RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3
[Candidatus Liberibacter asiaticus str. psy62]
         (227 letters)



>gnl|CDD|178972 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
          Length = 232

 Score =  357 bits (918), Expect = 2e-99
 Identities = 123/202 (60%), Positives = 159/202 (78%)

Query: 1   MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
           MGQK+NPI FRLG+   W+SRW+A   +Y  LLHEDLKIR++L+  LK+AGV++I IER 
Sbjct: 1   MGQKVNPIGFRLGIIKDWDSRWYADKKDYADLLHEDLKIRKFLKKKLKKAGVSRIEIERP 60

Query: 61  HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120
            K  R+ +++ARPG++IGKKG +IEK+RK+L  +T   + +++ EV KPE++A L+A+SI
Sbjct: 61  AKRVRVTIHTARPGIVIGKKGAEIEKLRKELEKLTGKPVQINIVEVKKPELDAQLVAESI 120

Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180
           AQQLERRV FRRAMKRA+Q AMR GA G+KV  SGRL GAE++RTE Y EGRVPL TLRA
Sbjct: 121 AQQLERRVSFRRAMKRAIQRAMRAGAKGIKVQVSGRLGGAEIARTEWYREGRVPLHTLRA 180

Query: 181 HIDYGTAVAETAYGSCGIKVYV 202
            IDYGTA A T YG  G+KV++
Sbjct: 181 DIDYGTAEAHTTYGIIGVKVWI 202


>gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type.
           TIGRFAMs model TIGR01008 describes S3 of the eukaryotic
           cytosol and of the archaea.
          Length = 211

 Score =  296 bits (761), Expect = 2e-81
 Identities = 115/202 (56%), Positives = 152/202 (75%)

Query: 1   MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
           MGQK+NPI FRLG+   W SRW+A   EY  LLHEDLKIR Y++  L  AG++ + IER 
Sbjct: 1   MGQKVNPIGFRLGITKDWKSRWYANPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERP 60

Query: 61  HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120
               R+ +++ARPG++IGKKG++IEK+RK L  +T  E+ +++ EV +PE++A L+A +I
Sbjct: 61  ADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNI 120

Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180
           A+QLE RV FRRAMK+A+QSAM+ GA G+KV  SGRL GAE++RTE Y EGRVPL TLRA
Sbjct: 121 ARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGAEIARTEWYKEGRVPLHTLRA 180

Query: 181 HIDYGTAVAETAYGSCGIKVYV 202
            IDY TA A T YG  G+KV++
Sbjct: 181 DIDYATAEAHTTYGIIGVKVWI 202


>gnl|CDD|179775 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
          Length = 207

 Score =  111 bits (279), Expect = 2e-25
 Identities = 64/172 (37%), Positives = 98/172 (56%), Gaps = 14/172 (8%)

Query: 37  LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS---N 93
           + I EYL   L +AG   + I++T    RI +Y+ RPG++IG+ G +I ++ + L     
Sbjct: 15  VMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFG 74

Query: 94  MTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIA 153
           + N +I   V EV  PE+NA ++A  +A  LER   FRRA   A++  M  GA GV++I 
Sbjct: 75  LENPQI--DVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIII 132

Query: 154 SGRLNGAELSRTECYLEGRV-----PLQTLRAHIDYGTAVAETAYGSCGIKV 200
           SG+L G E +RTE + EG +     P + L   +D G A+A+   G  G++V
Sbjct: 133 SGKLTG-ERARTEKFTEGYIKKSGEPAEEL---VDRGFAIAKLKLGIIGVEV 180


>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal
           type.  This model describes ribosomal protein S3 of the
           eukaryotic cytosol and of the archaea. TIGRFAMs model
           TIGR01009 describes the bacterial/organellar type,
           although the organellar types have a different
           architecture with long insertions and may score poorly.
          Length = 195

 Score =  102 bits (257), Expect = 6e-23
 Identities = 65/180 (36%), Positives = 98/180 (54%), Gaps = 9/180 (5%)

Query: 37  LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN 96
             I E+L+  L++AG + + +  T    ++I+++ RPGL+IG+ G  I ++ +KL     
Sbjct: 13  TLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFG 72

Query: 97  SE-IHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASG 155
            E   + V EV  PE+NA + A+ IA+ LER + FRRA   AV+  M  GA GV+V  SG
Sbjct: 73  LENPQIDVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISG 132

Query: 156 RLNGAELSRTECYLEGRVPL--QTLRAHIDYGTAVAETAYGSCGIKVY-----VSLRDEV 208
           +L G   +RTE +  G +    +     +D G A+A    G  G+KV      V L DEV
Sbjct: 133 KLTGER-ARTEKFAAGYLKHSGEPAEELVDKGFAIALLKLGVLGVKVKIMPPDVKLPDEV 191


>gnl|CDD|116265 pfam07650, KH_2, KH domain. 
          Length = 55

 Score = 64.0 bits (157), Expect = 3e-11
 Identities = 18/54 (33%), Positives = 35/54 (64%)

Query: 64  CRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIA 117
             +++ +++PG++IGK G++I+K+ K+L      ++ + V EV  PE+ A L A
Sbjct: 2   VIVVIRTSQPGIVIGKGGSNIKKLGKELRKRFGKKVQIEVLEVKNPELLAQLGA 55


>gnl|CDD|185435 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional.
          Length = 220

 Score = 49.7 bits (119), Expect = 6e-07
 Identities = 31/122 (25%), Positives = 54/122 (44%), Gaps = 3/122 (2%)

Query: 41  EYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIR---KKLSNMTNS 97
           E+L   L + G + + +  T     II+ + R   ++G KG  I ++    +K       
Sbjct: 23  EFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEG 82

Query: 98  EIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRL 157
           ++ L    V    + A   A+S+  +L   +  RRA    ++  M  GA G +VI SG+L
Sbjct: 83  KVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL 142

Query: 158 NG 159
             
Sbjct: 143 RA 144


>gnl|CDD|128617 smart00322, KH, K homology RNA-binding domain. 
          Length = 69

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 65  RIIVYSARPGLIIGKKGTDIEKIRKKLS---NMTNSEIHLSVNEVPKPEINATLIAQSIA 121
            +++ + + GLIIGK G+ I+KI ++     ++        V E+  P  N    A+ I 
Sbjct: 6   EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELIL 65

Query: 122 QQLE 125
           + LE
Sbjct: 66  EILE 69


>gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed.
          Length = 292

 Score = 32.3 bits (75), Expect = 0.10
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 16/54 (29%)

Query: 53  AKILIER-THKNCRIIVYSARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101
           A I +ER + K           G+IIGK G  ++KI    RK +  +   ++ L
Sbjct: 228 ATIYVERDSQK-----------GIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270


>gnl|CDD|132714 TIGR03675, arCOG00543, arCOG00543 universal archaeal
           KH-domain/beta-lactamase-domain protein.  This family of
           proteins is universal in the archaea and consistsof an
           N-terminal type-1 KH-domain (pfam00013) a central
           beta-lactamase-domain (pfam00753) with a C-terminal
           motif associated with RNA metabolism (pfam07521).
           KH-domains are associated with RNA-binding, so taken
           together, this protein is a likely metal-dependent
           RNAase. This family was defined in as arCOG01782.
          Length = 630

 Score = 30.7 bits (70), Expect = 0.29
 Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 5/53 (9%)

Query: 38  KIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKK 90
           KI+E +    ++AG+  I  +       +I+ + +PGL+IGK G+ + +I  +
Sbjct: 74  KIKEIVP---EEAGITDIYFDDV--TGEVIIEAEKPGLVIGKGGSTLREITAE 121


>gnl|CDD|177558 PHA03216, PHA03216, nuclear protein UL24; Provisional.
          Length = 272

 Score = 30.4 bits (68), Expect = 0.43
 Identities = 15/55 (27%), Positives = 26/55 (47%)

Query: 125 ERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLR 179
           E+R+  R  ++  ++   RF    V+ +AS + NG    R        VP +TL+
Sbjct: 4   EQRLTARSRLRAGIRCHNRFYNAMVQDLASAKANGVYGDRLAPLFSELVPAETLK 58


>gnl|CDD|184053 PRK13436, PRK13436, F0F1 ATP synthase subunit delta; Provisional.
          Length = 179

 Score = 30.0 bits (68), Expect = 0.58
 Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 6/36 (16%)

Query: 82  TDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIA 117
             I +   KLS   N ++HL        +I+  LIA
Sbjct: 122 VQISRFESKLSKKLNKKVHL------VNKIDPKLIA 151


>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era.  Era is an essential
           GTPase in Escherichia coli and many other bacteria. It
           plays a role in ribosome biogenesis. Few bacteria lack
           this protein.
          Length = 270

 Score = 28.9 bits (65), Expect = 1.1
 Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 4/32 (12%)

Query: 74  GLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101
            +IIGK G+ I+ I    RK +  + + ++ L
Sbjct: 234 KIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265


>gnl|CDD|179528 PRK03031, rnpA, ribonuclease P; Reviewed.
          Length = 122

 Score = 27.3 bits (61), Expect = 3.5
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 111 INATLIAQSIAQQLERRVVFRRAMKRAVQSAMR----FGADGVKVIASGRLNGAE 161
              T    SI+Q++ ++ V R  +KR +++A+R      A G  ++   +   AE
Sbjct: 44  PPPTRFGISISQKVSKKAVVRNRIKRQIRAALRQLLPRIAPGWDLVIIVKPTAAE 98


>gnl|CDD|163056 TIGR02877, spore_yhbH, sporulation protein YhbH.  This protein
           family, typified by YhbH in Bacillus subtilis, is found
           in nearly every endospore-forming bacterium and in no
           other genome (but note that the trusted cutoff score is
           set high to exclude a single high-scoring sequence from
           Nitrosococcus oceani ATCC 19707, which is classified in
           the Gammaproteobacteria). The gene in Bacillus subtilis
           was shown to be in the regulon of the sporulation sigma
           factor, sigma-E, and its mutation was shown to create a
           sporulation defect.
          Length = 371

 Score = 27.4 bits (61), Expect = 3.6
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 8/49 (16%)

Query: 77  IGKKGTDIEKIRKKLS-------NMTNSEIHLS-VNEVPKPEINATLIA 117
           + KK T IE +++           +T  ++      E  KPE NA +IA
Sbjct: 159 LDKKRTVIEALKRNQLRGRPELYPITKEDLRYKTWKENEKPESNAVVIA 207


>gnl|CDD|180352 PRK06019, PRK06019, phosphoribosylaminoimidazole carboxylase ATPase
           subunit; Reviewed.
          Length = 372

 Score = 27.0 bits (61), Expect = 3.8
 Identities = 16/46 (34%), Positives = 17/46 (36%), Gaps = 5/46 (10%)

Query: 136 RAVQSAMRFGADG--VKVIASG---RLNGAELSRTECYLEGRVPLQ 176
            AV    R G DG    VI S        A L    C LE  VP +
Sbjct: 137 PAVLKTRRGGYDGKGQWVIRSAEDLEAAWALLGSVPCILEEFVPFE 182


>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
          Length = 602

 Score = 27.1 bits (61), Expect = 3.8
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 7/56 (12%)

Query: 38  KIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARP--GLIIGKKGTDIEKIRKKL 91
           +I   ++ +L      +++      + + +VY        +IGK G  I+KI KKL
Sbjct: 460 EIEREIKRYLPGPVEVEVV-----SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKL 510


>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
           clpA. 
          Length = 731

 Score = 26.5 bits (59), Expect = 5.7
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 13/80 (16%)

Query: 76  IIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPK-PEINATLIAQSIAQQLERRVVFRRAM 134
           I+ + G D+E +RK L +      +L  N +P   E N     Q++  Q     V +RA+
Sbjct: 42  ILEECGGDVEALRKDLED------YLE-NNLPSITEENEADPEQTVGVQ----RVLQRAL 90

Query: 135 KRAVQSAMRFGADGVKVIAS 154
              V+SA +       ++ +
Sbjct: 91  -LHVKSAGKKEIGIGDILVA 109


>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
           domain fusion protein; Reviewed.
          Length = 725

 Score = 26.2 bits (58), Expect = 7.0
 Identities = 9/30 (30%), Positives = 15/30 (50%)

Query: 12  LGVNCTWNSRWFARGSEYGALLHEDLKIRE 41
           LG++     RW A+G +Y   L  +L+   
Sbjct: 665 LGIDSKLIKRWLAQGPDYRQALATNLEEER 694


>gnl|CDD|184049 PRK13429, PRK13429, F0F1 ATP synthase subunit delta; Provisional.
          Length = 181

 Score = 26.3 bits (59), Expect = 7.2
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 13/63 (20%)

Query: 83  DIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQ--------SIAQQLERRVVFRRAM 134
             E IR+KL  MT  ++ L    V  P +   ++ +        S+  QL R    +  +
Sbjct: 123 QQEAIRQKLEKMTGKKVELDT-AV-DPSLIGGVVVKIGDKVLDASVRTQLRR---LKETL 177

Query: 135 KRA 137
           K+ 
Sbjct: 178 KKG 180


>gnl|CDD|180527 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
           Validated.
          Length = 860

 Score = 25.9 bits (57), Expect = 8.4
 Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 11/66 (16%)

Query: 84  IEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLER-----RVVFRRAMKRAV 138
           I KI K         ++LS    P P+     IA  IA QL +     R+ F    K AV
Sbjct: 64  INKICKLAKKC--DVVYLS----PDPDREGEAIAWHIANQLPKNTKIQRISFNAITKGAV 117

Query: 139 QSAMRF 144
             A++ 
Sbjct: 118 TEALKH 123


  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
   0.320    0.134    0.387 

Gapped
Lambda     K      H
   0.267   0.0763    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,650,430
Number of extensions: 228435
Number of successful extensions: 518
Number of sequences better than 10.0: 1
Number of HSP's gapped: 514
Number of HSP's successfully gapped: 38
Length of query: 227
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 137
Effective length of database: 4,049,753
Effective search space: 554816161
Effective search space used: 554816161
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 (21.8 bits)
S2: 55 (24.9 bits)