Query gi|254781154|ref|YP_003065567.1| hypothetical protein CLIBASIA_05305 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 65 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 254781154.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG4687 Uncharacterized protei 75.9 1.1 2.9E-05 24.6 1.0 25 2-27 16-40 (122) 2 pfam06115 DUF956 Domain of unk 73.1 1.5 3.7E-05 24.1 0.9 25 2-27 16-40 (118) 3 COG1427 Predicted periplasmic 22.9 23 0.00059 18.2 -0.1 31 4-34 125-155 (252) 4 pfam10876 DUF2669 Protein of u 17.0 27 0.00069 17.9 -0.8 19 18-36 89-107 (133) 5 pfam08144 CPL CPL (NUC119) dom 14.3 60 0.0015 16.2 0.4 21 35-55 125-145 (148) 6 TIGR02782 TrbB_P P-type conjug 13.6 60 0.0015 16.2 0.3 20 34-53 130-149 (315) 7 COG5410 Uncharacterized protei 12.8 40 0.001 17.1 -0.8 27 19-45 27-60 (305) 8 pfam02621 DUF178 Putative peri 11.5 1.4E+02 0.0035 14.5 1.6 16 11-26 133-148 (248) 9 COG3825 Uncharacterized protei 10.8 1.2E+02 0.0031 14.7 1.1 21 5-25 297-317 (393) 10 TIGR01253 thiP thiamine/thiami 10.4 77 0.002 15.7 -0.0 15 9-23 469-484 (519) No 1 >COG4687 Uncharacterized protein conserved in bacteria [Function unknown] Probab=75.93 E-value=1.1 Score=24.61 Aligned_cols=25 Identities=40% Similarity=0.893 Sum_probs=21.2 Q ss_pred CCEEEEECCEEEEEEECHHHCCHHEE Q ss_conf 60024310200899851210001215 Q gi|254781154|r 2 TSWLKLQRDFGVVLIGDKAFNTYRSQ 27 (65) Q Consensus 2 tswlklqrdfgvvligdkafntyrsq 27 (65) |++|-+. +.|-.+|||++|.-|.+. T Consensus 16 taYlg~~-~~GkiliGDkgfEFYn~~ 40 (122) T COG4687 16 TAYLGFA-EYGKILIGDKGFEFYNDR 40 (122) T ss_pred EEEEEHH-HCCEEEECCCCEEECCCC T ss_conf 6896021-357598745214653787 No 2 >pfam06115 DUF956 Domain of unknown function (DUF956). Family of bacterial sequences with undetermined function. Probab=73.06 E-value=1.5 Score=24.06 Aligned_cols=25 Identities=44% Similarity=0.878 Sum_probs=19.2 Q ss_pred CCEEEEECCEEEEEEECHHHCCHHEE Q ss_conf 60024310200899851210001215 Q gi|254781154|r 2 TSWLKLQRDFGVVLIGDKAFNTYRSQ 27 (65) Q Consensus 2 tswlklqrdfgvvligdkafntyrsq 27 (65) ||.+-+ -+.|-++||||||.-|... T Consensus 16 ts~~G~-~~yGkimiGDkaFEFYn~~ 40 (118) T pfam06115 16 TSYLGL-GKYGKIMIGDKGFEFYNDR 40 (118) T ss_pred EEEECC-CCCCEEEECCCCEEECCCC T ss_conf 697266-6567498856427870799 No 3 >COG1427 Predicted periplasmic solute-binding protein [General function prediction only] Probab=22.86 E-value=23 Score=18.24 Aligned_cols=31 Identities=35% Similarity=0.319 Sum_probs=19.2 Q ss_pred EEEEECCEEEEEEECHHHCCHHEEEEEEEEC Q ss_conf 0243102008998512100012157888861 Q gi|254781154|r 4 WLKLQRDFGVVLIGDKAFNTYRSQLRILITD 34 (65) Q Consensus 4 wlklqrdfgvvligdkafntyrsqlrilitd 34 (65) |.-++.-=|++||||+|..++-+----+|+| T Consensus 125 ~~~le~~d~~LlIGDeAL~~~~~~~~~~~~D 155 (252) T COG1427 125 EELLEEADGALLIGDEALRAVYSLPGKLIYD 155 (252) T ss_pred HHHHHCCCCEEEECHHHHHHHCCCCCCEEHH T ss_conf 6776408903885589887511678822013 No 4 >pfam10876 DUF2669 Protein of unknown function (DUF2669). This family of proteins has no known function. Probab=16.98 E-value=27 Score=17.89 Aligned_cols=19 Identities=37% Similarity=0.725 Sum_probs=12.6 Q ss_pred CHHHCCHHEEEEEEEECCH Q ss_conf 1210001215788886152 Q gi|254781154|r 18 DKAFNTYRSQLRILITDNL 36 (65) Q Consensus 18 dkafntyrsqlrilitdnl 36 (65) +..|||||+.+--++.+.| T Consensus 89 n~HFNtyR~Hllpvl~eGl 107 (133) T pfam10876 89 NQHFNTYRGHLLPVLKEGL 107 (133) T ss_pred HHHHHHHHHHHHHHHHHHH T ss_conf 8898888888899999767 No 5 >pfam08144 CPL CPL (NUC119) domain. This C terminal domain is fund in Penguin-like proteins associated with Pumilio like repeats. Probab=14.29 E-value=60 Score=16.21 Aligned_cols=21 Identities=48% Similarity=0.586 Sum_probs=17.7 Q ss_pred CHHHHHHCCCCCCCCCCCCEE Q ss_conf 525533075320000222258 Q gi|254781154|r 35 NLSALISSDKNITESGKEGIV 55 (65) Q Consensus 35 nlsalissdknitesgkegiv 55 (65) -|..||..||..-|+|||+.. T Consensus 125 ~LK~LI~~dk~~~~~gke~~f 145 (148) T pfam08144 125 VLKWLIEQDKKKKENGKEGCF 145 (148) T ss_pred HHHHHHHCCHHHHHCCCCCCC T ss_conf 999999758777866764445 No 6 >TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB; InterPro: IPR014149 This entry represents TrbB, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbB is a homologue of the vir system VirB11 ATPase , and the Flp pilus system ATPase TadA .. Probab=13.63 E-value=60 Score=16.20 Aligned_cols=20 Identities=35% Similarity=0.483 Sum_probs=14.7 Q ss_pred CCHHHHHHCCCCCCCCCCCC Q ss_conf 15255330753200002222 Q gi|254781154|r 34 DNLSALISSDKNITESGKEG 53 (65) Q Consensus 34 dnlsalissdknitesgkeg 53 (65) |-|+..|.|-|||--+|--| T Consensus 130 d~l~~Av~ar~NIlv~GGTG 149 (315) T TIGR02782 130 DVLREAVAARKNILVVGGTG 149 (315) T ss_pred HHHHHHHHHCCCEEEECCCC T ss_conf 99999997129889981458 No 7 >COG5410 Uncharacterized protein conserved in bacteria [Function unknown] Probab=12.80 E-value=40 Score=17.06 Aligned_cols=27 Identities=33% Similarity=0.492 Sum_probs=20.6 Q ss_pred HHHCCHHEEEEE-------EEECCHHHHHHCCCC Q ss_conf 210001215788-------886152553307532 Q gi|254781154|r 19 KAFNTYRSQLRI-------LITDNLSALISSDKN 45 (65) Q Consensus 19 kafntyrsqlri-------litdnlsalissdkn 45 (65) +-||||+.+++- +|++-|.+.|+.+.| T Consensus 27 r~f~T~~~~~~Y~~~~H~~iI~~~L~~Vi~G~~k 60 (305) T COG5410 27 RYFFTQRQQLRYRVNWHHHVIAGVLDDVIAGRRK 60 (305) T ss_pred HHHHEECCCCEECCHHHHHHHHHHHHHHHCCCCE T ss_conf 7652116653002115579999888888636310 No 8 >pfam02621 DUF178 Putative periplasminc binding protein (DUF178). This family of proteins belong to the periplasmic binding protein clan. Probab=11.49 E-value=1.4e+02 Score=14.47 Aligned_cols=16 Identities=38% Similarity=0.432 Sum_probs=11.0 Q ss_pred EEEEEEECHHHCCHHE Q ss_conf 0089985121000121 Q gi|254781154|r 11 FGVVLIGDKAFNTYRS 26 (65) Q Consensus 11 fgvvligdkafntyrs 26 (65) =++++|||.|+.-.+. T Consensus 133 da~LlIGD~Al~~~~~ 148 (248) T pfam02621 133 DAGLLIGDEALTYARE 148 (248) T ss_pred CEEEEECHHHCCCCCC T ss_conf 7589975043450005 No 9 >COG3825 Uncharacterized protein conserved in bacteria [Function unknown] Probab=10.77 E-value=1.2e+02 Score=14.71 Aligned_cols=21 Identities=29% Similarity=0.648 Sum_probs=17.9 Q ss_pred EEEECCEEEEEEECHHHCCHH Q ss_conf 243102008998512100012 Q gi|254781154|r 5 LKLQRDFGVVLIGDKAFNTYR 25 (65) Q Consensus 5 lklqrdfgvvligdkafntyr 25 (65) -|+.+|+-|+++||.+..+|. T Consensus 297 ~K~~~dykvi~vgDA~mapye 317 (393) T COG3825 297 HKYGPDYKVIFVGDATMAPYE 317 (393) T ss_pred HHCCCCCEEEEEECCCCCCEE T ss_conf 651998379998326678323 No 10 >TIGR01253 thiP thiamine/thiamine pyrophosphate ABC transporter, permease protein; InterPro: IPR005947 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). This entry represents thiamine ABC transporter, permease protein in bacteria, believed to be involved in the specific translocation of thiamine and its phosphoesters across the inner membrane. The protein belongs to the larger ABC transport system. It has been experimentally demonstrated that mutants in the various steps in the de novo synthesis of thiamine and its biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP). Thiamine pyrophosphate (TPP)1 is a required cofactor synthesized de novo in Salmonella typhimurium. The primary role for TPP is in central metabolism as an electron carrier and nucleophile for such enzymes as pyruvate dehydrogenase (1.2.4.1 from EC), acetolactate synthase (4.1.3.18 from EC), and -ketoglutarate dehydrogenase (1.2.4.2 from EC). Despite its importance in cellular physiology, neither the de novo biosynthetic pathway nor the salvage systems for thiamine are fully understood in any organism.; GO: 0005215 transporter activity, 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=10.36 E-value=77 Score=15.67 Aligned_cols=15 Identities=47% Similarity=0.871 Sum_probs=9.5 Q ss_pred CCEEEE-EEECHHHCC Q ss_conf 020089-985121000 Q gi|254781154|r 9 RDFGVV-LIGDKAFNT 23 (65) Q Consensus 9 rdfgvv-ligdkafnt 23 (65) -|||+| |-|...|.| T Consensus 469 GDF~~~ALFGN~~F~~ 484 (519) T TIGR01253 469 GDFTVVALFGNDDFRS 484 (519) T ss_pred HHHHHEEEECCCCCCH T ss_conf 1156200103753211 Done!