RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780532|ref|YP_003064945.1| aminodeoxychorismate lyase
[Candidatus Liberibacter asiaticus str. psy62]
         (325 letters)



>gnl|CDD|161789 TIGR00247, TIGR00247, conserved hypothetical protein, YceG family. 
           This uncharacterized protein family, found in three of
           four microbial genomes, virtually always once per
           genome, includes YceG from Escherichia coli. This
           protein is encoded next to PabC,
           4-amino-4-deoxychorismate lyase, in E. coli and numerous
           other proteobacteria, but that proximity is not
           conserved in other lineages. Numerous members of this
           family have been misannotated as aminodeoxychorismate
           lyase, apparently because of promiximty to PabC.
          Length = 342

 Score =  221 bits (564), Expect = 2e-58
 Identities = 116/346 (33%), Positives = 176/346 (50%), Gaps = 26/346 (7%)

Query: 1   MLKFLI---PLITIFLLAIGVHIHVIRVYNATGPL-QNDTIFLVRNNMSLKEISKNLFNG 56
           M KFLI    L  +F +   +  + I   N +    +    F +     + +I+K L   
Sbjct: 1   MKKFLIIILLLFVLFFILGSILSYKIYFLNLSSLANKLVYEFNIEKGTGVSKIAKELKKQ 60

Query: 57  GVIVNPYIFRYVTQFYFGSRGLKTGEYEIEKGSSMSQIAEKIMYGKVLMH-SISFPEGFT 115
            +I +  + +Y+ +     +  K G Y +    ++ +I + ++ GK  +   ++ PEG+T
Sbjct: 61  KLIKSEKLLQYLLKIKGSLKQFKAGTYLLNGDMTVFEILKLLLSGKENVQFDVTIPEGYT 120

Query: 116 VKQMARRLKDNPLLVGELP-----------------LELPLEGTLCPSTYNFPLGTHRSE 158
           ++ +A++LK+ P ++  L                  L+ PLEG L P TY F  G    E
Sbjct: 121 LRDIAKKLKEAPQVIDTLQDFLFLINKKSTIYQLLELKNPLEGWLFPDTYKFTKGDTDLE 180

Query: 159 ILNQAMLKQKQVVDEVWEIRDVDHPIKSKEDLVILASIVEKETSRADERAHVASVFINRF 218
           +L +A +K  +   + W +R  D P K   +LVI+ASIVEKET    ER  VASVF NR 
Sbjct: 181 LLKRAFVKMFKAKLKAWGVRLSDLPSKELYNLVIMASIVEKETRVKSERPKVASVFYNRL 240

Query: 219 SKSIRLQSDSTVIYGILEGDYDLTNRKISRSDFSIKTPYNSYLMNGLPPTAISNPGRLSL 278
              + LQ+D TVIYG+ E      NR + + D  I +PYN+Y+  GLPPT I+N G  SL
Sbjct: 241 KSGMALQTDPTVIYGMGEE----YNRSLPKRDLEIDSPYNTYINTGLPPTPIANAGISSL 296

Query: 279 EAVAKPLHTEDLYFVGDGKGGHFFSTNFKDHTINVQKWRKMSLESK 324
           +A A P  T+ LYFV  G GGH F++N   H   VQ + K  +  K
Sbjct: 297 QAAAHPKKTDYLYFVAKGSGGHQFTSNLSSHNKAVQDYIKNFITKK 342


>gnl|CDD|182348 PRK10270, PRK10270, putative aminodeoxychorismate lyase;
           Provisional.
          Length = 340

 Score =  203 bits (517), Expect = 7e-53
 Identities = 112/333 (33%), Positives = 171/333 (51%), Gaps = 19/333 (5%)

Query: 1   MLKFLIPLITIFLLAIGVHIHVIR-VYNATGPLQNDTIFLVRNNMSLKEISKNLFNGGVI 59
           +L  ++ L+ +  +A GV +  +R + ++   ++ +TIF ++       + + L+   +I
Sbjct: 4   VLLIILLLLVVLGIAAGVGVWKVRHLADSKLLIKEETIFTLKPGTGRLALGEQLYADKII 63

Query: 60  VNPYIFRYVTQFYFGSRGLKTGEYEIEKGSSMSQIAEKIMYGKVLMHSISFPEGFTVKQM 119
             P +F+++ +        K G Y      ++ ++ + +  GK     +   EG  +   
Sbjct: 64  NRPRVFQWLLRIEPDLSHFKAGTYRFTPQMTVREMLKLLESGKEAQFPLRLVEGMRLSDY 123

Query: 120 ARRLKDNPLLVGELP------------LELP--LEGTLCPSTYNFPLGTHRSEILNQAML 165
            ++L++ P +   L             LE P  +EG   P T+ +   T    +L +A  
Sbjct: 124 LKQLREAPYIKHTLSDDKYATVAQALELENPEWIEGWFWPDTWMYTANTTDVALLKRAHK 183

Query: 166 KQKQVVDEVWEIRDVDHPIKSKEDLVILASIVEKETSRADERAHVASVFINRFSKSIRLQ 225
           K  + VD  WE R    P K K  LV +ASI+EKET+ A ER  VASVFINR    +RLQ
Sbjct: 184 KMVKAVDSAWEGRADGLPYKDKNQLVTMASIIEKETAVASERDQVASVFINRLRIGMRLQ 243

Query: 226 SDSTVIYGILEGDYDLTNRKISRSDFSIKTPYNSYLMNGLPPTAISNPGRLSLEAVAKPL 285
           +D TVIYG+ E  Y   N K+SR+D    T YN+Y + GLPP  I+ PG  SL+A A P 
Sbjct: 244 TDPTVIYGMGE-RY---NGKLSRADLETPTAYNTYTITGLPPGPIATPGEASLKAAAHPA 299

Query: 286 HTEDLYFVGDGKGGHFFSTNFKDHTINVQKWRK 318
            T  LYFV DGKGGH F+TN   H  +VQ + K
Sbjct: 300 KTPYLYFVADGKGGHTFNTNLASHNRSVQDYLK 332


>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
           Provisional.
          Length = 758

 Score = 29.8 bits (67), Expect = 0.97
 Identities = 10/18 (55%), Positives = 14/18 (77%)

Query: 115 TVKQMARRLKDNPLLVGE 132
            ++ + RR K+NPLLVGE
Sbjct: 198 AIQVLCRRRKNNPLLVGE 215


>gnl|CDD|152256 pfam11820, DUF3339, Protein of unknown function (DUF3339).  This
          family of proteins are functionally uncharacterized.
          This family is found in eukaryotes. Proteins in this
          family are about 70 amino acids in length.
          Length = 68

 Score = 28.4 bits (64), Expect = 2.9
 Identities = 11/14 (78%), Positives = 14/14 (100%)

Query: 8  LITIFLLAIGVHIH 21
          LITIFL+A+GVHI+
Sbjct: 54 LITIFLVALGVHIY 67


>gnl|CDD|151770 pfam11329, DUF3131, Protein of unknown function (DUF3131).  This
           bacterial family of proteins has no known function.
          Length = 368

 Score = 28.0 bits (63), Expect = 3.7
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 4/50 (8%)

Query: 230 VIYGILEGDYDLTNRKISRSDFSIKTP----YNSYLMNGLPPTAISNPGR 275
            +Y   E  YD T    + S+ ++       YN+   +G P   ++  G+
Sbjct: 243 RVYQAQERRYDQTGILTAVSEDAVDRAPYFVYNTIYADGKPWNTVTEDGK 292


>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2.  Members
           of this protein family are homologous to SecA and part
           of the accessory Sec system. This system, including both
           five core proteins for export and a variable number of
           proteins for glycosylation, operates in certain
           Gram-positive pathogens for the maturation and delivery
           of serine-rich glycoproteins such as the cell surface
           glycoprotein GspB in Streptococcus gordonii.
          Length = 762

 Score = 28.1 bits (63), Expect = 3.7
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 9/57 (15%)

Query: 195 SIVEKETSRADERAHVASVFINRFSKSIRLQSDSTVIYGILEGDYDLTNRKISRSDF 251
            IVEK    ++++   A    N F +S+ +Q ++          Y   NR I  SDF
Sbjct: 575 KIVEKAQRASEDKGESAREQTNEFEESLSIQRENI---------YAERNRLIEGSDF 622


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

 Score = 27.7 bits (62), Expect = 3.8
 Identities = 11/18 (61%), Positives = 15/18 (83%)

Query: 115 TVKQMARRLKDNPLLVGE 132
           T++ + RR K+NPLLVGE
Sbjct: 194 TIQVLCRRKKNNPLLVGE 211


>gnl|CDD|179640 PRK03739, PRK03739, 2-isopropylmalate synthase; Validated.
          Length = 552

 Score = 27.4 bits (62), Expect = 4.6
 Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 10/35 (28%)

Query: 15  AIGVHIHVIRVYNATGPLQNDTIFLVRNNMSLKEI 49
           AI VH     +YN+T PLQ   +F          I
Sbjct: 123 AI-VH-----LYNSTSPLQRRVVF----GKDRDGI 147


>gnl|CDD|163222 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
           Members of this protein family are homologs of ClpB, an
           ATPase associated with chaperone-related functions.
           These ClpB homologs, designated ClpV1, are a key
           component of the bacterial pathogenicity-associated type
           VI secretion system.
          Length = 852

 Score = 27.6 bits (62), Expect = 5.1
 Identities = 9/21 (42%), Positives = 14/21 (66%), Gaps = 4/21 (19%)

Query: 116 VKQM----ARRLKDNPLLVGE 132
           ++QM     RR ++NP+L GE
Sbjct: 196 IRQMIDILLRRRQNNPILTGE 216


>gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB.  Members
           of this protein family are the bacterial ATP-dependent
           chaperone ClpB. This protein belongs to the AAA family,
           ATPases associated with various cellular activities
           (pfam00004). This molecular chaperone does not act as a
           protease, but rather serves to disaggregate misfolded
           and aggregated proteins.
          Length = 852

 Score = 27.2 bits (61), Expect = 5.2
 Identities = 9/18 (50%), Positives = 16/18 (88%)

Query: 115 TVKQMARRLKDNPLLVGE 132
           T++ ++RR K+NP+L+GE
Sbjct: 185 TIQVLSRRTKNNPVLIGE 202


>gnl|CDD|183034 PRK11198, PRK11198, LysM domain/BON superfamily protein;
           Provisional.
          Length = 147

 Score = 27.2 bits (61), Expect = 5.3
 Identities = 8/20 (40%), Positives = 14/20 (70%), Gaps = 1/20 (5%)

Query: 83  YEIEKGSSMSQIAEKIMYGK 102
           Y ++ G ++S IA+K +YG 
Sbjct: 98  YTVKSGDTLSAIAKK-VYGN 116


>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
          Length = 857

 Score = 27.1 bits (60), Expect = 6.5
 Identities = 9/18 (50%), Positives = 15/18 (83%)

Query: 115 TVKQMARRLKDNPLLVGE 132
           T++ + RR K+NP+L+GE
Sbjct: 190 TIQVLQRRTKNNPVLIGE 207


>gnl|CDD|162129 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
           Family protei. 
          Length = 659

 Score = 26.6 bits (59), Expect = 8.9
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 185 KSKEDLVILASIVEKETSRADERAHVASVFINRFSKSIRL 224
             KE+L I+      E   A ++AHV  VF+ +    +++
Sbjct: 48  SGKEELTIVGKHSTIE--GAKKKAHVNGVFLGKLDFLLKI 85


>gnl|CDD|183435 PRK12319, PRK12319, acetyl-CoA carboxylase subunit alpha;
           Provisional.
          Length = 256

 Score = 26.7 bits (59), Expect = 9.2
 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 3/39 (7%)

Query: 170 VVDEVWEIRDVDHPIKSKEDLVILASIVEKETSRADERA 208
           V D+VW + +  + + S E     ASI+ K+ SRA E A
Sbjct: 157 VADQVWMLENTMYAVLSPEGF---ASILWKDGSRATEAA 192


  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    0.138    0.398 

Gapped
Lambda     K      H
   0.267   0.0711    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,286,059
Number of extensions: 337255
Number of successful extensions: 616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 610
Number of HSP's successfully gapped: 21
Length of query: 325
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 231
Effective length of database: 3,963,321
Effective search space: 915527151
Effective search space used: 915527151
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: 57 (25.8 bits)