Query         gi|254780159|ref|YP_003064572.1| hypothetical protein CLIBASIA_00210 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 96
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 22 18:59:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780159.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10654 dcuC C4-dicarboxylate  56.2      11 0.00028   18.8   2.8   35   27-61    412-446 (452)
  2 COG2263 Predicted RNA methylas  38.6      18 0.00046   17.6   1.6   28   29-56    132-159 (198)
  3 TIGR01601 PYST-C1 Plasmodium y  30.6      22 0.00056   17.1   1.0   15   19-33      8-22  (86)
  4 COG3788 Uncharacterized relati  29.4      49  0.0012   15.2   3.4   28   48-75      5-32  (131)
  5 TIGR02972 TMAO_torE trimethyla  25.2      58  0.0015   14.7   2.5   26   15-40     11-36  (50)
  6 pfam04547 Anoctamin Calcium-ac  25.1      58  0.0015   14.7   5.0   76    9-85    120-202 (446)
  7 pfam04971 Lysis_S Lysis protei  24.4      60  0.0015   14.6   3.3   39   38-77     28-66  (68)
  8 TIGR00956 3a01205 Pleiotropic   21.9      68  0.0017   14.3   3.6   34   36-70    540-573 (1466)
  9 PRK09499 sifB secreted effecto  21.6      37 0.00093   15.9   0.7   29   17-45     64-92  (316)
 10 TIGR02943 Sig70_famx1 RNA poly  21.1      59  0.0015   14.7   1.7   24    4-27    154-177 (194)

No 1  
>PRK10654 dcuC C4-dicarboxylate transporter DcuC; Provisional
Probab=56.19  E-value=11  Score=18.80  Aligned_cols=35  Identities=9%  Similarity=0.275  Sum_probs=17.7

Q ss_pred             HHHHHHHCCCCHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99998741320130015269999999999999999
Q gi|254780159|r   27 IVCASIIGNWQYSIHKRPALDMIASMICGLLMSLL   61 (96)
Q Consensus        27 ivcasiignwqysihkrpaldmiasmicgllmsll   61 (96)
                      |.||.+.|-=...+-||.++-|+..++.-+++|.+
T Consensus       412 IavAg~a~vsP~eiVKRtavPmi~~~i~~~i~s~i  446 (452)
T PRK10654        412 VAVAGMAKISPFEVVKRTSVPVLVGLVIVIVATEI  446 (452)
T ss_pred             HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88615158889999997188799999999999998


No 2  
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=38.61  E-value=18  Score=17.58  Aligned_cols=28  Identities=32%  Similarity=0.383  Sum_probs=23.2

Q ss_pred             HHHHHCCCCHHHHCCHHHHHHHHHHHHH
Q ss_conf             9987413201300152699999999999
Q gi|254780159|r   29 CASIIGNWQYSIHKRPALDMIASMICGL   56 (96)
Q Consensus        29 casiignwqysihkrpaldmiasmicgl   56 (96)
                      -|.-++++-|||||.+..|.+.+..-++
T Consensus       132 ~Ale~s~vVYsiH~a~~~~f~~~~~~~~  159 (198)
T COG2263         132 KALEISDVVYSIHKAGSRDFVEKFAADL  159 (198)
T ss_pred             HHHHHHHEEEEEECCCCHHHHHHHHHHC
T ss_conf             9997401478740166079999998854


No 3  
>TIGR01601 PYST-C1 Plasmodium yoelii subtelomeric domain PYST-C1; InterPro: IPR006488    This group of sequences are defined by the N-terminal domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism. The C-terminal portions of the genes that contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (IPR006491 from INTERPRO). .
Probab=30.62  E-value=22  Score=17.11  Aligned_cols=15  Identities=33%  Similarity=0.693  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999874
Q gi|254780159|r   19 FIFVVLYTIVCASII   33 (96)
Q Consensus        19 fifvvlytivcasii   33 (96)
                      .+|+|||++.-.||-
T Consensus         8 LVcIvLY~llaVsIH   22 (86)
T TIGR01601         8 LVCIVLYILLAVSIH   22 (86)
T ss_pred             HHHHHHHHHHCCCCC
T ss_conf             889999998717521


No 4  
>COG3788 Uncharacterized relative of glutathione S-transferase, MAPEG superfamily [General function prediction only]
Probab=29.39  E-value=49  Score=15.15  Aligned_cols=28  Identities=32%  Similarity=0.408  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999999999999999988875402348
Q gi|254780159|r   48 MIASMICGLLMSLLIILSFTIVQDRRSS   75 (96)
Q Consensus        48 miasmicgllmslliilsftivqdrrss   75 (96)
                      |.++.-.|+.--+|++|||..|..|+..
T Consensus         5 mvstlyavl~~llll~LS~~vVrlR~k~   32 (131)
T COG3788           5 MVSALYAVLNALLLLKLSFDVVRLRMKY   32 (131)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6989999999999999999999998876


No 5  
>TIGR02972 TMAO_torE trimethylamine N-oxide reductase system, TorE protein; InterPro: IPR014316   Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA..
Probab=25.22  E-value=58  Score=14.72  Aligned_cols=26  Identities=27%  Similarity=0.651  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHH
Q ss_conf             68999999999999998741320130
Q gi|254780159|r   15 VSAFFIFVVLYTIVCASIIGNWQYSI   40 (96)
Q Consensus        15 vsaffifvvlytivcasiignwqysi   40 (96)
                      -+-+||-|||+.+..-..||.+-.+|
T Consensus        11 Kal~FI~vvLFP~Lsv~~vg~YGfiv   36 (50)
T TIGR02972        11 KALGFIIVVLFPILSVAVVGGYGFIV   36 (50)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998998887689999999889999


No 6  
>pfam04547 Anoctamin Calcium-activated chloride channel. The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes.
Probab=25.13  E-value=58  Score=14.71  Aligned_cols=76  Identities=22%  Similarity=0.319  Sum_probs=47.8

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------CCCCCCCCCC
Q ss_conf             320587689999999999999987413201300152699999999999999999998887540-------2348864344
Q gi|254780159|r    9 ICSNFPVSAFFIFVVLYTIVCASIIGNWQYSIHKRPALDMIASMICGLLMSLLIILSFTIVQD-------RRSSPRIDSD   81 (96)
Q Consensus         9 icsnfpvsaffifvvlytivcasiignwqysihkrpaldmiasmicgllmslliilsftivqd-------rrsspridsd   81 (96)
                      .+..+|+..+++.++...+++--..-.|-.+....|.-.+.++++.+.+.++.|.. ++.+-.       ....+|..++
T Consensus       120 ~~~s~~vvl~~i~~~i~~~~~~f~~~~~~~~~~~~~~~~~~~~~~p~il~~v~i~i-l~~iY~~iA~~Lt~~ENhrt~~~  198 (446)
T pfam04547       120 QLLSIPVVLLFIGLVIGIIIGIFILRIFLSEIYSGPFKQTLESFLPAILNSVIILI-LNFIYEKVATKLTDWENHRTQSS  198 (446)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             99999999999999999999999999999987437406799999999999999999-99999999999998857675568


Q ss_pred             CCHH
Q ss_conf             4311
Q gi|254780159|r   82 IETS   85 (96)
Q Consensus        82 iets   85 (96)
                      -|.|
T Consensus       199 ye~s  202 (446)
T pfam04547       199 YENS  202 (446)
T ss_pred             HHHH
T ss_conf             9998


No 7  
>pfam04971 Lysis_S Lysis protein S. The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane.
Probab=24.36  E-value=60  Score=14.62  Aligned_cols=39  Identities=36%  Similarity=0.546  Sum_probs=29.7

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             1300152699999999999999999998887540234886
Q gi|254780159|r   38 YSIHKRPALDMIASMICGLLMSLLIILSFTIVQDRRSSPR   77 (96)
Q Consensus        38 ysihkrpaldmiasmicgllmslliilsftivqdrrsspr   77 (96)
                      +|-..-.|...+.|.+-|+|- .|.-|-|.|-.|||...|
T Consensus        28 ~sp~qWaAIGVlgsl~fg~LT-ylTNlYFKikedrRk~ar   66 (68)
T pfam04971        28 VSPSQWAAIGVLGSLVFGLLT-YLTNLYFKIREDRRKAAR   66 (68)
T ss_pred             CCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHC
T ss_conf             899999999999999999999-998889887786666543


No 8  
>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein; InterPro: IPR005285   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 family includes transporters, whose physiological function is not yet established. These proteins are thought to confer resistance to the chemicals cycloheximide and sulphomethuron methyl, BFA, azole antifungal agents, other antifungal agents: amorolfine and terbinafine. Some of them could serve as an efflux pump of various antibiotics..
Probab=21.94  E-value=68  Score=14.35  Aligned_cols=34  Identities=32%  Similarity=0.598  Sum_probs=27.0

Q ss_pred             CCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             20130015269999999999999999999888754
Q gi|254780159|r   36 WQYSIHKRPALDMIASMICGLLMSLLIILSFTIVQ   70 (96)
Q Consensus        36 wqysihkrpaldmiasmicgllmslliilsftivq   70 (96)
                      -.|+.| +|+-|-|||.|.++-.++.....|.||-
T Consensus       540 r~yaLY-hP~Ada~~S~i~~~P~k~~~~~~F~ii~  573 (1466)
T TIGR00956       540 RKYALY-HPSADALASIISELPFKLIISVVFNIIL  573 (1466)
T ss_pred             HHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             662057-8547889999974349999999999887


No 9  
>PRK09499 sifB secreted effector protein; Provisional
Probab=21.59  E-value=37  Score=15.85  Aligned_cols=29  Identities=28%  Similarity=0.496  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHCCHH
Q ss_conf             99999999999999874132013001526
Q gi|254780159|r   17 AFFIFVVLYTIVCASIIGNWQYSIHKRPA   45 (96)
Q Consensus        17 affifvvlytivcasiignwqysihkrpa   45 (96)
                      -+-||.-||...|+|--+|+||.-|+...
T Consensus        64 L~diFfeLk~Lac~S~rdrF~~~~~~d~~   92 (316)
T PRK09499         64 LFDLFCALYELSSPSCRGNFHFQHYKDAE   92 (316)
T ss_pred             HHHHHHHHHHHCCCCHHCCCCCCCCCCCC
T ss_conf             99999999872381021245678878873


No 10 
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This group of sigma factors are part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family..
Probab=21.06  E-value=59  Score=14.68  Aligned_cols=24  Identities=38%  Similarity=0.653  Sum_probs=21.0

Q ss_pred             CCCHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             000033205876899999999999
Q gi|254780159|r    4 FDSRAICSNFPVSAFFIFVVLYTI   27 (96)
Q Consensus         4 fdsraicsnfpvsaffifvvlyti   27 (96)
                      |++.-||++..+|+--..|.||--
T Consensus       154 ~~~~eIC~~l~is~~N~~VlLyRA  177 (194)
T TIGR02943       154 FESEEICQELEISASNCHVLLYRA  177 (194)
T ss_pred             CCHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             866887530031376799999999


Done!