Query gi|254780556|ref|YP_003064969.1| hypothetical protein CLIBASIA_02215 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 120 No_of_seqs 2 out of 4 Neff 1.4 Searched_HMMs 39220 Date Sun May 29 22:14:18 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780556.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01010 BexC_CtrB_KpsE polys 78.2 3.3 8.4E-05 22.2 3.9 60 33-93 152-212 (364) 2 pfam03448 MgtE_N MgtE intracel 64.7 9.9 0.00025 19.4 3.7 63 53-115 39-101 (102) 3 PRK10824 hypothetical protein; 46.9 7 0.00018 20.3 0.6 21 18-40 81-105 (115) 4 pfam09756 DDRGK DDRGK domain. 45.3 28 0.00071 16.8 4.9 87 31-119 40-130 (189) 5 KOG2651 consensus 38.3 26 0.00067 16.9 2.4 33 88-120 119-151 (476) 6 PHA00101 internal virion prote 35.4 40 0.001 15.9 7.2 79 27-105 34-123 (194) 7 PRK01326 prsA foldase protein 35.4 37 0.00094 16.1 2.8 22 1-22 1-22 (310) 8 COG5180 PBP1 Protein interacti 33.3 24 0.0006 17.2 1.5 34 39-79 184-217 (654) 9 pfam12575 DUF3753 Protein of u 32.8 27 0.00068 16.9 1.7 28 80-107 8-35 (72) 10 TIGR01116 ATPase-IIA1_Ca calci 31.4 31 0.00079 16.5 1.9 25 96-120 163-194 (800) 11 COG3445 Acid-induced glycyl ra 27.8 19 0.0005 17.7 0.3 21 74-94 9-29 (127) 12 TIGR00657 asp_kinases aspartat 26.4 34 0.00088 16.3 1.4 13 32-44 72-84 (504) 13 TIGR02982 heterocyst_DevA ABC 24.9 33 0.00085 16.4 1.1 28 60-88 115-143 (220) 14 PRK13731 conjugal transfer sur 23.3 66 0.0017 14.7 2.4 24 1-24 1-24 (243) 15 KOG3651 consensus 23.1 66 0.0017 14.6 2.8 59 57-117 135-199 (429) 16 pfam12085 DUF3562 Protein of u 22.3 50 0.0013 15.3 1.6 28 92-120 17-44 (65) 17 PRK11548 hypothetical protein; 22.3 69 0.0018 14.5 2.3 24 1-25 1-24 (113) 18 KOG2008 consensus 21.2 73 0.0018 14.4 4.1 22 49-70 125-146 (426) 19 pfam02216 B B domain. This fam 21.1 73 0.0019 14.4 3.6 34 79-112 8-47 (54) 20 pfam11853 DUF3373 Protein of u 20.7 75 0.0019 14.3 6.1 58 11-72 9-66 (485) 21 KOG1618 consensus 20.3 17 0.00044 18.0 -1.1 57 18-88 95-157 (389) 22 PRK03002 prsA peptidylprolyl i 20.3 76 0.0019 14.3 2.6 22 1-22 1-22 (285) 23 pfam03154 Atrophin-1 Atrophin- 20.1 77 0.002 14.3 3.2 40 27-66 544-595 (979) No 1 >TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; InterPro: IPR005705 This family contains gamma proteobacterial proteins involved in ATP-dependent capsule polysaccharide export , .; GO: 0015542 sugar efflux transmembrane transporter activity, 0006859 extracellular carbohydrate transport, 0009276 1-2nm peptidoglycan-based cell wall. Probab=78.19 E-value=3.3 Score=22.16 Aligned_cols=60 Identities=25% Similarity=0.299 Sum_probs=36.3 Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHH Q ss_conf 999986578999-8899999999999999999976547677137999999999366801146 Q gi|254780556|r 33 RMVKEAKMEVLE-AHKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFMNLDSQNQA 93 (120) Q Consensus 33 ~MvKEA~~~v~E-~HkLA~E~VE~A~~RVKE~EE~s~A~llk~L~~D~L~~~F~~L~~~~~~ 93 (120) +|.||+---|-+ .||.++|.|.=||+.||+|+++-++.-.. |+-=--.|-..|+.+|-.+ T Consensus 152 ~lLk~~E~~IN~l~~R~~~d~~~FaE~~V~~A~~~l~~~~~~-L~~yq~~n~~~Dp~~qs~a 212 (364) T TIGR01010 152 RLLKEGERLINRLNERARKDTIAFAEEEVKEAEQRLNATKAE-LLKYQIKNKVLDPKAQSEA 212 (364) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCCCCHHHHHH T ss_conf 999877799978989999999999999999999989999999-9998985478780789999 No 2 >pfam03448 MgtE_N MgtE intracellular N domain. This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family pfam01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains. Probab=64.68 E-value=9.9 Score=19.42 Aligned_cols=63 Identities=17% Similarity=0.262 Sum_probs=47.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999765476771379999999993668011466556688998988999999866 Q gi|254780556|r 53 VEQANQRVKEAEEQSNARLLKGLGMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEMEELSEFGE 115 (120) Q Consensus 53 VE~A~~RVKE~EE~s~A~llk~L~~D~L~~~F~~L~~~~~~~F~~~i~~~yqdemeelsefge 115 (120) .+....-++......-+.++.++..|+.+.-+.+|+...+..+......+-+.+.+++..|.+ T Consensus 39 ~~~~~~il~~l~~~~~~~il~~m~~Dd~~dll~~L~~~~~~~iL~~l~~~~r~~i~~ll~Y~e 101 (102) T pfam03448 39 EDVQAELLEALPPEELAELLEELDPDDAADLLEELPEEVREELLSLLDPEEREEIRELLSYPE 101 (102) T ss_pred HHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHCCCCC T ss_conf 999999998689898999998189278999998799999999998599999999999828998 No 3 >PRK10824 hypothetical protein; Provisional Probab=46.94 E-value=7 Score=20.27 Aligned_cols=21 Identities=24% Similarity=0.673 Sum_probs=12.4 Q ss_pred HHHCHHHCC----CHHHHHHHHHHHHH Q ss_conf 860002201----02679999998657 Q gi|254780556|r 18 IIGCSLVED----NRIESLRMVKEAKM 40 (120) Q Consensus 18 I~GC~lVED----Nri~S~~MvKEA~~ 40 (120) ||||||+.. ..|+ .++++|.- T Consensus 81 IGG~DI~~em~~~GeL~--~ll~ea~~ 105 (115) T PRK10824 81 VGGCDIVIEMYQRGELQ--QLIKETAA 105 (115) T ss_pred ECCHHHHHHHHHCCCHH--HHHHHHHC T ss_conf 64089999999778799--99999622 No 4 >pfam09756 DDRGK DDRGK domain. This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Probab=45.34 E-value=28 Score=16.83 Aligned_cols=87 Identities=29% Similarity=0.287 Sum_probs=49.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHH---HHHHHHHHHHHHHHH Q ss_conf 99999986578999889999999999999999997654767713799999999936680114---665566889989889 Q gi|254780556|r 31 SLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFMNLDSQNQ---AFFIDTIQNKYQDEM 107 (120) Q Consensus 31 S~~MvKEA~~~v~E~HkLA~E~VE~A~~RVKE~EE~s~A~llk~L~~D~L~~~F~~L~~~~~---~~F~~~i~~~yqdem 107 (120) ..++.++..-+--+.++-+-++-...++.-+|.||-..-. ...+|++-....-+-+++.+ ..||+-|+..----. T Consensus 40 ~er~~~ee~~ee~e~~kee~e~~~reek~~~e~eEy~kwk--~~f~veeeG~~~~~~~~~~~~ll~~Fi~~Ik~~Kvv~l 117 (189) T pfam09756 40 GERKEEEELEEEREKKKEEEERKEREEQARKEQEEYEKLK--SSFVVEEEGTDKLSADEESNELLEDFINYIKLKKVVNL 117 (189) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHCEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEH T ss_conf 9998888999999987347899977999887789999999--86203015530146667888899999999987765319 Q ss_pred HHH-HHHHHHHHC Q ss_conf 999-998666416 Q gi|254780556|r 108 EEL-SEFGEKVSD 119 (120) Q Consensus 108 eel-sefgekvsd 119 (120) ++| ++||-++.| T Consensus 118 edLa~~F~l~t~d 130 (189) T pfam09756 118 EELSAEFGLKTED 130 (189) T ss_pred HHHHHHCCCCHHH T ss_conf 9999881996899 No 5 >KOG2651 consensus Probab=38.31 E-value=26 Score=16.95 Aligned_cols=33 Identities=36% Similarity=0.509 Sum_probs=29.8 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 801146655668899898899999986664169 Q gi|254780556|r 88 DSQNQAFFIDTIQNKYQDEMEELSEFGEKVSDY 120 (120) Q Consensus 88 ~~~~~~~F~~~i~~~yqdemeelsefgekvsdy 120 (120) .+|+++.|-..+.-+||.|.+-+||.--+++|| T Consensus 119 ~sq~~~l~rkh~~~k~qhEi~~lselvSsi~~f 151 (476) T KOG2651 119 SSQLTALFRKHVRPKKQHEIRRLSELVSSISDF 151 (476) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 544101555100178898999999999988765 No 6 >PHA00101 internal virion protein B Probab=35.40 E-value=40 Score=15.91 Aligned_cols=79 Identities=16% Similarity=0.253 Sum_probs=52.5 Q ss_pred CHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHCCCHHHHHHHHHCCCCCHHHHH Q ss_conf 026799999986578-----9998899999999999999999976547------67713799999999936680114665 Q gi|254780556|r 27 NRIESLRMVKEAKME-----VLEAHKLAKEYVEQANQRVKEAEEQSNA------RLLKGLGMDDLVRYFMNLDSQNQAFF 95 (120) Q Consensus 27 Nri~S~~MvKEA~~~-----v~E~HkLA~E~VE~A~~RVKE~EE~s~A------~llk~L~~D~L~~~F~~L~~~~~~~F 95 (120) -|.|+.+|||+.|+- +-...+|-.-.-|-.++-..-+.-+.+- +.|-|-+||-..|---+--....+.. T Consensus 34 ~RrQa~emvKqmN~qnANl~Lq~rd~~e~a~~Elt~~nm~~vr~mGtIRaAIgEs~LEGnSM~RI~rv~Eg~~ire~~~i 113 (194) T PHA00101 34 GRRQAMEMVKQMNIQNANLSLEARDKLEEASSELTETNMQKVRNMGTIRAAIGESMLEGNSMDRIKRVTEGDFIREANGI 113 (194) T ss_pred HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 88999999998371122100554776999999999999999986105799873044455129999998620888885010 Q ss_pred HHHHHHHHHH Q ss_conf 5668899898 Q gi|254780556|r 96 IDTIQNKYQD 105 (120) Q Consensus 96 ~~~i~~~yqd 105 (120) |+|.+..|+. T Consensus 114 TenY~RDYas 123 (194) T PHA00101 114 TENYRRDYAS 123 (194) T ss_pred HHHHHHHHHH T ss_conf 5777766999 No 7 >PRK01326 prsA foldase protein PrsA; Reviewed Probab=35.38 E-value=37 Score=16.10 Aligned_cols=22 Identities=23% Similarity=0.462 Sum_probs=18.7 Q ss_pred CCHHHHHHHHHHHHHHHHHHCH Q ss_conf 9057887999999999986000 Q gi|254780556|r 1 MRAKTLLASTLVTTAITIIGCS 22 (120) Q Consensus 1 MrAK~Ll~S~~~TT~iTI~GC~ 22 (120) ||-|+++..+.....++..||+ T Consensus 1 MKKKl~~~~~~~~svl~LaaCs 22 (310) T PRK01326 1 MKKKLIAGAVTLLSVATLAACS 22 (310) T ss_pred CCHHHHHHHHHHHHHHHHHHHC T ss_conf 9088999999999999998716 No 8 >COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification] Probab=33.34 E-value=24 Score=17.24 Aligned_cols=34 Identities=47% Similarity=0.606 Sum_probs=21.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 57899988999999999999999999765476771379999 Q gi|254780556|r 39 KMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDD 79 (120) Q Consensus 39 ~~~v~E~HkLA~E~VE~A~~RVKE~EE~s~A~llk~L~~D~ 79 (120) +-++.|+.|+|||---++.-...-+|| |||++|| T Consensus 184 k~k~qeA~RIaKEIe~s~TtniHiaEe-------RGl~~DD 217 (654) T COG5180 184 KSKVQEARRIAKEIELSATTNIHIAEE-------RGLGNDD 217 (654) T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHH-------CCCCCCC T ss_conf 778889999999986313541123655-------1756666 No 9 >pfam12575 DUF3753 Protein of unknown function (DUF3753). This family of proteins is found in viruses. Proteins in this family are approximately 70 amino acids in length. There is a conserved YLK sequence motif. There are two completely conserved residues (D and F) that may be functionally important. Probab=32.84 E-value=27 Score=16.93 Aligned_cols=28 Identities=14% Similarity=0.350 Sum_probs=23.1 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 9999936680114665566889989889 Q gi|254780556|r 80 LVRYFMNLDSQNQAFFIDTIQNKYQDEM 107 (120) Q Consensus 80 L~~~F~~L~~~~~~~F~~~i~~~yqdem 107 (120) +...||..+|+|.+-|++.|++-..|+- T Consensus 8 ifGvFlss~ddDfe~Fi~vV~sVltdk~ 35 (72) T pfam12575 8 IFGVFLSSSDDDFENFINVVKSVLTDKK 35 (72) T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHCCCC T ss_conf 8866506876679999999999975996 No 10 >TIGR01116 ATPase-IIA1_Ca calcium-translocating P-type ATPase, SERCA-type; InterPro: IPR005782 This model describes Ca2+ ATPases (3.6.3.8 from EC) from eukaryotes and includes significant representatives from plants. Plasma membrane Ca2+ ATPases are primarily responsible for extrusion of calcium from cytoplasmic milieu to outside, coupled to the hydrolyis of ATP. Besides Ca2+ ATPases, Na+/Ca2+ exchangers are also involved in the maintenance of Ca2+ homestasis in the cell. ; GO: 0005388 calcium-transporting ATPase activity, 0006816 calcium ion transport, 0016021 integral to membrane. Probab=31.39 E-value=31 Score=16.53 Aligned_cols=25 Identities=32% Similarity=0.583 Sum_probs=17.8 Q ss_pred HHHHHHHHHHHHH-------HHHHHHHHHHCC Q ss_conf 5668899898899-------999986664169 Q gi|254780556|r 96 IDTIQNKYQDEME-------ELSEFGEKVSDY 120 (120) Q Consensus 96 ~~~i~~~yqdeme-------elsefgekvsdy 120 (120) ||.|+.+-+++-+ .|.|||++.|.| T Consensus 163 IG~I~~~~~~~e~~~TPL~~KLDEFG~~LsKv 194 (800) T TIGR01116 163 IGKIRDEVREAEQEDTPLKKKLDEFGELLSKV 194 (800) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 57789999877521583666657877787689 No 11 >COG3445 Acid-induced glycyl radical enzyme [General function prediction only] Probab=27.77 E-value=19 Score=17.71 Aligned_cols=21 Identities=33% Similarity=0.362 Sum_probs=15.9 Q ss_pred CCCHHHHHHHHHCCCCCHHHH Q ss_conf 379999999993668011466 Q gi|254780556|r 74 GLGMDDLVRYFMNLDSQNQAF 94 (120) Q Consensus 74 ~L~~D~L~~~F~~L~~~~~~~ 94 (120) +-.-|+|.|.||-|||+...+ T Consensus 9 kaand~llnsfwlldsek~ea 29 (127) T COG3445 9 KAANDDLLNSFWLLDSEKGEA 29 (127) T ss_pred ECCCHHHHHHEEEECCCCCCE T ss_conf 123375653214320566715 No 12 >TIGR00657 asp_kinases aspartate kinase; InterPro: IPR001341 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see . Aspartate kinase (2.7.2.4 from EC) (AK) catalyzes the first reaction in the aspartate pathway; the phosphorylation of aspartate. The product of this reaction can then be used in the biosynthesis of lysine or in the pathway leading to homoserine, which participates in the biosynthesis of threonine, isoleucine and methionine . In bacteria there are three different aspartate kinase isozymes which differ in sensitivity to repression and inhibition by Lys, Met and Thr. AK1 and AK2 are bifunctional enzymes which both consist of an N-terminal AK domain and a C-terminal homoserine dehydrogenase domain. AK1 is involved in threonine biosynthesis and AK2, in that of methionine. The third isozyme, AK3 is monofunctional and involved in lysine synthesis. In archaea and plants there may be a single isozyme of AK which in plants is multifunctional. This entry represents a region encoding aspartate kinase activity found in both the monofunctional and bifunctional enzymes. Synonym(s): Aspartokinase; GO: 0004072 aspartate kinase activity, 0008652 amino acid biosynthetic process. Probab=26.40 E-value=34 Score=16.28 Aligned_cols=13 Identities=38% Similarity=0.761 Sum_probs=4.3 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999986578999 Q gi|254780556|r 32 LRMVKEAKMEVLE 44 (120) Q Consensus 32 ~~MvKEA~~~v~E 44 (120) +.-|.+-.+++.+ T Consensus 72 ~~~Ir~~~~~~~~ 84 (504) T TIGR00657 72 LEKIREKHLEILE 84 (504) T ss_pred HHHHHHHCCCHHH T ss_conf 9999984000477 No 13 >TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family; InterPro: IPR014324 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 the ATP-binding subunit DevA, found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The ABC transporter encoded by the devBCA operon is induced by nitrogen deficiency and is necessary for the formation of the laminated layer which envelops heterocysts , . It is thought to be involved in the export of either the heterocyst-specific glycolipids found in the laminated layer, or an enzyme essential for their formation.. Probab=24.86 E-value=33 Score=16.37 Aligned_cols=28 Identities=36% Similarity=0.708 Sum_probs=17.5 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHH-CCC Q ss_conf 99999765476771379999999993-668 Q gi|254780556|r 60 VKEAEEQSNARLLKGLGMDDLVRYFM-NLD 88 (120) Q Consensus 60 VKE~EE~s~A~llk~L~~D~L~~~F~-~L~ 88 (120) -+|..++|.+ .|...|+.+-.+|+- ||| T Consensus 115 ~~~~~~~a~~-~L~~VGL~~~~~y~P~~LS 143 (220) T TIGR02982 115 AQEAREKARA-MLEAVGLGDRLDYYPENLS 143 (220) T ss_pred HHHHHHHHHH-HHHHHCHHHHHHHCCCCCC T ss_conf 8899999999-9986060125540524367 No 14 >PRK13731 conjugal transfer surface exclusion protein TraT; Provisional Probab=23.29 E-value=66 Score=14.66 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=21.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHCHHH Q ss_conf 905788799999999998600022 Q gi|254780556|r 1 MRAKTLLASTLVTTAITIIGCSLV 24 (120) Q Consensus 1 MrAK~Ll~S~~~TT~iTI~GC~lV 24 (120) |+-|.++-+.++...|.+-||.-+ T Consensus 1 m~~kk~~~~~~~~~~l~lsGC~a~ 24 (243) T PRK13731 1 MKTKKLMMVALVSSTLALSGCGAM 24 (243) T ss_pred CCHHHHHHHHHHHHHHHHCCHHHH T ss_conf 933775799999999997156876 No 15 >KOG3651 consensus Probab=23.08 E-value=66 Score=14.63 Aligned_cols=59 Identities=32% Similarity=0.533 Sum_probs=38.9 Q ss_pred HHHHHHHHHHHHHHHHHCCC--HHHHHHHHHCCCCCHHHH---HHHH-HHHHHHHHHHHHHHHHHHH Q ss_conf 99999999765476771379--999999993668011466---5566-8899898899999986664 Q gi|254780556|r 57 NQRVKEAEEQSNARLLKGLG--MDDLVRYFMNLDSQNQAF---FIDT-IQNKYQDEMEELSEFGEKV 117 (120) Q Consensus 57 ~~RVKE~EE~s~A~llk~L~--~D~L~~~F~~L~~~~~~~---F~~~-i~~~yqdemeelsefgekv 117 (120) -+|.+|.|+ ||-+.|||- ..++.+||.+|+.-.+.| |.+- +...-|..-|..+.||++- T Consensus 135 vkrleeLE~--tae~Ykglveh~~~ml~a~y~lsqt~k~FGd~F~~i~vhEpQq~AsEAF~~Fgd~H 199 (429) T KOG3651 135 VKRLEELEE--TAEFYKGLVEHFGDMLQAQYKLSQTQKEFGDIFCDIAVHEPQQTASEAFSSFGDKH 199 (429) T ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 899999876--89999999999999999999999999985115554441686444789999887888 No 16 >pfam12085 DUF3562 Protein of unknown function (DUF3562). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important. Probab=22.34 E-value=50 Score=15.34 Aligned_cols=28 Identities=36% Similarity=0.566 Sum_probs=18.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 46655668899898899999986664169 Q gi|254780556|r 92 QAFFIDTIQNKYQDEMEELSEFGEKVSDY 120 (120) Q Consensus 92 ~~~F~~~i~~~yqdemeelsefgekvsdy 120 (120) -..-.++|-+-|.|+|.+||. |-.|-|| T Consensus 17 t~~p~e~V~~my~d~~~~ls~-~ARV~DY 44 (65) T pfam12085 17 TGAPADLVRQMYDDEMRALSS-DARVHDY 44 (65) T ss_pred HCCCHHHHHHHHHHHHHHHHC-CCHHHHH T ss_conf 599799999999999999876-7807773 No 17 >PRK11548 hypothetical protein; Provisional Probab=22.26 E-value=69 Score=14.54 Aligned_cols=24 Identities=46% Similarity=0.638 Sum_probs=17.3 Q ss_pred CCHHHHHHHHHHHHHHHHHHCHHHC Q ss_conf 9057887999999999986000220 Q gi|254780556|r 1 MRAKTLLASTLVTTAITIIGCSLVE 25 (120) Q Consensus 1 MrAK~Ll~S~~~TT~iTI~GC~lVE 25 (120) ||-|.|.+.++.. .+-+.|||.++ T Consensus 1 m~~k~l~~a~ll~-~lllsgCS~~~ 24 (113) T PRK11548 1 MRCKTLTAAAAVL-LMLTAGCSTLE 24 (113) T ss_pred CCHHHHHHHHHHH-HHHHCCCCCCC T ss_conf 9257889999999-99980115787 No 18 >KOG2008 consensus Probab=21.25 E-value=73 Score=14.41 Aligned_cols=22 Identities=36% Similarity=0.440 Sum_probs=16.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999765476 Q gi|254780556|r 49 AKEYVEQANQRVKEAEEQSNAR 70 (120) Q Consensus 49 A~E~VE~A~~RVKE~EE~s~A~ 70 (120) -+|-.+++-|||+|||+.-++. T Consensus 125 ~~evlnh~~qrV~EaE~e~t~a 146 (426) T KOG2008 125 WQEVLNHATQRVMEAEQEKTRA 146 (426) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999998777889 No 19 >pfam02216 B B domain. This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G. Probab=21.07 E-value=73 Score=14.39 Aligned_cols=34 Identities=21% Similarity=0.327 Sum_probs=23.2 Q ss_pred HHHHHHH------CCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999993------668011466556688998988999999 Q gi|254780556|r 79 DLVRYFM------NLDSQNQAFFIDTIQNKYQDEMEELSE 112 (120) Q Consensus 79 ~L~~~F~------~L~~~~~~~F~~~i~~~yqdemeelse 112 (120) +..++|+ ||..+-++.||.+++..-.---+-|+| T Consensus 8 ~qq~Afyeil~lpNLte~qrn~fI~sLkddPs~S~~vlaE 47 (54) T pfam02216 8 AQQNAFYEVLHLPNLTEEQRNGFIQSLKDDPSQSQNVLAE 47 (54) T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCHHHHHHHHHH T ss_conf 9999999999389999899988999986185788999999 No 20 >pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length. Probab=20.66 E-value=75 Score=14.34 Aligned_cols=58 Identities=24% Similarity=0.310 Sum_probs=30.0 Q ss_pred HHHHHHHHHHCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999998600022010267999999865789998899999999999999999976547677 Q gi|254780556|r 11 LVTTAITIIGCSLVEDNRIESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLL 72 (120) Q Consensus 11 ~~TT~iTI~GC~lVEDNri~S~~MvKEA~~~v~E~HkLA~E~VE~A~~RVKE~EE~s~A~ll 72 (120) ++..+++..+-...-++-+...|-|.+-+-++.|- |+-....+.||+++|+++--+-| T Consensus 9 ~~aall~~s~~~~a~~~d~~~~qkI~~L~~ql~eL----k~~~~~~~~~v~~~e~~~a~~~l 66 (485) T pfam11853 9 LVAALLALSLPAAAAAADIDLLQKIEALKKELAEL----KAQLKDLNKRVDKTEKKSAGDRL 66 (485) T ss_pred HHHHHHHHCCCHHCCCCCHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHCCCCE T ss_conf 99999975041001344344999999999999999----99999877665556665303637 No 21 >KOG1618 consensus Probab=20.35 E-value=17 Score=18.02 Aligned_cols=57 Identities=26% Similarity=0.341 Sum_probs=30.3 Q ss_pred HHHCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH---HHHCCCHHHHHHHHHCCC Q ss_conf 86000220102679999998657899988999999999999999999---765476---771379999999993668 Q gi|254780556|r 18 IIGCSLVEDNRIESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAE---EQSNAR---LLKGLGMDDLVRYFMNLD 88 (120) Q Consensus 18 I~GC~lVEDNri~S~~MvKEA~~~v~E~HkLA~E~VE~A~~RVKE~E---E~s~A~---llk~L~~D~L~~~F~~L~ 88 (120) ..||++-+|+-|||-- --+-.||--++||--+- -|++|. .-.-..+|+++.||-+++ T Consensus 95 ~Lgv~Vs~dqviqSHs--------------P~r~l~~~~~k~vLv~G~~~vr~vAegyGFk~Vvt~D~l~k~f~~ld 157 (389) T KOG1618 95 LLGVEVSADQVIQSHS--------------PFRLLVEYHYKRVLVVGQGSVREVAEGYGFKNVVTVDELAKYFPLLD 157 (389) T ss_pred HHCCCCCHHHHHHHCC--------------HHHHHHHCCCCEEEEECCCCHHHHHHCCCCCCEEEHHHHHHHCCCCC T ss_conf 6287647778776158--------------38888640001699946876887865158640455889998577855 No 22 >PRK03002 prsA peptidylprolyl isomerase; Reviewed Probab=20.33 E-value=76 Score=14.30 Aligned_cols=22 Identities=23% Similarity=0.507 Sum_probs=16.2 Q ss_pred CCHHHHHHHHHHHHHHHHHHCH Q ss_conf 9057887999999999986000 Q gi|254780556|r 1 MRAKTLLASTLVTTAITIIGCS 22 (120) Q Consensus 1 MrAK~Ll~S~~~TT~iTI~GC~ 22 (120) ||-|.++.-+.....+++.||+ T Consensus 1 mkkK~i~~~~~~~svl~LaaC~ 22 (285) T PRK03002 1 MRGKHIFIITALISILMLSACG 22 (285) T ss_pred CCHHHHHHHHHHHHHHHHHHHC T ss_conf 9601899999999999999845 No 23 >pfam03154 Atrophin-1 Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-media Probab=20.14 E-value=77 Score=14.28 Aligned_cols=40 Identities=30% Similarity=0.343 Sum_probs=29.1 Q ss_pred CHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 026799999986------------5789998899999999999999999976 Q gi|254780556|r 27 NRIESLRMVKEA------------KMEVLEAHKLAKEYVEQANQRVKEAEEQ 66 (120) Q Consensus 27 Nri~S~~MvKEA------------~~~v~E~HkLA~E~VE~A~~RVKE~EE~ 66 (120) .--||-|.+|.- -|--+..-||||.|-|+++|--.|+|.+ T Consensus 544 HASQSARF~KHLdRGyNSCaRtDlYF~PL~~SKLAkKReea~EkakREAEqk 595 (979) T pfam03154 544 HASQSARFYKHLDRGYNSCARTDLYFTPLASSKLAKKREEAVEKAKREAEQK 595 (979) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 0567889998751334422012211113530066777899999888888888 Done!