Query gi|254781092|ref|YP_003065505.1| hypothetical protein CLIBASIA_04970 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 35 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 04:12:52 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781092.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK10921 twin-arginine protein 14.2 90 0.0023 15.0 1.3 23 11-33 220-242 (255) 2 TIGR00603 rad25 DNA repair hel 13.1 48 0.0012 16.3 -0.3 17 3-19 492-510 (756) 3 TIGR02275 DHB_AMP_lig 2,3-dihy 10.8 1.3E+02 0.0034 14.1 1.3 24 6-29 476-502 (534) 4 KOG0967 consensus 10.1 96 0.0024 14.8 0.4 18 8-25 458-477 (714) 5 TIGR01257 rim_protein rim ABC 9.8 1.4E+02 0.0035 14.1 1.1 20 12-31 1349-1368(2272) 6 pfam05756 S-antigen S-antigen 9.7 75 0.0019 15.4 -0.3 18 1-18 1-18 (310) 7 TIGR02015 BchY chlorophyllide 8.1 1.8E+02 0.0047 13.5 1.2 12 16-27 296-308 (426) 8 pfam05798 Phage_FRD3 Bacteriop 6.7 2.2E+02 0.0055 13.2 1.0 27 1-27 27-53 (75) 9 TIGR02745 ccoG_rdxA_fixG cytoc 6.6 1.6E+02 0.0041 13.8 0.3 8 6-13 189-196 (474) 10 TIGR00574 dnl1 DNA ligase I, A 5.7 1.1E+02 0.0028 14.6 -1.0 24 9-32 344-368 (705) No 1 >PRK10921 twin-arginine protein translocation system subunit TatC; Provisional Probab=14.23 E-value=90 Score=14.98 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=18.4 Q ss_pred EEEHHHHCCHHHHHHHHHHHHHC Q ss_conf 11010122079999996345521 Q gi|254781092|r 11 VFLILFYEGELLVKRFMHTKKKN 33 (35) Q Consensus 11 vflilfyegellvkrfmhtkkkn 33 (35) +-+++.||--++.-|+...|+++ T Consensus 220 ~Pl~~LYE~~i~i~~~~~~kr~~ 242 (255) T PRK10921 220 IPMYCLFEIGVFFSRFYVGKGRN 242 (255) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999986644 No 2 >TIGR00603 rad25 DNA repair helicase rad25; InterPro: IPR001161 Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region . XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents XP group B (XP-B) give rise to both XP and Cockayne syndrome . The DNA/RNA helicase domain IPR001650 from INTERPRO is also present in this group of proteins.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006289 nucleotide-excision repair, 0005634 nucleus. Probab=13.11 E-value=48 Score=16.26 Aligned_cols=17 Identities=53% Similarity=0.892 Sum_probs=11.2 Q ss_pred CHHCCHH--HEEEHHHHCC Q ss_conf 0010001--1110101220 Q gi|254781092|r 3 TMKREKF--CVFLILFYEG 19 (35) Q Consensus 3 tmkrekf--cvflilfyeg 19 (35) +|.-.|| |-|||-|-|- T Consensus 492 ~MNP~KFrACqFLI~fHE~ 510 (756) T TIGR00603 492 VMNPNKFRACQFLIRFHER 510 (756) T ss_pred ECCCCHHHHHHHHHHHHHH T ss_conf 0386443577898888541 No 3 >TIGR02275 DHB_AMP_lig 2,3-dihydroxybenzoate-AMP ligase; InterPro: IPR011963 Siderophores are low molecular weight iron-chelating compounds synthesised by many bacteria to aid in the aquisition of this vital trace element . Proteins in this entry are adenylation components of non-ribosomal peptide synthases (NRPSs) involved in the biosynthesis of siderophores. These proteins belong to the AMP-binding family and are mostly thought to activate 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate. One of these proteins, however, is believed to differ in function, activating salicylate rather than DHB. The crystal structure of 2,3-dihydroxybenzoate-AMP ligase (P40871 from SWISSPROT) from Bacillus subtilis has been examined . This protein is composed of a large N-terminal domain (~420 aa) and a more compact C-terminal domain (~110 aa), with an overall "hammer-and-anvil" fold similar to that of firefly luciferase . The active site is located in a deep compartment located at the interface of the domains, with a p-loop thought to be involved in catalysis located at the entrance to the cavity. Relatively little conformational change was observed during catalysis.; GO: 0008668 (23-dihydroxybenzoyl)adenylate synthase activity, 0019290 siderophore biosynthetic process. Probab=10.81 E-value=1.3e+02 Score=14.14 Aligned_cols=24 Identities=25% Similarity=0.591 Sum_probs=19.0 Q ss_pred CCHHHEEEHHHHCC---HHHHHHHHHH Q ss_conf 00011110101220---7999999634 Q gi|254781092|r 6 REKFCVFLILFYEG---ELLVKRFMHT 29 (35) Q Consensus 6 rekfcvflilfyeg---ellvkrfmht 29 (35) -||=|+|+|+--|. -+-+|||.|. T Consensus 476 GEkSCAfIV~~~p~s~~~~~LrrfLr~ 502 (534) T TIGR02275 476 GEKSCAFIVVKDPDSLKAVQLRRFLRE 502 (534) T ss_pred CCEEEEEEEECCCCCCCHHHHHHHHHH T ss_conf 740058888578877680899999986 No 4 >KOG0967 consensus Probab=10.07 E-value=96 Score=14.84 Aligned_cols=18 Identities=50% Similarity=1.075 Sum_probs=13.7 Q ss_pred HHHEEE--HHHHCCHHHHHH Q ss_conf 011110--101220799999 Q gi|254781092|r 8 KFCVFL--ILFYEGELLVKR 25 (35) Q Consensus 8 kfcvfl--ilfyegellvkr 25 (35) ++|||. |+|+.|+.|+.+ T Consensus 458 ~Vcvf~FDily~ng~~Li~~ 477 (714) T KOG0967 458 KVCVFVFDILYLNGESLIQE 477 (714) T ss_pred EEEEEEEEEEEECCHHHHHH T ss_conf 89999985466677456542 No 5 >TIGR01257 rim_protein rim ABC transporter; InterPro: IPR005951 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Rim protein (ABCR), is an ATP binding cassette (ABC)1 transporter found in vertebrate retinal photoreceptor cells. It is localized along the rim region of photoreceptor rod outer segment disc membranes and more recently has been found in human foveal and peripheral cone outer segments. Several studies have implicated ABCR in the retinoid cycle, possibly functioning as a retinal extruder or retinal-phosphatidylethanolamine flippase to facilitate the removal of all-trans-retinal from disc membranes following the photobleaching of rhodopsin . ABCR contains eight glycosylation sites. Four sites reside in a 600-amino acid exocytoplasmic domain of the N-terminal half between the first transmembrane segment H1 and the first multi-spanning membrane domain, and four sites are in a 275-amino acid domain of the C half between transmembrane segment H7 and the second multi-spanning membrane domain. This leads to a model in which each half has a transmembrane segment followed by a large exocytoplasmic domain, a multi-spanning membrane domain, and a nucleotide binding domain. ; GO: 0005524 ATP binding, 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0005887 integral to plasma membrane. Probab=9.82 E-value=1.4e+02 Score=14.08 Aligned_cols=20 Identities=55% Similarity=0.592 Sum_probs=15.0 Q ss_pred EEHHHHCCHHHHHHHHHHHH Q ss_conf 10101220799999963455 Q gi|254781092|r 12 FLILFYEGELLVKRFMHTKK 31 (35) Q Consensus 12 flilfyegellvkrfmhtkk 31 (35) -||+-.--.||||||-||-+ T Consensus 1349 ~l~~qhvqallvkrf~htir 1368 (2272) T TIGR01257 1349 RLILQHVQALLVKRFQHTIR 1368 (2272) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 67899999999998776553 No 6 >pfam05756 S-antigen S-antigen protein. S-antigens are heat stable proteins that are found in the blood of individuals infected with malaria. Probab=9.65 E-value=75 Score=15.36 Aligned_cols=18 Identities=33% Similarity=0.643 Sum_probs=14.1 Q ss_pred CCCHHCCHHHEEEHHHHC Q ss_conf 970010001111010122 Q gi|254781092|r 1 MNTMKREKFCVFLILFYE 18 (35) Q Consensus 1 mntmkrekfcvflilfye 18 (35) ||.+-.-.||.|.|..|- T Consensus 1 MNRILSVsfyLFFiYLYI 18 (310) T pfam05756 1 MNRILSVTFYLFFIYLYI 18 (310) T ss_pred CCCEEEEHHHHHHHHHHH T ss_conf 972353157899999999 No 7 >TIGR02015 BchY chlorophyllide reductase subunit Y; InterPro: IPR010245 This entry represents the Y subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase , . This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.; GO: 0016731 oxidoreductase activity acting on iron-sulfur proteins as donors NAD or NADP as acceptor, 0015979 photosynthesis, 0030494 bacteriochlorophyll biosynthetic process, 0016021 integral to membrane. Probab=8.12 E-value=1.8e+02 Score=13.48 Aligned_cols=12 Identities=67% Similarity=0.988 Sum_probs=6.5 Q ss_pred HHCC-HHHHHHHH Q ss_conf 1220-79999996 Q gi|254781092|r 16 FYEG-ELLVKRFM 27 (35) Q Consensus 16 fyeg-ellvkrfm 27 (35) =||| ||+|-|.+ T Consensus 296 GYEG~EL~~~RLL 308 (426) T TIGR02015 296 GYEGSELLVVRLL 308 (426) T ss_pred ECCCCHHHHHHHH T ss_conf 1156268888988 No 8 >pfam05798 Phage_FRD3 Bacteriophage FRD3 protein. This family consists of bacteriophage FRD3 proteins. Probab=6.70 E-value=2.2e+02 Score=13.16 Aligned_cols=27 Identities=22% Similarity=0.346 Sum_probs=0.0 Q ss_pred CCCHHCCHHHEEEHHHHCCHHHHHHHH Q ss_conf 970010001111010122079999996 Q gi|254781092|r 1 MNTMKREKFCVFLILFYEGELLVKRFM 27 (35) Q Consensus 1 mntmkrekfcvflilfyegellvkrfm 27 (35) |...+..+||-+-|..-.----++||| T Consensus 27 i~si~d~~f~~~~i~i~GPle~l~~FM 53 (75) T pfam05798 27 IDSVQDSKFWSIQIVIEGPLEDLKKFM 53 (75) T ss_pred EEEEECCCCCEEEEEEECCHHHHHHHH T ss_conf 776524886259999856599999999 No 9 >TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein CcoG; InterPro: IPR014116 Member of this ferredoxin-like protein family, include FixG, CcoG and RdxA,. They are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else; it is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.. Probab=6.64 E-value=1.6e+02 Score=13.77 Aligned_cols=8 Identities=50% Similarity=1.634 Sum_probs=0.0 Q ss_pred CCHHHEEE Q ss_conf 00011110 Q gi|254781092|r 6 REKFCVFL 13 (35) Q Consensus 6 rekfcvfl 13 (35) ||.||+++ T Consensus 189 RE~~Ciym 196 (474) T TIGR02745 189 REQFCIYM 196 (474) T ss_pred HHHHHEEE T ss_conf 66211034 No 10 >TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1); InterPro: IPR000977 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (220.127.116.11 from EC), the other NAD (18.104.22.168 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination ,. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold , . ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006260 DNA replication, 0006281 DNA repair, 0006310 DNA recombination. Probab=5.73 E-value=1.1e+02 Score=14.57 Aligned_cols=24 Identities=29% Similarity=0.570 Sum_probs=0.0 Q ss_pred HH-EEEHHHHCCHHHHHHHHHHHHH Q ss_conf 11-1101012207999999634552 Q gi|254781092|r 9 FC-VFLILFYEGELLVKRFMHTKKK 32 (35) Q Consensus 9 fc-vflilfyegellvkrfmhtkkk 32 (35) +| ||=|||+.|+-|+..=.+-.++ T Consensus 344 ~fl~FD~LY~ng~~L~~~pL~~RR~ 368 (705) T TIGR00574 344 LFLVFDILYLNGESLIDEPLIERRE 368 (705) T ss_pred EEEEEEEEEECCCCCCCCCHHHHHH T ss_conf 4444656232780355677388999 Done!