Query 043133
Match_columns 131
No_of_seqs 161 out of 335
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 13:12:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043133.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043133hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK04342 DNA topoisomerase VI 100.0 3.1E-33 6.8E-38 233.1 11.9 122 1-130 21-157 (367)
2 COG1697 DNA topoisomerase VI, 100.0 8.7E-31 1.9E-35 215.6 8.8 122 1-130 17-149 (356)
3 PLN00060 meiotic recombination 100.0 2.7E-28 5.8E-33 204.3 10.9 121 2-130 37-175 (384)
4 KOG2795 Catalytic subunit of t 100.0 2.9E-28 6.2E-33 201.6 9.1 127 1-130 31-159 (372)
5 PF04406 TP6A_N: Type IIB DNA 99.9 8.1E-27 1.8E-31 152.7 5.6 68 50-117 1-68 (68)
6 cd06405 PB1_Mekk2_3 The PB1 do 75.6 2.6 5.7E-05 28.3 2.2 27 79-105 36-65 (79)
7 PF08921 DUF1904: Domain of un 56.9 11 0.00024 26.6 2.5 25 93-117 15-39 (108)
8 PF14804 Jag_N: Jag N-terminus 46.0 18 0.0004 22.2 1.9 30 95-124 6-38 (52)
9 PF00126 HTH_1: Bacterial regu 42.9 28 0.00061 21.1 2.5 35 88-122 22-59 (60)
10 PRK09906 DNA-binding transcrip 36.1 33 0.00072 26.6 2.5 37 87-123 23-62 (296)
11 smart00391 MBD Methyl-CpG bind 35.6 36 0.00079 22.4 2.3 30 74-103 22-53 (77)
12 PF02594 DUF167: Uncharacteris 33.3 38 0.00083 22.3 2.1 26 97-122 43-68 (77)
13 cd00122 MBD MeCP2, MBD1, MBD2, 32.4 50 0.0011 20.5 2.4 27 76-102 21-49 (62)
14 PRK13348 chromosome replicatio 32.3 38 0.00083 26.3 2.3 36 87-123 24-62 (294)
15 TIGR02424 TF_pcaQ pca operon t 31.5 44 0.00096 25.9 2.6 36 87-122 25-63 (300)
16 cd01396 MeCP2_MBD MeCP2, MBD1, 31.3 42 0.00091 22.1 2.1 28 76-103 22-51 (77)
17 PF00325 Crp: Bacterial regula 30.4 26 0.00056 19.5 0.8 13 101-113 6-18 (32)
18 PRK11482 putative DNA-binding 30.3 45 0.00098 26.6 2.5 37 87-123 51-90 (317)
19 PF12039 DUF3525: Protein of u 30.0 23 0.0005 29.8 0.7 36 87-122 280-337 (453)
20 PF08796 DUF1797: Protein of u 30.0 40 0.00086 22.0 1.7 39 32-70 28-66 (67)
21 TIGR03339 phn_lysR aminoethylp 29.3 60 0.0013 24.6 2.9 37 87-123 19-58 (279)
22 PRK11062 nhaR transcriptional 27.7 62 0.0014 25.3 2.8 37 87-123 26-65 (296)
23 TIGR03418 chol_sulf_TF putativ 27.3 62 0.0013 25.0 2.7 37 87-123 23-62 (291)
24 PRK09986 DNA-binding transcrip 27.1 59 0.0013 25.0 2.6 57 61-123 9-68 (294)
25 PRK03635 chromosome replicatio 25.8 58 0.0013 25.4 2.3 35 87-122 24-61 (294)
26 PRK10837 putative DNA-binding 25.7 66 0.0014 24.7 2.6 36 87-122 25-63 (290)
27 PTZ00061 DNA-directed RNA poly 25.6 1.7E+02 0.0036 23.2 4.8 53 57-122 5-60 (205)
28 PRK11242 DNA-binding transcrip 25.3 73 0.0016 24.5 2.8 36 87-122 23-61 (296)
29 TIGR00323 eIF-6 translation in 24.7 56 0.0012 25.7 2.0 37 92-128 153-200 (215)
30 PRK11151 DNA-binding transcrip 24.3 94 0.002 24.2 3.3 37 87-123 23-62 (305)
31 TIGR03298 argP transcriptional 24.3 70 0.0015 24.7 2.5 36 87-123 23-61 (292)
32 TIGR02036 dsdC D-serine deamin 24.1 82 0.0018 24.7 2.9 36 87-122 30-68 (302)
33 PF02796 HTH_7: Helix-turn-hel 24.0 31 0.00066 20.0 0.3 14 100-113 24-37 (45)
34 TIGR03544 DivI1A_domain DivIVA 23.8 87 0.0019 17.2 2.2 15 92-106 19-33 (34)
35 PRK10341 DNA-binding transcrip 23.8 83 0.0018 24.8 2.9 37 87-123 29-68 (312)
36 PRK02220 4-oxalocrotonate taut 23.7 88 0.0019 18.7 2.4 27 92-118 17-43 (61)
37 PRK11233 nitrogen assimilation 23.6 83 0.0018 24.7 2.8 36 87-122 23-61 (305)
38 PRK10082 cell density-dependen 22.7 69 0.0015 25.1 2.2 36 87-122 33-71 (303)
39 CHL00180 rbcR LysR transcripti 22.7 75 0.0016 24.9 2.4 37 87-123 27-66 (305)
40 PRK09791 putative DNA-binding 22.1 1.1E+02 0.0023 23.8 3.2 36 87-122 27-65 (302)
41 PF05121 GvpK: Gas vesicle pro 21.9 64 0.0014 22.1 1.6 26 95-120 56-81 (88)
42 PRK01310 hypothetical protein; 21.8 94 0.002 21.7 2.5 26 97-122 55-80 (104)
43 PRK03601 transcriptional regul 21.3 1E+02 0.0022 23.8 2.9 37 87-123 23-62 (275)
44 PRK02289 4-oxalocrotonate taut 21.3 1.2E+02 0.0026 18.4 2.7 26 93-118 18-43 (60)
45 PRK02302 hypothetical protein; 21.0 78 0.0017 21.7 1.9 39 47-107 16-59 (89)
46 PRK15421 DNA-binding transcrip 20.7 1E+02 0.0023 24.5 2.9 36 87-122 24-62 (317)
47 PRK05090 hypothetical protein; 20.6 1E+02 0.0022 21.2 2.4 26 97-122 49-74 (95)
48 PRK00647 hypothetical protein; 20.2 1E+02 0.0023 21.3 2.4 26 97-122 44-69 (96)
49 smart00685 DM14 Repeats in fly 20.1 2E+02 0.0044 18.1 3.6 31 50-80 23-53 (59)
No 1
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=100.00 E-value=3.1e-33 Score=233.09 Aligned_cols=122 Identities=20% Similarity=0.317 Sum_probs=114.1
Q ss_pred CHHHHHHHHhcCCcceEEEecccCcccCCCCCceeEEeCCCCeEEEe-------ecchhhHHHHHHHHHHHHHHHHHHhc
Q 043133 1 FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILT-------LEKQCHARRIDILLSVLLIVQKLLQE 73 (131)
Q Consensus 1 ~~~~i~~~l~~g~~P~i~l~~r~~~~~n~~~~~~~~yd~~~g~~~l~-------~~~~~~~~kf~~~l~vl~~i~~ll~~ 73 (131)
+++++++++++|+.|.|++|+|+.+ | +.||+..|.++++ +.+..+++||+++++||+++|++|++
T Consensus 21 l~~~~~~~~~~g~~p~~~ip~r~~~--n------~~~d~~~~~~~~~~~~~~r~~~~~~~a~~f~~~~~vl~~i~~~l~~ 92 (367)
T PRK04342 21 LAEKIYEDIEKGKRPVLEIPKRTLS--N------IEYDEKKGLLVLGDKKSKRSFLNVKQAKKFMQTVLMAEFIKELLEE 92 (367)
T ss_pred HHHHHHHHHhcCCCCEEeccccccc--c------eEEccccCeEeeCCCceEEecCCHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3789999999999999999998655 9 9999999887764 56799999999999999999999999
Q ss_pred CCccceeeeeccCCC--------CCCchHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133 74 NIHMSKRDIYYMHPS--------LYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV 130 (131)
Q Consensus 74 ~~~~T~RdiYY~~~~--------lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~ 130 (131)
|+++|+|||||++++ +|++|++||++|+|||+++|++|++|||+|++||+|+|++.+
T Consensus 93 ~~~~T~RdiYY~~~~~~~~~~~~~F~~Q~~~d~~I~dl~~~l~~~R~~L~I~a~~KGlv~G~i~i 157 (367)
T PRK04342 93 NKSSTLRELYYMSKHWIPGLKENTFDDQDESDAVIEDLEVALGVLREELHIRPEEDGSVVGPLRI 157 (367)
T ss_pred CCccchhhhcccCcccccccccccCCCHHHHHHHHHHHHHHHCCCHHHCCeeECCCeEEEeceEE
Confidence 999999999999876 599999999999999999999999999999999999999875
No 2
>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]
Probab=99.97 E-value=8.7e-31 Score=215.56 Aligned_cols=122 Identities=23% Similarity=0.340 Sum_probs=115.4
Q ss_pred CHHHHHHHHhcCCcceEEEecccCcccCCCCCceeEEeCCCCeEEEe-------ecchhhHHHHHHHHHHHHHHHHHHhc
Q 043133 1 FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILT-------LEKQCHARRIDILLSVLLIVQKLLQE 73 (131)
Q Consensus 1 ~~~~i~~~l~~g~~P~i~l~~r~~~~~n~~~~~~~~yd~~~g~~~l~-------~~~~~~~~kf~~~l~vl~~i~~ll~~ 73 (131)
|+..+++|+++|+.|.+.+|.|+++ | +.||++.+.++++ +.++.++++|+++++++++|++++..
T Consensus 17 ~~~~~~~~l~~~~~p~~~vp~r~~s--n------~~~d~~~~~~~lg~r~~~r~~~~v~~a~k~~q~l~~~~~i~e~l~~ 88 (356)
T COG1697 17 FAHKIYEQLEKGQIPIVEVPTRTKS--N------IIYDEESDHIVLGDRKSERSFLTVKGARKLAQTLLMLDFIKELLEL 88 (356)
T ss_pred HHHHHHHHHhcCCCCceeccccccc--c------cccCccccceeccccccchhhhhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5789999999999999999999988 9 9999999998885 56799999999999999999999999
Q ss_pred CCccceeeeecc--CCCCCC--chHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133 74 NIHMSKRDIYYM--HPSLYS--EQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV 130 (131)
Q Consensus 74 ~~~~T~RdiYY~--~~~lF~--~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~ 130 (131)
|+++|+|||||. +..+|. +|++||++|+||+..+|++||+|||.|++||+|+||+.+
T Consensus 89 ~~~~TlReiYY~~~~~~~~k~~~Q~esd~lieDie~~~gl~Re~l~i~p~ekG~V~G~l~I 149 (356)
T COG1697 89 GKTSTLREIYYISKHVEVFKFDDQSESDRLIEDIEVTLGLSREDLGIRPEEKGLVYGPLRI 149 (356)
T ss_pred CCCccHHHHhhhccCcccccccchhHHHHHHHHHHHHhccCHHHcCCCcccCceEEcceEE
Confidence 999999999999 666787 999999999999999999999999999999999999976
No 3
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=99.95 E-value=2.7e-28 Score=204.33 Aligned_cols=121 Identities=20% Similarity=0.256 Sum_probs=103.1
Q ss_pred HHHHHHHHhcCCcce--EEEecccCcccCCCCCceeEEeCCC------------CeEEEeecchhhHHHHHHHHHHHHHH
Q 043133 2 CKSILKDITERRSLS--ISINQFRNYCKNLDAHCSCSYDFPQ------------GQEILTLEKQCHARRIDILLSVLLIV 67 (131)
Q Consensus 2 ~~~i~~~l~~g~~P~--i~l~~r~~~~~n~~~~~~~~yd~~~------------g~~~l~~~~~~~~~kf~~~l~vl~~i 67 (131)
+..++.+|.+|+.+. +++|+|++. | +.|.+.- .....++.+.++++||+++++||+++
T Consensus 37 ~~~~~~~l~~~~~~~~~~~~~~r~~~--n------~~~~~~~~~~~~~~~~l~~~~~~r~~~~~~~a~kf~~~~~vl~~i 108 (384)
T PLN00060 37 VLNFLAALNSPDPAISDLPLISRNCS--N------VLLRRGLLQGDVSSIFLSHLFCKRSLTKAGSAKAFVRVWKVMEMC 108 (384)
T ss_pred HHHHHHHHhcCCCccceecccccccc--c------ccccccccccccceeeeccceeeEecCCHHHHHHHHHHHHHHHHH
Confidence 567888999985444 777886644 7 6666532 11112366789999999999999999
Q ss_pred HHHHhcCCccceeeeecc----CCCCCCchHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133 68 QKLLQENIHMSKRDIYYM----HPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV 130 (131)
Q Consensus 68 ~~ll~~~~~~T~RdiYY~----~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~ 130 (131)
|++|.+|+++|+|||||+ ++++|++|++||++|+|||++++++|++|||+|++||+|+|++.+
T Consensus 109 ~~~l~~~~~~TkRdiYY~~~~~~~~lF~~Q~~vd~~I~Di~~~l~~~R~~L~I~a~~KGlV~G~l~i 175 (384)
T PLN00060 109 YQILGEGKLVTQRELFYKLLCDSPEYFSCQRHVNQTVQDVVSLLRCSRYSLGIMASSRGALIGRLVL 175 (384)
T ss_pred HHHHHcCCccchHHhhcccccCChhhcCCHHHHHHHHHHHHHHHCCCHHHCCeEecCCceEEeeeEE
Confidence 999999999999999999 889999999999999999999999999999999999999999865
No 4
>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]
Probab=99.95 E-value=2.9e-28 Score=201.62 Aligned_cols=127 Identities=31% Similarity=0.471 Sum_probs=106.0
Q ss_pred CHHHHHHHHhcCCcceEEEecccCc--ccCCCCCceeEEeCCCCeEEEeecchhhHHHHHHHHHHHHHHHHHHhcCCccc
Q 043133 1 FCKSILKDITERRSLSISINQFRNY--CKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMS 78 (131)
Q Consensus 1 ~~~~i~~~l~~g~~P~i~l~~r~~~--~~n~~~~~~~~yd~~~g~~~l~~~~~~~~~kf~~~l~vl~~i~~ll~~~~~~T 78 (131)
|...++.++++.+.+++++++|..+ +.|+.-.+.+.++.+...... ....+++|+++|++|++||++++.|+++|
T Consensus 31 ~v~~~~~~l~r~~~~sls~~~r~~~n~~~~~~l~~~~~~~~~~~~~~~---~~~~~~~~~~llrvL~~V~ell~~~~~~T 107 (372)
T KOG2795|consen 31 FVLSVLVQLARPEGFSLSVINRKRSNSLSSPDLDTLVSKSHNTLRFTF---SSKKAKKFAILLRVLEIVHELLELGKRVT 107 (372)
T ss_pred HHHHHHHHhhcccCCcccchhhhhcCCccCcchhhhhcccccccceee---ccccchHHHHHHHHHHHHHHHHHcCCcee
Confidence 4567889999877777777776544 444444555667666443211 13348999999999999999999999999
Q ss_pred eeeeeccCCCCCCchHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133 79 KRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV 130 (131)
Q Consensus 79 ~RdiYY~~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~ 130 (131)
+|||||+|+.+|++|.+||++++|||++|+|+|.+|||.|++||+|+|++.+
T Consensus 108 kRdiyY~dv~lF~~Qs~Vd~~l~dI~~~l~~SR~sLnI~a~~KGLV~G~l~~ 159 (372)
T KOG2795|consen 108 KRDIYYMDVDLFRRQSVVDRLLDDICCLLKCSRYSLNILAASKGLVAGRLRF 159 (372)
T ss_pred eeeeeecCHHHHhhHHHHHHHHHHHHHHhcCChhcCCeeeecCceEEeeEEE
Confidence 9999999999999999999999999999999999999999999999999875
No 5
>PF04406 TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR013049 This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, ]. These two types of proteins share structural homology. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination []. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (5.99.1.2 from EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003824 catalytic activity, 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1D3Y_B 2ZBK_A 2Q2E_A.
Probab=99.93 E-value=8.1e-27 Score=152.66 Aligned_cols=68 Identities=49% Similarity=0.734 Sum_probs=61.7
Q ss_pred chhhHHHHHHHHHHHHHHHHHHhcCCccceeeeeccCCCCCCchHHHHHHHHHHHHHhcCCcccccee
Q 043133 50 KQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVV 117 (131)
Q Consensus 50 ~~~~~~kf~~~l~vl~~i~~ll~~~~~~T~RdiYY~~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~ 117 (131)
|+++++||++++++|+.+|+++.+|+++|+|||||+++++|++|++||++|+|||.+|+++|++|||+
T Consensus 1 n~~~~~k~a~~l~vl~~i~~~l~~~~~~T~RdiYY~~~~lF~~Q~~vd~~i~di~~~l~~~R~~L~Iv 68 (68)
T PF04406_consen 1 NVKSARKFAQLLRVLAIIHELLQNNKTSTKRDIYYRNVSLFKSQREVDRAIDDICCLLGVSREDLNIV 68 (68)
T ss_dssp -TCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHHCSCS-SSHHHHHHHHHHHHHHHTS-GGGGTEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCccchHHHHHhchhhccCHHHHHHHHHHHHHHHCCCHHHcCCC
Confidence 46789999999999999999999999999999999999999999999999999999999999999996
No 6
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=75.60 E-value=2.6 Score=28.30 Aligned_cols=27 Identities=26% Similarity=0.289 Sum_probs=22.7
Q ss_pred eeeeeccCCCC---CCchHHHHHHHHHHHH
Q 043133 79 KRDIYYMHPSL---YSEQSIVDQAINDICI 105 (131)
Q Consensus 79 ~RdiYY~~~~l---F~~Q~~vd~~I~di~~ 105 (131)
+=|+||++.++ -.+|...|++|+-+..
T Consensus 36 ~mdl~ytn~eL~iPl~~Q~DLDkAie~ld~ 65 (79)
T cd06405 36 PMDLHYTNNELLIPLKNQEDLDRAIELLDR 65 (79)
T ss_pred eeeEEEecccEEEeccCHHHHHHHHHHHcc
Confidence 34999999986 5799999999997654
No 7
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=56.90 E-value=11 Score=26.58 Aligned_cols=25 Identities=20% Similarity=0.504 Sum_probs=19.1
Q ss_pred hHHHHHHHHHHHHHhcCCcccccee
Q 043133 93 QSIVDQAINDICILLQCSRHNINVV 117 (131)
Q Consensus 93 Q~~vd~~I~di~~~l~~~R~~L~i~ 117 (131)
+..|..++++||.+.+|+|+++-+-
T Consensus 15 ~~~S~~LideLa~i~~~p~e~ftlE 39 (108)
T PF08921_consen 15 QELSKELIDELAEICGCPRENFTLE 39 (108)
T ss_dssp HHHHHHHHHHHHHHHT--GGG-EEE
T ss_pred HHHhHHHHHHHHHHHCCCcceEEEE
Confidence 5678899999999999999998764
No 8
>PF14804 Jag_N: Jag N-terminus; PDB: 3GKU_B.
Probab=45.95 E-value=18 Score=22.17 Aligned_cols=30 Identities=17% Similarity=0.259 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHhcCCccccce--eec-CCceE
Q 043133 95 IVDQAINDICILLQCSRHNINV--VGT-SLELL 124 (131)
Q Consensus 95 ~vd~~I~di~~~l~~~R~~L~i--~a~-~KGlv 124 (131)
.++.+|+.-+..|+++|+++.+ +.. .||++
T Consensus 6 t~eeAi~~A~~~l~~~~~~~~~eVi~~g~kGf~ 38 (52)
T PF14804_consen 6 TVEEAIEKALKELGVPREELEYEVIEEGKKGFF 38 (52)
T ss_dssp SHHHHHHHHHHHTT--GGGEEEEEEE--B----
T ss_pred CHHHHHHHHHHHhCCChHHEEEEEEEcCCCcEE
Confidence 4789999999999999998875 343 56654
No 9
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=42.92 E-value=28 Score=21.15 Aligned_cols=35 Identities=23% Similarity=0.100 Sum_probs=25.2
Q ss_pred CCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 88 SLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 88 ~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
.+.-+|..+-+.|..++..+|++ |..=++.+++.|
T Consensus 22 ~l~is~~~vs~~i~~LE~~lg~~Lf~r~~~~~~lT~~G 59 (60)
T PF00126_consen 22 ELGISQSAVSRQIKQLEEELGVPLFERSGRGLRLTEAG 59 (60)
T ss_dssp HCTSSHHHHHHHHHHHHHHHTS-SEEECSSSEEE-HHH
T ss_pred HhhccchHHHHHHHHHHHHhCCeEEEECCCCeeEChhh
Confidence 46779999999999999999996 444345554433
No 10
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=36.10 E-value=33 Score=26.59 Aligned_cols=37 Identities=22% Similarity=0.159 Sum_probs=32.7
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
+.++-+|..+-+.|..++..+|++ |..=++.+++.|.
T Consensus 23 ~~L~isQ~avSr~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 62 (296)
T PRK09906 23 EKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGE 62 (296)
T ss_pred HHhCCCCcHHHHHHHHHHHHhCCeeeeeCCCcceEcHhHH
Confidence 457889999999999999999996 8888888888883
No 11
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=35.61 E-value=36 Score=22.39 Aligned_cols=30 Identities=20% Similarity=0.360 Sum_probs=23.6
Q ss_pred CCccceeeeeccCCC--CCCchHHHHHHHHHH
Q 043133 74 NIHMSKRDIYYMHPS--LYSEQSIVDQAINDI 103 (131)
Q Consensus 74 ~~~~T~RdiYY~~~~--lF~~Q~~vd~~I~di 103 (131)
|.+.-+.|+||.+|. -|.+..+|.+.+..-
T Consensus 22 g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~ 53 (77)
T smart00391 22 GRSAGKFDVYYISPCGKKLRSKSELARYLHKN 53 (77)
T ss_pred CCCCCcccEEEECCCCCeeeCHHHHHHHHHhC
Confidence 445568899999875 688999998888753
No 12
>PF02594 DUF167: Uncharacterised ACR, YggU family COG1872; InterPro: IPR003746 This entry describes proteins of unknown function. Structures for two of these proteins, YggU from Escherichia coli and MTH637 from the archaea Methanobacterium thermoautotrophicum, have been determined; they have a core 2-layer alpha/beta structure consisting of beta(2)-loop-alpha-beta(2)-alpha [, ].; PDB: 1YH5_A 1N91_A 1JRM_A.
Probab=33.26 E-value=38 Score=22.30 Aligned_cols=26 Identities=15% Similarity=0.212 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhcCCccccceeecCCc
Q 043133 97 DQAINDICILLQCSRHNINVVGTSLE 122 (131)
Q Consensus 97 d~~I~di~~~l~~~R~~L~i~a~~KG 122 (131)
+.+++-|+..|++++.++.|+.-.++
T Consensus 43 ~ali~~La~~l~v~ks~i~i~~G~~S 68 (77)
T PF02594_consen 43 KALIRFLAKALGVPKSDIEIVSGHTS 68 (77)
T ss_dssp HHHHHHHHHHCT--TTCEEECC-CCC
T ss_pred HHHHHHHHHHhCCCcccEEEEecCCC
Confidence 56778889999999999999877654
No 13
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=32.38 E-value=50 Score=20.53 Aligned_cols=27 Identities=22% Similarity=0.447 Sum_probs=21.9
Q ss_pred ccceeeeeccCCC--CCCchHHHHHHHHH
Q 043133 76 HMSKRDIYYMHPS--LYSEQSIVDQAIND 102 (131)
Q Consensus 76 ~~T~RdiYY~~~~--lF~~Q~~vd~~I~d 102 (131)
...+.|+||.+|. -|.+..+|.+.+.+
T Consensus 21 ~~~k~dv~Y~sP~Gk~~Rs~~ev~~yL~~ 49 (62)
T cd00122 21 SAGKGDVYYYSPCGKKLRSKPEVARYLEK 49 (62)
T ss_pred CCCcceEEEECCCCceecCHHHHHHHHHh
Confidence 3578899999885 58899998888775
No 14
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=32.34 E-value=38 Score=26.25 Aligned_cols=36 Identities=22% Similarity=0.055 Sum_probs=31.3
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..++-+|..+-+.|..++..||++ |.. ++.+++.|.
T Consensus 24 ~~L~iSQ~avS~~i~~LE~~lg~~Lf~R~r-~i~lT~~G~ 62 (294)
T PRK13348 24 RRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQ 62 (294)
T ss_pred HHhCCCchHHHHHHHHHHHHhCceeeecCC-CCccChhHH
Confidence 468889999999999999999986 765 899998883
No 15
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=31.52 E-value=44 Score=25.90 Aligned_cols=36 Identities=17% Similarity=0.178 Sum_probs=32.3
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..+|-+|..+-+.|..++..||++ |..=++.+++.|
T Consensus 25 ~~L~isq~avS~~I~~LE~~lg~~LF~R~~~~~~lT~~G 63 (300)
T TIGR02424 25 EALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYG 63 (300)
T ss_pred HHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCccccHhH
Confidence 457889999999999999999996 888888888888
No 16
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=31.35 E-value=42 Score=22.10 Aligned_cols=28 Identities=18% Similarity=0.445 Sum_probs=23.0
Q ss_pred ccceeeeeccCCC--CCCchHHHHHHHHHH
Q 043133 76 HMSKRDIYYMHPS--LYSEQSIVDQAINDI 103 (131)
Q Consensus 76 ~~T~RdiYY~~~~--lF~~Q~~vd~~I~di 103 (131)
+..+.|+||.++. -|.+..+|.+.++.-
T Consensus 22 s~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~ 51 (77)
T cd01396 22 SAGKFDVYYISPTGKKFRSKVELARYLEKN 51 (77)
T ss_pred CCCcceEEEECCCCCEEECHHHHHHHHHhC
Confidence 4568899999885 688999999988764
No 17
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=30.42 E-value=26 Score=19.49 Aligned_cols=13 Identities=31% Similarity=0.378 Sum_probs=10.2
Q ss_pred HHHHHHhcCCccc
Q 043133 101 NDICILLQCSRHN 113 (131)
Q Consensus 101 ~di~~~l~~~R~~ 113 (131)
+|||..+|++||.
T Consensus 6 ~diA~~lG~t~ET 18 (32)
T PF00325_consen 6 QDIADYLGLTRET 18 (32)
T ss_dssp HHHHHHHTS-HHH
T ss_pred HHHHHHhCCcHHH
Confidence 6899999999875
No 18
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=30.27 E-value=45 Score=26.64 Aligned_cols=37 Identities=19% Similarity=0.232 Sum_probs=32.7
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..|+-+|..+-+.|..|+..||++ |..=++.+++.|.
T Consensus 51 ~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~v~lT~~G~ 90 (317)
T PRK11482 51 KILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYAT 90 (317)
T ss_pred HHhCCChHHHHHHHHHHHHHhCCcceEecCCCccCCHHHH
Confidence 468899999999999999999996 8888888888883
No 19
>PF12039 DUF3525: Protein of unknown function (DUF3525); InterPro: IPR021912 This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are about 360 amino acids in length.
Probab=30.03 E-value=23 Score=29.78 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=29.5
Q ss_pred CCCCCchHHHHHHHHHHHHHhcC----------------------CccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQC----------------------SRHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~----------------------~R~~L~i~a~~KG 122 (131)
.+++++|..+|..-+|+|.+|.. .+++=+.+|++||
T Consensus 280 qEWWgSqDSidtV~NDlcYlLSFLkdT~IPEdvkLdvVELaytq~~~DEk~rIPEPkG 337 (453)
T PF12039_consen 280 QEWWGSQDSIDTVSNDLCYLLSFLKDTAIPEDVKLDVVELAYTQFIQDEKERIPEPKG 337 (453)
T ss_pred hhhhccCccHhHHhhhHHHHHHHhccCCCchhhhhhHHHHHHHHHHhhhcccCCCCCC
Confidence 35799999999999999999874 4556677888888
No 20
>PF08796 DUF1797: Protein of unknown function (DUF1797); InterPro: IPR014904 The function of this protein is unknown. It forms a central anti-parallel beta sheet with flanking alpha helical regions. ; PDB: 2FFG_B.
Probab=29.98 E-value=40 Score=22.01 Aligned_cols=39 Identities=21% Similarity=0.185 Sum_probs=21.7
Q ss_pred CceeEEeCCCCeEEEeecchhhHHHHHHHHHHHHHHHHH
Q 043133 32 HCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKL 70 (131)
Q Consensus 32 ~~~~~yd~~~g~~~l~~~~~~~~~kf~~~l~vl~~i~~l 70 (131)
-|.++||++.+.+.|.-....+.-.|--+=.+.-.||++
T Consensus 28 ~c~V~y~~~t~~F~l~~~~~~~~f~FDdIDLvAIEIydl 66 (67)
T PF08796_consen 28 VCTVTYDQETETFELEEYRQKQKFQFDDIDLVAIEIYDL 66 (67)
T ss_dssp EEEEEEETTTTEEEEEEEETTCEEEES-HHHHHHHHHHH
T ss_pred EEEEEEECCCCeEEEEEecCCCEeecccccchHhhHHhc
Confidence 466999999998877633333333333333334444444
No 21
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=29.30 E-value=60 Score=24.56 Aligned_cols=37 Identities=14% Similarity=0.010 Sum_probs=32.0
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..|+-+|..+-+.|..|+..+|++ |..=++.+++.|.
T Consensus 19 ~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 58 (279)
T TIGR03339 19 ERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGH 58 (279)
T ss_pred HHhcCCchHHHHHHHHHHHHhCCccEEEcCCeEEEChhHH
Confidence 357889999999999999999997 8888888888873
No 22
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=27.72 E-value=62 Score=25.29 Aligned_cols=37 Identities=19% Similarity=0.165 Sum_probs=31.9
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..|+-+|..+-+.|..|+..||++ |..=++.+++.|.
T Consensus 26 ~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~ 65 (296)
T PRK11062 26 EALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGE 65 (296)
T ss_pred HHhCCChHHHHHHHHHHHHHcCccceeecCCceeECHhHH
Confidence 358899999999999999999996 7888888888773
No 23
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=27.30 E-value=62 Score=24.98 Aligned_cols=37 Identities=22% Similarity=0.061 Sum_probs=31.8
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..|+-+|..+-+.|.+++..||++ |..=++.+++.|.
T Consensus 23 ~~L~itqpavS~~Ik~LE~~lg~~LF~R~~r~~~lT~~G~ 62 (291)
T TIGR03418 23 RELGSTQPAVSQQVKRLEEELGTPLFERGHRGIELTEDGQ 62 (291)
T ss_pred HHhCCCHHHHHHHHHHHHHHhCcHHhhcCCCceeEcHhHH
Confidence 357889999999999999999985 8778888888873
No 24
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=27.13 E-value=59 Score=24.99 Aligned_cols=57 Identities=21% Similarity=0.120 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhcCCccceeeeeccCCCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 61 LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 61 l~vl~~i~~ll~~~~~~T~RdiYY~~~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
++-|.......++|..+ + -...++-+|..+-+.|..++..||++ |..=++.+++.|.
T Consensus 9 l~~l~~f~~v~~~gs~t-~-----AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~ 68 (294)
T PRK09986 9 LKLLRYFLAVAEELHFG-R-----AAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGK 68 (294)
T ss_pred HHHHHHHHHHHHhcCHH-H-----HHHHhCCCCCHHHHHHHHHHHHhCCeeEeeCCCceeECHhHH
Confidence 34455555555555332 1 12457889999999999999999996 8888889888883
No 25
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=25.76 E-value=58 Score=25.39 Aligned_cols=35 Identities=23% Similarity=0.079 Sum_probs=30.5
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..++-+|..+-+.|..++..||++ |.. ++.+++-|
T Consensus 24 ~~L~isq~avS~~I~~LE~~lg~~LF~R~~-~~~lT~~G 61 (294)
T PRK03635 24 QKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAG 61 (294)
T ss_pred HHhCCChHHHHHHHHHHHHHhCceeeecCC-CCccCHHH
Confidence 357889999999999999999996 775 88888888
No 26
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=25.69 E-value=66 Score=24.69 Aligned_cols=36 Identities=25% Similarity=0.123 Sum_probs=31.4
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..++-+|..+-+.|..++..+|++ |..=++.+++.|
T Consensus 25 ~~L~isqpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G 63 (290)
T PRK10837 25 VMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHG 63 (290)
T ss_pred HHhCCCccHHHHHHHHHHHHhCCccEeecCCeEEECHhH
Confidence 457889999999999999999986 777788888877
No 27
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=25.57 E-value=1.7e+02 Score=23.15 Aligned_cols=53 Identities=6% Similarity=-0.057 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHhcCCccceeeeeccCCCCCCchHHHHHHHHHHHHHhcC---CccccceeecCCc
Q 043133 57 IDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQC---SRHNINVVGTSLE 122 (131)
Q Consensus 57 f~~~l~vl~~i~~ll~~~~~~T~RdiYY~~~~lF~~Q~~vd~~I~di~~~l~~---~R~~L~i~a~~KG 122 (131)
..++|++-..+++|+....+ +-+|.+.+.-.++....+|- .|+.|.+.++.+.
T Consensus 5 ~~rl~r~rrTv~eMl~DRGY-------------~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~ 60 (205)
T PTZ00061 5 ETRFFRCRRTCCEMLEDRGY-------------IITSQEKLETFATFKERFEENERLRSRMLMVASHKT 60 (205)
T ss_pred HHHHHHHHHHHHHHHhccCC-------------ccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCC
Confidence 45889999999999987554 44788999888888877765 3788998886544
No 28
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=25.33 E-value=73 Score=24.52 Aligned_cols=36 Identities=22% Similarity=0.125 Sum_probs=31.6
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..||-+|..+-+.|..++..+|++ |..=++.+++.|
T Consensus 23 ~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G 61 (296)
T PRK11242 23 EALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAG 61 (296)
T ss_pred HHcCCCchHHHHHHHHHHHHhCCeeEeEcCCceeechhH
Confidence 468999999999999999999986 777778888777
No 29
>TIGR00323 eIF-6 translation initiation factor eIF-6, putative. This model finds translation initiation factor eIF-6 of eukaryotes, which is a ribosome dissociation factor. It also finds a set of apparent archaeal orthologs, slightly shorter proteins not yet shown to act as initiation factors; these probably should be designated as translation initiation factor aIF-6, putative.
Probab=24.73 E-value=56 Score=25.72 Aligned_cols=37 Identities=16% Similarity=0.146 Sum_probs=30.3
Q ss_pred chHHHHHHHHHHHHHhcCC--ccccc---------eeecCCceEEeec
Q 043133 92 EQSIVDQAINDICILLQCS--RHNIN---------VVGTSLELLILPR 128 (131)
Q Consensus 92 ~Q~~vd~~I~di~~~l~~~--R~~L~---------i~a~~KGlv~G~i 128 (131)
+....+.-++.|+..||++ |-.+| .++..||.++||-
T Consensus 153 hP~~s~ee~~~i~d~LgV~v~~gTin~G~~~VGs~~Vann~G~lv~~~ 200 (215)
T TIGR00323 153 HPQTSVQEQEELSSLLGVELVAGTVNRGTTVVGAGMVANSKGAVVGLD 200 (215)
T ss_pred CCCCCHHHHHHHHHHhCCcEEEEEecCCCCceeEEEEEECCEEEECCC
Confidence 6667788899999999998 66665 7889999998874
No 30
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=24.32 E-value=94 Score=24.22 Aligned_cols=37 Identities=22% Similarity=0.080 Sum_probs=33.1
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..|+-+|..+-+.|..++..||++ |..=++.+++.|.
T Consensus 23 ~~L~itQpavS~~i~~LE~~lg~~LF~R~~r~~~lT~~G~ 62 (305)
T PRK11151 23 DSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGL 62 (305)
T ss_pred HHhCCCchHHHHHHHHHHHHhCchheeeCCCceeECccHH
Confidence 468889999999999999999996 8888999988884
No 31
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=24.27 E-value=70 Score=24.73 Aligned_cols=36 Identities=22% Similarity=0.111 Sum_probs=30.8
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..|+-+|..+-+.|..++..||++ |.. ++.+++.|.
T Consensus 23 ~~L~isQpavS~~I~~LE~~lg~~Lf~R~r-~~~lT~~G~ 61 (292)
T TIGR03298 23 AALSVTPSAVSQRIKALEERLGQPLLVRTQ-PCRATEAGQ 61 (292)
T ss_pred HHhCCCHHHHHHHHHHHHHHhCchheecCC-CCcCCHhHH
Confidence 457889999999999999999996 764 888888883
No 32
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=24.06 E-value=82 Score=24.73 Aligned_cols=36 Identities=22% Similarity=0.095 Sum_probs=31.5
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..|+-+|..|-+.|..||..||++ |..=++.+++-|
T Consensus 30 ~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G 68 (302)
T TIGR02036 30 EELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEG 68 (302)
T ss_pred HHHCCCHHHHHHHHHHHHHHhCCceEEECCCceeECHhH
Confidence 357889999999999999999996 888888888877
No 33
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=23.97 E-value=31 Score=19.98 Aligned_cols=14 Identities=29% Similarity=0.368 Sum_probs=10.4
Q ss_pred HHHHHHHhcCCccc
Q 043133 100 INDICILLQCSRHN 113 (131)
Q Consensus 100 I~di~~~l~~~R~~ 113 (131)
+.+||..+||+|..
T Consensus 24 i~~IA~~~gvsr~T 37 (45)
T PF02796_consen 24 IAEIAKQFGVSRST 37 (45)
T ss_dssp HHHHHHHTTS-HHH
T ss_pred HHHHHHHHCcCHHH
Confidence 66889999998854
No 34
>TIGR03544 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
Probab=23.80 E-value=87 Score=17.17 Aligned_cols=15 Identities=13% Similarity=0.158 Sum_probs=13.3
Q ss_pred chHHHHHHHHHHHHH
Q 043133 92 EQSIVDQAINDICIL 106 (131)
Q Consensus 92 ~Q~~vd~~I~di~~~ 106 (131)
++.+||..++.++..
T Consensus 19 ~~~eVD~fLd~v~~~ 33 (34)
T TIGR03544 19 DAAEVDAFLDRVADD 33 (34)
T ss_pred CHHHHHHHHHHHHHh
Confidence 899999999998864
No 35
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=23.80 E-value=83 Score=24.78 Aligned_cols=37 Identities=30% Similarity=0.204 Sum_probs=32.5
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..|+-+|..+-+.|..++..||++ |..=++.+++.|.
T Consensus 29 ~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~~lT~~G~ 68 (312)
T PRK10341 29 KELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQ 68 (312)
T ss_pred HHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCceEChhHH
Confidence 457889999999999999999986 8888888888883
No 36
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=23.73 E-value=88 Score=18.66 Aligned_cols=27 Identities=11% Similarity=0.140 Sum_probs=20.4
Q ss_pred chHHHHHHHHHHHHHhcCCccccceee
Q 043133 92 EQSIVDQAINDICILLQCSRHNINVVG 118 (131)
Q Consensus 92 ~Q~~vd~~I~di~~~l~~~R~~L~i~a 118 (131)
.|+-+..+-+.++..+|++++++-|+=
T Consensus 17 k~~l~~~it~~l~~~~~~p~~~v~V~i 43 (61)
T PRK02220 17 LKALVKDVTAAVSKNTGAPAEHIHVII 43 (61)
T ss_pred HHHHHHHHHHHHHHHhCcChhhEEEEE
Confidence 345667777778889999998887753
No 37
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=23.63 E-value=83 Score=24.70 Aligned_cols=36 Identities=19% Similarity=0.087 Sum_probs=31.2
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..|+-+|..|-+.|..++..+|++ |..=++.+++.|
T Consensus 23 ~~L~isQ~avS~~I~~LE~~lg~~LF~R~~r~v~lT~~G 61 (305)
T PRK11233 23 EVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAG 61 (305)
T ss_pred HHhCCCchHHHHHHHHHHHHhCCceEEeCCCCceECHhH
Confidence 357889999999999999999996 777788888777
No 38
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=22.71 E-value=69 Score=25.07 Aligned_cols=36 Identities=11% Similarity=0.002 Sum_probs=30.9
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..|+-+|..+-+.|..+|..||++ |..=++.+++.|
T Consensus 33 ~~L~iSQpavS~~I~~LE~~lG~~Lf~R~~r~~~lT~~G 71 (303)
T PRK10082 33 VSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQG 71 (303)
T ss_pred HHhCCChHHHHHHHHHHHHHcCCEEEEecCCCCccCHHH
Confidence 457889999999999999999996 776777777777
No 39
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=22.71 E-value=75 Score=24.89 Aligned_cols=37 Identities=24% Similarity=0.176 Sum_probs=32.4
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
..++-+|..+-+.|..++..||++ |..=++.+++.|.
T Consensus 27 ~~L~isqpavS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~ 66 (305)
T CHL00180 27 ESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGE 66 (305)
T ss_pred HHhcCCChHHHHHHHHHHHHhCCEEEEecCCCceECHhHH
Confidence 457889999999999999999996 8888888888873
No 40
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=22.13 E-value=1.1e+02 Score=23.84 Aligned_cols=36 Identities=19% Similarity=0.140 Sum_probs=31.7
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..|+-+|..+-+.|..++..+|++ |..=++.+++.|
T Consensus 27 ~~L~isQ~avS~~i~~LE~~lG~~LF~R~~r~~~lT~~G 65 (302)
T PRK09791 27 RMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAG 65 (302)
T ss_pred HHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCceECccH
Confidence 357889999999999999999996 888888888887
No 41
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=21.86 E-value=64 Score=22.15 Aligned_cols=26 Identities=12% Similarity=0.323 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhcCCccccceeecC
Q 043133 95 IVDQAINDICILLQCSRHNINVVGTS 120 (131)
Q Consensus 95 ~vd~~I~di~~~l~~~R~~L~i~a~~ 120 (131)
..+..++++|..+|++.++||+-=.+
T Consensus 56 ~Le~~~~~l~~~~gl~~~dLn~dLgp 81 (88)
T PF05121_consen 56 KLEEAMEELCERFGLTPEDLNLDLGP 81 (88)
T ss_pred HHHHHHHHHHHHcCCCHHHhcccccc
Confidence 46778999999999999999875433
No 42
>PRK01310 hypothetical protein; Validated
Probab=21.81 E-value=94 Score=21.75 Aligned_cols=26 Identities=8% Similarity=0.160 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhcCCccccceeecCCc
Q 043133 97 DQAINDICILLQCSRHNINVVGTSLE 122 (131)
Q Consensus 97 d~~I~di~~~l~~~R~~L~i~a~~KG 122 (131)
+.++.-|+..|++++.+..|+.-+++
T Consensus 55 ~ali~~LA~~l~v~ks~I~iv~G~ts 80 (104)
T PRK01310 55 RALIELLAKALGVPKSSVRLLSGATS 80 (104)
T ss_pred HHHHHHHHHHhCCChhhEEEEecCCC
Confidence 45677789999999999999876655
No 43
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=21.32 E-value=1e+02 Score=23.82 Aligned_cols=37 Identities=32% Similarity=0.255 Sum_probs=31.5
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCce
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLEL 123 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KGl 123 (131)
+.++-+|..+-+.|..|+..||++ |..=++..++.|.
T Consensus 23 ~~L~isqpavS~~I~~LE~~lG~~LF~R~~r~~~lT~~G~ 62 (275)
T PRK03601 23 ESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGE 62 (275)
T ss_pred HHhCCChHHHHHHHHHHHHHhCCceEEECCCceEECHhHH
Confidence 457889999999999999999996 7777788888773
No 44
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=21.28 E-value=1.2e+02 Score=18.37 Aligned_cols=26 Identities=8% Similarity=0.199 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHHHhcCCccccceee
Q 043133 93 QSIVDQAINDICILLQCSRHNINVVG 118 (131)
Q Consensus 93 Q~~vd~~I~di~~~l~~~R~~L~i~a 118 (131)
|+.++.+-+-++..+++|.+...|.=
T Consensus 18 ~~L~~~it~a~~~~~~~p~~~v~V~i 43 (60)
T PRK02289 18 NALAREVTEVVSRIAKAPKEAIHVFI 43 (60)
T ss_pred HHHHHHHHHHHHHHhCcCcceEEEEE
Confidence 46677777777889999998887753
No 45
>PRK02302 hypothetical protein; Provisional
Probab=20.97 E-value=78 Score=21.75 Aligned_cols=39 Identities=21% Similarity=0.301 Sum_probs=30.7
Q ss_pred eecchhhHHHHHHHHHHHHHHHHHHhcCCccceeeeeccCCC-----CCCchHHHHHHHHHHHHHh
Q 043133 47 TLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPS-----LYSEQSIVDQAINDICILL 107 (131)
Q Consensus 47 ~~~~~~~~~kf~~~l~vl~~i~~ll~~~~~~T~RdiYY~~~~-----lF~~Q~~vd~~I~di~~~l 107 (131)
+++..++.+||. +|.|.++. ++-+|.+++.+++.|..+=
T Consensus 16 ~~k~~r~LrkfG----------------------~I~Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~ 59 (89)
T PRK02302 16 YNRDARKLSKYG----------------------DIVYHSKRSRYLVLYVNKEDVEQKLEELSKLK 59 (89)
T ss_pred ecHhHHHHhhcC----------------------cEEEEeccccEEEEEECHHHHHHHHHHHhcCC
Confidence 355677777777 88888865 5889999999999997653
No 46
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=20.75 E-value=1e+02 Score=24.53 Aligned_cols=36 Identities=19% Similarity=0.131 Sum_probs=31.0
Q ss_pred CCCCCchHHHHHHHHHHHHHhcCC---ccccceeecCCc
Q 043133 87 PSLYSEQSIVDQAINDICILLQCS---RHNINVVGTSLE 122 (131)
Q Consensus 87 ~~lF~~Q~~vd~~I~di~~~l~~~---R~~L~i~a~~KG 122 (131)
..|+-+|..|-+.|..++..||++ |..=++.+++.|
T Consensus 24 ~~L~iSqpaVS~~Ik~LE~~lg~~LF~R~~r~v~lT~~G 62 (317)
T PRK15421 24 ATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQG 62 (317)
T ss_pred HHhCCCHHHHHHHHHHHHHHhCCEEEEecCCCceECHhH
Confidence 468899999999999999999986 777777887777
No 47
>PRK05090 hypothetical protein; Validated
Probab=20.56 E-value=1e+02 Score=21.23 Aligned_cols=26 Identities=4% Similarity=0.124 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhcCCccccceeecCCc
Q 043133 97 DQAINDICILLQCSRHNINVVGTSLE 122 (131)
Q Consensus 97 d~~I~di~~~l~~~R~~L~i~a~~KG 122 (131)
+.+++-|+..|++++.+..|++-.++
T Consensus 49 ~ali~~LAk~l~v~ks~I~i~~G~ts 74 (95)
T PRK05090 49 AHLLKFLAKQFRVAKSQVVIEKGELG 74 (95)
T ss_pred HHHHHHHHHHhCCChhhEEEEecCCC
Confidence 46677889999999999999887665
No 48
>PRK00647 hypothetical protein; Validated
Probab=20.22 E-value=1e+02 Score=21.33 Aligned_cols=26 Identities=12% Similarity=0.298 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhcCCccccceeecCCc
Q 043133 97 DQAINDICILLQCSRHNINVVGTSLE 122 (131)
Q Consensus 97 d~~I~di~~~l~~~R~~L~i~a~~KG 122 (131)
..++.-|+..|++++.+..|++-.++
T Consensus 44 ~ali~~LAk~l~vpks~I~Iv~G~tS 69 (96)
T PRK00647 44 DAVIALLAKFLSLPKRDVTLIAGETS 69 (96)
T ss_pred HHHHHHHHHHhCCChhhEEEEecCCC
Confidence 45677789999999999999987665
No 49
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=20.13 E-value=2e+02 Score=18.11 Aligned_cols=31 Identities=13% Similarity=-0.055 Sum_probs=26.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHhcCCcccee
Q 043133 50 KQCHARRIDILLSVLLIVQKLLQENIHMSKR 80 (131)
Q Consensus 50 ~~~~~~kf~~~l~vl~~i~~ll~~~~~~T~R 80 (131)
+...|++|.++.+-++-..++...|+..-.-
T Consensus 23 d~~kAr~~~R~~K~~~~~I~~~~aG~pVd~~ 53 (59)
T smart00685 23 DEEKARRHLRIAKQFDDAIKAARAGRPVDLS 53 (59)
T ss_pred CHHHHHHHHHHHhhHHHHHHHHHCCCCCChh
Confidence 4678999999999999999999999876443
Done!