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!