Query 047493
Match_columns 77
No_of_seqs 101 out of 262
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 11:35:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047493hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2189 Vacuolar H+-ATPase V0 99.9 3.8E-27 8.2E-32 196.9 3.6 58 20-77 1-58 (829)
2 PF01496 V_ATPase_I: V-type AT 98.6 7.5E-09 1.6E-13 85.2 0.0 33 45-77 1-33 (759)
3 PRK05771 V-type ATP synthase s 96.6 0.0019 4.2E-08 52.7 3.1 48 25-72 2-50 (646)
4 COG1269 NtpI Archaeal/vacuolar 91.3 0.21 4.6E-06 41.7 3.3 42 24-65 1-42 (660)
5 PF09902 DUF2129: Uncharacteri 83.8 1.9 4E-05 27.2 3.4 36 23-58 24-59 (71)
6 PRK02302 hypothetical protein; 82.9 2.6 5.6E-05 27.8 3.9 38 23-60 30-67 (89)
7 PRK02886 hypothetical protein; 78.7 3.6 7.8E-05 27.1 3.5 38 23-60 28-65 (87)
8 COG3323 Uncharacterized protei 60.3 9.5 0.00021 26.1 2.5 33 27-59 3-35 (109)
9 PF08029 HisG_C: HisG, C-termi 55.8 19 0.00041 22.5 3.2 27 26-52 37-63 (75)
10 COG4471 Uncharacterized protei 54.9 15 0.00032 24.5 2.7 49 24-73 30-78 (90)
11 TIGR03455 HisG_C-term ATP phos 54.8 12 0.00026 24.4 2.2 28 26-53 61-88 (100)
12 PF12339 DNAJ_related: DNA-J r 50.3 5.8 0.00013 27.4 0.2 31 41-71 22-54 (132)
13 PF14257 DUF4349: Domain of un 49.0 23 0.00051 25.7 3.2 31 31-61 97-127 (262)
14 PF01978 TrmB: Sugar-specific 47.1 16 0.00034 21.2 1.7 25 36-60 34-58 (68)
15 COG3454 Metal-dependent hydrol 46.1 34 0.00074 27.9 3.9 51 21-72 124-174 (377)
16 PF00679 EFG_C: Elongation fac 44.2 27 0.00059 21.4 2.6 27 27-53 4-30 (89)
17 cd03710 BipA_TypA_C BipA_TypA_ 38.1 41 0.00088 20.2 2.6 26 27-52 1-26 (79)
18 PF13783 DUF4177: Domain of un 35.6 29 0.00063 20.1 1.6 24 36-59 17-42 (61)
19 COG3602 Uncharacterized protei 35.4 23 0.00051 25.0 1.4 19 33-51 111-129 (134)
20 cd01514 Elongation_Factor_C El 32.9 42 0.00092 19.8 2.1 26 27-52 1-26 (79)
21 cd03713 EFG_mtEFG_C EFG_mtEFG_ 32.8 41 0.00089 19.8 2.0 25 27-51 1-25 (78)
22 cd03709 lepA_C lepA_C: This fa 32.5 44 0.00095 20.2 2.1 26 27-52 1-26 (80)
23 cd04096 eEF2_snRNP_like_C eEF2 31.7 44 0.00095 19.9 2.0 26 27-52 1-26 (80)
24 COG4110 Uncharacterized protei 31.2 41 0.0009 25.1 2.1 38 14-51 29-74 (200)
25 PF03235 DUF262: Protein of un 30.2 20 0.00044 24.0 0.3 11 61-71 12-22 (221)
26 cd04097 mtEFG1_C mtEFG1_C: C-t 28.9 57 0.0012 19.4 2.2 26 27-52 1-26 (78)
27 PF02629 CoA_binding: CoA bind 28.8 34 0.00074 21.2 1.2 26 29-54 63-88 (96)
28 PF09904 HTH_43: Winged helix- 27.9 46 0.00099 22.0 1.7 23 36-58 33-56 (90)
29 cd03711 Tet_C Tet_C: C-terminu 27.9 60 0.0013 19.3 2.1 26 27-52 1-26 (78)
30 PF13350 Y_phosphatase3: Tyros 27.3 65 0.0014 21.6 2.4 39 14-60 12-50 (164)
31 PRK00489 hisG ATP phosphoribos 27.3 52 0.0011 24.3 2.1 28 26-53 247-274 (287)
32 cd07153 Fur_like Ferric uptake 25.7 74 0.0016 19.8 2.4 31 36-66 33-63 (116)
33 smart00838 EFG_C Elongation fa 25.5 66 0.0014 19.4 2.1 25 27-51 3-27 (85)
34 PF00392 GntR: Bacterial regul 25.3 51 0.0011 18.9 1.4 23 36-58 36-58 (64)
35 PF13380 CoA_binding_2: CoA bi 25.2 51 0.0011 21.4 1.6 26 27-52 54-79 (116)
36 PF04567 RNA_pol_Rpb2_5: RNA p 22.8 1E+02 0.0023 17.4 2.4 20 47-66 3-22 (48)
37 PF11582 DUF3240: Protein of u 21.5 1.1E+02 0.0023 19.8 2.5 24 28-51 59-82 (102)
38 TIGR00341 conserved hypothetic 20.4 1.5E+02 0.0032 23.5 3.5 36 15-52 30-65 (325)
39 PF09339 HTH_IclR: IclR helix- 20.3 64 0.0014 17.8 1.2 21 36-56 30-50 (52)
40 PF10307 DUF2410: Hypothetical 20.0 42 0.0009 24.7 0.4 33 6-43 18-52 (197)
No 1
>KOG2189 consensus Vacuolar H+-ATPase V0 sector, subunit a [Energy production and conversion]
Probab=99.93 E-value=3.8e-27 Score=196.93 Aligned_cols=58 Identities=38% Similarity=0.427 Sum_probs=56.7
Q ss_pred CCCcccccccceEEEEeecccHHHHHHHhhcccceeeeeCCCCCCccchhhhhhhhcC
Q 047493 20 LPNDGSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLNAGKSLFQRTFAAQVRFM 77 (77)
Q Consensus 20 ~~~~~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN~~v~~FqR~FvneIrRc 77 (77)
.+++||||+|+|||||+|+|+||+||++||++|+|||+|||++|++|||+||||||||
T Consensus 1 ~~s~fRSE~M~L~Ql~l~~eaAy~~vaeLGelGlvqFrDLN~~v~afQR~fv~evrRc 58 (829)
T KOG2189|consen 1 MGSLFRSEEMCLVQLFLQSEAAYQCVAELGELGLVQFRDLNPDVSAFQRKFVNEVRRC 58 (829)
T ss_pred CccccccccceeeEEEecHHHHHHHHHHhhccCeeEeeeCCCccCHHHHHHHHHHHHH
Confidence 3689999999999999999999999999999999999999999999999999999998
No 2
>PF01496 V_ATPase_I: V-type ATPase 116kDa subunit family ; InterPro: IPR002490 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents the 116kDa subunit (or subunit a) and subunit I found in the V0 or A0 complex of V- or A-ATPases, respectively. The 116kDa subunit is a transmembrane glycoprotein required for the assembly and proton transport activity of the ATPase complex. Several isoforms of the 116kDa subunit exist, providing a potential role in the differential targeting and regulation of the V-ATPase for specific organelles []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015991 ATP hydrolysis coupled proton transport, 0033177 proton-transporting two-sector ATPase complex, proton-transporting domain; PDB: 2RPW_X 2NVJ_A 2JTW_A 3RRK_A.
Probab=98.60 E-value=7.5e-09 Score=85.17 Aligned_cols=33 Identities=52% Similarity=0.779 Sum_probs=0.0
Q ss_pred HHHhhcccceeeeeCCCCCCccchhhhhhhhcC
Q 047493 45 ISYLGGLGLFQFKDLNAGKSLFQRTFAAQVRFM 77 (77)
Q Consensus 45 V~eLG~lglvqF~DLN~~v~~FqR~FvneIrRc 77 (77)
|++||++|+|||+|+|+++++|||+|+++++||
T Consensus 1 V~eLgelG~VqF~Dln~~~~~fqr~f~~ev~r~ 33 (759)
T PF01496_consen 1 VNELGELGLVQFRDLNEDVSAFQRKFVNEVRRC 33 (759)
T ss_dssp ---------------------------------
T ss_pred CchhhcCCcEEEEECccchhHHHHHhhhccccH
Confidence 789999999999999999999999999999998
No 3
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=96.58 E-value=0.0019 Score=52.68 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=41.0
Q ss_pred cccccceEEEEeecccHHHHHHHhhcccceeeeeCCCCCC-ccchhhhh
Q 047493 25 SSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLNAGKS-LFQRTFAA 72 (77)
Q Consensus 25 RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN~~v~-~FqR~Fvn 72 (77)
+.++|..++++.|.+.+.++++.|.++|.||+.|++.... ...+.+.+
T Consensus 2 ~i~kM~kv~l~~~~~~~~~~l~~L~~lg~vhi~~~~~~~~~~~~~~~~~ 50 (646)
T PRK05771 2 APVRMKKVLIVTLKSYKDEVLEALHELGVVHIEDLKEELSNERLRKLRS 50 (646)
T ss_pred CceeeEEEEEEEEHHHHHHHHHHHHhCCCEEEeecccccchhHHhHHHH
Confidence 5689999999999999999999999999999999998875 33444433
No 4
>COG1269 NtpI Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion]
Probab=91.34 E-value=0.21 Score=41.71 Aligned_cols=42 Identities=17% Similarity=0.164 Sum_probs=38.1
Q ss_pred ccccccceEEEEeecccHHHHHHHhhcccceeeeeCCCCCCc
Q 047493 24 GSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLNAGKSL 65 (77)
Q Consensus 24 ~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN~~v~~ 65 (77)
+|-+.|..+.++.+.+..-+++.+|++.|++|+.|++.++..
T Consensus 1 ~~~~~M~kv~i~~~~~~~~~vi~~L~~~g~~~~~d~~~~~~~ 42 (660)
T COG1269 1 MRPEKMKKVSIIGLKSELDPVLAELHDFGLVHLEDLEEGEKG 42 (660)
T ss_pred CchhhheeEEEEeehhhhhHHHHHHHHcCeEEeecccccccc
Confidence 367899999999999999999999999999999999876543
No 5
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=83.81 E-value=1.9 Score=27.21 Aligned_cols=36 Identities=17% Similarity=-0.004 Sum_probs=32.8
Q ss_pred cccccccceEEEEeecccHHHHHHHhhcccceeeee
Q 047493 23 DGSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKD 58 (77)
Q Consensus 23 ~~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~D 58 (77)
.+-|..|.++.||+..|.+-+++..|.++..|.=++
T Consensus 24 ~Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve 59 (71)
T PF09902_consen 24 HYVSKKMKYVVLYVNEEDVEEIIEKLKKLKFVKKVE 59 (71)
T ss_pred EEEECCccEEEEEECHHHHHHHHHHHhcCCCeeEEe
Confidence 458999999999999999999999999999887665
No 6
>PRK02302 hypothetical protein; Provisional
Probab=82.91 E-value=2.6 Score=27.82 Aligned_cols=38 Identities=13% Similarity=-0.032 Sum_probs=34.1
Q ss_pred cccccccceEEEEeecccHHHHHHHhhcccceeeeeCC
Q 047493 23 DGSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLN 60 (77)
Q Consensus 23 ~~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN 60 (77)
.+=|..|.++-||+..|.|-+++..|.++..|.-++.-
T Consensus 30 ~Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~S 67 (89)
T PRK02302 30 VYHSKRSRYLVLYVNKEDVEQKLEELSKLKFVKKVRPS 67 (89)
T ss_pred EEEeccccEEEEEECHHHHHHHHHHHhcCCCeeEEccc
Confidence 45799999999999999999999999999988877644
No 7
>PRK02886 hypothetical protein; Provisional
Probab=78.72 E-value=3.6 Score=27.06 Aligned_cols=38 Identities=16% Similarity=0.016 Sum_probs=34.1
Q ss_pred cccccccceEEEEeecccHHHHHHHhhcccceeeeeCC
Q 047493 23 DGSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLN 60 (77)
Q Consensus 23 ~~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN 60 (77)
.+=|..|.++-||+..|.|-+++..|.++..|.-++.-
T Consensus 28 ~Y~Skr~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~S 65 (87)
T PRK02886 28 HYVSKRLKYAVLYCDMEQVEDIMNKLSSLPFVKRVEPS 65 (87)
T ss_pred EEEeccccEEEEEECHHHHHHHHHHHhcCCCeeEEccc
Confidence 35799999999999999999999999999998877644
No 8
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.25 E-value=9.5 Score=26.11 Aligned_cols=33 Identities=12% Similarity=-0.017 Sum_probs=29.5
Q ss_pred cccceEEEEeecccHHHHHHHhhcccceeeeeC
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLGLFQFKDL 59 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DL 59 (77)
+.|.-..+|+|.|-.-..-..|++.|.-|.-|.
T Consensus 3 ~~~~K~~vyVP~~~~e~vr~aL~~aGag~iG~Y 35 (109)
T COG3323 3 EPLYKIEVYVPEEYVEQVRDALFEAGAGHIGNY 35 (109)
T ss_pred cceeEEEEEeCHHHHHHHHHHHHhcCCcceecc
Confidence 467788999999999999999999999988874
No 9
>PF08029 HisG_C: HisG, C-terminal domain; InterPro: IPR013115 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. This entry represents the C-terminal portion of ATP phosphoribosyltransferase. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates [, ]. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. This domain is not directly involved in catalysis but appears to be responsible for the formation of hexamers induced by the binding of inhibitors to the enzyme, thus regulating activity.; GO: 0000287 magnesium ion binding, 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1Q1K_A 1H3D_A 2VD3_B 1NH7_A 1NH8_A.
Probab=55.81 E-value=19 Score=22.52 Aligned_cols=27 Identities=11% Similarity=0.132 Sum_probs=24.4
Q ss_pred ccccceEEEEeecccHHHHHHHhhccc
Q 047493 26 SAVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 26 SE~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
.+++.-++.++|.+..++.|++|=+.|
T Consensus 37 ~~~w~AV~~vV~~~~~~~~~~~Lk~~G 63 (75)
T PF08029_consen 37 DEDWVAVHAVVPEKQVWDLMDKLKAAG 63 (75)
T ss_dssp STTEEEEEEEEECCCHHHHHHHHHCTT
T ss_pred CCCEEEEEEEecHHHHHHHHHHHHHcC
Confidence 457888999999999999999998887
No 10
>COG4471 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.90 E-value=15 Score=24.50 Aligned_cols=49 Identities=10% Similarity=0.059 Sum_probs=37.6
Q ss_pred ccccccceEEEEeecccHHHHHHHhhcccceeeeeCCCCCCccchhhhhh
Q 047493 24 GSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLNAGKSLFQRTFAAQ 73 (77)
Q Consensus 24 ~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN~~v~~FqR~Fvne 73 (77)
+-|.++.++.||++.+..-++++.|..+-.|-=++.-+- +-.+++|.++
T Consensus 30 Y~Skk~kY~vlYvn~~~ve~~~~kl~~~kfVK~V~~s~~-~~Lk~~f~~~ 78 (90)
T COG4471 30 YVSKKSKYVVLYVNEQDVEQIVEKLSRLKFVKKVRVSHI-PYLKTEFEGN 78 (90)
T ss_pred EEecceeEEEEEECHHHHHHHHHHHhhceeeeecccccc-HHHHhHHhhc
Confidence 479999999999999999999999999988876665431 2334455543
No 11
>TIGR03455 HisG_C-term ATP phosphoribosyltransferase, C-terminal domain. This domain corresponds to the C-terminal third of the HisG protein. It is absent in many lineages.
Probab=54.82 E-value=12 Score=24.45 Aligned_cols=28 Identities=11% Similarity=0.039 Sum_probs=25.4
Q ss_pred ccccceEEEEeecccHHHHHHHhhcccc
Q 047493 26 SAVGADAQLIIPIESAHCTISYLGGLGL 53 (77)
Q Consensus 26 SE~M~l~qL~ip~E~A~~~V~eLG~lgl 53 (77)
+++|.-++.++|.+..++++++|-+.|-
T Consensus 61 ~~~w~AV~~vv~~~~v~~~~~~Lk~~GA 88 (100)
T TIGR03455 61 DEGWVAVHAVVDEKVVNELIDKLKAAGA 88 (100)
T ss_pred CCCeEEEEEEEcHHHHHHHHHHHHHcCC
Confidence 5788889999999999999999999883
No 12
>PF12339 DNAJ_related: DNA-J related protein ; InterPro: IPR021059 This domain family is approximately 130 amino acids in length and contains a conserved YYLD sequence motif. The proteins have a C-terminal DNA-J domain PF00226 from PFAM and most of the sequences are annotated as DNA-J related proteins, other annotations include: DnaJ-class molecular chaperon and formate dehydrogenase; but there is currently no publications to support these annotations.
Probab=50.33 E-value=5.8 Score=27.43 Aligned_cols=31 Identities=35% Similarity=0.419 Sum_probs=27.0
Q ss_pred HHHHHHHhhcccce--eeeeCCCCCCccchhhh
Q 047493 41 AHCTISYLGGLGLF--QFKDLNAGKSLFQRTFA 71 (77)
Q Consensus 41 A~~~V~eLG~lglv--qF~DLN~~v~~FqR~Fv 71 (77)
-++-+++|++.|.. ...|++++...|+|.|.
T Consensus 22 e~~L~~~L~~~~~~~f~~l~~~~~~~LFk~hFL 54 (132)
T PF12339_consen 22 EHELISQLQEQGYILFPELDLDPPLDLFKRHFL 54 (132)
T ss_pred HHHHHHHHhhCcCccCCCCCCCcHHHHHHHHHH
Confidence 47889999999988 77788899999999985
No 13
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=49.04 E-value=23 Score=25.74 Aligned_cols=31 Identities=13% Similarity=0.304 Sum_probs=27.6
Q ss_pred eEEEEeecccHHHHHHHhhcccceeeeeCCC
Q 047493 31 DAQLIIPIESAHCTISYLGGLGLFQFKDLNA 61 (77)
Q Consensus 31 l~qL~ip~E~A~~~V~eLG~lglvqF~DLN~ 61 (77)
...+-||++..-+.+++|+++|.|.-...+.
T Consensus 97 ~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~~ 127 (262)
T PF14257_consen 97 SLTIRVPADKFDSFLDELSELGKVTSRNISS 127 (262)
T ss_pred EEEEEECHHHHHHHHHHHhccCceeeeeccc
Confidence 6789999999999999999999888777664
No 14
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=47.08 E-value=16 Score=21.20 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=22.2
Q ss_pred eecccHHHHHHHhhcccceeeeeCC
Q 047493 36 IPIESAHCTISYLGGLGLFQFKDLN 60 (77)
Q Consensus 36 ip~E~A~~~V~eLG~lglvqF~DLN 60 (77)
+|...++.++..|-+.|+|+..+-+
T Consensus 34 i~~~~v~~~L~~L~~~GlV~~~~~~ 58 (68)
T PF01978_consen 34 ISRSTVYRALKSLEEKGLVEREEGR 58 (68)
T ss_dssp SSHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred cCHHHHHHHHHHHHHCCCEEEEcCc
Confidence 6788999999999999999988744
No 15
>COG3454 Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=46.10 E-value=34 Score=27.86 Aligned_cols=51 Identities=12% Similarity=-0.056 Sum_probs=41.2
Q ss_pred CCcccccccceEEEEeecccHHHHHHHhhcccceeeeeCCCCCCccchhhhh
Q 047493 21 PNDGSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLNAGKSLFQRTFAA 72 (77)
Q Consensus 21 ~~~~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN~~v~~FqR~Fvn 72 (77)
.+.+|++---..+.=++.+...+.+.++.+.+.|+.+-|+.+ +|-||.|.+
T Consensus 124 ~g~lradHr~HlRcEvs~~~~l~~~e~~~~~p~v~LiSlMDH-~PGQrQf~~ 174 (377)
T COG3454 124 AGRLRADHRLHLRCEVSHPATLPLFEDLMDHPRVKLISLMDH-TPGQRQFAN 174 (377)
T ss_pred ccchhhccceeeeeecCChhHHHHHHHHhcCCCeeEEEecCC-CCCcchhhh
Confidence 345666665556666789999999999999999999999988 677998865
No 16
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=44.23 E-value=27 Score=21.40 Aligned_cols=27 Identities=19% Similarity=-0.001 Sum_probs=23.7
Q ss_pred cccceEEEEeecccHHHHHHHhhcccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLGL 53 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lgl 53 (77)
|++-.+++.+|.|..-.+++.|++.+-
T Consensus 4 EP~~~~~I~~p~~~~g~v~~~l~~r~g 30 (89)
T PF00679_consen 4 EPIMSVEISVPEEYLGKVISDLSKRRG 30 (89)
T ss_dssp EEEEEEEEEEEGGGHHHHHHHHHHTT-
T ss_pred CCEEEEEEEECHHHHHHHHHHhccccc
Confidence 677889999999999999999999863
No 17
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=38.11 E-value=41 Score=20.20 Aligned_cols=26 Identities=19% Similarity=0.161 Sum_probs=23.3
Q ss_pred cccceEEEEeecccHHHHHHHhhccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
|+|-.+.+.+|.|..-.+++.|.+..
T Consensus 1 EPi~~v~I~~P~~~~g~V~~~l~~rr 26 (79)
T cd03710 1 EPIEELTIDVPEEYSGAVIEKLGKRK 26 (79)
T ss_pred CCEEEEEEEeCchhhHHHHHHHHhCC
Confidence 67788999999999999999998874
No 18
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=35.58 E-value=29 Score=20.11 Aligned_cols=24 Identities=21% Similarity=0.153 Sum_probs=21.1
Q ss_pred eecccHHHHHHHhhccc--ceeeeeC
Q 047493 36 IPIESAHCTISYLGGLG--LFQFKDL 59 (77)
Q Consensus 36 ip~E~A~~~V~eLG~lg--lvqF~DL 59 (77)
++.+...+.++++|+.| +|+..+-
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeLV~~~~~ 42 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWELVSIIPP 42 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEEEEEEcC
Confidence 56677889999999999 9999987
No 19
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.38 E-value=23 Score=24.98 Aligned_cols=19 Identities=37% Similarity=0.604 Sum_probs=17.2
Q ss_pred EEEeecccHHHHHHHhhcc
Q 047493 33 QLIIPIESAHCTISYLGGL 51 (77)
Q Consensus 33 qL~ip~E~A~~~V~eLG~l 51 (77)
++|+|.|.|.+.+..|+.+
T Consensus 111 HlFVp~e~a~~A~~~L~~l 129 (134)
T COG3602 111 HLFVPAERAKEALVVLQGL 129 (134)
T ss_pred eeeeeHHHHHHHHHHHHHH
Confidence 6999999999999998865
No 20
>cd01514 Elongation_Factor_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the
Probab=32.94 E-value=42 Score=19.77 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=23.0
Q ss_pred cccceEEEEeecccHHHHHHHhhccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
|+|-.+.+.+|.|..-.+++.|....
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (79)
T cd01514 1 EPIMKVEITVPEEYLGAVIGDLSKRR 26 (79)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHhcC
Confidence 67889999999999999999997764
No 21
>cd03713 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide
Probab=32.78 E-value=41 Score=19.84 Aligned_cols=25 Identities=16% Similarity=0.070 Sum_probs=22.5
Q ss_pred cccceEEEEeecccHHHHHHHhhcc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGL 51 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~l 51 (77)
|+|-.+.+.+|.+..-.+++.|.+.
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~r 25 (78)
T cd03713 1 EPIMKVEVTVPEEYMGDVIGDLSSR 25 (78)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHHc
Confidence 6788899999999999999999875
No 22
>cd03709 lepA_C lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=32.53 E-value=44 Score=20.22 Aligned_cols=26 Identities=15% Similarity=0.043 Sum_probs=23.2
Q ss_pred cccceEEEEeecccHHHHHHHhhccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
|++-.+.+.+|.|..-++++.|....
T Consensus 1 EPi~~v~i~vP~e~~G~V~~~l~~rr 26 (80)
T cd03709 1 EPFVKATIITPSEYLGAIMELCQERR 26 (80)
T ss_pred CCEEEEEEEeCHHhhHHHHHHHHHhC
Confidence 67888999999999999999999863
No 23
>cd04096 eEF2_snRNP_like_C eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=31.74 E-value=44 Score=19.89 Aligned_cols=26 Identities=12% Similarity=-0.088 Sum_probs=23.3
Q ss_pred cccceEEEEeecccHHHHHHHhhccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
|+|-.+.+.+|.|..-.+++.|+...
T Consensus 1 EPi~~~~I~~p~~~~g~V~~~l~~rr 26 (80)
T cd04096 1 EPIYLVEIQCPEDALGKVYSVLSKRR 26 (80)
T ss_pred CCEEEEEEEEcHHHhhHHHHhhhhCe
Confidence 67888999999999999999998875
No 24
>COG4110 Uncharacterized protein involved in stress response [General function prediction only]
Probab=31.19 E-value=41 Score=25.08 Aligned_cols=38 Identities=16% Similarity=-0.009 Sum_probs=32.7
Q ss_pred cCccccCC------Ccccc--cccceEEEEeecccHHHHHHHhhcc
Q 047493 14 NGRWWLLP------NDGSS--AVGADAQLIIPIESAHCTISYLGGL 51 (77)
Q Consensus 14 ~~~~~~~~------~~~RS--E~M~l~qL~ip~E~A~~~V~eLG~l 51 (77)
|..|=+-+ +||+| -|..|..+|.-.|-.+.+|..||+.
T Consensus 29 NLNW~rGg~~~f~~giF~~~giDLDLG~~~~LnDGskGviQALGN~ 74 (200)
T COG4110 29 NLNWHRGGSKSFFAGIFGSKGIDLDLGAFVELNDGSKGVIQALGNA 74 (200)
T ss_pred EeeeccCCCcchhhhhhccCccccccceEEEecCCchHHHHHHhhh
Confidence 56677777 89999 5677999999999999999999975
No 25
>PF03235 DUF262: Protein of unknown function DUF262; InterPro: IPR004919 This entry is found in prokaryotic proteins of unknown function.
Probab=30.21 E-value=20 Score=23.97 Aligned_cols=11 Identities=18% Similarity=0.241 Sum_probs=9.0
Q ss_pred CCCCccchhhh
Q 047493 61 AGKSLFQRTFA 71 (77)
Q Consensus 61 ~~v~~FqR~Fv 71 (77)
=.+|.|||+|+
T Consensus 12 ~~iP~yQR~yv 22 (221)
T PF03235_consen 12 IVIPDYQRDYV 22 (221)
T ss_pred ccCCCCCCCCc
Confidence 35789999997
No 26
>cd04097 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (desig
Probab=28.90 E-value=57 Score=19.39 Aligned_cols=26 Identities=15% Similarity=0.060 Sum_probs=23.0
Q ss_pred cccceEEEEeecccHHHHHHHhhccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
|+|-.+.+.+|.|..-.+++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (78)
T cd04097 1 EPIMKVEVTAPTEFQGNVIGLLNKRK 26 (78)
T ss_pred CCEEEEEEEecHHHHHHHHHHHHHCC
Confidence 67788999999999999999998864
No 27
>PF02629 CoA_binding: CoA binding domain; InterPro: IPR003781 This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.; GO: 0005488 binding; PDB: 3IL2_B 3IKT_A 3IKV_B 2SCU_D 1JKJ_D 2NU7_A 1CQI_A 1JLL_A 2NU8_D 1SCU_D ....
Probab=28.76 E-value=34 Score=21.18 Aligned_cols=26 Identities=23% Similarity=0.144 Sum_probs=19.5
Q ss_pred cceEEEEeecccHHHHHHHhhcccce
Q 047493 29 GADAQLIIPIESAHCTISYLGGLGLF 54 (77)
Q Consensus 29 M~l~qL~ip~E~A~~~V~eLG~lglv 54 (77)
....=+++|.+.|.+++.++-+.|+=
T Consensus 63 i~iaii~VP~~~a~~~~~~~~~~gIk 88 (96)
T PF02629_consen 63 IDIAIITVPAEAAQEVADELVEAGIK 88 (96)
T ss_dssp TSEEEEES-HHHHHHHHHHHHHTT-S
T ss_pred CCEEEEEcCHHHHHHHHHHHHHcCCC
Confidence 44556889999999999999887753
No 28
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=27.89 E-value=46 Score=22.05 Aligned_cols=23 Identities=30% Similarity=0.483 Sum_probs=17.3
Q ss_pred eecccHHHHHHHhhcccc-eeeee
Q 047493 36 IPIESAHCTISYLGGLGL-FQFKD 58 (77)
Q Consensus 36 ip~E~A~~~V~eLG~lgl-vqF~D 58 (77)
+|+..+.+++..|.++|+ +.|+.
T Consensus 33 mPrRT~Qd~i~aL~~~~I~~~Fvq 56 (90)
T PF09904_consen 33 MPRRTIQDTIKALPELGIECEFVQ 56 (90)
T ss_dssp --HHHHHHHHHGGGGGT-EEEEE-
T ss_pred CCHhHHHHHHHHhhcCCeEEEEEe
Confidence 689999999999999994 66775
No 29
>cd03711 Tet_C Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=27.89 E-value=60 Score=19.29 Aligned_cols=26 Identities=19% Similarity=0.213 Sum_probs=23.1
Q ss_pred cccceEEEEeecccHHHHHHHhhccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
|+|-.+.+.+|.|..-.+++.|++..
T Consensus 1 EPi~~~~i~~p~~~~g~v~~~l~~rr 26 (78)
T cd03711 1 EPYLRFELEVPQDALGRAMSDLAKMG 26 (78)
T ss_pred CCeEEEEEEcCHHHHHHHHHHHHHcC
Confidence 67888999999999999999998864
No 30
>PF13350 Y_phosphatase3: Tyrosine phosphatase family; PDB: 1YWF_A 2OZ5_B.
Probab=27.30 E-value=65 Score=21.57 Aligned_cols=39 Identities=21% Similarity=0.131 Sum_probs=19.4
Q ss_pred cCccccCCCcccccccceEEEEeecccHHHHHHHhhcccceeeeeCC
Q 047493 14 NGRWWLLPNDGSSAVGADAQLIIPIESAHCTISYLGGLGLFQFKDLN 60 (77)
Q Consensus 14 ~~~~~~~~~~~RSE~M~l~qL~ip~E~A~~~V~eLG~lglvqF~DLN 60 (77)
.++.=+.+-+|||...+ ...-+-+..|.++|+=..+||=
T Consensus 12 ~g~~ir~g~lyRS~~l~--------~lt~~d~~~L~~lgI~tIiDLR 50 (164)
T PF13350_consen 12 DGRRIRPGRLYRSGNLS--------NLTEADLERLRELGIRTIIDLR 50 (164)
T ss_dssp ---TS-TTSEEEES--T--------T--HHHHHHHHHTT--EEEE-S
T ss_pred ceeeecCCcEEecCCcC--------cCCHHHHHHHHhCCCCEEEECC
Confidence 34444567799999954 3344445566688888888863
No 31
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=27.27 E-value=52 Score=24.28 Aligned_cols=28 Identities=14% Similarity=0.163 Sum_probs=25.0
Q ss_pred ccccceEEEEeecccHHHHHHHhhcccc
Q 047493 26 SAVGADAQLIIPIESAHCTISYLGGLGL 53 (77)
Q Consensus 26 SE~M~l~qL~ip~E~A~~~V~eLG~lgl 53 (77)
.+++.-++.++|.+..++++++|-+.|-
T Consensus 247 ~~~~~av~~~~~~~~~~~~~~~l~~~ga 274 (287)
T PRK00489 247 DEGWVAVHAVVPEDLVWELMDKLKALGA 274 (287)
T ss_pred CCCeEEEEEEECHHHHHHHHHHHHHcCC
Confidence 4678889999999999999999998883
No 32
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=25.70 E-value=74 Score=19.79 Aligned_cols=31 Identities=26% Similarity=0.409 Sum_probs=24.8
Q ss_pred eecccHHHHHHHhhcccceeeeeCCCCCCcc
Q 047493 36 IPIESAHCTISYLGGLGLFQFKDLNAGKSLF 66 (77)
Q Consensus 36 ip~E~A~~~V~eLG~lglvqF~DLN~~v~~F 66 (77)
++....|.+++.|-+.|+|+-++...+...|
T Consensus 33 i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 33 ISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred CCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 5667899999999999999998876653333
No 33
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=25.54 E-value=66 Score=19.37 Aligned_cols=25 Identities=16% Similarity=0.070 Sum_probs=22.7
Q ss_pred cccceEEEEeecccHHHHHHHhhcc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGL 51 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~l 51 (77)
|+|-.+.+.+|.|..-.+++.|.+.
T Consensus 3 EPi~~~~I~~p~~~~g~v~~~l~~r 27 (85)
T smart00838 3 EPIMKVEVTVPEEYMGDVIGDLNSR 27 (85)
T ss_pred CCEEEEEEEeCHHHHHHHHHHHHHc
Confidence 7888999999999999999999775
No 34
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=25.32 E-value=51 Score=18.86 Aligned_cols=23 Identities=13% Similarity=0.213 Sum_probs=19.1
Q ss_pred eecccHHHHHHHhhcccceeeee
Q 047493 36 IPIESAHCTISYLGGLGLFQFKD 58 (77)
Q Consensus 36 ip~E~A~~~V~eLG~lglvqF~D 58 (77)
++...+++++..|-+.|+|+.++
T Consensus 36 vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 36 VSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEET
T ss_pred cCCcHHHHHHHHHHHCCcEEEEC
Confidence 66778899999999999998764
No 35
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=25.17 E-value=51 Score=21.37 Aligned_cols=26 Identities=15% Similarity=0.113 Sum_probs=21.4
Q ss_pred cccceEEEEeecccHHHHHHHhhccc
Q 047493 27 AVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 27 E~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
++..++-+++|.+..-+.+.+++++|
T Consensus 54 ~~iDlavv~~~~~~~~~~v~~~~~~g 79 (116)
T PF13380_consen 54 EPIDLAVVCVPPDKVPEIVDEAAALG 79 (116)
T ss_dssp ST-SEEEE-S-HHHHHHHHHHHHHHT
T ss_pred CCCCEEEEEcCHHHHHHHHHHHHHcC
Confidence 56779999999999999999999998
No 36
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=22.79 E-value=1e+02 Score=17.38 Aligned_cols=20 Identities=15% Similarity=0.210 Sum_probs=14.3
Q ss_pred HhhcccceeeeeCCCCCCcc
Q 047493 47 YLGGLGLFQFKDLNAGKSLF 66 (77)
Q Consensus 47 eLG~lglvqF~DLN~~v~~F 66 (77)
.|=+.|+|.|+|-+...++.
T Consensus 3 ~ll~~G~vE~id~eEEe~~~ 22 (48)
T PF04567_consen 3 DLLKEGVVEYIDAEEEETCM 22 (48)
T ss_dssp HHHHTTSEEEEETTTCTT--
T ss_pred hHhhCCCEEEecchhccccE
Confidence 45567999999988876554
No 37
>PF11582 DUF3240: Protein of unknown function (DUF3240); InterPro: IPR021634 This family of proteins with unknown function appears to be restricted to Proteobacteria. ; PDB: 3CE8_A.
Probab=21.46 E-value=1.1e+02 Score=19.82 Aligned_cols=24 Identities=25% Similarity=0.198 Sum_probs=21.2
Q ss_pred ccceEEEEeecccHHHHHHHhhcc
Q 047493 28 VGADAQLIIPIESAHCTISYLGGL 51 (77)
Q Consensus 28 ~M~l~qL~ip~E~A~~~V~eLG~l 51 (77)
++..+++++|.+.|.+.++.|.+.
T Consensus 59 ~~~~~~~~~~~~~~~~Ll~~L~~~ 82 (102)
T PF11582_consen 59 RRVRFQVILPEEDAEELLAALKQE 82 (102)
T ss_dssp EEEEEEEEEEGGGHHHHHHHHHHH
T ss_pred ceEEEEEEECHHHHHHHHHHHHHH
Confidence 667899999999999999999764
No 38
>TIGR00341 conserved hypothetical protein TIGR00341. This conserved hypothetical protein is found so far only in three archaeal genomes and in Streptomyces coelicolor. It shares a hydrophobic uncharacterized domain (see model TIGR00271) of about 180 residues with several eubacterial proteins, including the much longer protein sll1151 of Synechocystis PCC6803.
Probab=20.42 E-value=1.5e+02 Score=23.49 Aligned_cols=36 Identities=11% Similarity=-0.179 Sum_probs=29.0
Q ss_pred CccccCCCcccccccceEEEEeecccHHHHHHHhhccc
Q 047493 15 GRWWLLPNDGSSAVGADAQLIIPIESAHCTISYLGGLG 52 (77)
Q Consensus 15 ~~~~~~~~~~RSE~M~l~qL~ip~E~A~~~V~eLG~lg 52 (77)
-.||.....-..+ ..+++++|.|++-+.+++|-++|
T Consensus 30 i~~~~~~~~~~~~--~~i~~~v~~~~~e~vld~L~~lg 65 (325)
T TIGR00341 30 IAIELGDKTFIYD--DRIELYVQDSDTEKIVSRLKDKL 65 (325)
T ss_pred ceEEeccCCCCcc--eEEEEEcChhhHHHHHHHHHHcC
Confidence 5677776544444 68999999999999999999985
No 39
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=20.31 E-value=64 Score=17.81 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=17.6
Q ss_pred eecccHHHHHHHhhcccceee
Q 047493 36 IPIESAHCTISYLGGLGLFQF 56 (77)
Q Consensus 36 ip~E~A~~~V~eLG~lglvqF 56 (77)
+|+-.++..+..|-+.|.|+-
T Consensus 30 l~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 30 LPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp S-HHHHHHHHHHHHHTTSEEE
T ss_pred cCHHHHHHHHHHHHHCcCeec
Confidence 788899999999999998864
No 40
>PF10307 DUF2410: Hypothetical protein (DUF2410); InterPro: IPR018812 This entry represents a family of proteins conserved in fungi whose function is not known. There are two characteristic sequence motifs, GGWW and TGR.
Probab=20.03 E-value=42 Score=24.72 Aligned_cols=33 Identities=21% Similarity=0.340 Sum_probs=22.8
Q ss_pred HHHHhhhhcCccccCCCcccc--cccceEEEEeecccHHH
Q 047493 6 LFNQKRKKNGRWWLLPNDGSS--AVGADAQLIIPIESAHC 43 (77)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~RS--E~M~l~qL~ip~E~A~~ 43 (77)
|-++-.-.|+-||.+|+++.- +. +.++...||+
T Consensus 18 L~~~~~~~ngGWW~d~~~L~~t~~~-----~~~~~~~~w~ 52 (197)
T PF10307_consen 18 LMSPDSFSNGGWWHDPRILAATGEG-----MEVEEKRAWE 52 (197)
T ss_pred HhCcccCCCCCCcCCcHHHHhhccc-----ccccCccccc
Confidence 445555678999999999966 33 4456666665
Done!