Query psy653
Match_columns 91
No_of_seqs 102 out of 275
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 20:25:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy653.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/653hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2189|consensus 100.0 3.2E-31 7E-36 227.4 5.3 75 1-75 1-79 (829)
2 PF01496 V_ATPase_I: V-type AT 99.0 5.4E-11 1.2E-15 101.0 0.0 47 26-72 1-50 (759)
3 PRK05771 V-type ATP synthase s 97.6 0.00011 2.3E-09 62.0 5.4 67 5-71 1-68 (646)
4 COG1269 NtpI Archaeal/vacuolar 90.5 0.3 6.4E-06 42.2 3.5 43 5-47 1-43 (660)
5 PF09902 DUF2129: Uncharacteri 84.3 1.8 3.8E-05 28.0 3.5 36 5-40 25-60 (71)
6 PRK02302 hypothetical protein; 83.1 2.4 5.1E-05 28.7 3.9 51 5-56 31-81 (89)
7 PRK02886 hypothetical protein; 77.9 3.8 8.3E-05 27.6 3.6 38 5-42 29-66 (87)
8 PF14257 DUF4349: Domain of un 63.5 24 0.00051 26.5 5.5 31 12-42 97-127 (262)
9 COG4471 Uncharacterized protei 49.3 21 0.00045 24.4 2.8 52 5-57 30-81 (90)
10 KOG1154|consensus 46.5 16 0.00035 29.3 2.2 68 20-90 132-200 (285)
11 PF08029 HisG_C: HisG, C-termi 46.4 30 0.00066 22.2 3.1 26 8-33 38-63 (75)
12 TIGR03455 HisG_C-term ATP phos 45.5 22 0.00048 23.8 2.5 28 7-34 61-88 (100)
13 KOG3314|consensus 44.9 21 0.00046 27.2 2.5 45 46-91 15-67 (194)
14 COG3323 Uncharacterized protei 43.2 27 0.0006 24.5 2.7 34 8-41 3-36 (109)
15 PF01978 TrmB: Sugar-specific 40.9 20 0.00044 21.3 1.6 25 17-41 34-58 (68)
16 PF03618 Kinase-PPPase: Kinase 40.2 14 0.0003 29.0 0.9 51 15-67 1-51 (255)
17 PF12339 DNAJ_related: DNA-J r 37.3 8.8 0.00019 27.3 -0.5 31 22-52 22-54 (132)
18 PF00679 EFG_C: Elongation fac 36.6 42 0.00092 21.2 2.6 33 8-41 4-36 (89)
19 COG3454 Metal-dependent hydrol 31.2 1.4E+02 0.003 25.1 5.4 50 3-53 125-174 (377)
20 cd03710 BipA_TypA_C BipA_TypA_ 30.5 62 0.0013 20.0 2.6 26 8-33 1-26 (79)
21 TIGR00341 conserved hypothetic 29.1 1.3E+02 0.0028 24.5 4.8 60 9-68 2-64 (325)
22 COG3602 Uncharacterized protei 29.0 37 0.00081 24.5 1.5 19 14-32 111-129 (134)
23 PF11684 DUF3280: Protein of u 27.8 1.1E+02 0.0023 21.9 3.7 52 35-88 9-71 (140)
24 PF13783 DUF4177: Domain of un 26.6 66 0.0014 19.1 2.2 24 17-40 17-42 (61)
25 cd04096 eEF2_snRNP_like_C eEF2 26.4 64 0.0014 19.7 2.2 27 8-34 1-27 (80)
26 cd03709 lepA_C lepA_C: This fa 26.3 69 0.0015 19.9 2.3 26 8-33 1-26 (80)
27 cd03713 EFG_mtEFG_C EFG_mtEFG_ 24.8 71 0.0015 19.4 2.1 26 8-33 1-26 (78)
28 cd01514 Elongation_Factor_C El 24.5 75 0.0016 19.3 2.2 26 8-33 1-26 (79)
29 cd04097 mtEFG1_C mtEFG1_C: C-t 23.5 85 0.0018 19.2 2.3 26 8-33 1-26 (78)
30 cd03711 Tet_C Tet_C: C-terminu 22.1 91 0.002 19.1 2.2 26 8-33 1-26 (78)
31 PF10126 Nit_Regul_Hom: Unchar 22.1 1.2E+02 0.0027 21.3 3.1 26 12-37 6-31 (110)
32 PRK05339 PEP synthetase regula 21.9 88 0.0019 24.8 2.6 55 10-66 2-56 (269)
33 PF06305 DUF1049: Protein of u 20.8 98 0.0021 18.3 2.1 24 49-72 44-67 (68)
34 COG4003 Uncharacterized protei 20.8 60 0.0013 22.3 1.3 17 52-68 38-60 (98)
35 PF04567 RNA_pol_Rpb2_5: RNA p 20.7 1.1E+02 0.0024 17.8 2.3 21 27-47 2-22 (48)
36 smart00838 EFG_C Elongation fa 20.2 1.1E+02 0.0023 19.0 2.3 34 8-42 3-36 (85)
37 PF03235 DUF262: Protein of un 20.1 72 0.0016 22.0 1.6 22 42-63 12-33 (221)
No 1
>KOG2189|consensus
Probab=99.97 E-value=3.2e-31 Score=227.38 Aligned_cols=75 Identities=53% Similarity=0.816 Sum_probs=71.9
Q ss_pred CCCCccccCCceEEEEeecchHHHHHHHhhcccceeeeeCCCCCCCCCcchhhHHHHH---HHHHhhhhhhhhhh-hcc
Q psy653 1 MGSLFRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDRDIPLGYLHFDRINSERLV---SSRVGFSDSGVIRV-VPC 75 (91)
Q Consensus 1 mgslfRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~~v~~FqR~Fv~eIrRc---Er~l~~l~~ei~~~-~~~ 75 (91)
||||||||+|+|+|||+|+|+||+||++||++|+|||+|||++|++|||+|||||||| |||||||++||.+. +|.
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 8999999999999999999999999999999999999999999999999999999999 69999999999994 443
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=99.01 E-value=5.4e-11 Score=101.04 Aligned_cols=47 Identities=34% Similarity=0.545 Sum_probs=0.0
Q ss_pred HHHhhcccceeeeeCCCCCCCCCcchhhHHHHH---HHHHhhhhhhhhhh
Q psy653 26 VSELGELGLVQFRDRDIPLGYLHFDRINSERLV---SSRVGFSDSGVIRV 72 (91)
Q Consensus 26 V~eLG~LglvqF~DLN~~v~~FqR~Fv~eIrRc---Er~l~~l~~ei~~~ 72 (91)
|++||++|+|||+|+|+++++|||+|++++||| ||+|+++++++.++
T Consensus 1 V~eLgelG~VqF~Dln~~~~~fqr~f~~ev~r~de~erkL~~le~~I~k~ 50 (759)
T PF01496_consen 1 VNELGELGLVQFRDLNEDVSAFQRKFVNEVRRCDEMERKLRFLEEEIKKL 50 (759)
T ss_dssp --------------------------------------------------
T ss_pred CchhhcCCcEEEEECccchhHHHHHhhhccccHHHHHHHHHHHHHHHHHh
Confidence 689999999999999999999999999999999 59999999999985
No 3
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=97.60 E-value=0.00011 Score=61.96 Aligned_cols=67 Identities=15% Similarity=0.031 Sum_probs=58.3
Q ss_pred ccccCCceEEEEeecchHHHHHHHhhcccceeeeeCCCCCC-CCCcchhhHHHHHHHHHhhhhhhhhh
Q psy653 5 FRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDRDIPLG-YLHFDRINSERLVSSRVGFSDSGVIR 71 (91)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~~v~-~FqR~Fv~eIrRcEr~l~~l~~ei~~ 71 (91)
++.++|..++++.|.+.+.+++++|.++|.+|+.|++...+ ...+.+.+...++++.+++|++...+
T Consensus 1 m~i~kM~kv~l~~~~~~~~~~l~~L~~lg~vhi~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~~~ 68 (646)
T PRK05771 1 LAPVRMKKVLIVTLKSYKDEVLEALHELGVVHIEDLKEELSNERLRKLRSLLTKLSEALDKLRSYLPK 68 (646)
T ss_pred CCceeeEEEEEEEEHHHHHHHHHHHHhCCCEEEeecccccchhHHhHHHHHHHHHHHHHHHHHHhccc
Confidence 36789999999999999999999999999999999998875 55778888888888888888766554
No 4
>COG1269 NtpI Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion]
Probab=90.46 E-value=0.3 Score=42.17 Aligned_cols=43 Identities=23% Similarity=0.283 Sum_probs=39.0
Q ss_pred ccccCCceEEEEeecchHHHHHHHhhcccceeeeeCCCCCCCC
Q psy653 5 FRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDRDIPLGYL 47 (91)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~~v~~F 47 (91)
+|-+.|..+.++.+++..-+++.+|++.|++|+.|++.++..+
T Consensus 1 ~~~~~M~kv~i~~~~~~~~~vi~~L~~~g~~~~~d~~~~~~~~ 43 (660)
T COG1269 1 MRPEKMKKVSIIGLKSELDPVLAELHDFGLVHLEDLEEGEKGL 43 (660)
T ss_pred CchhhheeEEEEeehhhhhHHHHHHHHcCeEEeeccccccccc
Confidence 4789999999999999999999999999999999999776543
No 5
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=84.28 E-value=1.8 Score=28.05 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=32.4
Q ss_pred ccccCCceEEEEeecchHHHHHHHhhcccceeeeeC
Q psy653 5 FRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDR 40 (91)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DL 40 (91)
+-|..|.++.||+..|.+-+++++|.++..|.-+..
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 568999999999999999999999999998876654
No 6
>PRK02302 hypothetical protein; Provisional
Probab=83.14 E-value=2.4 Score=28.73 Aligned_cols=51 Identities=14% Similarity=0.148 Sum_probs=39.0
Q ss_pred ccccCCceEEEEeecchHHHHHHHhhcccceeeeeCCCCCCCCCcchhhHHH
Q psy653 5 FRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDRDIPLGYLHFDRINSER 56 (91)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~~v~~FqR~Fv~eIr 56 (91)
+=|..|.++-||+..|.|-+++.+|.++..|.-++..+- +-..-.|...+-
T Consensus 31 Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~S~~-~~l~~~f~~~l~ 81 (89)
T PRK02302 31 YHSKRSRYLVLYVNKEDVEQKLEELSKLKFVKKVRPSAI-DEIDQNFVGNLY 81 (89)
T ss_pred EEeccccEEEEEECHHHHHHHHHHHhcCCCeeEEcccCc-hhccchhhhhhh
Confidence 458899999999999999999999999999988775542 222444544443
No 7
>PRK02886 hypothetical protein; Provisional
Probab=77.95 E-value=3.8 Score=27.62 Aligned_cols=38 Identities=16% Similarity=0.254 Sum_probs=33.7
Q ss_pred ccccCCceEEEEeecchHHHHHHHhhcccceeeeeCCC
Q psy653 5 FRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDRDI 42 (91)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~ 42 (91)
+=|..|.++-||+..|.|-+++.+|.++..|.-++..+
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 45889999999999999999999999999988777543
No 8
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=63.51 E-value=24 Score=26.53 Aligned_cols=31 Identities=23% Similarity=0.243 Sum_probs=27.6
Q ss_pred eEEEEeecchHHHHHHHhhcccceeeeeCCC
Q psy653 12 LCQLFLQSEAAYACVSELGELGLVQFRDRDI 42 (91)
Q Consensus 12 l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~ 42 (91)
...+-||.+..-+.+++|+++|.|.-++.+.
T Consensus 97 ~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~~ 127 (262)
T PF14257_consen 97 SLTIRVPADKFDSFLDELSELGKVTSRNISS 127 (262)
T ss_pred EEEEEECHHHHHHHHHHHhccCceeeeeccc
Confidence 6789999999999999999999888777764
No 9
>COG4471 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.34 E-value=21 Score=24.39 Aligned_cols=52 Identities=15% Similarity=0.149 Sum_probs=39.7
Q ss_pred ccccCCceEEEEeecchHHHHHHHhhcccceeeeeCCCCCCCCCcchhhHHHH
Q psy653 5 FRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDRDIPLGYLHFDRINSERL 57 (91)
Q Consensus 5 fRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~~v~~FqR~Fv~eIrR 57 (91)
+-|.++.++.||++.+.--+++++|..+-.|--++...- +-.++.|.++.-+
T Consensus 30 Y~Skk~kY~vlYvn~~~ve~~~~kl~~~kfVK~V~~s~~-~~Lk~~f~~~~~~ 81 (90)
T COG4471 30 YVSKKSKYVVLYVNEQDVEQIVEKLSRLKFVKKVRVSHI-PYLKTEFEGNLHE 81 (90)
T ss_pred EEecceeEEEEEECHHHHHHHHHHHhhceeeeecccccc-HHHHhHHhhchhH
Confidence 348889999999999999999999999998877775542 2235666665444
No 10
>KOG1154|consensus
Probab=46.45 E-value=16 Score=29.35 Aligned_cols=68 Identities=16% Similarity=0.163 Sum_probs=48.6
Q ss_pred chHHHHHHHhhcccceeeeeCCCCCCCCCcchhhHHHHHHHHHhhhhhhhhh-hhcccchhhhhhccCCCCC
Q psy653 20 EAAYACVSELGELGLVQFRDRDIPLGYLHFDRINSERLVSSRVGFSDSGVIR-VVPCFSRLECLATCNPCPD 90 (91)
Q Consensus 20 E~A~~~V~eLG~LglvqF~DLN~~v~~FqR~Fv~eIrRcEr~l~~l~~ei~~-~~~~~~~~~~~~~~~~~~~ 90 (91)
.++.++++||=.+|.|-.++-|.-+++=.-+|-.. .-=+..-.-+..+|.+ +.=-+|..+||-| || ||
T Consensus 132 ~Nl~~Ti~eLL~m~viPIvNeNDavs~~~~~~~D~-~dNDsLsA~laaei~ADlLilLsDVdglYt-~P-Pd 200 (285)
T KOG1154|consen 132 KNLQNTISELLSMNVIPIVNENDAVSPREIPFGDS-SDNDSLAAILAAEIKADLLILLSDVDGLYT-GP-PD 200 (285)
T ss_pred HHHHHHHHHHHhCCceeeecCCCccCCcccccCCC-CcccHHHHHHHHHhccCEEEEEeccccccc-CC-CC
Confidence 35778999999999999999999887655444321 1112444455666666 4557899999999 88 65
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=46.39 E-value=30 Score=22.20 Aligned_cols=26 Identities=12% Similarity=0.272 Sum_probs=23.5
Q ss_pred cCCceEEEEeecchHHHHHHHhhccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELG 33 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lg 33 (91)
++|--++.+++.+..|+.|.+|=+.|
T Consensus 38 ~~w~AV~~vV~~~~~~~~~~~Lk~~G 63 (75)
T PF08029_consen 38 EDWVAVHAVVPEKQVWDLMDKLKAAG 63 (75)
T ss_dssp TTEEEEEEEEECCCHHHHHHHHHCTT
T ss_pred CCEEEEEEEecHHHHHHHHHHHHHcC
Confidence 57788999999999999999998877
No 12
>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=45.54 E-value=22 Score=23.84 Aligned_cols=28 Identities=11% Similarity=0.176 Sum_probs=24.8
Q ss_pred ccCCceEEEEeecchHHHHHHHhhcccc
Q psy653 7 SEEMALCQLFLQSEAAYACVSELGELGL 34 (91)
Q Consensus 7 SE~M~l~qL~ip~E~A~~~V~eLG~Lgl 34 (91)
+++|.-++..+|++..|+++.+|-+.|-
T Consensus 61 ~~~w~AV~~vv~~~~v~~~~~~Lk~~GA 88 (100)
T TIGR03455 61 DEGWVAVHAVVDEKVVNELIDKLKAAGA 88 (100)
T ss_pred CCCeEEEEEEEcHHHHHHHHHHHHHcCC
Confidence 5678889999999999999999988883
No 13
>KOG3314|consensus
Probab=44.92 E-value=21 Score=27.25 Aligned_cols=45 Identities=13% Similarity=0.163 Sum_probs=30.6
Q ss_pred CCCcchhhHHHHHHHHHhhhhh--hhhh-hhcccchhhhh-----hccCCCCCC
Q psy653 46 YLHFDRINSERLVSSRVGFSDS--GVIR-VVPCFSRLECL-----ATCNPCPDW 91 (91)
Q Consensus 46 ~FqR~Fv~eIrRcEr~l~~l~~--ei~~-~~~~~~~~~~~-----~~~~~~~~~ 91 (91)
|-+| +.++++.|++.++-+-+ -+.+ +..++.++.|- -.|.+||+|
T Consensus 15 pqar-~~ks~~kCq~~~~~~l~~nP~Vkfl~~am~k~~c~~~d~~isc~~C~~~ 67 (194)
T KOG3314|consen 15 PQAR-RGKSIDKCQDMIRRSLRTNPIVKFLMEAMEKSGCRVGDNFISCVVCTGP 67 (194)
T ss_pred chhh-hhhHHHHHHHHHHHHhccCcHHHHHHHHHHHcCCCccCCceEEeeCCCC
Confidence 3355 89999999755544433 2333 57777888775 358999987
No 14
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.23 E-value=27 Score=24.50 Aligned_cols=34 Identities=18% Similarity=0.175 Sum_probs=29.7
Q ss_pred cCCceEEEEeecchHHHHHHHhhcccceeeeeCC
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELGLVQFRDRD 41 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN 41 (91)
++|.-..+|||.|-.-.+-.+|++.|.-|.-|..
T Consensus 3 ~~~~K~~vyVP~~~~e~vr~aL~~aGag~iG~Y~ 36 (109)
T COG3323 3 EPLYKIEVYVPEEYVEQVRDALFEAGAGHIGNYD 36 (109)
T ss_pred cceeEEEEEeCHHHHHHHHHHHHhcCCcceeccc
Confidence 4677889999999999999999999998888743
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=40.89 E-value=20 Score=21.35 Aligned_cols=25 Identities=24% Similarity=0.434 Sum_probs=21.9
Q ss_pred eecchHHHHHHHhhcccceeeeeCC
Q psy653 17 LQSEAAYACVSELGELGLVQFRDRD 41 (91)
Q Consensus 17 ip~E~A~~~V~eLG~LglvqF~DLN 41 (91)
+|+..++..++.|-+.|+|+...-+
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 5778899999999999999988744
No 16
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=40.23 E-value=14 Score=28.96 Aligned_cols=51 Identities=16% Similarity=0.271 Sum_probs=39.1
Q ss_pred EEeecchHHHHHHHhhcccceeeeeCCCCCCCCCcchhhHHHHHHHHHhhhhh
Q psy653 15 LFLQSEAAYACVSELGELGLVQFRDRDIPLGYLHFDRINSERLVSSRVGFSDS 67 (91)
Q Consensus 15 L~ip~E~A~~~V~eLG~LglvqF~DLN~~v~~FqR~Fv~eIrRcEr~l~~l~~ 67 (91)
+|+-+|+.-++...+|+-.+.||-|.+-++ ...+|++...+.++.+.-.++
T Consensus 1 IyiVSDstGeTAe~v~~A~l~QF~~~~~~~--~~~p~I~~~~~~~~il~~i~~ 51 (255)
T PF03618_consen 1 IYIVSDSTGETAETVARAALAQFPDVEFEI--HRFPFIRTEEQLDEILEEIKE 51 (255)
T ss_pred CEEEecCchHHHHHHHHHHHHhCCCCceEE--EECCCcCCHHHHHHHHHHHhc
Confidence 477889999999999999999998877543 344788877777665555544
No 17
>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=37.32 E-value=8.8 Score=27.28 Aligned_cols=31 Identities=26% Similarity=0.296 Sum_probs=26.4
Q ss_pred HHHHHHHhhcccce--eeeeCCCCCCCCCcchh
Q psy653 22 AYACVSELGELGLV--QFRDRDIPLGYLHFDRI 52 (91)
Q Consensus 22 A~~~V~eLG~Lglv--qF~DLN~~v~~FqR~Fv 52 (91)
-++.+++|++.|.. ...|.+++..-|+|+|.
T Consensus 22 e~~L~~~L~~~~~~~f~~l~~~~~~~LFk~hFL 54 (132)
T PF12339_consen 22 EHELISQLQEQGYILFPELDLDPPLDLFKRHFL 54 (132)
T ss_pred HHHHHHHHhhCcCccCCCCCCCcHHHHHHHHHH
Confidence 46889999999998 66777888888999986
No 18
>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=36.58 E-value=42 Score=21.16 Aligned_cols=33 Identities=15% Similarity=0.124 Sum_probs=26.3
Q ss_pred cCCceEEEEeecchHHHHHHHhhcccceeeeeCC
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELGLVQFRDRD 41 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN 41 (91)
|++-.+++.+|.|..-.+++.|++.+- ++.+.+
T Consensus 4 EP~~~~~I~~p~~~~g~v~~~l~~r~g-~i~~~~ 36 (89)
T PF00679_consen 4 EPIMSVEISVPEEYLGKVISDLSKRRG-EILSMD 36 (89)
T ss_dssp EEEEEEEEEEEGGGHHHHHHHHHHTT--EEEEEE
T ss_pred CCEEEEEEEECHHHHHHHHHHhccccc-EEEech
Confidence 678889999999999999999999863 344433
No 19
>COG3454 Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=31.23 E-value=1.4e+02 Score=25.10 Aligned_cols=50 Identities=10% Similarity=-0.081 Sum_probs=40.5
Q ss_pred CCccccCCceEEEEeecchHHHHHHHhhcccceeeeeCCCCCCCCCcchhh
Q psy653 3 SLFRSEEMALCQLFLQSEAAYACVSELGELGLVQFRDRDIPLGYLHFDRIN 53 (91)
Q Consensus 3 slfRSE~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~~v~~FqR~Fv~ 53 (91)
+.+|++---..+.=++.....+.+.++.+.+.|+.+-|+.+ +|=||+|.+
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 35666665666666788899999999999999999999988 467888765
No 20
>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=30.49 E-value=62 Score=19.97 Aligned_cols=26 Identities=19% Similarity=0.198 Sum_probs=23.6
Q ss_pred cCCceEEEEeecchHHHHHHHhhccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELG 33 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lg 33 (91)
|+|-.+.+.+|.|..-.+++.|.+..
T Consensus 1 EPi~~v~I~~P~~~~g~V~~~l~~rr 26 (79)
T cd03710 1 EPIEELTIDVPEEYSGAVIEKLGKRK 26 (79)
T ss_pred CCEEEEEEEeCchhhHHHHHHHHhCC
Confidence 67888999999999999999998875
No 21
>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=29.12 E-value=1.3e+02 Score=24.50 Aligned_cols=60 Identities=3% Similarity=-0.175 Sum_probs=32.7
Q ss_pred CCceEEEEeecchHHHHHHHh---hcccceeeeeCCCCCCCCCcchhhHHHHHHHHHhhhhhh
Q psy653 9 EMALCQLFLQSEAAYACVSEL---GELGLVQFRDRDIPLGYLHFDRINSERLVSSRVGFSDSG 68 (91)
Q Consensus 9 ~M~l~qL~ip~E~A~~~V~eL---G~LglvqF~DLN~~v~~FqR~Fv~eIrRcEr~l~~l~~e 68 (91)
+|.++|+++|++.--.+...| ++.|.-.+...+.+.....=.|...=..-|..|+-|++-
T Consensus 2 ~mRliev~iP~~~~~~v~~~l~~~~~~~i~~~~~~~~~~~~~~i~~~v~~~~~e~vld~L~~l 64 (325)
T TIGR00341 2 RHRTNDCLIPKEGVVMRKEIVRGEDLEEIAIELGDKTFIYDDRIELYVQDSDTEKIVSRLKDK 64 (325)
T ss_pred CceEEEEEeccchHHHHHHHHhccCcccceEEeccCCCCcceEEEEEcChhhHHHHHHHHHHc
Confidence 588999999987666555555 555555665554332221112222222346555555554
No 22
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.95 E-value=37 Score=24.55 Aligned_cols=19 Identities=32% Similarity=0.419 Sum_probs=17.1
Q ss_pred EEEeecchHHHHHHHhhcc
Q psy653 14 QLFLQSEAAYACVSELGEL 32 (91)
Q Consensus 14 qL~ip~E~A~~~V~eLG~L 32 (91)
++|+|.|.|.+.+..|+.+
T Consensus 111 HlFVp~e~a~~A~~~L~~l 129 (134)
T COG3602 111 HLFVPAERAKEALVVLQGL 129 (134)
T ss_pred eeeeeHHHHHHHHHHHHHH
Confidence 6999999999999988865
No 23
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=27.78 E-value=1.1e+02 Score=21.90 Aligned_cols=52 Identities=12% Similarity=0.130 Sum_probs=30.1
Q ss_pred eeeeeCCCCCCCCCcchhhHHHHHHHHHhhhhhhhhh-----h------hcccchhhhhhccCCC
Q psy653 35 VQFRDRDIPLGYLHFDRINSERLVSSRVGFSDSGVIR-----V------VPCFSRLECLATCNPC 88 (91)
Q Consensus 35 vqF~DLN~~v~~FqR~Fv~eIrRcEr~l~~l~~ei~~-----~------~~~~~~~~~~~~~~~~ 88 (91)
++|.|.+.+-..=+ =-.|.+|+...=..|++.+.+ + -....+...+..||-|
T Consensus 9 fel~D~s~~~~~~~--~~~e~~RL~~~~~~lr~~L~~~G~y~vVd~~~~~a~i~~~~~l~~C~gC 71 (140)
T PF11684_consen 9 FELIDTSAEPAPGQ--TPAEAARLAALTDQLREALAESGRYRVVDLAPVAAEIAAAQNLRKCNGC 71 (140)
T ss_pred eEEecCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHhcCCeEEecCchhHHHhhccCCcccCCCH
Confidence 57888887744311 135666765444444444444 2 2334456778889888
No 24
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=26.63 E-value=66 Score=19.12 Aligned_cols=24 Identities=25% Similarity=0.347 Sum_probs=20.5
Q ss_pred eecchHHHHHHHhhccc--ceeeeeC
Q psy653 17 LQSEAAYACVSELGELG--LVQFRDR 40 (91)
Q Consensus 17 ip~E~A~~~V~eLG~Lg--lvqF~DL 40 (91)
++.+..-+.++++|+.| +|+..+-
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeLV~~~~~ 42 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWELVSIIPP 42 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEEEEEEcC
Confidence 45677788999999999 8999887
No 25
>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=26.36 E-value=64 Score=19.72 Aligned_cols=27 Identities=19% Similarity=0.058 Sum_probs=23.9
Q ss_pred cCCceEEEEeecchHHHHHHHhhcccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELGL 34 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lgl 34 (91)
|+|-.+.+.+|.|..-.+++.|++..-
T Consensus 1 EPi~~~~I~~p~~~~g~V~~~l~~rrg 27 (80)
T cd04096 1 EPIYLVEIQCPEDALGKVYSVLSKRRG 27 (80)
T ss_pred CCEEEEEEEEcHHHhhHHHHhhhhCee
Confidence 688899999999999999999988753
No 26
>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=26.33 E-value=69 Score=19.90 Aligned_cols=26 Identities=19% Similarity=0.029 Sum_probs=23.5
Q ss_pred cCCceEEEEeecchHHHHHHHhhccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELG 33 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lg 33 (91)
|+|-.+.+.+|.|..-++++.|....
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 67888999999999999999999864
No 27
>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=24.82 E-value=71 Score=19.36 Aligned_cols=26 Identities=12% Similarity=0.129 Sum_probs=23.0
Q ss_pred cCCceEEEEeecchHHHHHHHhhccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELG 33 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lg 33 (91)
|+|-.+.+.+|.+..-.+++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (78)
T cd03713 1 EPIMKVEVTVPEEYMGDVIGDLSSRR 26 (78)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHHcC
Confidence 68889999999999999999997753
No 28
>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=24.52 E-value=75 Score=19.25 Aligned_cols=26 Identities=15% Similarity=0.183 Sum_probs=23.1
Q ss_pred cCCceEEEEeecchHHHHHHHhhccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELG 33 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lg 33 (91)
|+|-.+.+.+|.+..-.+++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (79)
T cd01514 1 EPIMKVEITVPEEYLGAVIGDLSKRR 26 (79)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHhcC
Confidence 78889999999999999999997764
No 29
>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=23.53 E-value=85 Score=19.18 Aligned_cols=26 Identities=12% Similarity=0.054 Sum_probs=23.2
Q ss_pred cCCceEEEEeecchHHHHHHHhhccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELG 33 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lg 33 (91)
|+|-.+.+.+|.|..-.+++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (78)
T cd04097 1 EPIMKVEVTAPTEFQGNVIGLLNKRK 26 (78)
T ss_pred CCEEEEEEEecHHHHHHHHHHHHHCC
Confidence 67888999999999999999998864
No 30
>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=22.13 E-value=91 Score=19.05 Aligned_cols=26 Identities=23% Similarity=0.305 Sum_probs=23.4
Q ss_pred cCCceEEEEeecchHHHHHHHhhccc
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELG 33 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~Lg 33 (91)
|+|-.+.+.+|.|..-.+++.|++..
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 31
>PF10126 Nit_Regul_Hom: Uncharacterized protein, homolog of nitrogen regulatory protein PII; InterPro: IPR019296 This family consists of various hypothetical archaeal proteins. It includes a putative nitrogen regulatory protein PII homolog.
Probab=22.11 E-value=1.2e+02 Score=21.30 Aligned_cols=26 Identities=35% Similarity=0.519 Sum_probs=22.6
Q ss_pred eEEEEeecchHHHHHHHhhcccceee
Q psy653 12 LCQLFLQSEAAYACVSELGELGLVQF 37 (91)
Q Consensus 12 l~qL~ip~E~A~~~V~eLG~LglvqF 37 (91)
++++|+-+|.--.+++.|.+.|+-=|
T Consensus 6 l~klFVe~eNlGKaINaLte~GITGF 31 (110)
T PF10126_consen 6 LLKLFVESENLGKAINALTEGGITGF 31 (110)
T ss_pred EEEEEEehhHHHHHHHHHHhcCccEE
Confidence 88999999999999999999986544
No 32
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=21.92 E-value=88 Score=24.78 Aligned_cols=55 Identities=16% Similarity=0.230 Sum_probs=41.4
Q ss_pred CceEEEEeecchHHHHHHHhhcccceeeeeCCCCCCCCCcchhhHHHHHHHHHhhhh
Q psy653 10 MALCQLFLQSEAAYACVSELGELGLVQFRDRDIPLGYLHFDRINSERLVSSRVGFSD 66 (91)
Q Consensus 10 M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~~v~~FqR~Fv~eIrRcEr~l~~l~ 66 (91)
|.-.++|+-+|+.-++...+|+--+.||-+.+.. ....+|++...+.++.++-.+
T Consensus 2 ~~~~~i~~VSDstGeTAe~v~~A~l~QF~~~~~~--~~~~p~v~~~~~~~~i~~~~~ 56 (269)
T PRK05339 2 MMKRHVFLVSDSTGETAETVGRAALSQFPNVEFE--EHRYPFVRTEEKADEVLEEIN 56 (269)
T ss_pred CCceEEEEEeCCHHHHHHHHHHHHHHhCCCCCee--EEEeCCcCCHHHHHHHHHHHH
Confidence 4556899999999999999999999999765443 234577777777665555444
No 33
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.83 E-value=98 Score=18.28 Aligned_cols=24 Identities=4% Similarity=-0.014 Sum_probs=18.7
Q ss_pred cchhhHHHHHHHHHhhhhhhhhhh
Q psy653 49 FDRINSERLVSSRVGFSDSGVIRV 72 (91)
Q Consensus 49 R~Fv~eIrRcEr~l~~l~~ei~~~ 72 (91)
.+...++|+.+++++-++++++++
T Consensus 44 ~~~r~~~~~~~k~l~~le~e~~~l 67 (68)
T PF06305_consen 44 LRLRRRIRRLRKELKKLEKELEQL 67 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345667888889999999988765
No 34
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.80 E-value=60 Score=22.33 Aligned_cols=17 Identities=12% Similarity=0.192 Sum_probs=13.2
Q ss_pred hhHHHHHH------HHHhhhhhh
Q psy653 52 INSERLVS------SRVGFSDSG 68 (91)
Q Consensus 52 v~eIrRcE------r~l~~l~~e 68 (91)
...++||+ .+|+||++.
T Consensus 38 ~D~L~rCdT~EEAlEii~yleKr 60 (98)
T COG4003 38 IDFLRRCDTEEEALEIINYLEKR 60 (98)
T ss_pred HHHHHHhCcHHHHHHHHHHHHHh
Confidence 66789993 689998764
No 35
>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=20.73 E-value=1.1e+02 Score=17.77 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=14.8
Q ss_pred HHhhcccceeeeeCCCCCCCC
Q psy653 27 SELGELGLVQFRDRDIPLGYL 47 (91)
Q Consensus 27 ~eLG~LglvqF~DLN~~v~~F 47 (91)
+.|=+.|.|.|+|-|...++.
T Consensus 2 ~~ll~~G~vE~id~eEEe~~~ 22 (48)
T PF04567_consen 2 DDLLKEGVVEYIDAEEEETCM 22 (48)
T ss_dssp HHHHHTTSEEEEETTTCTT--
T ss_pred hhHhhCCCEEEecchhccccE
Confidence 345567999999999876654
No 36
>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=20.21 E-value=1.1e+02 Score=19.01 Aligned_cols=34 Identities=9% Similarity=0.077 Sum_probs=26.3
Q ss_pred cCCceEEEEeecchHHHHHHHhhcccceeeeeCCC
Q psy653 8 EEMALCQLFLQSEAAYACVSELGELGLVQFRDRDI 42 (91)
Q Consensus 8 E~M~l~qL~ip~E~A~~~V~eLG~LglvqF~DLN~ 42 (91)
|+|-.+.+.+|.|..-.+++.|.+..- ++.+.++
T Consensus 3 EPi~~~~I~~p~~~~g~v~~~l~~rrG-~i~~~~~ 36 (85)
T smart00838 3 EPIMKVEVTVPEEYMGDVIGDLNSRRG-KIEGMEQ 36 (85)
T ss_pred CCEEEEEEEeCHHHHHHHHHHHHHcCC-EEECeec
Confidence 788999999999999999999977532 2235443
No 37
>PF03235 DUF262: Protein of unknown function DUF262; InterPro: IPR004919 This entry is found in prokaryotic proteins of unknown function.
Probab=20.11 E-value=72 Score=21.98 Aligned_cols=22 Identities=14% Similarity=0.129 Sum_probs=15.3
Q ss_pred CCCCCCCcchhhHHHHHHHHHh
Q psy653 42 IPLGYLHFDRINSERLVSSRVG 63 (91)
Q Consensus 42 ~~v~~FqR~Fv~eIrRcEr~l~ 63 (91)
=.+|.|||+|+=.-+++++.++
T Consensus 12 ~~iP~yQR~yvW~~~~~~~Li~ 33 (221)
T PF03235_consen 12 IVIPDYQRDYVWDEEQIEELID 33 (221)
T ss_pred ccCCCCCCCCccCHHHHHHHHH
Confidence 4678999999966666554443
Done!