RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780272|ref|YP_003064685.1| ATP-dependent Clp protease
proteolytic subunit [Candidatus Liberibacter asiaticus str. psy62]
         (216 letters)



>gnl|CDD|178955 PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit;
           Reviewed.
          Length = 200

 Score =  399 bits (1028), Expect = e-112
 Identities = 132/192 (68%), Positives = 165/192 (85%)

Query: 17  GLVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEIS 76
            LVPMV+EQT+RGERSYDIYSRLLKERI+F+ G++EDHMA LI AQLLFLEAE+P K+I 
Sbjct: 6   NLVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEVEDHMANLIVAQLLFLEAEDPDKDIY 65

Query: 77  LYINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARIL 136
           LYINSPGG VTAG+AIYDTMQFIKP +ST C+GQAASMG+ LL+AG KG RFALPN+RI+
Sbjct: 66  LYINSPGGSVTAGLAIYDTMQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFALPNSRIM 125

Query: 137 LHQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEAC 196
           +HQP GGF GQA+DIE HA++I+K+K+RLNEI  ++ G+  E++EK  DRD+ MSA EA 
Sbjct: 126 IHQPLGGFQGQATDIEIHAREILKLKKRLNEILAEHTGQPLEKIEKDTDRDNFMSAEEAK 185

Query: 197 DWGVVDKVLMSR 208
           ++G++D+VL  R
Sbjct: 186 EYGLIDEVLTKR 197


>gnl|CDD|129584 TIGR00493, clpP, ATP-dependent Clp protease, proteolytic subunit
           ClpP.  This model for the proteolytic subunit ClpP has
           been rebuilt to a higher stringency. In every bacterial
           genome with the ClpXP machine, a ClpP protein will be
           found that scores with this model. In general, this ClpP
           member will be encoded adjacent to the clpX gene, as
           were all examples used in the seed alignment. A large
           fraction of genomes have one or more additional ClpP
           paralogs, sometimes encoded nearby and sometimes
           elsewhere. The stringency of the trusted cutoff used
           here excludes the more divergent ClpP paralogs from
           being called authentic ClpP by this model.
          Length = 191

 Score =  304 bits (780), Expect = 1e-83
 Identities = 120/189 (63%), Positives = 156/189 (82%)

Query: 17  GLVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEIS 76
            L+PMV+EQT RGERS+DIYSRLLKERI+F++G++ D +A LI AQLLFLEAE+P+K+I 
Sbjct: 1   NLIPMVIEQTGRGERSFDIYSRLLKERIIFLSGEVNDSVANLIVAQLLFLEAEDPEKDIY 60

Query: 77  LYINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARIL 136
           LYINSPGG +TAG+AIYDTMQFIKP +ST C+GQAASMG+ LLSAG KG RF+LPN+RI+
Sbjct: 61  LYINSPGGSITAGLAIYDTMQFIKPDVSTICIGQAASMGAFLLSAGAKGKRFSLPNSRIM 120

Query: 137 LHQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEAC 196
           +HQP GG  GQASDIE  A +I+++K  LN+I   + G++ E++EK  +RD  MSA EA 
Sbjct: 121 IHQPLGGAQGQASDIEIQANEILRLKGLLNDILANHTGQSLEQIEKDTERDFFMSAEEAK 180

Query: 197 DWGVVDKVL 205
           ++G++D VL
Sbjct: 181 EYGLIDSVL 189


>gnl|CDD|183589 PRK12553, PRK12553, ATP-dependent Clp protease proteolytic subunit;
           Reviewed.
          Length = 207

 Score =  281 bits (721), Expect = 1e-76
 Identities = 99/196 (50%), Positives = 146/196 (74%), Gaps = 2/196 (1%)

Query: 19  VPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLY 78
           +P  +E+T+ G +  D Y++L +ERI+F+ GQ++D  A  + AQLL LE+ +P ++I+LY
Sbjct: 12  LPSFIERTSYGVKESDPYNKLFEERIIFLGGQVDDASANDVMAQLLVLESIDPDRDITLY 71

Query: 79  INSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLH 138
           INSPGG VTAG AIYDT+QFI+P + T C GQAAS G++LL+AG  G RFALPNARIL+H
Sbjct: 72  INSPGGSVTAGDAIYDTIQFIRPDVQTVCTGQAASAGAVLLAAGTPGKRFALPNARILIH 131

Query: 139 QPS--GGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEAC 196
           QPS  GG  GQASD+E  A++I++++ RL  I  ++ G++ E++ K  DRD  ++A EA 
Sbjct: 132 QPSLGGGIRGQASDLEIQAREILRMRERLERILAEHTGQSVEKIRKDTDRDKWLTAEEAK 191

Query: 197 DWGVVDKVLMSRIDIE 212
           D+G+VD+++ S  D++
Sbjct: 192 DYGLVDQIITSYRDLK 207


>gnl|CDD|139060 PRK12551, PRK12551, ATP-dependent Clp protease proteolytic subunit;
           Reviewed.
          Length = 196

 Score =  226 bits (577), Expect = 5e-60
 Identities = 98/191 (51%), Positives = 137/191 (71%)

Query: 18  LVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISL 77
           ++P+V+E++ RGER++DIYSRLL+ERI+F+   +    A  I AQLLFLEAE+P+K+I L
Sbjct: 1   MIPIVIEESGRGERAFDIYSRLLRERIIFLGEPVTSDSANRIVAQLLFLEAEDPEKDIYL 60

Query: 78  YINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILL 137
           YINSPGG V  G+ I+DTMQ +KP + T C+G AASMG+ LL AG KG R +L ++RI++
Sbjct: 61  YINSPGGSVYDGLGIFDTMQHVKPDVHTVCVGLAASMGAFLLCAGAKGKRSSLQHSRIMI 120

Query: 138 HQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACD 197
           HQP GG  GQASDI   A +I+ +K RLN    +  G+  E +++  DRD  MS SEA +
Sbjct: 121 HQPLGGARGQASDIRIQADEILFLKERLNTELSERTGQPLERIQEDTDRDFFMSPSEAVE 180

Query: 198 WGVVDKVLMSR 208
           +G++D V+  R
Sbjct: 181 YGLIDLVIDKR 191


>gnl|CDD|184721 PRK14513, PRK14513, ATP-dependent Clp protease proteolytic subunit;
           Provisional.
          Length = 201

 Score =  225 bits (575), Expect = 7e-60
 Identities = 98/197 (49%), Positives = 141/197 (71%)

Query: 16  LGLVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEI 75
           + ++P V+EQT RGER YDIYSRLLK+RI+FV   IE  MA  I AQLL L+++NP++EI
Sbjct: 1   MSVIPYVIEQTGRGERMYDIYSRLLKDRIIFVGTPIESQMANTIVAQLLLLDSQNPEQEI 60

Query: 76  SLYINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARI 135
            +YIN PGG V AG+AIYDTM++IK P+ST C+G A SMGS+LL AG+KG R ALPN+RI
Sbjct: 61  QMYINCPGGEVYAGLAIYDTMRYIKAPVSTICVGIAMSMGSVLLMAGDKGKRMALPNSRI 120

Query: 136 LLHQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEA 195
           ++HQ S GF G   D+E  A++++ ++  L +IY ++    +E++ + ++RD+ MS  EA
Sbjct: 121 MIHQGSAGFRGNTPDLEVQAKEVLFLRDTLVDIYHRHTDLPHEKLLRDMERDYFMSPEEA 180

Query: 196 CDWGVVDKVLMSRIDIE 212
             +G++D V+       
Sbjct: 181 KAYGLIDSVIEPTRVKR 197


>gnl|CDD|184722 PRK14514, PRK14514, ATP-dependent Clp protease proteolytic subunit;
           Provisional.
          Length = 221

 Score =  209 bits (534), Expect = 4e-55
 Identities = 92/191 (48%), Positives = 135/191 (70%)

Query: 18  LVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISL 77
           L P ++E+        D++SRL+ +RI+F+  QI+D+ A  I AQLL+L++ +P K+IS+
Sbjct: 30  LNPYILEERQLNVTQMDVFSRLMMDRIIFLGTQIDDYTANTIQAQLLYLDSVDPGKDISI 89

Query: 78  YINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILL 137
           YINSPGG V AG+ IYDTMQFI   ++T C G AASM S+LL AG KG R ALP++R+++
Sbjct: 90  YINSPGGSVYAGLGIYDTMQFISSDVATICTGMAASMASVLLVAGTKGKRSALPHSRVMI 149

Query: 138 HQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACD 197
           HQP GG  GQASDIE  A++I K+K+ L  I   + G  +++V    DRD+ M+A EA +
Sbjct: 150 HQPLGGAQGQASDIEITAREIQKLKKELYTIIADHSGTPFDKVWADSDRDYWMTAQEAKE 209

Query: 198 WGVVDKVLMSR 208
           +G++D+VL+ +
Sbjct: 210 YGMIDEVLIKK 220


>gnl|CDD|183588 PRK12552, PRK12552, ATP-dependent Clp protease-like protein;
           Reviewed.
          Length = 222

 Score =  192 bits (489), Expect = 6e-50
 Identities = 87/218 (39%), Positives = 126/218 (57%), Gaps = 24/218 (11%)

Query: 18  LVPMVVEQTNRGERSY-----DIYSRLLKERIVF----------VTGQIEDHMATLICAQ 62
              M V+    G+        D+ S LLKERIV+             Q+   +  LI AQ
Sbjct: 1   SPIMAVQAPYYGDAVMRTPPPDLPSLLLKERIVYLGLPLFSDDDAKRQVGMDVTELIIAQ 60

Query: 63  LLFLEAENPQKEISLYINSPG---------GVVTAGMAIYDTMQFIKPPISTFCMGQAAS 113
           LL+LE ++P+K I  YINS G         G  T   AI DTM++IKPP+ T C+GQA  
Sbjct: 61  LLYLEFDDPEKPIYFYINSTGTSWYTGDAIGFETEAFAICDTMRYIKPPVHTICIGQAMG 120

Query: 114 MGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNC 173
             +++LSAG KG R +LP+A I+LHQP  G  GQA+DI+  A++++  KR + EI  +N 
Sbjct: 121 TAAMILSAGTKGQRASLPHATIVLHQPRSGARGQATDIQIRAKEVLHNKRTMLEILSRNT 180

Query: 174 GKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMSRIDI 211
           G+T E++ K  DR   ++  EA ++G++D+VL SR D+
Sbjct: 181 GQTVEKLSKDTDRMFYLTPQEAKEYGLIDRVLESRKDL 218


>gnl|CDD|184720 PRK14512, PRK14512, ATP-dependent Clp protease proteolytic subunit;
           Provisional.
          Length = 197

 Score =  165 bits (420), Expect = 7e-42
 Identities = 72/177 (40%), Positives = 115/177 (64%)

Query: 38  RLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQ 97
           + LK R + + G+I   ++ L   ++L LEA + +K I +YI+S GG + AG AI++ ++
Sbjct: 19  KFLKSRSIVIAGEINKDLSELFQEKILLLEALDSKKPIFVYIDSEGGDIDAGFAIFNMIR 78

Query: 98  FIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERHAQD 157
           F+KP + T  +G  AS  +L+  A +K  RF+LPNAR LLHQP  GF G A+DIE +A +
Sbjct: 79  FVKPKVFTIGVGLVASAAALIFLAAKKESRFSLPNARYLLHQPLSGFKGVATDIEIYANE 138

Query: 158 IVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMSRIDIEEK 214
           + K+K  LN+I  K  G+  ++VEK  DRD  + +S A  +G+V +V+ +R+++EE 
Sbjct: 139 LNKVKSELNDIIAKETGQELDKVEKDTDRDFWLDSSSAVKYGLVFEVVETRLELEEF 195


>gnl|CDD|162004 TIGR00705, SppA_67K, signal peptide peptidase SppA, 67K type.  E.
           coli SohB, which is most closely homologous to the
           C-terminal duplication of SppA, is predicted to perform
           a similar function of small peptide degradation, but in
           the periplasm. Many prokaryotes have a single SppA/SohB
           homolog that may perform the function of either or both.
          Length = 584

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 38/121 (31%), Positives = 49/121 (40%), Gaps = 24/121 (19%)

Query: 32  SYDIYSRLLKER--------IVFVTGQIEDHMAT-------LICAQLLFLEAENPQKEIS 76
           S D Y+R   +R        IV + G I D   T        + A L    ++   K + 
Sbjct: 292 SLDDYNRDRPQRHDVQDKIGIVHLEGPIADGRDTEGNTGGDTVAALLRVARSDPDIKAVV 351

Query: 77  LYINSPGGVVTAGMAIYDTMQFI----KPPISTFCMGQ-AASMGSLLLSAGEKGMRFALP 131
           L INSPGG V A   I   +       KP I +  MG  AAS G  + SA +     A P
Sbjct: 352 LRINSPGGSVFASEIIRRELARAQARGKPVIVS--MGAMAASGGYWIASAADY--IVASP 407

Query: 132 N 132
           N
Sbjct: 408 N 408


>gnl|CDD|129789 TIGR00706, SppA_dom, signal peptide peptidase SppA, 36K type.  The
           member of this family from Bacillus subtilis was shown
           to have properties consistent with a role in degrading
           signal peptides after cleavage from precursor proteins,
           although it was not demonstrated conclusively.
          Length = 207

 Score = 30.8 bits (70), Expect = 0.29
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 73  KEISLYINSPGGVVTAGMAIYDTMQFI--KPPISTFCMGQAASMGSLLLSAGEK 124
           K + L INSPGG V A   IY+ ++ +  K P+     G AAS G  +  A ++
Sbjct: 32  KALLLRINSPGGTVVASEEIYEKLKKLKAKKPVVASMGGVAASGGYYIAMAADE 85


>gnl|CDD|162635 TIGR01976, am_tr_V_VC1184, cysteine desulfurase family protein,
           VC1184 subfamily.  This model describes a subfamily of
           probable pyridoxal phosphate-dependent enzymes in the
           aminotransferase class V family (pfam00266). The most
           closely related characterized proteins are active as
           cysteine desulfurases, selenocysteine lyases, or both;
           some are involved in FeS cofactor biosynthesis and are
           designated NifS. An active site Cys residue present in
           those sequences, in motifs resembling GHHC or GSAC, is
           not found in this family. The function of members of
           this family is unknown, but seems unlike to be as an
           aminotransferase.
          Length = 397

 Score = 28.2 bits (63), Expect = 1.5
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 77  LYINSPGGVVTAGMAIYDTMQ 97
           L +N  GGVV  G+A Y+T +
Sbjct: 368 LGLNDEGGVVRVGLAHYNTAE 388


>gnl|CDD|182860 PRK10949, PRK10949, protease 4; Provisional.
          Length = 618

 Score = 28.1 bits (63), Expect = 2.0
 Identities = 12/20 (60%), Positives = 13/20 (65%)

Query: 73  KEISLYINSPGGVVTAGMAI 92
           K I L +NSPGG VTA   I
Sbjct: 366 KAIVLRVNSPGGSVTASEVI 385


>gnl|CDD|182806 PRK10881, PRK10881, putative hydrogenase 2 b cytochrome subunit;
           Provisional.
          Length = 394

 Score = 27.2 bits (61), Expect = 3.5
 Identities = 9/17 (52%), Positives = 13/17 (76%), Gaps = 1/17 (5%)

Query: 108 MGQAASMGSLLLSAGEK 124
           M Q+ S+GSL++ AG K
Sbjct: 185 MHQS-SLGSLMIIAGYK 200


>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
          Length = 2435

 Score = 26.7 bits (58), Expect = 4.3
 Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 95  TMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSG 142
           T  F  P   T  MG     GS   S   +GM  A  NA +++ QP G
Sbjct: 791 TTGFTDPSDGTLVMG-GTPFGSSQASMTYQGMTDAEGNATLVIEQPQG 837


>gnl|CDD|147832 pfam05894, Podovirus_Gp16, Podovirus DNA encapsidation protein
           (Gp16).  This family consists of several DNA
           encapsidation protein (Gp16) sequences from the
           phi-29-like viruses. Gene product 16 catalyses the in
           vivo and in vitro genome-encapsidation reaction.
          Length = 333

 Score = 26.7 bits (59), Expect = 4.5
 Identities = 7/37 (18%), Positives = 15/37 (40%)

Query: 78  YINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASM 114
           Y +     V   + + DT+   +  +   C+  A S+
Sbjct: 127 YGSYDPNEVRNFLNLMDTVFRARERVRCICLSNAVSI 163


>gnl|CDD|180473 PRK06213, PRK06213, enoyl-CoA hydratase; Provisional.
          Length = 229

 Score = 25.7 bits (57), Expect = 8.5
 Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 2/41 (4%)

Query: 84  GVVTAGM-AIYDTMQFIKPPISTFCMGQAASMGSLLLSAGE 123
            ++TAG       +   KP I   C G A + G+ LL + +
Sbjct: 75  ALLTAGSTLARRLLSHPKPVIVA-CTGHAIAKGAFLLLSAD 114


  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
   0.319    0.135    0.387 

Gapped
Lambda     K      H
   0.267   0.0664    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,502,594
Number of extensions: 219762
Number of successful extensions: 474
Number of sequences better than 10.0: 1
Number of HSP's gapped: 471
Number of HSP's successfully gapped: 21
Length of query: 216
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 127
Effective length of database: 4,071,361
Effective search space: 517062847
Effective search space used: 517062847
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 (25.1 bits)