RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780856|ref|YP_003065269.1| NADH-quinone oxidoreductase, E
subunit [Candidatus Liberibacter asiaticus str. psy62]
         (218 letters)



>gnl|CDD|183479 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional.
          Length = 400

 Score =  372 bits (956), Expect = e-104
 Identities = 147/214 (68%), Positives = 170/214 (79%), Gaps = 2/214 (0%)

Query: 2   SVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAI 61
            +RRL E+  QP SF+F+ E+A W  + I++YP  R  SAVIPLLMRAQEQEGWV+RAAI
Sbjct: 1   MLRRLHED--QPDSFAFTPENAAWAEKQITKYPEGRQASAVIPLLMRAQEQEGWVTRAAI 58

Query: 62  EVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIH 121
           E VA++LDMAYIRVLE+ATFYTQFQL PVGTRAH+QVCGTTPCMLRG E L+ VC++KIH
Sbjct: 59  EKVADMLDMAYIRVLEVATFYTQFQLQPVGTRAHIQVCGTTPCMLRGSEALMAVCKSKIH 118

Query: 122 QKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIR 181
             P   N+DGTLSWEEVEC GACVNAPMV IGKD YEDLTPERLEEIIDAF+ G+G  ++
Sbjct: 119 AHPHELNADGTLSWEEVECLGACVNAPMVQIGKDYYEDLTPERLEEIIDAFAAGKGPVVK 178

Query: 182 PGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDD 215
           PGPQI R +S PAGGLTSL +   K R    K  
Sbjct: 179 PGPQIGRYASEPAGGLTSLTEEAGKARYNASKAL 212


>gnl|CDD|181024 PRK07539, PRK07539, NADH dehydrogenase subunit E; Validated.
          Length = 154

 Score =  237 bits (608), Expect = 1e-63
 Identities = 75/157 (47%), Positives = 95/157 (60%), Gaps = 3/157 (1%)

Query: 17  SFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVL 76
             S E    +   I++YP  R  SAVIP L   QEQ GWV   AIE VA+ L M  I V 
Sbjct: 1   MLSAEELAAIEREIAKYPRPR--SAVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58

Query: 77  EIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWE 136
           E+ATFY+     PVG R  +QVC +TPC LRG E ++   + K+  KP    +DG  +  
Sbjct: 59  EVATFYSMIFRQPVG-RHVIQVCTSTPCWLRGGEAILAALKKKLGIKPGETTADGRFTLL 117

Query: 137 EVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFS 173
           EVEC GAC NAP+VMI  DTYEDLTPE+++E++D   
Sbjct: 118 EVECLGACDNAPVVMINDDTYEDLTPEKIDELLDELK 154


>gnl|CDD|131013 TIGR01958, nuoE_fam, NADH-quinone oxidoreductase, E subunit.  This
           model describes the E chain of complexes that resemble
           NADH-quinone oxidoreductases. The electron acceptor is a
           quinone, ubiquinone, in mitochondria and most bacteria,
           including Escherichia coli, where the recommended gene
           symbol is nuoB. This model does not identify proteins
           from chloroplast and cyanobacteria.
          Length = 148

 Score =  209 bits (533), Expect = 5e-55
 Identities = 70/148 (47%), Positives = 98/148 (66%), Gaps = 1/148 (0%)

Query: 25  WVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQ 84
            + E+I++YP  + +SA++P LM AQEQ+GWV+  AI  VA +L +  + V E+ATFY+ 
Sbjct: 1   LIEEIIAKYPDDQKRSAIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVATFYSM 60

Query: 85  FQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGAC 144
           F   PVG R H+QVC   PC LRG E L++   NK+  KP     DG  +  EVEC GAC
Sbjct: 61  FDTEPVG-RYHLQVCTNVPCALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGAC 119

Query: 145 VNAPMVMIGKDTYEDLTPERLEEIIDAF 172
            NAP++MI  D YE LTPE+L+E+++ +
Sbjct: 120 GNAPVMMINDDYYEFLTPEKLDELLERY 147


>gnl|CDD|136420 PRK07571, PRK07571, bidirectional hydrogenase complex protein HoxE;
           Reviewed.
          Length = 169

 Score = 82.9 bits (205), Expect = 5e-17
 Identities = 46/135 (34%), Positives = 65/135 (48%), Gaps = 1/135 (0%)

Query: 39  QSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQV 98
           Q A+I +L +AQE  G++ R  +  VA  L +   RV  +ATFY  F L P G    V V
Sbjct: 35  QDALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFYHLFSLKPSGEHTCV-V 93

Query: 99  CGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYE 158
           C  T C ++G   ++E   N++  K     +DG LS     C GAC  AP V+       
Sbjct: 94  CTGTACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDGKVAG 153

Query: 159 DLTPERLEEIIDAFS 173
             TPE + E +  + 
Sbjct: 154 KQTPESVLEKVQGWL 168


>gnl|CDD|180339 PRK05988, PRK05988, formate dehydrogenase subunit gamma; Validated.
          Length = 156

 Score = 66.9 bits (164), Expect = 4e-12
 Identities = 38/135 (28%), Positives = 68/135 (50%), Gaps = 11/135 (8%)

Query: 41  AVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHV-QVC 99
           A++P+L   Q++ G+V   A+ V+A  L+++   V  + TFY  F+  P G   HV ++C
Sbjct: 24  ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPG--RHVLKLC 81

Query: 100 GTTPCMLRGCEKLIEVCRNKI----HQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKD 155
               C   G + L    + ++    HQ      +DG ++ E V C G C  +P  M+  +
Sbjct: 82  RAEACQAMGGDALAAHAKARLGIDFHQ----TTADGAVTLEPVYCLGLCACSPAAMLDGE 137

Query: 156 TYEDLTPERLEEIID 170
            +  L P+RL+ ++ 
Sbjct: 138 VHGRLDPQRLDALLA 152


>gnl|CDD|185473 PTZ00139, PTZ00139, Succinate dehydrogenase [ubiquinone]
           flavoprotein subunit; Provisional.
          Length = 617

 Score = 30.1 bits (68), Expect = 0.44
 Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 9/64 (14%)

Query: 95  HVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSW-----EEVECQGACVNAPM 149
           H  V      +  G EK+ E+  +    K      D +L W     E +E +     A  
Sbjct: 492 HAAVFRIGESLQEGVEKIKEIYSDFKDVKI----KDKSLVWNTDLIETLELENLLTQAKQ 547

Query: 150 VMIG 153
            ++ 
Sbjct: 548 TILS 551


>gnl|CDD|161886 TIGR00456, argS, arginyl-tRNA synthetase.  This model recognizes
          arginyl-tRNA synthetase in every completed genome to
          date. An interesting feature of the alignment of all
          arginyl-tRNA synthetases is a fairly deep split between
          two families. One family includes archaeal, eukaryotic
          and organellar, spirochete, E. coli, and Synechocystis
          sp. The second, sharing a deletion of about 25 residues
          in the central region relative to the first, includes
          Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas
          and Mycobacteria, and the Gram-negative bacterium
          Helicobacter pylori.
          Length = 566

 Score = 28.1 bits (63), Expect = 2.0
 Identities = 10/30 (33%), Positives = 14/30 (46%)

Query: 60 AIEVVANILDMAYIRVLEIATFYTQFQLSP 89
          A E+V  +     I  +E A  +  F LSP
Sbjct: 57 AEEIVLKLKTGEIIEKVEAAGPFINFFLSP 86


>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein;
          Provisional.
          Length = 267

 Score = 27.8 bits (62), Expect = 2.1
 Identities = 9/18 (50%), Positives = 10/18 (55%)

Query: 54 GWVSRAAIEVVANILDMA 71
          G V  A  E V  IL+MA
Sbjct: 16 GVVDPAHREEVKRILEMA 33


>gnl|CDD|178672 PLN03126, PLN03126, Elongation factor Tu; Provisional.
          Length = 478

 Score = 27.3 bits (60), Expect = 3.0
 Identities = 15/36 (41%), Positives = 20/36 (55%)

Query: 182 PGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDDKI 217
           PG  I  IS +    L +L++N + KRG  K  DKI
Sbjct: 233 PGDDIPIISGSALLALEALMENPNIKRGDNKWVDKI 268


>gnl|CDD|183390 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
          Length = 556

 Score = 27.5 bits (62), Expect = 3.1
 Identities = 10/20 (50%), Positives = 13/20 (65%)

Query: 16  FSFSEESAIWVNEVISRYPP 35
           FS S    IWV++ + RYPP
Sbjct: 335 FSKSRGWGIWVDDALERYPP 354


>gnl|CDD|180170 PRK05626, rpsO, 30S ribosomal protein S15; Reviewed.
          Length = 89

 Score = 27.4 bits (62), Expect = 3.1
 Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 13/58 (22%)

Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQI----DRISSAPAGGLTSLLDNNSK----KRG 209
           LT E+  EII  +   +GDT  P  Q+    +RI+      LT  L  + K    +RG
Sbjct: 3   LTKEKKAEIIKEYGRHEGDTGSPEVQVALLTERINH-----LTEHLKEHKKDHHSRRG 55


>gnl|CDD|162887 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
           family.  This subset of the radical-SAM family
           (pfam04055) includes a number of probable activating
           proteins acting on different enzymes all requiring an
           amino-acid-centered radical. The closest relatives to
           this family are the pyruvate-formate lyase activating
           enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
           ribonucleotide reductase activating enzyme (TIGR02491).
           Included within this subfamily are activators of
           hydroxyphenyl acetate decarboxylase (HdpA, ),
           benzylsuccinate synthase (BssD, ), gycerol dehydratase
           (DhaB2, ) as well as enzymes annotated in E. coli as
           activators of different isozymes of pyruvate-formate
           lyase (PFLC and PFLE) however, these appear to lack
           characterization and may activate enzymes with
           distinctive functions. Most of the sequence-level
           variability between these forms is concentrated within
           an N-terminal domain which follows a conserved group of
           three cysteines and contains a variable pattern of 0 to
           8 additional cysteines.
          Length = 295

 Score = 27.3 bits (61), Expect = 3.5
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 7/83 (8%)

Query: 108 GCEKLIEVCRNKIHQKPLHRNSDGTLSWEEV------ECQGACVNAPMVMIGKD-TYEDL 160
           GC K +EVC     +     +    +           +C  AC +  + ++G++ T E++
Sbjct: 52  GCGKCVEVCPAGTARLSELADGRNRIIIRREKCTHCGKCTEACPSGALSIVGEEMTVEEV 111

Query: 161 TPERLEEIIDAFSTGQGDTIRPG 183
               L + I   ++G G T+  G
Sbjct: 112 MRVVLRDSIFYRNSGGGVTLSGG 134


>gnl|CDD|177740 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
           iron-sulfur subunit.
          Length = 276

 Score = 27.1 bits (60), Expect = 3.6
 Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 11/46 (23%)

Query: 155 DTYEDLTPERLEEIIDAFSTGQGDTIR-----------PGPQIDRI 189
           D+ ++ T ERLE + D F   +  TIR           P   I +I
Sbjct: 224 DSRDEYTKERLEALDDEFKLYRCHTIRNCSNACPKGLNPAKAIAKI 269


>gnl|CDD|177871 PLN02226, PLN02226, 2-oxoglutarate dehydrogenase E2 component.
          Length = 463

 Score = 26.3 bits (57), Expect = 5.8
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 168 IIDAFSTGQGDTIRPGPQIDRISSA 192
           +I  F   +GDT+ PG ++  IS +
Sbjct: 144 VIQEFLVKEGDTVEPGTKVAIISKS 168


>gnl|CDD|178776 PLN03238, PLN03238, probable histone acetyltransferase MYST;
           Provisional.
          Length = 290

 Score = 26.0 bits (57), Expect = 8.5
 Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 11/55 (20%)

Query: 119 KIHQKP----LHRNSDGTLSWEEVE-------CQGACVNAPMVMIGKDTYEDLTP 162
            I Q P        ++G LS  EV+       CQ  C+ A + +  K  Y D+ P
Sbjct: 72  DIRQPPGGGIYGAVTEGPLSVFEVDGKKAKVYCQNLCLLAKLFLDHKTLYYDVDP 126


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.317    0.132    0.393 

Gapped
Lambda     K      H
   0.267   0.0718    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,595,000
Number of extensions: 219092
Number of successful extensions: 489
Number of sequences better than 10.0: 1
Number of HSP's gapped: 484
Number of HSP's successfully gapped: 16
Length of query: 218
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,049,753
Effective search space: 518368384
Effective search space used: 518368384
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 (21.7 bits)
S2: 55 (25.0 bits)