Query 040313
Match_columns 123
No_of_seqs 124 out of 197
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 07:12:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040313.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040313hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4103 Mitochondrial F1F0-ATP 100.0 1.8E-35 4E-40 210.7 6.9 97 25-123 3-103 (103)
2 PF04718 ATP-synt_G: Mitochond 100.0 3.4E-31 7.3E-36 189.2 6.5 90 32-123 2-103 (103)
3 PF04718 ATP-synt_G: Mitochond 91.1 0.69 1.5E-05 33.0 5.3 57 19-75 7-67 (103)
4 PF10958 DUF2759: Protein of u 28.7 74 0.0016 20.5 2.7 22 92-113 24-45 (52)
5 TIGR01470 cysG_Nterm siroheme 26.5 1.8E+02 0.0039 22.5 5.2 57 46-102 128-184 (205)
6 PRK06718 precorrin-2 dehydroge 26.1 1.7E+02 0.0037 22.6 4.9 40 45-84 127-166 (202)
7 PHA01757 hypothetical protein 24.4 99 0.0021 22.0 3.0 26 87-112 3-30 (98)
8 PF04719 TAFII28: hTAFII28-lik 21.6 2.4E+02 0.0052 19.7 4.5 36 75-113 28-63 (90)
9 smart00648 SWAP Suppressor-of- 21.2 1.4E+02 0.0031 18.1 3.0 23 12-34 4-26 (54)
10 KOG4103 Mitochondrial F1F0-ATP 21.0 3.4E+02 0.0073 19.8 5.4 50 1-54 1-53 (103)
No 1
>KOG4103 consensus Mitochondrial F1F0-ATP synthase, subunit g/ATP20 [Energy production and conversion]
Probab=100.00 E-value=1.8e-35 Score=210.69 Aligned_cols=97 Identities=26% Similarity=0.364 Sum_probs=92.1
Q ss_pred HHHHHHHHhcchhccCCCchhHHHHHHHHHHHHHhhcCCCChHHHHHHHHhHHHHHH----hhhhcCcHHHHHHHHHHHH
Q 040313 25 AYIKQLLEDNKQHIKDPPNTETCQLLAKQLFYTRLASIPNRVDAFWKELDGLKQFMK----NRELEMNLDNAGLAALFGV 100 (123)
Q Consensus 25 ~~~~~l~~k~~~lv~~~~~~~k~~~L~k~~~Y~k~~l~PP~~~~~~~~~~~~k~~~~----~~~~~ltv~ea~~~~l~~~ 100 (123)
.|+.++++|.+.+++...+.++ |+|..+|.|+|+||+||+++|||++++++.++.+ +.++|+|++|+++|++|++
T Consensus 3 ~~~~~l~~K~~~L~~~~~~~~~-p~l~~~~~y~K~eL~PPt~Ad~pai~q~l~~~~~~~~t~~~Knltv~Eall~~~v~~ 81 (103)
T KOG4103|consen 3 NYMSGLVEKAANLVNAALTYAK-PRLAIFWKYAKVELAPPTPADIPAIKQDLAKLKKFAQTGCYKNLTVKEALLNGLVTL 81 (103)
T ss_pred hHHHHHHHHHHHHHHHHHHhcC-chHHHHHHHHhcccCCCChhhHHHHHHHHHHhHHHHhhhhhhhhhHHHHHHHHHHHH
Confidence 4788999999999999999999 9999999999999999999999999999876555 7789999999999999999
Q ss_pred HHHHHHHhhhhcccCCccccccC
Q 040313 101 ECFAWFCGGEIIGRGFTITGYHV 123 (123)
Q Consensus 101 Ev~~wF~vGEiIGRr~~lvGY~V 123 (123)
|+++||+|||||||| +||||+|
T Consensus 82 Evi~wf~vGEiIGrR-~ivGY~v 103 (103)
T KOG4103|consen 82 EVIFWFYVGEIIGRR-HIVGYKV 103 (103)
T ss_pred HHHHHHHHHHHhccc-ccccccC
Confidence 999999999999999 9999997
No 2
>PF04718 ATP-synt_G: Mitochondrial ATP synthase g subunit; InterPro: IPR006808 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. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents the G subunit found in the F0 complex of F-ATPases in mitochondria. The function of subunit G is currently unknown. There is no counterpart in chloroplast or bacterial F-ATPases identified so far []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=99.97 E-value=3.4e-31 Score=189.21 Aligned_cols=90 Identities=23% Similarity=0.313 Sum_probs=80.0
Q ss_pred HhcchhccCCCchhHHHHHHHHHHHHHhhcCCCChHHHHHHHHhHHHHHH------------hhhhcCcHHHHHHHHHHH
Q 040313 32 EDNKQHIKDPPNTETCQLLAKQLFYTRLASIPNRVDAFWKELDGLKQFMK------------NRELEMNLDNAGLAALFG 99 (123)
Q Consensus 32 ~k~~~lv~~~~~~~k~~~L~k~~~Y~k~~l~PP~~~~~~~~~~~~k~~~~------------~~~~~ltv~ea~~~~l~~ 99 (123)
++.+.++++.++++| +.+.++..|.+.||.||+++||++.++++.+.++ ++++|+|++|++++|++|
T Consensus 2 ~~~~~l~~~~v~~~k-v~le~~k~v~k~El~PPt~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~e~~~~~l~~ 80 (103)
T PF04718_consen 2 AKVTSLVNPAVYYSK-VGLELFKQVYKKELAPPTPAEFQSVYQQLFKTVKSAKSGSSPKSKLKQWKNLTVKEAAKNGLVG 80 (103)
T ss_pred chHHHHHHHHHHHhH-HHHHHHhHHHhhccCCcCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHhhcCCHHHHHHHHHHH
Confidence 456777888889999 8888888888999999999999999988776655 225799999999999999
Q ss_pred HHHHHHHHhhhhcccCCccccccC
Q 040313 100 VECFAWFCGGEIIGRGFTITGYHV 123 (123)
Q Consensus 100 ~Ev~~wF~vGEiIGRr~~lvGY~V 123 (123)
+||+|||||||||||| |||||+|
T Consensus 81 ~Ev~~wF~vGEiIGRr-~ivGY~V 103 (103)
T PF04718_consen 81 AEVYGWFFVGEIIGRR-SIVGYKV 103 (103)
T ss_pred HHHHHHHhhheeeccC-ceeCccC
Confidence 9999999999999999 9999998
No 3
>PF04718 ATP-synt_G: Mitochondrial ATP synthase g subunit; InterPro: IPR006808 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. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents the G subunit found in the F0 complex of F-ATPases in mitochondria. The function of subunit G is currently unknown. There is no counterpart in chloroplast or bacterial F-ATPases identified so far []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=91.11 E-value=0.69 Score=32.98 Aligned_cols=57 Identities=25% Similarity=0.207 Sum_probs=39.8
Q ss_pred HhhhhHHHHHHHHHhcchhc---cCCCchhHHHHHHHHHHHHHhhcCCC-ChHHHHHHHHh
Q 040313 19 FIKNGSAYIKQLLEDNKQHI---KDPPNTETCQLLAKQLFYTRLASIPN-RVDAFWKELDG 75 (123)
Q Consensus 19 ~~k~~~~~~~~l~~k~~~lv---~~~~~~~k~~~L~k~~~Y~k~~l~PP-~~~~~~~~~~~ 75 (123)
..+|+..|.+-.+|.++++. ..||+.++||++.+++.+.......+ .++++++..++
T Consensus 7 l~~~~v~~~kv~le~~k~v~k~El~PPt~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 67 (103)
T PF04718_consen 7 LVNPAVYYSKVGLELFKQVYKKELAPPTPAEFQSVYQQLFKTVKSAKSGSSPKSKLKQWKN 67 (103)
T ss_pred HHHHHHHHhHHHHHHHhHHHhhccCCcCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHhhc
Confidence 45556777777789999988 88999999999999997665522222 34455544433
No 4
>PF10958 DUF2759: Protein of unknown function (DUF2759); InterPro: IPR024490 This family of proteins with unknown function appear to be restricted to Bacillales.
Probab=28.75 E-value=74 Score=20.49 Aligned_cols=22 Identities=36% Similarity=0.377 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHhhhhcc
Q 040313 92 AGLAALFGVECFAWFCGGEIIG 113 (123)
Q Consensus 92 a~~~~l~~~Ev~~wF~vGEiIG 113 (123)
+...++..+=+.|||+|--+|=
T Consensus 24 ~i~F~~~t~~VFGwFtimTii~ 45 (52)
T PF10958_consen 24 GIGFALVTVAVFGWFTIMTIIH 45 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5778889999999999987763
No 5
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=26.49 E-value=1.8e+02 Score=22.49 Aligned_cols=57 Identities=12% Similarity=0.033 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhhcCCCChHHHHHHHHhHHHHHHhhhhcCcHHHHHHHHHHHHHH
Q 040313 46 TCQLLAKQLFYTRLASIPNRVDAFWKELDGLKQFMKNRELEMNLDNAGLAALFGVEC 102 (123)
Q Consensus 46 k~~~L~k~~~Y~k~~l~PP~~~~~~~~~~~~k~~~~~~~~~ltv~ea~~~~l~~~Ev 102 (123)
+.|.+++.+.-.=+++.|+.++++-+....+.+.++....+.+.+......++.-++
T Consensus 128 ~sP~la~~lr~~ie~~l~~~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~ 184 (205)
T TIGR01470 128 AAPVLARLLRERIETLLPPSLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAF 184 (205)
T ss_pred CCcHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHH
Confidence 447888877666677889999998888888877777543333333333333443333
No 6
>PRK06718 precorrin-2 dehydrogenase; Reviewed
Probab=26.14 E-value=1.7e+02 Score=22.55 Aligned_cols=40 Identities=18% Similarity=0.083 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHHHHhhcCCCChHHHHHHHHhHHHHHHhhh
Q 040313 45 ETCQLLAKQLFYTRLASIPNRVDAFWKELDGLKQFMKNRE 84 (123)
Q Consensus 45 ~k~~~L~k~~~Y~k~~l~PP~~~~~~~~~~~~k~~~~~~~ 84 (123)
.+.|.|++.+.-.=+++.||.++++-+....+.+.++.+.
T Consensus 127 G~sP~la~~lr~~ie~~~~~~~~~~~~~~~~~R~~~k~~~ 166 (202)
T PRK06718 127 GASPKLAKKIRDELEALYDESYESYIDFLYECRQKIKELQ 166 (202)
T ss_pred CCChHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHHHHhC
Confidence 3458888887554455689999999888888887777543
No 7
>PHA01757 hypothetical protein
Probab=24.41 E-value=99 Score=21.98 Aligned_cols=26 Identities=35% Similarity=0.432 Sum_probs=19.1
Q ss_pred CcHHHHHHHHHHHH--HHHHHHHhhhhc
Q 040313 87 MNLDNAGLAALFGV--ECFAWFCGGEII 112 (123)
Q Consensus 87 ltv~ea~~~~l~~~--Ev~~wF~vGEiI 112 (123)
++.-|..++|.+++ -+.+-|.||||+
T Consensus 3 i~l~e~al~gf~a~~g~l~~~fii~e~~ 30 (98)
T PHA01757 3 ITLLEGALYGFFAVTGALSASFIIGEIV 30 (98)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567777777765 367889999986
No 8
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=21.65 E-value=2.4e+02 Score=19.70 Aligned_cols=36 Identities=17% Similarity=0.238 Sum_probs=20.4
Q ss_pred hHHHHHHhhhhcCcHHHHHHHHHHHHHHHHHHHhhhhcc
Q 040313 75 GLKQFMKNRELEMNLDNAGLAALFGVECFAWFCGGEIIG 113 (123)
Q Consensus 75 ~~k~~~~~~~~~ltv~ea~~~~l~~~Ev~~wF~vGEiIG 113 (123)
.+++++++-..|-++.+ +.+.++--++=.||||||=
T Consensus 28 ~ikkli~~~~~~qsv~~---~v~i~v~g~aKvFVGEiVE 63 (90)
T PF04719_consen 28 AIKKLINQVLGNQSVSQ---NVVIAVAGIAKVFVGEIVE 63 (90)
T ss_dssp HHHHHHHHHHS-S---H---HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCCh---hHHHHHHHHHHHHHHHHHH
Confidence 44555554433355554 4446677788889999983
No 9
>smart00648 SWAP Suppressor-of-White-APricot splicing regulator. domain present in regulators which are responsible for pre-mRNA splicing processes
Probab=21.20 E-value=1.4e+02 Score=18.12 Aligned_cols=23 Identities=22% Similarity=0.564 Sum_probs=18.7
Q ss_pred HHHHHHHHhhhhHHHHHHHHHhc
Q 040313 12 ASQASEFFIKNGSAYIKQLLEDN 34 (123)
Q Consensus 12 ~~~a~~~~~k~~~~~~~~l~~k~ 34 (123)
....|++++++|..+-..++++.
T Consensus 4 I~~tA~~Va~~G~~fe~~l~~~~ 26 (54)
T smart00648 4 IDKTAQFVARNGPEFEAKLMERE 26 (54)
T ss_pred HHHHHHHHHHhhHHHHHHHHHhc
Confidence 34567899999999999999765
No 10
>KOG4103 consensus Mitochondrial F1F0-ATP synthase, subunit g/ATP20 [Energy production and conversion]
Probab=20.96 E-value=3.4e+02 Score=19.75 Aligned_cols=50 Identities=20% Similarity=0.183 Sum_probs=28.9
Q ss_pred CccchhhHHhHHHHHHHHH---hhhhHHHHHHHHHhcchhccCCCchhHHHHHHHHH
Q 040313 1 MASKLPQLQSKASQASEFF---IKNGSAYIKQLLEDNKQHIKDPPNTETCQLLAKQL 54 (123)
Q Consensus 1 mas~~~~~~~~~~~a~~~~---~k~~~~~~~~l~~k~~~lv~~~~~~~k~~~L~k~~ 54 (123)
||.-..+|.+|+..-++.+ ++|-..-.... ...=..||+.+++|.+-..+
T Consensus 1 ma~~~~~l~~K~~~L~~~~~~~~~p~l~~~~~y----~K~eL~PPt~Ad~pai~q~l 53 (103)
T KOG4103|consen 1 MANYMSGLVEKAANLVNAALTYAKPRLAIFWKY----AKVELAPPTPADIPAIKQDL 53 (103)
T ss_pred CchHHHHHHHHHHHHHHHHHHhcCchHHHHHHH----HhcccCCCChhhHHHHHHHH
Confidence 6666777777777655522 23221111111 11227899999999777666
Done!