083 rpl12 ribosomal prote 100.0 3.5E-42 7.5E-47 269.5 14.1 131 37-169 1-131 (131)
2 KOG1715 Mitochondrial/chloropl 100.0 9.7E-42 2.1E-46 279.4 15.0 136 33-169 52-187 (187)
3 cd00387 Ribosomal_L7_L12 Ribos 100.0 1.5E-41 3.3E-46 264.5 14.0 127 39-168 1-127 (127)
4 TIGR00855 L12 ribosomal protei 100.0 1.5E-39 3.2E-44 253.3 13.5 122 40-169 5-126 (126)
5 PRK00157 rplL 50S ribosomal pr 100.0 3.5E-39 7.5E-44 250.3 13.5 122 38-169 2-123 (123)
6 COG0222 RplL Ribosomal protein 100.0 5.5E-39 1.2E-43 248.6 12.4 122 39-169 3-124 (124)
7 PF00542 Ribosomal_L12: Riboso 99.9 4E-25 8.7E-30 155.7 5.7 68 101-169 1-68 (68)
8 PRK06771 hypothetical protein; 97.9 1.2E-05 2.7E-10 60.3 3.2 29 111-139 65-93 (93)
9 PF02617 ClpS: ATP-dependent C 90.0 0.82 1.8E-05 32.4 5.0 65 98-163 3-71 (82)
10 PRK00033 clpS ATP-dependent Cl 78.9 16 0.00034 27.6 7.5 72 97-169 23-98 (100)
11 PRK13019 clpS ATP-dependent Cl 65.1 39 0.00084 25.2 6.8 72 96-167 16-91 (94)
12 COG0264 Tsf Translation elonga 60.6 8.8 0.00019 34.4 3.1 27 113-139 4-30 (296)
13 KOG3449 60S acidic ribosomal p 58.7 36 0.00078 26.6 5.8 39 33-74 31-70 (112)
14 PRK10664 transcriptional regul 56.5 5.5 0.00012 29.0 0.9 36 113-148 2-37 (90)
15 PRK12332 tsf elongation factor 56.0 14 0.00029 31.0 3.3 29 115-143 5-33 (198)
16 PRK10753 transcriptional regul 55.1 5.9 0.00013 28.7 0.9 35 113-147 2-36 (90)
17 cd04788 HTH_NolA-AlbR Helix-Tu 53.8 29 0.00063 25.1 4.4 47 112-160 44-90 (96)
18 TIGR00116 tsf translation elon 53.5 15 0.00032 32.6 3.3 29 115-143 5-33 (290)
19 PRK09377 tsf elongation factor 53.4 14 0.00031 32.6 3.2 29 115-143 6-34 (290)
20 PF09278 MerR-DNA-bind: MerR, 51.6 21 0.00045 23.5 3.1 22 114-136 3-24 (65)
21 PF10925 DUF2680: Protein of u 49.5 28 0.00061 23.9 3.5 26 133-161 21-47 (59)
22 cd04774 HTH_YfmP Helix-Turn-He 48.2 48 0.001 24.2 4.8 31 112-142 43-73 (96)
23 PF14520 HHH_5: Helix-hairpin- 48.1 54 0.0012 21.5 4.7 46 116-161 2-60 (60)
24 PF02022 Integrase_Zn: Integra 48.0 26 0.00056 22.3 2.9 27 118-144 12-38 (40)
25 cd00591 HU_IHF Integration hos 46.9 18 0.00038 25.1 2.3 35 113-147 1-35 (87)
26 smart00411 BHL bacterial (prok 45.6 18 0.00039 25.3 2.1 36 113-148 2-37 (90)
27 cd01107 HTH_BmrR Helix-Turn-He 43.5 48 0.001 24.4 4.3 29 112-141 45-73 (108)
28 PF13411 MerR_1: MerR HTH fami 41.0 27 0.00059 22.9 2.4 26 112-138 43-68 (69)
29 PF10044 Ret_tiss: Retinal tis 39.8 22 0.00047 26.9 1.9 23 116-138 62-88 (95)
30 cd04766 HTH_HspR Helix-Turn-He 37.9 92 0.002 22.0 4.9 41 112-162 44-84 (91)
31 PRK00285 ihfA integration host 34.5 33 0.00072 24.8 2.1 35 113-147 4-38 (99)
32 PF11363 DUF3164: Protein of u 32.9 69 0.0015 26.8 4.0 82 41-148 36-117 (195)
33 cd04768 HTH_BmrR-like Helix-Tu 32.6 99 0.0021 22.3 4.4 28 112-140 44-71 (96)
34 TIGR02043 ZntR Zn(II)-responsi 32.2 80 0.0017 24.1 4.0 26 112-138 45-70 (131)
35 cd04763 HTH_MlrA-like Helix-Tu 31.9 55 0.0012 21.7 2.8 23 113-136 45-67 (68)
36 cd01104 HTH_MlrA-CarA Helix-Tu 31.5 56 0.0012 21.3 2.7 24 113-137 45-68 (68)
37 cd04782 HTH_BltR Helix-Turn-He 31.3 90 0.0019 22.5 4.0 26 113-139 45-70 (97)
38 cd04780 HTH_MerR-like_sg5 Heli 31.2 63 0.0014 23.5 3.2 27 112-138 44-70 (95)
39 PF11272 DUF3072: Protein of u 29.7 59 0.0013 22.6 2.6 19 50-68 38-56 (57)
40 cd04781 HTH_MerR-like_sg6 Heli 29.6 1.6E+02 0.0035 21.9 5.3 27 112-139 43-69 (120)
41 cd01105 HTH_GlnR-like Helix-Tu 28.5 74 0.0016 22.6 3.1 26 112-138 45-70 (88)
42 cd01106 HTH_TipAL-Mta Helix-Tu 28.1 1.5E+02 0.0031 21.5 4.7 28 112-140 44-71 (103)
43 PRK13752 putative transcriptio 27.2 1.1E+02 0.0024 24.0 4.1 25 113-138 52-76 (144)
44 PRK05412 putative nucleotide-b 26.6 64 0.0014 26.6 2.7 64 103-167 45-120 (161)
45 PF00828 Ribosomal_L18e: Ribos 26.3 62 0.0013 24.5 2.5 27 138-168 101-128 (129)
46 cd01109 HTH_YyaN Helix-Turn-He 25.9 83 0.0018 23.1 3.1 26 113-139 45-70 (113)
47 cd02810 DHOD_DHPD_FMN Dihydroo 25.8 1E+02 0.0023 25.9 4.0 40 115-166 151-192 (289)
48 cd01108 HTH_CueR Helix-Turn-He 25.5 1.3E+02 0.0028 22.7 4.1 26 112-138 44-69 (127)
49 PRK10227 DNA-binding transcrip 25.4 1.1E+02 0.0024 23.6 3.8 25 113-138 45-69 (135)
50 PRK08385 nicotinate-nucleotide 24.9 1E+02 0.0022 27.1 3.9 43 127-169 190-235 (278)
51 PF04461 DUF520: Protein of un 24.9 52 0.0011 27.1 1.9 64 103-167 45-120 (160)
52 cd04777 HTH_MerR-like_sg1 Heli 24.7 91 0.002 22.7 3.0 25 113-138 43-67 (107)
53 COG4575 ElaB Uncharacterized c 24.6 81 0.0018 24.3 2.8 33 130-162 15-49 (104)
54 PF10584 Proteasome_A_N: Prote 24.4 34 0.00073 19.6 0.5 12 4-15 4-15 (23)
55 PRK06419 rpl15p 50S ribosomal 24.2 71 0.0015 25.5 2.5 25 140-168 119-144 (148)
56 cd04764 HTH_MlrA-like_sg1 Heli 24.1 92 0.002 20.5 2.7 24 113-137 44-67 (67)
57 PRK00199 ihfB integration host 23.9 35 0.00076 24.4 0.7 35 113-147 2-37 (94)
58 TIGR01037 pyrD_sub1_fam dihydr 23.0 1.1E+02 0.0023 26.1 3.6 41 114-166 145-185 (300)
59 PRK05350 acyl carrier protein; 23.0 1.1E+02 0.0023 21.3 3.0 26 44-70 32-57 (82)
60 cd04740 DHOD_1B_like Dihydroor 22.9 1.1E+02 0.0024 26.0 3.6 38 116-165 144-181 (296)
61 cd04784 HTH_CadR-PbrR Helix-Tu 22.5 98 0.0021 23.2 2.9 25 113-138 45-69 (127)
62 cd04767 HTH_HspR-like_MBC Heli 22.5 1.1E+02 0.0025 23.6 3.3 32 112-143 43-74 (120)
63 cd04411 Ribosomal_P1_P2_L12p R 22.4 2.7E+02 0.0059 21.0 5.3 31 35-68 32-62 (105)
64 smart00422 HTH_MERR helix_turn 22.1 1.2E+02 0.0026 19.7 3.0 25 112-137 44-68 (70)
65 PRK07379 coproporphyrinogen II 22.0 5.9E+02 0.013 22.9 9.7 38 125-165 129-166 (400)
66 cd08494 PBP2_NikA_DppA_OppA_li 21.7 1.5E+02 0.0032 26.0 4.3 44 126-169 297-349 (448)
67 COG3797 Uncharacterized protei 21.4 69 0.0015 26.9 2.0 50 109-162 13-63 (178)
68 cd08499 PBP2_Ylib_like The sub 21.4 1.5E+02 0.0032 26.4 4.3 44 126-169 300-352 (474)
69 TIGR00517 acyl_carrier acyl ca 21.1 1E+02 0.0022 20.9 2.5 23 49-71 33-55 (77)
70 PF00216 Bac_DNA_binding: Bact 20.9 74 0.0016 22.0 1.8 33 113-145 2-34 (90)
71 PRK15002 redox-sensitivie tran 20.7 1.7E+02 0.0037 23.3 4.1 25 113-138 55-79 (154)
72 COG0236 AcpP Acyl carrier prot 20.4 1E+02 0.0022 21.3 2.5 23 49-71 35-57 (80)
73 cd04770 HTH_HMRTR Helix-Turn-H 20.4 1.6E+02 0.0034 21.8 3.6 26 113-139 45-70 (123)
74 cd05833 Ribosomal_P2 Ribosomal 20.2 3.7E+02 0.0079 20.5 5.6 32 35-69 33-64 (109)
75 COG0789 SoxR Predicted transcr 20.2 1.2E+02 0.0027 21.9 3.0 29 112-141 44-72 (124)
76 PRK13562 acetolactate synthase 20.2 55 0.0012 24.1 1.1 48 4-51 19-68 (84)
77 PF08542 Rep_fac_C: Replicatio 20.0 1.7E+02 0.0037 20.0 3.6 33 37-70 4-36 (89)
No 1
>CHL00083 rpl12 ribosomal protein L12
Probab=100.00 E-value=3.5e-42 Score=269.55 Aligned_cols=131 Identities=39% Similarity=0.583 Sum_probs=112.4
Q ss_pred CChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhccceeEEEeecCcchhHH
Q 030926 37 RTQKLERISDELLDLTKLERYDFATLFGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQATKIK 116 (169)
Q Consensus 37 ~s~kv~~Ivd~I~~LTLlE~seLv~~leekfgv~~~~~~~~~~~~~~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~ 116 (169)
.|+++++|+|+|++|||+|++||++.|+++|||+++++++++++ +++++++ +.++++.+|||+|||+|++||+++||+
T Consensus 1 ~s~k~~~ivd~i~~LTllE~~eLv~~le~~fgv~~~~~~a~~~~-~~~a~~~-~~~~~~~~EKT~F~V~L~~~~~~~Ki~ 78 (131)
T CHL00083 1 MSTKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMM-SAPAAAA-AQAAEEVEEKTEFDVILEEVPADKRIA 78 (131)
T ss_pred CCchHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhhhhhc-cccCccc-ccccchhhhcceeeEEEeecCCcchHH
Confidence 37899999999999999999999999999999998765432211 1111111 112345689999999999998899999
Q ss_pred HHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 117 IIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 117 vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
|||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 79 vIK~vr~it~lgLkeaK~lVe~~P~~ike~v~KeeAe~ik~~le~~Ga~v~lk 131 (131)
T CHL00083 79 VLKVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131 (131)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 99999999999999999999999999999999999999999999999999983
No 2
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.7e-42 Score=279.41 Aligned_cols=136 Identities=46% Similarity=0.644 Sum_probs=116.8
Q ss_pred ccccCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhccceeEEEeecCcc
Q 030926 33 VTESRTQKLERISDELLDLTKLERYDFATLFGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQA 112 (169)
Q Consensus 33 ~~~~~s~kv~~Ivd~I~~LTLlE~seLv~~leekfgv~~~~~~~~~~~~~~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~ 112 (169)
.+.++++||.+|+|+|++|||+|.+||+++|+++|||+..+.++++++.++++.+ +...++++.|+|.|||+|++||+.
T Consensus 52 ~~~~~~~KI~~iv~eIssLtLlE~s~L~~~Lk~kl~i~e~~~~~a~~~g~~~~~~-~~a~ee~k~ekt~FdVkL~~fda~ 130 (187)
T KOG1715|consen 52 AAVPPPPKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGAAAPDA-GGAEEEAKKEKTTFDVKLEKFDAS 130 (187)
T ss_pred cccCCCHHHHHHHHHHHhcCHHHHHHHHHHHHHHcCCCcccchhhccccCCCCCc-ccccccchhhcceEEEEEeecCcc
Confidence 3467899999999999999999999999999999999987654432221121111 222345667888899999999999
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
.||+|||+||.+|||||+|||+|||++|+++|+|++|||||+||++|+++||+|+||
T Consensus 131 ~KIkVIKEVR~~tgL~LkeAKklVE~aP~ilKegvtKeEAEkik~kLea~GakV~le 187 (187)
T KOG1715|consen 131 SKIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEKLEAAGAKVVLE 187 (187)
T ss_pred chhHHHHHHHHhccccHHHHHHHHHhccHHHHcCCCHHHHHHHHHHHHHcCCeEeeC
Confidence 999999999999999999999999999999999999999999999999999999997
No 3
>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
Probab=100.00 E-value=1.5e-41 Score=264.52 Aligned_cols=127 Identities=47% Similarity=0.658 Sum_probs=107.6
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhccceeEEEeecCcchhHHHH
Q 030926 39 QKLERISDELLDLTKLERYDFATLFGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQATKIKII 118 (169)
Q Consensus 39 ~kv~~Ivd~I~~LTLlE~seLv~~leekfgv~~~~~~~~~~~~~~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vI 118 (169)
+++++|+|+|++|||+|+++|++.|+++|||++.++.++++ +++|+++ ...++..+|||+|||+|++||+++||+||
T Consensus 1 ~~~~~i~d~i~~LtllE~~eLv~~le~~~gv~~~~~~~~~~-~~a~~~~--~~~~~~~~EKt~F~V~L~~~~~~~Ki~vI 77 (127)
T cd00387 1 LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAA-AAAPAAA--AAAAAEAEEKTEFDVVLESFGAAKKIAVI 77 (127)
T ss_pred CcHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCccccccccc-ccCcccc--cccccchhhcceEEEEEeeCCchhhHHHH
Confidence 36899999999999999999999999999999763222111 1112211 11223357999999999999988999999
Q ss_pred HHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEe
Q 030926 119 KEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVL 168 (169)
Q Consensus 119 K~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~Vei 168 (169)
|+||++|||||+|||+|||++|++||+|+||+|||+||++|+++||+|+|
T Consensus 78 K~VR~it~LgLkEAK~lVe~~P~~iKe~vsKeeAE~ik~kLe~aGA~Vel 127 (127)
T cd00387 78 KEVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127 (127)
T ss_pred HHHHHHhCCChHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEeC
Confidence 99999999999999999999999999999999999999999999999986
No 4
>TIGR00855 L12 ribosomal protein L7/L12. THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus.
Probab=100.00 E-value=1.5e-39 Score=253.27 Aligned_cols=122 Identities=43% Similarity=0.592 Sum_probs=105.9
Q ss_pred hHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhccceeEEEeecCcchhHHHHH
Q 030926 40 KLERISDELLDLTKLERYDFATLFGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQATKIKIIK 119 (169)
Q Consensus 40 kv~~Ivd~I~~LTLlE~seLv~~leekfgv~~~~~~~~~~~~~~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vIK 119 (169)
+.++|+|+|++|||+|++||++.|+++|||++++++++++ + ++++ +++..+|||+|||+|+.++ ++||+|||
T Consensus 5 ~~~~ive~i~~LTllE~~eLv~~lee~fgV~a~a~~a~~~--a--~~~~---~~~~~eEKt~f~V~L~~~~-~~Ki~vIK 76 (126)
T TIGR00855 5 SKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAGA--A--GAAA---AAAAAEEKTEFDVILKGAG-DNKIAVIK 76 (126)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCccchhhhcc--c--cccc---ccccccccceeeEEEecCC-cchhHHHH
Confidence 4589999999999999999999999999999876543211 1 1111 1234579999999999885 68999999
Q ss_pred HHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 120 EVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 120 ~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 77 ~vR~itgLgLkEAK~lVe~~P~~ike~vsKeeAe~ik~~Le~aGa~veik 126 (126)
T TIGR00855 77 VVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEVK 126 (126)
T ss_pred HHHHHcCCcHHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 99999999999999999999999999999999999999999999999983
No 5
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=100.00 E-value=3.5e-39 Score=250.35 Aligned_cols=122 Identities=46% Similarity=0.617 Sum_probs=107.1
Q ss_pred ChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhccceeEEEeecCcchhHHH
Q 030926 38 TQKLERISDELLDLTKLERYDFATLFGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQATKIKI 117 (169)
Q Consensus 38 s~kv~~Ivd~I~~LTLlE~seLv~~leekfgv~~~~~~~~~~~~~~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~v 117 (169)
+-++++|+|+|++|||+|++||++.|+++|||++.++++++ ++++ .++.++|||+|||+|++| +++||+|
T Consensus 2 ~~~~~~i~e~i~~LtllE~~eLv~~lee~fgv~a~~~~~~~-----~~~~----~~~~~eEkt~f~V~L~~~-~~kKi~v 71 (123)
T PRK00157 2 ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAA-----AAAA----AAAAAEEKTEFDVVLKSA-GDKKIAV 71 (123)
T ss_pred CccHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhccc-----cccc----cccccccccceeEEEecc-chhhHHH
Confidence 44689999999999999999999999999999987643221 1111 123457999999999999 5799999
Q ss_pred HHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 118 IKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 118 IK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 72 IK~vR~itgLgLkEAK~lVe~~P~~ike~v~keeAe~ik~~Le~aGa~velk 123 (123)
T PRK00157 72 IKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGAKVELK 123 (123)
T ss_pred HHHHHHHhCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEeeC
Confidence 9999999999999999999999999999999999999999999999999984
No 6
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-39 Score=248.55 Aligned_cols=122 Identities=47% Similarity=0.620 Sum_probs=107.5
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhccceeEEEeecCcchhHHHH
Q 030926 39 QKLERISDELLDLTKLERYDFATLFGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQATKIKII 118 (169)
Q Consensus 39 ~kv~~Ivd~I~~LTLlE~seLv~~leekfgv~~~~~~~~~~~~~~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vI 118 (169)
-.+++|+++|++||++|+++|++.++++|||++.+|++++++ + + + ..+..+|||+|||+|.++ +++||+||
T Consensus 3 ~~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa~va~a~~--~-a-~----a~~aaeEktefdVvL~~~-g~kKI~VI 73 (124)
T COG0222 3 LTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAA--G-A-A----AAEAAEEKTEFDVVLKSA-GGKKIAVI 73 (124)
T ss_pred CcHHHHHHHHHHhhHHHHHHHHHHHHHHhCCccchhhhhccc--c-c-c----ccccccccceeEEEeccc-CCcchhHH
Confidence 457899999999999999999999999999998876443211 1 1 1 122367999999999998 58999999
Q ss_pred HHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 119 KEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 119 K~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
|.||++|||||||||++||++|++||+|++|+|||+||++|+++||+|++.
T Consensus 74 K~vR~itGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~V~~k 124 (124)
T COG0222 74 KVVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124 (124)
T ss_pred HHHHHHhcccHHHHHHHHHhCcHHHHccCCHHHHHHHHHHHHHcCCeEeeC
Confidence 999999999999999999999999999999999999999999999999984
No 7
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=99.91 E-value=4e-25 Score=155.74 Aligned_cols=68 Identities=54% Similarity=0.803 Sum_probs=60.4
Q ss_pred ceeEEEeecCcchhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 101 AFDVKLEKYDQATKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 101 ~fdV~L~~~~~~kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
+|||+|+++ +++||++||.||++|||||+|||++||++|++|+++++++|||+|+++|+++||+|+|+
T Consensus 1 ef~V~L~~~-~~~ki~vIK~vR~~tgl~L~eAK~~vd~~p~~ik~~v~keeAe~ik~~Le~aGa~v~l~ 68 (68)
T PF00542_consen 1 EFDVVLKSF-GEKKIKVIKEVREITGLGLKEAKKLVDSLPKVIKEGVSKEEAEEIKKKLEAAGAKVELK 68 (68)
T ss_dssp SEEEEEEE--TTGHHHHHHHHHHHC---HHHHHHHHCTTTEEEEEEE-HHHHHHHHHHHHCCT-EEEEE
T ss_pred CeEEEEeec-ccchHHHHHHHHHHhCCcHHHHHHHHHhCCHHHHcCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 699999999 79999999999999999999999999999999999999999999999999999999985
No 8
>PRK06771 hypothetical protein; Provisional
Probab=97.86 E-value=1.2e-05 Score=60.27 Aligned_cols=29 Identities=28% Similarity=0.469 Sum_probs=27.2
Q ss_pred cchhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030926 111 QATKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 111 ~~kKi~vIK~VR~it~LgLkEaK~lVe~~ 139 (169)
.++||+.||.+|+.||+||+|||++||++
T Consensus 65 ~Gkki~AIK~~Re~tG~~L~eAK~yVD~L 93 (93)
T PRK06771 65 EGQTVTAVKRVREAFGFSLLEAKQYVDKL 93 (93)
T ss_pred cCCchHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 46999999999999999999999999975
No 9
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=90.02 E-value=0.82 Score=32.45 Aligned_cols=65 Identities=22% Similarity=0.298 Sum_probs=48.1
Q ss_pred hccceeEEEeecCcchhHHHHHHHHHhhCCChhHHHHHHhhcc----hhhhcCCCHHHHHHHHHHHHHcC
Q 030926 98 EKTAFDVKLEKYDQATKIKIIKEVKTFTGLGLKESKDLVEKAP----AVIKKGVTKEEADKIVEKLKELN 163 (169)
Q Consensus 98 EKt~fdV~L~~~~~~kKi~vIK~VR~it~LgLkEaK~lVe~~P----~~IKe~vsKeEAEeik~kLe~aG 163 (169)
+...|.|+|-+-+-..--.||..++...|+...+|..+...+- .+|.. -++++||....+|...|
T Consensus 3 ~~~~~~vvL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~avv~~-~~~e~ae~~~~~l~~~g 71 (82)
T PF02617_consen 3 EPDMYRVVLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREGRAVVGT-GSREEAEEYAEKLQRAG 71 (82)
T ss_dssp S--EEEEEEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHSEEEEEE-EEHHHHHHHHHHHHHHH
T ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcCCEeeee-CCHHHHHHHHHHHHHHh
Confidence 4467999997655556779999999999999999999877553 35544 58999999999999998
No 10
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=78.87 E-value=16 Score=27.64 Aligned_cols=72 Identities=17% Similarity=0.262 Sum_probs=57.1
Q ss_pred hhccceeEEEeecCcchhHHHHHHHHHhhCCChhHHHHHHhhcc---h-hhhcCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 97 AEKTAFDVKLEKYDQATKIKIIKEVKTFTGLGLKESKDLVEKAP---A-VIKKGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 97 ~EKt~fdV~L~~~~~~kKi~vIK~VR~it~LgLkEaK~lVe~~P---~-~IKe~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
.....|.|+|-+-|-...==||..++.+.+++..+|.++...+= + ++.. -++|.||-...+|...|-.+.||
T Consensus 23 ~~~~~y~ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~-~~~e~AE~~~~~l~~~~L~~~ie 98 (100)
T PRK00033 23 KPPPMYKVLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGV-CTREVAETKVEQVHQHGLLCTME 98 (100)
T ss_pred CCCCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEE-EcHHHHHHHHHHHHcCCCeEEEe
Confidence 33456999997754445557999999999999999998877542 2 4443 59999999999999999988886
No 11
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=65.15 E-value=39 Score=25.19 Aligned_cols=72 Identities=14% Similarity=0.099 Sum_probs=55.2
Q ss_pred hhhccceeEEEeecCcchhHHHH-HHHHHhhCCChhHHHHHHhhcc---hhhhcCCCHHHHHHHHHHHHHcCcEEE
Q 030926 96 AAEKTAFDVKLEKYDQATKIKII-KEVKTFTGLGLKESKDLVEKAP---AVIKKGVTKEEADKIVEKLKELNAIVV 167 (169)
Q Consensus 96 ~~EKt~fdV~L~~~~~~kKi~vI-K~VR~it~LgLkEaK~lVe~~P---~~IKe~vsKeEAEeik~kLe~aGA~Ve 167 (169)
......|.|+|-+-|-.--==|| ..++.+.+++..+|..+.-.+= +-|----++|.||-...+|...|.++|
T Consensus 16 ~~~p~~ykViL~NDd~~t~dfVi~~vl~~vf~~s~~~A~~iml~vH~~G~avv~~~~~E~AE~~~~~l~~~glt~e 91 (94)
T PRK13019 16 LERYPLYKVIVLNDDFNTFEHVVNCLLKAIPGMSEDRAWRLMITAHKEGSAVVWVGPLEQAELYHQQLTDAGLTMA 91 (94)
T ss_pred ccCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHHcccccC
Confidence 34456799999775444455688 6778889999999999887552 233334799999999999999998765
No 12
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=60.60 E-value=8.8 Score=34.38 Aligned_cols=27 Identities=30% Similarity=0.523 Sum_probs=23.4
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~ 139 (169)
-+.+.+|++|+.||-|++++|+.++..
T Consensus 4 ita~~VKeLRe~TgAGMmdCKkAL~E~ 30 (296)
T COG0264 4 ITAALVKELREKTGAGMMDCKKALEEA 30 (296)
T ss_pred ccHHHHHHHHHHhCCcHHHHHHHHHHc
Confidence 456899999999999999999987654
No 13
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=58.75 E-value=36 Score=26.58 Aligned_cols=39 Identities=18% Similarity=0.088 Sum_probs=24.8
Q ss_pred ccccCChhHHHHHHHHhcCCHHHHHHHHHHHHHHh-CCCCCCC
Q 030926 33 VTESRTQKLERISDELLDLTKLERYDFATLFGCKL-GLDRFGP 74 (169)
Q Consensus 33 ~~~~~s~kv~~Ivd~I~~LTLlE~seLv~~leekf-gv~~~~~ 74 (169)
.+.....+++.++.+|+.-|+-| |+..=+++| .||..++
T Consensus 31 G~E~d~e~i~~visel~GK~i~E---lIA~G~eklAsvpsGGa 70 (112)
T KOG3449|consen 31 GAEIDDERINLVLSELKGKDIEE---LIAAGREKLASVPSGGA 70 (112)
T ss_pred CcccCHHHHHHHHHHhcCCCHHH---HHHHhHHHHhcCCCCCc
Confidence 34556788888888888887655 444444444 4554443
No 14
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=56.49 E-value=5.5 Score=28.99 Aligned_cols=36 Identities=8% Similarity=0.175 Sum_probs=30.5
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCC
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVT 148 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vs 148 (169)
+|-.+|+.|.+-+|+.-++++.+||.+=..|.+.+.
T Consensus 2 tK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~ 37 (90)
T PRK10664 2 NKSQLIDKIAAGADISKAAAGRALDAIIASVTESLK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 466899999999999999999999998777765543
No 15
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=56.01 E-value=14 Score=31.02 Aligned_cols=29 Identities=31% Similarity=0.525 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhh
Q 030926 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVI 143 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEaK~lVe~~P~~I 143 (169)
...||++|+.||.|+.+.|+.+.....-+
T Consensus 5 a~~ik~LR~~tga~~~~ck~AL~~~~gd~ 33 (198)
T PRK12332 5 AKLVKELREKTGAGMMDCKKALEEANGDM 33 (198)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 47899999999999999999887766555
No 16
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=55.14 E-value=5.9 Score=28.73 Aligned_cols=35 Identities=20% Similarity=0.286 Sum_probs=29.9
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCC
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+-+++.-++++..|+.+-.+|.+.+
T Consensus 2 ~K~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L 36 (90)
T PRK10753 2 NKTQLIDVIADKAELSKTQAKAALESTLAAITESL 36 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999877776544
No 17
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=53.78 E-value=29 Score=25.09 Aligned_cols=47 Identities=13% Similarity=0.250 Sum_probs=29.7
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHH
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLK 160 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe 160 (169)
-.++..|+.+|+ +|++|+|.+.+++.....+++ +=.+..+.+..+++
T Consensus 44 l~~l~~I~~lr~-~G~~l~eI~~~l~~~~~~~~~-~l~~~~~~l~~~i~ 90 (96)
T cd04788 44 IRRLHQIIALRR-LGFSLREIGRALDGPDFDPLE-LLRRQLARLEEQLE 90 (96)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhCCChhHHH-HHHHHHHHHHHHHH
Confidence 367777777776 699999999999876532222 22334444444444
No 18
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=53.54 E-value=15 Score=32.57 Aligned_cols=29 Identities=24% Similarity=0.447 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhh
Q 030926 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVI 143 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEaK~lVe~~P~~I 143 (169)
.+.||++|+.||-|+.+.|+.++....-+
T Consensus 5 a~~IK~LRe~Tgagm~dCKkAL~e~~gDi 33 (290)
T TIGR00116 5 AQLVKELRERTGAGMMDCKKALTEANGDF 33 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 36799999999999999999988776655
No 19
>PRK09377 tsf elongation factor Ts; Provisional
Probab=53.36 E-value=14 Score=32.64 Aligned_cols=29 Identities=28% Similarity=0.462 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhh
Q 030926 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVI 143 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEaK~lVe~~P~~I 143 (169)
.+.||++|+.||-|+.+.|+.++....-+
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ 34 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDI 34 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 47899999999999999999988776554
No 20
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=51.58 E-value=21 Score=23.48 Aligned_cols=22 Identities=23% Similarity=0.688 Sum_probs=15.9
Q ss_pred hHHHHHHHHHhhCCChhHHHHHH
Q 030926 114 KIKIIKEVKTFTGLGLKESKDLV 136 (169)
Q Consensus 114 Ki~vIK~VR~it~LgLkEaK~lV 136 (169)
++..|+..|. .|++|.|-|+++
T Consensus 3 rL~~I~~~r~-lGfsL~eI~~~l 24 (65)
T PF09278_consen 3 RLQFIRRLRE-LGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHHHH-TT--HHHHHHHH
T ss_pred HHHHHHHHHH-cCCCHHHHHHHH
Confidence 4566666665 799999999999
No 21
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=49.53 E-value=28 Score=23.85 Aligned_cols=26 Identities=27% Similarity=0.640 Sum_probs=20.8
Q ss_pred HHHHhhcchhhhcC-CCHHHHHHHHHHHHH
Q 030926 133 KDLVEKAPAVIKKG-VTKEEADKIVEKLKE 161 (169)
Q Consensus 133 K~lVe~~P~~IKe~-vsKeEAEeik~kLe~ 161 (169)
|.+|+ +.|+.| +|+|.|+.|++.++.
T Consensus 21 K~~id---k~Ve~G~iTqeqAd~ik~~id~ 47 (59)
T PF10925_consen 21 KQIID---KYVEAGVITQEQADAIKKHIDQ 47 (59)
T ss_pred HHHHH---HHHHcCCCCHHHHHHHHHHHHH
Confidence 45665 467777 899999999998875
No 22
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=48.21 E-value=48 Score=24.16 Aligned_cols=31 Identities=16% Similarity=0.352 Sum_probs=27.1
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAPAV 142 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P~~ 142 (169)
-.++..|+.+|+..|++|.+.+.+++..+..
T Consensus 43 v~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 43 LKRLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 4788999999988899999999999887765
No 23
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=48.09 E-value=54 Score=21.53 Aligned_cols=46 Identities=24% Similarity=0.486 Sum_probs=31.0
Q ss_pred HHHHHHHHhhCCChhHHHHHHhhcchhh-------------hcCCCHHHHHHHHHHHHH
Q 030926 116 KIIKEVKTFTGLGLKESKDLVEKAPAVI-------------KKGVTKEEADKIVEKLKE 161 (169)
Q Consensus 116 ~vIK~VR~it~LgLkEaK~lVe~~P~~I-------------Ke~vsKeEAEeik~kLe~ 161 (169)
.++..+.++.|+|-+-++.|++.--.++ -.|+++..|+.|...+.+
T Consensus 2 ~~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 2 GVFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAARE 60 (60)
T ss_dssp HHHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHHH
T ss_pred HHHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence 4566667777888777777777622222 247888888888877653
No 24
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=48.01 E-value=26 Score=22.35 Aligned_cols=27 Identities=19% Similarity=0.295 Sum_probs=20.5
Q ss_pred HHHHHHhhCCChhHHHHHHhhcchhhh
Q 030926 118 IKEVKTFTGLGLKESKDLVEKAPAVIK 144 (169)
Q Consensus 118 IK~VR~it~LgLkEaK~lVe~~P~~IK 144 (169)
.|.+|.-.||-..+||++|.+.|.=-.
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~C~~Cq~ 38 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQCPKCQQ 38 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHHSCCHHS
T ss_pred HHHHHHHHccCHHHHHHHHHHCHHHhh
Confidence 467788889999999999999997443
No 25
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=46.94 E-value=18 Score=25.10 Aligned_cols=35 Identities=29% Similarity=0.404 Sum_probs=29.4
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCC
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+.+++.-++++.+++.+-.+|.+.+
T Consensus 1 ~K~~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L 35 (87)
T cd00591 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLDVITEAL 35 (87)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 36689999999999999999999998877766543
No 26
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=45.65 E-value=18 Score=25.30 Aligned_cols=36 Identities=25% Similarity=0.388 Sum_probs=30.6
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCC
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVT 148 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vs 148 (169)
+|-.+|+.|.+.+++.-++++..++.+..+|.+.+.
T Consensus 2 tk~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~ 37 (90)
T smart00411 2 TKSELIDAIAEKAGLSKKDAKAAVDAFLEIITEALK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 356899999999999999999999999888776543
No 27
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.48 E-value=48 Score=24.39 Aligned_cols=29 Identities=21% Similarity=0.410 Sum_probs=23.7
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcch
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAPA 141 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P~ 141 (169)
-..+..|+.+|. +|++|.|.+.+++..+.
T Consensus 45 i~~l~~I~~lr~-~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 45 LERLNRIKYLRD-LGFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhcCCH
Confidence 367777777776 89999999999998764
No 28
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=40.95 E-value=27 Score=22.92 Aligned_cols=26 Identities=31% Similarity=0.640 Sum_probs=20.9
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
-..+..|+.+++ .|+.+.+.+++++.
T Consensus 43 v~~l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 43 VERLREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHHHHHH-TTTHHHHHHHHH--
T ss_pred HHHHHHHHHHHH-CcCCHHHHHHHHcc
Confidence 478888888888 99999999998763
No 29
>PF10044 Ret_tiss: Retinal tissue protein; InterPro: IPR018737 Rtp is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. Rtp is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein [].
Probab=39.85 E-value=22 Score=26.88 Aligned_cols=23 Identities=30% Similarity=0.648 Sum_probs=16.3
Q ss_pred HHHHHHHHh----hCCChhHHHHHHhh
Q 030926 116 KIIKEVKTF----TGLGLKESKDLVEK 138 (169)
Q Consensus 116 ~vIK~VR~i----t~LgLkEaK~lVe~ 138 (169)
++++.||++ -.|||.|||++--+
T Consensus 62 ~L~~~Ik~L~~~aYqLGl~EaKEmtRG 88 (95)
T PF10044_consen 62 QLIEKIKKLQDEAYQLGLEEAKEMTRG 88 (95)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHhh
Confidence 455555544 68999999998543
No 30
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.92 E-value=92 Score=22.03 Aligned_cols=41 Identities=24% Similarity=0.408 Sum_probs=30.8
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHc
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKEL 162 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~a 162 (169)
-.++..|+.++.-.|++|.+.+.+++ =.++-+.+...|+..
T Consensus 44 v~~l~~i~~L~~d~g~~l~~i~~~l~----------l~~~~~~l~~~l~~l 84 (91)
T cd04766 44 IERLRRIQRLTQELGVNLAGVKRILE----------LEEELAELRAELDEL 84 (91)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHH----------HHHHHHHHHHHHHHH
Confidence 47888888888889999999999998 345556666655543
No 31
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=34.51 E-value=33 Score=24.82 Aligned_cols=35 Identities=29% Similarity=0.347 Sum_probs=30.2
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCC
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+.+++.-++++..++.+-..|.+.+
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 38 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDAL 38 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999999999888776644
No 32
>PF11363 DUF3164: Protein of unknown function (DUF3164); InterPro: IPR021505 This entry is represented by Bacteriophage B3, Orf6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.93 E-value=69 Score=26.76 Aligned_cols=82 Identities=21% Similarity=0.182 Sum_probs=50.7
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCCCchhhhhhhccceeEEEeecCcchhHHHHHH
Q 030926 41 LERISDELLDLTKLERYDFATLFGCKLGLDRFGPVVPAFPSSGPAASGSTSAETKAAEKTAFDVKLEKYDQATKIKIIKE 120 (169)
Q Consensus 41 v~~Ivd~I~~LTLlE~seLv~~leekfgv~~~~~~~~~~~~~~~~a~~~~~~~~~~~EKt~fdV~L~~~~~~kKi~vIK~ 120 (169)
+.+.+...+.-+.-++..+++++.+.+|+...+ ..-++.|.+||+..||.+--.
T Consensus 36 l~~~l~~fK~~~f~d~~af~~l~~e~Yg~k~gg--------------------------~kGn~Tl~sfDG~~kV~i~~~ 89 (195)
T PF11363_consen 36 LSEQLAEFKAHTFEDIEAFIELSAEEYGVKLGG--------------------------KKGNVTLTSFDGRYKVTIAVQ 89 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCC--------------------------CcCcEEEEEeCCCEEEEEEec
Confidence 445556666777888899999999999985311 111456667776555544322
Q ss_pred HHHhhCCChhHHHHHHhhcchhhhcCCC
Q 030926 121 VKTFTGLGLKESKDLVEKAPAVIKKGVT 148 (169)
Q Consensus 121 VR~it~LgLkEaK~lVe~~P~~IKe~vs 148 (169)
-+--.+=.|.-||++|+.+=.-.-+|.+
T Consensus 90 ~~~~Fde~l~~Ak~lIde~l~~w~~g~~ 117 (195)
T PF11363_consen 90 DRISFDERLQAAKALIDECLNEWAKGAD 117 (195)
T ss_pred ccCCcChHHHHHHHHHHHHHHHHhcCCC
Confidence 2222344577778888766555555543
No 33
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.58 E-value=99 Score=22.27 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=22.6
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcc
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAP 140 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P 140 (169)
-.++..|+.+|+ .|+.|++.+.+++...
T Consensus 44 l~~l~~I~~lr~-~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 44 LYQLQFILFLRE-LGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhcCc
Confidence 367777887776 5999999999998754
No 34
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=32.21 E-value=80 Score=24.11 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=21.5
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
-.++..|+.+|+ .|++|+|.+++++.
T Consensus 45 l~~l~~I~~lr~-~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 45 QKRLRFILKAKE-LGFTLDEIKELLSI 70 (131)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 367778888775 79999999999984
No 35
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=31.85 E-value=55 Score=21.69 Aligned_cols=23 Identities=26% Similarity=0.354 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHH
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLV 136 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lV 136 (169)
.++..|+.+++ .|+.|.|.+.++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~l 67 (68)
T cd04763 45 DRILEIKRWID-NGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHh
Confidence 57777777777 999999999886
No 36
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=31.46 E-value=56 Score=21.28 Aligned_cols=24 Identities=13% Similarity=0.497 Sum_probs=17.4
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHh
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVE 137 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe 137 (169)
..+..|+.+++ .|+.|.|.+++++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~~~ 68 (68)
T cd01104 45 ARLRLIRRLTS-EGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 45555555555 8999999998863
No 37
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.32 E-value=90 Score=22.53 Aligned_cols=26 Identities=35% Similarity=0.549 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~ 139 (169)
..+..|+.+|. .|+.|.|.+++++..
T Consensus 45 ~~l~~I~~lr~-~G~~l~eI~~~l~~~ 70 (97)
T cd04782 45 EQLDIILLLKE-LGISLKEIKDYLDNR 70 (97)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcC
Confidence 57777777765 599999999999753
No 38
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.23 E-value=63 Score=23.51 Aligned_cols=27 Identities=15% Similarity=0.490 Sum_probs=24.0
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
-.++..|+.+|...|++|.+.+.+++.
T Consensus 44 v~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 44 VERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 478888888888899999999999986
No 39
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=29.75 E-value=59 Score=22.56 Aligned_cols=19 Identities=32% Similarity=0.326 Sum_probs=17.4
Q ss_pred cCCHHHHHHHHHHHHHHhC
Q 030926 50 DLTKLERYDFATLFGCKLG 68 (169)
Q Consensus 50 ~LTLlE~seLv~~leekfg 68 (169)
.||-.|++++++.|+.+.|
T Consensus 38 ~LtkaeAs~rId~L~~~~g 56 (57)
T PF11272_consen 38 DLTKAEASERIDELQAQTG 56 (57)
T ss_pred cccHHHHHHHHHHHHHHhC
Confidence 7999999999999998876
No 40
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=29.58 E-value=1.6e+02 Score=21.92 Aligned_cols=27 Identities=15% Similarity=0.368 Sum_probs=21.3
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~ 139 (169)
-.++..|+.+|+ .|++|+|.+.+++..
T Consensus 43 l~~l~~I~~lr~-~G~~L~eI~~~l~~~ 69 (120)
T cd04781 43 LDRLALIALGRA-AGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 356777777775 699999999999864
No 41
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.52 E-value=74 Score=22.61 Aligned_cols=26 Identities=19% Similarity=0.424 Sum_probs=21.9
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
-.++..|+.+|+ .|+.|.+.+++++.
T Consensus 45 v~~l~~I~~Lr~-~G~sl~~i~~~l~~ 70 (88)
T cd01105 45 VDRLLVIKELLD-EGFTLAAAVEKLRR 70 (88)
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence 467788888887 89999999999973
No 42
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=28.10 E-value=1.5e+02 Score=21.45 Aligned_cols=28 Identities=29% Similarity=0.447 Sum_probs=22.5
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcc
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAP 140 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P 140 (169)
-..+..|+.+|. .|++|.+.+.+++...
T Consensus 44 i~~l~~i~~lr~-~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 44 LERLQQILFLKE-LGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHHcCc
Confidence 366777777776 6999999999998764
No 43
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=27.19 E-value=1.1e+02 Score=24.00 Aligned_cols=25 Identities=24% Similarity=0.498 Sum_probs=19.9
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
.++..|+..| -+|++|.|.+++++.
T Consensus 52 ~rl~~I~~lr-~~G~sL~eI~~ll~~ 76 (144)
T PRK13752 52 TRVRFVKSAQ-RLGFSLDEIAELLRL 76 (144)
T ss_pred HHHHHHHHHH-HcCCCHHHHHHHHhc
Confidence 5666676666 479999999999974
No 44
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=26.61 E-value=64 Score=26.60 Aligned_cols=64 Identities=28% Similarity=0.378 Sum_probs=41.3
Q ss_pred eEEEeecCcchhHHHHH-HHHHh---hCCChhHHHH-HHh-------hcchhhhcCCCHHHHHHHHHHHHHcCcEEE
Q 030926 103 DVKLEKYDQATKIKIIK-EVKTF---TGLGLKESKD-LVE-------KAPAVIKKGVTKEEADKIVEKLKELNAIVV 167 (169)
Q Consensus 103 dV~L~~~~~~kKi~vIK-~VR~i---t~LgLkEaK~-lVe-------~~P~~IKe~vsKeEAEeik~kLe~aGA~Ve 167 (169)
.++|..- .+.|+.-++ .++.- -|++++--.- -.+ .-...|++|+++|.|.+|.+.+++.+-+|.
T Consensus 45 ~i~l~a~-~d~kl~~v~diL~~kl~KR~i~~k~ld~~~~e~~sG~~vrq~i~lk~GI~~e~AKkIvK~IKd~klKVq 120 (161)
T PRK05412 45 EITLTAE-SDFQLKQVKDILRSKLIKRGIDLKALDYGKVEKASGKTVKQEVKLKQGIDQELAKKIVKLIKDSKLKVQ 120 (161)
T ss_pred EEEEEeC-CHHHHHHHHHHHHHHHHHcCCCHHHcCCCCccccCCCEEEEEEehhhccCHHHHHHHHHHHHhcCCcee
Confidence 4777765 467776544 44422 3666552211 111 123478999999999999999999988764
No 45
>PF00828 Ribosomal_L18e: Ribosomal protein L18e/L15; InterPro: IPR021131 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents both L15 and L18e ribosomal proteins, which share a common structure consisting mainly of parallel beta sheets (beta-alpha-beta units) with a core of three turns of irregular (beta-beta-alpha)n superhelix [, ].; PDB: 3O58_Y 1S1I_V 3O5H_Y 3IZS_O 3IZR_R 2OTL_L 1M1K_M 3G6E_L 1VQ9_L 1YIT_L ....
Probab=26.26 E-value=62 Score=24.53 Aligned_cols=27 Identities=30% Similarity=0.342 Sum_probs=18.4
Q ss_pred hcchhhhc-CCCHHHHHHHHHHHHHcCcEEEe
Q 030926 138 KAPAVIKK-GVTKEEADKIVEKLKELNAIVVL 168 (169)
Q Consensus 138 ~~P~~IKe-~vsKeEAEeik~kLe~aGA~Vei 168 (169)
+.|-+|+. .+|+ ..++++|++|++|++
T Consensus 101 ~~~l~I~a~~~S~----~A~ekIe~aGG~v~~ 128 (129)
T PF00828_consen 101 TKPLTIKAHRFSK----SAKEKIEAAGGEVVT 128 (129)
T ss_dssp SSSEEEEESEETH----HHHHHHHHTSEEEEE
T ss_pred ccceEEEEEecCH----HHHHHHHHcCCEEEe
Confidence 45555554 3454 467789999999975
No 46
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.92 E-value=83 Score=23.15 Aligned_cols=26 Identities=27% Similarity=0.472 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~ 139 (169)
.++..|+.+|+ .|++|+|.+++++..
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~~ 70 (113)
T cd01109 45 EWLEFIKCLRN-TGMSIKDIKEYAELR 70 (113)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHHH
Confidence 57777777775 799999999998753
No 47
>cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
Probab=25.82 E-value=1e+02 Score=25.85 Aligned_cols=40 Identities=18% Similarity=0.199 Sum_probs=29.9
Q ss_pred HHHHHHHHHhhCCChhHHHHHHhhcchhhh--cCCCHHHHHHHHHHHHHcCcEE
Q 030926 115 IKIIKEVKTFTGLGLKESKDLVEKAPAVIK--KGVTKEEADKIVEKLKELNAIV 166 (169)
Q Consensus 115 i~vIK~VR~it~LgLkEaK~lVe~~P~~IK--e~vsKeEAEeik~kLe~aGA~V 166 (169)
..+++.||+.+ +.|-.+| -+++.+|..++.+.++++|+..
T Consensus 151 ~eiv~~vr~~~------------~~pv~vKl~~~~~~~~~~~~a~~l~~~Gad~ 192 (289)
T cd02810 151 ANLLKAVKAAV------------DIPLLVKLSPYFDLEDIVELAKAAERAGADG 192 (289)
T ss_pred HHHHHHHHHcc------------CCCEEEEeCCCCCHHHHHHHHHHHHHcCCCE
Confidence 35677777544 3677777 3467789999999999999874
No 48
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=25.50 E-value=1.3e+02 Score=22.73 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=21.2
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
-.++..|+.+|. +|++|+|-+.+++.
T Consensus 44 ~~~l~~I~~lr~-~G~sL~eI~~~l~~ 69 (127)
T cd01108 44 IEELRFIRRARD-LGFSLEEIRELLAL 69 (127)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 367777777774 89999999999973
No 49
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=25.38 E-value=1.1e+02 Score=23.65 Aligned_cols=25 Identities=24% Similarity=0.603 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
.++..|+..|. +|++|+|.+++++.
T Consensus 45 ~~l~~I~~lr~-~G~sl~eI~~~l~~ 69 (135)
T PRK10227 45 NELTLLRQARQ-VGFNLEESGELVNL 69 (135)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHh
Confidence 56666666664 69999999999974
No 50
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=24.93 E-value=1e+02 Score=27.07 Aligned_cols=43 Identities=21% Similarity=0.317 Sum_probs=35.4
Q ss_pred CChhHHHHHHhhcch-hhhcCCCHHHHHHHHHHHHHcC--cEEEeC
Q 030926 127 LGLKESKDLVEKAPA-VIKKGVTKEEADKIVEKLKELN--AIVVLE 169 (169)
Q Consensus 127 LgLkEaK~lVe~~P~-~IKe~vsKeEAEeik~kLe~aG--A~VeiE 169 (169)
=+|.|+++.++.-+. +..+|++.++..++.+.+.+.| ..+.||
T Consensus 190 ~~leea~~a~~agaDiI~LDn~~~e~l~~~v~~l~~~~~~~~~~le 235 (278)
T PRK08385 190 ESLEDALKAAKAGADIIMLDNMTPEEIREVIEALKREGLRERVKIE 235 (278)
T ss_pred CCHHHHHHHHHcCcCEEEECCCCHHHHHHHHHHHHhcCcCCCEEEE
Confidence 479999999997666 5599999999999999998876 456554
No 51
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=24.93 E-value=52 Score=27.10 Aligned_cols=64 Identities=28% Similarity=0.399 Sum_probs=34.3
Q ss_pred eEEEeecCcchhHHHHHH-HHHh---hCCChhHHHHH-Hhhc-------chhhhcCCCHHHHHHHHHHHHHcCcEEE
Q 030926 103 DVKLEKYDQATKIKIIKE-VKTF---TGLGLKESKDL-VEKA-------PAVIKKGVTKEEADKIVEKLKELNAIVV 167 (169)
Q Consensus 103 dV~L~~~~~~kKi~vIK~-VR~i---t~LgLkEaK~l-Ve~~-------P~~IKe~vsKeEAEeik~kLe~aGA~Ve 167 (169)
.++|..-+ +.|+.-+.. ++.- -|++++--.-- .+.+ ...+++|+++|.|.+|.+.+++.+-+|.
T Consensus 45 ~i~l~a~~-e~kl~~v~diL~~kl~KR~i~~k~ld~~k~e~asg~~vrq~i~lk~GI~~d~AKkIvK~IKd~klKVq 120 (160)
T PF04461_consen 45 TITLTAED-EFKLKQVKDILRSKLIKRGIDLKALDFGKIESASGGTVRQVIKLKQGIDQDTAKKIVKLIKDSKLKVQ 120 (160)
T ss_dssp EEEEEESS-HHHHHHHHHHHHHHHHHTT--GGGEE--SS-EEETTEEEEEEEE--S--HHHHHHHHHHHHHH--SEE
T ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHcCCCHHHcCCCCCccccCCEEEEEEEeecccCHHHHHHHHHHHHhcCCcee
Confidence 77887754 677655444 3432 26666522211 1211 2468999999999999999999987764
No 52
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.68 E-value=91 Score=22.70 Aligned_cols=25 Identities=24% Similarity=0.392 Sum_probs=20.4
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
.++..|+.+|+ +|++|+|-+++++.
T Consensus 43 ~~l~~I~~lr~-~G~sL~eI~~~l~~ 67 (107)
T cd04777 43 DDLEFILELKG-LGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHh
Confidence 56777777776 69999999999974
No 53
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=24.59 E-value=81 Score=24.31 Aligned_cols=33 Identities=21% Similarity=0.397 Sum_probs=26.2
Q ss_pred hHHHHHHhhcchhhhcC--CCHHHHHHHHHHHHHc
Q 030926 130 KESKDLVEKAPAVIKKG--VTKEEADKIVEKLKEL 162 (169)
Q Consensus 130 kEaK~lVe~~P~~IKe~--vsKeEAEeik~kLe~a 162 (169)
-|-+.|++++-.+++.. .+++|+++++.+++.+
T Consensus 15 ~el~~L~d~lEevL~ssg~~a~~e~~~lR~r~~~~ 49 (104)
T COG4575 15 AELQELLDTLEEVLKSSGSLAGDEAEELRSKAESA 49 (104)
T ss_pred HHHHHHHHHHHHHHHhcccchhhHHHHHHHHHHHH
Confidence 45668888888888865 7889999999988753
No 54
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=24.41 E-value=34 Score=19.61 Aligned_cols=12 Identities=33% Similarity=0.581 Sum_probs=9.6
Q ss_pred ccccCCCCCccc
Q 030926 4 VTRKFPRLGRVF 15 (169)
Q Consensus 4 ~~~~~~~~~~~~ 15 (169)
-..-|+|-||.|
T Consensus 4 ~~t~FSp~Grl~ 15 (23)
T PF10584_consen 4 SITTFSPDGRLF 15 (23)
T ss_dssp STTSBBTTSSBH
T ss_pred CceeECCCCeEE
Confidence 346799999987
No 55
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=24.21 E-value=71 Score=25.46 Aligned_cols=25 Identities=40% Similarity=0.602 Sum_probs=17.9
Q ss_pred chhhhcC-CCHHHHHHHHHHHHHcCcEEEe
Q 030926 140 PAVIKKG-VTKEEADKIVEKLKELNAIVVL 168 (169)
Q Consensus 140 P~~IKe~-vsKeEAEeik~kLe~aGA~Vei 168 (169)
|-+|+.. +| +..++++|++|++|++
T Consensus 119 pl~Vka~~fS----~~A~ekIe~aGG~v~l 144 (148)
T PRK06419 119 PLVIKADAFS----EKAIEKIEAAGGEVVL 144 (148)
T ss_pred CEEEEEeccC----HHHHHHHHHcCCEEEE
Confidence 6667643 34 3567789999999875
No 56
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=24.12 E-value=92 Score=20.48 Aligned_cols=24 Identities=33% Similarity=0.538 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHh
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVE 137 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe 137 (169)
..+..|+.+++ .|+.|.|.+.+++
T Consensus 44 ~~l~~i~~l~~-~g~~l~~i~~~l~ 67 (67)
T cd04764 44 ELLKKIKTLLE-KGLSIKEIKEILN 67 (67)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 56677777777 8999999998763
No 57
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=23.87 E-value=35 Score=24.44 Aligned_cols=35 Identities=17% Similarity=0.264 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHh-hCCChhHHHHHHhhcchhhhcCC
Q 030926 113 TKIKIIKEVKTF-TGLGLKESKDLVEKAPAVIKKGV 147 (169)
Q Consensus 113 kKi~vIK~VR~i-t~LgLkEaK~lVe~~P~~IKe~v 147 (169)
+|-.+|+.|.+. ++++-++++..|+.+-..|.+.+
T Consensus 2 tk~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L 37 (94)
T PRK00199 2 TKSELIERLAARNPHLSAKDVENAVKEILEEMSDAL 37 (94)
T ss_pred CHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 356789999864 79999999999999888777654
No 58
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase (subfamily 1) family protein. This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.
Probab=23.04 E-value=1.1e+02 Score=26.12 Aligned_cols=41 Identities=22% Similarity=0.222 Sum_probs=31.4
Q ss_pred hHHHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcEE
Q 030926 114 KIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIV 166 (169)
Q Consensus 114 Ki~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~V 166 (169)
-..+++.||+.+ ..|-.+|=..+-++..++.+.++++|+..
T Consensus 145 ~~eiv~~vr~~~------------~~pv~vKi~~~~~~~~~~a~~l~~~G~d~ 185 (300)
T TIGR01037 145 SADVVKAVKDKT------------DVPVFAKLSPNVTDITEIAKAAEEAGADG 185 (300)
T ss_pred HHHHHHHHHHhc------------CCCEEEECCCChhhHHHHHHHHHHcCCCE
Confidence 356677776543 36888887777789999999999999864
No 59
>PRK05350 acyl carrier protein; Provisional
Probab=22.99 E-value=1.1e+02 Score=21.29 Aligned_cols=26 Identities=19% Similarity=0.355 Sum_probs=21.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHHHHhCCC
Q 030926 44 ISDELLDLTKLERYDFATLFGCKLGLD 70 (169)
Q Consensus 44 Ivd~I~~LTLlE~seLv~~leekfgv~ 70 (169)
+.+.+ ++.=+...+|+-.|+++|||.
T Consensus 32 l~~dl-g~DSld~veli~~lE~~fgI~ 57 (82)
T PRK05350 32 LYEDL-DLDSIDAVDLVVHLQKLTGKK 57 (82)
T ss_pred chhhc-CCCHHHHHHHHHHHHHHHCCc
Confidence 33444 788889999999999999997
No 60
>cd04740 DHOD_1B_like Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
Probab=22.91 E-value=1.1e+02 Score=25.96 Aligned_cols=38 Identities=26% Similarity=0.313 Sum_probs=29.3
Q ss_pred HHHHHHHHhhCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcE
Q 030926 116 KIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAI 165 (169)
Q Consensus 116 ~vIK~VR~it~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~ 165 (169)
.+++.||+.+ ..|-.+|=+...++..++.+.++++|+.
T Consensus 144 eiv~~vr~~~------------~~Pv~vKl~~~~~~~~~~a~~~~~~G~d 181 (296)
T cd04740 144 EIVKAVKKAT------------DVPVIVKLTPNVTDIVEIARAAEEAGAD 181 (296)
T ss_pred HHHHHHHhcc------------CCCEEEEeCCCchhHHHHHHHHHHcCCC
Confidence 4666666544 4788888777777899999999999986
No 61
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.52 E-value=98 Score=23.24 Aligned_cols=25 Identities=16% Similarity=0.428 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
.++..|+..|+ +|++|.|.|++++.
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~ 69 (127)
T cd04784 45 ERLLFIRRCRS-LDMSLDEIRTLLQL 69 (127)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 45666666664 59999999999974
No 62
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=22.50 E-value=1.1e+02 Score=23.61 Aligned_cols=32 Identities=19% Similarity=0.350 Sum_probs=26.2
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcchhh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAPAVI 143 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P~~I 143 (169)
-..++.|+.+|+-.|+.|.+.+.+++-.|...
T Consensus 43 v~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~ 74 (120)
T cd04767 43 LKRLRFIKKLINEKGLNIAGVKQILSMYPCWS 74 (120)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhCcccc
Confidence 36777777777778999999999999988754
No 63
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=22.43 E-value=2.7e+02 Score=21.02 Aligned_cols=31 Identities=6% Similarity=-0.054 Sum_probs=21.5
Q ss_pred ccCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhC
Q 030926 35 ESRTQKLERISDELLDLTKLERYDFATLFGCKLG 68 (169)
Q Consensus 35 ~~~s~kv~~Ivd~I~~LTLlE~seLv~~leekfg 68 (169)
.....++..+++.|.+.++ .+|+.....+++
T Consensus 32 eVe~~~~~~~~~aLaGk~V---~eli~~g~~kl~ 62 (105)
T cd04411 32 EIEPERVKLFLSALNGKNI---DEVISKGKELMS 62 (105)
T ss_pred CcCHHHHHHHHHHHcCCCH---HHHHHHHHhhcc
Confidence 3455677888888888776 456677777764
No 64
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=22.13 E-value=1.2e+02 Score=19.66 Aligned_cols=25 Identities=36% Similarity=0.672 Sum_probs=20.6
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHh
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVE 137 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe 137 (169)
-..+..|+.+|+ .|+++.+.+.+++
T Consensus 44 l~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 44 LERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 367788888877 8999999998876
No 65
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=22.03 E-value=5.9e+02 Score=22.94 Aligned_cols=38 Identities=11% Similarity=0.163 Sum_probs=24.1
Q ss_pred hCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHcCcE
Q 030926 125 TGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAI 165 (169)
Q Consensus 125 t~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~aGA~ 165 (169)
..+|.. .+-+.+=+.+..+.+.+++.+....+.++|-.
T Consensus 129 islGvQ---S~~d~~L~~l~R~~~~~~~~~ai~~l~~~G~~ 166 (400)
T PRK07379 129 VSLGVQ---AFQDELLALCGRSHRVKDIFAAVDLIHQAGIE 166 (400)
T ss_pred EEEEcc---cCCHHHHHHhCCCCCHHHHHHHHHHHHHcCCC
Confidence 355544 22233334556778888888888888888765
No 66
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=21.69 E-value=1.5e+02 Score=25.99 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=31.1
Q ss_pred CCChhHHHHHHhhcch------hh--h-cCCCHHHHHHHHHHHHHcCcEEEeC
Q 030926 126 GLGLKESKDLVEKAPA------VI--K-KGVTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 126 ~LgLkEaK~lVe~~P~------~I--K-e~vsKeEAEeik~kLe~aGA~VeiE 169 (169)
..++++||++++.+-. .| - ....+.-|+.|+..|+++|-+|+++
T Consensus 297 ~~d~~kA~~lL~~aG~~~g~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i~ 349 (448)
T cd08494 297 PYDPDKARQLLAEAGAAYGLTLTLTLPPLPYARRIGEIIASQLAEVGITVKIE 349 (448)
T ss_pred CCCHHHHHHHHHHcCCCCCeEEEEEecCCcchhHHHHHHHHHHHhcCcEEEEE
Confidence 4567778888776521 11 1 2235789999999999999998863
No 67
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.40 E-value=69 Score=26.87 Aligned_cols=50 Identities=18% Similarity=0.304 Sum_probs=36.6
Q ss_pred cCcchhHHHHHHHHHh-hCCChhHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHc
Q 030926 109 YDQATKIKIIKEVKTF-TGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKEL 162 (169)
Q Consensus 109 ~~~~kKi~vIK~VR~i-t~LgLkEaK~lVe~~P~~IKe~vsKeEAEeik~kLe~a 162 (169)
+++.+| =+...+|.. |+||+..++-+|.+---+.-.+.+ +.++.++||++
T Consensus 13 VGgg~k-V~MAdLka~~~dlGf~~v~T~iaSGNlvf~s~~~---~~el~~klE~a 63 (178)
T COG3797 13 VGGGRK-VVMADLKAALTDLGFANVRTYIASGNLVFESEAG---AAELEAKLEAA 63 (178)
T ss_pred ecCCce-EeHHHHHHHHHHcCcchhhHhhhcCCEEEEcCCC---hHHHHHHHHHH
Confidence 444444 456777877 899999999999998777766666 55677777754
No 68
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=21.36 E-value=1.5e+02 Score=26.37 Aligned_cols=44 Identities=18% Similarity=0.216 Sum_probs=30.5
Q ss_pred CCChhHHHHHHhhcchh------h--hcC-CCHHHHHHHHHHHHHcCcEEEeC
Q 030926 126 GLGLKESKDLVEKAPAV------I--KKG-VTKEEADKIVEKLKELNAIVVLE 169 (169)
Q Consensus 126 ~LgLkEaK~lVe~~P~~------I--Ke~-vsKeEAEeik~kLe~aGA~VeiE 169 (169)
..++.+||++++.+-.. | -.+ ...+.|+.|++.|+++|-+|+++
T Consensus 300 ~~d~~~A~~lL~eaG~~~~~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i~ 352 (474)
T cd08499 300 EYDPEKAKELLAEAGYPDGFETTLWTNDNRERIKIAEFIQQQLAQIGIDVEIE 352 (474)
T ss_pred CCCHHHHHHHHHHcCCCCCceEEEEecCCCchhHHHHHHHHHHHHcCceEEEE
Confidence 45677788887755321 1 111 34678999999999999998863
No 69
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=21.13 E-value=1e+02 Score=20.88 Aligned_cols=23 Identities=9% Similarity=0.234 Sum_probs=19.6
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCC
Q 030926 49 LDLTKLERYDFATLFGCKLGLDR 71 (169)
Q Consensus 49 ~~LTLlE~seLv~~leekfgv~~ 71 (169)
..+.=+...+|+-.||++|||.-
T Consensus 33 lglDSl~~veli~~lE~~f~i~i 55 (77)
T TIGR00517 33 LGADSLDTVELVMALEEEFDIEI 55 (77)
T ss_pred cCCcHHHHHHHHHHHHHHHCCCC
Confidence 36777888999999999999973
No 70
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=20.93 E-value=74 Score=21.98 Aligned_cols=33 Identities=33% Similarity=0.447 Sum_probs=27.1
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhcchhhhc
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKK 145 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~P~~IKe 145 (169)
+|-.+|+.|.+-+++.-++++..++.+=.+|.+
T Consensus 2 tk~eli~~ia~~~~~s~~~v~~vl~~~~~~i~~ 34 (90)
T PF00216_consen 2 TKKELIKRIAEKTGLSKKDVEAVLDALFDVIKE 34 (90)
T ss_dssp BHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 356899999999999999999999987655554
No 71
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=20.73 E-value=1.7e+02 Score=23.33 Aligned_cols=25 Identities=20% Similarity=0.231 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhh
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEK 138 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~ 138 (169)
.++..|+..|+ +|++|.|-+++++.
T Consensus 55 ~~L~~I~~lr~-lG~sL~eIk~ll~~ 79 (154)
T PRK15002 55 RYVAIIKIAQR-IGIPLATIGEAFGV 79 (154)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 56666666664 79999999999974
No 72
>COG0236 AcpP Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.39 E-value=1e+02 Score=21.28 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=19.6
Q ss_pred hcCCHHHHHHHHHHHHHHhCCCC
Q 030926 49 LDLTKLERYDFATLFGCKLGLDR 71 (169)
Q Consensus 49 ~~LTLlE~seLv~~leekfgv~~ 71 (169)
..+.=+.+.+|+-.||++||+.-
T Consensus 35 lg~DSld~veLi~~lE~~f~i~i 57 (80)
T COG0236 35 LGLDSLDLVELVMALEEEFGIEI 57 (80)
T ss_pred cCccHHHHHHHHHHHHHHHCCcC
Confidence 46667789999999999999973
No 73
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.35 E-value=1.6e+02 Score=21.81 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHhhCCChhHHHHHHhhc
Q 030926 113 TKIKIIKEVKTFTGLGLKESKDLVEKA 139 (169)
Q Consensus 113 kKi~vIK~VR~it~LgLkEaK~lVe~~ 139 (169)
..+..|+.+|+ +|++|+|.+.+++..
T Consensus 45 ~~l~~I~~lr~-~G~sl~eI~~~l~~~ 70 (123)
T cd04770 45 ARLRFIRRAQA-LGFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHhh
Confidence 56666766653 599999999999854
No 74
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=20.23 E-value=3.7e+02 Score=20.49 Aligned_cols=32 Identities=22% Similarity=0.154 Sum_probs=22.5
Q ss_pred ccCChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Q 030926 35 ESRTQKLERISDELLDLTKLERYDFATLFGCKLGL 69 (169)
Q Consensus 35 ~~~s~kv~~Ivd~I~~LTLlE~seLv~~leekfgv 69 (169)
......+..+++.|..-++ .+|+.....+++-
T Consensus 33 eVe~~~~~lf~~~L~GKdi---~eLIa~g~~kl~s 64 (109)
T cd05833 33 EVDDEKLNKVISELEGKDV---EELIAAGKEKLAS 64 (109)
T ss_pred CccHHHHHHHHHHHcCCCH---HHHHHHhHhhhcC
Confidence 4455667778888888665 5677777777764
No 75
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=20.22 E-value=1.2e+02 Score=21.93 Aligned_cols=29 Identities=31% Similarity=0.456 Sum_probs=21.9
Q ss_pred chhHHHHHHHHHhhCCChhHHHHHHhhcch
Q 030926 112 ATKIKIIKEVKTFTGLGLKESKDLVEKAPA 141 (169)
Q Consensus 112 ~kKi~vIK~VR~it~LgLkEaK~lVe~~P~ 141 (169)
-..+.+|+..| .+|++|++-|++++....
T Consensus 44 l~~l~~I~~~r-~~G~~L~~I~~~l~~~~~ 72 (124)
T COG0789 44 LELLQIIKTLR-ELGFSLAEIKELLDLLSA 72 (124)
T ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHhcccc
Confidence 35566666555 589999999999987653
No 76
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=20.16 E-value=55 Score=24.13 Aligned_cols=48 Identities=23% Similarity=0.198 Sum_probs=35.2
Q ss_pred ccccCCCCCcccccceeehhhhccccccc-ccc-cCChhHHHHHHHHhcC
Q 030926 4 VTRKFPRLGRVFATLKVTEAVTLSRSLCT-VTE-SRTQKLERISDELLDL 51 (169)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~~s~kv~~Ivd~I~~L 51 (169)
+++-|+|-|=|..++.+.+--....|+-+ ... .....+++|..+|..|
T Consensus 19 it~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~Kl 68 (84)
T PRK13562 19 ITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQ 68 (84)
T ss_pred HHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCC
Confidence 56678898999999999887766777666 443 5556668888777654
No 77
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=20.04 E-value=1.7e+02 Score=20.05 Aligned_cols=33 Identities=15% Similarity=0.044 Sum_probs=27.5
Q ss_pred CChhHHHHHHHHhcCCHHHHHHHHHHHHHHhCCC
Q 030926 37 RTQKLERISDELLDLTKLERYDFATLFGCKLGLD 70 (169)
Q Consensus 37 ~s~kv~~Ivd~I~~LTLlE~seLv~~leekfgv~ 70 (169)
.+..+++|++.+.+=++.++...++.|-.. |++
T Consensus 4 ~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s 36 (89)
T PF08542_consen 4 PPEVIEEILESCLNGDFKEARKKLYELLVE-GYS 36 (89)
T ss_dssp -HHHHHHHHHHHHHTCHHHHHHHHHHHHHT-T--
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-CCC
Confidence 456789999999999999999999999888 887
Done!