RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780620|ref|YP_003065033.1| iron-responsive
transcriptional regulator [Candidatus Liberibacter asiaticus str.
psy62]
         (144 letters)



>gnl|CDD|171344 PRK11920, rirA, iron-responsive transcriptional regulator;
           Reviewed.
          Length = 153

 Score =  261 bits (669), Expect = 4e-71
 Identities = 87/144 (60%), Positives = 110/144 (76%)

Query: 1   MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
           M LTK+T+Y IR+LMYCA ++   +RI +IA A  +SELFLFKILQPLV+AG+VETVRGR
Sbjct: 1   MRLTKQTNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGR 60

Query: 61  RGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFD 120
            GGVRL RPA  I++ DVV+ TE+SF +AECF +   +CPLV SCGL S LRKALNAFF 
Sbjct: 61  NGGVRLGRPAADISLFDVVRVTEDSFSMAECFENDASECPLVDSCGLNSALRKALNAFFA 120

Query: 121 VLTQYSIECLVRNRSSIKKIFNAG 144
           VL++YSI  LV+ R +I+ +    
Sbjct: 121 VLSKYSIADLVKARPNIRFLLGLD 144


>gnl|CDD|129821 TIGR00738, rrf2_super, rrf2 family protein (putative
           transcriptional regulator).  This model represents a
           superfamily of probable transcriptional regulators. One
           member, RRF2 of Desulfovibrio vulgaris is an apparent
           regulatory protein experimentally (MEDLINE:97293189).
           The N-terminal region appears related to the DNA-binding
           biotin repressor region of the BirA bifunctional
           according to results after three rounds of PSI-BLAST
           with a fairly high stringency.
          Length = 132

 Score =  118 bits (297), Expect = 7e-28
 Identities = 52/133 (39%), Positives = 78/133 (58%), Gaps = 2/133 (1%)

Query: 1   MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
           M LTK+T+Y +R L+  A++ D  P  + +IAE   IS  +L KIL+ L +AG+VE+VRG
Sbjct: 1   MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRG 60

Query: 60  RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFF 119
             GG RL RP ++IT+ DVV+A E      +C   +    P    C L +V R+  +A  
Sbjct: 61  PGGGYRLARPPEEITVGDVVRAVEGPLAPVQCIGLNG-CHPGEEVCLLHAVWRELEDAIE 119

Query: 120 DVLTQYSIECLVR 132
           D L + ++  LV+
Sbjct: 120 DFLREITLADLVK 132


>gnl|CDD|182900 PRK11014, PRK11014, transcriptional repressor NsrR; Provisional.
          Length = 141

 Score = 89.3 bits (222), Expect = 3e-19
 Identities = 50/141 (35%), Positives = 72/141 (51%), Gaps = 5/141 (3%)

Query: 1   MHLTKRTDYGIRVLMYCA-IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
           M LT  TDYG+R L+Y A +       IS++ E   +S   + KI+  L +AG V  VRG
Sbjct: 1   MQLTSFTDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60

Query: 60  RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFF 119
           + GG+RL +PA  I I DVV+  E    V  C +     C +  +C L   L KA+ +F 
Sbjct: 61  KNGGIRLGKPASTIRIGDVVRELEPLSLV-NCSSEF---CHITPACRLKQALSKAVQSFL 116

Query: 120 DVLTQYSIECLVRNRSSIKKI 140
             L  Y++  LV     + K+
Sbjct: 117 KELDNYTLADLVEENQPLYKL 137


>gnl|CDD|131989 TIGR02944, suf_reg_Xantho, FeS assembly SUF system regulator,
           gammaproteobacterial.  The SUF system is an
           oxygen-resistant iron-sulfur cluster assembly system
           found in both aerobes and facultative anaerobes. Its
           presence appears to be a marker of oxygen tolerance;
           strict anaerobes and microaerophiles tend to have
           different FeS cluster biosynthesis systems. Members of
           this protein family belong to the rrf2 family of
           transcriptional regulators and are found, typically, as
           the first gene of a SUF operon. It is found only in a
           subset of genomes that encode the SUF system, including
           the genus Xanthomonas. The conserved location suggests
           an autoregulatory role.
          Length = 130

 Score = 76.0 bits (187), Expect = 4e-15
 Identities = 44/127 (34%), Positives = 65/127 (51%), Gaps = 1/127 (0%)

Query: 1   MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
           + ++K TDY   VL   A ++  P   ++IAE   ++   + KIL+ L  AGIV + RG 
Sbjct: 2   LKISKLTDYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGV 61

Query: 61  RGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFD 120
            GG  L R    IT+ D+VKA E    + EC    K  C L  SCG+ S  +   +   D
Sbjct: 62  EGGYTLARAPRDITVADIVKAVEGPVALTECSDDQKK-CSLGNSCGVRSNWKVINSQVLD 120

Query: 121 VLTQYSI 127
           +L+  S+
Sbjct: 121 LLSSVSL 127


>gnl|CDD|131065 TIGR02010, IscR, iron-sulfur cluster assembly transcription factor
           IscR.  This model describes IscR, an iron-sulfur binding
           transcription factor of the ISC iron-sulfur cluster
           assembly system.
          Length = 135

 Score = 62.4 bits (152), Expect = 4e-11
 Identities = 43/137 (31%), Positives = 71/137 (51%), Gaps = 5/137 (3%)

Query: 1   MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
           M LT +  Y +  ++  A++ +  P  ++ I+E   IS  +L ++   L KAG+V++VRG
Sbjct: 1   MRLTTKGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRG 60

Query: 60  RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNA-F 118
             GG +L RPA+ I++ D++ A +ES     C    K +C     C LT  L   L+   
Sbjct: 61  PGGGYQLGRPAEDISVADIIDAVDESVDATRCQG--KGNCRHGTRC-LTHDLWADLSKHI 117

Query: 119 FDVLTQYSIECLVRNRS 135
            D L   S+  LV  ++
Sbjct: 118 RDYLESISLADLVNQQN 134


>gnl|CDD|182783 PRK10857, PRK10857, DNA-binding transcriptional regulator IscR;
           Provisional.
          Length = 164

 Score = 49.9 bits (119), Expect = 2e-07
 Identities = 39/136 (28%), Positives = 65/136 (47%), Gaps = 5/136 (3%)

Query: 1   MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
           M LT +  Y +  ++  A++++  P  ++ I+E   IS  +L ++   L K G+V +VRG
Sbjct: 1   MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRG 60

Query: 60  RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNA-F 118
             GG  L + A  I + +V+ A +ES     C    K  C     C LT  L + L+   
Sbjct: 61  PGGGYLLGKDASSIAVGEVISAVDESVDATRC--QGKGGCQGGDKC-LTHALWRDLSDRL 117

Query: 119 FDVLTQYSIECLVRNR 134
              L   ++  LV N+
Sbjct: 118 TGFLNNITLGELVNNQ 133


>gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional.
          Length = 588

 Score = 29.2 bits (66), Expect = 0.38
 Identities = 11/18 (61%), Positives = 12/18 (66%)

Query: 48 LVKAGIVETVRGRRGGVR 65
          L K GI  T+ GRR GVR
Sbjct: 4  LPKIGIRPTIDGRRMGVR 21


>gnl|CDD|184474 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
          Length = 392

 Score = 28.5 bits (64), Expect = 0.71
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 49 VKAGIVETVRGRRGGVRLCRPADQI 73
          VKA I    RG+ GG++LCR  +++
Sbjct: 45 VKAQIHSGARGKAGGIKLCRTYNEV 69


>gnl|CDD|162403 TIGR01531, glyc_debranch, glycogen debranching enzymye.  glycogen
           debranching enzyme possesses two different catalytic
           activities; oligo-1,4-->1,4-glucantransferase (EC
           2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
           directed mutagenesis studies in S. cerevisiae indicate
           that the transferase and glucosidase activities are
           independent and located in different regions of the
           polypeptide chain. Proteins in this model belong to the
           larger alpha-amylase family. The model covers eukaryotic
           proteins with a seed composed of human, nematode and
           yeast sequences. Yeast seed sequence is well
           characterized. The model is quite rigorous; either query
           sequence yields large bit score or it fails to hit the
           model altogether. There doesn't appear to be any middle
           ground.
          Length = 1464

 Score = 28.3 bits (63), Expect = 0.77
 Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 86  FFVAECFA-SHKIDCPLVGSCGLTSVLRKALNAF 118
           + VAE F  S  +D   V   G++S++R+A++A+
Sbjct: 537 YVVAELFTGSETLDNVFVNRLGISSLIREAMSAW 570


>gnl|CDD|181783 PRK09333, PRK09333, 30S ribosomal protein S19e; Provisional.
          Length = 150

 Score = 27.1 bits (61), Expect = 1.6
 Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)

Query: 43  KILQPLVKAGIVETV-RGRR 61
           KILQ L KAG+VE   +GR 
Sbjct: 100 KILQQLEKAGLVEKTKKGRV 119


>gnl|CDD|177992 PLN02363, PLN02363, phosphoribosylanthranilate isomerase.
          Length = 256

 Score = 27.1 bits (60), Expect = 1.9
 Identities = 13/30 (43%), Positives = 14/30 (46%), Gaps = 1/30 (3%)

Query: 88  VAECFASHKIDCPLVGSCGLTSVLRKALNA 117
           VA        D PLV  CG+TS  R A  A
Sbjct: 35  VAPKDDERGKDRPLVKMCGITSA-RDAAMA 63


>gnl|CDD|130161 TIGR01089, fucI, L-fucose isomerase.  This enzyme catalyzes the
          first step in fucose metabolism, and has been
          characterized in Escherichia coli and Bacteroides
          thetaiotaomicron.
          Length = 587

 Score = 26.4 bits (58), Expect = 3.0
 Identities = 11/18 (61%), Positives = 12/18 (66%)

Query: 48 LVKAGIVETVRGRRGGVR 65
          L K GI  T+ GRR GVR
Sbjct: 3  LPKIGIRPTIDGRRMGVR 20


>gnl|CDD|162205 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit.  This
           model describes the bacterial oxaloacetate decarboxylase
           alpha subunit and its equivalents in archaea. The
           oxaloacetate decarboxylase Na+ pump is the paradigm of
           the family of Na+ transport decarboxylases that present
           in bacteria and archaea. It a multi subunit enzyme
           consisting of a peripheral alpha-subunit and integral
           membrane subunits beta and gamma. The energy released by
           the decarboxylation reaction of oxaloacetate is coupled
           to Na+ ion pumping across the membrane.
          Length = 582

 Score = 26.3 bits (58), Expect = 3.2
 Identities = 7/23 (30%), Positives = 11/23 (47%)

Query: 49  VKAGIVETVRGRRGGVRLCRPAD 71
           + A +   + G    +  CRPAD
Sbjct: 375 INAELQRKILGDEKPIVDCRPAD 397


>gnl|CDD|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase
           N; Provisional.
          Length = 343

 Score = 25.9 bits (57), Expect = 4.1
 Identities = 6/21 (28%), Positives = 12/21 (57%)

Query: 112 RKALNAFFDVLTQYSIECLVR 132
           R+ +  F ++L +  IE  +R
Sbjct: 300 RERIERFKEILLKNGIEAEIR 320


>gnl|CDD|170049 PRK09692, PRK09692, integrase; Provisional.
          Length = 413

 Score = 25.8 bits (56), Expect = 4.5
 Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 6/35 (17%)

Query: 41  LFKILQPLVKAGIVETVRGRRGGVRLCRPADQITI 75
           L + +QP+   G +ETVR      RLC+  +++ I
Sbjct: 155 LVQAVQPVQARGALETVR------RLCQRINEVMI 183


>gnl|CDD|171489 PRK12423, PRK12423, LexA repressor; Provisional.
          Length = 202

 Score = 25.9 bits (57), Expect = 4.5
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 36 ISELFLF-------KILQPLVKAGIVETVRGRRGGVRLCRPADQITILDV 78
          I++ F F       K +Q L +AG++E V  +  G+RL   A +  +L++
Sbjct: 31 IAQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIRLPGGAGRPELLEL 80


>gnl|CDD|184952 PRK14990, PRK14990, anaerobic dimethyl sulfoxide reductase subunit
           A; Provisional.
          Length = 814

 Score = 25.4 bits (55), Expect = 5.2
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 87  FVAECFASHKIDCPLVGSCGLTSVL---RKALNAFFDVLTQYSIECLVRNRSSIKKIFNA 143
            + +C AS ++D  L  SCG  S +    + +   F+  T Y +   +  R  +++ F  
Sbjct: 526 LLPDCTASEQMDFALDASCGNMSYVIFNDQVIKPRFECKTIYEMTSELAKRLGVEQQFTE 585

Query: 144 G 144
           G
Sbjct: 586 G 586


>gnl|CDD|184448 PRK14010, PRK14010, potassium-transporting ATPase subunit B;
           Provisional.
          Length = 673

 Score = 25.4 bits (55), Expect = 5.4
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 3/57 (5%)

Query: 45  LQPLVKAGIVETVRGRRG-GVR--LCRPADQITILDVVKATEESFFVAECFASHKID 98
           L+ ++K G+VE  R  R  G+   +C   +++T   + K      FVAEC    KI+
Sbjct: 438 LKDVIKDGLVERFRELREMGIETVMCTGDNELTAATIAKEAGVDRFVAECKPEDKIN 494


>gnl|CDD|116493 pfam07881, Fucose_iso_N1, L-fucose isomerase, first N-terminal
          domain.  The members of this family are similar to
          L-fucose isomerase expressed by E. coli (EC:5.3.1.3).
          This enzyme corresponds to glucose-6-phosphate
          isomerase in glycolysis, and converts an aldo-hexose to
          a ketose to prepare it for aldol cleavage. The enzyme
          is a hexamer, with each subunit being wedge-shaped and
          composed of three domains. Both domains 1 and 2 contain
          central parallel beta-sheets with surrounding alpha
          helices. Domain 1 demonstrates the
          beta-alpha-beta-alpha- beta Rossman fold. The active
          centre is shared between pairs of subunits related
          along the molecular three-fold axis, with domains 2 and
          3 from one subunit providing most of the
          substrate-contacting residues, and domain 1 from the
          adjacent subunit contributing some other residues.
          Length = 171

 Score = 25.0 bits (55), Expect = 6.9
 Identities = 11/16 (68%), Positives = 12/16 (75%)

Query: 50 KAGIVETVRGRRGGVR 65
          K GI  T+ GRRGGVR
Sbjct: 5  KIGIRPTIDGRRGGVR 20


>gnl|CDD|182200 PRK10026, PRK10026, arsenate reductase; Provisional.
          Length = 141

 Score = 24.8 bits (54), Expect = 8.8
 Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 2/28 (7%)

Query: 63  GVRLCRPADQITILDVVKATEESFFVAE 90
           G RLCRP++   +L+++   ++  F  E
Sbjct: 102 GTRLCRPSE--VVLEILPDAQKGAFTKE 127


  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
   0.329    0.141    0.428 

Gapped
Lambda     K      H
   0.267   0.0639    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,209,520
Number of extensions: 126646
Number of successful extensions: 313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 27
Length of query: 144
Length of database: 5,994,473
Length adjustment: 84
Effective length of query: 60
Effective length of database: 4,179,401
Effective search space: 250764060
Effective search space used: 250764060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.0 bits)