RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780556|ref|YP_003064969.1| hypothetical protein
CLIBASIA_02215 [Candidatus Liberibacter asiaticus str. psy62]
         (120 letters)



>gnl|CDD|36212 KOG0994, KOG0994, KOG0994, Extracellular matrix glycoprotein Laminin
            subunit beta [Extracellular structures].
          Length = 1758

 Score = 29.7 bits (66), Expect = 0.19
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 30   ESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARL 71
            ++L MV+EAK+   EA + A+  +EQAN   +   E+SN  L
Sbjct: 1433 QTLSMVREAKLSASEAQQSAQRALEQAN-ASRSQMEESNREL 1473


>gnl|CDD|36831 KOG1618, KOG1618, KOG1618, Predicted phosphatase [General function
           prediction only].
          Length = 389

 Score = 29.6 bits (66), Expect = 0.20
 Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 13/92 (14%)

Query: 28  RIESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLG------MDDLV 81
            + +L  V+ +  +V+++H   +  VE   +RV    + S   + +G G      +D+L 
Sbjct: 91  ELSALLGVEVSADQVIQSHSPFRLLVEYHYKRVLVVGQGSVREVAEGYGFKNVVTVDELA 150

Query: 82  RYFMNLDSQNQAFFIDTIQNKYQDEMEELSEF 113
           +YF  LD      F D   ++     +   + 
Sbjct: 151 KYFPLLDP-----FTDL--SRELKTTKLARDR 175


>gnl|CDD|109977 pfam00942, CBM_3, Cellulose binding domain. 
          Length = 83

 Score = 26.1 bits (58), Expect = 2.2
 Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)

Query: 78  DDL-VRYFMNLDS-QNQAFFIDTIQ 100
            DL  RY+  LD  + Q F+ D  Q
Sbjct: 32  SDLKFRYYYTLDGNKAQGFWCDWAQ 56


>gnl|CDD|37862 KOG2651, KOG2651, KOG2651, rRNA adenine N-6-methyltransferase [RNA
           processing and modification].
          Length = 476

 Score = 26.1 bits (57), Expect = 2.3
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 69  ARLLKGLGMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEMEELSEFGEKVSDY 120
            R+       + +       SQ  A F   ++ K Q E+  LSE    +SD+
Sbjct: 101 TRMQGIQTPSEFLENPSQS-SQLTALFRKHVRPKKQHEIRRLSELVSSISDF 151


>gnl|CDD|31731 COG1542, COG1542, Uncharacterized conserved protein [Function
           unknown].
          Length = 593

 Score = 25.3 bits (55), Expect = 4.1
 Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 9/87 (10%)

Query: 35  VKEAKMEVLEA-HKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFM-NLDSQNQ 92
           + E ++ +L+A  KL K++       +K  E++    +     +DDLV   +  L+S   
Sbjct: 282 ILEDEIRLLKAIDKLKKKHETNPAPEIKPIEKE----IKWETKIDDLVTAALYTLESFG- 336

Query: 93  AFFIDTIQNKYQDEMEELSEFGEKVSD 119
              I     K  D    L+EFGEKV +
Sbjct: 337 --LIKREVVKNGDLTYVLTEFGEKVLE 361


>gnl|CDD|30536 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
           topoisomerase IV), B subunit [DNA replication,
           recombination, and repair].
          Length = 635

 Score = 25.5 bits (56), Expect = 4.2
 Identities = 10/32 (31%), Positives = 17/32 (53%)

Query: 2   RAKTLLASTLVTTAITIIGCSLVEDNRIESLR 33
           R   +L +  + T IT +G  + +D  +E LR
Sbjct: 458 RLDKILKNEEIQTIITALGTGIGKDFDLEKLR 489


>gnl|CDD|35692 KOG0471, KOG0471, KOG0471, Alpha-amylase [Carbohydrate transport
           and metabolism].
          Length = 545

 Score = 25.4 bits (55), Expect = 4.3
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 76  GMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEM------EELSEFGEKVSD 119
            + + +R F  L+     F ID ++    +        E + + GEK+ D
Sbjct: 193 AIKEWLRDFW-LEKGVDGFRIDAVKGYAGENFKNMWPDEPVFDVGEKLQD 241


>gnl|CDD|146587 pfam04029, 2-ph_phosp, 2-phosphosulpholactate phosphatase.  Thought
           to catalyse 2-phosphosulpholactate = sulpholactate +
           phosphate. Probable magnesium cofactor. Involved in the
           second step of coenzyme M biosynthesis. Inhibited by
           vanadate in Methanococcus jannaschii. Also known as the
           ComB family.
          Length = 231

 Score = 25.2 bits (56), Expect = 4.7
 Identities = 13/59 (22%), Positives = 27/59 (45%)

Query: 33  RMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFMNLDSQN 91
            ++   + E+ +  + A     Q N  ++     S+ R LK LG++D + +   LD  +
Sbjct: 160 LLLGLGEEELNDEARAALALYRQENDLLELLRNSSHGRRLKALGLEDDLEFCAQLDILD 218


>gnl|CDD|145014 pfam01650, Peptidase_C13, Peptidase C13 family.  Members of this
           family are asparaginyl peptidases. The blood fluke
           parasite Schistosoma mansoni has at least five Clan CA
           cysteine peptidases in its digestive tract including
           cathepsins B (2 isoforms), C, F and L. All have been
           recombinantly expressed as active enzymes, albeit in
           various stages of activation. In addition, a Clan CD
           peptidase, termed asparaginyl endopeptidase or
           'legumain' has been identified. This has formerly been
           characterized as a 'haemoglobinase', but this term is
           probably incorrect. Two cDNAs have been described for
           Schistosoma mansoni legumain; one encodes an active
           enzyme whereas the active site cysteine residue encoded
           by the second cDNA is substituted by an asparagine
           residue. Both forms have been recombinantly expressed.
          Length = 258

 Score = 24.9 bits (55), Expect = 4.9
 Identities = 11/29 (37%), Positives = 16/29 (55%)

Query: 40  MEVLEAHKLAKEYVEQANQRVKEAEEQSN 68
           ME  + H L+KE +EQ  + VK     S+
Sbjct: 210 MEDSDDHDLSKETLEQQFELVKNRTTGSH 238


>gnl|CDD|48129 cd03202, GST_C_etherase_LigE, GST_C family, Beta etherase LigE
           subfamily; composed of proteins similar to Sphingomonas
           paucimobilis beta etherase, LigE, a GST-like protein
           that catalyzes the cleavage of the beta-aryl ether
           linkages present in low-moleculer weight lignins using
           GSH as the hydrogen donor. This reaction is an essential
           step in the degradation of lignin, a complex phenolic
           polymer that is the most abundant aromatic material in
           the biosphere. The beta etherase activity of LigE is
           enantioselective and it complements the activity of the
           other GST family beta etherase, LigF. The GST fold
           contains an N-terminal thioredoxin-fold domain and a
           C-terminal alpha helical domain, with an active site
           located in a cleft between the two domains..
          Length = 124

 Score = 24.8 bits (54), Expect = 5.2
 Identities = 13/47 (27%), Positives = 23/47 (48%)

Query: 64  EEQSNARLLKGLGMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEMEEL 110
           E  SN  L+ GL    +      LD  +QA+F  + + ++   +EE+
Sbjct: 6   ERWSNTTLVPGLFPLIVPDIHDLLDPPDQAYFRQSREKRFGRSLEEV 52


>gnl|CDD|143803 pfam00012, HSP70, Hsp70 protein.  Hsp70 chaperones help to fold
           many proteins. Hsp70 assisted folding involves repeated
           cycles of substrate binding and release. Hsp70 activity
           is ATP dependent. Hsp70 proteins are made up of two
           regions: the amino terminus is the ATPase domain and the
           carboxyl terminus is the substrate binding region.
          Length = 598

 Score = 24.9 bits (55), Expect = 5.8
 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 11/67 (16%)

Query: 9   STLVTTAITIIGCSLVEDNRIESLRMVKEA---------KMEVLEAHKLAKEYVEQANQR 59
            T     ITI   S + D+ IE  RMVK+A         + E +EA   A+EYV    + 
Sbjct: 486 GTGKEQKITITNSSGLSDDEIE--RMVKDAEEYAAEDKKRKERIEAKNEAEEYVYSLEKS 543

Query: 60  VKEAEEQ 66
           +KE  ++
Sbjct: 544 LKEEGDK 550


>gnl|CDD|37327 KOG2116, KOG2116, KOG2116, Protein involved in plasmid
           maintenance/nuclear protein involved in lipid metabolism
           [Cell motility, Lipid transport and metabolism].
          Length = 738

 Score = 24.6 bits (53), Expect = 6.4
 Identities = 8/27 (29%), Positives = 15/27 (55%)

Query: 85  MNLDSQNQAFFIDTIQNKYQDEMEELS 111
           M L    +AFF++  ++  +D  +EL 
Sbjct: 74  MKLGDSGEAFFVEETEDDVEDVPDELL 100


>gnl|CDD|185706 cd07895, Adenylation_mRNA_capping, Adenylation domain of
          GTP-dependent mRNA capping enzymes.  RNA capping
          enzymes transfer GMP from GTP to the 5'-diphosphate end
          of nascent mRNAs to form a G(5')ppp(5')RNA cap
          structure. The RNA cap is found only in eukarya. RNA
          capping is chemically analogous to the first two steps
          of polynucleotide ligation. ATP-dependent
          polynucleotide ligases catalyze phosphodiester bond
          formation of nicked nucleic acid substrates using the
          high energy nucleotide of ATP as a cofactor in a three
          step reaction mechanism. Structural studies reveal a
          shared structure for DNA ligases and capping enzymes,
          with a common catalytic core composed of an adenylation
          or nucleotidyltransferase domain and a C-terminal
          OB-fold domain containing conserved sequence motifs.
          The adenylation domain binds ATP and contains many
          active site residues.
          Length = 215

 Score = 24.5 bits (54), Expect = 6.4
 Identities = 5/17 (29%), Positives = 10/17 (58%)

Query: 81 VRYFMNLDSQNQAFFID 97
          VRY + +  + + + ID
Sbjct: 52 VRYLLLITGRGEVYLID 68


>gnl|CDD|177069 CHL00149, odpA, pyruvate dehydrogenase E1 component alpha subunit;
           Reviewed.
          Length = 341

 Score = 24.4 bits (53), Expect = 6.9
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 40  MEVLEAHKLAKEYVEQANQ 58
           M+VL   ++AKE VE+A Q
Sbjct: 229 MDVLAVREVAKEAVERARQ 247


>gnl|CDD|177000 CHL00060, atpB, ATP synthase CF1 beta subunit.
          Length = 494

 Score = 24.2 bits (53), Expect = 7.6
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 65  EQSNARLLKGLGMDDLVRYFMNLDSQNQAFFIDTI 99
           E   AR+  GL    +  YF +++ Q+   FID I
Sbjct: 237 EPPGARMRVGLTALTMAEYFRDVNKQDVLLFIDNI 271


>gnl|CDD|36143 KOG0925, KOG0925, KOG0925, mRNA splicing factor ATP-dependent RNA
           helicase [RNA processing and modification].
          Length = 699

 Score = 24.1 bits (52), Expect = 9.0
 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 48  LAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRY-FMN 86
             KE   Q    +  +   S    LK LG+DDLV + FM+
Sbjct: 389 FEKEMQPQTYPEILRSNLSSTVLQLKKLGIDDLVHFDFMD 428


>gnl|CDD|107325 cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain
           of active transport proteins.  Periplasmic
           solute-binding domain of active transport proteins found
           in bacteria and Archaea that is predicted to be involved
           in the efflux of toxic compounds.  Members of this
           subgroup include proteins from Herminiimonas
           arsenicoxydans, which is resistant to arsenic and
           various heavy metals such as cadmium and zinc. Moreover,
           they show significant sequence similarity to the cluster
           of AmiC and active transport systems for short-chain
           amides and urea (FmdDEF), and thus are likely to exhibit
           a ligand-binding mode similar to that of the amide
           sensor protein AmiC from Pseudomonas aeruginosa.
          Length = 346

 Score = 24.1 bits (53), Expect = 9.2
 Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 2/43 (4%)

Query: 50  KEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRY--FMNLDSQ 90
              VE+A      A  +  A  L+GL  +           D Q
Sbjct: 294 AAAVEKAGATDGGAPPEQIAAALEGLSFETPGGPITMRAADHQ 336


>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
           head-to-tail.  These trans-Isoprenyl Diphosphate
           Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
           condensation reactions. This CD includes all-trans
           (E)-isoprenyl diphosphate synthases which synthesize
           various chain length (C10, C15, C20, C25, C30, C35, C40,
           C45, and C50) linear isoprenyl diphosphates from
           precursors,  isopentenyl diphosphate (IPP) and
           dimethylallyl diphosphate (DMAPP). They catalyze the
           successive 1'-4 condensation of the 5-carbon IPP to
           allylic substrates geranyl-, farnesyl-, or
           geranylgeranyl-diphosphate. Isoprenoid chain elongation
           reactions proceed via electrophilic alkylations in which
           a new carbon-carbon single bond is generated through
           interaction between a highly reactive electron-deficient
           allylic carbocation and an electron-rich carbon-carbon
           double bond. The catalytic site consists of a large
           central cavity formed by mostly antiparallel alpha
           helices with two aspartate-rich regions (DDXX(XX)D)
           located on opposite walls. These residues mediate
           binding of prenyl phosphates via bridging Mg2+ ions,
           inducing proposed conformational changes that close the
           active site to solvent, protecting and stabilizing
           reactive carbocation intermediates. Farnesyl diphosphate
           synthases produce the precursors of steroids,
           cholesterol, sesquiterpenes, farnsylated proteins, heme,
           and vitamin K12; and geranylgeranyl diphosphate and
           longer chain synthases produce the precursors of
           carotenoids, retinoids, diterpenes, geranylgeranylated
           chlorophylls, ubiquinone, and archaeal ether linked
           lipids. Isoprenyl diphosphate synthases are widely
           distributed among archaea, bacteria, and eukareya.
          Length = 259

 Score = 24.0 bits (53), Expect = 9.9
 Identities = 10/29 (34%), Positives = 16/29 (55%)

Query: 47  KLAKEYVEQANQRVKEAEEQSNARLLKGL 75
           +LA+EY E+A + +K   E      L+ L
Sbjct: 224 ELAREYEEKALEALKALPESPAREALRAL 252


>gnl|CDD|147308 pfam05059, Orbi_VP4, Orbivirus VP4 core protein.  Orbiviruses are
           double stranded RNA retroviruses of which the bluetongue
           virus is a member. The core of bluetongue virus (BTV) is
           a multienzyme complex composed of two major proteins
           (VP7 and VP3) and three minor proteins (VP1, VP4 and
           VP6) in addition to the viral genome. VP4 has been shown
           to perform all RNA capping activities and has both
           methyltransferase type 1 and type 2 activities
           associated with it.
          Length = 642

 Score = 23.9 bits (52), Expect = 10.0
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 27  NRIESLRMVKEAKMEVLE 44
           NR + LR + EAK EV+E
Sbjct: 581 NREQKLRDLSEAKAEVIE 598


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.314    0.129    0.334 

Gapped
Lambda     K      H
   0.267   0.0753    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,217,809
Number of extensions: 54255
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 262
Number of HSP's successfully gapped: 53
Length of query: 120
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,491,799
Effective search space: 170688362
Effective search space used: 170688362
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.4 bits)