RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780757|ref|YP_003065170.1| glycyl-tRNA synthetase subunit
alpha [Candidatus Liberibacter asiaticus str. psy62]
         (307 letters)



>gnl|CDD|31095 COG0752, GlyQ, Glycyl-tRNA synthetase, alpha subunit [Translation,
           ribosomal structure and biogenesis].
          Length = 298

 Score =  517 bits (1333), Expect = e-147
 Identities = 203/294 (69%), Positives = 234/294 (79%), Gaps = 10/294 (3%)

Query: 7   KKNDLSFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPS 66
               L+FQ +ILTL  YWA+QGCTILQPYDMEVGAGTFHP+T LRALGP  W AAYVQPS
Sbjct: 1   MNKKLTFQGLILTLQNYWAEQGCTILQPYDMEVGAGTFHPATFLRALGPEPWNAAYVQPS 60

Query: 67  RRPLDGRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWE 126
           RRP DGRY ENPNRLQHYYQFQVIIKP+P N+Q LY+ SL+A+GIDPL HD+RFVEDNWE
Sbjct: 61  RRPTDGRYGENPNRLQHYYQFQVIIKPSPDNIQELYLGSLEALGIDPLEHDIRFVEDNWE 120

Query: 127 SPTLGAWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYD 186
           +PTLGAWGLGWE W DGME++QFTYFQQV G+EC P+SGEITYGLERLAMY+Q V++VYD
Sbjct: 121 NPTLGAWGLGWEVWLDGMEVTQFTYFQQVGGLECKPVSGEITYGLERLAMYIQGVDNVYD 180

Query: 187 IVFNAIEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEH 246
           + +N   G  V YGD+F Q+E E S+YNFEYA+ ++L  HF D EKE   LL+ G     
Sbjct: 181 LEWNDGPGGKVTYGDVFLQNEVEQSKYNFEYADVDMLFRHFDDYEKEAKRLLELG----- 235

Query: 247 HRHHLCVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFL 300
                 V PAYD  +KASH FNLLDARG IS TERQRYILRIR+LA+A  EA+L
Sbjct: 236 -----LVLPAYDYVLKASHTFNLLDARGAISVTERQRYILRIRNLARAVAEAYL 284


>gnl|CDD|111033 pfam02091, tRNA-synt_2e, Glycyl-tRNA synthetase alpha subunit. 
          Length = 284

 Score =  479 bits (1235), Expect = e-136
 Identities = 195/288 (67%), Positives = 226/288 (78%), Gaps = 14/288 (4%)

Query: 13  FQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLDG 72
           FQ++ILTL +YWA QGC I+QPYDMEVGAGTF+P+T LRALGP  W  AYV+PSRRP DG
Sbjct: 1   FQSMILTLQEYWASQGCVIMQPYDMEVGAGTFNPATFLRALGPEPWNVAYVEPSRRPTDG 60

Query: 73  RYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGA 132
           RY ENPNRLQHYYQFQVI+KP+P N+Q LY+ SLKA+GIDPL HD+RFVEDNWESPTLGA
Sbjct: 61  RYGENPNRLQHYYQFQVILKPSPDNIQELYLGSLKALGIDPLDHDIRFVEDNWESPTLGA 120

Query: 133 WGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFNAI 192
           WGLGWE W DGMEI+QFTYFQQV G+EC P+SGEITYGLERLAMY+Q V+SVYD+V+   
Sbjct: 121 WGLGWEVWLDGMEITQFTYFQQVGGLECKPVSGEITYGLERLAMYLQKVDSVYDLVWA-- 178

Query: 193 EGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHHLC 252
               + YGDIF Q+E E S YNFE AN ++L  HF D E+E L LL+ G+P         
Sbjct: 179 --DGLTYGDIFQQNEVEQSTYNFETANVDMLFKHFDDYEEEALQLLENGLP--------- 227

Query: 253 VFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFL 300
             PAYD  +KASH FNLLDARG IS TER RYILRIR LA+A  + + 
Sbjct: 228 -LPAYDFVLKASHAFNLLDARGAISVTERTRYILRIRQLARAVADLYY 274


>gnl|CDD|29812 cd00733, GlyRS_alpha_core, Class II Glycyl-tRNA synthetase (GlyRS)
           alpha subunit core catalytic domain. GlyRS functions as
           a homodimer in eukaryotes, archaea and some bacteria and
           as a heterotetramer in the remainder of prokaryotes and
           in arabidopsis. It is responsible for the attachment of
           glycine to the 3' OH group of ribose of the appropriate
           tRNA. This domain is primarily responsible for the
           ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. This alignment contains only
           sequences from the GlyRS form which heterotetramerizes.
           The homodimer form of GlyRS is in a different family of
           class II aaRS. Class II assignment is based upon
           structure and the presence of three characteristic
           sequence motifs..
          Length = 279

 Score =  474 bits (1222), Expect = e-134
 Identities = 189/289 (65%), Positives = 225/289 (77%), Gaps = 14/289 (4%)

Query: 12  SFQNIILTLTQYWAQQGCTILQPYDMEVGAGTFHPSTTLRALGPLSWKAAYVQPSRRPLD 71
           +FQ++IL L ++WA QGC I+QPYDMEVGAGTFHP+T LRALGP  W  AYV+PSRRP D
Sbjct: 1   TFQDLILKLQKFWASQGCLIIQPYDMEVGAGTFHPATFLRALGPEPWNVAYVEPSRRPTD 60

Query: 72  GRYAENPNRLQHYYQFQVIIKPNPLNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLG 131
           GRY ENPNRLQHYYQFQVIIKP+P N+Q LY+ESL+A+GI+P  HD+RFVEDNWESPTLG
Sbjct: 61  GRYGENPNRLQHYYQFQVIIKPSPDNIQELYLESLEALGINPKEHDIRFVEDNWESPTLG 120

Query: 132 AWGLGWECWCDGMEISQFTYFQQVCGIECSPISGEITYGLERLAMYVQNVNSVYDIVFNA 191
           AWGLGWE W DGME++QFTYFQQV GI C PIS EITYGLER+AMY+Q V++VYDI +N 
Sbjct: 121 AWGLGWEVWLDGMEVTQFTYFQQVGGIPCKPISVEITYGLERIAMYLQGVDNVYDIEWN- 179

Query: 192 IEGQNVLYGDIFAQSEQEYSRYNFEYANPEILHNHFIDSEKECLDLLKKGIPNEHHRHHL 251
              + + YGD+F Q+E E S YNFEYAN ++L   F D EKE   LL+ G+P        
Sbjct: 180 ---KKITYGDVFLQNEIEQSVYNFEYANVDMLFQLFEDYEKEAKRLLELGLP-------- 228

Query: 252 CVFPAYDQCIKASHIFNLLDARGVISTTERQRYILRIRSLAKACGEAFL 300
              PAYD  +K SH FNLLDARG IS TERQRYILRIR+LA+   + ++
Sbjct: 229 --LPAYDYVLKCSHTFNLLDARGAISVTERQRYILRIRNLAREIAKLYV 275


>gnl|CDD|29813 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl
           synthetase-like catalytic core domain. Class II amino
           acyl-tRNA synthetases (aaRS) share a common fold and
           generally attach an amino acid to the 3' OH of ribose of
           the appropriate tRNA.   PheRS is an exception in that it
           attaches the amino acid at the 2'-OH group, like class I
           aaRSs. These enzymes are usually homodimers. This domain
           is primarily responsible for ATP-dependent formation of
           the enzyme bound aminoacyl-adenylate. The substrate
           specificity of this reaction is further determined by
           additional domains. Intererestingly, this domain is also
           found is asparagine synthase A (AsnA), in the accessory
           subunit of mitochondrial polymerase gamma and in the
           bacterial  ATP  phosphoribosyltransferase regulatory
           subunit HisZ..
          Length = 211

 Score = 53.5 bits (128), Expect = 7e-08
 Identities = 35/161 (21%), Positives = 52/161 (32%), Gaps = 30/161 (18%)

Query: 39  VGAGTFHPSTTLRA-LGPLSWKAAYVQPSRRPLDGRYAENPNRLQHYYQFQVIIKPNP-- 95
                        + +  L  + A + P+ R   GR      R++ + Q +  +      
Sbjct: 56  RPTLEPGLVRLFVSHIRKLPLRLAEIGPAFRNEGGRR--GLRRVREFTQLEGEVFGEDGE 113

Query: 96  -----LNLQNLYIESLKAVGIDPLIHDVRFVEDNWESPTLGAWGLGWECWCD-----GME 145
                  L  L  E L+A+GI     D+ FVE      + G  G G+E   D     G+E
Sbjct: 114 EASEFEELIELTEELLRALGIK---LDIVFVEKTPGEFSPGGAGPGFEIEVDHPEGRGLE 170

Query: 146 ISQFT------------YFQQVCGIECSPISGEITYGLERL 174
           I                YF         P +     GLERL
Sbjct: 171 IGSGGYRQDEQARAADLYFLDEALEYRYPPTIGFGLGLERL 211


>gnl|CDD|30363 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 879

 Score = 33.7 bits (77), Expect = 0.072
 Identities = 9/21 (42%), Positives = 12/21 (57%)

Query: 169 YGLERLAMYVQNVNSVYDIVF 189
            GLER+A  +Q V + YD   
Sbjct: 229 MGLERIAAVLQGVPTNYDTDL 249


>gnl|CDD|37622 KOG2411, KOG2411, KOG2411, Aspartyl-tRNA synthetase, mitochondrial
           [Translation, ribosomal structure and biogenesis].
          Length = 628

 Score = 31.9 bits (72), Expect = 0.21
 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 161 SPISGEITYGLERLAMYVQNVNSVYD-IVF-NAIEGQNVLYGDIFAQSEQEYSRYNFEYA 218
           +P  G I  GL+RL   +    S+ D I F     G ++L        E++   YN   +
Sbjct: 565 APPHGGIALGLDRLVAMLTGAPSIRDVIAFPKTTTGADLLSNSPSEIPEEQLEDYNIRVS 624

Query: 219 NPE 221
           N  
Sbjct: 625 NST 627


>gnl|CDD|144852 pfam01411, tRNA-synt_2c, tRNA synthetases class II (A).  Other tRNA
           synthetase sub-families are too dissimilar to be
           included. This family includes only alanyl-tRNA
           synthetases.
          Length = 545

 Score = 28.4 bits (64), Expect = 2.3
 Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 5/29 (17%)

Query: 170 GLERLAMYVQNVNSVYDI-----VFNAIE 193
           GLERL   +QNV S YD      +   IE
Sbjct: 223 GLERLVAVLQNVRSNYDTDVFIPLIELIE 251


>gnl|CDD|35409 KOG0188, KOG0188, KOG0188, Alanyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 895

 Score = 28.4 bits (63), Expect = 2.6
 Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 5/29 (17%)

Query: 170 GLERLAMYVQNVNSVYDI-----VFNAIE 193
           G ERL   +QN  S YD      +F AI+
Sbjct: 234 GFERLVSVLQNKTSNYDTDLFTPIFEAIQ 262


>gnl|CDD|185676 cd00807, GlnRS_core, catalytic core domain of glutaminyl-tRNA
           synthetase.  Glutaminyl-tRNA synthetase (GlnRS) cataytic
           core domain. These enzymes attach Gln to the appropriate
           tRNA. Like other class I tRNA synthetases, they
           aminoacylate the 2'-OH of the nucleotide at the 3' end
           of the tRNA. The core domain is based on the Rossman
           fold and is responsible for the ATP-dependent formation
           of the enzyme bound aminoacyl-adenylate. GlnRS contains
           the characteristic class I HIGH and KMSKS motifs, which
           are involved in ATP binding. These enzymes function as
           monomers. Archaea and most bacteria lack GlnRS. In these
           organisms, the "non-discriminating" form of GluRS
           aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu,
           which is converted to Gln when appropriate by a
           transamidation enzyme.
          Length = 238

 Score = 27.6 bits (62), Expect = 4.0
 Identities = 22/86 (25%), Positives = 27/86 (31%), Gaps = 41/86 (47%)

Query: 214 NFEYA--------------NPEILHNHFIDSEKE-------------------------C 234
           NF YA              NPE     ++DS KE                          
Sbjct: 25  NFGYAKKYGGRCNLRFDDTNPEKEEEEYVDSIKEDVKWLGIKPYKVTYASDYFDQLYEYA 84

Query: 235 LDLLKKGIPNEHHRHHL--CVFPAYD 258
             L+KKG    HHR     C++P YD
Sbjct: 85  EQLIKKGKAYVHHRTGDKWCIYPTYD 110


>gnl|CDD|36401 KOG1187, KOG1187, KOG1187, Serine/threonine protein kinase [Signal
           transduction mechanisms].
          Length = 361

 Score = 27.0 bits (59), Expect = 6.6
 Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 14/66 (21%)

Query: 215 FEYANPEILHNHFIDSEKECLDLLK---------KGIPNEHHRHHLCVFPAYDQCIKASH 265
           +EY     L +H    + E LD            +G+    + H  C  P   + IK+S+
Sbjct: 151 YEYMPNGSLEDHLHGKKGEPLDWETRLKIALGAARGL---AYLHEGCPPPIIHRDIKSSN 207

Query: 266 IFNLLD 271
           I  LLD
Sbjct: 208 I--LLD 211


>gnl|CDD|173736 cd07832, STKc_CCRK, Catalytic domain of the Serine/Threonine
           Kinase, Cell Cycle-Related Kinase.  Serine/Threonine
           Kinases (STKs), Cell Cycle-Related Kinase (CCRK) p42
           subfamily, catalytic (c) domain. STKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           serine/threonine residues on protein substrates. The
           CCRK subfamily is part of a larger superfamily that
           includes the catalytic domains of other protein STKs,
           protein tyrosine kinases, RIO kinases, aminoglycoside
           phosphotransferase, choline kinase, and phosphoinositide
           3-kinase. CCRK was previously called p42. It is a
           Cyclin-Dependent Kinase (CDK)-Activating Kinase (CAK)
           which is essential for the activation of CDK2. It is
           indispensable for cell growth and has been implicated in
           the progression of glioblastoma multiforme. In the
           heart, a splice variant of CCRK with a different
           C-terminal half is expressed, this variant promotes
           cardiac cell growth and survival and is significantly
           down-regulated during the development of heart failure.
          Length = 286

 Score = 26.9 bits (60), Expect = 7.5
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 210 YSRYNFEYANPEILHNHFIDSEKECLDLLKK 240
           Y++  F  + P  L   F D+  E LDLLK 
Sbjct: 234 YNKITFPESKPIPLEEIFPDASPEALDLLKG 264


>gnl|CDD|37006 KOG1795, KOG1795, KOG1795, U5 snRNP spliceosome subunit [RNA
           processing and modification].
          Length = 2321

 Score = 26.5 bits (58), Expect = 9.3
 Identities = 8/25 (32%), Positives = 9/25 (36%)

Query: 117 DVRFVEDNWESPTLGAWGLGWECWC 141
             RF     + P  G W  GW  W 
Sbjct: 609 YYRFNTGVGKGPGCGFWAPGWRVWL 633


>gnl|CDD|80330 cd04447, DEP_BRCC3, DEP (Dishevelled, Egl-10, and Pleckstrin)
           domain found in BBRC3-like proteins. BBRC3, also known
           as DEPDC1B, is a DEP containing protein of unknown
           function..
          Length = 92

 Score = 26.5 bits (58), Expect = 9.8
 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 233 ECLDLLKKGIPNEHHRHHLCVFPAYDQCIKASHIFNLL 270
           E  +L + G+P   HR H   F +Y+ C  AS   + L
Sbjct: 5   EVTELFRAGMPLRKHRQH---FKSYENCFTASEAVDWL 39


  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
   0.322    0.139    0.443 

Gapped
Lambda     K      H
   0.267   0.0784    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,977,461
Number of extensions: 211484
Number of successful extensions: 442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 16
Length of query: 307
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 213
Effective length of database: 4,232,491
Effective search space: 901520583
Effective search space used: 901520583
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.6 bits)