Query 029444
Match_columns 193
No_of_seqs 166 out of 1121
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 13:01:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029444.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029444hhsearch_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 6.3E-50 1.4E-54 334.6 16.0 187 1-193 1-187 (187)
2 CHL00083 rpl12 ribosomal prote 100.0 1E-42 2.2E-47 278.4 14.3 130 60-193 2-131 (131)
3 cd00387 Ribosomal_L7_L12 Ribos 100.0 1.9E-42 4.2E-47 275.2 14.4 127 61-192 1-127 (127)
4 TIGR00855 L12 ribosomal protei 100.0 1.7E-40 3.7E-45 264.0 13.6 122 62-193 5-126 (126)
5 COG0222 RplL Ribosomal protein 100.0 5.9E-40 1.3E-44 259.4 12.7 122 61-193 3-124 (124)
6 PRK00157 rplL 50S ribosomal pr 100.0 1.2E-39 2.7E-44 258.2 13.8 122 60-193 2-123 (123)
7 PF00542 Ribosomal_L12: Riboso 99.9 1.5E-25 3.3E-30 161.2 5.5 68 125-193 1-68 (68)
8 PRK06771 hypothetical protein; 97.8 1.5E-05 3.3E-10 61.2 3.2 28 136-163 66-93 (93)
9 PF02617 ClpS: ATP-dependent C 85.3 2.6 5.7E-05 30.5 5.3 65 122-187 3-71 (82)
10 PRK00033 clpS ATP-dependent Cl 60.8 47 0.001 25.7 6.8 70 123-193 25-98 (100)
11 COG0264 Tsf Translation elonga 60.5 9.4 0.0002 35.0 3.3 28 137-164 4-31 (296)
12 cd04788 HTH_NolA-AlbR Helix-Tu 56.8 28 0.00061 25.8 4.9 48 136-185 44-91 (96)
13 PRK09377 tsf elongation factor 53.5 15 0.00032 33.3 3.4 29 139-167 6-34 (290)
14 PRK10664 transcriptional regul 50.5 8.2 0.00018 28.7 1.1 36 137-172 2-37 (90)
15 PF10925 DUF2680: Protein of u 49.6 28 0.00061 24.4 3.6 27 156-185 20-47 (59)
16 PF02022 Integrase_Zn: Integra 48.9 27 0.00058 22.8 3.2 28 142-169 12-39 (40)
17 PRK10753 transcriptional regul 48.0 9.4 0.0002 28.3 1.0 35 137-171 2-36 (90)
18 cd01107 HTH_BmrR Helix-Turn-He 47.8 40 0.00086 25.5 4.5 29 136-165 45-73 (108)
19 PF09278 MerR-DNA-bind: MerR, 47.8 27 0.00059 23.4 3.3 22 138-160 3-24 (65)
20 cd00591 HU_IHF Integration hos 45.9 20 0.00042 25.5 2.4 34 138-171 2-35 (87)
21 PF10044 Ret_tiss: Retinal tis 45.5 17 0.00037 28.1 2.2 24 138-161 60-87 (95)
22 PF09999 DUF2240: Uncharacteri 44.3 40 0.00088 27.7 4.3 34 60-93 84-122 (144)
23 smart00411 BHL bacterial (prok 42.2 23 0.00049 25.4 2.3 34 138-171 3-36 (90)
24 cd04774 HTH_YfmP Helix-Turn-He 41.7 77 0.0017 23.6 5.2 31 136-166 43-73 (96)
25 PF11363 DUF3164: Protein of u 41.2 43 0.00093 28.7 4.1 80 63-172 36-117 (195)
26 KOG3449 60S acidic ribosomal p 40.7 95 0.0021 24.9 5.7 27 60-89 36-62 (112)
27 PF14520 HHH_5: Helix-hairpin- 40.4 82 0.0018 21.2 4.7 46 140-185 2-60 (60)
28 PF13411 MerR_1: MerR HTH fami 40.0 31 0.00067 23.2 2.6 26 136-162 43-68 (69)
29 cd04766 HTH_HspR Helix-Turn-He 39.0 91 0.002 22.6 5.1 40 136-185 44-83 (91)
30 COG3797 Uncharacterized protei 37.1 29 0.00063 29.7 2.5 50 133-186 13-63 (178)
31 COG3612 Uncharacterized protei 35.5 51 0.0011 27.8 3.6 35 56-90 86-123 (157)
32 cd04768 HTH_BmrR-like Helix-Tu 34.5 1E+02 0.0023 22.7 4.9 28 136-164 44-71 (96)
33 TIGR02043 ZntR Zn(II)-responsi 32.7 92 0.002 24.4 4.5 26 136-162 45-70 (131)
34 cd04782 HTH_BltR Helix-Turn-He 32.3 1E+02 0.0022 22.8 4.5 26 137-163 45-70 (97)
35 PF08542 Rep_fac_C: Replicatio 31.8 67 0.0015 22.7 3.4 36 58-94 3-38 (89)
36 PRK13019 clpS ATP-dependent Cl 30.9 2.2E+02 0.0047 21.7 6.2 70 122-191 18-91 (94)
37 PF13565 HTH_32: Homeodomain-l 30.7 93 0.002 21.3 3.8 33 61-93 33-66 (77)
38 PRK00285 ihfA integration host 29.6 47 0.001 24.6 2.3 35 137-171 4-38 (99)
39 cd01104 HTH_MlrA-CarA Helix-Tu 29.0 68 0.0015 21.4 2.9 24 137-161 45-68 (68)
40 COG4575 ElaB Uncharacterized c 29.0 64 0.0014 25.5 3.0 33 154-186 15-49 (104)
41 PF08958 DUF1871: Domain of un 28.0 48 0.001 24.6 2.1 39 50-90 10-49 (79)
42 PF00828 Ribosomal_L18e: Ribos 27.6 51 0.0011 25.6 2.3 27 162-192 101-128 (129)
43 cd04763 HTH_MlrA-like Helix-Tu 27.6 75 0.0016 21.6 2.9 23 137-160 45-67 (68)
44 KOG2003 TPR repeat-containing 27.2 60 0.0013 32.5 3.1 30 132-163 689-719 (840)
45 cd04781 HTH_MerR-like_sg6 Heli 27.1 2E+02 0.0043 22.0 5.5 27 136-163 43-69 (120)
46 PRK06419 rpl15p 50S ribosomal 27.0 56 0.0012 26.7 2.5 25 164-192 119-144 (148)
47 COG0151 PurD Phosphoribosylami 26.9 47 0.001 32.0 2.3 47 145-193 121-186 (428)
48 PRK05412 putative nucleotide-b 26.9 61 0.0013 27.4 2.7 64 127-191 45-120 (161)
49 cd01105 HTH_GlnR-like Helix-Tu 26.8 87 0.0019 22.8 3.3 26 136-162 45-70 (88)
50 PRK13752 putative transcriptio 26.2 1.2E+02 0.0027 24.3 4.3 25 137-162 52-76 (144)
51 cd05833 Ribosomal_P2 Ribosomal 25.7 1.6E+02 0.0035 23.0 4.7 28 61-91 37-64 (109)
52 cd04780 HTH_MerR-like_sg5 Heli 25.5 95 0.0021 23.1 3.3 27 136-162 44-70 (95)
53 PF04461 DUF520: Protein of un 25.4 46 0.001 28.1 1.7 64 127-191 45-120 (160)
54 PRK05350 acyl carrier protein; 25.1 85 0.0018 22.3 2.9 21 72-92 37-57 (82)
55 cd01108 HTH_CueR Helix-Turn-He 25.1 1.6E+02 0.0034 22.8 4.6 25 137-162 45-69 (127)
56 PF11272 DUF3072: Protein of u 25.0 97 0.0021 22.1 3.0 29 158-186 26-54 (57)
57 PRK10227 DNA-binding transcrip 24.5 1.4E+02 0.003 23.7 4.3 25 137-162 45-69 (135)
58 PF07037 DUF1323: Putative tra 23.5 2.1E+02 0.0046 23.2 5.1 31 57-87 77-107 (122)
59 cd01109 HTH_YyaN Helix-Turn-He 23.5 1E+02 0.0022 23.2 3.2 26 137-163 45-70 (113)
60 cd02810 DHOD_DHPD_FMN Dihydroo 23.5 1.2E+02 0.0025 26.2 4.0 40 140-191 152-193 (289)
61 cd01106 HTH_TipAL-Mta Helix-Tu 23.4 2.1E+02 0.0046 21.1 4.9 27 137-164 45-71 (103)
62 PF03608 EII-GUT: PTS system e 23.3 22 0.00048 30.2 -0.5 49 5-54 52-101 (168)
63 PF10410 DnaB_bind: DnaB-helic 23.2 2.2E+02 0.0048 18.4 4.6 34 61-94 23-57 (59)
64 PF06698 DUF1192: Protein of u 22.6 71 0.0015 22.7 2.0 33 55-89 5-37 (59)
65 TIGR02044 CueR Cu(I)-responsiv 21.8 2E+02 0.0043 22.2 4.6 24 137-161 45-68 (127)
66 PF00416 Ribosomal_S13: Riboso 21.6 1.3E+02 0.0028 22.9 3.5 46 140-185 12-60 (107)
67 cd01282 HTH_MerR-like_sg3 Heli 21.6 2E+02 0.0044 21.7 4.5 25 137-162 44-68 (112)
68 cd04783 HTH_MerR1 Helix-Turn-H 21.5 1.9E+02 0.0042 22.1 4.5 26 137-163 45-70 (126)
69 COG1480 Predicted membrane-ass 21.0 1E+02 0.0022 31.5 3.5 74 17-90 581-683 (700)
70 cd04777 HTH_MerR-like_sg1 Heli 21.0 1.2E+02 0.0027 22.5 3.2 25 137-162 43-67 (107)
71 cd04740 DHOD_1B_like Dihydroor 20.7 1.1E+02 0.0024 26.5 3.3 39 140-190 144-182 (296)
72 cd08499 PBP2_Ylib_like The sub 20.2 1.6E+02 0.0035 26.8 4.3 44 150-193 300-352 (474)
73 cd04784 HTH_CadR-PbrR Helix-Tu 20.2 1.2E+02 0.0026 23.3 3.1 25 137-162 45-69 (127)
No 1
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-50 Score=334.61 Aligned_cols=187 Identities=40% Similarity=0.508 Sum_probs=154.4
Q ss_pred CchhhhhHhhhcCCCCCCccchhhhhhhcccCCCCCCCCCCccCCCCCcCCCCCCCCCCChhHHHHHHHHhcCCHHHHHH
Q 029444 1 MKLTALAKSICSRPFLPRITGPLQFRLLQHDFVPRDPKSKPIKYKYPAFYDPYGPRPPPSDKVVQLAERIASLTPEERRQ 80 (193)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~s~kV~~ivd~I~~LtllE~se 80 (193)
|..+++.+++.++.|++.++++.+.+.-..+... . .....+.++.+|+|++++.++++||.+|+|+|++|||+|.+|
T Consensus 1 ~~~~s~~~~~~sr~~~r~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~KI~~iv~eIssLtLlE~s~ 77 (187)
T KOG1715|consen 1 SIATSIRSSSLSRLALRSISRSVPRSIEYPHAFS--S-SKSSTLSHRATPLPPIAAVPPPPKISKIVDEISSLTLLETSD 77 (187)
T ss_pred CcccchhhhhhhhhhhhhhcccccceecchhhcC--c-ccccccccccCCCCcccccCCCHHHHHHHHHHHhcCHHHHHH
Confidence 4567788888877888888888887554444222 1 245556679999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCCCCccccccccCCCCCCCCCCCchhhhhcccceeEEEEeecccchhHHHHHHHHHhhcCChHHHHHHH
Q 029444 81 ISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAKVEEKKEKTTFDVKLEKFEAAAKLKIVKEVKTFFDLGMKEAKELV 160 (193)
Q Consensus 81 Lv~~leekfgv~~~~~~~~~~~~~~~~~~aa~~~a~~e~~~EKT~FdV~L~~~~a~kKI~VIKeVR~iT~LGLKEAK~lV 160 (193)
|+++|+++|||+..+.+++++. |++++ +++++.++.++|+|.|||+|++||+.+||+||||||.+|||||+|||+||
T Consensus 78 L~~~Lk~kl~i~e~~~~~a~~~--g~~~~-~~~~a~ee~k~ekt~FdVkL~~fda~~KIkVIKEVR~~tgL~LkeAKklV 154 (187)
T KOG1715|consen 78 LVDLLKKKLNIPELPLAPAAAA--GAAAP-DAGGAEEEAKKEKTTFDVKLEKFDASSKIKVIKEVRALTGLGLKEAKKLV 154 (187)
T ss_pred HHHHHHHHcCCCcccchhhccc--cCCCC-CcccccccchhhcceEEEEEeecCccchhHHHHHHHHhccccHHHHHHHH
Confidence 9999999999998865543222 11111 11222334455888899999999999999999999999999999999999
Q ss_pred HhCchhhhcCCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 161 EKAPVVLKQGLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 161 Es~P~vIKe~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
|++|+++|+||+|||||+||++|+++||+|+||
T Consensus 155 E~aP~ilKegvtKeEAEkik~kLea~GakV~le 187 (187)
T KOG1715|consen 155 EKAPKILKEGVTKEEAEEIKEKLEAAGAKVVLE 187 (187)
T ss_pred HhccHHHHcCCCHHHHHHHHHHHHHcCCeEeeC
Confidence 999999999999999999999999999999998
No 2
>CHL00083 rpl12 ribosomal protein L12
Probab=100.00 E-value=1e-42 Score=278.36 Aligned_cols=130 Identities=34% Similarity=0.510 Sum_probs=110.8
Q ss_pred ChhHHHHHHHHhcCCHHHHHHHHHHHHHHcCCCCCCccccccccCCCCCCCCCCCchhhhhcccceeEEEEeecccchhH
Q 029444 60 SDKVVQLAERIASLTPEERRQISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAKVEEKKEKTTFDVKLEKFEAAAKL 139 (193)
Q Consensus 60 s~kV~~ivd~I~~LtllE~seLv~~leekfgv~~~~~~~~~~~~~~~~~~aa~~~a~~e~~~EKT~FdV~L~~~~a~kKI 139 (193)
|+++++|+|+|++|||+|++||++.|+++|||++.+++++++++ + +++++ ++.+++.+|||+|||+|++|++++||
T Consensus 2 s~k~~~ivd~i~~LTllE~~eLv~~le~~fgv~~~~~~a~~~~~-~--~a~~~-~~~~~~~~EKT~F~V~L~~~~~~~Ki 77 (131)
T CHL00083 2 STKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMS-A--PAAAA-AQAAEEVEEKTEFDVILEEVPADKRI 77 (131)
T ss_pred CchHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhhhhhcc-c--cCccc-ccccchhhhcceeeEEEeecCCcchH
Confidence 68999999999999999999999999999999987654321111 1 01111 11123456999999999999888999
Q ss_pred HHHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 140 KIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 140 ~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
+|||+||++|||||+|||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 78 ~vIK~vr~it~lgLkeaK~lVe~~P~~ike~v~KeeAe~ik~~le~~Ga~v~lk 131 (131)
T CHL00083 78 AVLKVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQLEEAGAKVIIK 131 (131)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 999999999999999999999999999999999999999999999999999983
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=1.9e-42 Score=275.23 Aligned_cols=127 Identities=39% Similarity=0.536 Sum_probs=106.7
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHcCCCCCCccccccccCCCCCCCCCCCchhhhhcccceeEEEEeecccchhHH
Q 029444 61 DKVVQLAERIASLTPEERRQISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAKVEEKKEKTTFDVKLEKFEAAAKLK 140 (193)
Q Consensus 61 ~kV~~ivd~I~~LtllE~seLv~~leekfgv~~~~~~~~~~~~~~~~~~aa~~~a~~e~~~EKT~FdV~L~~~~a~kKI~ 140 (193)
.++++|+|+|++|||+|++||++.|+++|||++.++.++ +++ ++++ ++++..++++|||+|||+|++||+++||+
T Consensus 1 ~~~~~i~d~i~~LtllE~~eLv~~le~~~gv~~~~~~~~-~~~--~a~~--~~~~~~~~~~EKt~F~V~L~~~~~~~Ki~ 75 (127)
T cd00387 1 LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAA-AAA--AAPA--AAAAAAAEAEEKTEFDVVLESFGAAKKIA 75 (127)
T ss_pred CcHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCccccccc-ccc--cCcc--cccccccchhhcceEEEEEeeCCchhhHH
Confidence 368999999999999999999999999999987632111 111 1111 11111223469999999999999889999
Q ss_pred HHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHcCCeEee
Q 029444 141 IVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAGGVAIM 192 (193)
Q Consensus 141 VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaaGA~V~i 192 (193)
|||+||++|||||||||+|||++|++||+|+||+|||+||++|+++||+|+|
T Consensus 76 vIK~VR~it~LgLkEAK~lVe~~P~~iKe~vsKeeAE~ik~kLe~aGA~Vel 127 (127)
T cd00387 76 VIKEVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127 (127)
T ss_pred HHHHHHHHhCCChHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEeC
Confidence 9999999999999999999999999999999999999999999999999986
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=1.7e-40 Score=264.02 Aligned_cols=122 Identities=35% Similarity=0.532 Sum_probs=105.3
Q ss_pred hHHHHHHHHhcCCHHHHHHHHHHHHHHcCCCCCCccccccccCCCCCCCCCCCchhhhhcccceeEEEEeecccchhHHH
Q 029444 62 KVVQLAERIASLTPEERRQISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAKVEEKKEKTTFDVKLEKFEAAAKLKI 141 (193)
Q Consensus 62 kV~~ivd~I~~LtllE~seLv~~leekfgv~~~~~~~~~~~~~~~~~~aa~~~a~~e~~~EKT~FdV~L~~~~a~kKI~V 141 (193)
..++|+|+|++|||+|++||++.|+++|||++.+++++ ++++++ + ++++++|||+|||+|+.++ ++||+|
T Consensus 5 ~~~~ive~i~~LTllE~~eLv~~lee~fgV~a~a~~a~-----~~a~~~-~---~~~~~eEKt~f~V~L~~~~-~~Ki~v 74 (126)
T TIGR00855 5 SKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAA-----GAAGAA-A---AAAAAEEKTEFDVILKGAG-DNKIAV 74 (126)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCccchhhh-----cccccc-c---ccccccccceeeEEEecCC-cchhHH
Confidence 45899999999999999999999999999998765421 111111 1 1233469999999999987 689999
Q ss_pred HHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 142 VKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 142 IKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
||+||++|||||||||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 75 IK~vR~itgLgLkEAK~lVe~~P~~ike~vsKeeAe~ik~~Le~aGa~veik 126 (126)
T TIGR00855 75 IKVVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEVK 126 (126)
T ss_pred HHHHHHHcCCcHHHHHHHHHhCcHHHHhCCCHHHHHHHHHHHHHcCCEEEeC
Confidence 9999999999999999999999999999999999999999999999999983
No 5
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.9e-40 Score=259.42 Aligned_cols=122 Identities=37% Similarity=0.529 Sum_probs=106.8
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHcCCCCCCccccccccCCCCCCCCCCCchhhhhcccceeEEEEeecccchhHH
Q 029444 61 DKVVQLAERIASLTPEERRQISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAKVEEKKEKTTFDVKLEKFEAAAKLK 140 (193)
Q Consensus 61 ~kV~~ivd~I~~LtllE~seLv~~leekfgv~~~~~~~~~~~~~~~~~~aa~~~a~~e~~~EKT~FdV~L~~~~a~kKI~ 140 (193)
-.+++|+++|++||++|+++|++.++++|||++.++++++++ + +++ .+..+|||+|||+|++++ ++||+
T Consensus 3 ~~~e~iie~i~~~svlel~eLvk~~eekfgVsaaa~va~a~~-----~-a~a----~~aaeEktefdVvL~~~g-~kKI~ 71 (124)
T COG0222 3 LTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAA-----G-AAA----AEAAEEKTEFDVVLKSAG-GKKIA 71 (124)
T ss_pred CcHHHHHHHHHHhhHHHHHHHHHHHHHHhCCccchhhhhccc-----c-ccc----cccccccceeEEEecccC-Ccchh
Confidence 357899999999999999999999999999999877543211 1 111 122458999999999995 79999
Q ss_pred HHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 141 IVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 141 VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
|||+||++|||||||||+|||++|++||+|++|+|||+||++|+++||+|++.
T Consensus 72 VIK~vR~itGLGLKEAKdlVe~aP~~~KE~v~k~eAe~~kkkleeaGa~V~~k 124 (124)
T COG0222 72 VIKVVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124 (124)
T ss_pred HHHHHHHHhcccHHHHHHHHHhCcHHHHccCCHHHHHHHHHHHHHcCCeEeeC
Confidence 99999999999999999999999999999999999999999999999999974
No 6
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=100.00 E-value=1.2e-39 Score=258.23 Aligned_cols=122 Identities=33% Similarity=0.499 Sum_probs=106.1
Q ss_pred ChhHHHHHHHHhcCCHHHHHHHHHHHHHHcCCCCCCccccccccCCCCCCCCCCCchhhhhcccceeEEEEeecccchhH
Q 029444 60 SDKVVQLAERIASLTPEERRQISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAKVEEKKEKTTFDVKLEKFEAAAKL 139 (193)
Q Consensus 60 s~kV~~ivd~I~~LtllE~seLv~~leekfgv~~~~~~~~~~~~~~~~~~aa~~~a~~e~~~EKT~FdV~L~~~~a~kKI 139 (193)
+-++++|+|+|++|||+|++||++.|+++|||++.+++++ +++++ + +++++|||+|||+|++| +++||
T Consensus 2 ~~~~~~i~e~i~~LtllE~~eLv~~lee~fgv~a~~~~~~-----~~~~~--~----~~~~eEkt~f~V~L~~~-~~kKi 69 (123)
T PRK00157 2 ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAA-----AAAAA--A----AAAAEEKTEFDVVLKSA-GDKKI 69 (123)
T ss_pred CccHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCccchhcc-----ccccc--c----ccccccccceeEEEecc-chhhH
Confidence 3468999999999999999999999999999998754321 11111 1 12345999999999999 47999
Q ss_pred HHHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 140 KIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 140 ~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
+|||+||++|||||||||+|||++|++||+|++|+|||+||++|+++||+|+|.
T Consensus 70 ~vIK~vR~itgLgLkEAK~lVe~~P~~ike~v~keeAe~ik~~Le~aGa~velk 123 (123)
T PRK00157 70 AVIKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAGAKVELK 123 (123)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHhCCHHHHhCCCHHHHHHHHHHHHHcCCEEeeC
Confidence 999999999999999999999999999999999999999999999999999984
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=99.92 E-value=1.5e-25 Score=161.22 Aligned_cols=68 Identities=46% Similarity=0.743 Sum_probs=60.3
Q ss_pred eeEEEEeecccchhHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 125 TFDVKLEKFEAAAKLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 125 ~FdV~L~~~~a~kKI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
+|||+|++| +++||++||+||++|||||+|||++||++|.+|+++++++|||+|+++|+++||+|+|+
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 68999999999999999999999999999999999999999999999999999999985
No 8
>PRK06771 hypothetical protein; Provisional
Probab=97.82 E-value=1.5e-05 Score=61.17 Aligned_cols=28 Identities=32% Similarity=0.494 Sum_probs=26.5
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHhC
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEKA 163 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs~ 163 (193)
.+||+.||.+|+.||+||+|||+.||++
T Consensus 66 Gkki~AIK~~Re~tG~~L~eAK~yVD~L 93 (93)
T PRK06771 66 GQTVTAVKRVREAFGFSLLEAKQYVDKL 93 (93)
T ss_pred CCchHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 5899999999999999999999999975
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=85.29 E-value=2.6 Score=30.54 Aligned_cols=65 Identities=22% Similarity=0.312 Sum_probs=47.9
Q ss_pred ccceeEEEEeecccchhHHHHHHHHHhhcCChHHHHHHHHhCc----hhhhcCCCHHHHHHHHHHHHHcC
Q 029444 122 EKTTFDVKLEKFEAAAKLKIVKEVKTFFDLGMKEAKELVEKAP----VVLKQGLTKEEASNIIEKIKAAG 187 (193)
Q Consensus 122 EKT~FdV~L~~~~a~kKI~VIKeVR~iT~LGLKEAK~lVEs~P----~vIKe~vsKeEAEeik~kLeaaG 187 (193)
+...|.|+|=+=+-..--.||..++...|+...+|.++...+- .+|.. -++++||....+|...|
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 3468999996655456779999999999999999999987542 35544 58999999999999999
No 10
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=60.84 E-value=47 Score=25.65 Aligned_cols=70 Identities=20% Similarity=0.281 Sum_probs=55.8
Q ss_pred cceeEEEEeecccchhHHHHHHHHHhhcCChHHHHHHHHhC----chhhhcCCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 123 KTTFDVKLEKFEAAAKLKIVKEVKTFFDLGMKEAKELVEKA----PVVLKQGLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 123 KT~FdV~L~~~~a~kKI~VIKeVR~iT~LGLKEAK~lVEs~----P~vIKe~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
..-|.|+|-+=|-..-==||..++.+.+++..+|-++.-.+ =.++.. -++|.||....+|...|-.+.||
T Consensus 25 ~~~y~ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~-~~~e~AE~~~~~l~~~~L~~~ie 98 (100)
T PRK00033 25 PPMYKVLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGV-CTREVAETKVEQVHQHGLLCTME 98 (100)
T ss_pred CCceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEE-EcHHHHHHHHHHHHcCCCeEEEe
Confidence 34699999764444455799999999999999999887643 224443 49999999999999999999886
No 11
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=60.51 E-value=9.4 Score=34.99 Aligned_cols=28 Identities=29% Similarity=0.388 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhCc
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKAP 164 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~P 164 (193)
-+.+.||++|+.||.|.++.|+.++.+-
T Consensus 4 ita~~VKeLRe~TgAGMmdCKkAL~E~~ 31 (296)
T COG0264 4 ITAALVKELREKTGAGMMDCKKALEEAN 31 (296)
T ss_pred ccHHHHHHHHHHhCCcHHHHHHHHHHcC
Confidence 3568999999999999999999876543
No 12
>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=56.78 E-value=28 Score=25.76 Aligned_cols=48 Identities=8% Similarity=0.234 Sum_probs=31.0
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHH
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKA 185 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLea 185 (193)
-.++..|+..|+ +|+.|+|.+.+++.....+++ +-.+..+++.+++++
T Consensus 44 l~~l~~I~~lr~-~G~~l~eI~~~l~~~~~~~~~-~l~~~~~~l~~~i~~ 91 (96)
T cd04788 44 IRRLHQIIALRR-LGFSLREIGRALDGPDFDPLE-LLRRQLARLEEQLEL 91 (96)
T ss_pred HHHHHHHHHHHH-cCCCHHHHHHHHhCCChhHHH-HHHHHHHHHHHHHHH
Confidence 357777777776 699999999999876532222 334444555555543
No 13
>PRK09377 tsf elongation factor Ts; Provisional
Probab=53.49 E-value=15 Score=33.34 Aligned_cols=29 Identities=24% Similarity=0.305 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhcCChHHHHHHHHhCchhh
Q 029444 139 LKIVKEVKTFFDLGMKEAKELVEKAPVVL 167 (193)
Q Consensus 139 I~VIKeVR~iT~LGLKEAK~lVEs~P~vI 167 (193)
.+.||++|+.||-|+.+.|+..+.+..-+
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ 34 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDI 34 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCH
Confidence 47899999999999999999988776554
No 14
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=50.48 E-value=8.2 Score=28.73 Aligned_cols=36 Identities=11% Similarity=0.189 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCCC
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLT 172 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vs 172 (193)
+|-.+|+.|.+-++|.-++++.+||..=.+|.+.+.
T Consensus 2 tK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~ 37 (90)
T PRK10664 2 NKSQLIDKIAAGADISKAAAGRALDAIIASVTESLK 37 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 366899999999999999999999998777765443
No 15
>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=49.61 E-value=28 Score=24.45 Aligned_cols=27 Identities=30% Similarity=0.585 Sum_probs=21.9
Q ss_pred HHHHHHhCchhhhcC-CCHHHHHHHHHHHHH
Q 029444 156 AKELVEKAPVVLKQG-LTKEEASNIIEKIKA 185 (193)
Q Consensus 156 AK~lVEs~P~vIKe~-vsKeEAEeik~kLea 185 (193)
=|.+|+. -++.| +|+|.|+.|++.++.
T Consensus 20 kK~~idk---~Ve~G~iTqeqAd~ik~~id~ 47 (59)
T PF10925_consen 20 KKQIIDK---YVEAGVITQEQADAIKKHIDQ 47 (59)
T ss_pred HHHHHHH---HHHcCCCCHHHHHHHHHHHHH
Confidence 3667764 67888 899999999998875
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=48.91 E-value=27 Score=22.84 Aligned_cols=28 Identities=21% Similarity=0.364 Sum_probs=20.7
Q ss_pred HHHHHHhhcCChHHHHHHHHhCchhhhc
Q 029444 142 VKEVKTFFDLGMKEAKELVEKAPVVLKQ 169 (193)
Q Consensus 142 IKeVR~iT~LGLKEAK~lVEs~P~vIKe 169 (193)
.|.+|.-.||-..+||++|.++|.=-.+
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 4677777899999999999999975443
No 17
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=48.00 E-value=9.4 Score=28.31 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=29.5
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCC
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGL 171 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~v 171 (193)
+|-.+|+.|.+-+++.-++++..|+.+-.+|.+.+
T Consensus 2 ~K~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L 36 (90)
T PRK10753 2 NKTQLIDVIADKAELSKTQAKAALESTLAAITESL 36 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999877665544
No 18
>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=47.85 E-value=40 Score=25.45 Aligned_cols=29 Identities=17% Similarity=0.356 Sum_probs=23.9
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHhCch
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEKAPV 165 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs~P~ 165 (193)
-..+..|+..|+ +|++|.|.+.+++..+.
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 357778888776 89999999999988764
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=47.80 E-value=27 Score=23.43 Aligned_cols=22 Identities=18% Similarity=0.655 Sum_probs=16.3
Q ss_pred hHHHHHHHHHhhcCChHHHHHHH
Q 029444 138 KLKIVKEVKTFFDLGMKEAKELV 160 (193)
Q Consensus 138 KI~VIKeVR~iT~LGLKEAK~lV 160 (193)
++..|+..|+ .|++|.|-|+++
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
>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=45.87 E-value=20 Score=25.46 Aligned_cols=34 Identities=21% Similarity=0.282 Sum_probs=28.9
Q ss_pred hHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCC
Q 029444 138 KLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGL 171 (193)
Q Consensus 138 KI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~v 171 (193)
|-.+|++|...+++.-++++.+|+.+-.+|.+.+
T Consensus 2 K~~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L 35 (87)
T cd00591 2 KSELIEAIAEKTGLSKKDAEAAVDAFLDVITEAL 35 (87)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 6689999999999999999999998877666543
No 21
>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=45.54 E-value=17 Score=28.09 Aligned_cols=24 Identities=29% Similarity=0.697 Sum_probs=17.4
Q ss_pred hHHHHHHHHHh----hcCChHHHHHHHH
Q 029444 138 KLKIVKEVKTF----FDLGMKEAKELVE 161 (193)
Q Consensus 138 KI~VIKeVR~i----T~LGLKEAK~lVE 161 (193)
.-.+++.||++ -.|||.|||++--
T Consensus 60 ~~~L~~~Ik~L~~~aYqLGl~EaKEmtR 87 (95)
T PF10044_consen 60 PDQLIEKIKKLQDEAYQLGLEEAKEMTR 87 (95)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHh
Confidence 33566666655 4799999999854
No 22
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=44.27 E-value=40 Score=27.74 Aligned_cols=34 Identities=18% Similarity=0.172 Sum_probs=28.2
Q ss_pred ChhHHHHHHHHhc---CCHHHHHHHHHHHHHHcC--CCC
Q 029444 60 SDKVVQLAERIAS---LTPEERRQISLTLFKRFS--LPK 93 (193)
Q Consensus 60 s~kV~~ivd~I~~---LtllE~seLv~~leekfg--v~~ 93 (193)
.+-.++|+|.|.. ++-.|+...++.++++|| |+.
T Consensus 84 ~~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l~~ 122 (144)
T PF09999_consen 84 RDPFERILDYIAAKTGIEKQEVVAEINELQEELGGLLDP 122 (144)
T ss_pred ccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCCH
Confidence 3457788888876 899999999999999999 653
No 23
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=42.24 E-value=23 Score=25.36 Aligned_cols=34 Identities=21% Similarity=0.301 Sum_probs=29.7
Q ss_pred hHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCC
Q 029444 138 KLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGL 171 (193)
Q Consensus 138 KI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~v 171 (193)
|-.+|++|.+.|++.-++++..++.+-.+|.+.+
T Consensus 3 k~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L 36 (90)
T smart00411 3 KSELIDAIAEKAGLSKKDAKAAVDAFLEIITEAL 36 (90)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999888777644
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=41.67 E-value=77 Score=23.60 Aligned_cols=31 Identities=10% Similarity=0.294 Sum_probs=26.7
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHhCchh
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEKAPVV 166 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs~P~v 166 (193)
-.++..|+..|+..|++|.+.+.+++..+..
T Consensus 43 v~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 43 LKRLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 3688999999988899999999999877664
No 25
>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=41.20 E-value=43 Score=28.65 Aligned_cols=80 Identities=19% Similarity=0.224 Sum_probs=50.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHcCCCCCCccccccccCCCCCCCCCCCchhhhhcccceeEEEEeecccchhHHHH
Q 029444 63 VVQLAERIASLTPEERRQISLTLFKRFSLPKLQPISTEGLDLGPQGGAPAGSAKVEEKKEKTTFDVKLEKFEAAAKLKIV 142 (193)
Q Consensus 63 V~~ivd~I~~LtllE~seLv~~leekfgv~~~~~~~~~~~~~~~~~~aa~~~a~~e~~~EKT~FdV~L~~~~a~kKI~VI 142 (193)
+.+.+...+.-+..++..+++++.+++|+..- | +.=++.|++||+..||.+
T Consensus 36 l~~~l~~fK~~~f~d~~af~~l~~e~Yg~k~g--------------g--------------~kGn~Tl~sfDG~~kV~i- 86 (195)
T PF11363_consen 36 LSEQLAEFKAHTFEDIEAFIELSAEEYGVKLG--------------G--------------KKGNVTLTSFDGRYKVTI- 86 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcC--------------C--------------CcCcEEEEEeCCCEEEEE-
Confidence 34445555666778889999999999998321 0 111456668876555544
Q ss_pred HHHHHh--hcCChHHHHHHHHhCchhhhcCCC
Q 029444 143 KEVKTF--FDLGMKEAKELVEKAPVVLKQGLT 172 (193)
Q Consensus 143 KeVR~i--T~LGLKEAK~lVEs~P~vIKe~vs 172 (193)
.+++. .+=.|.-||+||+.+=...-+|..
T Consensus 87 -~~~~~~~Fde~l~~Ak~lIde~l~~w~~g~~ 117 (195)
T PF11363_consen 87 -AVQDRISFDERLQAAKALIDECLNEWAKGAD 117 (195)
T ss_pred -EecccCCcChHHHHHHHHHHHHHHHHhcCCC
Confidence 23332 344678888888876666666644
No 26
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=40.68 E-value=95 Score=24.86 Aligned_cols=27 Identities=4% Similarity=0.107 Sum_probs=16.4
Q ss_pred ChhHHHHHHHHhcCCHHHHHHHHHHHHHHc
Q 029444 60 SDKVVQLAERIASLTPEERRQISLTLFKRF 89 (193)
Q Consensus 60 s~kV~~ivd~I~~LtllE~seLv~~leekf 89 (193)
.++++.++.+|+.-++. ||+..=+++|
T Consensus 36 ~e~i~~visel~GK~i~---ElIA~G~ekl 62 (112)
T KOG3449|consen 36 DERINLVLSELKGKDIE---ELIAAGREKL 62 (112)
T ss_pred HHHHHHHHHHhcCCCHH---HHHHHhHHHH
Confidence 45677777777776654 4555555555
No 27
>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=40.40 E-value=82 Score=21.16 Aligned_cols=46 Identities=24% Similarity=0.366 Sum_probs=31.1
Q ss_pred HHHHHHHHhhcCChHHHHHHHHhCchhh-------------hcCCCHHHHHHHHHHHHH
Q 029444 140 KIVKEVKTFFDLGMKEAKELVEKAPVVL-------------KQGLTKEEASNIIEKIKA 185 (193)
Q Consensus 140 ~VIKeVR~iT~LGLKEAK~lVEs~P~vI-------------Ke~vsKeEAEeik~kLea 185 (193)
.++..+.++.|+|-+-|+.|++.--..+ -.|+++.-|+.|++.+.+
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 3556666777888888877777622222 247888888888887753
No 28
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=39.98 E-value=31 Score=23.20 Aligned_cols=26 Identities=23% Similarity=0.535 Sum_probs=20.9
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
-..+..|+..++ .|+.|.|.+++++.
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 468888888888 99999999998763
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=38.97 E-value=91 Score=22.61 Aligned_cols=40 Identities=13% Similarity=0.333 Sum_probs=30.2
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHH
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKA 185 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLea 185 (193)
=.++..|+..+.-.|++|.+.+.+++ =.++-+.+.+.|+.
T Consensus 44 v~~l~~i~~L~~d~g~~l~~i~~~l~----------l~~~~~~l~~~l~~ 83 (91)
T cd04766 44 IERLRRIQRLTQELGVNLAGVKRILE----------LEEELAELRAELDE 83 (91)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHH----------HHHHHHHHHHHHHH
Confidence 36788888888878999999999997 34555666665554
No 30
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.10 E-value=29 Score=29.74 Aligned_cols=50 Identities=20% Similarity=0.363 Sum_probs=37.1
Q ss_pred cccchhHHHHHHHHHh-hcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHc
Q 029444 133 FEAAAKLKIVKEVKTF-FDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAA 186 (193)
Q Consensus 133 ~~a~kKI~VIKeVR~i-T~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaa 186 (193)
+++.+| =+..++|+. |+||+..++-+|.|---++-...+ +.++.+|||++
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 343334 456788877 899999999999998777776666 56677777764
No 31
>COG3612 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.51 E-value=51 Score=27.76 Aligned_cols=35 Identities=14% Similarity=0.136 Sum_probs=27.7
Q ss_pred CCCCChhHHHHHHHHhc---CCHHHHHHHHHHHHHHcC
Q 029444 56 RPPPSDKVVQLAERIAS---LTPEERRQISLTLFKRFS 90 (193)
Q Consensus 56 ~~~~s~kV~~ivd~I~~---LtllE~seLv~~leekfg 90 (193)
+..+-+-+++|+|.+.. +|-.|+---++-+++.+|
T Consensus 86 rsk~~~~~driLDa~aA~g~~~rqe~Va~vn~~qe~l~ 123 (157)
T COG3612 86 RSKDKPSFDRILDAAAASGKLDRQEAVAEVNSLQENLG 123 (157)
T ss_pred ccCCcchHHHHHHHHHHhcCccHHHHHHHHHHHHHHhc
Confidence 44455578999999874 778888888888999999
No 32
>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=34.46 E-value=1e+02 Score=22.69 Aligned_cols=28 Identities=18% Similarity=0.344 Sum_probs=22.8
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHhCc
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEKAP 164 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs~P 164 (193)
-.++..|+..|+ .|+.|+|.+++++...
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 367888888776 5999999999998754
No 33
>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=32.74 E-value=92 Score=24.36 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=21.5
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
-.++..|+..|+ .|+.|+|.|++++.
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 357788888775 79999999999974
No 34
>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=32.27 E-value=1e+02 Score=22.84 Aligned_cols=26 Identities=23% Similarity=0.486 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhC
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKA 163 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~ 163 (193)
..+..|+..|. +|+.|.|-+++++..
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 57777777775 599999999999753
No 35
>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=31.81 E-value=67 Score=22.67 Aligned_cols=36 Identities=17% Similarity=0.224 Sum_probs=28.8
Q ss_pred CCChhHHHHHHHHhcCCHHHHHHHHHHHHHHcCCCCC
Q 029444 58 PPSDKVVQLAERIASLTPEERRQISLTLFKRFSLPKL 94 (193)
Q Consensus 58 ~~s~kV~~ivd~I~~LtllE~seLv~~leekfgv~~~ 94 (193)
||...|++|++.+.+=++.++...+..|-.. |++..
T Consensus 3 p~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~~ 38 (89)
T PF08542_consen 3 PPPEVIEEILESCLNGDFKEARKKLYELLVE-GYSAS 38 (89)
T ss_dssp --HHHHHHHHHHHHHTCHHHHHHHHHHHHHT-T--HH
T ss_pred CCHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCHH
Confidence 4567899999999999999999999999988 88643
No 36
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=30.89 E-value=2.2e+02 Score=21.71 Aligned_cols=70 Identities=14% Similarity=0.007 Sum_probs=52.1
Q ss_pred ccceeEEEEeecccchhHHHH-HHHHHhhcCChHHHHHHHHhCch---hhhcCCCHHHHHHHHHHHHHcCCeEe
Q 029444 122 EKTTFDVKLEKFEAAAKLKIV-KEVKTFFDLGMKEAKELVEKAPV---VLKQGLTKEEASNIIEKIKAAGGVAI 191 (193)
Q Consensus 122 EKT~FdV~L~~~~a~kKI~VI-KeVR~iT~LGLKEAK~lVEs~P~---vIKe~vsKeEAEeik~kLeaaGA~V~ 191 (193)
....|.|+|-+=|-.--==|| ..++.+.++...+|-.+.-.+=. -+=---++|.||-...+|...|.+++
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 445799999764434444688 57788899999999998764421 11122689999999999999998765
No 37
>PF13565 HTH_32: Homeodomain-like domain
Probab=30.66 E-value=93 Score=21.25 Aligned_cols=33 Identities=15% Similarity=0.123 Sum_probs=23.1
Q ss_pred hhH-HHHHHHHhcCCHHHHHHHHHHHHHHcCCCC
Q 029444 61 DKV-VQLAERIASLTPEERRQISLTLFKRFSLPK 93 (193)
Q Consensus 61 ~kV-~~ivd~I~~LtllE~seLv~~leekfgv~~ 93 (193)
+.+ ..|++-+.+-...-..+|...|+++||++.
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC
Confidence 455 667777665545556667778999999854
No 38
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=29.63 E-value=47 Score=24.61 Aligned_cols=35 Identities=29% Similarity=0.296 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhCchhhhcCC
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKAPVVLKQGL 171 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~v 171 (193)
.|-.+|+.|.+.+++.-++++..|+.+-.+|.+.+
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 38 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDAL 38 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999999999887776543
No 39
>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=28.99 E-value=68 Score=21.39 Aligned_cols=24 Identities=17% Similarity=0.401 Sum_probs=17.9
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHH
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVE 161 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVE 161 (193)
..+..|+..++ .|+.|.|.+++++
T Consensus 45 ~~l~~i~~l~~-~g~~l~~i~~~~~ 68 (68)
T cd01104 45 ARLRLIRRLTS-EGVRISQAAALAL 68 (68)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 45666666665 8999999999863
No 40
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=28.96 E-value=64 Score=25.49 Aligned_cols=33 Identities=33% Similarity=0.449 Sum_probs=26.6
Q ss_pred HHHHHHHHhCchhhhcC--CCHHHHHHHHHHHHHc
Q 029444 154 KEAKELVEKAPVVLKQG--LTKEEASNIIEKIKAA 186 (193)
Q Consensus 154 KEAK~lVEs~P~vIKe~--vsKeEAEeik~kLeaa 186 (193)
-|-++|++++-.+++.. .+++|+++|+.+++.+
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 45668888888888875 7889999999998753
No 41
>PF08958 DUF1871: Domain of unknown function (DUF1871); InterPro: IPR015053 This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus. ; PDB: 1U84_A.
Probab=27.97 E-value=48 Score=24.61 Aligned_cols=39 Identities=10% Similarity=0.342 Sum_probs=25.1
Q ss_pred CCCCCC-CCCCChhHHHHHHHHhcCCHHHHHHHHHHHHHHcC
Q 029444 50 YDPYGP-RPPPSDKVVQLAERIASLTPEERRQISLTLFKRFS 90 (193)
Q Consensus 50 ~dp~~~-~~~~s~kV~~ivd~I~~LtllE~seLv~~leekfg 90 (193)
+||++= .--.+.-+.+|+..+.... ...+|.+.|+.-|-
T Consensus 10 WDP~~~g~deY~~Ei~~Iv~~v~~~~--~~~~LA~~Iq~If~ 49 (79)
T PF08958_consen 10 WDPFGLGEDEYDTEINDIVQAVHEND--DPEELAKKIQSIFE 49 (79)
T ss_dssp H-TTSS-GGGGHHHHHHHHHHHTT-S---HHHHHHHHHHHHH
T ss_pred CCCCcCCCcccHHHHHHHHHHHHhCC--CHHHHHHHHHHHHH
Confidence 466652 2234577889999998876 66778887777664
No 42
>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=27.64 E-value=51 Score=25.57 Aligned_cols=27 Identities=37% Similarity=0.609 Sum_probs=17.0
Q ss_pred hCchhhhc-CCCHHHHHHHHHHHHHcCCeEee
Q 029444 162 KAPVVLKQ-GLTKEEASNIIEKIKAAGGVAIM 192 (193)
Q Consensus 162 s~P~vIKe-~vsKeEAEeik~kLeaaGA~V~i 192 (193)
+.|-+|+. .+|+ ..+++||+||++|++
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 457788899998875
No 43
>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=27.60 E-value=75 Score=21.56 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHH
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELV 160 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lV 160 (193)
..+..|+..|+ .|+.|.|.|+++
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 899999999886
No 44
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=27.18 E-value=60 Score=32.52 Aligned_cols=30 Identities=43% Similarity=0.564 Sum_probs=21.2
Q ss_pred ecccchhHHHHHH-HHHhhcCChHHHHHHHHhC
Q 029444 132 KFEAAAKLKIVKE-VKTFFDLGMKEAKELVEKA 163 (193)
Q Consensus 132 ~~~a~kKI~VIKe-VR~iT~LGLKEAK~lVEs~ 163 (193)
+|+ .-+.-+|- ||=.++|||+++|+.-+++
T Consensus 689 kfp--edldclkflvri~~dlgl~d~key~~kl 719 (840)
T KOG2003|consen 689 KFP--EDLDCLKFLVRIAGDLGLKDAKEYADKL 719 (840)
T ss_pred hCc--cchHHHHHHHHHhccccchhHHHHHHHH
Confidence 464 23455664 4555899999999998875
No 45
>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=27.15 E-value=2e+02 Score=21.95 Aligned_cols=27 Identities=7% Similarity=0.254 Sum_probs=21.6
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHhC
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEKA 163 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs~ 163 (193)
-..+..|+..|+ +|+.|+|.+++++..
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 357777777776 599999999999864
No 46
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=26.98 E-value=56 Score=26.68 Aligned_cols=25 Identities=44% Similarity=0.806 Sum_probs=17.9
Q ss_pred chhhhcC-CCHHHHHHHHHHHHHcCCeEee
Q 029444 164 PVVLKQG-LTKEEASNIIEKIKAAGGVAIM 192 (193)
Q Consensus 164 P~vIKe~-vsKeEAEeik~kLeaaGA~V~i 192 (193)
|-+|+.. +| +..+++||++|++|++
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 6677643 44 3467789999999986
No 47
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=26.90 E-value=47 Score=31.99 Aligned_cols=47 Identities=32% Similarity=0.549 Sum_probs=33.7
Q ss_pred HHHhhcCChHHHHHHHH--hCchhhhcC-----------CCHHHHHHHHH-HHH-----HcCCeEeeC
Q 029444 145 VKTFFDLGMKEAKELVE--KAPVVLKQG-----------LTKEEASNIIE-KIK-----AAGGVAIME 193 (193)
Q Consensus 145 VR~iT~LGLKEAK~lVE--s~P~vIKe~-----------vsKeEAEeik~-kLe-----aaGA~V~iE 193 (193)
.+.++ ...|||++++ +.|-+||.. .+.|||.+... -|+ ++|+.|+||
T Consensus 121 y~~f~--~~e~a~ayi~~~g~piVVKadGLaaGKGV~V~~~~eeA~~a~~~~l~~~~fg~~g~~VVIE 186 (428)
T COG0151 121 YEVFT--DPEEAKAYIDEKGAPIVVKADGLAAGKGVIVAMTLEEAEAAVDEMLEGNAFGSAGARVVIE 186 (428)
T ss_pred ccccC--CHHHHHHHHHHcCCCEEEecccccCCCCeEEcCCHHHHHHHHHHHHhhccccCCCCcEEEE
Confidence 34555 8899999999 558899862 46889988433 333 356889987
No 48
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=26.88 E-value=61 Score=27.37 Aligned_cols=64 Identities=30% Similarity=0.339 Sum_probs=40.6
Q ss_pred EEEEeecccchhHHHHHHH-HHh---hcCChHHHHH-HHHh-------CchhhhcCCCHHHHHHHHHHHHHcCCeEe
Q 029444 127 DVKLEKFEAAAKLKIVKEV-KTF---FDLGMKEAKE-LVEK-------APVVLKQGLTKEEASNIIEKIKAAGGVAI 191 (193)
Q Consensus 127 dV~L~~~~a~kKI~VIKeV-R~i---T~LGLKEAK~-lVEs-------~P~vIKe~vsKeEAEeik~kLeaaGA~V~ 191 (193)
.++|.+-+ +-|+.-++.| +.- -|+.++=-.- -+|. -...||+|+++|.|.+|.+.+++.+-+|.
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 EITLTAES-DFQLKQVKDILRSKLIKRGIDLKALDYGKVEKASGKTVKQEVKLKQGIDQELAKKIVKLIKDSKLKVQ 120 (161)
T ss_pred EEEEEeCC-HHHHHHHHHHHHHHHHHcCCCHHHcCCCCccccCCCEEEEEEehhhccCHHHHHHHHHHHHhcCCcee
Confidence 46776643 6777654443 322 2555552110 1111 13469999999999999999999988763
No 49
>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=26.78 E-value=87 Score=22.78 Aligned_cols=26 Identities=19% Similarity=0.305 Sum_probs=22.0
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
=..+..|+.+|+ .|+.|+|++++++.
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 357888888887 89999999999973
No 50
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=26.19 E-value=1.2e+02 Score=24.32 Aligned_cols=25 Identities=20% Similarity=0.426 Sum_probs=20.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
.++..|+..| -+|+.|+|-+++++.
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 5677777766 479999999999974
No 51
>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=25.68 E-value=1.6e+02 Score=23.03 Aligned_cols=28 Identities=4% Similarity=0.093 Sum_probs=18.5
Q ss_pred hhHHHHHHHHhcCCHHHHHHHHHHHHHHcCC
Q 029444 61 DKVVQLAERIASLTPEERRQISLTLFKRFSL 91 (193)
Q Consensus 61 ~kV~~ivd~I~~LtllE~seLv~~leekfgv 91 (193)
.++.-+++.|+.-++ .||+.....+++-
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 355666666666554 6677777787763
No 52
>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=25.50 E-value=95 Score=23.11 Aligned_cols=27 Identities=15% Similarity=0.384 Sum_probs=23.4
Q ss_pred chhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 136 AAKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 136 ~kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
-..+..|+..|.-.|++|.+.|++++.
T Consensus 44 v~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 44 VERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 468888888887789999999999986
No 53
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=25.37 E-value=46 Score=28.07 Aligned_cols=64 Identities=27% Similarity=0.327 Sum_probs=33.5
Q ss_pred EEEEeecccchhHHHHHHH-HHh---hcCChHHHHHH-HHhC-------chhhhcCCCHHHHHHHHHHHHHcCCeEe
Q 029444 127 DVKLEKFEAAAKLKIVKEV-KTF---FDLGMKEAKEL-VEKA-------PVVLKQGLTKEEASNIIEKIKAAGGVAI 191 (193)
Q Consensus 127 dV~L~~~~a~kKI~VIKeV-R~i---T~LGLKEAK~l-VEs~-------P~vIKe~vsKeEAEeik~kLeaaGA~V~ 191 (193)
.++|.+-+ +-|+.-+..| +.- -|+.|+=-.-- .|.+ ...||+|+++|.|.+|.+.+++.+-+|.
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 77887654 6676655444 322 25554411111 1211 2368999999999999999999887763
No 54
>PRK05350 acyl carrier protein; Provisional
Probab=25.14 E-value=85 Score=22.32 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=18.9
Q ss_pred cCCHHHHHHHHHHHHHHcCCC
Q 029444 72 SLTPEERRQISLTLFKRFSLP 92 (193)
Q Consensus 72 ~LtllE~seLv~~leekfgv~ 92 (193)
++.=+...+|+-.||++|||.
T Consensus 37 g~DSld~veli~~lE~~fgI~ 57 (82)
T PRK05350 37 DLDSIDAVDLVVHLQKLTGKK 57 (82)
T ss_pred CCCHHHHHHHHHHHHHHHCCc
Confidence 777788999999999999995
No 55
>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=25.11 E-value=1.6e+02 Score=22.81 Aligned_cols=25 Identities=16% Similarity=0.523 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
.++..|+..|. +|++|+|-|++++.
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 57888888875 89999999999973
No 56
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=25.02 E-value=97 Score=22.06 Aligned_cols=29 Identities=38% Similarity=0.438 Sum_probs=21.6
Q ss_pred HHHHhCchhhhcCCCHHHHHHHHHHHHHc
Q 029444 158 ELVEKAPVVLKQGLTKEEASNIIEKIKAA 186 (193)
Q Consensus 158 ~lVEs~P~vIKe~vsKeEAEeik~kLeaa 186 (193)
.|-+.+-..+-+++||.||.+.+..|++.
T Consensus 26 tL~e~Age~~~~~LtkaeAs~rId~L~~~ 54 (57)
T PF11272_consen 26 TLSEEAGEPFPDDLTKAEASERIDELQAQ 54 (57)
T ss_pred HHHHHhCCCCCCcccHHHHHHHHHHHHHH
Confidence 34444445566799999999999999864
No 57
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=24.46 E-value=1.4e+02 Score=23.67 Aligned_cols=25 Identities=20% Similarity=0.492 Sum_probs=19.7
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
..+..|+..|. +|++|+|.|++++.
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 56667776664 69999999999974
No 58
>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=23.52 E-value=2.1e+02 Score=23.21 Aligned_cols=31 Identities=23% Similarity=0.333 Sum_probs=24.9
Q ss_pred CCCChhHHHHHHHHhcCCHHHHHHHHHHHHH
Q 029444 57 PPPSDKVVQLAERIASLTPEERRQISLTLFK 87 (193)
Q Consensus 57 ~~~s~kV~~ivd~I~~LtllE~seLv~~lee 87 (193)
...++--..|++.+.+||..|-..|...|-.
T Consensus 77 ~~~~~l~~~ii~~~~~Mt~~EQ~~L~~lL~R 107 (122)
T PF07037_consen 77 TWDSPLERQIIDTLEEMTPAEQEQLTSLLLR 107 (122)
T ss_pred CCcchHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 3455556689999999999999999887643
No 59
>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=23.49 E-value=1e+02 Score=23.21 Aligned_cols=26 Identities=23% Similarity=0.354 Sum_probs=21.2
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhC
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKA 163 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~ 163 (193)
.++..|+..|+ .|++|+|.+++++..
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 57777887775 699999999998753
No 60
>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=23.46 E-value=1.2e+02 Score=26.17 Aligned_cols=40 Identities=20% Similarity=0.349 Sum_probs=30.1
Q ss_pred HHHHHHHHhhcCChHHHHHHHHhCchhhhc--CCCHHHHHHHHHHHHHcCCeEe
Q 029444 140 KIVKEVKTFFDLGMKEAKELVEKAPVVLKQ--GLTKEEASNIIEKIKAAGGVAI 191 (193)
Q Consensus 140 ~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe--~vsKeEAEeik~kLeaaGA~V~ 191 (193)
.+|+.||+.+ +.|-.+|- +++.++..++-+.++++|+...
T Consensus 152 eiv~~vr~~~------------~~pv~vKl~~~~~~~~~~~~a~~l~~~Gad~i 193 (289)
T cd02810 152 NLLKAVKAAV------------DIPLLVKLSPYFDLEDIVELAKAAERAGADGL 193 (289)
T ss_pred HHHHHHHHcc------------CCCEEEEeCCCCCHHHHHHHHHHHHHcCCCEE
Confidence 5777777655 35777773 4677899999999999998653
No 61
>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=23.41 E-value=2.1e+02 Score=21.10 Aligned_cols=27 Identities=26% Similarity=0.453 Sum_probs=22.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhCc
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKAP 164 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~P 164 (193)
..+..|+.+|. .|++|.+.+.+++...
T Consensus 45 ~~l~~i~~lr~-~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 45 ERLQQILFLKE-LGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHcCc
Confidence 56777777776 6999999999998764
No 62
>PF03608 EII-GUT: PTS system enzyme II sorbitol-specific factor; InterPro: IPR004699 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The Gut family consists only of glucitol-specific transporters, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli consists of IIA protein, a IIC protein and a IIBC protein. This family is specific for the IIC component.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=23.27 E-value=22 Score=30.20 Aligned_cols=49 Identities=22% Similarity=0.291 Sum_probs=34.3
Q ss_pred hhhHhhhcCCCCCCccchhhhhhhcccCCC-CCCCCCCccCCCCCcCCCCC
Q 029444 5 ALAKSICSRPFLPRITGPLQFRLLQHDFVP-RDPKSKPIKYKYPAFYDPYG 54 (193)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~-~~~~~~~~~~~~~~~~dp~~ 54 (193)
.++|.....+..+....|+.+-+|-+.--. .--|=+|.+|| |++||...
T Consensus 52 k~a~~~~kn~i~RY~vLP~i~~F~l~NPM~~t~GrFlpEkyK-Payydaa~ 101 (168)
T PF03608_consen 52 KFAQKCAKNPITRYTVLPVIAVFFLGNPMAYTFGRFLPEKYK-PAYYDAAV 101 (168)
T ss_pred HHHHHHcCCchHHHHHHHHHHHHHhcCccHHHHhccCccccC-ccHHHHHH
Confidence 455555566677777888888887766221 23456899999 99999765
No 63
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=23.18 E-value=2.2e+02 Score=18.44 Aligned_cols=34 Identities=26% Similarity=0.304 Sum_probs=26.3
Q ss_pred hhHHHHHHHHhcC-CHHHHHHHHHHHHHHcCCCCC
Q 029444 61 DKVVQLAERIASL-TPEERRQISLTLFKRFSLPKL 94 (193)
Q Consensus 61 ~kV~~ivd~I~~L-tllE~seLv~~leekfgv~~~ 94 (193)
.-+.++..-|..+ +-++...+++.|.+++||+..
T Consensus 23 ~~~~~~~~~i~~i~~~i~r~~y~~~la~~~~i~~~ 57 (59)
T PF10410_consen 23 EAVREAAPLIAQIPDPIERELYIRELAERLGISED 57 (59)
T ss_dssp HHHHHHHHHHTT--SHHHHHHHHHHHHHHCT-SST
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCcCcc
Confidence 3456777777777 899999999999999999753
No 64
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=22.57 E-value=71 Score=22.68 Aligned_cols=33 Identities=27% Similarity=0.348 Sum_probs=24.7
Q ss_pred CCCCCChhHHHHHHHHhcCCHHHHHHHHHHHHHHc
Q 029444 55 PRPPPSDKVVQLAERIASLTPEERRQISLTLFKRF 89 (193)
Q Consensus 55 ~~~~~s~kV~~ivd~I~~LtllE~seLv~~leekf 89 (193)
|+++++. ..|-+.|+.||+-|+.+=+..|+.+.
T Consensus 5 Pr~~~~~--~~ig~dLs~lSv~EL~~RIa~L~aEI 37 (59)
T PF06698_consen 5 PRKKPSG--HEIGEDLSLLSVEELEERIALLEAEI 37 (59)
T ss_pred cCCCCCc--cccCCCchhcCHHHHHHHHHHHHHHH
Confidence 4445544 55677899999999999988888765
No 65
>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=21.79 E-value=2e+02 Score=22.19 Aligned_cols=24 Identities=21% Similarity=0.534 Sum_probs=19.4
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHH
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVE 161 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVE 161 (193)
..+..|+..| -+|++|+|.|++++
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 5667777766 38999999999997
No 66
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=21.60 E-value=1.3e+02 Score=22.92 Aligned_cols=46 Identities=20% Similarity=0.352 Sum_probs=38.4
Q ss_pred HHHHHHHHhhcCChHHHHHHHHhC---chhhhcCCCHHHHHHHHHHHHH
Q 029444 140 KIVKEVKTFFDLGMKEAKELVEKA---PVVLKQGLTKEEASNIIEKIKA 185 (193)
Q Consensus 140 ~VIKeVR~iT~LGLKEAK~lVEs~---P~vIKe~vsKeEAEeik~kLea 185 (193)
.|.-.+..|-|+|..-|+.+...+ |..--..++.++-+.|.+.|+.
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~ 60 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK 60 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT
T ss_pred chHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH
Confidence 577788899999999999999876 5444556999999999988875
No 67
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=21.56 E-value=2e+02 Score=21.74 Aligned_cols=25 Identities=12% Similarity=0.345 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
..+..|+..|+ +|++|.|.|++++.
T Consensus 44 ~~l~~I~~lr~-~G~sl~eI~~~l~~ 68 (112)
T cd01282 44 DRVRQIRRLLA-AGLTLEEIREFLPC 68 (112)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHH
Confidence 46666666664 79999999999874
No 68
>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=21.54 E-value=1.9e+02 Score=22.14 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=20.0
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHhC
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEKA 163 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs~ 163 (193)
.++..|+..|+ +|++|+|-|++++..
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 46666666663 799999999999854
No 69
>COG1480 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]
Probab=21.03 E-value=1e+02 Score=31.53 Aligned_cols=74 Identities=19% Similarity=0.369 Sum_probs=46.8
Q ss_pred CCccchhhhhhhcccCCCCCCCCCCccCCCCCcC------------CCCC-----CCCCCChhHHHHHHHH---------
Q 029444 17 PRITGPLQFRLLQHDFVPRDPKSKPIKYKYPAFY------------DPYG-----PRPPPSDKVVQLAERI--------- 70 (193)
Q Consensus 17 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~------------dp~~-----~~~~~s~kV~~ivd~I--------- 70 (193)
..|||--..+||-...-..+|+-.+.+|.||--- |-+. -+.|-.+++.++||.|
T Consensus 581 ~eHhGTsLikYFY~kAke~~~~v~Ee~FRY~GPkPqSKEtaIImlADSvEAAvRSl~~p~~~ki~~~v~~II~~rl~DgQ 660 (700)
T COG1480 581 PEHHGTSLIKYFYYKAKEENPNVKEEEFRYPGPKPQSKETAIIMLADSVEAAVRSLKEPNPEKIEEMVDKIIQARLQDGQ 660 (700)
T ss_pred HHhcCccHHHHHHHHHHHhCCCCCHhhccCCCCCCCcchhheehhHhHHHHHHhhccCCCHHHHHHHHHHHHHHHHhcCC
Confidence 4678888888887764456777777777776211 0000 0111246777777777
Q ss_pred ---hcCCHHHHHHHHHHHHHHcC
Q 029444 71 ---ASLTPEERRQISLTLFKRFS 90 (193)
Q Consensus 71 ---~~LtllE~seLv~~leekfg 90 (193)
++||+.|+....+.+=++|+
T Consensus 661 l~~s~lT~~El~~I~~~fv~tl~ 683 (700)
T COG1480 661 LSESGLTLKELEIIADSFVQTLQ 683 (700)
T ss_pred ccccCCcHHHHHHHHHHHHHHHH
Confidence 56888888888777776664
No 70
>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=21.01 E-value=1.2e+02 Score=22.50 Aligned_cols=25 Identities=16% Similarity=0.356 Sum_probs=20.9
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
..+..|+..|+ +|++|+|-+++++.
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 57778887776 69999999999974
No 71
>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=20.65 E-value=1.1e+02 Score=26.52 Aligned_cols=39 Identities=28% Similarity=0.342 Sum_probs=29.8
Q ss_pred HHHHHHHHhhcCChHHHHHHHHhCchhhhcCCCHHHHHHHHHHHHHcCCeE
Q 029444 140 KIVKEVKTFFDLGMKEAKELVEKAPVVLKQGLTKEEASNIIEKIKAAGGVA 190 (193)
Q Consensus 140 ~VIKeVR~iT~LGLKEAK~lVEs~P~vIKe~vsKeEAEeik~kLeaaGA~V 190 (193)
.+++.||+.+ ..|-.+|=+...++..++-+.++++|+..
T Consensus 144 eiv~~vr~~~------------~~Pv~vKl~~~~~~~~~~a~~~~~~G~d~ 182 (296)
T cd04740 144 EIVKAVKKAT------------DVPVIVKLTPNVTDIVEIARAAEEAGADG 182 (296)
T ss_pred HHHHHHHhcc------------CCCEEEEeCCCchhHHHHHHHHHHcCCCE
Confidence 5666666554 46888887777778999999999999853
No 72
>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=20.23 E-value=1.6e+02 Score=26.77 Aligned_cols=44 Identities=20% Similarity=0.143 Sum_probs=31.8
Q ss_pred cCChHHHHHHHHhCchh----h----hc-CCCHHHHHHHHHHHHHcCCeEeeC
Q 029444 150 DLGMKEAKELVEKAPVV----L----KQ-GLTKEEASNIIEKIKAAGGVAIME 193 (193)
Q Consensus 150 ~LGLKEAK~lVEs~P~v----I----Ke-~vsKeEAEeik~kLeaaGA~V~iE 193 (193)
..++.+||+|++.+-.. | -. ....+.|+.|++.|+++|-+|+++
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 46788889988865421 1 11 134678999999999999998863
No 73
>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=20.18 E-value=1.2e+02 Score=23.26 Aligned_cols=25 Identities=16% Similarity=0.534 Sum_probs=19.2
Q ss_pred hhHHHHHHHHHhhcCChHHHHHHHHh
Q 029444 137 AKLKIVKEVKTFFDLGMKEAKELVEK 162 (193)
Q Consensus 137 kKI~VIKeVR~iT~LGLKEAK~lVEs 162 (193)
.++..|+..|+ +|++|+|.|++++.
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
Done!