Query psy15628
Match_columns 90
No_of_seqs 105 out of 282
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 17:34:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15628.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15628hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2189|consensus 100.0 3.8E-33 8.3E-38 238.3 3.1 78 1-78 1-79 (829)
2 PF01496 V_ATPase_I: V-type AT 99.2 4.2E-12 9.1E-17 107.4 0.0 48 26-73 1-49 (759)
3 PRK05771 V-type ATP synthase s 96.7 0.00085 1.8E-08 56.5 2.2 62 5-69 1-64 (646)
4 COG1269 NtpI Archaeal/vacuolar 90.2 0.31 6.7E-06 41.9 3.4 41 5-45 1-41 (660)
5 PRK02302 hypothetical protein; 86.5 1.2 2.7E-05 30.0 3.7 53 5-58 31-83 (89)
6 PF09902 DUF2129: Uncharacteri 82.1 2.5 5.4E-05 27.2 3.6 36 5-40 25-60 (71)
7 PRK02886 hypothetical protein; 75.5 5 0.00011 27.0 3.6 38 5-42 29-66 (87)
8 COG4471 Uncharacterized protei 58.5 9.4 0.0002 25.9 2.3 51 6-57 31-81 (90)
9 COG3454 Metal-dependent hydrol 54.2 20 0.00043 29.8 3.9 50 3-53 125-174 (377)
10 TIGR03455 HisG_C-term ATP phos 46.0 22 0.00047 23.8 2.5 28 7-34 61-88 (100)
11 PF08029 HisG_C: HisG, C-termi 45.4 29 0.00063 22.2 2.9 27 7-33 37-63 (75)
12 COG3323 Uncharacterized protei 45.3 24 0.00051 24.7 2.6 33 8-40 3-35 (109)
13 PF12339 DNAJ_related: DNA-J r 41.4 7.9 0.00017 27.4 -0.2 31 22-52 22-54 (132)
14 PF14257 DUF4349: Domain of un 38.2 41 0.0009 25.2 3.2 32 12-43 97-128 (262)
15 PF01978 TrmB: Sugar-specific 36.3 32 0.0007 20.4 2.0 25 17-41 34-58 (68)
16 PF00679 EFG_C: Elongation fac 29.3 58 0.0013 20.4 2.4 26 8-33 4-29 (89)
17 COG3602 Uncharacterized protei 28.8 36 0.00078 24.5 1.5 19 14-32 111-129 (134)
18 PF13783 DUF4177: Domain of un 27.6 60 0.0013 19.2 2.1 24 17-40 17-42 (61)
19 cd03710 BipA_TypA_C BipA_TypA_ 25.7 90 0.002 19.2 2.7 26 8-33 1-26 (79)
20 cd03713 EFG_mtEFG_C EFG_mtEFG_ 23.7 79 0.0017 19.1 2.2 25 8-32 1-25 (78)
21 cd01306 PhnM PhnM is believed 23.4 1.4E+02 0.003 23.7 4.0 48 4-52 79-126 (325)
22 cd03709 lepA_C lepA_C: This fa 23.4 86 0.0019 19.4 2.3 25 8-32 1-25 (80)
23 cd01514 Elongation_Factor_C El 22.0 90 0.002 18.8 2.2 26 8-33 1-26 (79)
24 cd04096 eEF2_snRNP_like_C eEF2 21.5 93 0.002 18.9 2.2 26 8-33 1-26 (80)
25 PF09904 HTH_43: Winged helix- 21.2 82 0.0018 21.3 2.0 23 17-39 33-56 (90)
26 PRK00489 hisG ATP phosphoribos 20.9 89 0.0019 23.7 2.4 27 7-33 247-273 (287)
27 PF03235 DUF262: Protein of un 20.6 40 0.00087 23.2 0.4 15 43-57 13-27 (221)
No 1
>KOG2189|consensus
Probab=99.97 E-value=3.8e-33 Score=238.33 Aligned_cols=78 Identities=41% Similarity=0.606 Sum_probs=73.6
Q ss_pred CCCcccccCCceEEEEeccchHHHHHHhhhhccceEEeecCCCccccccccccCcccchhhhhh-hhhhhccccCCCcc
Q psy15628 1 MGAMFRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSITLDTQFNRFQEERPMCVSSSRV-DWNTSHAFRHTPFV 78 (90)
Q Consensus 1 mgslfRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~v~~fqR~f~~eIrRcdEmeR~-~~l~~~~~~~~~~~ 78 (90)
||||||||+|+|||||+|+|+||+||++||++|+|||+|||++|++|||+|+|||||||||||+ +|+++++.++-...
T Consensus 1 ~~s~fRSE~M~L~Ql~l~~eaAy~~vaeLGelGlvqFrDLN~~v~afQR~fv~evrRcdemeRklrfl~~ei~k~~i~~ 79 (829)
T KOG2189|consen 1 MGSLFRSEEMCLVQLFLQSEAAYQCVAELGELGLVQFRDLNPDVSAFQRKFVNEVRRCDEMERKLRFLESEIKKAGIPL 79 (829)
T ss_pred CccccccccceeeEEEecHHHHHHHHHHhhccCeeEeeeCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 8999999999999999999999999999999999999999999999999999999999999995 99999887765333
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=99.17 E-value=4.2e-12 Score=107.42 Aligned_cols=48 Identities=29% Similarity=0.454 Sum_probs=0.0
Q ss_pred HHhhhhccceEEeecCCCccccccccccCcccchhhhhh-hhhhhcccc
Q psy15628 26 VSTLGEAGIVQFRDVSITLDTQFNRFQEERPMCVSSSRV-DWNTSHAFR 73 (90)
Q Consensus 26 v~eLG~lg~vqF~DlN~~v~~fqR~f~~eIrRcdEmeR~-~~l~~~~~~ 73 (90)
|++||++|+|||+|+|+++++|||+|++++||||||+|+ +++.++..+
T Consensus 1 V~eLgelG~VqF~Dln~~~~~fqr~f~~ev~r~de~erkL~~le~~I~k 49 (759)
T PF01496_consen 1 VNELGELGLVQFRDLNEDVSAFQRKFVNEVRRCDEMERKLRFLEEEIKK 49 (759)
T ss_dssp -------------------------------------------------
T ss_pred CchhhcCCcEEEEECccchhHHHHHhhhccccHHHHHHHHHHHHHHHHH
Confidence 789999999999999999999999999999999999995 788875443
No 3
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=96.74 E-value=0.00085 Score=56.45 Aligned_cols=62 Identities=16% Similarity=0.218 Sum_probs=48.5
Q ss_pred ccccCCceEEEEeccchHHHHHHhhhhccceEEeecCCCcc-ccccccccCcccchhhhh-hhhhhh
Q psy15628 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSITLD-TQFNRFQEERPMCVSSSR-VDWNTS 69 (90)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~v~-~fqR~f~~eIrRcdEmeR-~~~l~~ 69 (90)
++.++|..++++.|.+.+.+++++|.++|.||+.|+|.... ...+.+.+ +++++.+ .+++.+
T Consensus 1 m~i~kM~kv~l~~~~~~~~~~l~~L~~lg~vhi~~~~~~~~~~~~~~~~~---~~~~~~~~l~~L~~ 64 (646)
T PRK05771 1 LAPVRMKKVLIVTLKSYKDEVLEALHELGVVHIEDLKEELSNERLRKLRS---LLTKLSEALDKLRS 64 (646)
T ss_pred CCceeeEEEEEEEEHHHHHHHHHHHHhCCCEEEeecccccchhHHhHHHH---HHHHHHHHHHHHHH
Confidence 46799999999999999999999999999999999998875 44555544 4555555 244544
No 4
>COG1269 NtpI Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion]
Probab=90.24 E-value=0.31 Score=41.93 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=38.3
Q ss_pred ccccCCceEEEEeccchHHHHHHhhhhccceEEeecCCCcc
Q psy15628 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSITLD 45 (90)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~v~ 45 (90)
+|.+.|+.+.++.+.+..-+++.+|++.|++||.|++.++.
T Consensus 1 ~~~~~M~kv~i~~~~~~~~~vi~~L~~~g~~~~~d~~~~~~ 41 (660)
T COG1269 1 MRPEKMKKVSIIGLKSELDPVLAELHDFGLVHLEDLEEGEK 41 (660)
T ss_pred CchhhheeEEEEeehhhhhHHHHHHHHcCeEEeeccccccc
Confidence 57899999999999999999999999999999999998754
No 5
>PRK02302 hypothetical protein; Provisional
Probab=86.49 E-value=1.2 Score=29.97 Aligned_cols=53 Identities=15% Similarity=0.108 Sum_probs=40.9
Q ss_pred ccccCCceEEEEeccchHHHHHHhhhhccceEEeecCCCccccccccccCcccc
Q psy15628 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSITLDTQFNRFQEERPMC 58 (90)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~v~~fqR~f~~eIrRc 58 (90)
+=|..|.++-||+..+.|-+++..|.++..|.=++..+- +-..-.|...+-|-
T Consensus 31 Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~S~~-~~l~~~f~~~l~r~ 83 (89)
T PRK02302 31 YHSKRSRYLVLYVNKEDVEQKLEELSKLKFVKKVRPSAI-DEIDQNFVGNLYRD 83 (89)
T ss_pred EEeccccEEEEEECHHHHHHHHHHHhcCCCeeEEcccCc-hhccchhhhhhhcc
Confidence 348899999999999999999999999999988776553 33344455555543
No 6
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=82.09 E-value=2.5 Score=27.22 Aligned_cols=36 Identities=17% Similarity=0.264 Sum_probs=31.9
Q ss_pred ccccCCceEEEEeccchHHHHHHhhhhccceEEeec
Q psy15628 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDV 40 (90)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~Dl 40 (90)
+-|..|.++.||+..|.+-+++..|.++..|.=+..
T Consensus 25 Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~ 60 (71)
T PF09902_consen 25 YVSKKMKYVVLYVNEEDVEEIIEKLKKLKFVKKVEP 60 (71)
T ss_pred EEECCccEEEEEECHHHHHHHHHHHhcCCCeeEEec
Confidence 568999999999999999999999999987766553
No 7
>PRK02886 hypothetical protein; Provisional
Probab=75.55 E-value=5 Score=26.97 Aligned_cols=38 Identities=16% Similarity=0.193 Sum_probs=33.6
Q ss_pred ccccCCceEEEEeccchHHHHHHhhhhccceEEeecCC
Q psy15628 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSI 42 (90)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~ 42 (90)
+=|..|.++.||+..|.|-+++..|.++..|.=++..+
T Consensus 29 Y~Skr~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~S~ 66 (87)
T PRK02886 29 YVSKRLKYAVLYCDMEQVEDIMNKLSSLPFVKRVEPSY 66 (87)
T ss_pred EEeccccEEEEEECHHHHHHHHHHHhcCCCeeEEcccC
Confidence 34889999999999999999999999999888777554
No 8
>COG4471 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.54 E-value=9.4 Score=25.93 Aligned_cols=51 Identities=16% Similarity=0.101 Sum_probs=40.0
Q ss_pred cccCCceEEEEeccchHHHHHHhhhhccceEEeecCCCccccccccccCccc
Q psy15628 6 RSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSITLDTQFNRFQEERPM 57 (90)
Q Consensus 6 RSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~v~~fqR~f~~eIrR 57 (90)
-|.++.++.||++.+.--+++++|-.+-.|-=++...- +-.++.|.++.-+
T Consensus 31 ~Skk~kY~vlYvn~~~ve~~~~kl~~~kfVK~V~~s~~-~~Lk~~f~~~~~~ 81 (90)
T COG4471 31 VSKKSKYVVLYVNEQDVEQIVEKLSRLKFVKKVRVSHI-PYLKTEFEGNLHE 81 (90)
T ss_pred EecceeEEEEEECHHHHHHHHHHHhhceeeeecccccc-HHHHhHHhhchhH
Confidence 47889999999999999999999999988877776553 4455666664433
No 9
>COG3454 Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=54.23 E-value=20 Score=29.84 Aligned_cols=50 Identities=10% Similarity=0.059 Sum_probs=43.2
Q ss_pred CcccccCCceEEEEeccchHHHHHHhhhhccceEEeecCCCcccccccccc
Q psy15628 3 AMFRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSITLDTQFNRFQE 53 (90)
Q Consensus 3 slfRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~v~~fqR~f~~ 53 (90)
+.+|++---+...=++.....+.+.++.+.+.|+.+-|+.+ +|-||+|.+
T Consensus 125 g~lradHr~HlRcEvs~~~~l~~~e~~~~~p~v~LiSlMDH-~PGQrQf~~ 174 (377)
T COG3454 125 GRLRADHRLHLRCEVSHPATLPLFEDLMDHPRVKLISLMDH-TPGQRQFAN 174 (377)
T ss_pred cchhhccceeeeeecCChhHHHHHHHHhcCCCeeEEEecCC-CCCcchhhh
Confidence 46777777777777889999999999999999999999998 788998765
No 10
>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=45.97 E-value=22 Score=23.79 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=25.0
Q ss_pred ccCCceEEEEeccchHHHHHHhhhhccc
Q psy15628 7 SEEMALCQLFIQPEAAYSSVSTLGEAGI 34 (90)
Q Consensus 7 SE~M~l~qL~ip~E~A~~~v~eLG~lg~ 34 (90)
+++|.-++.++|.+..|+++++|-+.|-
T Consensus 61 ~~~w~AV~~vv~~~~v~~~~~~Lk~~GA 88 (100)
T TIGR03455 61 DEGWVAVHAVVDEKVVNELIDKLKAAGA 88 (100)
T ss_pred CCCeEEEEEEEcHHHHHHHHHHHHHcCC
Confidence 5778889999999999999999998873
No 11
>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=45.39 E-value=29 Score=22.19 Aligned_cols=27 Identities=15% Similarity=0.309 Sum_probs=24.0
Q ss_pred ccCCceEEEEeccchHHHHHHhhhhcc
Q psy15628 7 SEEMALCQLFIQPEAAYSSVSTLGEAG 33 (90)
Q Consensus 7 SE~M~l~qL~ip~E~A~~~v~eLG~lg 33 (90)
.++|.-++.+++.+..|+.+++|=+.|
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 357888999999999999999998887
No 12
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.31 E-value=24 Score=24.71 Aligned_cols=33 Identities=18% Similarity=0.186 Sum_probs=29.5
Q ss_pred cCCceEEEEeccchHHHHHHhhhhccceEEeec
Q psy15628 8 EEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDV 40 (90)
Q Consensus 8 E~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~Dl 40 (90)
+.|.-..+|+|.|-.-..-.+|++.|.-|.-|.
T Consensus 3 ~~~~K~~vyVP~~~~e~vr~aL~~aGag~iG~Y 35 (109)
T COG3323 3 EPLYKIEVYVPEEYVEQVRDALFEAGAGHIGNY 35 (109)
T ss_pred cceeEEEEEeCHHHHHHHHHHHHhcCCcceecc
Confidence 567888999999999999999999999888874
No 13
>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=41.41 E-value=7.9 Score=27.42 Aligned_cols=31 Identities=26% Similarity=0.245 Sum_probs=27.2
Q ss_pred HHHHHHhhhhccce--EEeecCCCccccccccc
Q psy15628 22 AYSSVSTLGEAGIV--QFRDVSITLDTQFNRFQ 52 (90)
Q Consensus 22 A~~~v~eLG~lg~v--qF~DlN~~v~~fqR~f~ 52 (90)
-|+.++.|.+.|.. ...|.+++...|+|.|.
T Consensus 22 e~~L~~~L~~~~~~~f~~l~~~~~~~LFk~hFL 54 (132)
T PF12339_consen 22 EHELISQLQEQGYILFPELDLDPPLDLFKRHFL 54 (132)
T ss_pred HHHHHHHHhhCcCccCCCCCCCcHHHHHHHHHH
Confidence 46789999999988 77889999999999985
No 14
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=38.19 E-value=41 Score=25.16 Aligned_cols=32 Identities=22% Similarity=0.212 Sum_probs=28.7
Q ss_pred eEEEEeccchHHHHHHhhhhccceEEeecCCC
Q psy15628 12 LCQLFIQPEAAYSSVSTLGEAGIVQFRDVSIT 43 (90)
Q Consensus 12 l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~ 43 (90)
...+-||++..-+.+++|+++|.|.-++.+.+
T Consensus 97 ~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~~~ 128 (262)
T PF14257_consen 97 SLTIRVPADKFDSFLDELSELGKVTSRNISSE 128 (262)
T ss_pred EEEEEECHHHHHHHHHHHhccCceeeeecccc
Confidence 67899999999999999999998888887664
No 15
>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=36.25 E-value=32 Score=20.37 Aligned_cols=25 Identities=24% Similarity=0.449 Sum_probs=22.1
Q ss_pred eccchHHHHHHhhhhccceEEeecC
Q psy15628 17 IQPEAAYSSVSTLGEAGIVQFRDVS 41 (90)
Q Consensus 17 ip~E~A~~~v~eLG~lg~vqF~DlN 41 (90)
+|+..++.+++.|-+.|+|+...-+
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 5778899999999999999998844
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=29.34 E-value=58 Score=20.44 Aligned_cols=26 Identities=15% Similarity=0.150 Sum_probs=23.8
Q ss_pred cCCceEEEEeccchHHHHHHhhhhcc
Q psy15628 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (90)
Q Consensus 8 E~M~l~qL~ip~E~A~~~v~eLG~lg 33 (90)
|++-.+++.+|.|..-.+++.|.+.+
T Consensus 4 EP~~~~~I~~p~~~~g~v~~~l~~r~ 29 (89)
T PF00679_consen 4 EPIMSVEISVPEEYLGKVISDLSKRR 29 (89)
T ss_dssp EEEEEEEEEEEGGGHHHHHHHHHHTT
T ss_pred CCEEEEEEEECHHHHHHHHHHhcccc
Confidence 67888999999999999999999985
No 17
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.79 E-value=36 Score=24.51 Aligned_cols=19 Identities=26% Similarity=0.384 Sum_probs=17.2
Q ss_pred EEEeccchHHHHHHhhhhc
Q psy15628 14 QLFIQPEAAYSSVSTLGEA 32 (90)
Q Consensus 14 qL~ip~E~A~~~v~eLG~l 32 (90)
++|+|.|.|.+.+..|+.+
T Consensus 111 HlFVp~e~a~~A~~~L~~l 129 (134)
T COG3602 111 HLFVPAERAKEALVVLQGL 129 (134)
T ss_pred eeeeeHHHHHHHHHHHHHH
Confidence 6999999999999988865
No 18
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=27.61 E-value=60 Score=19.23 Aligned_cols=24 Identities=25% Similarity=0.415 Sum_probs=20.7
Q ss_pred eccchHHHHHHhhhhcc--ceEEeec
Q psy15628 17 IQPEAAYSSVSTLGEAG--IVQFRDV 40 (90)
Q Consensus 17 ip~E~A~~~v~eLG~lg--~vqF~Dl 40 (90)
++.+...+.++++|+.| +|+..+-
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeLV~~~~~ 42 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWELVSIIPP 42 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEEEEEEcC
Confidence 45677788999999999 9999987
No 19
>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=25.66 E-value=90 Score=19.15 Aligned_cols=26 Identities=15% Similarity=0.183 Sum_probs=23.4
Q ss_pred cCCceEEEEeccchHHHHHHhhhhcc
Q psy15628 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (90)
Q Consensus 8 E~M~l~qL~ip~E~A~~~v~eLG~lg 33 (90)
|+|-.+.+.+|.|..-.+++.|.+..
T Consensus 1 EPi~~v~I~~P~~~~g~V~~~l~~rr 26 (79)
T cd03710 1 EPIEELTIDVPEEYSGAVIEKLGKRK 26 (79)
T ss_pred CCEEEEEEEeCchhhHHHHHHHHhCC
Confidence 67888999999999999999998874
No 20
>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=23.72 E-value=79 Score=19.09 Aligned_cols=25 Identities=12% Similarity=0.138 Sum_probs=22.6
Q ss_pred cCCceEEEEeccchHHHHHHhhhhc
Q psy15628 8 EEMALCQLFIQPEAAYSSVSTLGEA 32 (90)
Q Consensus 8 E~M~l~qL~ip~E~A~~~v~eLG~l 32 (90)
|+|-.+.+.+|.+..-.+++.|.+.
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~r 25 (78)
T cd03713 1 EPIMKVEVTVPEEYMGDVIGDLSSR 25 (78)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHHc
Confidence 7888999999999999999999875
No 21
>cd01306 PhnM PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage of alkylphosphonates, which are utilized as sole phosphorus sources by many bacteria.
Probab=23.41 E-value=1.4e+02 Score=23.70 Aligned_cols=48 Identities=10% Similarity=0.104 Sum_probs=36.4
Q ss_pred cccccCCceEEEEeccchHHHHHHhhhhccceEEeecCCCccccccccc
Q psy15628 4 MFRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDVSITLDTQFNRFQ 52 (90)
Q Consensus 4 lfRSE~M~l~qL~ip~E~A~~~v~eLG~lg~vqF~DlN~~v~~fqR~f~ 52 (90)
.+|.+---....=++...+.+.+..+-+.+.|+++-+|.+ +|-||+|.
T Consensus 79 ~~~~d~~~hlR~E~~~~~~~~~~~~~~~~~~v~lvs~~dH-~pg~~q~~ 126 (325)
T cd01306 79 VLRADHRLHLRCELADPAVLPELESLMADPRVHLVSLMDH-TPGQRQFR 126 (325)
T ss_pred cchhhcceEEEEeecCccHHHHHHHHhcCCCcCEEEEeCC-CCcccccc
Confidence 4445544455555678889999999999999999999988 57888654
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=23.37 E-value=86 Score=19.39 Aligned_cols=25 Identities=12% Similarity=0.044 Sum_probs=23.0
Q ss_pred cCCceEEEEeccchHHHHHHhhhhc
Q psy15628 8 EEMALCQLFIQPEAAYSSVSTLGEA 32 (90)
Q Consensus 8 E~M~l~qL~ip~E~A~~~v~eLG~l 32 (90)
|++-.+.+.+|.|..-++++.|...
T Consensus 1 EPi~~v~i~vP~e~~G~V~~~l~~r 25 (80)
T cd03709 1 EPFVKATIITPSEYLGAIMELCQER 25 (80)
T ss_pred CCEEEEEEEeCHHhhHHHHHHHHHh
Confidence 6788899999999999999999986
No 23
>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=22.05 E-value=90 Score=18.82 Aligned_cols=26 Identities=12% Similarity=0.147 Sum_probs=23.0
Q ss_pred cCCceEEEEeccchHHHHHHhhhhcc
Q psy15628 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (90)
Q Consensus 8 E~M~l~qL~ip~E~A~~~v~eLG~lg 33 (90)
|+|-.+.+.+|.+..-.+++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (79)
T cd01514 1 EPIMKVEITVPEEYLGAVIGDLSKRR 26 (79)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHhcC
Confidence 78899999999999999999997763
No 24
>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=21.55 E-value=93 Score=18.93 Aligned_cols=26 Identities=19% Similarity=0.151 Sum_probs=23.3
Q ss_pred cCCceEEEEeccchHHHHHHhhhhcc
Q psy15628 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (90)
Q Consensus 8 E~M~l~qL~ip~E~A~~~v~eLG~lg 33 (90)
|+|-.+.+.+|.|..-.+++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~V~~~l~~rr 26 (80)
T cd04096 1 EPIYLVEIQCPEDALGKVYSVLSKRR 26 (80)
T ss_pred CCEEEEEEEEcHHHhhHHHHhhhhCe
Confidence 67888999999999999999998874
No 25
>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=21.23 E-value=82 Score=21.31 Aligned_cols=23 Identities=22% Similarity=0.417 Sum_probs=17.2
Q ss_pred eccchHHHHHHhhhhccc-eEEee
Q psy15628 17 IQPEAAYSSVSTLGEAGI-VQFRD 39 (90)
Q Consensus 17 ip~E~A~~~v~eLG~lg~-vqF~D 39 (90)
+|+..+.++++.|.++|+ +.|+.
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 688899999999999994 66775
No 26
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=20.94 E-value=89 Score=23.75 Aligned_cols=27 Identities=11% Similarity=0.224 Sum_probs=24.5
Q ss_pred ccCCceEEEEeccchHHHHHHhhhhcc
Q psy15628 7 SEEMALCQLFIQPEAAYSSVSTLGEAG 33 (90)
Q Consensus 7 SE~M~l~qL~ip~E~A~~~v~eLG~lg 33 (90)
.++|.-++.++|.+..|+++++|-+.|
T Consensus 247 ~~~~~av~~~~~~~~~~~~~~~l~~~g 273 (287)
T PRK00489 247 DEGWVAVHAVVPEDLVWELMDKLKALG 273 (287)
T ss_pred CCCeEEEEEEECHHHHHHHHHHHHHcC
Confidence 467888999999999999999999887
No 27
>PF03235 DUF262: Protein of unknown function DUF262; InterPro: IPR004919 This entry is found in prokaryotic proteins of unknown function.
Probab=20.64 E-value=40 Score=23.21 Aligned_cols=15 Identities=0% Similarity=-0.026 Sum_probs=11.0
Q ss_pred CccccccccccCccc
Q psy15628 43 TLDTQFNRFQEERPM 57 (90)
Q Consensus 43 ~v~~fqR~f~~eIrR 57 (90)
.+|.|||+|+=.-+.
T Consensus 13 ~iP~yQR~yvW~~~~ 27 (221)
T PF03235_consen 13 VIPDYQRDYVWDEEQ 27 (221)
T ss_pred cCCCCCCCCccCHHH
Confidence 578999999854443
Done!