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!