Query 045414
Match_columns 214
No_of_seqs 159 out of 1116
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 13:01:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045414.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045414hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1715 Mitochondrial/chloropl 100.0 1.1E-44 2.4E-49 308.1 15.3 152 56-214 33-187 (187)
2 CHL00083 rpl12 ribosomal prote 100.0 2.3E-41 5E-46 274.8 13.6 130 77-214 2-131 (131)
3 cd00387 Ribosomal_L7_L12 Ribos 100.0 2.6E-41 5.7E-46 272.8 13.8 126 79-213 2-127 (127)
4 TIGR00855 L12 ribosomal protei 100.0 5.1E-39 1.1E-43 259.7 13.5 123 78-214 4-126 (126)
5 PRK00157 rplL 50S ribosomal pr 100.0 1.5E-38 3.3E-43 256.1 13.4 121 78-214 3-123 (123)
6 COG0222 RplL Ribosomal protein 100.0 2.7E-38 5.8E-43 254.3 12.3 121 79-214 4-124 (124)
7 PF00542 Ribosomal_L12: Riboso 99.9 1.5E-24 3.2E-29 158.5 5.8 68 146-214 1-68 (68)
8 PRK06771 hypothetical protein; 97.7 2.4E-05 5.2E-10 61.2 3.2 29 156-184 65-93 (93)
9 PF02617 ClpS: ATP-dependent C 85.5 2.5 5.3E-05 31.2 5.3 64 144-208 4-71 (82)
10 PRK00033 clpS ATP-dependent Cl 67.8 35 0.00076 26.9 7.3 69 145-214 26-98 (100)
11 KOG3449 60S acidic ribosomal p 67.5 16 0.00034 29.8 5.4 31 77-110 36-67 (112)
12 PF09999 DUF2240: Uncharacteri 62.0 11 0.00025 31.6 3.8 95 5-110 8-122 (144)
13 COG0264 Tsf Translation elonga 57.3 11 0.00023 35.3 3.2 28 158-185 4-31 (296)
14 cd04788 HTH_NolA-AlbR Helix-Tu 55.8 29 0.00063 26.2 4.8 47 158-206 45-91 (96)
15 cd05833 Ribosomal_P2 Ribosomal 53.9 35 0.00077 27.2 5.2 28 78-108 37-64 (109)
16 PF02022 Integrase_Zn: Integra 53.7 17 0.00037 24.3 2.9 28 163-190 12-39 (40)
17 PRK09377 tsf elongation factor 52.7 14 0.00031 34.0 3.2 30 159-188 5-34 (290)
18 PRK10664 transcriptional regul 50.5 8.9 0.00019 29.1 1.3 36 158-193 2-37 (90)
19 PF09278 MerR-DNA-bind: MerR, 50.2 26 0.00055 24.0 3.5 22 159-181 3-24 (65)
20 cd04411 Ribosomal_P1_P2_L12p R 48.8 45 0.00096 26.5 5.0 27 78-107 36-62 (105)
21 PRK10753 transcriptional regul 46.8 11 0.00023 28.5 1.2 35 158-192 2-36 (90)
22 cd01107 HTH_BmrR Helix-Turn-He 45.9 42 0.00092 25.7 4.4 28 158-186 46-73 (108)
23 PRK13019 clpS ATP-dependent Cl 45.3 1.1E+02 0.0023 23.9 6.6 70 143-212 18-91 (94)
24 cd04774 HTH_YfmP Helix-Turn-He 44.6 59 0.0013 24.7 5.0 31 157-187 43-73 (96)
25 PF14520 HHH_5: Helix-hairpin- 43.4 70 0.0015 21.9 4.8 46 161-206 2-60 (60)
26 PF11272 DUF3072: Protein of u 42.9 72 0.0016 23.3 4.9 49 59-107 3-56 (57)
27 cd00591 HU_IHF Integration hos 41.3 26 0.00057 25.2 2.5 34 159-192 2-35 (87)
28 smart00411 BHL bacterial (prok 40.7 25 0.00055 25.5 2.4 35 159-193 3-37 (90)
29 cd04766 HTH_HspR Helix-Turn-He 40.6 76 0.0016 23.5 5.0 41 157-207 44-84 (91)
30 PF10925 DUF2680: Protein of u 40.4 45 0.00097 23.9 3.5 26 178-206 21-47 (59)
31 PF13411 MerR_1: MerR HTH fami 39.2 30 0.00066 23.6 2.5 26 157-183 43-68 (69)
32 KOG1748 Acyl carrier protein/N 33.6 29 0.00062 29.0 1.8 21 89-109 84-104 (131)
33 PF08106 Antimicrobial11: Form 32.7 32 0.0007 19.1 1.4 14 58-71 1-14 (16)
34 cd04768 HTH_BmrR-like Helix-Tu 32.7 1.1E+02 0.0025 22.9 4.9 27 158-185 45-71 (96)
35 cd01104 HTH_MlrA-CarA Helix-Tu 32.0 56 0.0012 22.2 2.9 24 158-182 45-68 (68)
36 TIGR02043 ZntR Zn(II)-responsi 31.3 96 0.0021 24.7 4.5 25 158-183 46-70 (131)
37 cd04763 HTH_MlrA-like Helix-Tu 30.2 63 0.0014 22.4 2.9 24 158-182 45-68 (68)
38 PRK00285 ihfA integration host 29.7 41 0.0009 25.3 2.0 35 158-192 4-38 (99)
39 cd04782 HTH_BltR Helix-Turn-He 29.5 1.1E+02 0.0025 23.0 4.4 26 158-184 45-70 (97)
40 cd04781 HTH_MerR-like_sg6 Heli 29.1 1.5E+02 0.0033 23.0 5.2 26 158-184 44-69 (120)
41 cd04780 HTH_MerR-like_sg5 Heli 28.5 73 0.0016 24.2 3.2 27 157-183 44-70 (95)
42 PF11363 DUF3164: Protein of u 27.1 60 0.0013 28.3 2.8 81 79-193 35-117 (195)
43 PRK05412 putative nucleotide-b 27.0 60 0.0013 28.0 2.7 64 148-212 45-120 (161)
44 PRK13752 putative transcriptio 27.0 1.1E+02 0.0025 24.9 4.3 25 158-183 52-76 (144)
45 cd01105 HTH_GlnR-like Helix-Tu 26.1 86 0.0019 23.3 3.2 25 158-183 46-70 (88)
46 cd01108 HTH_CueR Helix-Turn-He 25.6 1.4E+02 0.0031 23.4 4.5 25 158-183 45-69 (127)
47 cd01109 HTH_YyaN Helix-Turn-He 25.0 87 0.0019 24.0 3.1 26 158-184 45-70 (113)
48 PF08542 Rep_fac_C: Replicatio 24.4 1.4E+02 0.0031 21.4 4.0 35 75-110 3-37 (89)
49 cd01106 HTH_TipAL-Mta Helix-Tu 24.4 1.8E+02 0.0039 21.9 4.7 27 158-185 45-71 (103)
50 PF04461 DUF520: Protein of un 23.5 48 0.0011 28.5 1.6 64 148-212 45-120 (160)
51 cd04777 HTH_MerR-like_sg1 Heli 22.8 1E+02 0.0022 23.4 3.1 25 158-183 43-67 (107)
52 cd02810 DHOD_DHPD_FMN Dihydroo 22.5 1.2E+02 0.0026 26.5 3.9 40 160-211 151-192 (289)
53 cd04783 HTH_MerR1 Helix-Turn-H 22.0 1.8E+02 0.0039 22.7 4.4 26 158-184 45-70 (126)
54 cd04764 HTH_MlrA-like_sg1 Heli 22.0 1.1E+02 0.0024 21.0 2.9 23 158-181 44-66 (67)
55 TIGR02044 CueR Cu(I)-responsiv 21.8 1.9E+02 0.0041 22.7 4.5 24 158-182 45-68 (127)
56 PF00828 Ribosomal_L18e: Ribos 21.7 82 0.0018 24.8 2.5 27 183-213 101-128 (129)
57 COG3797 Uncharacterized protei 21.4 71 0.0015 28.0 2.2 50 154-207 13-63 (178)
58 PRK10227 DNA-binding transcrip 21.3 1.7E+02 0.0038 23.6 4.3 25 158-183 45-69 (135)
59 smart00422 HTH_MERR helix_turn 20.5 1.4E+02 0.0029 20.2 3.1 24 158-182 45-68 (70)
60 PF07037 DUF1323: Putative tra 20.3 2.3E+02 0.0051 23.5 4.8 29 75-103 78-106 (122)
61 COG4575 ElaB Uncharacterized c 20.3 1.1E+02 0.0024 24.7 2.9 33 175-207 15-49 (104)
62 cd04784 HTH_CadR-PbrR Helix-Tu 20.1 1.2E+02 0.0025 23.8 3.0 25 158-183 45-69 (127)
No 1
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-44 Score=308.06 Aligned_cols=152 Identities=44% Similarity=0.608 Sum_probs=131.6
Q ss_pred hccccCCCCCCCCCCCCC---chhhhhHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCCCCcccccCCCcccccccccccC
Q 045414 56 IDQRRLPANYNPATFDYQ---SIQVLRLHELVDEVSGLTLSESAELGLIMMKKQGMTEPPVVGVLKPGAAGFTGMAMKTG 132 (214)
Q Consensus 56 ~~~~~~p~d~~p~~~~p~---~~~S~KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~~~~~~~~~~ga~~~~g~a~~a~ 132 (214)
..+.+.+..+.+.+|+|. +++++||.+|+|+|++|||+|+++|+++|+++|||+..+.++++++|+ |+ .+
T Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~KI~~iv~eIssLtLlE~s~L~~~Lk~kl~i~e~~~~~a~~~g~----~~---~~ 105 (187)
T KOG1715|consen 33 FSSSKSSTLSHRATPLPPIAAVPPPPKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGA----AA---PD 105 (187)
T ss_pred cCcccccccccccCCCCcccccCCCHHHHHHHHHHHhcCHHHHHHHHHHHHHHcCCCcccchhhccccC----CC---CC
Confidence 667778888888888888 889999999999999999999999999999999999876443222111 11 11
Q ss_pred cchhhhcccCccceeeEEEeecCCchhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHCCcEEE
Q 045414 133 GAAAKEELKPEKTAFDLKLESYDANAKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAVGGKVI 212 (214)
Q Consensus 133 ~aa~~ee~~~EKT~FdV~L~~~~a~kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaaGA~Ve 212 (214)
++++.+++++|||+|||+|++||+.+||+|||+||.+|||||+|||+|||++|+++|+|++|||||+||++|+++||+|+
T Consensus 106 ~~~a~ee~k~ekt~FdVkL~~fda~~KIkVIKEVR~~tgL~LkeAKklVE~aP~ilKegvtKeEAEkik~kLea~GakV~ 185 (187)
T KOG1715|consen 106 AGGAEEEAKKEKTTFDVKLEKFDASSKIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEKLEAAGAKVV 185 (187)
T ss_pred cccccccchhhcceEEEEEeecCccchhHHHHHHHHhccccHHHHHHHHHhccHHHHcCCCHHHHHHHHHHHHHcCCeEe
Confidence 23334566778889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eC
Q 045414 213 ME 214 (214)
Q Consensus 213 lE 214 (214)
||
T Consensus 186 le 187 (187)
T KOG1715|consen 186 LE 187 (187)
T ss_pred eC
Confidence 97
No 2
>CHL00083 rpl12 ribosomal protein L12
Probab=100.00 E-value=2.3e-41 Score=274.81 Aligned_cols=130 Identities=38% Similarity=0.540 Sum_probs=110.1
Q ss_pred hhhHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCCCCcccccCCCcccccccccccCcchhhhcccCccceeeEEEeecCC
Q 045414 77 VLRLHELVDEVSGLTLSESAELGLIMMKKQGMTEPPVVGVLKPGAAGFTGMAMKTGGAAAKEELKPEKTAFDLKLESYDA 156 (214)
Q Consensus 77 S~KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~~~~~~~~~~ga~~~~g~a~~a~~aa~~ee~~~EKT~FdV~L~~~~a 156 (214)
|+++++|+|+|++|||+|++||++.|+++|||++++++++++ +++ +++ +++.++++++|||+|||+|++|++
T Consensus 2 s~k~~~ivd~i~~LTllE~~eLv~~le~~fgv~~~~~~a~~~--~~~--~a~----~~~~~~~~~~EKT~F~V~L~~~~~ 73 (131)
T CHL00083 2 STKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGM--MSA--PAA----AAAQAAEEVEEKTEFDVILEEVPA 73 (131)
T ss_pred CchHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhhhhh--ccc--cCc----ccccccchhhhcceeeEEEeecCC
Confidence 579999999999999999999999999999999875432211 100 000 111122346799999999999988
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHCCcEEEeC
Q 045414 157 NAKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAVGGKVIME 214 (214)
Q Consensus 157 ~kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaaGA~VelE 214 (214)
++||+|||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 74 ~~Ki~vIK~vr~it~lgLkeaK~lVe~~P~~ike~v~KeeAe~ik~~le~~Ga~v~lk 131 (131)
T CHL00083 74 DKRIAVLKVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131 (131)
T ss_pred cchHHHHHHHHHHcCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 9999999999999999999999999999999999999999999999999999999973
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=2.6e-41 Score=272.79 Aligned_cols=126 Identities=45% Similarity=0.613 Sum_probs=106.6
Q ss_pred hHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCCCCcccccCCCcccccccccccCcchhhhcccCccceeeEEEeecCCch
Q 045414 79 RLHELVDEVSGLTLSESAELGLIMMKKQGMTEPPVVGVLKPGAAGFTGMAMKTGGAAAKEELKPEKTAFDLKLESYDANA 158 (214)
Q Consensus 79 KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~~~~~~~~~~ga~~~~g~a~~a~~aa~~ee~~~EKT~FdV~L~~~~a~k 158 (214)
++++|+|+|++|||+|++||++.|+++|||++.++.+++ +++++ + +++++++.++|||+|||+|++||+++
T Consensus 2 ~~~~i~d~i~~LtllE~~eLv~~le~~~gv~~~~~~~~~----~~~a~----~-~~~~~~~~~~EKt~F~V~L~~~~~~~ 72 (127)
T cd00387 2 KVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAA----AAAAP----A-AAAAAAAEAEEKTEFDVVLESFGAAK 72 (127)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCcccccccc----cccCc----c-cccccccchhhcceEEEEEeeCCchh
Confidence 789999999999999999999999999999986322111 10001 0 11111223579999999999999889
Q ss_pred hHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHCCcEEEe
Q 045414 159 KVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAVGGKVIM 213 (214)
Q Consensus 159 KI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaaGA~Vel 213 (214)
||+|||+||++|||||+|||+|||++|++||+|+||+|||+||++|+++||+|+|
T Consensus 73 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~iKe~vsKeeAE~ik~kLe~aGA~Vel 127 (127)
T cd00387 73 KIAVIKEVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127 (127)
T ss_pred hHHHHHHHHHHhCCChHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEeC
Confidence 9999999999999999999999999999999999999999999999999999986
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=5.1e-39 Score=259.67 Aligned_cols=123 Identities=39% Similarity=0.537 Sum_probs=105.4
Q ss_pred hhHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCCCCcccccCCCcccccccccccCcchhhhcccCccceeeEEEeecCCc
Q 045414 78 LRLHELVDEVSGLTLSESAELGLIMMKKQGMTEPPVVGVLKPGAAGFTGMAMKTGGAAAKEELKPEKTAFDLKLESYDAN 157 (214)
Q Consensus 78 ~KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~~~~~~~~~~ga~~~~g~a~~a~~aa~~ee~~~EKT~FdV~L~~~~a~ 157 (214)
-..++|+|+|++|||+|++||++.|+++|||+++++++++ ++ ++ + + +.+.++|||+|||+|+.++ +
T Consensus 4 ~~~~~ive~i~~LTllE~~eLv~~lee~fgV~a~a~~a~~---~a--~~-~----~---~~~~~eEKt~f~V~L~~~~-~ 69 (126)
T TIGR00855 4 LSKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAG---AA--GA-A----A---AAAAAEEKTEFDVILKGAG-D 69 (126)
T ss_pred ccHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCccchhhhc---cc--cc-c----c---ccccccccceeeEEEecCC-c
Confidence 3569999999999999999999999999999987643211 10 01 0 1 1123479999999999986 5
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHCCcEEEeC
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAVGGKVIME 214 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaaGA~VelE 214 (214)
+||+|||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 70 ~Ki~vIK~vR~itgLgLkEAK~lVe~~P~~ike~vsKeeAe~ik~~Le~aGa~veik 126 (126)
T TIGR00855 70 NKIAVIKVVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEVK 126 (126)
T ss_pred chhHHHHHHHHHcCCcHHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 799999999999999999999999999999999999999999999999999999973
No 5
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=100.00 E-value=1.5e-38 Score=256.06 Aligned_cols=121 Identities=40% Similarity=0.567 Sum_probs=105.5
Q ss_pred hhHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCCCCcccccCCCcccccccccccCcchhhhcccCccceeeEEEeecCCc
Q 045414 78 LRLHELVDEVSGLTLSESAELGLIMMKKQGMTEPPVVGVLKPGAAGFTGMAMKTGGAAAKEELKPEKTAFDLKLESYDAN 157 (214)
Q Consensus 78 ~KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~~~~~~~~~~ga~~~~g~a~~a~~aa~~ee~~~EKT~FdV~L~~~~a~ 157 (214)
-.+++|+|+|++|||+|++||++.|+++|||+++++++++ + ++ ++ .+..+|||+|||+|++| ++
T Consensus 3 ~~~~~i~e~i~~LtllE~~eLv~~lee~fgv~a~~~~~~~---~---~~------~~---~~~~eEkt~f~V~L~~~-~~ 66 (123)
T PRK00157 3 LTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAA---A---AA------AA---AAAAEEKTEFDVVLKSA-GD 66 (123)
T ss_pred ccHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhccc---c---cc------cc---ccccccccceeEEEecc-ch
Confidence 4689999999999999999999999999999987543211 0 01 00 12347999999999999 57
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHCCcEEEeC
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAVGGKVIME 214 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaaGA~VelE 214 (214)
+||+|||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 67 kKi~vIK~vR~itgLgLkEAK~lVe~~P~~ike~v~keeAe~ik~~Le~aGa~velk 123 (123)
T PRK00157 67 KKIAVIKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGAKVELK 123 (123)
T ss_pred hhHHHHHHHHHHhCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEeeC
Confidence 999999999999999999999999999999999999999999999999999999984
No 6
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-38 Score=254.32 Aligned_cols=121 Identities=42% Similarity=0.580 Sum_probs=105.8
Q ss_pred hHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCCCCcccccCCCcccccccccccCcchhhhcccCccceeeEEEeecCCch
Q 045414 79 RLHELVDEVSGLTLSESAELGLIMMKKQGMTEPPVVGVLKPGAAGFTGMAMKTGGAAAKEELKPEKTAFDLKLESYDANA 158 (214)
Q Consensus 79 KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~~~~~~~~~~ga~~~~g~a~~a~~aa~~ee~~~EKT~FdV~L~~~~a~k 158 (214)
.+++|++.|++||++|+++|++.++++|||++++++++++++ + + + + +..+|||+|||+|++++ ++
T Consensus 4 ~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa~va~a~~~-----a-~--a-~-----~aaeEktefdVvL~~~g-~k 68 (124)
T COG0222 4 TKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAAG-----A-A--A-A-----EAAEEKTEFDVVLKSAG-GK 68 (124)
T ss_pred cHHHHHHHHHHhhHHHHHHHHHHHHHHhCCccchhhhhcccc-----c-c--c-c-----ccccccceeEEEecccC-Cc
Confidence 578999999999999999999999999999998764422111 0 0 0 1 12469999999999995 79
Q ss_pred hHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHCCcEEEeC
Q 045414 159 KVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAVGGKVIME 214 (214)
Q Consensus 159 KI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaaGA~VelE 214 (214)
||+|||.||++|||||||||++||++|++||+|++|+|||+||++|+++||+|++.
T Consensus 69 KI~VIK~vR~itGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~V~~k 124 (124)
T COG0222 69 KIAVIKVVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124 (124)
T ss_pred chhHHHHHHHHhcccHHHHHHHHHhCcHHHHccCCHHHHHHHHHHHHHcCCeEeeC
Confidence 99999999999999999999999999999999999999999999999999999984
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=99.90 E-value=1.5e-24 Score=158.51 Aligned_cols=68 Identities=53% Similarity=0.815 Sum_probs=60.2
Q ss_pred eeeEEEeecCCchhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHCCcEEEeC
Q 045414 146 AFDLKLESYDANAKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAVGGKVIME 214 (214)
Q Consensus 146 ~FdV~L~~~~a~kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaaGA~VelE 214 (214)
+|||+|++| +++||++||.||++|||||+|||++||++|.+|+++++++|||+|+++|+++||+|+|+
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 599999999 78999999999999999999999999999999999999999999999999999999985
No 8
>PRK06771 hypothetical protein; Provisional
Probab=97.74 E-value=2.4e-05 Score=61.22 Aligned_cols=29 Identities=31% Similarity=0.393 Sum_probs=27.0
Q ss_pred CchhHHHHHHHHHhhcCChHHHHHHHhhc
Q 045414 156 ANAKVKIIKELRTFTDLGLKEAKDLVEKT 184 (214)
Q Consensus 156 a~kKI~vIK~VR~iT~LgLkEAK~lVE~~ 184 (214)
..+||+.||.+|+.||+||+|||++||++
T Consensus 65 ~Gkki~AIK~~Re~tG~~L~eAK~yVD~L 93 (93)
T PRK06771 65 EGQTVTAVKRVREAFGFSLLEAKQYVDKL 93 (93)
T ss_pred cCCchHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 35899999999999999999999999975
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=85.49 E-value=2.5 Score=31.22 Aligned_cols=64 Identities=22% Similarity=0.285 Sum_probs=47.9
Q ss_pred cceeeEEEeecCCchhHHHHHHHHHhhcCChHHHHHHHhhcc----hhhhcCCCHHHHHHHHHHHHHCC
Q 045414 144 KTAFDLKLESYDANAKVKIIKELRTFTDLGLKEAKDLVEKTP----AVLKKGVLKEEAEKIIEKMKAVG 208 (214)
Q Consensus 144 KT~FdV~L~~~~a~kKI~vIK~VR~iT~LgLkEAK~lVE~~P----~vIKe~vsKEEAE~iKkkLEaaG 208 (214)
...|.|+|=.=+-..--.||..++.+.|+...+|..+...+- .+|.. -++++||....+|...|
T Consensus 4 ~~~~~vvL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~avv~~-~~~e~ae~~~~~l~~~g 71 (82)
T PF02617_consen 4 PDMYRVVLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREGRAVVGT-GSREEAEEYAEKLQRAG 71 (82)
T ss_dssp --EEEEEEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHSEEEEEE-EEHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcCCEeeee-CCHHHHHHHHHHHHHHh
Confidence 357999997655566779999999999999999999987552 45544 58999999999999998
No 10
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=67.83 E-value=35 Score=26.91 Aligned_cols=69 Identities=20% Similarity=0.237 Sum_probs=55.8
Q ss_pred ceeeEEEeecCCchhHHHHHHHHHhhcCChHHHHHHHhhcc----hhhhcCCCHHHHHHHHHHHHHCCcEEEeC
Q 045414 145 TAFDLKLESYDANAKVKIIKELRTFTDLGLKEAKDLVEKTP----AVLKKGVLKEEAEKIIEKMKAVGGKVIME 214 (214)
Q Consensus 145 T~FdV~L~~~~a~kKI~vIK~VR~iT~LgLkEAK~lVE~~P----~vIKe~vsKEEAE~iKkkLEaaGA~VelE 214 (214)
.-|.|+|-.=|-...==||..++.+.|++..+|.++...+= .++.. -++|.||....+|...|-.+.||
T Consensus 26 ~~y~ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~-~~~e~AE~~~~~l~~~~L~~~ie 98 (100)
T PRK00033 26 PMYKVLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGV-CTREVAETKVEQVHQHGLLCTME 98 (100)
T ss_pred CceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEE-EcHHHHHHHHHHHHcCCCeEEEe
Confidence 45999997644445567999999999999999999876542 34444 48999999999999999988886
No 11
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=67.48 E-value=16 Score=29.84 Aligned_cols=31 Identities=19% Similarity=0.197 Sum_probs=21.4
Q ss_pred hhhHHHHHHHHhCCCHHHHHHHHHHHHHhh-CCCC
Q 045414 77 VLRLHELVDEVSGLTLSESAELGLIMMKKQ-GMTE 110 (214)
Q Consensus 77 S~KV~~Ivd~I~~LTLlE~sELv~~leekf-GVs~ 110 (214)
.++++.++.+|+.=|+ .||+..=+++| .|+.
T Consensus 36 ~e~i~~visel~GK~i---~ElIA~G~eklAsvps 67 (112)
T KOG3449|consen 36 DERINLVLSELKGKDI---EELIAAGREKLASVPS 67 (112)
T ss_pred HHHHHHHHHHhcCCCH---HHHHHHhHHHHhcCCC
Confidence 3688888888888876 45666666666 3443
No 12
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=62.04 E-value=11 Score=31.56 Aligned_cols=95 Identities=18% Similarity=0.289 Sum_probs=54.2
Q ss_pred hhhhhhcCCcccCCCCchhhHhhhhcccccchhhcccc-chhh--hhh-hhhhHh-----------hccccCCCCCCCCC
Q 045414 5 SKLRHHLPNRLSRNPSVYPILALRSLSFNGVASRSFGQ-TVKK--EEE-EEEEVE-----------IDQRRLPANYNPAT 69 (214)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~--~~~-~~~~~~-----------~~~~~~p~d~~p~~ 69 (214)
.-+||+-.+.|+++-+++ +|+|.= +.+|. +|++ +.. ++-=++ ...-..|.+|.|+.
T Consensus 8 apFk~kg~~~L~~sefv~------~Ls~D~---~WmspdqAk~li~~A~~eGLl~~~~~~l~~~Fd~~~v~iP~~FkP~~ 78 (144)
T PF09999_consen 8 APFKQKGKDRLSKSEFVF------ALSFDR---KWMSPDQAKRLIDEAIEEGLLEEEGGYLVPNFDPSEVEIPLGFKPDE 78 (144)
T ss_pred HHHHHcCccccChhheEe------eEeeec---CCCCHHHHHHHHHHHHHCCCeeecCCEEEEecCccccccCCCCCCcH
Confidence 347899999999999986 333321 12333 2222 111 111122 22334455555531
Q ss_pred CCCCchhhhhHHHHHHHHhC---CCHHHHHHHHHHHHHhhC--CCC
Q 045414 70 FDYQSIQVLRLHELVDEVSG---LTLSESAELGLIMMKKQG--MTE 110 (214)
Q Consensus 70 ~~p~~~~S~KV~~Ivd~I~~---LTLlE~sELv~~leekfG--Vs~ 110 (214)
=- =...+-.++|+|.|.. ++-.|+-..++.++++|| |+.
T Consensus 79 ~~--l~e~~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l~~ 122 (144)
T PF09999_consen 79 EI--LQERDPFERILDYIAAKTGIEKQEVVAEINELQEELGGLLDP 122 (144)
T ss_pred HH--HhcccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCCH
Confidence 00 0112346677777755 999999999999999999 753
No 13
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=57.35 E-value=11 Score=35.29 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcc
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTP 185 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P 185 (214)
-+.+.+|++|+.||-|..++|+.++-+-
T Consensus 4 ita~~VKeLRe~TgAGMmdCKkAL~E~~ 31 (296)
T COG0264 4 ITAALVKELREKTGAGMMDCKKALEEAN 31 (296)
T ss_pred ccHHHHHHHHHHhCCcHHHHHHHHHHcC
Confidence 4678999999999999999999876543
No 14
>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=55.83 E-value=29 Score=26.16 Aligned_cols=47 Identities=15% Similarity=0.254 Sum_probs=30.5
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHH
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKA 206 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEa 206 (214)
.++..|+.+|+ +|+.|+|.+.+++.....+++ +-.+..+.+..++++
T Consensus 45 ~~l~~I~~lr~-~G~~l~eI~~~l~~~~~~~~~-~l~~~~~~l~~~i~~ 91 (96)
T cd04788 45 RRLHQIIALRR-LGFSLREIGRALDGPDFDPLE-LLRRQLARLEEQLEL 91 (96)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhCCChhHHH-HHHHHHHHHHHHHHH
Confidence 57777777775 699999999999876543222 224444555555443
No 15
>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=53.89 E-value=35 Score=27.22 Aligned_cols=28 Identities=21% Similarity=0.260 Sum_probs=21.3
Q ss_pred hhHHHHHHHHhCCCHHHHHHHHHHHHHhhCC
Q 045414 78 LRLHELVDEVSGLTLSESAELGLIMMKKQGM 108 (214)
Q Consensus 78 ~KV~~Ivd~I~~LTLlE~sELv~~leekfGV 108 (214)
.++.-+++.|.+-++ .+|+.....+++-
T Consensus 37 ~~~~lf~~~L~GKdi---~eLIa~g~~kl~s 64 (109)
T cd05833 37 EKLNKVISELEGKDV---EELIAAGKEKLAS 64 (109)
T ss_pred HHHHHHHHHHcCCCH---HHHHHHhHhhhcC
Confidence 577788888888665 6788888888863
No 16
>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=53.65 E-value=17 Score=24.29 Aligned_cols=28 Identities=29% Similarity=0.303 Sum_probs=21.4
Q ss_pred HHHHHHhhcCChHHHHHHHhhcchhhhc
Q 045414 163 IKELRTFTDLGLKEAKDLVEKTPAVLKK 190 (214)
Q Consensus 163 IK~VR~iT~LgLkEAK~lVE~~P~vIKe 190 (214)
.|.+|.-.||...+||++|..+|+=-.+
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~C~~Cq~~ 39 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQCPKCQQK 39 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHHSCCHHST
T ss_pred HHHHHHHHccCHHHHHHHHHHCHHHhhC
Confidence 4678888999999999999999975443
No 17
>PRK09377 tsf elongation factor Ts; Provisional
Probab=52.67 E-value=14 Score=34.00 Aligned_cols=30 Identities=23% Similarity=0.403 Sum_probs=25.7
Q ss_pred hHHHHHHHHHhhcCChHHHHHHHhhcchhh
Q 045414 159 KVKIIKELRTFTDLGLKEAKDLVEKTPAVL 188 (214)
Q Consensus 159 KI~vIK~VR~iT~LgLkEAK~lVE~~P~vI 188 (214)
..+.||++|+.||-|+.+.|+.++.+..-+
T Consensus 5 s~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ 34 (290)
T PRK09377 5 TAALVKELRERTGAGMMDCKKALTEADGDI 34 (290)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 357899999999999999999988776554
No 18
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=50.48 E-value=8.9 Score=29.07 Aligned_cols=36 Identities=14% Similarity=0.195 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCC
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVL 193 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vs 193 (214)
+|-.+|+.|.+-+|+.-++++.+||.+=.+|.+.+.
T Consensus 2 tK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~ 37 (90)
T PRK10664 2 NKSQLIDKIAAGADISKAAAGRALDAIIASVTESLK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 366899999999999999999999998877766554
No 19
>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=50.24 E-value=26 Score=24.00 Aligned_cols=22 Identities=27% Similarity=0.653 Sum_probs=16.4
Q ss_pred hHHHHHHHHHhhcCChHHHHHHH
Q 045414 159 KVKIIKELRTFTDLGLKEAKDLV 181 (214)
Q Consensus 159 KI~vIK~VR~iT~LgLkEAK~lV 181 (214)
++..|+..|. +|++|.|-|+++
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 5667777775 799999999999
No 20
>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=48.82 E-value=45 Score=26.45 Aligned_cols=27 Identities=11% Similarity=0.080 Sum_probs=20.7
Q ss_pred hhHHHHHHHHhCCCHHHHHHHHHHHHHhhC
Q 045414 78 LRLHELVDEVSGLTLSESAELGLIMMKKQG 107 (214)
Q Consensus 78 ~KV~~Ivd~I~~LTLlE~sELv~~leekfG 107 (214)
.++..+++.|.+-++ .+|+.....+++
T Consensus 36 ~~~~~~~~aLaGk~V---~eli~~g~~kl~ 62 (105)
T cd04411 36 ERVKLFLSALNGKNI---DEVISKGKELMS 62 (105)
T ss_pred HHHHHHHHHHcCCCH---HHHHHHHHhhcc
Confidence 578888888888876 566777777775
No 21
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=46.83 E-value=11 Score=28.50 Aligned_cols=35 Identities=23% Similarity=0.332 Sum_probs=29.9
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCC
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGV 192 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~v 192 (214)
+|-.+|+.|.+-+++.-++++..|+.+-.+|.+.+
T Consensus 2 ~K~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L 36 (90)
T PRK10753 2 NKTQLIDVIADKAELSKTQAKAALESTLAAITESL 36 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999877776554
No 22
>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=45.89 E-value=42 Score=25.74 Aligned_cols=28 Identities=25% Similarity=0.417 Sum_probs=23.3
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcch
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTPA 186 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P~ 186 (214)
..+..|+.+|. +|++|.|.+.+++..+.
T Consensus 46 ~~l~~I~~lr~-~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 46 ERLNRIKYLRD-LGFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcCCH
Confidence 57777777776 89999999999998764
No 23
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=45.28 E-value=1.1e+02 Score=23.86 Aligned_cols=70 Identities=13% Similarity=0.076 Sum_probs=52.7
Q ss_pred ccceeeEEEeecCCchhHHHH-HHHHHhhcCChHHHHHHHhhcc---hhhhcCCCHHHHHHHHHHHHHCCcEEE
Q 045414 143 EKTAFDLKLESYDANAKVKII-KELRTFTDLGLKEAKDLVEKTP---AVLKKGVLKEEAEKIIEKMKAVGGKVI 212 (214)
Q Consensus 143 EKT~FdV~L~~~~a~kKI~vI-K~VR~iT~LgLkEAK~lVE~~P---~vIKe~vsKEEAE~iKkkLEaaGA~Ve 212 (214)
....|.|+|-.=|-..-==|| ..++.+.+++..+|..+.-.+= +-+=---++|.||-...+|...|.+++
T Consensus 18 ~p~~ykViL~NDd~~t~dfVi~~vl~~vf~~s~~~A~~iml~vH~~G~avv~~~~~E~AE~~~~~l~~~glt~e 91 (94)
T PRK13019 18 RYPLYKVIVLNDDFNTFEHVVNCLLKAIPGMSEDRAWRLMITAHKEGSAVVWVGPLEQAELYHQQLTDAGLTMA 91 (94)
T ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHHcccccC
Confidence 345699999775444455788 6778889999999999986542 112222589999999999999998775
No 24
>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=44.64 E-value=59 Score=24.70 Aligned_cols=31 Identities=19% Similarity=0.301 Sum_probs=26.8
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHhhcchh
Q 045414 157 NAKVKIIKELRTFTDLGLKEAKDLVEKTPAV 187 (214)
Q Consensus 157 ~kKI~vIK~VR~iT~LgLkEAK~lVE~~P~v 187 (214)
=.++..|+.+|+..|++|.+.+.+++..+..
T Consensus 43 v~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 43 LKRLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 3688899999988899999999999887765
No 25
>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=43.40 E-value=70 Score=21.93 Aligned_cols=46 Identities=30% Similarity=0.427 Sum_probs=31.6
Q ss_pred HHHHHHHHhhcCChHHHHHHHhhcchhh-------------hcCCCHHHHHHHHHHHHH
Q 045414 161 KIIKELRTFTDLGLKEAKDLVEKTPAVL-------------KKGVLKEEAEKIIEKMKA 206 (214)
Q Consensus 161 ~vIK~VR~iT~LgLkEAK~lVE~~P~vI-------------Ke~vsKEEAE~iKkkLEa 206 (214)
.++..+.++.|+|-+-|+.|++.--.++ -.|+++.-|+.|...+.+
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 4566777778888888888877622222 147888888888877653
No 26
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=42.89 E-value=72 Score=23.26 Aligned_cols=49 Identities=20% Similarity=0.208 Sum_probs=34.1
Q ss_pred ccCCCCCCCCCCCCCchhhhhHHHHHHHH-----hCCCHHHHHHHHHHHHHhhC
Q 045414 59 RRLPANYNPATFDYQSIQVLRLHELVDEV-----SGLTLSESAELGLIMMKKQG 107 (214)
Q Consensus 59 ~~~p~d~~p~~~~p~~~~S~KV~~Ivd~I-----~~LTLlE~sELv~~leekfG 107 (214)
-|.|.||.+---+.|...-..+..|.++- ..||-.|++++++.|+.+.|
T Consensus 3 ekdp~dw~tGDePmT~aQ~syL~tL~e~Age~~~~~LtkaeAs~rId~L~~~~g 56 (57)
T PF11272_consen 3 EKDPDDWVTGDEPMTGAQASYLKTLSEEAGEPFPDDLTKAEASERIDELQAQTG 56 (57)
T ss_pred ccCHhhccCCCCCCcHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHhC
Confidence 35677777764444444444555555443 37999999999999999876
No 27
>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=41.30 E-value=26 Score=25.21 Aligned_cols=34 Identities=24% Similarity=0.333 Sum_probs=29.4
Q ss_pred hHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCC
Q 045414 159 KVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGV 192 (214)
Q Consensus 159 KI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~v 192 (214)
|-.+|+.|...+|+.-++++.+++.+-.++++.+
T Consensus 2 K~~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L 35 (87)
T cd00591 2 KSELIEAIAEKTGLSKKDAEAAVDAFLDVITEAL 35 (87)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 6689999999999999999999999877776544
No 28
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=40.69 E-value=25 Score=25.51 Aligned_cols=35 Identities=20% Similarity=0.298 Sum_probs=30.5
Q ss_pred hHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCC
Q 045414 159 KVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVL 193 (214)
Q Consensus 159 KI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vs 193 (214)
|-.+|+.|.+.+++.-++++..++.+-.+|.+.+.
T Consensus 3 k~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~ 37 (90)
T smart00411 3 KSELIDAIAEKAGLSKKDAKAAVDAFLEIITEALK 37 (90)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 56899999999999999999999999888876553
No 29
>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=40.62 E-value=76 Score=23.46 Aligned_cols=41 Identities=20% Similarity=0.342 Sum_probs=31.0
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHC
Q 045414 157 NAKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAV 207 (214)
Q Consensus 157 ~kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaa 207 (214)
=.++..|+.++.-.|++|.+.+.+++ =+++-+.+...|+..
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 36788888888889999999999997 355566666666543
No 30
>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=40.42 E-value=45 Score=23.94 Aligned_cols=26 Identities=19% Similarity=0.516 Sum_probs=21.0
Q ss_pred HHHHhhcchhhhcC-CCHHHHHHHHHHHHH
Q 045414 178 KDLVEKTPAVLKKG-VLKEEAEKIIEKMKA 206 (214)
Q Consensus 178 K~lVE~~P~vIKe~-vsKEEAE~iKkkLEa 206 (214)
|.+|+ +-|+.| +|+|.|+.|++.++.
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 56666 467777 899999999998875
No 31
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=39.21 E-value=30 Score=23.62 Aligned_cols=26 Identities=35% Similarity=0.583 Sum_probs=20.6
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 157 NAKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 157 ~kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
=..+..|+.+++ .|+.+.+++++++.
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 367888888888 89999999998763
No 32
>KOG1748 consensus Acyl carrier protein/NADH-ubiquinone oxidoreductase, NDUFAB1/SDAP subunit [Energy production and conversion; Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=33.57 E-value=29 Score=28.99 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=17.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCC
Q 045414 89 GLTLSESAELGLIMMKKQGMT 109 (214)
Q Consensus 89 ~LTLlE~sELv~~leekfGVs 109 (214)
+|-=|..-|+|=+||+.||+.
T Consensus 84 GlDSLD~VEiVMAlEEEFgiE 104 (131)
T KOG1748|consen 84 GLDSLDTVEIVMALEEEFGIE 104 (131)
T ss_pred CCcccccchhhhhhHHHhCCc
Confidence 566677789999999999985
No 33
>PF08106 Antimicrobial11: Formaecin family; InterPro: IPR012514 This entry consists of the formaecin family of antimicrobial peptides isolated from the bulldog ant Myrmecia gulosa in response to bacterial infection. Formaecins are inducible peptide antibiotics and are active against growing Escherichia coli but were inactive against other Gram-negative and Gram-positive bacteria. Formaecin peptides are 16 amino acids long, are rich in proline and have N-acetylgalactosamine O-linked to a conserved threonine [].; GO: 0042381 hemolymph coagulation, 0042742 defense response to bacterium
Probab=32.75 E-value=32 Score=19.09 Aligned_cols=14 Identities=29% Similarity=0.434 Sum_probs=11.9
Q ss_pred cccCCCCCCCCCCC
Q 045414 58 QRRLPANYNPATFD 71 (214)
Q Consensus 58 ~~~~p~d~~p~~~~ 71 (214)
+|.+|.+.+|.+|+
T Consensus 1 grpnpvn~kptp~p 14 (16)
T PF08106_consen 1 GRPNPVNNKPTPHP 14 (16)
T ss_pred CCCCcccCCCCCCC
Confidence 58899999998876
No 34
>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=32.65 E-value=1.1e+02 Score=22.91 Aligned_cols=27 Identities=26% Similarity=0.369 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcc
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTP 185 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P 185 (214)
.++..|+.+|+ .|+.|++.|.+++...
T Consensus 45 ~~l~~I~~lr~-~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 45 YQLQFILFLRE-LGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcCc
Confidence 57778887776 6999999999998754
No 35
>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=32.03 E-value=56 Score=22.22 Aligned_cols=24 Identities=21% Similarity=0.462 Sum_probs=17.8
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVE 182 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE 182 (214)
..+..|+.+++ .|+.|.|.+++++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~~~ 68 (68)
T cd01104 45 ARLRLIRRLTS-EGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 35556666665 8999999999863
No 36
>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=31.27 E-value=96 Score=24.69 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
.++..|+.+|+ +|++|+|.|++++.
T Consensus 46 ~~l~~I~~lr~-~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 46 KRLRFILKAKE-LGFTLDEIKELLSI 70 (131)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHh
Confidence 57777887775 79999999999974
No 37
>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=30.18 E-value=63 Score=22.36 Aligned_cols=24 Identities=17% Similarity=0.273 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVE 182 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE 182 (214)
.++..|+.+++ .|+.|.++|.++.
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~l~ 68 (68)
T cd04763 45 DRILEIKRWID-NGVQVSKVKKLLS 68 (68)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHhC
Confidence 57777777777 8999999999863
No 38
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=29.73 E-value=41 Score=25.34 Aligned_cols=35 Identities=26% Similarity=0.300 Sum_probs=30.3
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcchhhhcCC
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTPAVLKKGV 192 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe~v 192 (214)
.|-.+|+.|.+.+++.-++++..|+.+-.+|.+.+
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 38 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDAL 38 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999999999988877654
No 39
>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=29.47 E-value=1.1e+02 Score=22.96 Aligned_cols=26 Identities=31% Similarity=0.494 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhc
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKT 184 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~ 184 (214)
.++..|+.+|. +|+.|.|.|++++..
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 47777777775 599999999999753
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=29.12 E-value=1.5e+02 Score=23.03 Aligned_cols=26 Identities=15% Similarity=0.326 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhc
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKT 184 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~ 184 (214)
.++..|+.+|+ +|++|+|.+.+++..
T Consensus 44 ~~l~~I~~lr~-~G~~L~eI~~~l~~~ 69 (120)
T cd04781 44 DRLALIALGRA-AGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 56777777775 699999999999864
No 41
>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=28.52 E-value=73 Score=24.18 Aligned_cols=27 Identities=15% Similarity=0.410 Sum_probs=23.7
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 157 NAKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 157 ~kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
-.++..|+.+|...|++|.+.|.+++.
T Consensus 44 v~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 44 VERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 468888888888889999999999986
No 42
>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=27.10 E-value=60 Score=28.26 Aligned_cols=81 Identities=23% Similarity=0.275 Sum_probs=51.3
Q ss_pred hHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCCCCcccccCCCcccccccccccCcchhhhcccCccceeeEEEeecCCch
Q 045414 79 RLHELVDEVSGLTLSESAELGLIMMKKQGMTEPPVVGVLKPGAAGFTGMAMKTGGAAAKEELKPEKTAFDLKLESYDANA 158 (214)
Q Consensus 79 KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~~~~~~~~~~ga~~~~g~a~~a~~aa~~ee~~~EKT~FdV~L~~~~a~k 158 (214)
.+.+.+...+.-+.-++..+++++.+.+|+.-. | +.=+++|++||+..
T Consensus 35 ~l~~~l~~fK~~~f~d~~af~~l~~e~Yg~k~g--------------g------------------~kGn~Tl~sfDG~~ 82 (195)
T PF11363_consen 35 ELSEQLAEFKAHTFEDIEAFIELSAEEYGVKLG--------------G------------------KKGNVTLTSFDGRY 82 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcC--------------C------------------CcCcEEEEEeCCCE
Confidence 444455555666778888899999999998421 0 01256667887655
Q ss_pred hHHHHHHHHHh--hcCChHHHHHHHhhcchhhhcCCC
Q 045414 159 KVKIIKELRTF--TDLGLKEAKDLVEKTPAVLKKGVL 193 (214)
Q Consensus 159 KI~vIK~VR~i--T~LgLkEAK~lVE~~P~vIKe~vs 193 (214)
||.+ .+++. .+=.|.-||+||+.+=...-+|..
T Consensus 83 kV~i--~~~~~~~Fde~l~~Ak~lIde~l~~w~~g~~ 117 (195)
T PF11363_consen 83 KVTI--AVQDRISFDERLQAAKALIDECLNEWAKGAD 117 (195)
T ss_pred EEEE--EecccCCcChHHHHHHHHHHHHHHHHhcCCC
Confidence 5443 33333 355677888888877666666643
No 43
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=26.98 E-value=60 Score=27.99 Aligned_cols=64 Identities=31% Similarity=0.365 Sum_probs=41.8
Q ss_pred eEEEeecCCchhHHHHH-HHHHh---hcCChHHHHH-HHhh-------cchhhhcCCCHHHHHHHHHHHHHCCcEEE
Q 045414 148 DLKLESYDANAKVKIIK-ELRTF---TDLGLKEAKD-LVEK-------TPAVLKKGVLKEEAEKIIEKMKAVGGKVI 212 (214)
Q Consensus 148 dV~L~~~~a~kKI~vIK-~VR~i---T~LgLkEAK~-lVE~-------~P~vIKe~vsKEEAE~iKkkLEaaGA~Ve 212 (214)
.++|.+- .+.|+.-++ .++.- -|++++=-.- -++. -.-.||+|+++|-|.+|.+.+++.+-+|.
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 4777764 467766544 34432 2666652211 1111 13579999999999999999999998874
No 44
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=26.97 E-value=1.1e+02 Score=24.95 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=19.9
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
.++..|+..| -+|++|+|.+++++.
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 5666776666 479999999999974
No 45
>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=26.14 E-value=86 Score=23.26 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=21.4
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
.++..|+.+|+ .|+.|.+++++++.
T Consensus 46 ~~l~~I~~Lr~-~G~sl~~i~~~l~~ 70 (88)
T cd01105 46 DRLLVIKELLD-EGFTLAAAVEKLRR 70 (88)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence 57788888887 89999999999973
No 46
>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=25.56 E-value=1.4e+02 Score=23.44 Aligned_cols=25 Identities=20% Similarity=0.476 Sum_probs=20.9
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
.++..|+.+|. +|++|+|-|.+++.
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~ 69 (127)
T cd01108 45 EELRFIRRARD-LGFSLEEIRELLAL 69 (127)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 57788887775 89999999999973
No 47
>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=24.97 E-value=87 Score=24.02 Aligned_cols=26 Identities=31% Similarity=0.449 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhc
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKT 184 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~ 184 (214)
.++..|+.+|+ +|++|+|.|++++..
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 48
>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=24.43 E-value=1.4e+02 Score=21.36 Aligned_cols=35 Identities=9% Similarity=0.097 Sum_probs=28.6
Q ss_pred hhhhhHHHHHHHHhCCCHHHHHHHHHHHHHhhCCCC
Q 045414 75 IQVLRLHELVDEVSGLTLSESAELGLIMMKKQGMTE 110 (214)
Q Consensus 75 ~~S~KV~~Ivd~I~~LTLlE~sELv~~leekfGVs~ 110 (214)
||.+.|++|++.+.+=++.++...+..|... |++.
T Consensus 3 p~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~ 37 (89)
T PF08542_consen 3 PPPEVIEEILESCLNGDFKEARKKLYELLVE-GYSA 37 (89)
T ss_dssp --HHHHHHHHHHHHHTCHHHHHHHHHHHHHT-T--H
T ss_pred CCHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCH
Confidence 4567999999999999999999999999988 9864
No 49
>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=24.37 E-value=1.8e+02 Score=21.86 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=21.9
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhcc
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKTP 185 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~P 185 (214)
..+..|+.+|. .|++|.+.+.+++...
T Consensus 45 ~~l~~i~~lr~-~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 45 ERLQQILFLKE-LGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHcCc
Confidence 56677777776 6999999999998764
No 50
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=23.53 E-value=48 Score=28.50 Aligned_cols=64 Identities=28% Similarity=0.356 Sum_probs=34.8
Q ss_pred eEEEeecCCchhHHHHHHH-HHh---hcCChHHHHHH-Hhhc-------chhhhcCCCHHHHHHHHHHHHHCCcEEE
Q 045414 148 DLKLESYDANAKVKIIKEL-RTF---TDLGLKEAKDL-VEKT-------PAVLKKGVLKEEAEKIIEKMKAVGGKVI 212 (214)
Q Consensus 148 dV~L~~~~a~kKI~vIK~V-R~i---T~LgLkEAK~l-VE~~-------P~vIKe~vsKEEAE~iKkkLEaaGA~Ve 212 (214)
.++|.+-+ +.|+.-+..| +.- -|+.++=-.-- .+.+ ...||+|+++|.|.+|.+.+++.+-+|.
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 78888754 6676555443 432 26666522211 1222 3478999999999999999999887764
No 51
>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=22.84 E-value=1e+02 Score=23.42 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
.++..|+.+|+ +|++|+|-|++++.
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 57777777776 69999999999974
No 52
>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=22.52 E-value=1.2e+02 Score=26.51 Aligned_cols=40 Identities=13% Similarity=0.214 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcCChHHHHHHHhhcchhhhc--CCCHHHHHHHHHHHHHCCcEE
Q 045414 160 VKIIKELRTFTDLGLKEAKDLVEKTPAVLKK--GVLKEEAEKIIEKMKAVGGKV 211 (214)
Q Consensus 160 I~vIK~VR~iT~LgLkEAK~lVE~~P~vIKe--~vsKEEAE~iKkkLEaaGA~V 211 (214)
..+++.||+.+ +.|-.+|- +.+.++..++.+.++++|+..
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 35677777654 36777773 467789999999999999874
No 53
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury 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=22.04 E-value=1.8e+02 Score=22.75 Aligned_cols=26 Identities=23% Similarity=0.427 Sum_probs=20.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhhc
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEKT 184 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~~ 184 (214)
.++..|+.+|. +|++|+|.|++++..
T Consensus 45 ~~l~~I~~lr~-~G~sL~eI~~~l~~~ 70 (126)
T cd04783 45 TRLRFIKRAQE-LGFTLDEIAELLELD 70 (126)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHhcc
Confidence 45666666663 799999999999854
No 54
>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=22.02 E-value=1.1e+02 Score=21.00 Aligned_cols=23 Identities=35% Similarity=0.486 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHH
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLV 181 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lV 181 (214)
..+..|+.+++ .|+.|.|.+.++
T Consensus 44 ~~l~~i~~l~~-~g~~l~~i~~~l 66 (67)
T cd04764 44 ELLKKIKTLLE-KGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHh
Confidence 46777777777 899999999876
No 55
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper 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-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=21.82 E-value=1.9e+02 Score=22.73 Aligned_cols=24 Identities=25% Similarity=0.529 Sum_probs=19.3
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVE 182 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE 182 (214)
..+..|+..| -+|++|+|.|++++
T Consensus 45 ~~l~~I~~lr-~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 45 DELRLISRAR-QVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHHHHH-HCCCCHHHHHHHHH
Confidence 5666676666 38999999999997
No 56
>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=21.71 E-value=82 Score=24.83 Aligned_cols=27 Identities=33% Similarity=0.530 Sum_probs=17.0
Q ss_pred hcchhhhc-CCCHHHHHHHHHHHHHCCcEEEe
Q 045414 183 KTPAVLKK-GVLKEEAEKIIEKMKAVGGKVIM 213 (214)
Q Consensus 183 ~~P~vIKe-~vsKEEAE~iKkkLEaaGA~Vel 213 (214)
+.|-+|+- .+|+ ..++++|+||++|++
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 44544443 2443 456788899999875
No 57
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.39 E-value=71 Score=28.00 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=36.7
Q ss_pred cCCchhHHHHHHHHHh-hcCChHHHHHHHhhcchhhhcCCCHHHHHHHHHHHHHC
Q 045414 154 YDANAKVKIIKELRTF-TDLGLKEAKDLVEKTPAVLKKGVLKEEAEKIIEKMKAV 207 (214)
Q Consensus 154 ~~a~kKI~vIK~VR~i-T~LgLkEAK~lVE~~P~vIKe~vsKEEAE~iKkkLEaa 207 (214)
+++.+| =+..++|+. |+||+..++-+|.+---++-.+.+ +.++..+||++
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 444344 456788877 899999999999998777766666 55667777754
No 58
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=21.28 E-value=1.7e+02 Score=23.59 Aligned_cols=25 Identities=20% Similarity=0.488 Sum_probs=19.5
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
.++..|+..|. +|++|+|.|++++.
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 46666666654 69999999999974
No 59
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.52 E-value=1.4e+02 Score=20.25 Aligned_cols=24 Identities=33% Similarity=0.652 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVE 182 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE 182 (214)
..+..|+.+|+ .|+++.+++.+++
T Consensus 45 ~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 45 ERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 57788888877 8999999998875
No 60
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=20.32 E-value=2.3e+02 Score=23.49 Aligned_cols=29 Identities=14% Similarity=0.273 Sum_probs=23.3
Q ss_pred hhhhhHHHHHHHHhCCCHHHHHHHHHHHH
Q 045414 75 IQVLRLHELVDEVSGLTLSESAELGLIMM 103 (214)
Q Consensus 75 ~~S~KV~~Ivd~I~~LTLlE~sELv~~le 103 (214)
.+++=-..|++.+.+||..|=..|...|-
T Consensus 78 ~~~~l~~~ii~~~~~Mt~~EQ~~L~~lL~ 106 (122)
T PF07037_consen 78 WDSPLERQIIDTLEEMTPAEQEQLTSLLL 106 (122)
T ss_pred CcchHHHHHHHHHHHCCHHHHHHHHHHHH
Confidence 33445568999999999999999988764
No 61
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=20.25 E-value=1.1e+02 Score=24.69 Aligned_cols=33 Identities=27% Similarity=0.431 Sum_probs=26.3
Q ss_pred HHHHHHHhhcchhhhcC--CCHHHHHHHHHHHHHC
Q 045414 175 KEAKDLVEKTPAVLKKG--VLKEEAEKIIEKMKAV 207 (214)
Q Consensus 175 kEAK~lVE~~P~vIKe~--vsKEEAE~iKkkLEaa 207 (214)
-|-+.|++++-.+++.. .+++|+++|+.+++.+
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 46678888888888865 7789999999988753
No 62
>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=20.07 E-value=1.2e+02 Score=23.77 Aligned_cols=25 Identities=24% Similarity=0.497 Sum_probs=19.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHhh
Q 045414 158 AKVKIIKELRTFTDLGLKEAKDLVEK 183 (214)
Q Consensus 158 kKI~vIK~VR~iT~LgLkEAK~lVE~ 183 (214)
.++..|+.+|. +|++|+|.|++++.
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 45566666663 59999999999974
Done!