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!