Query gi|254781153|ref|YP_003065566.1| hypothetical protein CLIBASIA_05300 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 30
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 05:29:20 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781153.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07209 ribonucleotide-diphos 87.4 0.16 4E-06 28.0 0.1 26 3-28 42-67 (391)
2 TIGR01978 sufC FeS assembly AT 12.9 35 0.0009 17.7 -1.1 13 16-28 7-19 (248)
3 TIGR02343 chap_CCT_epsi T-comp 9.1 95 0.0024 15.8 0.1 13 1-13 466-478 (541)
4 KOG0088 consensus 8.7 53 0.0013 16.9 -1.4 28 3-30 39-68 (218)
5 KOG0357 consensus 7.8 1.3E+02 0.0032 15.3 0.2 13 1-13 321-333 (400)
6 TIGR02342 chap_CCT_delta T-com 7.0 1.4E+02 0.0035 15.1 0.1 11 1-11 452-462 (526)
7 TIGR02339 thermosome_arch ther 6.3 1.2E+02 0.0032 15.3 -0.4 11 2-12 447-457 (522)
8 pfam10375 GRAB GRIP-related Ar 6.1 2.3E+02 0.0058 14.2 0.8 10 20-29 6-15 (26)
9 cd01204 IRS_PTB Insulin recept 5.7 3E+02 0.0077 13.6 1.3 23 7-29 69-91 (104)
10 COG0832 UreB Urea amidohydrola 5.4 2E+02 0.0052 14.4 0.2 13 3-15 27-39 (106)
No 1
>PRK07209 ribonucleotide-diphosphate reductase subunit beta; Validated
Probab=87.36 E-value=0.16 Score=27.98 Aligned_cols=26 Identities=50% Similarity=0.733 Sum_probs=21.7
Q ss_pred CCCCCCHHHCCCEECCCCHHHHHHHH
Q ss_conf 67567701104302054246678763
Q gi|254781153|r 3 NNTGLSPIQAGEKRVNVDDKRILTNI 28 (30)
Q Consensus 3 nntglspiqagekrvnvddkriltni 28 (30)
..+|+..+..|..||+|||||+...-
T Consensus 42 ~~~~~~~~~~~~~r~~~~~k~~in~~ 67 (391)
T PRK07209 42 VATGLEELEGGAARVNVDDKRIINCR 67 (391)
T ss_pred CCCCHHHHHCCCCCCCCCCCCEECCC
T ss_conf 55536676434776674521002265
No 2
>TIGR01978 sufC FeS assembly ATPase SufC; InterPro: IPR010230 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents SufC, which acts as an ATPase in the SUF system. SufC belongs to the ATP-binding cassette transporter family (IPR003439 from INTERPRO) but is no longer thought to be part of a transporter. The complex is reported as cytosolic or associated with the membrane.; GO: 0005524 ATP binding, 0006810 transport.
Probab=12.91 E-value=35 Score=17.71 Aligned_cols=13 Identities=46% Similarity=0.792 Sum_probs=8.2
Q ss_pred ECCCCHHHHHHHH
Q ss_conf 2054246678763
Q gi|254781153|r 16 RVNVDDKRILTNI 28 (30)
Q Consensus 16 rvnvddkriltni 28 (30)
.|.|+||+||.++
T Consensus 7 hv~~edk~IL~gv 19 (248)
T TIGR01978 7 HVSVEDKEILKGV 19 (248)
T ss_pred EEEECCEECCCCC
T ss_conf 8887788616786
No 3
>TIGR02343 chap_CCT_epsi T-complex protein 1, epsilon subunit; InterPro: IPR012718 Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT epsilon chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=9.07 E-value=95 Score=15.81 Aligned_cols=13 Identities=46% Similarity=0.820 Sum_probs=9.8
Q ss_pred CCCCCCCCHHHCC
Q ss_conf 9867567701104
Q gi|254781153|r 1 MANNTGLSPIQAG 13 (30)
Q Consensus 1 manntglspiqag 13 (30)
+|.|.|+.||++-
T Consensus 466 LA~NSGl~PI~~~ 478 (541)
T TIGR02343 466 LAENSGLDPIETL 478 (541)
T ss_pred HHHHCCCCHHHHH
T ss_conf 7640687768999
No 4
>KOG0088 consensus
Probab=8.73 E-value=53 Score=16.94 Aligned_cols=28 Identities=46% Similarity=0.515 Sum_probs=20.2
Q ss_pred CCCCCCHHHCC--CEECCCCHHHHHHHHCC
Q ss_conf 67567701104--30205424667876329
Q gi|254781153|r 3 NNTGLSPIQAG--EKRVNVDDKRILTNIVD 30 (30)
Q Consensus 3 nntglspiqag--ekrvnvddkriltnivd 30 (30)
|..-||.+||. .|.+|+.|+|.--+|-|
T Consensus 39 n~kHlsTlQASF~~kk~n~ed~ra~L~IWD 68 (218)
T KOG0088 39 NCKHLSTLQASFQNKKVNVEDCRADLHIWD 68 (218)
T ss_pred CHHHHHHHHHHHHHCCCCCCCCEEEEEEEE
T ss_conf 304678999887633046211131143212
No 5
>KOG0357 consensus
Probab=7.77 E-value=1.3e+02 Score=15.27 Aligned_cols=13 Identities=46% Similarity=0.820 Sum_probs=9.8
Q ss_pred CCCCCCCCHHHCC
Q ss_conf 9867567701104
Q gi|254781153|r 1 MANNTGLSPIQAG 13 (30)
Q Consensus 1 manntglspiqag 13 (30)
.|.|.||.||++-
T Consensus 321 laensgl~pi~~l 333 (400)
T KOG0357 321 LAENSGLDPIETL 333 (400)
T ss_pred HHHCCCCCCHHHH
T ss_conf 5541688830346
No 6
>TIGR02342 chap_CCT_delta T-complex protein 1, delta subunit; InterPro: IPR012717 Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=7.04 E-value=1.4e+02 Score=15.10 Aligned_cols=11 Identities=55% Similarity=1.063 Sum_probs=8.3
Q ss_pred CCCCCCCCHHH
Q ss_conf 98675677011
Q gi|254781153|r 1 MANNTGLSPIQ 11 (30)
Q Consensus 1 manntglspiq 11 (30)
+|.|.||+||.
T Consensus 452 LAENAGL~pi~ 462 (526)
T TIGR02342 452 LAENAGLNPIK 462 (526)
T ss_pred HHHHCCCCHHH
T ss_conf 44540677257
No 7
>TIGR02339 thermosome_arch thermosome, various subunits, archaeal; InterPro: IPR012714 Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacteria), a toroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=6.34 E-value=1.2e+02 Score=15.31 Aligned_cols=11 Identities=64% Similarity=1.020 Sum_probs=7.9
Q ss_pred CCCCCCCHHHC
Q ss_conf 86756770110
Q gi|254781153|r 2 ANNTGLSPIQA 12 (30)
Q Consensus 2 anntglspiqa 12 (30)
|.|.||-||++
T Consensus 447 AENAGlDPID~ 457 (522)
T TIGR02339 447 AENAGLDPIDA 457 (522)
T ss_pred HHHCCCCHHHH
T ss_conf 86338688899
No 8
>pfam10375 GRAB GRIP-related Arf-binding domain. The GRAB (GRIP-related Arf-binding) domain is towards the C-terminus of Rud3 type proteins. This domain is related to the GRIP domain, but the conserved tyrosine residue found at position 4 in all GRIP domains is replaced by a leucine residue. The Arf small GTPase is localized to the cis-Golgi where it recruits proteins via their GRAB domain, as part of the transport of cargo from the endoplasmic reticulum to the plasma membrane.
Probab=6.06 E-value=2.3e+02 Score=14.18 Aligned_cols=10 Identities=40% Similarity=0.840 Sum_probs=7.4
Q ss_pred CHHHHHHHHC
Q ss_conf 2466787632
Q gi|254781153|r 20 DDKRILTNIV 29 (30)
Q Consensus 20 ddkriltniv 29 (30)
-|||+.+|..
T Consensus 6 VDK~lISNll 15 (26)
T pfam10375 6 VDKRLISNLL 15 (26)
T ss_pred HHHHHHHHHH
T ss_conf 8899999999
No 9
>cd01204 IRS_PTB Insulin receptor substrate (IRS) Phosphotyrosine-binding domain(PTB). This domain has a PH-like fold and is found in insulin receptor substrate molecules. IRS molecules have an N-terminal PH domain , which is followed by an IRS-like PTB domain. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs in the insulin receptor, IGF-I receptor and the IL-4 receptor.
Probab=5.73 E-value=3e+02 Score=13.62 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=19.2
Q ss_pred CCHHHCCCEECCCCHHHHHHHHC
Q ss_conf 77011043020542466787632
Q gi|254781153|r 7 LSPIQAGEKRVNVDDKRILTNIV 29 (30)
Q Consensus 7 lspiqagekrvnvddkriltniv 29 (30)
-|++-+||--..+||.-|-.|+-
T Consensus 69 ss~~G~GElWMq~~D~~vAqnmH 91 (104)
T cd01204 69 SAVTGPGELWMQVDDAVVAQNMH 91 (104)
T ss_pred CCCCCCCEEEEECCCHHHHHHHH
T ss_conf 36779963899846389999999
No 10
>COG0832 UreB Urea amidohydrolase (urease) beta subunit [Amino acid transport and metabolism]
Probab=5.42 E-value=2e+02 Score=14.38 Aligned_cols=13 Identities=54% Similarity=0.774 Sum_probs=10.5
Q ss_pred CCCCCCHHHCCCE
Q ss_conf 6756770110430
Q gi|254781153|r 3 NNTGLSPIQAGEK 15 (30)
Q Consensus 3 nntglspiqagek 15 (30)
.|||--|||.|..
T Consensus 27 ~NtGDRPIQVGSH 39 (106)
T COG0832 27 ANTGDRPIQVGSH 39 (106)
T ss_pred EECCCCCEEEECC
T ss_conf 6169985275041
Done!