Query gi|254780691|ref|YP_003065104.1| hypothetical protein CLIBASIA_02890 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 55
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Sun May 29 20:05:46 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780691.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01286 nifK nitrogenase mol 44.5 13 0.00032 18.8 1.5 24 1-43 117-140 (526)
2 smart00076 IFabd Interferon al 24.3 50 0.0013 15.6 1.9 22 33-54 81-102 (117)
3 cd00095 IFab Interferon alpha, 23.1 59 0.0015 15.2 2.1 21 34-54 114-134 (152)
4 PRK08561 rps15p 30S ribosomal 18.1 83 0.0021 14.4 1.9 27 21-47 109-135 (151)
5 TIGR01485 SPP_plant-cyano sucr 17.4 27 0.00068 17.1 -0.7 14 3-16 200-213 (257)
6 PTZ00072 40S ribosomal protein 17.1 45 0.0012 15.8 0.4 28 21-48 106-133 (148)
7 pfam00143 Interferon Interfero 16.9 96 0.0024 14.1 2.1 20 35-54 121-140 (167)
8 TIGR01945 rnfC electron transp 15.3 95 0.0024 14.1 1.7 20 33-52 425-444 (444)
9 KOG4704 consensus 13.9 79 0.002 14.5 1.0 30 16-45 342-371 (431)
10 KOG1349 consensus 11.4 1.4E+02 0.0036 13.2 1.9 31 25-55 152-182 (309)
No 1
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain; InterPro: IPR005976 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene , . Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes . It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0016612 molybdenum-iron nitrogenase complex.
Probab=44.48 E-value=13 Score=18.85 Aligned_cols=24 Identities=54% Similarity=0.769 Sum_probs=14.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9715888856545569999975568897632331129999999
Q gi|254780691|r 1 MEEDAEVFRTSHVRGVHDILLRSSFFLKLQNMKNIGLQRYYKR 43 (55)
Q Consensus 1 meedaevfrtshvrgvhdillrssfflklqnmkniglqryykr 43 (55)
|-|||-||- -|+||+. |||--|+-
T Consensus 117 MTEdAAVFG------------------Gl~Nmvd-GL~N~~al 140 (526)
T TIGR01286 117 MTEDAAVFG------------------GLKNMVD-GLQNIYAL 140 (526)
T ss_pred CCHHHHHHC------------------CHHHHHH-HHHHHHHH
T ss_conf 413578742------------------5677999-99740432
No 2
>smart00076 IFabd Interferon alpha, beta and delta. Interferons produce antiviral and antiproliferative responses in cells. They are classified into five groups, all of them related but gamma-interferon.
Probab=24.34 E-value=50 Score=15.57 Aligned_cols=22 Identities=27% Similarity=0.818 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 3112999999999999776404
Q gi|254780691|r 33 KNIGLQRYYKRVKTVIRAKKYQ 54 (55)
Q Consensus 33 kniglqryykrvktvirakkyq 54 (55)
..+.+.+||.|.......|+|.
T Consensus 81 ~~L~lkkYF~rI~~yLk~K~yS 102 (117)
T smart00076 81 THLALRKYFQRIQLYLKEKKYS 102 (117)
T ss_pred CCHHHHHHHHHHHHHHHHCCCC
T ss_conf 4269999998999999847996
No 3
>cd00095 IFab Interferon alpha, beta. Includes also interferon omega and tau. Different from interferon gamma family. Type I interferons(alpha, beta) belong to the larger helical cytokine superfamily, which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules. All function as regulators of cellular activty by interacting with cell-surface receptors and activating various signalling pathways. Interferons produce antiviral and antiproliferative responses in cells. Receptor specificity determines function of the various members of the family.
Probab=23.15 E-value=59 Score=15.21 Aligned_cols=21 Identities=29% Similarity=0.825 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHC
Q ss_conf 112999999999999776404
Q gi|254780691|r 34 NIGLQRYYKRVKTVIRAKKYQ 54 (55)
Q Consensus 34 niglqryykrvktvirakkyq 54 (55)
.+.+.+||.|.......|+|-
T Consensus 114 ~L~lk~YF~rI~~yLk~K~YS 134 (152)
T cd00095 114 HLHLRKYFQRIQLYLKEKKYS 134 (152)
T ss_pred CHHHHHHHHHHHHHHHHCCCC
T ss_conf 169999987999998747996
No 4
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=18.05 E-value=83 Score=14.40 Aligned_cols=27 Identities=33% Similarity=0.380 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 755688976323311299999999999
Q gi|254780691|r 21 LRSSFFLKLQNMKNIGLQRYYKRVKTV 47 (55)
Q Consensus 21 lrssfflklqnmkniglqryykrvktv 47 (55)
..+.|-|.|-.-|---|-||||+.+..
T Consensus 109 ~~~Kr~L~LiESkI~RL~rYYk~~~~L 135 (151)
T PRK08561 109 LHNKRGLQLIESKIRRLVKYYKRTGVL 135 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 666899999999999999998714848
No 5
>TIGR01485 SPP_plant-cyano sucrose phosphatase; InterPro: IPR012847 This entry describes the sucrose phosphate phosphohydrolase from plants and cyanobacteria (SPP). However, a closely related group of sequences from bacteria and archaea may prove to catalyze the same reaction. SPP is a member of the Class IIB subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain, which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain..
Probab=17.39 E-value=27 Score=17.09 Aligned_cols=14 Identities=50% Similarity=0.840 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 15888856545569
Q gi|254780691|r 3 EDAEVFRTSHVRGV 16 (55)
Q Consensus 3 edaevfrtshvrgv 16 (55)
.|++.|.++.+|||
T Consensus 200 NDi~LF~~~~~~Gv 213 (257)
T TIGR01485 200 NDIELFEIGSVRGV 213 (257)
T ss_pred CCHHHHCCCCCCEE
T ss_conf 34765217973148
No 6
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=17.11 E-value=45 Score=15.84 Aligned_cols=28 Identities=43% Similarity=0.502 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7556889763233112999999999999
Q gi|254780691|r 21 LRSSFFLKLQNMKNIGLQRYYKRVKTVI 48 (55)
Q Consensus 21 lrssfflklqnmkniglqryykrvktvi 48 (55)
..+.|-|.|-.-|---|-||||+.+..-
T Consensus 106 ~~~kr~L~LiESkI~RL~rYYk~~~~LP 133 (148)
T PTZ00072 106 KDSKFRLILVESRIHRLARYYKRVKQLP 133 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 2457899999999999999986067079
No 7
>pfam00143 Interferon Interferon alpha/beta domain.
Probab=16.93 E-value=96 Score=14.06 Aligned_cols=20 Identities=30% Similarity=0.863 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHC
Q ss_conf 12999999999999776404
Q gi|254780691|r 35 IGLQRYYKRVKTVIRAKKYQ 54 (55)
Q Consensus 35 iglqryykrvktvirakkyq 54 (55)
+.+.+||.|.......|+|-
T Consensus 121 L~lkkYF~rI~~yLk~K~YS 140 (167)
T pfam00143 121 LALKKYFQRIHLYLKEKKYS 140 (167)
T ss_pred HHHHHHHHHHHHHHHHCCCC
T ss_conf 89999997999998748996
No 8
>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit; InterPro: IPR010208 The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase (IPR003667 from INTERPRO), but is distinct. This entry describes the C subunit.; GO: 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport, 0016020 membrane.
Probab=15.28 E-value=95 Score=14.07 Aligned_cols=20 Identities=40% Similarity=0.629 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 31129999999999997764
Q gi|254780691|r 33 KNIGLQRYYKRVKTVIRAKK 52 (55)
Q Consensus 33 kniglqryykrvktvirakk 52 (55)
-||-|-+||+--|..||+++
T Consensus 425 s~iPLV~Y~R~aK~~~~~~~ 444 (444)
T TIGR01945 425 SNIPLVQYIRQAKAKLREKK 444 (444)
T ss_pred CCCHHHHHHHHHHHHHHCCC
T ss_conf 75258999988789861379
No 9
>KOG4704 consensus
Probab=13.93 E-value=79 Score=14.50 Aligned_cols=30 Identities=30% Similarity=0.478 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999997556889763233112999999999
Q gi|254780691|r 16 VHDILLRSSFFLKLQNMKNIGLQRYYKRVK 45 (55)
Q Consensus 16 vhdillrssfflklqnmkniglqryykrvk 45 (55)
-.+|.+-|.|||.-|...|-.+-||+.|+-
T Consensus 342 s~~~F~~~~ffL~~~E~nNen~~~yf~R~~ 371 (431)
T KOG4704 342 SKYIFNTSHFFLTDQEFNNENMLDYFQRYN 371 (431)
T ss_pred HHHHHHHCCCEECCCCCCCHHHHHHHHHHH
T ss_conf 656653112120474646447899999999
No 10
>KOG1349 consensus
Probab=11.38 E-value=1.4e+02 Score=13.17 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 8897632331129999999999997764049
Q gi|254780691|r 25 FFLKLQNMKNIGLQRYYKRVKTVIRAKKYQE 55 (55)
Q Consensus 25 fflklqnmkniglqryykrvktvirakkyqe 55 (55)
-|||.|+...|.-+..-.+++..-.+|.|.|
T Consensus 152 ~FlKFqd~eelts~dLadai~qm~e~~Ryne 182 (309)
T KOG1349 152 GFLKFQDAEELTSDDLADAIQQMWEKKRYNE 182 (309)
T ss_pred CCEECCCHHHHHHHHHHHHHHHHHHHHHHCE
T ss_conf 2033266887646788999999998632324
Done!