Query psy15627
Match_columns 77
No_of_seqs 104 out of 271
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 17:32:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15627.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15627hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2189|consensus 99.9 9.4E-24 2E-28 177.6 2.6 54 1-54 1-54 (829)
2 PF01496 V_ATPase_I: V-type AT 97.8 4.4E-06 9.5E-11 69.1 0.0 31 26-56 1-31 (759)
3 PRK05771 V-type ATP synthase s 96.1 0.0045 9.8E-08 50.6 2.6 41 5-45 1-41 (646)
4 PF03235 DUF262: Protein of un 93.8 0.011 2.3E-07 40.0 -1.0 33 42-77 12-46 (221)
5 COG1269 NtpI Archaeal/vacuolar 91.8 0.17 3.7E-06 42.4 3.2 43 5-47 1-43 (660)
6 PF09902 DUF2129: Uncharacteri 85.9 1.4 3E-05 28.0 3.5 36 5-40 25-60 (71)
7 PRK02302 hypothetical protein; 81.7 2.4 5.3E-05 28.1 3.5 37 5-41 31-67 (89)
8 PRK02886 hypothetical protein; 79.3 3.3 7.1E-05 27.4 3.5 37 5-41 29-65 (87)
9 PF14257 DUF4349: Domain of un 61.7 10 0.00022 27.6 3.1 31 12-42 97-127 (262)
10 PF08029 HisG_C: HisG, C-termi 55.6 17 0.00036 22.9 2.9 27 7-33 37-63 (75)
11 TIGR03455 HisG_C-term ATP phos 54.7 12 0.00027 24.5 2.3 28 7-34 61-88 (100)
12 TIGR02549 CRISPR_DxTHG CRISPR- 51.8 4.1 8.8E-05 21.6 -0.3 17 52-68 3-19 (26)
13 COG3323 Uncharacterized protei 48.6 20 0.00042 24.8 2.6 34 8-41 3-36 (109)
14 COG1479 Uncharacterized conser 48.2 7.3 0.00016 28.7 0.5 16 43-58 21-36 (409)
15 PF08473 VGCC_alpha2: Neuronal 44.7 13 0.00028 25.1 1.2 40 30-74 20-64 (94)
16 COG0301 ThiI Thiamine biosynth 43.6 11 0.00024 30.5 0.9 35 38-76 139-174 (383)
17 COG4471 Uncharacterized protei 43.2 29 0.00064 23.2 2.7 35 6-40 31-65 (90)
18 PF01978 TrmB: Sugar-specific 39.9 25 0.00054 20.4 1.8 25 17-41 34-58 (68)
19 TIGR02913 HAF_rpt probable ext 35.1 14 0.00031 20.6 0.2 10 55-64 20-29 (39)
20 PF13783 DUF4177: Domain of un 34.0 58 0.0012 18.9 2.7 24 17-40 17-42 (61)
21 PF00679 EFG_C: Elongation fac 32.4 44 0.00096 20.5 2.2 33 8-41 4-36 (89)
22 COG3602 Uncharacterized protei 32.1 28 0.00061 24.8 1.3 19 14-32 111-129 (134)
23 cd03713 EFG_mtEFG_C EFG_mtEFG_ 31.8 44 0.00095 19.8 2.0 25 8-32 1-25 (78)
24 cd03710 BipA_TypA_C BipA_TypA_ 31.5 63 0.0014 19.4 2.7 26 8-33 1-26 (79)
25 PRK00489 hisG ATP phosphoribos 29.1 48 0.001 24.6 2.2 27 7-33 247-273 (287)
26 cd03709 lepA_C lepA_C: This fa 29.0 58 0.0013 19.7 2.2 25 8-32 1-25 (80)
27 PF04567 RNA_pol_Rpb2_5: RNA p 28.0 73 0.0016 18.1 2.4 21 27-47 2-22 (48)
28 cd01514 Elongation_Factor_C El 27.4 60 0.0013 19.2 2.1 26 8-33 1-26 (79)
29 cd03711 Tet_C Tet_C: C-terminu 26.9 63 0.0014 19.3 2.1 26 8-33 1-26 (78)
30 cd04096 eEF2_snRNP_like_C eEF2 26.8 60 0.0013 19.3 2.0 27 8-34 1-27 (80)
31 cd04097 mtEFG1_C mtEFG1_C: C-t 25.6 71 0.0015 19.0 2.2 26 8-33 1-26 (78)
32 PRK05256 condesin subunit E; P 25.1 51 0.0011 25.5 1.8 24 19-42 152-175 (238)
33 smart00838 EFG_C Elongation fa 23.6 76 0.0017 19.1 2.1 33 8-42 3-36 (85)
34 COG3454 Metal-dependent hydrol 23.0 1.4E+02 0.0031 24.6 4.0 50 2-52 124-173 (377)
35 PF02629 CoA_binding: CoA bind 22.3 48 0.001 20.5 1.0 28 10-37 63-90 (96)
36 TIGR00341 conserved hypothetic 21.8 1.6E+02 0.0034 23.4 4.0 21 9-29 2-22 (325)
37 PF08003 Methyltransf_9: Prote 21.7 92 0.002 24.9 2.7 45 15-59 243-287 (315)
No 1
>KOG2189|consensus
Probab=99.88 E-value=9.4e-24 Score=177.56 Aligned_cols=54 Identities=50% Similarity=0.758 Sum_probs=52.0
Q ss_pred CCCcccccCCceEEEEecCccHHHHHHHhhcccceeEeecCCCCCccccceecC
Q psy15627 1 MGAMFRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEERPMCVSSSRVDWN 54 (77)
Q Consensus 1 m~slfRSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN~~v~afqR~y~~~ 54 (77)
|++|||||+|+|||+|+|+|+||+||++|||+|+|||+|||++|++|||+|+=.
T Consensus 1 ~~s~fRSE~M~L~Ql~l~~eaAy~~vaeLGelGlvqFrDLN~~v~afQR~fv~e 54 (829)
T KOG2189|consen 1 MGSLFRSEEMCLVQLFLQSEAAYQCVAELGELGLVQFRDLNPDVSAFQRKFVNE 54 (829)
T ss_pred CccccccccceeeEEEecHHHHHHHHHHhhccCeeEeeeCCCccCHHHHHHHHH
Confidence 799999999999999999999999999999999999999999999999998743
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=97.80 E-value=4.4e-06 Score=69.10 Aligned_cols=31 Identities=32% Similarity=0.462 Sum_probs=0.0
Q ss_pred HHHhhcccceeEeecCCCCCccccceecCCC
Q psy15627 26 VSTLGEAGIVQFRDEERPMCVSSSRVDWNTS 56 (77)
Q Consensus 26 V~eLGeLGlVQF~DLN~~v~afqR~y~~~~~ 56 (77)
|++||++|+|||+|+|+++++|||+|+-...
T Consensus 1 V~eLgelG~VqF~Dln~~~~~fqr~f~~ev~ 31 (759)
T PF01496_consen 1 VNELGELGLVQFRDLNEDVSAFQRKFVNEVR 31 (759)
T ss_dssp -------------------------------
T ss_pred CchhhcCCcEEEEECccchhHHHHHhhhccc
Confidence 6899999999999999999999999765543
No 3
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=96.06 E-value=0.0045 Score=50.63 Aligned_cols=41 Identities=15% Similarity=0.195 Sum_probs=38.4
Q ss_pred ccccCCceEEEEecCccHHHHHHHhhcccceeEeecCCCCC
Q psy15627 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEERPMC 45 (77)
Q Consensus 5 fRSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN~~v~ 45 (77)
++.++|+.++++.|.+.+.+++++|.++|.+|+.|+|...+
T Consensus 1 m~i~kM~kv~l~~~~~~~~~~l~~L~~lg~vhi~~~~~~~~ 41 (646)
T PRK05771 1 LAPVRMKKVLIVTLKSYKDEVLEALHELGVVHIEDLKEELS 41 (646)
T ss_pred CCceeeEEEEEEEEHHHHHHHHHHHHhCCCEEEeecccccc
Confidence 46799999999999999999999999999999999998775
No 4
>PF03235 DUF262: Protein of unknown function DUF262; InterPro: IPR004919 This entry is found in prokaryotic proteins of unknown function.
Probab=93.84 E-value=0.011 Score=39.96 Aligned_cols=33 Identities=15% Similarity=0.285 Sum_probs=22.3
Q ss_pred CCCCccccceecCCCcccccccccccc--eeeccCCCC
Q psy15627 42 RPMCVSSSRVDWNTSHAFRHTPFVKGL--GIALPLGSI 77 (77)
Q Consensus 42 ~~v~afqR~y~~~~~~~~~~~~~~~~~--~~~~~~~~~ 77 (77)
=.+|.|||.|+|...+. .-|..-+ .-..|+|+|
T Consensus 12 ~~iP~yQR~yvW~~~~~---~~Li~si~~~~~~~iG~i 46 (221)
T PF03235_consen 12 IVIPDYQRDYVWDEEQI---EELIDSILELRGYPIGSI 46 (221)
T ss_pred ccCCCCCCCCccCHHHH---HHHHHHHHhccCCccceE
Confidence 36799999999988773 2344444 555566653
No 5
>COG1269 NtpI Archaeal/vacuolar-type H+-ATPase subunit I [Energy production and conversion]
Probab=91.78 E-value=0.17 Score=42.36 Aligned_cols=43 Identities=19% Similarity=0.176 Sum_probs=39.3
Q ss_pred ccccCCceEEEEecCccHHHHHHHhhcccceeEeecCCCCCcc
Q psy15627 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEERPMCVS 47 (77)
Q Consensus 5 fRSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN~~v~af 47 (77)
+|-|+|+.+.++.+.+..-+++.+|++.|++|+.|++..+...
T Consensus 1 ~~~~~M~kv~i~~~~~~~~~vi~~L~~~g~~~~~d~~~~~~~~ 43 (660)
T COG1269 1 MRPEKMKKVSIIGLKSELDPVLAELHDFGLVHLEDLEEGEKGL 43 (660)
T ss_pred CchhhheeEEEEeehhhhhHHHHHHHHcCeEEeeccccccccc
Confidence 5789999999999999999999999999999999999876543
No 6
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=85.86 E-value=1.4 Score=27.96 Aligned_cols=36 Identities=17% Similarity=0.276 Sum_probs=32.1
Q ss_pred ccccCCceEEEEecCccHHHHHHHhhcccceeEeec
Q psy15627 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDE 40 (77)
Q Consensus 5 fRSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DL 40 (77)
+-|.+|.++.||+..|.+-+++++|.++.-|.-+..
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 468999999999999999999999999988876653
No 7
>PRK02302 hypothetical protein; Provisional
Probab=81.67 E-value=2.4 Score=28.10 Aligned_cols=37 Identities=14% Similarity=0.209 Sum_probs=32.6
Q ss_pred ccccCCceEEEEecCccHHHHHHHhhcccceeEeecC
Q psy15627 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEE 41 (77)
Q Consensus 5 fRSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN 41 (77)
.=|.+|.++-||+..|.|-+++..|.++--|.-++.-
T Consensus 31 Y~Skk~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~S 67 (89)
T PRK02302 31 YHSKRSRYLVLYVNKEDVEQKLEELSKLKFVKKVRPS 67 (89)
T ss_pred EEeccccEEEEEECHHHHHHHHHHHhcCCCeeEEccc
Confidence 3488999999999999999999999999988776643
No 8
>PRK02886 hypothetical protein; Provisional
Probab=79.35 E-value=3.3 Score=27.40 Aligned_cols=37 Identities=14% Similarity=0.198 Sum_probs=32.9
Q ss_pred ccccCCceEEEEecCccHHHHHHHhhcccceeEeecC
Q psy15627 5 FRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEE 41 (77)
Q Consensus 5 fRSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN 41 (77)
.=|..|.++.||+..|.+-+++..|.++-.|.-++.-
T Consensus 29 Y~Skr~kYvvlYvn~~~~e~~~~kl~~l~fVk~Ve~S 65 (87)
T PRK02886 29 YVSKRLKYAVLYCDMEQVEDIMNKLSSLPFVKRVEPS 65 (87)
T ss_pred EEeccccEEEEEECHHHHHHHHHHHhcCCCeeEEccc
Confidence 3488999999999999999999999999988877644
No 9
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=61.72 E-value=10 Score=27.64 Aligned_cols=31 Identities=19% Similarity=0.154 Sum_probs=27.7
Q ss_pred eEEEEecCccHHHHHHHhhcccceeEeecCC
Q psy15627 12 LCQLFIQPEAAYSSVSTLGEAGIVQFRDEER 42 (77)
Q Consensus 12 l~qLiip~E~A~d~V~eLGeLGlVQF~DLN~ 42 (77)
...+.||++..-+.+++|+++|.|.-++.+.
T Consensus 97 ~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~~ 127 (262)
T PF14257_consen 97 SLTIRVPADKFDSFLDELSELGKVTSRNISS 127 (262)
T ss_pred EEEEEECHHHHHHHHHHHhccCceeeeeccc
Confidence 7789999999999999999999888777763
No 10
>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=55.56 E-value=17 Score=22.87 Aligned_cols=27 Identities=15% Similarity=0.309 Sum_probs=24.3
Q ss_pred ccCCceEEEEecCccHHHHHHHhhccc
Q psy15627 7 SEEMALCQLFIQPEAAYSSVSTLGEAG 33 (77)
Q Consensus 7 SE~M~l~qLiip~E~A~d~V~eLGeLG 33 (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 357888999999999999999998887
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=54.65 E-value=12 Score=24.51 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=25.2
Q ss_pred ccCCceEEEEecCccHHHHHHHhhcccc
Q psy15627 7 SEEMALCQLFIQPEAAYSSVSTLGEAGI 34 (77)
Q Consensus 7 SE~M~l~qLiip~E~A~d~V~eLGeLGl 34 (77)
+++|.-++.++|.+..++++++|-+.|-
T Consensus 61 ~~~w~AV~~vv~~~~v~~~~~~Lk~~GA 88 (100)
T TIGR03455 61 DEGWVAVHAVVDEKVVNELIDKLKAAGA 88 (100)
T ss_pred CCCeEEEEEEEcHHHHHHHHHHHHHcCC
Confidence 5788889999999999999999998883
No 12
>TIGR02549 CRISPR_DxTHG CRISPR-associated DxTHG motif protein. This model describes a short region highly conserved between two otherwise substantially different CRISPR-associated (cas) proteins, TIGR02221 and TIGR01987. This region includes the motif [VIL]-D-x-[ST]-H-[GS].
Probab=51.82 E-value=4.1 Score=21.64 Aligned_cols=17 Identities=18% Similarity=0.325 Sum_probs=12.9
Q ss_pred ecCCCcccccccccccc
Q psy15627 52 DWNTSHAFRHTPFVKGL 68 (77)
Q Consensus 52 ~~~~~~~~~~~~~~~~~ 68 (77)
..+..|+||+-|++--.
T Consensus 3 ilDiTHGfr~~P~la~~ 19 (26)
T TIGR02549 3 ILDVTHGFNFMPLLAYE 19 (26)
T ss_pred EEEecCcccchHHHHHH
Confidence 34678999999987543
No 13
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.59 E-value=20 Score=24.75 Aligned_cols=34 Identities=18% Similarity=0.191 Sum_probs=30.4
Q ss_pred cCCceEEEEecCccHHHHHHHhhcccceeEeecC
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEE 41 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN 41 (77)
+.|.-..+++|.|-.-+.-..|++.|.-|..|..
T Consensus 3 ~~~~K~~vyVP~~~~e~vr~aL~~aGag~iG~Y~ 36 (109)
T COG3323 3 EPLYKIEVYVPEEYVEQVRDALFEAGAGHIGNYD 36 (109)
T ss_pred cceeEEEEEeCHHHHHHHHHHHHhcCCcceeccc
Confidence 4677889999999999999999999999998744
No 14
>COG1479 Uncharacterized conserved protein [Function unknown]
Probab=48.23 E-value=7.3 Score=28.71 Aligned_cols=16 Identities=6% Similarity=0.083 Sum_probs=13.1
Q ss_pred CCCccccceecCCCcc
Q psy15627 43 PMCVSSSRVDWNTSHA 58 (77)
Q Consensus 43 ~v~afqR~y~~~~~~~ 58 (77)
.++-+||+|+|...+.
T Consensus 21 ~ip~yQR~Y~W~~~~~ 36 (409)
T COG1479 21 IIPDYQRPYVWDEKNI 36 (409)
T ss_pred eccCccCCCcCcHHHH
Confidence 4578999999998665
No 15
>PF08473 VGCC_alpha2: Neuronal voltage-dependent calcium channel alpha 2acd; InterPro: IPR013680 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2/delta subunits to the N terminus of a Cache domain (IPR004010 from INTERPRO).
Probab=44.73 E-value=13 Score=25.12 Aligned_cols=40 Identities=23% Similarity=0.375 Sum_probs=26.9
Q ss_pred hcccceeEeecC-----CCCCccccceecCCCcccccccccccceeeccC
Q psy15627 30 GEAGIVQFRDEE-----RPMCVSSSRVDWNTSHAFRHTPFVKGLGIALPL 74 (77)
Q Consensus 30 GeLGlVQF~DLN-----~~v~afqR~y~~~~~~~~~~~~~~~~~~~~~~~ 74 (77)
|+-|-.+|.-+. .-+.--+|.|+|..- +-||| .||++||-
T Consensus 20 g~~Ge~~i~tlvks~DeRYId~~~RtYtw~PI---~gT~y--SLaLVLP~ 64 (94)
T PF08473_consen 20 GRSGEKTIRTLVKSQDERYIDEVNRTYTWTPI---NGTDY--SLALVLPS 64 (94)
T ss_pred CCCCcEEEEEEEeeccceeeeeeceeEEEecc---CCCcc--eeEEEcCC
Confidence 455555554433 345667899999754 46888 58999985
No 16
>COG0301 ThiI Thiamine biosynthesis ATP pyrophosphatase [Coenzyme metabolism]
Probab=43.63 E-value=11 Score=30.46 Aligned_cols=35 Identities=26% Similarity=0.448 Sum_probs=27.5
Q ss_pred eec-CCCCCccccceecCCCcccccccccccceeeccCCC
Q psy15627 38 RDE-ERPMCVSSSRVDWNTSHAFRHTPFVKGLGIALPLGS 76 (77)
Q Consensus 38 ~DL-N~~v~afqR~y~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (77)
+|| |||+..+ ...--.+||=||.=.||.| .||+|+
T Consensus 139 Vdl~~Pdv~i~---iEIr~~~ayi~~~~~~G~G-GLPvGt 174 (383)
T COG0301 139 VDLKNPDVEIH---IEIREDKAYIYTERIKGPG-GLPVGT 174 (383)
T ss_pred eecCCCCeEEE---EEEecCeEEEEEeeeccCC-CCcccc
Confidence 566 8887764 3445578999999999998 799986
No 17
>COG4471 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.19 E-value=29 Score=23.25 Aligned_cols=35 Identities=14% Similarity=0.131 Sum_probs=30.8
Q ss_pred cccCCceEEEEecCccHHHHHHHhhcccceeEeec
Q psy15627 6 RSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDE 40 (77)
Q Consensus 6 RSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DL 40 (77)
-|.++.++.||++.+..-+.+++|-.+-.|--++.
T Consensus 31 ~Skk~kY~vlYvn~~~ve~~~~kl~~~kfVK~V~~ 65 (90)
T COG4471 31 VSKKSKYVVLYVNEQDVEQIVEKLSRLKFVKKVRV 65 (90)
T ss_pred EecceeEEEEEECHHHHHHHHHHHhhceeeeeccc
Confidence 48899999999999999999999999888766654
No 18
>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=39.91 E-value=25 Score=20.39 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=21.9
Q ss_pred ecCccHHHHHHHhhcccceeEeecC
Q psy15627 17 IQPEAAYSSVSTLGEAGIVQFRDEE 41 (77)
Q Consensus 17 ip~E~A~d~V~eLGeLGlVQF~DLN 41 (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 5778899999999999999998844
No 19
>TIGR02913 HAF_rpt probable extracellular repeat, HAF family. The model for this family detects a homology domain of about 40 amino acids. Member proteins always have a least two tandem copies and as many as seven. The spacing between repeats as defined here usually is four residues exactly. This repeat is named for a tripeptide motif HAF found in most members. Some members proteins are found in species with no outer membrane (archaea and Gram-positive bacteria) while others have C-terminal autotransporter domains that suggest that the repeat region is transported across the outer membrane. This domain seems likely to be an extracellular protein repeat.
Probab=35.08 E-value=14 Score=20.59 Aligned_cols=10 Identities=30% Similarity=0.268 Sum_probs=7.8
Q ss_pred CCcccccccc
Q psy15627 55 TSHAFRHTPF 64 (77)
Q Consensus 55 ~~~~~~~~~~ 64 (77)
..|||++++=
T Consensus 20 ~~hAF~W~~g 29 (39)
T TIGR02913 20 ETHAFLYSDG 29 (39)
T ss_pred CEeEEEECCC
Confidence 3599999874
No 20
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=33.96 E-value=58 Score=18.91 Aligned_cols=24 Identities=25% Similarity=0.433 Sum_probs=20.6
Q ss_pred ecCccHHHHHHHhhccc--ceeEeec
Q psy15627 17 IQPEAAYSSVSTLGEAG--IVQFRDE 40 (77)
Q Consensus 17 ip~E~A~d~V~eLGeLG--lVQF~DL 40 (77)
++.+...+.++++|+.| +|+..+-
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeLV~~~~~ 42 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWELVSIIPP 42 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEEEEEEcC
Confidence 45677889999999999 9999886
No 21
>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=32.38 E-value=44 Score=20.49 Aligned_cols=33 Identities=12% Similarity=0.090 Sum_probs=26.0
Q ss_pred cCCceEEEEecCccHHHHHHHhhcccceeEeecC
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEE 41 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN 41 (77)
|++-.+++.+|.|..-.+++.|.+.+- ++.+.+
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 677889999999999999999998753 344433
No 22
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.10 E-value=28 Score=24.77 Aligned_cols=19 Identities=26% Similarity=0.384 Sum_probs=17.3
Q ss_pred EEEecCccHHHHHHHhhcc
Q psy15627 14 QLFIQPEAAYSSVSTLGEA 32 (77)
Q Consensus 14 qLiip~E~A~d~V~eLGeL 32 (77)
++++|.|.|.+.+..|+.+
T Consensus 111 HlFVp~e~a~~A~~~L~~l 129 (134)
T COG3602 111 HLFVPAERAKEALVVLQGL 129 (134)
T ss_pred eeeeeHHHHHHHHHHHHHH
Confidence 6999999999999998875
No 23
>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=31.76 E-value=44 Score=19.77 Aligned_cols=25 Identities=12% Similarity=0.138 Sum_probs=22.5
Q ss_pred cCCceEEEEecCccHHHHHHHhhcc
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEA 32 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeL 32 (77)
|+|-.+.+.+|.|..-.+++.|.+.
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~r 25 (78)
T cd03713 1 EPIMKVEVTVPEEYMGDVIGDLSSR 25 (78)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHHc
Confidence 7888999999999999999999864
No 24
>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=31.51 E-value=63 Score=19.42 Aligned_cols=26 Identities=15% Similarity=0.183 Sum_probs=23.2
Q ss_pred cCCceEEEEecCccHHHHHHHhhccc
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeLG 33 (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 67888999999999999999998764
No 25
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=29.06 E-value=48 Score=24.55 Aligned_cols=27 Identities=11% Similarity=0.224 Sum_probs=24.6
Q ss_pred ccCCceEEEEecCccHHHHHHHhhccc
Q psy15627 7 SEEMALCQLFIQPEAAYSSVSTLGEAG 33 (77)
Q Consensus 7 SE~M~l~qLiip~E~A~d~V~eLGeLG 33 (77)
.++|.-++.++|.+..|+++++|-+.|
T Consensus 247 ~~~~~av~~~~~~~~~~~~~~~l~~~g 273 (287)
T PRK00489 247 DEGWVAVHAVVPEDLVWELMDKLKALG 273 (287)
T ss_pred CCCeEEEEEEECHHHHHHHHHHHHHcC
Confidence 467888999999999999999999888
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=29.01 E-value=58 Score=19.74 Aligned_cols=25 Identities=12% Similarity=0.044 Sum_probs=22.7
Q ss_pred cCCceEEEEecCccHHHHHHHhhcc
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEA 32 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeL 32 (77)
|+|-.+.+.+|.|..-++++.|...
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 6788899999999999999999975
No 27
>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=27.97 E-value=73 Score=18.12 Aligned_cols=21 Identities=24% Similarity=0.368 Sum_probs=15.1
Q ss_pred HHhhcccceeEeecCCCCCcc
Q psy15627 27 STLGEAGIVQFRDEERPMCVS 47 (77)
Q Consensus 27 ~eLGeLGlVQF~DLN~~v~af 47 (77)
+.|=+.|.|.|+|-|...+++
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 345567999999999877653
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=27.43 E-value=60 Score=19.16 Aligned_cols=26 Identities=12% Similarity=0.147 Sum_probs=22.9
Q ss_pred cCCceEEEEecCccHHHHHHHhhccc
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeLG 33 (77)
|+|-.+.+.+|.|..-.+++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (79)
T cd01514 1 EPIMKVEITVPEEYLGAVIGDLSKRR 26 (79)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHhcC
Confidence 78889999999999999999997654
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=26.93 E-value=63 Score=19.26 Aligned_cols=26 Identities=23% Similarity=0.250 Sum_probs=23.3
Q ss_pred cCCceEEEEecCccHHHHHHHhhccc
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeLG 33 (77)
|+|-.+.+.+|.|..-++++.|.+..
T Consensus 1 EPi~~~~i~~p~~~~g~v~~~l~~rr 26 (78)
T cd03711 1 EPYLRFELEVPQDALGRAMSDLAKMG 26 (78)
T ss_pred CCeEEEEEEcCHHHHHHHHHHHHHcC
Confidence 67889999999999999999998764
No 30
>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=26.82 E-value=60 Score=19.32 Aligned_cols=27 Identities=19% Similarity=0.090 Sum_probs=23.6
Q ss_pred cCCceEEEEecCccHHHHHHHhhcccc
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEAGI 34 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeLGl 34 (77)
|+|-.+.+.+|.|..-+.++.|.+..-
T Consensus 1 EPi~~~~I~~p~~~~g~V~~~l~~rrg 27 (80)
T cd04096 1 EPIYLVEIQCPEDALGKVYSVLSKRRG 27 (80)
T ss_pred CCEEEEEEEEcHHHhhHHHHhhhhCee
Confidence 678889999999999999999987653
No 31
>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=25.60 E-value=71 Score=19.02 Aligned_cols=26 Identities=12% Similarity=0.083 Sum_probs=23.0
Q ss_pred cCCceEEEEecCccHHHHHHHhhccc
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEAG 33 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeLG 33 (77)
|+|-.+.+.+|.|..-++++.|.+..
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rr 26 (78)
T cd04097 1 EPIMKVEVTAPTEFQGNVIGLLNKRK 26 (78)
T ss_pred CCEEEEEEEecHHHHHHHHHHHHHCC
Confidence 67888999999999999999998754
No 32
>PRK05256 condesin subunit E; Provisional
Probab=25.14 E-value=51 Score=25.52 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=20.0
Q ss_pred CccHHHHHHHhhcccceeEeecCC
Q psy15627 19 PEAAYSSVSTLGEAGIVQFRDEER 42 (77)
Q Consensus 19 ~E~A~d~V~eLGeLGlVQF~DLN~ 42 (77)
.|..+.++..|..+|.|+|.+=|.
T Consensus 152 ~ekvr~sLrrLrRlgmI~~l~~d~ 175 (238)
T PRK05256 152 QEKVRTSLNRLRRLGMVWFMGHDS 175 (238)
T ss_pred HHHHHHHHHHHHhccceeeecCCC
Confidence 367788999999999999988443
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=23.65 E-value=76 Score=19.13 Aligned_cols=33 Identities=15% Similarity=0.218 Sum_probs=26.1
Q ss_pred cCCceEEEEecCccHHHHHHHhhcc-cceeEeecCC
Q psy15627 8 EEMALCQLFIQPEAAYSSVSTLGEA-GIVQFRDEER 42 (77)
Q Consensus 8 E~M~l~qLiip~E~A~d~V~eLGeL-GlVQF~DLN~ 42 (77)
|+|-.+.+.+|.|..-.+++.|.+. |.+ .+.++
T Consensus 3 EPi~~~~I~~p~~~~g~v~~~l~~rrG~i--~~~~~ 36 (85)
T smart00838 3 EPIMKVEVTVPEEYMGDVIGDLNSRRGKI--EGMEQ 36 (85)
T ss_pred CCEEEEEEEeCHHHHHHHHHHHHHcCCEE--ECeec
Confidence 7889999999999999999999764 433 34443
No 34
>COG3454 Metal-dependent hydrolase involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=22.97 E-value=1.4e+02 Score=24.57 Aligned_cols=50 Identities=8% Similarity=-0.007 Sum_probs=40.8
Q ss_pred CCcccccCCceEEEEecCccHHHHHHHhhcccceeEeecCCCCCcccccee
Q psy15627 2 GAMFRSEEMALCQLFIQPEAAYSSVSTLGEAGIVQFRDEERPMCVSSSRVD 52 (77)
Q Consensus 2 ~slfRSE~M~l~qLiip~E~A~d~V~eLGeLGlVQF~DLN~~v~afqR~y~ 52 (77)
.+.+|++---+.++=++.+...+.++++.+.+.|+.+-|+.+.+ =||+|.
T Consensus 124 ~g~lradHr~HlRcEvs~~~~l~~~e~~~~~p~v~LiSlMDH~P-GQrQf~ 173 (377)
T COG3454 124 AGRLRADHRLHLRCEVSHPATLPLFEDLMDHPRVKLISLMDHTP-GQRQFA 173 (377)
T ss_pred ccchhhccceeeeeecCChhHHHHHHHHhcCCCeeEEEecCCCC-Ccchhh
Confidence 35677777777777789999999999999999999999998754 477764
No 35
>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=22.32 E-value=48 Score=20.54 Aligned_cols=28 Identities=29% Similarity=0.351 Sum_probs=20.0
Q ss_pred CceEEEEecCccHHHHHHHhhcccceeE
Q psy15627 10 MALCQLFIQPEAAYSSVSTLGEAGIVQF 37 (77)
Q Consensus 10 M~l~qLiip~E~A~d~V~eLGeLGlVQF 37 (77)
....=+.+|.+.|.+++.++=+.|+=-+
T Consensus 63 i~iaii~VP~~~a~~~~~~~~~~gIk~i 90 (96)
T PF02629_consen 63 IDIAIITVPAEAAQEVADELVEAGIKGI 90 (96)
T ss_dssp TSEEEEES-HHHHHHHHHHHHHTT-SEE
T ss_pred CCEEEEEcCHHHHHHHHHHHHHcCCCEE
Confidence 3445578999999999999988775433
No 36
>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=21.82 E-value=1.6e+02 Score=23.42 Aligned_cols=21 Identities=10% Similarity=0.021 Sum_probs=12.2
Q ss_pred CCceEEEEecCccHHHHHHHh
Q psy15627 9 EMALCQLFIQPEAAYSSVSTL 29 (77)
Q Consensus 9 ~M~l~qLiip~E~A~d~V~eL 29 (77)
+|.++|+++|++.--.....|
T Consensus 2 ~mRliev~iP~~~~~~v~~~l 22 (325)
T TIGR00341 2 RHRTNDCLIPKEGVVMRKEIV 22 (325)
T ss_pred CceEEEEEeccchHHHHHHHH
Confidence 467777777765544444444
No 37
>PF08003 Methyltransf_9: Protein of unknown function (DUF1698); InterPro: IPR010017 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This entry represents a set of bacterial AdoMet-dependent tRNA (mo5U34)-methyltransferases. These enzymes catalyse the conversion of 5-hydroxyuridine (ho5U) to 5-methoxyuridine (mo5U) at the wobble position (34) of tRNA []. The 5-methoxyuridine is subsequently converted to uridine-5-oxyacetic acid, a modified nucleoside that is apparently necessary for the efficient decoding of G-ending Pro, Ala, and Val codons in these organisms [].; GO: 0016300 tRNA (uracil) methyltransferase activity, 0002098 tRNA wobble uridine modification
Probab=21.72 E-value=92 Score=24.85 Aligned_cols=45 Identities=18% Similarity=0.163 Sum_probs=37.3
Q ss_pred EEecCccHHHHHHHhhcccceeEeecCCCCCccccceecCCCccc
Q psy15627 15 LFIQPEAAYSSVSTLGEAGIVQFRDEERPMCVSSSRVDWNTSHAF 59 (77)
Q Consensus 15 Liip~E~A~d~V~eLGeLGlVQF~DLN~~v~afqR~y~~~~~~~~ 59 (77)
-+||+-.|-..+.+=.-.-.|..+|.++--..=||+-+|-+.+..
T Consensus 243 ~FiPs~~~L~~wl~r~gF~~v~~v~~~~Tt~~EQR~T~Wm~~~SL 287 (315)
T PF08003_consen 243 WFIPSVAALKNWLERAGFKDVRCVDVSPTTIEEQRKTDWMDFQSL 287 (315)
T ss_pred EEeCCHHHHHHHHHHcCCceEEEecCccCCHHHhccCCCcCcccH
Confidence 367888887777776667789999999999999999999887754
Done!