Query gi|254780543|ref|YP_003064956.1| NADH dehydrogenase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 131
No_of_seqs 109 out of 570
Neff 5.1
Searched_HMMs 39220
Date Sun May 29 22:34:35 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780543.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08183 NADH dehydrogenase; V 100.0 0 0 370.4 8.6 129 2-130 1-132 (133)
2 COG3761 NADH:ubiquinone oxidor 100.0 0 0 277.8 5.1 116 9-130 1-118 (118)
3 pfam05071 NDUFA12 NADH ubiquin 100.0 2.8E-45 0 262.6 6.8 100 27-129 1-100 (100)
4 PRK06630 hypothetical protein; 100.0 6.7E-41 1.4E-45 239.6 6.0 87 15-103 1-93 (99)
5 KOG3382 consensus 100.0 5.9E-34 1.5E-38 202.3 3.6 98 24-130 44-147 (151)
6 pfam11385 DUF3189 Protein of u 42.9 15 0.00039 17.9 1.8 15 28-42 53-67 (148)
7 pfam10743 Phage_Cox Regulatory 30.8 14 0.00037 18.0 0.1 34 40-74 43-86 (87)
8 TIGR01967 DEAH_box_HrpA ATP-de 20.2 75 0.0019 14.2 2.8 63 36-107 661-732 (1320)
9 TIGR02984 Sig-70_plancto1 RNA 18.6 17 0.00043 17.7 -1.5 15 65-79 60-74 (190)
10 KOG3731 consensus 18.3 48 0.0012 15.2 0.8 18 56-73 136-153 (541)
No 1
>PRK08183 NADH dehydrogenase; Validated
Probab=100.00 E-value=0 Score=370.37 Aligned_cols=129 Identities=53% Similarity=1.030 Sum_probs=119.9
Q ss_pred HHHHHHHHHCCCCCEEHHHHHHHHHCEEEEEECCCCEEEEECCC--CCCCCCEEEEECCCCCCCCCCCCCCCEEECCCCC
Q ss_conf 66778673314796610214331307043666658786550577--7777620899478667553686532003214168
Q gi|254780543|r 2 KNFLLQIFTWWNGQTLGTRFFTWRFGHIVGKDEFGNTYYESRKN--INGSSRRWVIYNGYTDPSSIPPMWHGWIHHRRIG 79 (131)
Q Consensus 2 ~~~l~~iftWwn~~TlgT~l~t~~~g~~VG~D~~GNkYye~~~~--~~~~~rRwV~Y~~~~d~s~IppeWh~WLh~~~d~ 79 (131)
++||++||||||+|||||+|||+|+|++||+|+|||+|||++++ ..+++||||||++++|||+||||||+||||++|+
T Consensus 1 ~~~~~~~ftwwn~~t~gT~l~t~~~G~lVG~D~~GNkYYe~k~~~~~~~~~~RWViY~g~~eaS~VPpeWh~WLH~t~d~ 80 (133)
T PRK08183 1 KSFLLQIFTWWNGQTLGTRLFTWRKGERVGEDEFGNRYYRTKGGKPSLGRERRWVIYNGYAEASRIPPEWHGWLHHTVDV 80 (133)
T ss_pred CCHHHHEEHEECCCCHHHHHHHEECCEEEEECCCCCEECCCCCCCCCCCCCCEEEEECCCCCCCCCCCHHEEECCCCCCC
T ss_conf 94563200102797187840211824683770888870334777666787536889699887262582320001046677
Q ss_pred CCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCC
Q ss_conf 8985645676110167687788710327873334666-44444787779999
Q gi|254780543|r 80 VPKAEEENSFDWQKPHCVNATGSLNSYYPRFRRDNMA-GTSTKGKYSAWSPD 130 (131)
Q Consensus 80 ~P~~~~~~~~~Wqk~h~~N~TGT~~AY~P~~~~~~~~-~~~~~~~Y~aW~Pe 130 (131)
||++++..++.||++|+||+|||..||+|+||+++.+ +....+|||||+||
T Consensus 81 ~P~~~~~~~~~Wqk~H~pNlTGT~~AY~P~g~~~~~~~~~~~~~dYe~W~P~ 132 (133)
T PRK08183 81 PPTEEPYAPREWEKPHQPNLTGTPLAYRPKGSILRGGERPRATGDYEAWTPG 132 (133)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 9874767687656677888889965786998534678663012786678989
No 2
>COG3761 NADH:ubiquinone oxidoreductase 17.2 kD subunit [Energy production and conversion]
Probab=100.00 E-value=0 Score=277.78 Aligned_cols=116 Identities=53% Similarity=1.064 Sum_probs=107.9
Q ss_pred HHCCCCCEEHHHHHHHHHCEEEEEECCCCEEEEEC-CCCCCCCCEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCCCC
Q ss_conf 33147966102143313070436666587865505-77777762089947866755368653200321416889856456
Q gi|254780543|r 9 FTWWNGQTLGTRFFTWRFGHIVGKDEFGNTYYESR-KNINGSSRRWVIYNGYTDPSSIPPMWHGWIHHRRIGVPKAEEEN 87 (131)
Q Consensus 9 ftWwn~~TlgT~l~t~~~g~~VG~D~~GNkYye~~-~~~~~~~rRwV~Y~~~~d~s~IppeWh~WLh~~~d~~P~~~~~~ 87 (131)
||||| |||||+|+ +.||+|+|||.|||.+ .+..++.||||||++..|||+|||+||+||||++|++|+.+.+.
T Consensus 1 ftWwn-qt~gTrfh-----~kvGeDefgN~Yye~r~~ds~gr~RRwVIYngyaEas~IPp~WhgWlHh~vd~~P~~~~~~ 74 (118)
T COG3761 1 FTWWN-QTFGTRFH-----KKVGEDEFGNVYYEGRNIDSEGRTRRWVIYNGYAEASKIPPGWHGWLHHRVDEPPKSEQLF 74 (118)
T ss_pred CCHHH-HHHHHHHH-----HHCCCHHCCCEEEECCCCCCCCCEEEEEEECCCCHHCCCCCCHHHHHHHHCCCCCCCCCCC
T ss_conf 93677-67888998-----8605110053444315776678704689975852011489731445555316896444446
Q ss_pred CCCHHCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCC
Q ss_conf 76110167687788710327873334666-44444787779999
Q gi|254780543|r 88 SFDWQKPHCVNATGSLNSYYPRFRRDNMA-GTSTKGKYSAWSPD 130 (131)
Q Consensus 88 ~~~Wqk~h~~N~TGT~~AY~P~~~~~~~~-~~~~~~~Y~aW~Pe 130 (131)
..+|||+|+||+|||..||+|+|++...+ ++...+||.+|+|+
T Consensus 75 ~reWqKph~pn~tgt~~a~rPkgs~~~~gerp~~t~dYdaWtP~ 118 (118)
T COG3761 75 PREWQKPHLPNLTGTPHAYRPKGSLARAGERPRVTGDYDAWTPG 118 (118)
T ss_pred HHHHCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 43412555668789821235676413567676423553456799
No 3
>pfam05071 NDUFA12 NADH ubiquinone oxidoreductase subunit NDUFA12. This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologues. The family also contains a second related eukaryotic protein of unknown function.
Probab=100.00 E-value=2.8e-45 Score=262.61 Aligned_cols=100 Identities=45% Similarity=0.951 Sum_probs=91.1
Q ss_pred CEEEEEECCCCEEEEECCCCCCCCCEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCC
Q ss_conf 70436666587865505777777620899478667553686532003214168898564567611016768778871032
Q gi|254780543|r 27 GHIVGKDEFGNTYYESRKNINGSSRRWVIYNGYTDPSSIPPMWHGWIHHRRIGVPKAEEENSFDWQKPHCVNATGSLNSY 106 (131)
Q Consensus 27 g~~VG~D~~GNkYye~~~~~~~~~rRwV~Y~~~~d~s~IppeWh~WLh~~~d~~P~~~~~~~~~Wqk~h~~N~TGT~~AY 106 (131)
|++||+|+|||+|||+++.. +++||||||++++|||+||||||+||||++|++|++.+..++.||++|++|+|||+.||
T Consensus 1 G~~VG~D~~GNkYYe~~~~~-~~~~RWV~Y~~~~daS~IppeWh~WLh~~~d~~P~~~~~~~~~Wqk~h~~N~TGT~~aY 79 (100)
T pfam05071 1 GTLVGEDEFGNKYYENKDEL-GGRRRWVIYNGKAEASRVPPEWHGWLHHTTDEPPTEEPLKPRAWEKPHQPNLTGTPGAY 79 (100)
T ss_pred CCEEEECCCCCCCCCCCCCC-CCCEEEEEECCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 98820618887846778877-88545888599877352880111022226678986466667654467788788996678
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 78733346664444478777999
Q gi|254780543|r 107 YPRFRRDNMAGTSTKGKYSAWSP 129 (131)
Q Consensus 107 ~P~~~~~~~~~~~~~~~Y~aW~P 129 (131)
+|.++++. ....++||++|+|
T Consensus 80 ~P~~~~~~--~~~~~~~Ye~W~P 100 (100)
T pfam05071 80 RPYGSLLR--RPRATGDYEAWTP 100 (100)
T ss_pred CCCCCCCC--CCCCCCCCCCCCC
T ss_conf 18985002--3113478677796
No 4
>PRK06630 hypothetical protein; Provisional
Probab=100.00 E-value=6.7e-41 Score=239.56 Aligned_cols=87 Identities=40% Similarity=0.744 Sum_probs=78.0
Q ss_pred CEEHHHHHHHHHCEEEEEECCCCEEEEECCC-CCCCCCEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHC
Q ss_conf 6610214331307043666658786550577-777762089947866755368653200321416889856456761101
Q gi|254780543|r 15 QTLGTRFFTWRFGHIVGKDEFGNTYYESRKN-INGSSRRWVIYNGYTDPSSIPPMWHGWIHHRRIGVPKAEEENSFDWQK 93 (131)
Q Consensus 15 ~TlgT~l~t~~~g~~VG~D~~GNkYye~~~~-~~~~~rRwV~Y~~~~d~s~IppeWh~WLh~~~d~~P~~~~~~~~~Wqk 93 (131)
|+|+|+|||+|+|++||+|+|||+|||++.. ..++.||||||+|++|||+||||||+||||+.|++|+. ..+++|||
T Consensus 1 M~~~~klyt~f~gk~VG~DefGNkYYe~k~~~~~~r~rRWViY~g~~EASkIPpeWH~WLHht~d~~P~~--~~~~~WQK 78 (99)
T PRK06630 1 MSWIDKFFITFFHKKVGEDEFLNQYYESRNIDYLGRPRRFVIYKNVNEPTKIPPSWHAWLHHLVNEIPKN--IQLFPWQK 78 (99)
T ss_pred CCHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCHHHHHHHCCCCCCCCC--CCCCCCCC
T ss_conf 9478876987204571571878880345887777886178984897645608805654441477868875--55566544
Q ss_pred CC-----CCCCCCCC
Q ss_conf 67-----68778871
Q gi|254780543|r 94 PH-----CVNATGSL 103 (131)
Q Consensus 94 ~h-----~~N~TGT~ 103 (131)
+| +||+|||.
T Consensus 79 ~Hk~~~~lpn~tgtk 93 (99)
T PRK06630 79 NNKIVKKLPKTSNLK 93 (99)
T ss_pred CCCCCCCCCCCCCCC
T ss_conf 765232277766764
No 5
>KOG3382 consensus
Probab=100.00 E-value=5.9e-34 Score=202.33 Aligned_cols=98 Identities=35% Similarity=0.730 Sum_probs=88.0
Q ss_pred HHHCEEEEEECCCCEEEEECCCCCCCCCEEEEECC----CCCCCCCCCCCCCEEECCCCCCCCCC-CCCCCCHHCCCCCC
Q ss_conf 13070436666587865505777777620899478----66755368653200321416889856-45676110167687
Q gi|254780543|r 24 WRFGHIVGKDEFGNTYYESRKNINGSSRRWVIYNG----YTDPSSIPPMWHGWIHHRRIGVPKAE-EENSFDWQKPHCVN 98 (131)
Q Consensus 24 ~~~g~~VG~D~~GNkYye~~~~~~~~~rRwV~Y~~----~~d~s~IppeWh~WLh~~~d~~P~~~-~~~~~~Wqk~h~~N 98 (131)
.+-|+|||+|.|||||||+.+...||. |||+|.. ++|+|+||||||+|||+++|+||+.. .+.++.|-.+|.+|
T Consensus 44 ~kiGTLVG~DkfGNkYyen~~~fygRh-RWVeya~kv~~Dyd~S~VP~EWh~WlH~iTD~~p~~~~~~~~~k~i~eHkeN 122 (151)
T KOG3382 44 HKIGTLVGVDKFGNKYYENNDYFYGRH-RWVEYASKVNWDYDASQVPAEWHGWLHFITDDPPDEKLPLPPKKWILEHKEN 122 (151)
T ss_pred CCCEEEEEECCCCCCHHCCCCEECCCC-EEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCC
T ss_conf 310035600134520112652112432-0477056234355546788888747674036896344798777886741223
Q ss_pred CCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 788-71032787333466644444787779999
Q gi|254780543|r 99 ATG-SLNSYYPRFRRDNMAGTSTKGKYSAWSPD 130 (131)
Q Consensus 99 ~TG-T~~AY~P~~~~~~~~~~~~~~~Y~aW~Pe 130 (131)
++| |..+|.| ++++..+|++|.|-
T Consensus 123 ~Sg~t~e~y~P--------ystt~tkiq~W~P~ 147 (151)
T KOG3382 123 FSGETGETYVP--------YSTTRTKIQSWVPT 147 (151)
T ss_pred CCCCCCCEECC--------CCCCHHHHHEECCC
T ss_conf 56668850056--------76775674100688
No 6
>pfam11385 DUF3189 Protein of unknown function (DUF3189). This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=42.87 E-value=15 Score=17.86 Aligned_cols=15 Identities=47% Similarity=0.849 Sum_probs=12.8
Q ss_pred EEEEEECCCCEEEEE
Q ss_conf 043666658786550
Q gi|254780543|r 28 HIVGKDEFGNTYYES 42 (131)
Q Consensus 28 ~~VG~D~~GNkYye~ 42 (131)
.++|+|++||.=|.-
T Consensus 53 ~y~G~De~gN~VY~~ 67 (148)
T pfam11385 53 IYIGKDEYGNEVYTL 67 (148)
T ss_pred EEEEECCCCCEEEEE
T ss_conf 997775999988998
No 7
>pfam10743 Phage_Cox Regulatory phage protein cox. This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes.
Probab=30.76 E-value=14 Score=18.03 Aligned_cols=34 Identities=21% Similarity=0.404 Sum_probs=20.1
Q ss_pred EEECCCCCCCCCEEEEECCCC------CCCCCCCC----CCCEEE
Q ss_conf 550577777762089947866------75536865----320032
Q gi|254780543|r 40 YESRKNINGSSRRWVIYNGYT------DPSSIPPM----WHGWIH 74 (131)
Q Consensus 40 ye~~~~~~~~~rRwV~Y~~~~------d~s~Ippe----Wh~WLh 74 (131)
..+..+..++..+|| |-.+. -...-|+| ||.||-
T Consensus 43 ~~dP~~~~~rgE~wi-~~pewn~~~r~a~~~~P~E~Rd~Wl~Wlg 86 (87)
T pfam10743 43 MRDPQKPKGRGELWV-HRPEWNKYAKQAFETRPPEIRDGWLMWKG 86 (87)
T ss_pred CCCCCCCCCCCEEEE-EHHHHHHHHHHHHHHCCHHHHHHHHHHCC
T ss_conf 568999887733887-64887899999887178788778988636
No 8
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA; InterPro: IPR010222 This entry represents HrpA, one of two related but uncharacterised DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterised, is about 800 amino acids long. Related characterised eukaryotic proteins are RNA helicases associated with pre-mRNA processing.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity.
Probab=20.18 E-value=75 Score=14.18 Aligned_cols=63 Identities=21% Similarity=0.377 Sum_probs=45.9
Q ss_pred CCEEEEECCCCCCC-CCEEEEECCCCCCCC--------CCCCCCCEEECCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCC
Q ss_conf 87865505777777-620899478667553--------686532003214168898564567611016768778871032
Q gi|254780543|r 36 GNTYYESRKNINGS-SRRWVIYNGYTDPSS--------IPPMWHGWIHHRRIGVPKAEEENSFDWQKPHCVNATGSLNSY 106 (131)
Q Consensus 36 GNkYye~~~~~~~~-~rRwV~Y~~~~d~s~--------IppeWh~WLh~~~d~~P~~~~~~~~~Wqk~h~~N~TGT~~AY 106 (131)
|-+|+..+.+..++ +=.||.-+.-+|.|+ |.|||- | |-...+.|+.+-.||=+.--|..-||
T Consensus 661 ~~~F~iFPGS~L~kK~PkWvmAAELVETSkL~AR~~AkIEPEWv--------E-~~A~HLiKk~~~EPHWE~k~G~vmA~ 731 (1320)
T TIGR01967 661 GRKFFIFPGSGLFKKPPKWVMAAELVETSKLYARLVAKIEPEWV--------E-PVAGHLIKKNYFEPHWEKKRGAVMAY 731 (1320)
T ss_pred CCEEEEECCCCCCCCCCCEEEECCHHHHHHHHHHHHCCCCCCCC--------C-HHCCCCCCCCCCCCCHHHHHCCEEEE
T ss_conf 76357734876677888148860104566888854201484410--------0-23052136888886476552037755
Q ss_pred C
Q ss_conf 7
Q gi|254780543|r 107 Y 107 (131)
Q Consensus 107 ~ 107 (131)
-
T Consensus 732 E 732 (1320)
T TIGR01967 732 E 732 (1320)
T ss_pred E
T ss_conf 3
No 9
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=18.62 E-value=17 Score=17.67 Aligned_cols=15 Identities=13% Similarity=0.412 Sum_probs=10.8
Q ss_pred CCCCCCCEEECCCCC
Q ss_conf 686532003214168
Q gi|254780543|r 65 IPPMWHGWIHHRRIG 79 (131)
Q Consensus 65 IppeWh~WLh~~~d~ 79 (131)
-.-||++||+.+-.+
T Consensus 60 t~~Ef~~WLR~IL~~ 74 (190)
T TIGR02984 60 TEGEFAGWLRQILAN 74 (190)
T ss_pred CHHHHHHHHHHHHHH
T ss_conf 857899999999999
No 10
>KOG3731 consensus
Probab=18.31 E-value=48 Score=15.22 Aligned_cols=18 Identities=39% Similarity=0.811 Sum_probs=0.0
Q ss_pred ECCCCCCCCCCCCCCCEE
Q ss_conf 478667553686532003
Q gi|254780543|r 56 YNGYTDPSSIPPMWHGWI 73 (131)
Q Consensus 56 Y~~~~d~s~IppeWh~WL 73 (131)
|-.++++|-|||.|..|.
T Consensus 136 ylney~gsyiPpgW~ew~ 153 (541)
T KOG3731 136 YLNEYNGSYIPPGWSEWA 153 (541)
T ss_pred HCCCCCCCCCCCCCHHHH
T ss_conf 226667555899713320
Done!