RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780444|ref|YP_003064857.1| bacteriophage repressor
protein C1 [Candidatus Liberibacter asiaticus str. psy62]
         (223 letters)



>gnl|CDD|32756 COG2932, COG2932, Predicted transcriptional regulator
           [Transcription].
          Length = 214

 Score =  127 bits (319), Expect = 3e-30
 Identities = 78/221 (35%), Positives = 108/221 (48%), Gaps = 14/221 (6%)

Query: 5   SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA 64
           SH     AID +AER   + SGLARK GLDPTSFN SKR   +   RW ST S  K+L A
Sbjct: 3   SHDSGGRAIDALAERGKASSSGLARKEGLDPTSFNLSKRASADVSARWLSTGSGEKVLEA 62

Query: 65  TNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIR 124
                    DL   D          IP+     +G+ GFFD   FP G  W+ +  P   
Sbjct: 63  AGAPT----DLTAGDASENPVV-PLIPVSGAAGAGADGFFDENGFPVGFGWDEIERPPGI 117

Query: 125 SPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKV 184
            P +G++A++           SM P Y  GD L+++  +    GDR+ ++   G++  K 
Sbjct: 118 DPDSGVFALR-------VTGDSMEPTYEDGDTLLVDPGVNTRRGDRVYVETDGGELYVKK 170

Query: 185 LISRRGRSIDLMSLNCCYPVDTV--EMSDIEWIARILWASQ 223
           L    G  + L+SLN  Y  D +  E  D+E I R++W S+
Sbjct: 171 LQREPGGLLRLVSLNPDYYPDEIFSEDDDVEIIGRVVWVSR 211


>gnl|CDD|119397 cd06529, S24_LexA-like, Peptidase S24 LexA-like proteins are
           involved in the SOS response leading to the repair of
           single-stranded DNA within the bacterial cell. This
           family includes: the lambda repressor CI/C2 family and
           related bacterial prophage repressor proteins; LexA (EC
           3.4.21.88), the repressor of genes in the cellular SOS
           response to DNA damage; MucA and the related UmuD
           proteins, which are lesion-bypass DNA polymerases,
           induced in response to mitogenic DNA damage; RulA, a
           component of the rulAB locus that confers resistance to
           UV, and RuvA, which is a component of the RuvABC
           resolvasome that catalyzes the resolution of Holliday
           junctions that arise during genetic recombination and
           DNA repair. The LexA-like proteins contain two-domains: 
           an N-terminal DNA binding domain and a C-terminal domain
           (CTD) that provides LexA dimerization as well as
           cleavage activity. They undergo autolysis, cleaving at
           an Ala-Gly or a Cys-Gly bond, separating the DNA-binding
           domain from the rest of the protein. In the presence of
           single-stranded DNA, the LexA, UmuD and MucA proteins
           interact with RecA, activating self cleavage, thus
           either derepressing transcription in the case of LexA or
           activating the lesion-bypass polymerase in the case of
           UmuD and MucA. The LexA proteins are serine proteases
           that carry out catalysis using a serine/lysine dyad
           instead of the prototypical serine/histidine/aspartic
           acid triad found in most serine proteases. LexA sequence
           homologs are found in almost all of the bacterial
           genomes sequenced to date, covering a large number of
           phyla, suggesting both, an ancient origin and a
           widespread distribution of lexA and the SOS response..
          Length = 81

 Score = 49.1 bits (118), Expect = 8e-07
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 143 QDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCY 202
           +  SM P    GD+++++ +     GD ++ +   G++  K L  R G  + L+S N  Y
Sbjct: 6   KGDSMEPTIPDGDLVLVDPSDTPRDGDIVVAR-LDGELTVKRLQRRGGGRLRLISDNPAY 64

Query: 203 PVDTVEMSDIEWIARI 218
           P   ++  ++E +  +
Sbjct: 65  PPIEIDEEELEIVGVV 80


>gnl|CDD|119396 cd06462, Peptidase_S24_S26, The S24, S26 LexA/signal peptidase
           superfamily contains LexA-related and type I signal
           peptidase families. The S24 LexA protein domains
           include: the lambda repressor CI/C2 family and related
           bacterial prophage repressor proteins; LexA (EC
           3.4.21.88), the repressor of genes in the cellular SOS
           response to DNA damage; MucA and the related UmuD
           proteins, which are lesion-bypass DNA polymerases,
           induced in response to mitogenic DNA damage; RulA, a
           component of the rulAB locus that confers resistance to
           UV, and RuvA, which is a component of the RuvABC
           resolvasome that catalyzes the resolution of Holliday
           junctions that arise during genetic recombination and
           DNA repair. The S26 type I signal peptidase (SPase)
           family also includes mitochondrial inner membrane
           protease (IMP)-like members. SPases are essential
           membrane-bound proteases which function to cleave away
           the amino-terminal signal peptide from the translocated
           pre-protein, thus playing a crucial role in the
           transport of proteins across membranes in all living
           organisms. All members in this superfamily are unique
           serine proteases that carry out catalysis using a
           serine/lysine dyad instead of the prototypical
           serine/histidine/aspartic acid triad found in most
           serine proteases..
          Length = 84

 Score = 36.5 bits (85), Expect = 0.006
 Identities = 18/81 (22%), Positives = 29/81 (35%), Gaps = 20/81 (24%)

Query: 146 SMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVA----------KVLISRRGR-SID 194
           SM P    GD++++         D+   +P+ GDIV           K +I   G     
Sbjct: 9   SMEPTIPDGDLVLV---------DKSSYEPKRGDIVVFRLPGGELTVKRVIGLPGEGHYF 59

Query: 195 LMSLNCCYPVDTVEMSDIEWI 215
           L+  N   P   ++      I
Sbjct: 60  LLGDNPNSPDSRIDGPPELDI 80


>gnl|CDD|144350 pfam00717, Peptidase_S24, Peptidase S24-like. 
          Length = 67

 Score = 34.5 bits (80), Expect = 0.021
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 146 SMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYP 203
           SM P    GD+L+++   +   GD ++ +    +   K LI   G  I L+  N  YP
Sbjct: 6   SMEPTIPDGDLLLVDKTSEPKRGDIVVARLPGEEAYVKRLIGLPGDII-LLPSNPEYP 62


>gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
          Prokaryotic DNA binding proteins belonging to the
          xenobiotic response element family of transcriptional
          regulators..
          Length = 58

 Score = 31.3 bits (71), Expect = 0.21
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69
          E +  + +   LT   LA K G+  ++ ++     IE   R PS E++ K+  A   ++
Sbjct: 2  ERLKELRKEKGLTQEELAEKLGVSRSTISR-----IENGKRNPSLETLEKLAKALGVSL 55


>gnl|CDD|29994 cd01128, rho_factor, Transcription termination factor rho is a
           bacterial ATP-dependent RNA/DNA helicase. It is a
           homohexamer. Each monomer consists of an N-terminal
           domain of the OB fold, which is responsible for binding
           to cysteine rich nucleotides. This alignment is of the
           C-terminal ATP binding domain..
          Length = 249

 Score = 31.4 bits (71), Expect = 0.23
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 11  EAIDRMAERHNLT--PSGLARKAGLDPTSFNKSKRFGIEGRN 50
           ++I R+A  +N    PSG     G+D  + +K KRF    RN
Sbjct: 110 DSITRLARAYNTVVPPSGKILSGGVDANALHKPKRFFGAARN 151


>gnl|CDD|31352 COG1158, Rho, Transcription termination factor [Transcription].
          Length = 422

 Score = 31.0 bits (70), Expect = 0.26
 Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 11  EAIDRMAERHNLT--PSGLARKAGLDPTSFNKSKRFGIEGRN 50
           ++I R+A  +N     SG     G+D  + ++ KRF    RN
Sbjct: 267 DSITRLARAYNTVVPSSGKVLSGGVDANALHRPKRFFGAARN 308


>gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators
          [Transcription].
          Length = 120

 Score = 29.6 bits (64), Expect = 0.69
 Identities = 15/80 (18%), Positives = 38/80 (47%), Gaps = 4/80 (5%)

Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70
          E +  + ++  L+   LA + G+  ++ ++ +R    GR+  PS E + ++ AA   ++ 
Sbjct: 4  ERLKELRKKKGLSQEELAERLGVSRSTISRIER----GRSESPSLELLARLAAALGVSLD 59

Query: 71 QLLDLPFSDGRTTEKKEKEI 90
          +LL+           +  ++
Sbjct: 60 ELLEEEEELEIEELNELAKL 79


>gnl|CDD|145926 pfam03036, Perilipin, Perilipin family.  The perilipin family
           includes lipid droplet-associated protein (perilipin)
           and adipose differentiation-related protein
           (adipophilin).
          Length = 390

 Score = 28.2 bits (63), Expect = 1.9
 Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 10/36 (27%)

Query: 62  LAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPP 97
           +AA NE  C+ LD          K E+++P+L  PP
Sbjct: 78  IAAANELACKGLD----------KLEEKLPILQQPP 103


>gnl|CDD|30773 COG0424, Maf, Nucleotide-binding protein implicated in inhibition
           of septum formation [Cell division and chromosome
           partitioning].
          Length = 193

 Score = 28.2 bits (63), Expect = 2.0
 Identities = 12/59 (20%), Positives = 25/59 (42%)

Query: 155 DILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIE 213
           D L++ +   V    R+L KP+  +   ++L    GR+  + +            S++E
Sbjct: 64  DALVIGADTVVVLDGRILGKPKDEEEAREMLRKLSGRTHQVYTGVALIDPGKRVQSEVE 122


>gnl|CDD|119398 cd06530, S26_SPase_I, The S26 Type I signal peptidase (SPase; LepB;
           leader peptidase B; leader peptidase I; EC 3.4.21.89)
           family members are essential membrane-bound serine
           proteases that function to cleave the amino-terminal
           signal peptide extension from proteins that are
           translocated across biological membranes. The bacterial
           signal peptidase I, which is the most intensively
           studied, has two N-terminal transmembrane segments
           inserted in the plasma membrane and a hydrophilic,
           C-terminal catalytic region that is located in the
           periplasmic space. Although the bacterial signal
           peptidase I is monomeric, signal peptidases of
           eukaryotic cells commonly function as oligomeric
           complexes containing two divergent copies of the
           catalytic monomer. These are the IMP1 and IMP2 signal
           peptidases of the mitochondrial inner membrane that
           remove leader peptides from nuclear- and
           mitochondrial-encoded proteins. Also, two components of
           the endoplasmic reticulum signal peptidase in mammals
           (18-kDa and 21-kDa) belong to this family and they
           process many proteins that enter the ER for retention or
           for export to the Golgi apparatus, secretory vesicles,
           plasma membranes or vacuole. An atypical member of the
           S26 SPase type I family is the TraF peptidase which has
           the remarkable activity of producing a cyclic protein of
           the Pseudomonas pilin system. The type I signal
           peptidases are unique serine proteases that utilize a
           serine/lysine catalytic dyad mechanism in place of the
           classical serine/histidine/aspartic acid catalytic triad
           mechanism..
          Length = 85

 Score = 27.5 bits (62), Expect = 2.7
 Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 6/36 (16%)

Query: 146 SMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIV 181
           SM P  + GD++++N             +P+ GD+V
Sbjct: 9   SMEPTLQPGDLVLVNKL------SYGFREPKRGDVV 38


>gnl|CDD|144828 pfam01381, HTH_3, Helix-turn-helix.  This large family of DNA
          binding helix-turn helix proteins includes Cro and CI.
          Length = 55

 Score = 27.5 bits (62), Expect = 2.8
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 5/55 (9%)

Query: 18 ERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72
          E   L+   LA K G+  ++ +K     IE   R PS E++ K+  A   ++ +L
Sbjct: 6  EELGLSQEELAEKLGVSRSTISK-----IENGKREPSLETLKKLAEALGVSLDEL 55


>gnl|CDD|31036 COG0692, Ung, Uracil DNA glycosylase [DNA replication,
           recombination, and repair].
          Length = 223

 Score = 26.7 bits (59), Expect = 5.2
 Identities = 18/70 (25%), Positives = 26/70 (37%), Gaps = 14/70 (20%)

Query: 55  TESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYF---------PPSGSGGFFD 105
           T+++ K L    E +  +L      G   +KK+K I              P S   GFF 
Sbjct: 145 TDAVIKALNERREPVVFVLW-----GSHAQKKKKLIDNKKHLILEAPHPSPLSAHRGFFG 199

Query: 106 SGVFPTGNKW 115
              F   N+W
Sbjct: 200 CKHFSKANEW 209


>gnl|CDD|33190 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
           function prediction only].
          Length = 978

 Score = 26.5 bits (58), Expect = 6.2
 Identities = 6/22 (27%), Positives = 12/22 (54%)

Query: 168 GDRLLIKPRTGDIVAKVLISRR 189
           GD + +    G+I  + L++ R
Sbjct: 872 GDLVRLTSEFGEIKLRALVTDR 893


>gnl|CDD|146768 pfam04303, PrpF, PrpF protein.  PrpF is a protein found in the
           2-methylcitrate pathway. It is structurally similar to
           DAP epimerase and proline racemase. This protein is
           likely to acts to isomerize trans-aconitate to
           cis-aconitate.
          Length = 371

 Score = 26.3 bits (58), Expect = 6.5
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 15/69 (21%)

Query: 63  AATNETICQLLDLPFSDGRTTEKKE----------KEIPLLYFPPSGSGGFFDSGVFPTG 112
             T +TI     +P  +G+     +            I L +   +G G      +FPTG
Sbjct: 124 VNTGKTI--EAHVPTPNGQVQYDGDFEIDGVPGPGAPIALTFLDAAGDGT---GALFPTG 178

Query: 113 NKWNTVGVP 121
           N  +T+ VP
Sbjct: 179 NLIDTLDVP 187


>gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system,
           permease and ATPase components [General function
           prediction only].
          Length = 604

 Score = 26.0 bits (57), Expect = 8.6
 Identities = 9/25 (36%), Positives = 13/25 (52%)

Query: 154 GDILILNSAIQVNCGDRLLIKPRTG 178
           G  L+     +V  G+RLLI   +G
Sbjct: 405 GQTLLSELNFEVRPGERLLITGESG 429


  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
   0.319    0.136    0.418 

Gapped
Lambda     K      H
   0.267   0.0616    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,815,335
Number of extensions: 141586
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 307
Number of HSP's successfully gapped: 24
Length of query: 223
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 133
Effective length of database: 4,318,927
Effective search space: 574417291
Effective search space used: 574417291
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 (25.2 bits)